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BUG: Remove extra cell from LabelImages example
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‎examples/LabelImages.ipynb‎

Lines changed: 72 additions & 38 deletions
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@@ -31,7 +31,7 @@
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},
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{
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"cell_type": "code",
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"execution_count": 2,
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"execution_count": 3,
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"metadata": {},
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"outputs": [],
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"source": [
@@ -45,15 +45,15 @@
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{
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"cell_type": "code",
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"execution_count": 3,
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"execution_count": 4,
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"metadata": {
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"scrolled": true
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"scrolled": false
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},
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"outputs": [
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{
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"data": {
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"application/vnd.jupyter.widget-view+json": {
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"model_id": "65c6b074eac64e7e9a26d65104a9d6ba",
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"model_id": "c46a472354864866871a66c73d09b99f",
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"version_major": 2,
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"version_minor": 0
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},
@@ -73,17 +73,7 @@
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},
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{
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"cell_type": "code",
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"execution_count": 10,
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"metadata": {},
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"outputs": [],
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"source": [
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"LabelImageType = itk.Image[itk.UL, 3]\n",
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"connected_components = itk.connected_component_image_filter(thresholded, ttype=(type(thresholded), LabelImageType))"
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]
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},
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{
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"cell_type": "code",
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"execution_count": 8,
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"execution_count": 7,
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"metadata": {},
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"outputs": [],
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"source": [
@@ -99,23 +89,22 @@
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},
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{
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"cell_type": "code",
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"execution_count": 11,
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"execution_count": 8,
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"metadata": {},
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"outputs": [
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{
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"ename": "TemplateTypeError",
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"evalue": "itk.ExtractImageFilter is not wrapped for input type `None`.\n\nTo limit the size of the package, only a limited number of\ntypes are available in ITK Python. To print the supported\ntypes, run the following command in your python environment:\n\n itk.ExtractImageFilter.GetTypes()\n\nPossible solutions:\n* If you are an application user:\n** Convert your input image into a supported format (see below).\n** Contact developer to report the issue.\n* If you are an application developer, force input images to be\nloaded in a supported pixel type.\n\n e.g.: instance = itk.ExtractImageFilter[itk.Image[itk.RGBPixel[itk.UC],2], itk.Image[itk.RGBPixel[itk.UC],2]].New(my_input)\n\n* (Advanced) If you are an application developer, build ITK Python yourself and\nturned to `ON` the corresponding CMake option to wrap the pixel type or image\ndimension you need. When configuring ITK with CMake, you can set\n`ITK_WRAP_${type}` (replace ${type} with appropriate pixel type such as\n`double`). If you need to support images with 4 or 5 dimensions, you can add\nthese dimensions to the list of dimensions in the CMake variable\n`ITK_WRAP_IMAGE_DIMS`.\n\nSupported input types:\n\nitk.Image[itk.RGBPixel[itk.UC],2]\nitk.Image[itk.RGBPixel[itk.UC],3]\nitk.Image[itk.RGBAPixel[itk.UC],2]\nitk.Image[itk.RGBAPixel[itk.UC],3]\nitk.Image[itk.Vector[itk.F,2],2]\nitk.Image[itk.Vector[itk.F,2],3]\nitk.Image[itk.Vector[itk.F,3],2]\nitk.Image[itk.Vector[itk.F,3],3]\nitk.Image[itk.Vector[itk.F,4],2]\nitk.Image[itk.Vector[itk.F,4],3]\nitk.Image[itk.CovariantVector[itk.F,2],2]\nitk.Image[itk.CovariantVector[itk.F,2],3]\nitk.Image[itk.CovariantVector[itk.F,3],2]\nitk.Image[itk.CovariantVector[itk.F,3],3]\nitk.Image[itk.CovariantVector[itk.F,4],2]\nitk.Image[itk.CovariantVector[itk.F,4],3]\nitk.Image[itk.SS,2]\nitk.Image[itk.SS,3]\nitk.Image[itk.UC,2]\nitk.Image[itk.UC,3]\nitk.Image[itk.US,2]\nitk.Image[itk.US,3]\nitk.Image[itk.F,2]\nitk.Image[itk.F,3]\nitk.Image[itk.D,2]\nitk.Image[itk.D,3]\nitk.Image[itk.complex[itk.F],2]\nitk.Image[itk.complex[itk.F],3]\nitk.Image[itk.SS,3]\nitk.Image[itk.UC,3]\nitk.Image[itk.US,3]\nitk.Image[itk.F,3]\nitk.Image[itk.D,3]\nitk.Image[itk.RGBPixel[itk.UC],3]\nitk.Image[itk.complex[itk.F],3]\n",
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"output_type": "error",
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"traceback": [
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"\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
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"\u001b[0;31mTemplateTypeError\u001b[0m Traceback (most recent call last)",
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"\u001b[0;32m<ipython-input-11-6e811847302e>\u001b[0m in \u001b[0;36m<module>\u001b[0;34m\u001b[0m\n\u001b[0;32m----> 1\u001b[0;31m \u001b[0mview\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mlabel_image\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0mconnected_components\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m",
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"\u001b[0;32m~/src/itkwidgets/itkwidgets/widget_viewer.py\u001b[0m in \u001b[0;36mview\u001b[0;34m(image, label_image, label_image_names, label_image_weights, label_image_blend, cmap, lut, select_roi, interpolation, gradient_opacity, opacity_gaussians, channels, slicing_planes, shadow, blend_mode, point_sets, point_set_colors, point_set_opacities, point_set_representations, point_set_sizes, geometries, geometry_colors, geometry_opacities, ui_collapsed, rotate, annotations, mode, **kwargs)\u001b[0m\n\u001b[1;32m 1076\u001b[0m \u001b[0mgeometries\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0mgeometries\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mgeometry_colors\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0mgeometry_colors\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mgeometry_opacities\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0mgeometry_opacities\u001b[0m\u001b[0;34m,\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 1077\u001b[0m \u001b[0mrotate\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0mrotate\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mui_collapsed\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0mui_collapsed\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mannotations\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0mannotations\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mmode\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0mmode\u001b[0m\u001b[0;34m,\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m-> 1078\u001b[0;31m **kwargs)\n\u001b[0m\u001b[1;32m 1079\u001b[0m \u001b[0;32mreturn\u001b[0m \u001b[0mviewer\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
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"\u001b[0;32m~/src/itkwidgets/itkwidgets/widget_viewer.py\u001b[0m in \u001b[0;36m__init__\u001b[0;34m(self, **kwargs)\u001b[0m\n\u001b[1;32m 404\u001b[0m \u001b[0;32mif\u001b[0m \u001b[0msize\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0mdim\u001b[0m\u001b[0;34m]\u001b[0m \u001b[0;34m>\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0msize_limit_3d\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0mdim\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 405\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_downsampling\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0;32mTrue\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 406\u001b[0;31m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_update_rendered_image\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 407\u001b[0m \u001b[0;32mif\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_downsampling\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 408\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mobserve\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_on_roi_changed\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m[\u001b[0m\u001b[0;34m'roi'\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
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"\u001b[0;32m~/src/itkwidgets/itkwidgets/widget_viewer.py\u001b[0m in \u001b[0;36m_update_rendered_image\u001b[0;34m(self)\u001b[0m\n\u001b[1;32m 487\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mshrinker\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mSetShrinkFactors\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mscale_factors\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0mdimension\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 488\u001b[0m \u001b[0;32mif\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mlabel_image\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 489\u001b[0;31m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mlabel_image_extractor\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mitk\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mExtractImageFilter\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mNew\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mlabel_image\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 490\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mlabel_image_shrinker\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mitk\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mShrinkImageFilter\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mNew\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mlabel_image_extractor\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 491\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mlabel_image_shrinker\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mSetShrinkFactors\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mscale_factors\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0mdimension\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
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"\u001b[0;32m~/bin/miniconda3/envs/itkwidgets/lib/python3.7/site-packages/itkTemplate.py\u001b[0m in \u001b[0;36mNew\u001b[0;34m(self, *args, **kwargs)\u001b[0m\n\u001b[1;32m 522\u001b[0m or via one of the following keyword arguments: %s\"\"\" % \", \".join(primary_input_methods))\n\u001b[1;32m 523\u001b[0m \u001b[0;32melse\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 524\u001b[0;31m \u001b[0;32mraise\u001b[0m \u001b[0mTemplateTypeError\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0minput_type\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 525\u001b[0m \u001b[0;32mreturn\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0mlist\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mkeys\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;36m0\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mNew\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m*\u001b[0m\u001b[0margs\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m**\u001b[0m\u001b[0mkwargs\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 526\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n",
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"\u001b[0;31mTemplateTypeError\u001b[0m: itk.ExtractImageFilter is not wrapped for input type `None`.\n\nTo limit the size of the package, only a limited number of\ntypes are available in ITK Python. To print the supported\ntypes, run the following command in your python environment:\n\n itk.ExtractImageFilter.GetTypes()\n\nPossible solutions:\n* If you are an application user:\n** Convert your input image into a supported format (see below).\n** Contact developer to report the issue.\n* If you are an application developer, force input images to be\nloaded in a supported pixel type.\n\n e.g.: instance = itk.ExtractImageFilter[itk.Image[itk.RGBPixel[itk.UC],2], itk.Image[itk.RGBPixel[itk.UC],2]].New(my_input)\n\n* (Advanced) If you are an application developer, build ITK Python yourself and\nturned to `ON` the corresponding CMake option to wrap the pixel type or image\ndimension you need. When configuring ITK with CMake, you can set\n`ITK_WRAP_${type}` (replace ${type} with appropriate pixel type such as\n`double`). If you need to support images with 4 or 5 dimensions, you can add\nthese dimensions to the list of dimensions in the CMake variable\n`ITK_WRAP_IMAGE_DIMS`.\n\nSupported input types:\n\nitk.Image[itk.RGBPixel[itk.UC],2]\nitk.Image[itk.RGBPixel[itk.UC],3]\nitk.Image[itk.RGBAPixel[itk.UC],2]\nitk.Image[itk.RGBAPixel[itk.UC],3]\nitk.Image[itk.Vector[itk.F,2],2]\nitk.Image[itk.Vector[itk.F,2],3]\nitk.Image[itk.Vector[itk.F,3],2]\nitk.Image[itk.Vector[itk.F,3],3]\nitk.Image[itk.Vector[itk.F,4],2]\nitk.Image[itk.Vector[itk.F,4],3]\nitk.Image[itk.CovariantVector[itk.F,2],2]\nitk.Image[itk.CovariantVector[itk.F,2],3]\nitk.Image[itk.CovariantVector[itk.F,3],2]\nitk.Image[itk.CovariantVector[itk.F,3],3]\nitk.Image[itk.CovariantVector[itk.F,4],2]\nitk.Image[itk.CovariantVector[itk.F,4],3]\nitk.Image[itk.SS,2]\nitk.Image[itk.SS,3]\nitk.Image[itk.UC,2]\nitk.Image[itk.UC,3]\nitk.Image[itk.US,2]\nitk.Image[itk.US,3]\nitk.Image[itk.F,2]\nitk.Image[itk.F,3]\nitk.Image[itk.D,2]\nitk.Image[itk.D,3]\nitk.Image[itk.complex[itk.F],2]\nitk.Image[itk.complex[itk.F],3]\nitk.Image[itk.SS,3]\nitk.Image[itk.UC,3]\nitk.Image[itk.US,3]\nitk.Image[itk.F,3]\nitk.Image[itk.D,3]\nitk.Image[itk.RGBPixel[itk.UC],3]\nitk.Image[itk.complex[itk.F],3]\n"
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]
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"data": {
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"application/vnd.jupyter.widget-view+json": {
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"model_id": "4960333a0feb4b25825d9b62ad0ea607",
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"version_major": 2,
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"version_minor": 0
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},
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"text/plain": [
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"Viewer(geometries=[], gradient_opacity=0.22, interpolation=False, point_sets=[], rendered_label_image=<itk.itk…"
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]
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},
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"metadata": {},
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"output_type": "display_data"
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}
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],
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"source": [
@@ -124,11 +113,26 @@
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"execution_count": 9,
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"metadata": {
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"scrolled": true
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"scrolled": false
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},
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"outputs": [],
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"outputs": [
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{
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"data": {
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"application/vnd.jupyter.widget-view+json": {
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"model_id": "e8ab46d59acd41438530b6ce34b42cdd",
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"version_major": 2,
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"version_minor": 0
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},
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"text/plain": [
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"Viewer(geometries=[], gradient_opacity=0.5, interpolation=False, label_image_blend=0.8, label_image_names=[(0,…"
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]
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},
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"metadata": {},
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"output_type": "display_data"
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}
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],
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"source": [
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"# We can combine the label map with the intensity image, add names for the labels, etc.\n",
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"names = [(0, 'Background'), (1, 'First cell'), (2, 'Second cell')]\n",
@@ -152,7 +156,7 @@
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"execution_count": 10,
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"metadata": {},
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"outputs": [],
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"source": [
@@ -172,9 +176,24 @@
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"execution_count": 11,
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"metadata": {},
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"outputs": [],
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"outputs": [
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{
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"data": {
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"application/vnd.jupyter.widget-view+json": {
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"model_id": "505009ada82e40249b35243fbe7d2bb5",
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"version_major": 2,
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"version_minor": 0
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},
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"text/plain": [
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"Viewer(annotations=False, cmap=['BrBG'], geometries=[], gradient_opacity=0.22, point_sets=[], rendered_image=<…"
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]
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},
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"metadata": {},
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"output_type": "display_data"
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}
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],
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"source": [
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"image = skimage.io.imread(file_name)\n",
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"\n",
@@ -183,7 +202,7 @@
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"execution_count": 12,
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"metadata": {},
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"outputs": [],
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"source": [
@@ -198,9 +217,24 @@
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"execution_count": 13,
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"metadata": {},
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"outputs": [],
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"outputs": [
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{
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"data": {
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"application/vnd.jupyter.widget-view+json": {
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"model_id": "58576171783c44ceae961c0a6682201b",
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"version_major": 2,
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"version_minor": 0
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},
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"text/plain": [
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"Viewer(geometries=[], gradient_opacity=0.22, interpolation=False, point_sets=[], rendered_label_image=<itk.itk…"
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]
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},
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"metadata": {},
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"output_type": "display_data"
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}
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],
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"source": [
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"view(label_image=connected_components)"
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]

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