Mercurial > repos > imgteam > libcarna_render

annotate render.py @ 4:a9f10dceb17e draft default tip

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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 99d6ebe67515f1362ea4412b143ab2a140c8d631
author imgteam
date Tue, 13 Jan 2026 12:21:55 +0000
parents 31a2e1909ae5
children
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7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
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diff changeset
1 import giatools
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
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2 import libcarna
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
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3 import libcarna._imshow
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
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4 import pandas as pd
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
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7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
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6 # Fail early if an optional backend is not available
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
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7 giatools.require_backend('omezarr')
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
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7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
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9 # Patch `libcarna._imshow` to return plain HTML
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
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10 libcarna._imshow.IPythonHTML = lambda html: html
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
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7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
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7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
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13 GEOMETRY_TYPE_INTENSITIES = 0
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
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14 GEOMETRY_TYPE_MASK = 1
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
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7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
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7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
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17 def wrap_color(params: dict) -> dict:
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
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18 """
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
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19 Return the `params` dictionary but wrap values for `color` with `libcarna.color`.
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
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20 """
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
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21 result = dict()
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
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22 for key, value in params.items():
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
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23 if key == 'color':
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
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24 value = libcarna.color(value)
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
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25 result[key] = value
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
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26 return result
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
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7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
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7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
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29 if __name__ == "__main__":
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
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30 tool = giatools.ToolBaseplate()
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
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31 tool.add_input_image('intensities')
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
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32 tool.add_input_image('mask', required=False)
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
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33 tool.parser.add_argument('--colormap', type=str)
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
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34 tool.parser.add_argument('--html', type=str)
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
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35 tool.parse_args()
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
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36
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
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37 # Load custom colormap
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
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38 if tool.args.raw_args.colormap:
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
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39 df_colormap = pd.read_csv(tool.args.raw_args.colormap, delimiter='\t')
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
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40
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
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41 # Validate the input image(s)
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
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42 try:
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
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43 for image in tool.args.input_images.values():
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
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44 if any(image.shape[image.axes.index(axis)] > 1 for axis in image.axes if axis not in 'ZYX'):
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
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45 raise ValueError(f'This tool is not applicable to images with {image.original_axes} axes.')
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
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46
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
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47 # Create and configure frame renderer
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
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48 print('Sample rate:', tool.args.params['sample_rate'])
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
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49 mode = getattr(libcarna, tool.args.params['mode'])(
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
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50 GEOMETRY_TYPE_INTENSITIES,
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
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51 sr=tool.args.params['sample_rate'],
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
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52 **tool.args.params['mode_kwargs']
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
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53 )
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
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54 mask_renderer = libcarna.mask_renderer(
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
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55 GEOMETRY_TYPE_MASK,
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
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56 sr=tool.args.params['sample_rate'],
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
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57 **wrap_color(tool.args.params['mask_renderer_kwargs']),
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
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58 )
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
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59 r = libcarna.renderer(
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
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60 tool.args.params['width'],
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
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61 tool.args.params['height'],
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
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62 [mode, mask_renderer],
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
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63 )
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
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64 print('EGL Vendor:', r.gl_context.vendor)
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
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65
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66 # Build the scene graph
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
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67 root = libcarna.node()
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
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68 intensities = tool.args.input_images['intensities']
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69 intensities_volume = libcarna.volume(
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
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70 GEOMETRY_TYPE_INTENSITIES,
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71 intensities.normalize_axes_like(tool.args.params['axes']).data,
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
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72 parent=root,
4
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73 units=tool.args.params['units'],
0
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
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74 spacing=[
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
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75 {
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
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76 'X': intensities.metadata.pixel_size[0] or 1,
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
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77 'Y': intensities.metadata.pixel_size[1] or 1,
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
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78 'Z': intensities.metadata.z_spacing or 1,
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
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79 }
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
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80 [axis] for axis in tool.args.params['axes']
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
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81 ],
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
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82 normals=(tool.args.params['mode'] == 'dvr'),
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
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83 )
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
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84 camera = libcarna.camera(
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
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85 parent=root,
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86 ).frustum(
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
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87 **tool.args.params['camera']['kwargs'],
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88 ).translate(
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89 z=tool.args.params['camera']['distance'],
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90 )
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91 if (mask := tool.args.input_images.get('mask')):
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92 libcarna.volume(
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93 GEOMETRY_TYPE_MASK,
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94 mask.normalize_axes_like(tool.args.params['axes']).data,
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95 parent=intensities_volume,
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96 spacing=intensities_volume.spacing,
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97 )
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98
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99 # Apply colormap
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100 if tool.args.params['colormap'] == 'custom':
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101 mode.cmap.clear()
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102 i0, color0 = None, None
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103 for row in df_colormap.to_dict(orient='records'):
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104 match row['type']:
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105 case 'relative':
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106 i1 = row['intensity']
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107 case 'absolute':
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108 i1 = intensities_volume.normalized(row['intensity'])
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109 case _:
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110 raise ValueError('Unknown intensity type: "{}"'.format(row['type']))
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111 color1 = libcarna.color(row['color'])
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112 if i0 is not None:
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113 mode.cmap.linear_segment(i0, i1, color0, color1)
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114 i0, color0 = i1, color1
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115 else:
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116 cmap_kwargs = dict()
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117 if (ramp_params := tool.args.params['ramp']):
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118 ramp_values = list()
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119 for val_type, value in (
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120 (ramp_params['start_type'], ramp_params['start_value']),
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121 (ramp_params['end_type'], ramp_params['end_value']),
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122 ):
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123 ramp_values.append(
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124 value if val_type == 'relative' else intensities_volume.normalized(value),
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125 )
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126 cmap_kwargs['ramp'] = tuple(ramp_values)
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127 cmap_kwargs['n_samples'] = 1000 # high precision is required when sampling ramps to avoid "soft" corners
0
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128 mode.cmap(tool.args.params['colormap'], **cmap_kwargs)
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129
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130 # Render
3
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131 colorbars = list()
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132 if tool.args.params['colorbar']:
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133 colorbars.append(mode.cmap.bar(intensities_volume))
0
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134 html = libcarna.imshow(
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135 libcarna.animate(
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136 libcarna.animate.rotate_local(camera),
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137 n_frames=tool.args.params['video']['frames'],
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138 ).render(r, camera),
3
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139 *colorbars,
0
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140 fps=tool.args.params['video']['fps'],
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141 )
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142
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143 # Write the result
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144 with open(tool.args.raw_args.html, 'w') as fhtml:
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145 fhtml.write(html)
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146
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147 except ValueError as err:
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148 exit(err.args[0])