Mercurial > repos > imgteam > colorize_labels
changeset 4:5907be5a8d7c draft default tip
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit 4344f548f365dba87c20188d6e3c2df8630d2313
| author | imgteam |
|---|---|
| date | Tue, 24 Sep 2024 17:30:20 +0000 |
| parents | 2d1de6e7b113 |
| children | |
| files | colorize_labels.py colorize_labels.xml creators.xml test-data/input3.tif test-data/output1.png test-data/output2.png test-data/output3.png |
| diffstat | 7 files changed, 33 insertions(+), 7 deletions(-) [+] |
line wrap: on
line diff
--- a/colorize_labels.py Wed Apr 24 08:12:15 2024 +0000 +++ b/colorize_labels.py Tue Sep 24 17:30:20 2024 +0000 @@ -1,12 +1,11 @@ import argparse import giatools.io -import matplotlib.colors as mpl +import matplotlib.pyplot as plt import networkx as nx import numpy as np import scipy.ndimage as ndi import skimage.io -import skimage.morphology as morph import skimage.util @@ -22,7 +21,6 @@ def build_label_adjacency_graph(im, radius, bg_label): G = nx.Graph() - selem = morph.disk(radius) for label in np.unique(im): if label == bg_label: @@ -31,7 +29,7 @@ G.add_node(label) cc = (im == label) - neighborhood = ndi.binary_dilation(cc, selem) + neighborhood = (ndi.distance_transform_edt(~cc) <= radius) adjacent_labels = np.unique(im[neighborhood]) for adjacent_label in adjacent_labels: @@ -45,6 +43,18 @@ return G +def get_n_unique_mpl_colors(n, colormap='jet', cyclic=False): + """ + Yields `n` unique colors from the given `colormap`. + + Set `cyclic` to `True` if the `colormap` is cyclic. + """ + cmap = plt.get_cmap(colormap) + m = n if cyclic else n - 1 + for i in range(n): + yield np.multiply(255, cmap(i / m)) + + if __name__ == '__main__': parser = argparse.ArgumentParser() @@ -68,7 +78,7 @@ unique_colors = frozenset(graph_coloring.values()) # Assign colors to nodes based on the greedy coloring - graph_color_to_mpl_color = dict(zip(unique_colors, mpl.TABLEAU_COLORS.values())) + graph_color_to_mpl_color = dict(zip(unique_colors, get_n_unique_mpl_colors(len(unique_colors)))) node_colors = [graph_color_to_mpl_color[graph_coloring[n]] for n in G.nodes()] # Render result @@ -77,7 +87,6 @@ for label, label_color in zip(G.nodes(), node_colors): cc = (im == label) - label_color = color_hex_to_rgb_tuple(label_color) for ch in range(3): result[:, :, ch][cc] = label_color[ch]
--- a/colorize_labels.xml Wed Apr 24 08:12:15 2024 +0000 +++ b/colorize_labels.xml Tue Sep 24 17:30:20 2024 +0000 @@ -4,7 +4,7 @@ <import>creators.xml</import> <import>tests.xml</import> <token name="@TOOL_VERSION@">3.2.1</token> - <token name="@VERSION_SUFFIX@">2</token> + <token name="@VERSION_SUFFIX@">3</token> </macros> <creator> <expand macro="creators/bmcv" /> @@ -43,6 +43,7 @@ <data format="png" name="output" from_work_dir="output.png" /> </outputs> <tests> + <!-- int64 --> <test> <param name="input" value="input1.tif" /> <param name="radius" value="1" /> @@ -52,6 +53,7 @@ <has_image_channels channels="3"/> </expand> </test> + <!-- uint8 --> <test> <param name="input" value="input2.tif" /> <param name="radius" value="10" /> @@ -61,6 +63,16 @@ <has_image_channels channels="3"/> </expand> </test> + <!-- uint16 --> + <test> + <param name="input" value="input3.tif" /> + <param name="radius" value="100" /> + <param name="bg_label" value="0" /> + <param name="bg_color" value="#ffffff" /> + <expand macro="tests/intensity_image_diff" name="output" value="output3.png" ftype="png"> + <has_image_channels channels="3"/> + </expand> + </test> </tests> <help>
--- a/creators.xml Wed Apr 24 08:12:15 2024 +0000 +++ b/creators.xml Tue Sep 24 17:30:20 2024 +0000 @@ -5,6 +5,11 @@ <yield /> </xml> + <xml name="creators/rmassei"> + <person givenName="Riccardo" familyName="Massei"/> + <yield/> + </xml> + <xml name="creators/alliecreason"> <person givenName="Allison" familyName="Creason"/> <yield/>