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ENH: Add label_statistics widget
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‎README.rst‎

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@@ -78,9 +78,10 @@ Interactive Jupyter_ widgets to visualize images, point sets, and meshes.
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- Exquisite volume rendering
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- Tri-plane volume slicing
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- Innovative, powerful opacity transfer function / window / level widget
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- Label map segmentation 2D and 3D rendering
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- Label image segmentation 2D and 3D rendering
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- Anisotropic voxel spacing supported
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- Image line profile widget
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- Image statistics widget
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- Compare images widget
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- Widgets to select solid colors for geometry or colormaps when point data or
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cell data is availble
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- `Binder: ITK Mesh <https://mybinder.org/v2/gh/InsightSoftwareConsortium/itkwidgets/master?urlpath=lab/tree/examples/Mesh.ipynb>`_
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- `Binder: ITK PointBasedSpatialObject <https://mybinder.org/v2/gh/InsightSoftwareConsortium/itkwidgets/master?urlpath=lab/tree/examples/PointBasedSpatialObject.ipynb>`_
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- `Binder: skan segmentation skeleton <https://mybinder.org/v2/gh/InsightSoftwareConsortium/itkwidgets/master?urlpath=lab/tree/examples/SegmentationSkeleton.ipynb>`_
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- `Binder: skan segmentation skeleton <https://mybinder.org/v2/gh/InsightSoftwareConsortium/itkwidgets/master?urlpath=lab/tree/examples/SegmentationSkeleton.ipynb>`_
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Recipes:
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- `Binder: Compare images with a checkerboard pattern <https://mybinder.org/v2/gh/InsightSoftwareConsortium/itkwidgets/master?urlpath=lab/tree/examples/Checkerboard.ipynb>`_
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- `Binder: Compare images side by side <https://mybinder.org/v2/gh/InsightSoftwareConsortium/itkwidgets/master?urlpath=lab/tree/examples/CompareImages.ipynb>`_
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- `Binder: Examine a line profile <https://mybinder.org/v2/gh/InsightSoftwareConsortium/itkwidgets/master?urlpath=lab/tree/examples/LineProfile.ipynb>`_
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- `Binder: Inspect image label statistics <https://mybinder.org/v2/gh/InsightSoftwareConsortium/itkwidgets/master?urlpath=lab/tree/examples/ImageLabelStatistics.ipynb>`_
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- `Binder: Interactively explore algorithm parameters <https://mybinder.org/v2/gh/InsightSoftwareConsortium/itkwidgets/master?urlpath=lab/tree/examples/InteractiveParameterExploration.ipynb>`_
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- `Binder: Record a video <https://mybinder.org/v2/gh/InsightSoftwareConsortium/itkwidgets/master?urlpath=lab/tree/examples/RecordAVideo.ipynb>`_
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- `Binder: Restore a volume opacity transfer function <https://mybinder.org/v2/gh/InsightSoftwareConsortium/itkwidgets/master?urlpath=lab/tree/examples/VolumeOpacityTransferFunction.ipynb>`_
@@ -290,6 +293,7 @@ or how to:
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- `Compares images with a checkerboard pattern <https://github.com/InsightSoftwareConsortium/itkwidgets/blob/master/examples/Checkerboard.ipynb>`_
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- `Compares images side by side <https://github.com/InsightSoftwareConsortium/itkwidgets/blob/master/examples/CompareImages.ipynb>`_
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- `Examine a line profile <https://github.com/InsightSoftwareConsortium/itkwidgets/blob/master/examples/LineProfile.ipynb>`_
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- `Inspect image label statistcs <https://github.com/InsightSoftwareConsortium/itkwidgets/blob/master/examples/ImageLabelStatistics.ipynb>`_
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- `Interatively explore algorithm parameters <https://github.com/InsightSoftwareConsortium/itkwidgets/blob/master/examples/InteractiveParameterExploration.ipynb>`_
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- `Record a video <https://github.com/InsightSoftwareConsortium/itkwidgets/blob/master/examples/RecordAVideo.ipynb>`_
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- `Restore a volume opacity transfer function <https://github.com/InsightSoftwareConsortium/itkwidgets/blob/master/examples/VolumeOpacityTransferFunction.ipynb>`_

‎examples/ImageLabelStatistics.ipynb‎

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{
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"cells": [
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": [
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"# Install dependencies for this example\n",
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"# Note: This does not include itkwidgets, itself\n",
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"import sys\n",
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"!{sys.executable} -m pip install -U itk plotly"
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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": 1,
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"metadata": {},
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"outputs": [],
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"source": [
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"from urllib.request import urlretrieve\n",
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"import os\n",
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"\n",
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"import itk\n",
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"import numpy as np\n",
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"\n",
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"from itkwidgets import label_statistics, view\n",
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"import itkwidgets"
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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": 2,
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"metadata": {},
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"outputs": [],
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"source": [
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"# Download data\n",
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"# Source: Simulated nuclei of HL60 cells stained with Hoescht\n",
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"# Dr. V. Ulman and Dr. D. Svoboda. Centre for Biomedical Image Analysis (CBIA),\n",
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"# http://doi.org/10.1109/TMI.2016.2606545\n",
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"file_name = 'Fluo-N3DH-SIM+-01-t148.nrrd'\n",
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"if not os.path.exists(file_name):\n",
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" url = 'https://data.kitware.com/api/v1/file/5f20d3a79014a6d84e462462/download'\n",
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" urlretrieve(url, file_name)\n",
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"label_file_name = 'Fluo-N3DH-SIM+-01_GT-SEG-man_seg148.nrrd'\n",
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"if not os.path.exists(label_file_name):\n",
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" url = 'https://data.kitware.com/api/v1/file/5f20d3a69014a6d84e462457/download'\n",
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" urlretrieve(url, label_file_name)"
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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": 3,
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"metadata": {},
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"outputs": [],
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"source": [
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"image = itk.imread(file_name)\n",
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"binary_labels = itk.imread(label_file_name)\n",
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"\n",
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"label_image = itk.connected_component_image_filter(binary_labels)"
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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": 4,
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"metadata": {},
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"outputs": [],
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"source": [
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"# A few viewer settings that work nicely with this dataset.\n",
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"opacity_gaussians = [[{'position': 0.17082204155374883,\n",
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" 'height': 1,\n",
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" 'width': 0.17082204155374883,\n",
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" 'xBias': 0.06522802840370252,\n",
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" 'yBias': 0.40466784651165977}]]\n",
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"camera = np.array([[ 6.6004913e+01, 4.5845730e+01, 1.1898222e+02],\n",
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" [ 4.0518013e+01, 2.3266140e+01, 1.5647539e+01],\n",
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" [-2.4525525e-02, 9.7789967e-01, -2.0763110e-01]], dtype=np.float32)"
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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": 5,
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"metadata": {},
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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": "3c1d54940fec4eb08e648bbef430b721",
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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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"AppLayout(children=(Viewer(camera=array([[ 6.6004913e+01, 4.5845730e+01, 1.1898222e+02],\n",
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" [ 4.0518013e…"
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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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"label_statistics(image=image,\n",
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" label_image=label_image,\n",
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" histogram=True,\n",
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" opacity_gaussians=opacity_gaussians,\n",
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" camera=camera)"
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]
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},
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{
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"cell_type": "markdown",
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"metadata": {},
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"source": [
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"Select label markers from the statistics graph in the lower left to highlight them in the image visualization and provide their intensity histograms."
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]
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}
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],
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"metadata": {
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"kernelspec": {
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"display_name": "Python 3",
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"language": "python",
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"name": "python3"
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},
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"language_info": {
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"codemirror_mode": {
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"name": "ipython",
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"version": 3
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},
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"file_extension": ".py",
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"mimetype": "text/x-python",
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"name": "python",
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"nbconvert_exporter": "python",
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"pygments_lexer": "ipython3",
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"version": "3.7.6"
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}
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},
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"nbformat": 4,
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"nbformat_minor": 4
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}

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