2d_simple_filter: filter.xml annotate

annotate filter.xml @ 4:5ab62693dca5 draft default tip

planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48

author	imgteam
date	Sat, 20 Dec 2025 18:28:21 +0000
parents	53c55776a974
children

rev	line source
4 5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1 <tool id="ip_filter_standard" name="Apply standard image filter" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.05">
2 b2d9c92bc431 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit a6fd77be465068f709a71d377900da99becf94d8 imgteam parents: 1 diff changeset	2 <description>with scipy</description>
b2d9c92bc431 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit a6fd77be465068f709a71d377900da99becf94d8 imgteam parents: 1 diff changeset	3 <macros>
4 5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	4 <!--
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	5 === BEGIN OF MACROS ===
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	6 -->
2 b2d9c92bc431 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit a6fd77be465068f709a71d377900da99becf94d8 imgteam parents: 1 diff changeset	7 <import>creators.xml</import>
b2d9c92bc431 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit a6fd77be465068f709a71d377900da99becf94d8 imgteam parents: 1 diff changeset	8 <import>tests.xml</import>
b2d9c92bc431 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit a6fd77be465068f709a71d377900da99becf94d8 imgteam parents: 1 diff changeset	9 <token name="@TOOL_VERSION@">1.16.3</token>
4 5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	10 <token name="@VERSION_SUFFIX@">1</token>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	11 <!--
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	12 === MACROS: UI text tokens ===
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	13 -->
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	14 <token name="@DEFAULT_AXIS_LABEL@">Direction</token>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	15 <token name="@DERIVATIVE_AXIS_LABEL@">Direction of the derivative</token>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	16 <token name="@DERIVATIVE_AXIS_HELP@">The axis to compute the derivative along.</token>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	17 <token name="@PREWITT_AXIS_HELP@">
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	18 The Prewitt filter is a 2-D image filter that computes an approximation of the derivative of the image intensities in the given direction.
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	19 </token>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	20 <token name="@SOBEL_AXIS_HELP@">
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	21 The Sobel filter is a 2-D image filter that computes an approximation of the derivative of the image intensities in the given direction.
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	22 </token>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	23 <!--
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	24 === MACROS: Direction selectors ===
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	25 -->
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	26 <xml name="select_direction" tokens="axis1,axis2,axis1_label,axis2_label,label,help"
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	27 token_axis1="1" token_axis1_label="Horizontal" token_axis2="0" token_axis2_label="Vertical" token_label="@DEFAULT_AXIS_LABEL@" token_help="">
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	28 <param name="direction" type="select" label="@LABEL@" help="@HELP@">
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	29 <option value="@AXIS1@" selected="true">@AXIS1_LABEL@</option>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	30 <option value="@AXIS2@">@AXIS2_LABEL@</option>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	31 <yield/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	32 </param>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	33 </xml>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	34 <xml name="select_direction_3d" tokens="label,help" token_label="@DEFAULT_AXIS_LABEL@" token_help="">
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	35 <!-- Normalized axes layout for 3-D images: ZYX -->
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	36 <expand macro="select_direction" axis1="2" axis1_label="Horizontal" axis2="1" axis2_label="Vertical" label="@LABEL@" help="@HELP@">
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	37 <option value="0">Orthogonal</option>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	38 </expand>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	39 </xml>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	40 <!--
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	41 === MACROS: Groups of fields for 3-D processing setup ===
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	42 -->
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	43 <xml name="select_axes_2d" tokens="yx_selected" token_yx_selected="true">
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	44 <param name="axes" type="select" label="Processing of 3-D images"
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	45 help="This governs which axes are processed jointly.">
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	46 <yield/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	47 <option value="YX" selected="@YX_SELECTED@">Perform 2-D filtering of all XY-slices</option>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	48 <option value="YZ">Perform 2-D filtering of all YZ-slices</option>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	49 <option value="XZ">Perform 2-D filtering of all XZ-slices</option>
2 b2d9c92bc431 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit a6fd77be465068f709a71d377900da99becf94d8 imgteam parents: 1 diff changeset	50 </param>
b2d9c92bc431 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit a6fd77be465068f709a71d377900da99becf94d8 imgteam parents: 1 diff changeset	51 </xml>
4 5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	52 <xml name="select_axes_2d_or_3d">
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	53 <expand macro="select_axes_2d" yx_selected="false">
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	54 <option value="ZYX" selected="true">Perform 3-D filtering</option>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	55 </expand>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	56 </xml>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	57 <xml name="directed_3d" tokens="selector,axis_label,axis_help"
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	58 token_selector="select_axes_2d" token_axis_label="@DEFAULT_AXIS_LABEL@" token_axis_help="">
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	59 <conditional name="directed_3d">
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	60 <expand macro="@SELECTOR@"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	61 <yield/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	62 <when value="YX">
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	63 <expand macro="select_direction" label="@AXIS_LABEL@" help="@AXIS_HELP@"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	64 </when>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	65 <when value="YZ">
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	66 <expand macro="select_direction" label="@AXIS_LABEL@" help="@AXIS_HELP@"
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	67 axis1="0" axis1_label="Vertical" axis2="1" axis2_label="Orthogonal"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	68 </when>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	69 <when value="XZ">
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	70 <expand macro="select_direction" label="@AXIS_LABEL@" help="@AXIS_HELP@"
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	71 axis1="0" axis1_label="Horizontal" axis2="1" axis2_label="Orthogonal"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	72 </when>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	73 </conditional>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	74 </xml>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	75 <xml name="directed_3d_full" tokens="axis_label,axis_help"
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	76 token_axis_label="@DEFAULT_AXIS_LABEL@" token_axis_help="">
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	77 <expand macro="directed_3d" selector="select_axes_2d_or_3d">
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	78 <when value="ZYX">
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	79 <expand macro="select_direction_3d" label="@AXIS_LABEL@" help="@AXIS_HELP@"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	80 </when>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	81 </expand>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	82 </xml>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	83 <!--
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	84 === MACROS: Field for optional anisotropic filtering ===
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	85 -->
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	86 <xml name="anisotropic" tokens="entities" token_entities="pixels/voxels">
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	87 <param name="anisotropic" type="boolean" checked="true" label="Anisotropic filtering"
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	88 help="Perform anisotropic filtering if the image @ENTITIES@ are anistropic. Has no effect if the @ENTITIES@ are isotropic or no information about the size of the @ENTITIES@ is available from the matadata of the image."/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	89 </xml>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	90 <!--
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	91 === MACROS: Group of fields for filter setup ===
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	92 -->
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	93 <xml name="filter" tokens="entities" token_entities="pixels/voxels">
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	94 <conditional name="filter">
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	95 <param name="filter_type" type="select" label="Filter type"
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	96 help="Gaussian filters include smoothing filters for pre-processing (denoising, scale selection) and Gaussian derivatives for edge and feature detection. Box filters use uniform rectangular averaging. Median filters remove impulse noise and suit binary images and label maps. Prewitt and Sobel filters compute first-order derivatives, with Sobel providing better isotropy.">
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	97 <option value="gaussian" selected="True">Gaussian</option>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	98 <option value="uniform">Box filter</option>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	99 <option value="median">Median</option>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	100 <option value="prewitt">Prewitt</option>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	101 <option value="sobel">Sobel</option>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	102 </param>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	103 <when value="gaussian">
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	104 <param name="sigma" type="float" value="3" min="0.1" label="Sigma"
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	105 help="The half width of the Gaussian bell (in pixels)."/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	106 <expand macro="anisotropic" entities="@ENTITIES@"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	107 <conditional name="derivative">
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	108 <param name="order" type="select" label="Advanced kernel options"
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	109 help="Kernels based on the Gaussian bell are low-pass filters. Kernels based on the 1st-order and 2nd-order derivative act like high-pass and band-pass filters, respectively.">
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	110 <option value="0">No derivative (Gaussian bell)</option>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	111 <option value="1">1st-order derivative of the Gaussian bell</option>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	112 <option value="2">2nd-order derivative of the Gaussian bell</option>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	113 </param>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	114 <when value="0">
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	115 <yield name="gaussian_order0"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	116 </when>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	117 <when value="1">
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	118 <yield name="gaussian_order1"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	119 </when>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	120 <when value="2">
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	121 <yield name="gaussian_order2"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	122 </when>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	123 </conditional>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	124 </when>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	125 <when value="uniform">
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	126 <param name="size" type="integer" min="2" value="3" label="Size"
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	127 help="Edge length of the neighborhood (square, in pixels)."/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	128 <expand macro="anisotropic" entities="@ENTITIES@"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	129 <yield name="uniform"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	130 </when>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	131 <when value="median">
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	132 <param name="size" type="integer" min="2" value="3" label="Size"
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	133 help="Edge length of the neighborhood (square, in pixels)."/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	134 <expand macro="anisotropic" entities="@ENTITIES@"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	135 <yield name="median"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	136 </when>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	137 <when value="prewitt">
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	138 <yield name="prewitt"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	139 </when>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	140 <when value="sobel">
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	141 <yield name="sobel"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	142 </when>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	143 </conditional>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	144 </xml>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	145 <xml name="select_dtype">
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	146 <param name="dtype" type="select" label="Output pixel type"
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	147 help="Data type used to store the pixel values in the output image.">
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	148 <option value="floating" selected="True">Same as the input image (if floating point, and 64-bit floating point otherwise)</option>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	149 <option value="float64">64-bit floating point</option>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	150 <option value="float32">32-bit floating point</option>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	151 <option value="float16">16-bit floating point</option>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	152 </param>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	153 </xml>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	154 <!--
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	155 === END OF MACROS ===
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	156 -->
2 b2d9c92bc431 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit a6fd77be465068f709a71d377900da99becf94d8 imgteam parents: 1 diff changeset	157 </macros>
b2d9c92bc431 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit a6fd77be465068f709a71d377900da99becf94d8 imgteam parents: 1 diff changeset	158 <creator>
b2d9c92bc431 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit a6fd77be465068f709a71d377900da99becf94d8 imgteam parents: 1 diff changeset	159 <expand macro="creators/bmcv"/>
b2d9c92bc431 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit a6fd77be465068f709a71d377900da99becf94d8 imgteam parents: 1 diff changeset	160 <expand macro="creators/kostrykin"/>
b2d9c92bc431 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit a6fd77be465068f709a71d377900da99becf94d8 imgteam parents: 1 diff changeset	161 </creator>
b2d9c92bc431 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit a6fd77be465068f709a71d377900da99becf94d8 imgteam parents: 1 diff changeset	162 <edam_operations>
b2d9c92bc431 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit a6fd77be465068f709a71d377900da99becf94d8 imgteam parents: 1 diff changeset	163 <edam_operation>operation_3443</edam_operation>
b2d9c92bc431 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit a6fd77be465068f709a71d377900da99becf94d8 imgteam parents: 1 diff changeset	164 </edam_operations>
b2d9c92bc431 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit a6fd77be465068f709a71d377900da99becf94d8 imgteam parents: 1 diff changeset	165 <xrefs>
b2d9c92bc431 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit a6fd77be465068f709a71d377900da99becf94d8 imgteam parents: 1 diff changeset	166 <xref type="bio.tools">galaxy_image_analysis</xref>
b2d9c92bc431 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit a6fd77be465068f709a71d377900da99becf94d8 imgteam parents: 1 diff changeset	167 <xref type="biii">scipy</xref>
b2d9c92bc431 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit a6fd77be465068f709a71d377900da99becf94d8 imgteam parents: 1 diff changeset	168 </xrefs>
0 96fe54355774 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_simple_filter/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581 imgteam parents: diff changeset	169 <requirements>
2 b2d9c92bc431 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit a6fd77be465068f709a71d377900da99becf94d8 imgteam parents: 1 diff changeset	170 <requirement type="package" version="@TOOL_VERSION@">scipy</requirement>
b2d9c92bc431 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit a6fd77be465068f709a71d377900da99becf94d8 imgteam parents: 1 diff changeset	171 <requirement type="package" version="2.3.5">numpy</requirement>
4 5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	172 <requirement type="package" version="0.12.2">ome-zarr</requirement>
2 b2d9c92bc431 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit a6fd77be465068f709a71d377900da99becf94d8 imgteam parents: 1 diff changeset	173 <requirement type="package" version="2025.10.16">tifffile</requirement>
4 5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	174 <requirement type="package" version="0.6.0">giatools</requirement>
0 96fe54355774 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_simple_filter/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581 imgteam parents: diff changeset	175 </requirements>
4 5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	176 <required_files>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	177 <include type="literal" path="filter.py"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	178 </required_files>
2 b2d9c92bc431 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit a6fd77be465068f709a71d377900da99becf94d8 imgteam parents: 1 diff changeset	179 <command detect_errors="aggressive"><![CDATA[
b2d9c92bc431 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit a6fd77be465068f709a71d377900da99becf94d8 imgteam parents: 1 diff changeset	180
b2d9c92bc431 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit a6fd77be465068f709a71d377900da99becf94d8 imgteam parents: 1 diff changeset	181 python '$__tool_directory__/filter.py'
b2d9c92bc431 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit a6fd77be465068f709a71d377900da99becf94d8 imgteam parents: 1 diff changeset	182
4 5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	183 #if $input.extension == "zarr"
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	184 '$setup.input.extra_files_path/$setup.input.metadata.store_root'
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	185 #else
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	186 '$setup.input'
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	187 #end if
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	188
2 b2d9c92bc431 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit a6fd77be465068f709a71d377900da99becf94d8 imgteam parents: 1 diff changeset	189 '$output'
b2d9c92bc431 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit a6fd77be465068f709a71d377900da99becf94d8 imgteam parents: 1 diff changeset	190 '$params'
b2d9c92bc431 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit a6fd77be465068f709a71d377900da99becf94d8 imgteam parents: 1 diff changeset	191
b2d9c92bc431 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit a6fd77be465068f709a71d377900da99becf94d8 imgteam parents: 1 diff changeset	192 ]]></command>
b2d9c92bc431 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit a6fd77be465068f709a71d377900da99becf94d8 imgteam parents: 1 diff changeset	193 <configfiles>
b2d9c92bc431 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit a6fd77be465068f709a71d377900da99becf94d8 imgteam parents: 1 diff changeset	194 <configfile name="params"><![CDATA[
b2d9c92bc431 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit a6fd77be465068f709a71d377900da99becf94d8 imgteam parents: 1 diff changeset	195 {
b2d9c92bc431 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit a6fd77be465068f709a71d377900da99becf94d8 imgteam parents: 1 diff changeset	196
4 5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	197 ## =================================================================================
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	198 #if $setup.filter.filter_type == "gaussian"
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	199 "sigma": $setup.filter.sigma,
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	200 "order": $setup.filter.derivative.order,
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	201 "anisotropic": $setup.filter.anisotropic,
2 b2d9c92bc431 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit a6fd77be465068f709a71d377900da99becf94d8 imgteam parents: 1 diff changeset	202
4 5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	203 #if $setup.target == "2d"
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	204 #if $setup.filter.derivative.order != "0"
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	205 "direction": $setup.filter.derivative.direction,
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	206 "dtype": "$setup.filter.derivative.dtype",
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	207 #end if
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	208 #else
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	209 #if $setup.filter.derivative.order == "0"
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	210 "axes": "$setup.filter.derivative.axes",
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	211 #else
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	212 "axes": "$setup.filter.derivative.directed_3d.axes",
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	213 "direction": $setup.filter.derivative.directed_3d.direction,
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	214 "dtype": "$setup.filter.derivative.dtype",
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	215 #end if
2 b2d9c92bc431 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit a6fd77be465068f709a71d377900da99becf94d8 imgteam parents: 1 diff changeset	216 #end if
b2d9c92bc431 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit a6fd77be465068f709a71d377900da99becf94d8 imgteam parents: 1 diff changeset	217
4 5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	218 ## =================================================================================
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	219 #elif $setup.filter.filter_type == "uniform"
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	220 "size": $setup.filter.size,
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	221 "anisotropic": $setup.filter.anisotropic,
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	222
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	223 #if $setup.target == "3d"
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	224 "axes": "$setup.filter.axes",
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	225 #end if
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	226
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	227 ## =================================================================================
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	228 #elif $setup.filter.filter_type == "median"
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	229 "size": $setup.filter.size,
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	230 "anisotropic": $setup.filter.anisotropic,
2 b2d9c92bc431 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit a6fd77be465068f709a71d377900da99becf94d8 imgteam parents: 1 diff changeset	231
4 5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	232 #if $setup.target == "3d"
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	233 "axes": "$setup.filter.axes",
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	234 #end if
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	235
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	236 ## =================================================================================
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	237 #elif $setup.filter.filter_type == "prewitt" or $setup.filter.filter_type == "sobel"
2 b2d9c92bc431 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit a6fd77be465068f709a71d377900da99becf94d8 imgteam parents: 1 diff changeset	238
4 5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	239 #if $setup.target == "2d"
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	240 "direction": $setup.filter.direction,
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	241 "dtype": "$setup.filter.dtype",
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	242 #else
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	243 "axes": "$setup.filter.directed_3d.axes",
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	244 "direction": $setup.filter.directed_3d.direction,
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	245 "dtype": "$setup.filter.dtype",
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	246 #end if
2 b2d9c92bc431 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit a6fd77be465068f709a71d377900da99becf94d8 imgteam parents: 1 diff changeset	247
4 5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	248 ## =================================================================================
2 b2d9c92bc431 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit a6fd77be465068f709a71d377900da99becf94d8 imgteam parents: 1 diff changeset	249 #end if
b2d9c92bc431 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit a6fd77be465068f709a71d377900da99becf94d8 imgteam parents: 1 diff changeset	250
4 5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	251 "filter_type": "$setup.filter.filter_type"
2 b2d9c92bc431 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit a6fd77be465068f709a71d377900da99becf94d8 imgteam parents: 1 diff changeset	252
b2d9c92bc431 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit a6fd77be465068f709a71d377900da99becf94d8 imgteam parents: 1 diff changeset	253 }
b2d9c92bc431 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit a6fd77be465068f709a71d377900da99becf94d8 imgteam parents: 1 diff changeset	254 ]]></configfile>
b2d9c92bc431 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit a6fd77be465068f709a71d377900da99becf94d8 imgteam parents: 1 diff changeset	255 </configfiles>
0 96fe54355774 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_simple_filter/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581 imgteam parents: diff changeset	256 <inputs>
4 5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	257 <conditional name="setup">
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	258 <param name="target" type="select" label="Type of image data to process"
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	259 help='Select "2-D image data" or "3-D image data" if you want to filter 2-D images or 3-D images, respectively, or series thereof (e.g., stacks or hyperstacks, such as temporal image sequences).'>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	260 <option value="2d" selected="true">2-D image data (or series thereof)</option>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	261 <option value="3d">3-D image data (or series thereof)</option>
2 b2d9c92bc431 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit a6fd77be465068f709a71d377900da99becf94d8 imgteam parents: 1 diff changeset	262 </param>
4 5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	263 <!-- Processing 2-D image data -->
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	264 <when value="2d">
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	265 <param name="input" type="data" format="tiff,zarr,png,jpg" label="Input image (2-D)">
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	266 <!--
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	267 The OME-Zarr datatype in Galaxy is currently not derived from the Image datatype, and it does
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	268 hence not inherit the metadata fields like `depth`. To cope with that, we allow all datasets
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	269 for 2-D processing except those which are known to be 3-D.
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	270 -->
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	271 <validator type="expression" message="Dataset is not a 2-D image"
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	272 ><![CDATA[getattr(value.metadata, "depth", None) in (None, '') or int(value.metadata.depth) < 2]]></validator>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	273 </param>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	274 <expand macro="filter" entities="pixels">
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	275 <token name="gaussian_order1">
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	276 <expand macro="select_direction" label="@DERIVATIVE_AXIS_LABEL@" help="@DERIVATIVE_AXIS_HELP@"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	277 <expand macro="select_dtype"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	278 </token>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	279 <token name="gaussian_order2">
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	280 <expand macro="select_direction" label="@DERIVATIVE_AXIS_LABEL@" help="@DERIVATIVE_AXIS_HELP@"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	281 <expand macro="select_dtype"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	282 </token>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	283 <token name="prewitt">
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	284 <expand macro="select_direction" label="@DERIVATIVE_AXIS_LABEL@" help="@PREWITT_AXIS_HELP@"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	285 <expand macro="select_dtype"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	286 </token>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	287 <token name="sobel">
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	288 <expand macro="select_direction" label="@DERIVATIVE_AXIS_LABEL@" help="@SOBEL_AXIS_HELP@"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	289 <expand macro="select_dtype"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	290 </token>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	291 </expand>
2 b2d9c92bc431 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit a6fd77be465068f709a71d377900da99becf94d8 imgteam parents: 1 diff changeset	292 </when>
4 5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	293 <!-- Processing 3-D image data -->
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	294 <when value="3d">
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	295 <param name="input" type="data" format="tiff,zarr" label="Input image (3-D)">
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	296 <!--
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	297 The OME-Zarr datatype in Galaxy is currently not derived from the Image datatype, and it does
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	298 hence not inherit the metadata fields like `depth`. To cope with that, we allow all datasets
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	299 for 3-D processing except those which are known to be 2-D.
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	300 -->
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	301 <validator type="expression" message="Dataset is not a 3-D image"
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	302 ><![CDATA[getattr(value.metadata, "depth", None) in (None, '') or int(value.metadata.depth) >= 2]]></validator>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	303 </param>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	304 <expand macro="filter" entities="voxels">
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	305 <token name="gaussian_order0">
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	306 <expand macro="select_axes_2d_or_3d"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	307 </token>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	308 <token name="gaussian_order1">
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	309 <expand macro="select_dtype"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	310 <expand macro="directed_3d_full" axis_label="@DERIVATIVE_AXIS_LABEL@" axis_help="@DERIVATIVE_AXIS_HELP@"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	311 </token>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	312 <token name="gaussian_order2">
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	313 <expand macro="select_dtype"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	314 <expand macro="directed_3d_full" axis_label="@DERIVATIVE_AXIS_LABEL@" axis_help="@DERIVATIVE_AXIS_HELP@"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	315 </token>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	316 <token name="uniform">
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	317 <expand macro="select_axes_2d_or_3d"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	318 </token>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	319 <token name="median">
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	320 <expand macro="select_axes_2d_or_3d"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	321 </token>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	322 <token name="prewitt">
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	323 <expand macro="select_dtype"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	324 <expand macro="directed_3d" axis_label="@DERIVATIVE_AXIS_LABEL@" axis_help="@PREWITT_AXIS_HELP@"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	325 </token>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	326 <token name="sobel">
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	327 <expand macro="select_dtype"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	328 <expand macro="directed_3d" axis_label="@DERIVATIVE_AXIS_LABEL@" axis_help="@SOBEL_AXIS_HELP@"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	329 </token>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	330 </expand>
2 b2d9c92bc431 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit a6fd77be465068f709a71d377900da99becf94d8 imgteam parents: 1 diff changeset	331 </when>
b2d9c92bc431 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit a6fd77be465068f709a71d377900da99becf94d8 imgteam parents: 1 diff changeset	332 </conditional>
0 96fe54355774 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_simple_filter/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581 imgteam parents: diff changeset	333 </inputs>
96fe54355774 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_simple_filter/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581 imgteam parents: diff changeset	334 <outputs>
3 53c55776a974 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit 8e99ddb62ceab1da15996906a0813826b62d38fe imgteam parents: 2 diff changeset	335 <data format="tiff" name="output"/>
0 96fe54355774 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_simple_filter/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581 imgteam parents: diff changeset	336 </outputs>
96fe54355774 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_simple_filter/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581 imgteam parents: diff changeset	337 <tests>
4 5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	338 <!--
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	339 =========================================================================================================
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	340 === TESTS: 2-D images
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	341 =========================================================================================================
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	342 -->
2 b2d9c92bc431 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit a6fd77be465068f709a71d377900da99becf94d8 imgteam parents: 1 diff changeset	343 <test>
4 5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	344 <!--
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	345 Test 1: GAUSSIAN, range of values is preserved
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	346 ==============================================
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	347
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	348 The input file `input1_uint8.tiff` has values ranging between 23 and 254, with a mean value of 63.67.
2 b2d9c92bc431 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit a6fd77be465068f709a71d377900da99becf94d8 imgteam parents: 1 diff changeset	349
4 5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	350 Below, we use an assertion in addition to the `image_diff` comparison, to ensure that the range of
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	351 values is preserved. The motiviation behind this is that the expectation images are usually checked
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	352 visually, which means that the `image_diff` comparison is likely to ensure that the brightness of
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	353 the image is correct, thus it's good to double-check the range of values (hence the comparably large
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	354 value for `eps`). This also concerns the Median and Box filters (see below).
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	355 -->
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	356 <conditional name="setup">
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	357 <param name="target" value="2d"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	358 <param name="input" value="input/input1_uint8.tiff"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	359 <conditional name="filter">
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	360 <param name="filter_type" value="gaussian"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	361 </conditional>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	362 </conditional>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	363 <expand macro="tests/intensity_image_diff" name="output" value="output/input1_gaussian.tiff" ftype="tiff">
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	364 <!-- Mean of Gaussian filter is approximately the mean intensity value of the image: -->
2 b2d9c92bc431 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit a6fd77be465068f709a71d377900da99becf94d8 imgteam parents: 1 diff changeset	365 <has_image_mean_intensity mean_intensity="63.67" eps="10"/>
b2d9c92bc431 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit a6fd77be465068f709a71d377900da99becf94d8 imgteam parents: 1 diff changeset	366 </expand>
4 5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	367 <assert_stdout>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	368 <has_line line="Input image shape: (1, 1, 1, 265, 329, 1)"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	369 <has_line line="Input image axes: QTZYXC"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	370 <has_line line="Input image dtype: uint8"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	371 <has_line line="Applying filter: gaussian_filter with sigma=3.0, order=0, axes='YX'"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	372 <has_line line="Output image shape: (265, 329)"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	373 <has_line line="Output image axes: YX"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	374 <has_line line="Output image dtype: uint8"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	375 </assert_stdout>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	376 </test>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	377 <test>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	378 <!--
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	379 Test 2: GAUSSIAN, test `sigma` parameter
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	380 ========================================
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	381 -->
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	382 <conditional name="setup">
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	383 <param name="target" value="2d"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	384 <param name="input" value="input/input1_uint8.tiff"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	385 <conditional name="filter">
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	386 <param name="filter_type" value="gaussian"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	387 <param name="sigma" value="1.0"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	388 </conditional>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	389 </conditional>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	390 <expand macro="tests/intensity_image_diff" name="output" value="output/input1_gaussian_sigma1.tiff" ftype="tiff"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	391 <assert_stdout>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	392 <has_line line="Input image shape: (1, 1, 1, 265, 329, 1)"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	393 <has_line line="Input image axes: QTZYXC"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	394 <has_line line="Input image dtype: uint8"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	395 <has_line line="Applying filter: gaussian_filter with sigma=1.0, order=0, axes='YX'"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	396 <has_line line="Output image shape: (265, 329)"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	397 <has_line line="Output image axes: YX"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	398 <has_line line="Output image dtype: uint8"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	399 </assert_stdout>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	400 </test>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	401 <test>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	402 <!--
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	403 Test 3: GAUSSIAN, test data with anisotropic pixels
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	404 ===================================================
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	405 -->
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	406 <conditional name="setup">
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	407 <param name="target" value="2d"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	408 <param name="input" value="input/input3_uint16.tiff"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	409 <conditional name="filter">
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	410 <param name="filter_type" value="gaussian"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	411 </conditional>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	412 </conditional>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	413 <expand macro="tests/intensity_image_diff" name="output" value="output/input3_gaussian.tiff" ftype="tiff"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	414 <assert_stdout>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	415 <has_line line="Input image shape: (1, 1, 1, 58, 64, 3)"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	416 <has_line line="Input image axes: QTZYXC"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	417 <has_line line="Input image dtype: uint16"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	418 <has_line_matching expression="^Anisotropy of YX pixels/voxels: $1\.414[0-9]+, 0\.707[0-9]+$$"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	419 <has_line_matching expression="^Applying filter: gaussian_filter with sigma=$2\.121[0-9]+, 4\.242[0-9]+$, order=0, axes='YX'$"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	420 <has_line line="Output image shape: (58, 64, 3)"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	421 <has_line line="Output image axes: YXC"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	422 <has_line line="Output image dtype: uint16"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	423 </assert_stdout>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	424 </test>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	425 <test>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	426 <!--
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	427 Test 4: GAUSSIAN, test data with anisotropic pixels and `"anisotropic": false`
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	428 ==============================================================================
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	429 -->
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	430 <conditional name="setup">
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	431 <param name="target" value="2d"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	432 <param name="input" value="input/input3_uint16.tiff"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	433 <conditional name="filter">
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	434 <param name="filter_type" value="gaussian"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	435 <param name="anisotropic" value="false"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	436 </conditional>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	437 </conditional>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	438 <expand macro="tests/intensity_image_diff" name="output" value="output/input3_gaussian_anisotropic-off.tiff" ftype="tiff"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	439 <assert_stdout>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	440 <has_line line="Input image shape: (1, 1, 1, 58, 64, 3)"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	441 <has_line line="Input image axes: QTZYXC"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	442 <has_line line="Input image dtype: uint16"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	443 <has_line line="Applying filter: gaussian_filter with sigma=3.0, order=0, axes='YX'"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	444 <has_line line="Output image shape: (58, 64, 3)"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	445 <has_line line="Output image axes: YXC"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	446 <has_line line="Output image dtype: uint16"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	447 </assert_stdout>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	448 </test>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	449 <test>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	450 <!--
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	451 Test 5: GAUSSIAN, test `"order": 1` (default is horizontal)
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	452 ===========================================================
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	453 -->
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	454 <conditional name="setup">
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	455 <param name="target" value="2d"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	456 <param name="input" value="input/input1_uint8.tiff"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	457 <conditional name="filter">
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	458 <param name="filter_type" value="gaussian"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	459 <conditional name="derivative">
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	460 <param name="order" value="1"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	461 </conditional>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	462 </conditional>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	463 </conditional>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	464 <expand macro="tests/intensity_image_diff" name="output" value="output/input1_gaussian_order1.tiff" ftype="tiff"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	465 <assert_stdout>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	466 <has_line line="Input image shape: (1, 1, 1, 265, 329, 1)"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	467 <has_line line="Input image axes: QTZYXC"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	468 <has_line line="Input image dtype: uint8"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	469 <has_line line="Applying filter: gaussian_filter with sigma=3.0, order=(0, 1), axes='YX'"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	470 <has_line line="Output image shape: (265, 329)"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	471 <has_line line="Output image axes: YX"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	472 <has_line line="Output image dtype: float64"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	473 </assert_stdout>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	474 </test>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	475 <test>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	476 <!--
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	477 Test 6: GAUSSIAN, test `"order": 1`, `"direction": 0` (vertical)
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	478 ================================================================
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	479 -->
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	480 <conditional name="setup">
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	481 <param name="target" value="2d"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	482 <param name="input" value="input/input1_uint8.tiff"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	483 <conditional name="filter">
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	484 <param name="filter_type" value="gaussian"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	485 <conditional name="derivative">
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	486 <param name="order" value="1"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	487 <param name="direction" value="0"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	488 </conditional>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	489 </conditional>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	490 </conditional>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	491 <expand macro="tests/intensity_image_diff" name="output" value="output/input1_gaussian_order1_direction0.tiff" ftype="tiff"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	492 <assert_stdout>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	493 <has_line line="Input image shape: (1, 1, 1, 265, 329, 1)"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	494 <has_line line="Input image axes: QTZYXC"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	495 <has_line line="Input image dtype: uint8"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	496 <has_line line="Applying filter: gaussian_filter with sigma=3.0, order=(1, 0), axes='YX'"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	497 <has_line line="Output image shape: (265, 329)"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	498 <has_line line="Output image axes: YX"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	499 <has_line line="Output image dtype: float64"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	500 </assert_stdout>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	501 </test>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	502 <test>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	503 <!--
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	504 Test 7: GAUSSAIN, test `"order": 2`
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	505 ===================================
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	506 -->
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	507 <conditional name="setup">
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	508 <param name="target" value="2d"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	509 <param name="input" value="input/input1_uint8.tiff"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	510 <conditional name="filter">
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	511 <param name="filter_type" value="gaussian"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	512 <conditional name="derivative">
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	513 <param name="order" value="2"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	514 </conditional>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	515 </conditional>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	516 </conditional>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	517 <expand macro="tests/intensity_image_diff" name="output" value="output/input1_gaussian_order2.tiff" ftype="tiff"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	518 <assert_stdout>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	519 <has_line line="Input image shape: (1, 1, 1, 265, 329, 1)"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	520 <has_line line="Input image axes: QTZYXC"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	521 <has_line line="Input image dtype: uint8"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	522 <has_line line="Applying filter: gaussian_filter with sigma=3.0, order=(0, 2), axes='YX'"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	523 <has_line line="Output image shape: (265, 329)"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	524 <has_line line="Output image axes: YX"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	525 <has_line line="Output image dtype: float64"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	526 </assert_stdout>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	527 </test>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	528 <test>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	529 <!--
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	530 Test 8: BOX, range of values is preserved
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	531 =========================================
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	532
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	533 The input file `input1_uint8.tiff` has values ranging between 23 and 254, with a mean value of 63.67.
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	534
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	535 Below, we use an assertion in addition to the `image_diff` comparison, to ensure that the range of
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	536 values is preserved. The motiviation behind this is that the expectation images are usually checked
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	537 visually, which means that the `image_diff` comparison is likely to ensure that the brightness of
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	538 the image is correct, thus it's good to double-check the range of values (hence the comparably large
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	539 value for `eps`). This also concerns the Gaussian (see above) and Median filters (see below).
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	540 -->
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	541 <conditional name="setup">
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	542 <param name="target" value="2d"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	543 <param name="input" value="input/input1_uint8.tiff"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	544 <conditional name="filter">
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	545 <param name="filter_type" value="uniform"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	546 </conditional>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	547 </conditional>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	548 <expand macro="tests/intensity_image_diff" name="output" value="output/input1_uniform.tiff" ftype="tiff">
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	549 <!-- Mean of Box filter is approximately the mean intensity value of the image: -->
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	550 <has_image_mean_intensity mean_intensity="63.67" eps="10"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	551 </expand>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	552 <assert_stdout>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	553 <has_line line="Input image shape: (1, 1, 1, 265, 329, 1)"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	554 <has_line line="Input image axes: QTZYXC"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	555 <has_line line="Input image dtype: uint8"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	556 <has_line line="Applying filter: uniform_filter with size=3, axes='YX'"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	557 <has_line line="Output image shape: (265, 329)"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	558 <has_line line="Output image axes: YX"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	559 <has_line line="Output image dtype: uint8"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	560 </assert_stdout>
2 b2d9c92bc431 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit a6fd77be465068f709a71d377900da99becf94d8 imgteam parents: 1 diff changeset	561 </test>
b2d9c92bc431 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit a6fd77be465068f709a71d377900da99becf94d8 imgteam parents: 1 diff changeset	562 <test>
4 5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	563 <!--
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	564 Test 9: BOX, test `size` parameter
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	565 ==================================
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	566 -->
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	567 <conditional name="setup">
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	568 <param name="target" value="2d"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	569 <param name="input" value="input/input1_uint8.tiff"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	570 <conditional name="filter">
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	571 <param name="filter_type" value="uniform"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	572 <param name="size" value="5"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	573 </conditional>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	574 </conditional>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	575 <expand macro="tests/intensity_image_diff" name="output" value="output/input1_uniform_size5.tiff" ftype="tiff"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	576 <assert_stdout>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	577 <has_line line="Input image shape: (1, 1, 1, 265, 329, 1)"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	578 <has_line line="Input image axes: QTZYXC"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	579 <has_line line="Input image dtype: uint8"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	580 <has_line line="Applying filter: uniform_filter with size=5, axes='YX'"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	581 <has_line line="Output image shape: (265, 329)"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	582 <has_line line="Output image axes: YX"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	583 <has_line line="Output image dtype: uint8"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	584 </assert_stdout>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	585 </test>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	586 <test>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	587 <!--
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	588 Test 10: BOX, test data with anisotropic pixels
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	589 ===============================================
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	590 -->
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	591 <conditional name="setup">
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	592 <param name="target" value="2d"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	593 <param name="input" value="input/input3_uint16.tiff"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	594 <conditional name="filter">
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	595 <param name="filter_type" value="uniform"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	596 </conditional>
2 b2d9c92bc431 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit a6fd77be465068f709a71d377900da99becf94d8 imgteam parents: 1 diff changeset	597 </conditional>
4 5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	598 <expand macro="tests/intensity_image_diff" name="output" value="output/input3_uniform.tiff" ftype="tiff"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	599 <assert_stdout>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	600 <has_line line="Input image shape: (1, 1, 1, 58, 64, 3)"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	601 <has_line line="Input image axes: QTZYXC"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	602 <has_line line="Input image dtype: uint16"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	603 <has_line_matching expression="^Anisotropy of YX pixels/voxels: $1\.414[0-9]+, 0\.707[0-9]+$$"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	604 <has_line line="Applying filter: uniform_filter with size=(2, 4), axes='YX'"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	605 <has_line line="Output image shape: (58, 64, 3)"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	606 <has_line line="Output image axes: YXC"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	607 <has_line line="Output image dtype: uint16"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	608 </assert_stdout>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	609 </test>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	610 <test>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	611 <!--
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	612 Test 11: BOX, test data with anisotropic pixels and `"anisotropic": false`
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	613 ==========================================================================
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	614 -->
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	615 <conditional name="setup">
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	616 <param name="target" value="2d"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	617 <param name="input" value="input/input3_uint16.tiff"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	618 <conditional name="filter">
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	619 <param name="filter_type" value="uniform"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	620 <param name="anisotropic" value="false"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	621 </conditional>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	622 </conditional>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	623 <expand macro="tests/intensity_image_diff" name="output" value="output/input3_uniform_anisotropic-off.tiff" ftype="tiff"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	624 <assert_stdout>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	625 <has_line line="Input image shape: (1, 1, 1, 58, 64, 3)"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	626 <has_line line="Input image axes: QTZYXC"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	627 <has_line line="Input image dtype: uint16"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	628 <has_line line="Applying filter: uniform_filter with size=3, axes='YX'"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	629 <has_line line="Output image shape: (58, 64, 3)"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	630 <has_line line="Output image axes: YXC"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	631 <has_line line="Output image dtype: uint16"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	632 </assert_stdout>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	633 </test>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	634 <test>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	635 <!--
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	636 Test 12: MEDIAN, range of values is preserved
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	637 =============================================
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	638
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	639 The input file `input1_uint8.tiff` has values ranging between 23 and 254, with a mean value of 63.67.
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	640
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	641 Below, we use an assertion in addition to the `image_diff` comparison, to ensure that the range of
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	642 values is preserved. The motiviation behind this is that the expectation images are usually checked
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	643 visually, which means that the `image_diff` comparison is likely to ensure that the brightness of
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	644 the image is correct, thus it's good to double-check the range of values (hence the comparably large
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	645 value for `eps`). This also concerns the Gaussian and Box filters (see above).
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	646 -->
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	647 <conditional name="setup">
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	648 <param name="target" value="2d"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	649 <param name="input" value="input/input1_uint8.tiff"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	650 <conditional name="filter">
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	651 <param name="filter_type" value="median"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	652 </conditional>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	653 </conditional>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	654 <expand macro="tests/intensity_image_diff" name="output" value="output/input1_median.tiff" ftype="tiff">
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	655 <!-- Mean of Median filter is approximately the mean intensity value of the image: -->
2 b2d9c92bc431 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit a6fd77be465068f709a71d377900da99becf94d8 imgteam parents: 1 diff changeset	656 <has_image_mean_intensity mean_intensity="63.67" eps="10"/>
b2d9c92bc431 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit a6fd77be465068f709a71d377900da99becf94d8 imgteam parents: 1 diff changeset	657 </expand>
4 5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	658 <assert_stdout>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	659 <has_line line="Input image shape: (1, 1, 1, 265, 329, 1)"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	660 <has_line line="Input image axes: QTZYXC"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	661 <has_line line="Input image dtype: uint8"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	662 <has_line line="Applying filter: median_filter with size=3, axes='YX'"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	663 <has_line line="Output image shape: (265, 329)"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	664 <has_line line="Output image axes: YX"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	665 <has_line line="Output image dtype: uint8"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	666 </assert_stdout>
2 b2d9c92bc431 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit a6fd77be465068f709a71d377900da99becf94d8 imgteam parents: 1 diff changeset	667 </test>
b2d9c92bc431 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit a6fd77be465068f709a71d377900da99becf94d8 imgteam parents: 1 diff changeset	668 <test>
4 5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	669 <!--
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	670 Test 13: MEDIAN, test `size` parameter
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	671 ======================================
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	672 -->
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	673 <conditional name="setup">
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	674 <param name="target" value="2d"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	675 <param name="input" value="input/input1_uint8.tiff"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	676 <conditional name="filter">
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	677 <param name="filter_type" value="median"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	678 <param name="size" value="5"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	679 </conditional>
2 b2d9c92bc431 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit a6fd77be465068f709a71d377900da99becf94d8 imgteam parents: 1 diff changeset	680 </conditional>
4 5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	681 <expand macro="tests/intensity_image_diff" name="output" value="output/input1_median_size5.tiff" ftype="tiff"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	682 <assert_stdout>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	683 <has_line line="Input image shape: (1, 1, 1, 265, 329, 1)"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	684 <has_line line="Input image axes: QTZYXC"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	685 <has_line line="Input image dtype: uint8"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	686 <has_line line="Applying filter: median_filter with size=5, axes='YX'"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	687 <has_line line="Output image shape: (265, 329)"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	688 <has_line line="Output image axes: YX"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	689 <has_line line="Output image dtype: uint8"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	690 </assert_stdout>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	691 </test>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	692 <test>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	693 <!--
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	694 Test 14: MEDIAN, test data with anisotropic pixels
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	695 ==================================================
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	696 -->
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	697 <conditional name="setup">
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	698 <param name="target" value="2d"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	699 <param name="input" value="input/input3_uint16.tiff"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	700 <conditional name="filter">
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	701 <param name="filter_type" value="median"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	702 </conditional>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	703 </conditional>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	704 <expand macro="tests/intensity_image_diff" name="output" value="output/input3_median.tiff" ftype="tiff"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	705 <assert_stdout>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	706 <has_line line="Input image shape: (1, 1, 1, 58, 64, 3)"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	707 <has_line line="Input image axes: QTZYXC"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	708 <has_line line="Input image dtype: uint16"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	709 <has_line_matching expression="^Anisotropy of YX pixels/voxels: $1\.414[0-9]+, 0\.707[0-9]+$$"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	710 <has_line line="Applying filter: median_filter with size=(2, 4), axes='YX'"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	711 <has_line line="Output image shape: (58, 64, 3)"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	712 <has_line line="Output image axes: YXC"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	713 <has_line line="Output image dtype: uint16"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	714 </assert_stdout>
2 b2d9c92bc431 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit a6fd77be465068f709a71d377900da99becf94d8 imgteam parents: 1 diff changeset	715 </test>
b2d9c92bc431 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit a6fd77be465068f709a71d377900da99becf94d8 imgteam parents: 1 diff changeset	716 <test>
4 5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	717 <!--
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	718 Test 15: MEDIAN, test data with anisotropic pixels and `"anisotropic": false`
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	719 =============================================================================
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	720 -->
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	721 <conditional name="setup">
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	722 <param name="target" value="2d"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	723 <param name="input" value="input/input3_uint16.tiff"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	724 <conditional name="filter">
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	725 <param name="filter_type" value="median"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	726 <param name="anisotropic" value="false"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	727 </conditional>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	728 </conditional>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	729 <expand macro="tests/intensity_image_diff" name="output" value="output/input3_median_anisotropic-off.tiff" ftype="tiff"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	730 <assert_stdout>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	731 <has_line line="Input image shape: (1, 1, 1, 58, 64, 3)"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	732 <has_line line="Input image axes: QTZYXC"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	733 <has_line line="Input image dtype: uint16"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	734 <has_line line="Applying filter: median_filter with size=3, axes='YX'"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	735 <has_line line="Output image shape: (58, 64, 3)"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	736 <has_line line="Output image axes: YXC"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	737 <has_line line="Output image dtype: uint16"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	738 </assert_stdout>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	739 </test>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	740 <test>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	741 <!--
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	742 Test 16: PREWITT (default is horizontal)
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	743 ========================================
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	744 -->
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	745 <conditional name="setup">
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	746 <param name="target" value="2d"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	747 <param name="input" value="input/input1_uint8.tiff"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	748 <conditional name="filter">
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	749 <param name="filter_type" value="prewitt"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	750 </conditional>
2 b2d9c92bc431 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit a6fd77be465068f709a71d377900da99becf94d8 imgteam parents: 1 diff changeset	751 </conditional>
4 5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	752 <expand macro="tests/intensity_image_diff" name="output" value="output/input1_prewitt.tiff" ftype="tiff"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	753 <assert_stdout>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	754 <has_line line="Input image shape: (1, 1, 1, 265, 329, 1)"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	755 <has_line line="Input image axes: QTZYXC"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	756 <has_line line="Input image dtype: uint8"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	757 <has_line line="Applying filter: prewitt with axis=1, axes='YX'"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	758 <has_line line="Output image shape: (265, 329)"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	759 <has_line line="Output image axes: YX"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	760 <has_line line="Output image dtype: float64"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	761 </assert_stdout>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	762 </test>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	763 <test>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	764 <!--
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	765 Test 17: PREWITT, test `"direction": 0` (vertical)
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	766 ==================================================
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	767 -->
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	768 <conditional name="setup">
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	769 <param name="target" value="2d"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	770 <param name="input" value="input/input1_uint8.tiff"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	771 <conditional name="filter">
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	772 <param name="filter_type" value="prewitt"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	773 <param name="direction" value="0"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	774 </conditional>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	775 </conditional>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	776 <expand macro="tests/intensity_image_diff" name="output" value="output/input1_prewitt_direction0.tiff" ftype="tiff"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	777 <assert_stdout>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	778 <has_line line="Input image shape: (1, 1, 1, 265, 329, 1)"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	779 <has_line line="Input image axes: QTZYXC"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	780 <has_line line="Input image dtype: uint8"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	781 <has_line line="Applying filter: prewitt with axis=0, axes='YX'"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	782 <has_line line="Output image shape: (265, 329)"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	783 <has_line line="Output image axes: YX"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	784 <has_line line="Output image dtype: float64"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	785 </assert_stdout>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	786 </test>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	787 <test>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	788 <!--
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	789 Test 18: SOBEL (default is horizontal)
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	790 ======================================
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	791 -->
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	792 <conditional name="setup">
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	793 <param name="target" value="2d"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	794 <param name="input" value="input/input1_uint8.tiff"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	795 <conditional name="filter">
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	796 <param name="filter_type" value="sobel"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	797 </conditional>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	798 </conditional>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	799 <expand macro="tests/intensity_image_diff" name="output" value="output/input1_sobel.tiff" ftype="tiff"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	800 <assert_stdout>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	801 <has_line line="Input image shape: (1, 1, 1, 265, 329, 1)"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	802 <has_line line="Input image axes: QTZYXC"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	803 <has_line line="Input image dtype: uint8"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	804 <has_line line="Applying filter: sobel with axis=1, axes='YX'"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	805 <has_line line="Output image shape: (265, 329)"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	806 <has_line line="Output image axes: YX"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	807 <has_line line="Output image dtype: float64"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	808 </assert_stdout>
2 b2d9c92bc431 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit a6fd77be465068f709a71d377900da99becf94d8 imgteam parents: 1 diff changeset	809 </test>
b2d9c92bc431 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit a6fd77be465068f709a71d377900da99becf94d8 imgteam parents: 1 diff changeset	810 <test>
4 5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	811 <!--
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	812 Test 19: SOBEL, test `"direction": 0` (vertical)
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	813 ================================================
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	814 -->
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	815 <conditional name="setup">
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	816 <param name="target" value="2d"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	817 <param name="input" value="input/input1_uint8.tiff"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	818 <conditional name="filter">
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	819 <param name="filter_type" value="sobel"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	820 <param name="direction" value="0"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	821 </conditional>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	822 </conditional>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	823 <expand macro="tests/intensity_image_diff" name="output" value="output/input1_sobel_direction0.tiff" ftype="tiff"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	824 <assert_stdout>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	825 <has_line line="Input image shape: (1, 1, 1, 265, 329, 1)"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	826 <has_line line="Input image axes: QTZYXC"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	827 <has_line line="Input image dtype: uint8"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	828 <has_line line="Applying filter: sobel with axis=0, axes='YX'"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	829 <has_line line="Output image shape: (265, 329)"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	830 <has_line line="Output image axes: YX"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	831 <has_line line="Output image dtype: float64"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	832 </assert_stdout>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	833 </test>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	834 <!--
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	835 =========================================================================================================
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	836 === TESTS: 3-D images
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	837 =========================================================================================================
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	838 -->
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	839 <test>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	840 <!--
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	841 Test 20: GAUSSIAN, defaults
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	842 ===========================
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	843 -->
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	844 <conditional name="setup">
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	845 <param name="target" value="3d"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	846 <param name="input" value="input/input4_float16.tiff"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	847 <conditional name="filter">
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	848 <param name="filter_type" value="gaussian"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	849 </conditional>
2 b2d9c92bc431 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit a6fd77be465068f709a71d377900da99becf94d8 imgteam parents: 1 diff changeset	850 </conditional>
4 5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	851 <expand macro="tests/intensity_image_diff" name="output" value="output/input4_gaussian.tiff" ftype="tiff"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	852 <assert_stdout>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	853 <has_line line="Input image shape: (1, 1, 10, 15, 18, 1)"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	854 <has_line line="Input image axes: QTZYXC"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	855 <has_line line="Input image dtype: float16"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	856 <has_line line="Anisotropy of ZYX pixels/voxels: (2.0, 1.0, 0.5)"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	857 <has_line line="Applying filter: gaussian_filter with sigma=(1.5, 3.0, 6.0), order=0, axes='ZYX'"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	858 <has_line line="Output image shape: (10, 15, 18)"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	859 <has_line line="Output image axes: ZYX"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	860 <has_line line="Output image dtype: float16"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	861 </assert_stdout>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	862 </test>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	863 <test>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	864 <!--
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	865 Test 21: GAUSSIAN, test `"anisotropic": false`
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	866 ==============================================
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	867 -->
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	868 <conditional name="setup">
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	869 <param name="target" value="3d"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	870 <param name="input" value="input/input4_float16.tiff"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	871 <conditional name="filter">
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	872 <param name="filter_type" value="gaussian"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	873 <param name="anisotropic" value="false"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	874 </conditional>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	875 </conditional>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	876 <expand macro="tests/intensity_image_diff" name="output" value="output/input4_gaussian_anisotropic-off.tiff" ftype="tiff"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	877 <assert_stdout>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	878 <has_line line="Input image shape: (1, 1, 10, 15, 18, 1)"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	879 <has_line line="Input image axes: QTZYXC"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	880 <has_line line="Input image dtype: float16"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	881 <has_line line="Applying filter: gaussian_filter with sigma=3.0, order=0, axes='ZYX'"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	882 <has_line line="Output image shape: (10, 15, 18)"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	883 <has_line line="Output image axes: ZYX"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	884 <has_line line="Output image dtype: float16"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	885 </assert_stdout>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	886 </test>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	887 <test>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	888 <!--
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	889 Test 22: GAUSSIAN, test `"axes": "YX"`
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	890 ======================================
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	891 -->
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	892 <conditional name="setup">
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	893 <param name="target" value="3d"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	894 <param name="input" value="input/input4_float16.tiff"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	895 <conditional name="filter">
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	896 <param name="filter_type" value="gaussian"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	897 <conditional name="derivative">
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	898 <param name="axes" value="YX"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	899 </conditional>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	900 </conditional>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	901 </conditional>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	902 <expand macro="tests/intensity_image_diff" name="output" value="output/input4_gaussian_yx.tiff" ftype="tiff"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	903 <assert_stdout>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	904 <has_line line="Input image shape: (1, 1, 10, 15, 18, 1)"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	905 <has_line line="Input image axes: QTZYXC"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	906 <has_line line="Input image dtype: float16"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	907 <has_line_matching expression="^Anisotropy of YX pixels/voxels: $1\.414[0-9]+, 0\.707[0-9]+$$"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	908 <has_line_matching expression="^Applying filter: gaussian_filter with sigma=$2\.121[0-9]+, 4\.242[0-9]+$, order=0, axes='YX'$"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	909 <has_line line="Output image shape: (10, 15, 18)"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	910 <has_line line="Output image axes: ZYX"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	911 <has_line line="Output image dtype: float16"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	912 </assert_stdout>
2 b2d9c92bc431 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit a6fd77be465068f709a71d377900da99becf94d8 imgteam parents: 1 diff changeset	913 </test>
b2d9c92bc431 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit a6fd77be465068f709a71d377900da99becf94d8 imgteam parents: 1 diff changeset	914 <test>
4 5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	915 <!--
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	916 Test 23: GAUSSIAN, test `"axes": "YZ"`
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	917 ======================================
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	918 -->
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	919 <conditional name="setup">
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	920 <param name="target" value="3d"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	921 <param name="input" value="input/input4_float16.tiff"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	922 <conditional name="filter">
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	923 <param name="filter_type" value="gaussian"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	924 <conditional name="derivative">
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	925 <param name="axes" value="YZ"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	926 </conditional>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	927 </conditional>
2 b2d9c92bc431 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit a6fd77be465068f709a71d377900da99becf94d8 imgteam parents: 1 diff changeset	928 </conditional>
4 5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	929 <expand macro="tests/intensity_image_diff" name="output" value="output/input4_gaussian_yz.tiff" ftype="tiff"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	930 <assert_stdout>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	931 <has_line line="Input image shape: (1, 1, 10, 15, 18, 1)"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	932 <has_line line="Input image axes: QTZYXC"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	933 <has_line line="Input image dtype: float16"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	934 <has_line_matching expression="^Anisotropy of YZ pixels/voxels: $0\.707[0-9]+, 1\.414[0-9]+$$"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	935 <has_line_matching expression="^Applying filter: gaussian_filter with sigma=$4\.242[0-9]+, 2\.121[0-9]+$, order=0, axes='YZ'$"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	936 <has_line line="Output image shape: (10, 15, 18)"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	937 <has_line line="Output image axes: ZYX"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	938 <has_line line="Output image dtype: float16"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	939 </assert_stdout>
2 b2d9c92bc431 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit a6fd77be465068f709a71d377900da99becf94d8 imgteam parents: 1 diff changeset	940 </test>
4 5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	941 <test>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	942 <!--
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	943 Test 24: GAUSSIAN, test `"order": 1` (default is horizontal)
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	944 ============================================================
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	945 -->
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	946 <conditional name="setup">
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	947 <param name="target" value="3d"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	948 <param name="input" value="input/input4_float16.tiff"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	949 <conditional name="filter">
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	950 <param name="filter_type" value="gaussian"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	951 <conditional name="derivative">
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	952 <param name="order" value="1"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	953 </conditional>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	954 </conditional>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	955 </conditional>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	956 <expand macro="tests/intensity_image_diff" name="output" value="output/input4_gaussian_order1.tiff" ftype="tiff"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	957 <assert_stdout>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	958 <has_line line="Input image shape: (1, 1, 10, 15, 18, 1)"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	959 <has_line line="Input image axes: QTZYXC"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	960 <has_line line="Input image dtype: float16"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	961 <has_line line="Anisotropy of ZYX pixels/voxels: (2.0, 1.0, 0.5)"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	962 <has_line line="Applying filter: gaussian_filter with sigma=(1.5, 3.0, 6.0), order=(0, 0, 1), axes='ZYX'"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	963 <has_line line="Output image shape: (10, 15, 18)"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	964 <has_line line="Output image axes: ZYX"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	965 <has_line line="Output image dtype: float16"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	966 </assert_stdout>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	967 </test>
2 b2d9c92bc431 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit a6fd77be465068f709a71d377900da99becf94d8 imgteam parents: 1 diff changeset	968 <test>
4 5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	969 <!--
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	970 Test 25: GAUSSIAN, test `"order": 1`, `"direction": 1` (vertical)
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	971 =================================================================
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	972 -->
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	973 <conditional name="setup">
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	974 <param name="target" value="3d"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	975 <param name="input" value="input/input4_float16.tiff"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	976 <conditional name="filter">
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	977 <param name="filter_type" value="gaussian"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	978 <conditional name="derivative">
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	979 <param name="order" value="1"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	980 <conditional name="directed_3d">
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	981 <param name="direction" value="1"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	982 </conditional>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	983 </conditional>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	984 </conditional>
2 b2d9c92bc431 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit a6fd77be465068f709a71d377900da99becf94d8 imgteam parents: 1 diff changeset	985 </conditional>
4 5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	986 <expand macro="tests/intensity_image_diff" name="output" value="output/input4_gaussian_order1_direction1.tiff" ftype="tiff"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	987 <assert_stdout>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	988 <has_line line="Input image shape: (1, 1, 10, 15, 18, 1)"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	989 <has_line line="Input image axes: QTZYXC"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	990 <has_line line="Input image dtype: float16"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	991 <has_line line="Anisotropy of ZYX pixels/voxels: (2.0, 1.0, 0.5)"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	992 <has_line line="Applying filter: gaussian_filter with sigma=(1.5, 3.0, 6.0), order=(0, 1, 0), axes='ZYX'"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	993 <has_line line="Output image shape: (10, 15, 18)"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	994 <has_line line="Output image axes: ZYX"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	995 <has_line line="Output image dtype: float16"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	996 </assert_stdout>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	997 </test>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	998 <test>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	999 <!--
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1000 Test 26: GAUSSIAN, test `"order": 1`, `"axes": "XZ"`, `"direction": 1` (orthogonal)
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1001 ===================================================================================
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1002 -->
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1003 <conditional name="setup">
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1004 <param name="target" value="3d"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1005 <param name="input" value="input/input4_float16.tiff"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1006 <conditional name="filter">
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1007 <param name="filter_type" value="gaussian"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1008 <conditional name="derivative">
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1009 <param name="order" value="1"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1010 <conditional name="directed_3d">
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1011 <param name="axes" value="XZ"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1012 <param name="direction" value="1"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1013 </conditional>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1014 </conditional>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1015 </conditional>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1016 </conditional>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1017 <expand macro="tests/intensity_image_diff" name="output" value="output/input4_gaussian_order1_xz_direction1.tiff" ftype="tiff"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1018 <assert_stdout>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1019 <has_line line="Input image shape: (1, 1, 10, 15, 18, 1)"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1020 <has_line line="Input image axes: QTZYXC"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1021 <has_line line="Input image dtype: float16"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1022 <has_line line="Anisotropy of XZ pixels/voxels: (0.5, 2.0)"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1023 <has_line line="Applying filter: gaussian_filter with sigma=(6.0, 1.5), order=(0, 1), axes='XZ'"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1024 <has_line line="Output image shape: (10, 15, 18)"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1025 <has_line line="Output image axes: ZYX"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1026 <has_line line="Output image dtype: float16"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1027 </assert_stdout>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1028 </test>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1029 <test>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1030 <!--
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1031 Test 27: BOX, defaults
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1032 ======================
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1033 -->
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1034 <conditional name="setup">
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1035 <param name="target" value="3d"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1036 <param name="input" value="input/input4_float16.tiff"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1037 <conditional name="filter">
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1038 <param name="filter_type" value="uniform"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1039 </conditional>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1040 </conditional>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1041 <expand macro="tests/intensity_image_diff" name="output" value="output/input4_uniform.tiff" ftype="tiff"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1042 <assert_stdout>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1043 <has_line line="Input image shape: (1, 1, 10, 15, 18, 1)"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1044 <has_line line="Input image axes: QTZYXC"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1045 <has_line line="Input image dtype: float16"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1046 <has_line line="Anisotropy of ZYX pixels/voxels: (2.0, 1.0, 0.5)"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1047 <has_line line="Applying filter: uniform_filter with size=(2, 3, 6), axes='ZYX'"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1048 <has_line line="Output image shape: (10, 15, 18)"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1049 <has_line line="Output image axes: ZYX"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1050 <has_line line="Output image dtype: float16"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1051 </assert_stdout>
2 b2d9c92bc431 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit a6fd77be465068f709a71d377900da99becf94d8 imgteam parents: 1 diff changeset	1052 </test>
b2d9c92bc431 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit a6fd77be465068f709a71d377900da99becf94d8 imgteam parents: 1 diff changeset	1053 <test>
4 5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1054 <!--
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1055 Test 28: MEDIAN, defaults
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1056 =========================
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1057 -->
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1058 <conditional name="setup">
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1059 <param name="target" value="3d"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1060 <param name="input" value="input/input4_float16.tiff"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1061 <conditional name="filter">
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1062 <param name="filter_type" value="median"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1063 </conditional>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1064 </conditional>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1065 <expand macro="tests/intensity_image_diff" name="output" value="output/input4_median.tiff" ftype="tiff"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1066 <assert_stdout>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1067 <has_line line="Input image shape: (1, 1, 10, 15, 18, 1)"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1068 <has_line line="Input image axes: QTZYXC"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1069 <has_line line="Input image dtype: float16"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1070 <has_line line="Anisotropy of ZYX pixels/voxels: (2.0, 1.0, 0.5)"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1071 <has_line line="Applying filter: median_filter with size=(2, 3, 6), axes='ZYX'"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1072 <has_line line="Output image shape: (10, 15, 18)"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1073 <has_line line="Output image axes: ZYX"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1074 <has_line line="Output image dtype: float16"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1075 </assert_stdout>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1076 </test>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1077 <test>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1078 <!--
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1079 Test 29: PREWITT, defaults
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1080 =========================
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1081 -->
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1082 <conditional name="setup">
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1083 <param name="target" value="3d"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1084 <param name="input" value="input/input4_float16.tiff"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1085 <conditional name="filter">
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1086 <param name="filter_type" value="prewitt"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1087 </conditional>
2 b2d9c92bc431 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit a6fd77be465068f709a71d377900da99becf94d8 imgteam parents: 1 diff changeset	1088 </conditional>
4 5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1089 <expand macro="tests/intensity_image_diff" name="output" value="output/input4_prewitt.tiff" ftype="tiff"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1090 <assert_stdout>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1091 <has_line line="Input image shape: (1, 1, 10, 15, 18, 1)"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1092 <has_line line="Input image axes: QTZYXC"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1093 <has_line line="Input image dtype: float16"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1094 <has_line line="Applying filter: prewitt with axis=1, axes='YX'"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1095 <has_line line="Output image shape: (10, 15, 18)"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1096 <has_line line="Output image axes: ZYX"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1097 <has_line line="Output image dtype: float16"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1098 </assert_stdout>
2 b2d9c92bc431 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit a6fd77be465068f709a71d377900da99becf94d8 imgteam parents: 1 diff changeset	1099 </test>
b2d9c92bc431 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit a6fd77be465068f709a71d377900da99becf94d8 imgteam parents: 1 diff changeset	1100 <test>
4 5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1101 <!--
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1102 Test 30: SOBEL, defaults
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1103 =========================
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1104 -->
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1105 <conditional name="setup">
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1106 <param name="target" value="3d"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1107 <param name="input" value="input/input4_float16.tiff"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1108 <conditional name="filter">
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1109 <param name="filter_type" value="sobel"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1110 </conditional>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1111 </conditional>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1112 <expand macro="tests/intensity_image_diff" name="output" value="output/input4_sobel.tiff" ftype="tiff"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1113 <assert_stdout>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1114 <has_line line="Input image shape: (1, 1, 10, 15, 18, 1)"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1115 <has_line line="Input image axes: QTZYXC"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1116 <has_line line="Input image dtype: float16"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1117 <has_line line="Applying filter: sobel with axis=1, axes='YX'"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1118 <has_line line="Output image shape: (10, 15, 18)"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1119 <has_line line="Output image axes: ZYX"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1120 <has_line line="Output image dtype: float16"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1121 </assert_stdout>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1122 </test>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1123 <!--
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1124 =========================================================================================================
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1125 === TESTS: Explicit `dtype` conversion
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1126 =========================================================================================================
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1127 -->
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1128 <test>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1129 <!--
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1130 Test 31: GAUSSIAN, uint8 input, test `"order": 1` (default is horizontal), `"dtype": "float16"`
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1131 ===============================================================================================
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1132 -->
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1133 <conditional name="setup">
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1134 <param name="target" value="2d"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1135 <param name="input" value="input/input1_uint8.tiff"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1136 <conditional name="filter">
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1137 <param name="filter_type" value="gaussian"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1138 <conditional name="derivative">
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1139 <param name="order" value="1"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1140 <param name="dtype" value="float16"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1141 </conditional>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1142 </conditional>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1143 </conditional>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1144 <expand macro="tests/intensity_image_diff" name="output" value="output/input1_gaussian_order1_float16.tiff" ftype="tiff"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1145 <assert_stdout>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1146 <has_line line="Input image shape: (1, 1, 1, 265, 329, 1)"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1147 <has_line line="Input image axes: QTZYXC"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1148 <has_line line="Input image dtype: uint8"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1149 <has_line line="Applying filter: gaussian_filter with sigma=3.0, order=(0, 1), axes='YX'"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1150 <has_line line="Output image shape: (265, 329)"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1151 <has_line line="Output image axes: YX"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1152 <has_line line="Output image dtype: float16"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1153 </assert_stdout>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1154 </test>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1155 <test>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1156 <!--
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1157 Test 32: PREWITT, uint8 input, `"dtype": "float16"`
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1158 ===================================================
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1159 -->
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1160 <conditional name="setup">
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1161 <param name="target" value="2d"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1162 <param name="input" value="input/input1_uint8.tiff"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1163 <conditional name="filter">
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1164 <param name="filter_type" value="prewitt"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1165 <param name="dtype" value="float16"/>
2 b2d9c92bc431 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit a6fd77be465068f709a71d377900da99becf94d8 imgteam parents: 1 diff changeset	1166 </conditional>
b2d9c92bc431 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit a6fd77be465068f709a71d377900da99becf94d8 imgteam parents: 1 diff changeset	1167 </conditional>
4 5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1168 <expand macro="tests/intensity_image_diff" name="output" value="output/input1_prewitt_float16.tiff" ftype="tiff"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1169 <assert_stdout>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1170 <has_line line="Input image shape: (1, 1, 1, 265, 329, 1)"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1171 <has_line line="Input image axes: QTZYXC"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1172 <has_line line="Input image dtype: uint8"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1173 <has_line line="Applying filter: prewitt with axis=1, axes='YX'"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1174 <has_line line="Output image shape: (265, 329)"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1175 <has_line line="Output image axes: YX"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1176 <has_line line="Output image dtype: float16"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1177 </assert_stdout>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1178 </test>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1179 <test>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1180 <!--
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1181 Test 33: SOBEL, float16 input, `"dtype": "float32"`
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1182 ===================================================
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1183 -->
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1184 <conditional name="setup">
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1185 <param name="target" value="3d"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1186 <param name="input" value="input/input4_float16.tiff"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1187 <conditional name="filter">
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1188 <param name="filter_type" value="sobel"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1189 <param name="dtype" value="float32"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1190 </conditional>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1191 </conditional>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1192 <expand macro="tests/intensity_image_diff" name="output" value="output/input4_sobel_float32.tiff" ftype="tiff"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1193 <assert_stdout>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1194 <has_line line="Input image shape: (1, 1, 10, 15, 18, 1)"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1195 <has_line line="Input image axes: QTZYXC"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1196 <has_line line="Input image dtype: float16"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1197 <has_line line="Applying filter: sobel with axis=1, axes='YX'"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1198 <has_line line="Output image shape: (10, 15, 18)"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1199 <has_line line="Output image axes: ZYX"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1200 <has_line line="Output image dtype: float32"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1201 </assert_stdout>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1202 </test>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1203 <!--
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1204 =========================================================================================================
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1205 === TESTS: Exotic datatypes
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1206 =========================================================================================================
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1207 -->
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1208 <test>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1209 <!--
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1210 Test 34: JPG
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1211 ============
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1212 -->
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1213 <conditional name="setup">
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1214 <param name="target" value="2d"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1215 <param name="input" value="input/input5.jpg"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1216 <conditional name="filter">
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1217 <param name="filter_type" value="gaussian"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1218 </conditional>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1219 </conditional>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1220 <expand macro="tests/intensity_image_diff" name="output" value="output/input5_gaussian.tiff" ftype="tiff"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1221 <assert_stdout>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1222 <has_line line="Input image shape: (1, 1, 1, 10, 10, 3)"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1223 <has_line line="Input image axes: QTZYXC"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1224 <has_line line="Input image dtype: uint8"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1225 <has_line line="Applying filter: gaussian_filter with sigma=3.0, order=0, axes='YX'"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1226 <has_line line="Output image shape: (10, 10, 3)"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1227 <has_line line="Output image axes: YXC"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1228 <has_line line="Output image dtype: uint8"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1229 </assert_stdout>
2 b2d9c92bc431 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit a6fd77be465068f709a71d377900da99becf94d8 imgteam parents: 1 diff changeset	1230 </test>
b2d9c92bc431 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit a6fd77be465068f709a71d377900da99becf94d8 imgteam parents: 1 diff changeset	1231 <test>
4 5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1232 <!--
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1233 Test 35: 2-D OME-Zarr
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1234 =====================
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1235 -->
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1236 <conditional name="setup">
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1237 <param name="target" value="2d"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1238 <param name="input" value="input/input6_yx.zarr"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1239 <conditional name="filter">
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1240 <param name="filter_type" value="gaussian"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1241 </conditional>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1242 </conditional>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1243 <expand macro="tests/intensity_image_diff" name="output" value="output/input6_gaussian.tiff" ftype="tiff"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1244 <assert_stdout>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1245 <has_line line="Input image shape: (1, 1, 1, 200, 200, 1)"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1246 <has_line line="Input image axes: QTZYXC"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1247 <has_line line="Input image dtype: float64"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1248 <has_line line="Anisotropy of YX pixels/voxels: (1.0, 1.0)"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1249 <has_line line="Applying filter: gaussian_filter with sigma=(3.0, 3.0), order=0, axes='YX'"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1250 <has_line line="Output image shape: (200, 200)"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1251 <has_line line="Output image axes: YX"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1252 <has_line line="Output image dtype: float64"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1253 </assert_stdout>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1254 </test>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1255 <test>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1256 <!--
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1257 Test 36: 3-D OME-Zarr
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1258 =====================
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1259 -->
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1260 <conditional name="setup">
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1261 <param name="target" value="3d"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1262 <param name="input" value="input/input7_zyx.zarr"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1263 <conditional name="filter">
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1264 <param name="filter_type" value="gaussian"/>
2 b2d9c92bc431 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit a6fd77be465068f709a71d377900da99becf94d8 imgteam parents: 1 diff changeset	1265 </conditional>
b2d9c92bc431 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit a6fd77be465068f709a71d377900da99becf94d8 imgteam parents: 1 diff changeset	1266 </conditional>
4 5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1267 <expand macro="tests/intensity_image_diff" name="output" value="output/input7_gaussian.tiff" ftype="tiff"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1268 <assert_stdout>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1269 <has_line line="Input image shape: (1, 1, 2, 64, 64, 1)"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1270 <has_line line="Input image axes: QTZYXC"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1271 <has_line line="Input image dtype: float64"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1272 <has_line line="Anisotropy of ZYX pixels/voxels: (1.0, 1.0, 1.0)"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1273 <has_line line="Applying filter: gaussian_filter with sigma=(3.0, 3.0, 3.0), order=0, axes='ZYX'"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1274 <has_line line="Output image shape: (2, 64, 64)"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1275 <has_line line="Output image axes: ZYX"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1276 <has_line line="Output image dtype: float64"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1277 </assert_stdout>
2 b2d9c92bc431 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit a6fd77be465068f709a71d377900da99becf94d8 imgteam parents: 1 diff changeset	1278 </test>
4 5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1279 <!--
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1280 =========================================================================================================
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1281 === TESTS: Illegal input images
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1282 =========================================================================================================
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1283 -->
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1284 <test expect_failure="true">
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1285 <!--
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1286 Test 37: Using 3-D image (with metadata) with `"target": "2d"`
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1287 ==============================================================
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1288 -->
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1289 <conditional name="setup">
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1290 <param name="target" value="2d"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1291 <param name="input" value="input/input4_float16.tiff"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1292 </conditional>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1293 </test>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1294 <test expect_failure="true">
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1295 <!--
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1296 Test 38: Using 2-D image (with metadata) with `"target": "3d"`
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1297 ==============================================================
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1298 -->
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1299 <conditional name="setup">
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1300 <param name="target" value="3d"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1301 <param name="input" value="input/input1_uint8.tiff"/>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1302 </conditional>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1303 </test>
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1304 <!-- TODO: Add test for wrong `target` with OME-Zarr -->
0 96fe54355774 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_simple_filter/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581 imgteam parents: diff changeset	1305 </tests>
96fe54355774 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_simple_filter/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581 imgteam parents: diff changeset	1306 <help>
2 b2d9c92bc431 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit a6fd77be465068f709a71d377900da99becf94d8 imgteam parents: 1 diff changeset	1307
4 5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1308 Applies a standard, general-purpose image filter to an image.
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1309
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1310 Support for different image types:
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1311
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1312 - For 3-D images, filters can either be applied jointly to the 3-D image data, or separately to all 2-D slices of the image.
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1313 - For multi-channel images, filters are applied separately to all channels of the image.
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1314 - For time-series images, filter also are applied separately for all time steps.
2 b2d9c92bc431 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit a6fd77be465068f709a71d377900da99becf94d8 imgteam parents: 1 diff changeset	1315
4 5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1316 Mean filters like the Gaussian filter, the box filter, or the median filter preserve the brightness of the image and the range
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1317 of values. Derivative filters like 1st and 2nd order Gaussians, Prewitt filters, and Sobel filters naturally may yield negative
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1318 or fractional values, and thus generally produce floating point-encoded images. The different filters are described below.
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1319
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1320 Gaussian filters are crucial for pre-processing in many image analysis tasks like edge detection and object recognition.
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1321 They are also employed for image denoising, when images are deteriorated by—or approximately by—white additive Gaussian noise.
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1322 Gaussian filters are linear filters that smoothen images and blur out fine details, which is why they are also used for scale
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1323 selection. These filters use a Gaussian bell-shaped kernel for weighted averaging of pixels, giving more importance to central
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1324 pixels and less to distant ones.
0 96fe54355774 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_simple_filter/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581 imgteam parents: diff changeset	1325
4 5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1326 Gaussian derivative operators (1st and 2nd order Gaussians) are filters that are used in image analysis for approximate
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1327 computation of the 1st and 2nd order derivatives of the image intensities. Due to their scale-space theoretical and
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1328 noise-reducing properties, they are popular candidates for edge and feature detection. They are implemented by convolving an
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1329 image with the derivative of a Gaussian function.
2 b2d9c92bc431 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit a6fd77be465068f709a71d377900da99becf94d8 imgteam parents: 1 diff changeset	1330
4 5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1331 Box filters are another family of linear smoothing filter, that uses a uniform kernel for arithmetic averaging of pixels.
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1332 The name stems from the rectangular shape of the kernel. The box filter corresponds to a sinc function in the frequency
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1333 domain. This causes smoothing artifacts in the spatial domain. It is rarely used as a low-pass filter and is more of academic
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1334 interest.
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1335
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1336 Median filters are non-linear filters, specifically well suited for reduction of impulse noise (e.g., salt-&-pepper
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1337 noise). Median filters compute the local median intensity value. An important advantage of median filters is that they
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1338 preserve the set of intensity values in the image (or yield a subset). This trait makes them specifically well suited for
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1339 smoothing of label maps and binary images. The median filters implemented in this tool uses rectangular neighborhoods for the
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1340 computation of the local median values.
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1341
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1342 Prewitt and Sobel filters are popular 2-D filters for approximate computation of the 1-st order derivatives of the image
5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1343 intensities. Sobel filters have better isotropy properties than Prewitt filters.
2 b2d9c92bc431 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit a6fd77be465068f709a71d377900da99becf94d8 imgteam parents: 1 diff changeset	1344
0 96fe54355774 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_simple_filter/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581 imgteam parents: diff changeset	1345 </help>
96fe54355774 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_simple_filter/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581 imgteam parents: diff changeset	1346 <citations>
3 53c55776a974 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit 8e99ddb62ceab1da15996906a0813826b62d38fe imgteam parents: 2 diff changeset	1347 <citation type="doi">10.1016/j.jbiotec.2017.07.019</citation>
4 5ab62693dca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c9cc62c508da3804872d105800993746c36cca48 imgteam parents: 3 diff changeset	1348 <citation type="doi">10.1038/s41592-019-0686-2</citation>
0 96fe54355774 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_simple_filter/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581 imgteam parents: diff changeset	1349 </citations>
96fe54355774 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_simple_filter/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581 imgteam parents: diff changeset	1350 </tool>

Mercurial > repos > imgteam > 2d_simple_filter

annotate filter.xml @ 4:5ab62693dca5 draft default tip