.. DO NOT EDIT. .. THIS FILE WAS AUTOMATICALLY GENERATED BY SPHINX-GALLERY. .. TO MAKE CHANGES, EDIT THE SOURCE PYTHON FILE: .. "auto_examples/segmentation/plot_regionprops_table.py" .. LINE NUMBERS ARE GIVEN BELOW. .. only:: html .. note:: :class: sphx-glr-download-link-note :ref:`Go to the end ` to download the full example code. or to run this example in your browser via Binder .. rst-class:: sphx-glr-example-title .. _sphx_glr_auto_examples_segmentation_plot_regionprops_table.py: =================================================== Explore and visualize region properties with pandas =================================================== This toy example shows how to compute the size of every labelled region in a series of 10 images. We use 2D images and then 3D images. The blob-like regions are generated synthetically. As the volume fraction (i.e., ratio of pixels or voxels covered by the blobs) increases, the number of blobs (regions) decreases, and the size (area or volume) of a single region can get larger and larger. The area (size) values are available in a pandas-compatible format, which makes for convenient data analysis and visualization. Besides area, many other region properties are available. .. GENERATED FROM PYTHON SOURCE LINES 17-28 .. code-block:: Python import matplotlib.pyplot as plt import numpy as np import pandas as pd import seaborn as sns from skimage import data, measure fractions = np.linspace(0.05, 0.5, 10) .. GENERATED FROM PYTHON SOURCE LINES 29-31 2D images ========= .. GENERATED FROM PYTHON SOURCE LINES 31-65 .. code-block:: Python images = [data.binary_blobs(volume_fraction=f) for f in fractions] labeled_images = [measure.label(image) for image in images] properties = ['label', 'area'] tables = [ measure.regionprops_table(image, properties=properties) for image in labeled_images ] tables = [pd.DataFrame(table) for table in tables] for fraction, table in zip(fractions, tables): table['volume fraction'] = fraction areas = pd.concat(tables, axis=0) # Create custom grid of subplots grid = plt.GridSpec(2, 2) ax1 = plt.subplot(grid[0, 0]) ax2 = plt.subplot(grid[0, 1]) ax = plt.subplot(grid[1, :]) # Show image with lowest volume fraction ax1.imshow(images[0], cmap='gray_r') ax1.set_axis_off() ax1.set_title(f'fraction {fractions[0]}') # Show image with highest volume fraction ax2.imshow(images[-1], cmap='gray_r') ax2.set_axis_off() ax2.set_title(f'fraction {fractions[-1]}') # Plot area vs volume fraction areas.plot(x='volume fraction', y='area', kind='scatter', ax=ax) plt.show() .. image-sg:: /auto_examples/segmentation/images/sphx_glr_plot_regionprops_table_001.png :alt: fraction 0.05, fraction 0.5 :srcset: /auto_examples/segmentation/images/sphx_glr_plot_regionprops_table_001.png :class: sphx-glr-single-img .. GENERATED FROM PYTHON SOURCE LINES 66-71 In the scatterplot, many points seem to be overlapping at low area values. To get a better sense of the distribution, we may want to add some 'jitter' to the visualization. To this end, we use :obj:`seaborn.stripplot` (from `seaborn library `_ for statistical data visualization) with argument ``jitter=True``. .. GENERATED FROM PYTHON SOURCE LINES 71-78 .. code-block:: Python fig, ax = plt.subplots() sns.stripplot(x='volume fraction', y='area', data=areas, jitter=True, ax=ax) # Fix floating point rendering ax.set_xticklabels([f'{frac:.2f}' for frac in fractions]) plt.show() .. image-sg:: /auto_examples/segmentation/images/sphx_glr_plot_regionprops_table_002.png :alt: plot regionprops table :srcset: /auto_examples/segmentation/images/sphx_glr_plot_regionprops_table_002.png :class: sphx-glr-single-img .. rst-class:: sphx-glr-script-out .. code-block:: none /home/runner/work/scikit-image/scikit-image/doc/examples/segmentation/plot_regionprops_table.py:75: UserWarning: set_ticklabels() should only be used with a fixed number of ticks, i.e. after set_ticks() or using a FixedLocator. .. GENERATED FROM PYTHON SOURCE LINES 79-86 3D images ========= Doing the same analysis in 3D, we find a much more dramatic behaviour: blobs coalesce into a single, giant piece as the volume fraction crosses ~0.25. This corresponds to the `percolation threshold `_ in statistical physics and graph theory. .. GENERATED FROM PYTHON SOURCE LINES 86-109 .. code-block:: Python images = [data.binary_blobs(length=128, n_dim=3, volume_fraction=f) for f in fractions] labeled_images = [measure.label(image) for image in images] properties = ['label', 'area'] tables = [ measure.regionprops_table(image, properties=properties) for image in labeled_images ] tables = [pd.DataFrame(table) for table in tables] for fraction, table in zip(fractions, tables): table['volume fraction'] = fraction blob_volumes = pd.concat(tables, axis=0) fig, ax = plt.subplots() sns.stripplot(x='volume fraction', y='area', data=blob_volumes, jitter=True, ax=ax) ax.set_ylabel('blob size (3D)') # Fix floating point rendering ax.set_xticklabels([f'{frac:.2f}' for frac in fractions]) plt.show() .. image-sg:: /auto_examples/segmentation/images/sphx_glr_plot_regionprops_table_003.png :alt: plot regionprops table :srcset: /auto_examples/segmentation/images/sphx_glr_plot_regionprops_table_003.png :class: sphx-glr-single-img .. rst-class:: sphx-glr-script-out .. code-block:: none /home/runner/work/scikit-image/scikit-image/doc/examples/segmentation/plot_regionprops_table.py:107: UserWarning: set_ticklabels() should only be used with a fixed number of ticks, i.e. after set_ticks() or using a FixedLocator. .. rst-class:: sphx-glr-timing **Total running time of the script:** (0 minutes 2.532 seconds) .. _sphx_glr_download_auto_examples_segmentation_plot_regionprops_table.py: .. only:: html .. container:: sphx-glr-footer sphx-glr-footer-example .. container:: binder-badge .. image:: images/binder_badge_logo.svg :target: https://mybinder.org/v2/gh/scikit-image/scikit-image/v0.24.0?filepath=notebooks/auto_examples/segmentation/plot_regionprops_table.ipynb :alt: Launch binder :width: 150 px .. container:: sphx-glr-download sphx-glr-download-jupyter :download:`Download Jupyter notebook: plot_regionprops_table.ipynb ` .. container:: sphx-glr-download sphx-glr-download-python :download:`Download Python source code: plot_regionprops_table.py ` .. only:: html .. rst-class:: sphx-glr-signature `Gallery generated by Sphinx-Gallery `_