Mercurial > repos > imgteam > libcarna_render

comparison 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
comparison
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3:31a2e1909ae5 4:a9f10dceb17e
68 intensities = tool.args.input_images['intensities'] 68 intensities = tool.args.input_images['intensities']
69 intensities_volume = libcarna.volume( 69 intensities_volume = libcarna.volume(
70 GEOMETRY_TYPE_INTENSITIES, 70 GEOMETRY_TYPE_INTENSITIES,
71 intensities.normalize_axes_like(tool.args.params['axes']).data, 71 intensities.normalize_axes_like(tool.args.params['axes']).data,
72 parent=root, 72 parent=root,
73 units=tool.args.params['units'],
73 spacing=[ 74 spacing=[
74 { 75 {
75 'X': intensities.metadata.pixel_size[0] or 1, 76 'X': intensities.metadata.pixel_size[0] or 1,
76 'Y': intensities.metadata.pixel_size[1] or 1, 77 'Y': intensities.metadata.pixel_size[1] or 1,
77 'Z': intensities.metadata.z_spacing or 1, 78 'Z': intensities.metadata.z_spacing or 1,
121 ): 122 ):
122 ramp_values.append( 123 ramp_values.append(
123 value if val_type == 'relative' else intensities_volume.normalized(value), 124 value if val_type == 'relative' else intensities_volume.normalized(value),
124 ) 125 )
125 cmap_kwargs['ramp'] = tuple(ramp_values) 126 cmap_kwargs['ramp'] = tuple(ramp_values)
127 cmap_kwargs['n_samples'] = 1000 # high precision is required when sampling ramps to avoid "soft" corners
126 mode.cmap(tool.args.params['colormap'], **cmap_kwargs) 128 mode.cmap(tool.args.params['colormap'], **cmap_kwargs)
127 129
128 # Render 130 # Render
129 colorbars = list() 131 colorbars = list()
130 if tool.args.params['colorbar']: 132 if tool.args.params['colorbar']: