comparison render.xml @ 0:7d6be2b7e1e2 draft

planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee

0:7d6be2b7e1e2

<tool id="libcarna_render" name="Render 3-D image data" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.05">
    <description>with LibCarna</description>
    <macros>
        <import>creators.xml</import>
        <import>validators.xml</import>
        <import>colormaps.xml</import>
        <token name="@TOOL_VERSION@">0.2.0</token>
        <token name="@VERSION_SUFFIX@">0</token>
        <xml name="params/intensity" tokens="name,label">
            <section name="@NAME@" title="@LABEL@" expanded="true">
                <param name="type" type="select" label="@LABEL@"
                       help="For relative intensity values, 0 is the minimum intensity of the image, and 1 is the maximum intensity.">
                    <option value="absolute" selected="true">Absolute intensity value</option>
                    <option value="relative">Relative intensity value</option>
                </param>
                <param name="value" type="float" label="Intensity value"/>
            </section>
        </xml>
        <xml name="params/builtin_cmap">
            <conditional name="ramp">
                <param name="enabled" type="select" label="Ramp function"
                       help="Use a piecewise linear ramp function for the alpha channel of the colormap.">
                    <option value="false" selected="true">Disabled</option>
                    <option value="true">Enabled</option>
                </param>
                <when value="true">
                    <expand macro="params/intensity" name="start" label="Ramp start"/>
                    <expand macro="params/intensity" name="end" label="Ramp end"/>
                </when>
                <when value="false"/>
            </conditional>
        </xml>
        <xml name="when/builtin_cmap" tokens="value">
            <when value="@VALUE@">
                <expand macro="params/builtin_cmap"/>
            </when>
        </xml>
        <xml name="test/params">
            <!-- CI tests use software rendering which requires very low sample rates -->
            <param name="sample_rate_override" value="5"/>
            <param name="width" value="200"/>
            <param name="height" value="110"/>
        </xml>
        <xml name="test/assert_stdout">
            <assert_stdout>
                <has_line_matching expression="^EGL Vendor: .+"/>
                <yield/>
            </assert_stdout>
        </xml>
    </macros>
    <creator>
        <expand macro="creators/bmcv"/>
        <expand macro="creators/kostrykin"/>
    </creator>
    <edam_operations>
        <edam_operation>operation_3443</edam_operation>
    </edam_operations>
    <xrefs>
        <xref type="bio.tools">galaxy_image_analysis</xref>
        <xref type="bio.tools">giatools</xref>
    </xrefs>
    <requirements>
    <!--
        We employ here a custom Docker image until https://github.com/bioconda/bioconda-containers/issues/87 gets a better solution.

        The Docker image is an extension of the BioContainer for the following packages:

            <requirement type="package" version="@TOOL_VERSION@">libcarna-python</requirement>
            <requirement type="package" version="1.26.4">numpy</requirement>
            <requirement type="package" version="4.3.2">ffmpeg</requirement>
            <requirement type="package" version="0.7.3">giatools</requirement>
            <requirement type="package" version="0.12.2">ome-zarr</requirement>
            <requirement type="package" version="2.3.3">pandas</requirement>

        See https://github.com/kostrykin/LibCarna-Python-Docker for details of the image.
        -->
        <container type="docker">docker.io/kostrykin/libcarna-python:@TOOL_VERSION@-0</container>
    </requirements>
    <required_files>
        <include type="literal" path="clip_image.py"/>
        <exclude type="literal" path="README.md"/>
    </required_files>
    <command detect_errors="aggressive"><![CDATA[

        python '$__tool_directory__/render.py'

        #if $intensities.extension == "zarr"
            --intensities '$intensities.extra_files_path/$intensities.metadata.store_root'
        #else
            --intensities '$intensities'
        #end if
        
        #if str($colormap.name) == "custom"
            --colormap '$colormap.custom'
        #end if

        #if str($mask.enabled) == "true":
            #if $mask.image.extension == "zarr"
                --mask '$mask.image.extra_files_path/$mask.image.metadata.store_root'
            #else
                --mask '$mask.image'
            #end if
        #end if

        --html '$html'
        --params '$params'
        --verbose

    ]]></command>
    <configfiles>
        <configfile name="params"><![CDATA[
            {

                #if str($sample_rate_override) != ""
                    #set $sample_rate = int($sample_rate_override)
                #end if

                "sample_rate": $sample_rate,
                "axes": "$axes",
                "width": $width,
                "height": $height,
                "mode": "$mode.name",

                "mode_kwargs": {
                    #if str($mode.name) == "dvr"
                        "translucency": $mode.translucency,
                        "diffuse": $mode.diffuse
                    #end if
                },

                "colormap": "$colormap.name",

                #if str($colormap.name) != "custom"
                    "ramp": {
                        #if str($colormap.ramp.enabled) == "true"
                            "start_type": "$colormap.ramp.start.type",
                            "start_value": $colormap.ramp.start.value,
                            "end_type": "$colormap.ramp.end.type",
                            "end_value": $colormap.ramp.end.value
                        #end if
                    },
                #end if

                "camera": {
                    "distance": $camera.distance,
                    "kwargs": {
                        "fov": $camera.fov,
                        "z_near": $camera.z_near,
                        "z_far": $camera.z_far
                    }
                },
                "video": {
                    "frames": $video.frames,
                    "fps": $video.fps
                },

                "mask": $mask.enabled,
                "mask_renderer_kwargs": {
                    #if str($mask.enabled) == "true"
                        "color": "$mask.color"
                    #end if
                }

            }
        ]]></configfile>
    </configfiles>
    <inputs>
        <param name="intensities" type="data" format="tiff,zarr" label="Input image (3-D)">
            <expand macro="validators/is_single_channel"/>
            <expand macro="validators/is_single_frame"/>
            <expand macro="validators/is_3d"/>
        </param>
        <param name="axes" type="select" label="Coordinate system">
            <option value="XZY" selected="true">Point Z to the top</option>
            <option value="XYZ">Point Y to the top</option>
        </param>
        <param name="sample_rate" type="integer" min="100" value="800" label="Sample rate"
               help="Samples per pixel for volume rendering (ray marching)."/>
        <param name="sample_rate_override" type="hidden" value="0"/><!-- For testing purposes -->
        <param name="width" type="integer" min="50" max="1024" value="800" label="Width of the video (in pixels)"/>
        <param name="height" type="integer" min="50" max="1024" value="450" label="Height of the video (in pixels)"/>
        <conditional name="mode">
            <param name="name" type="select" label="Rendering mode">
                <option value="mip" selected="true">Maximum Intensity Projection (MIP)</option>
                <option value="dvr">Direct Volume Rendering (DVR)</option>
            </param>
            <when value="mip"/>
            <when value="dvr">
                <param name="translucency" type="float" min="0" value="1" label="Translucency"/>
                <param name="diffuse" type="float" min="0" max="1" value="0.8" label="Directional light"
                       help="Balances the amount of ambient vs directional light. The light is fully ambient for 0 and fully directional for 1."/>
            </when>
        </conditional>
        <conditional name="colormap">
            <param name="name" type="select" label="Color map">
                <option value="custom">Custom</option>
                <expand macro="option/builtin_cmap_list"/>
            </param>
            <when value="custom">
                <param name="custom" type="data" format="tabular" label="Custom colormap">
                    <validator type="dataset_metadata_in_range" metadata_name="columns" min="3" message="Colormap needs to have at least 3 columns."/>
                </param>
            </when>
            <expand macro="when/builtin_cmap_list"/>
        </conditional>
        <section name="camera" title="Camera parameters" expanded="true">
            <param name="fov" type="float" min="10" max="170" value="90" label="Field of view (in degrees)"/>
            <param name="distance" type="float" min="1" value="200" label="Distance"
                   help="Distance between the camera and the center of the 3-D image."/>
            <param name="z_near" type="float" min="0.01" value="10" label="Near clipping plane"
                   help="Position of the near clipping plane along the z-axis."/>
            <param name="z_far" type="float" min="100" value="1000" label="Far clipping plane"
                   help="Position of the far clipping plane along the z-axis."/>
        </section>
        <conditional name="mask">
            <param name="enabled" type="select" label="Render mask overlay">
                <option value="false" selected="true">No overlay</option>
                <option value="true">Render mask overlay</option>
            </param>
            <when value="false"/>
            <when value="true">
                <param name="image" type="data" format="tiff,zarr" label="Mask overlay (3-D)">
                    <expand macro="validators/is_single_channel"/>
                    <expand macro="validators/is_single_frame"/>
                    <expand macro="validators/is_3d"/>
                </param>
                <param name="color" type="color" value="#00ff00" label="Color of the overlay"/>
            </when>
        </conditional>
        <section name="video" title="Video parameters" expanded="false">
            <param name="frames" type="integer" min="10" value="200" label="Frames"/>
            <param name="fps" type="integer" min="1" max="60" value="25" label="Frames per second"/>
        </section>
    </inputs>
    <outputs>
        <data format="html" name="html"/>
    </outputs>
    <tests>
        <!-- Test with MIP -->
        <test>
            <param name="intensities" value="input/float32_10z_32y_40x.tiff"/>
            <section name="camera">
                <param name="distance" value="50"/>
            </section>
            <output name="html" ftype="html" value="output/float32_10z_32y_40x-mip.html" compare="sim_size" delta="1000"/>
            <expand macro="test/params"/>
            <expand macro="test/assert_stdout"/>
        </test>
        <!-- Test with DVR, ramp colormap, and mask -->
        <test>
            <param name="intensities" value="input/float32_10z_32y_40x.tiff"/>
            <conditional name="mode">
                <param name="name" value="dvr"/>
                <param name="translucency" value="0"/>
            </conditional>
            <conditional name="colormap">
                <param name="name" value="BrBG"/>
                <conditional name="ramp">
                    <param name="enabled" value="true"/>
                    <section name="start">
                        <param name="type" value="relative"/>
                        <param name="value" value="0.33"/>
                    </section>
                    <section name="end">
                        <param name="type" value="relative"/>
                        <param name="value" value="0.37"/>
                    </section>
                </conditional>
            </conditional>
            <section name="camera">
                <param name="distance" value="50"/>
            </section>
            <conditional name="mask">
                <param name="enabled" value="true"/>
                <param name="image" value="input/uint8_10z_32y_40x.tiff"/>
            </conditional>
            <output name="html" ftype="html" value="output/float32_10z_32y_40x-dvr-mask.html" compare="sim_size" delta="1000"/>
            <expand macro="test/params"/>
            <expand macro="test/assert_stdout"/>
        </test>
        <!-- Test with custom colormap -->
        <test>
            <param name="intensities" value="input/float32_10z_32y_40x.tiff"/>
            <param name="axes" value="XYZ"/>
            <conditional name="colormap">
                <param name="name" value="custom"/>
                <param name="custom" value="input/colormap.tsv"/>
            </conditional>
            <section name="camera">
                <param name="distance" value="50"/>
            </section>
            <output name="html" ftype="html" value="output/float32_10z_32y_40x-colormap.html" compare="sim_size" delta="1000"/>
            <expand macro="test/params"/>
            <expand macro="test/assert_stdout"/>
        </test>
        <!-- Test with Zarr and missing `z_spacing` metadata -->
        <test>
            <param name="intensities" value="input/float32_5z_16y_20x-no_z_spacing.zarr"/>
            <section name="camera">
                <param name="distance" value="50"/>
            </section>
            <output name="html" ftype="html" value="output/float32_5z_16y_20x.html" compare="sim_size" delta="1000"/>
            <expand macro="test/params"/>
            <expand macro="test/assert_stdout"/>
        </test>
    </tests>
    <help>

**Renders videos for visualization of 3-D image data.**

The image data is rotated to facilitate grasping visual information from different angles.

LibCarna employs a volume rendering technique called *ray marching* and permits different visualization modes, including *maximum intensity projections* (MIP) and *direct volume rendering* (DVR). In addition, the renderings can be augmented with binary or label masks (e.g., segmentation overlays).

.. image:: dvr.gif
  :width: 438px
  :scale: 100%

An overview of the available colormaps is available at `matplotlib.org`_.

.. _matplotlib.org: https://matplotlib.org/stable/users/explain/colors/colormaps.html

When using custom colormaps, a tabular file with at least 3 columns must be used (`intensity`, `type`, `color`). Each pair of consecutive rows defines a linear segment of the colormap. The `intensity` values can be given either as absolute intensity values, or as relative values where 0 and 1 correspond to the minimum and maximum intensities of the image data, respectively. The `type` column indicates whether the corresponding `intensity` value is `absolute` or `relative`. The `color` must be given in hexadecimal notation with a ``#`` prefix and must be either 6 or 8 digits long (6 for RGB and 8 for RGBA). An example is given below.

+-----------+------------+----------+
| color     | intensity  | type     |
+-----------+------------+----------+
| #ff00007f | 0          | absolute |
+-----------+------------+----------+
| #ffff00ff | 0.5        | absolute |
+-----------+------------+----------+
| #00ffffff | 1.0        | relative |
+-----------+------------+----------+

    </help>
    <citations>
        <citation type="doi">10.1016/j.jbiotec.2017.07.019</citation>
    </citations>
</tool>