23169211772

Committed 16 Mar 2026 10:37PM UTC coverage: 94.953%. Remained the same

Build # 23169211772

Build Type

Pull #21

github

Committed by

web-flow

Commit Message

Merge 31815bcf3 into f10b9569e

Pull Request Pull Request #21: [pre-commit.ci] pre-commit autoupdate

Coverage Stats

8 of 8 new or added lines in 8 files covered. (100.0%)

21 existing lines in 4 files now uncovered.

809 of 852 relevant lines covered (94.95%)

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97.83

/ximage/labels/plot_labels.py

# -----------------------------------------------------------------------------.
# MIT License

# Copyright (c) 2024-2026 ximage developers
#
# This file is part of ximage.

# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without limitation the rights
# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
# copies of the Software, and to permit persons to whom the Software is
# furnished to do so, subject to the following conditions:
#
# The above copyright notice and this permission notice shall be included in all
# copies or substantial portions of the Software.
#
# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
# SOFTWARE.

# -----------------------------------------------------------------------------.
"""Utilities to plot labels."""
import matplotlib as mpl
import matplotlib.pyplot as plt
import numpy as np

from ximage.labels.labels import get_label_indices


def get_label_colorbar_settings(label_indices, cmap="Paired"):
    """Return plot and cbar kwargs to plot properly a label array."""
    # Cast to int the label_indices
    label_indices = label_indices.astype(int)
    # Compute number of required colors
    n_labels = len(label_indices)

    # Get colormap if string
    if isinstance(cmap, str):
        cmap = plt.get_cmap(cmap)

    # Extract colors
    color_list = [cmap(i) for i in range(cmap.N)]

    # Create the new colormap
    cmap_new = mpl.colors.LinearSegmentedColormap.from_list("Label Classes", color_list, n_labels)

    # Define the bins and normalize
    bounds = np.linspace(1, n_labels + 1, n_labels + 1)
    norm = mpl.colors.BoundaryNorm(bounds, cmap_new.N)

    # Define the plot kwargs
    plot_kwargs = {}
    plot_kwargs["cmap"] = cmap_new
    plot_kwargs["norm"] = norm

    # Define colorbar kwargs
    ticks = bounds[:-1] + 0.5
    ticklabels = label_indices
    assert len(ticks) == len(ticklabels)
    cbar_kwargs = {}
    cbar_kwargs["label"] = "Label IDs"
    cbar_kwargs["ticks"] = ticks
    cbar_kwargs["ticklabels"] = ticklabels
    return plot_kwargs, cbar_kwargs


def plot_labels(
    dataarray,
    x=None,
    y=None,
    ax=None,
    max_n_labels=50,
    add_colorbar=True,
    cmap="Paired",
    use_imshow=False,
    **plot_kwargs,
):
    """Plot labels.

    The maximum allowed number of labels to plot is 'max_n_labels'.
    """
    # Check that datarray has two dimensions only
    if len(dataarray.dims) != 2:
        raise ValueError(f"The dataarray must have two dimensions only to be plotted. Got {dataarray.dims}")

    # Compute the dataarray if needed
    dataarray = dataarray.compute()

    # Retrieve label indices
    label_indices = get_label_indices(dataarray)
    n_labels = len(label_indices)
    if add_colorbar and n_labels > max_n_labels:
        msg = f"""The array currently contains {n_labels} labels and 'max_n_labels'
            is set to {max_n_labels}. The colorbar is not displayed!"""
        print(msg)
        add_colorbar = False

    # Redefine label array to have consecutive integers starting from 1
    # dataarray = redefine_label_array(dataarray, label_indices=label_indices)

    # Replace 0 with nan
    dataarray = dataarray.where(dataarray > 0)

    # Define appropriate colormap
    plot_kwargs, cbar_kwargs = get_label_colorbar_settings(label_indices, cmap=cmap)

    # Plot image
    ticklabels = cbar_kwargs.pop("ticklabels", None)
    if not add_colorbar:
        cbar_kwargs = {}
    if use_imshow:
        p = dataarray.plot.imshow(
            x=x,
            y=y,
            ax=ax,
            add_colorbar=add_colorbar,
            cbar_kwargs=cbar_kwargs,
            **plot_kwargs,
        )
    else:
        p = dataarray.plot.pcolormesh(
            x=x,
            y=y,
            ax=ax,
            add_colorbar=add_colorbar,
            cbar_kwargs=cbar_kwargs,
            **plot_kwargs,
        )
    plt.title(dataarray.name)
    if add_colorbar and ticklabels is not None:
        p.colorbar.ax.set_yticklabels(ticklabels)
    return p

1	# -----------------------------------------------------------------------------.
2	# MIT License
3
4	# Copyright (c) 2024-2026 ximage developers
5	#
6	# This file is part of ximage.
7
8	# Permission is hereby granted, free of charge, to any person obtaining a copy
9	# of this software and associated documentation files (the "Software"), to deal
10	# in the Software without restriction, including without limitation the rights
11	# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
12	# copies of the Software, and to permit persons to whom the Software is
13	# furnished to do so, subject to the following conditions:
14	#
15	# The above copyright notice and this permission notice shall be included in all
16	# copies or substantial portions of the Software.
17	#
18	# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
19	# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
20	# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
21	# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
22	# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
23	# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
24	# SOFTWARE.
25
26	# -----------------------------------------------------------------------------.
27	"""Utilities to plot labels."""
28	import matplotlib as mpl	1✔
29	import matplotlib.pyplot as plt	1✔
30	import numpy as np	1✔
31
32	from ximage.labels.labels import get_label_indices	1✔
33
34
35	def get_label_colorbar_settings(label_indices, cmap="Paired"):	1✔
36	"""Return plot and cbar kwargs to plot properly a label array."""
37	# Cast to int the label_indices
38	label_indices = label_indices.astype(int)	1✔
39	# Compute number of required colors
40	n_labels = len(label_indices)	1✔
41
42	# Get colormap if string
43	if isinstance(cmap, str):	1✔
44	cmap = plt.get_cmap(cmap)	1✔
45
46	# Extract colors
47	color_list = [cmap(i) for i in range(cmap.N)]	1✔
48
49	# Create the new colormap
50	cmap_new = mpl.colors.LinearSegmentedColormap.from_list("Label Classes", color_list, n_labels)	1✔
51
52	# Define the bins and normalize
53	bounds = np.linspace(1, n_labels + 1, n_labels + 1)	1✔
54	norm = mpl.colors.BoundaryNorm(bounds, cmap_new.N)	1✔
55
56	# Define the plot kwargs
57	plot_kwargs = {}	1✔
58	plot_kwargs["cmap"] = cmap_new	1✔
59	plot_kwargs["norm"] = norm	1✔
60
61	# Define colorbar kwargs
62	ticks = bounds[:-1] + 0.5	1✔
63	ticklabels = label_indices	1✔
64	assert len(ticks) == len(ticklabels)	1✔
65	cbar_kwargs = {}	1✔
66	cbar_kwargs["label"] = "Label IDs"	1✔
67	cbar_kwargs["ticks"] = ticks	1✔
68	cbar_kwargs["ticklabels"] = ticklabels	1✔
69	return plot_kwargs, cbar_kwargs	1✔
70
71
72	def plot_labels(	1✔
73	dataarray,
74	x=None,
75	y=None,
76	ax=None,
77	max_n_labels=50,
78	add_colorbar=True,
79	cmap="Paired",
80	use_imshow=False,
81	**plot_kwargs,
82	):
83	"""Plot labels.
84
85	The maximum allowed number of labels to plot is 'max_n_labels'.
86	"""
87	# Check that datarray has two dimensions only
88	if len(dataarray.dims) != 2:	1✔
UNCOV 89	raise ValueError(f"The dataarray must have two dimensions only to be plotted. Got {dataarray.dims}")	×
90
91	# Compute the dataarray if needed
92	dataarray = dataarray.compute()	1✔
93
94	# Retrieve label indices
95	label_indices = get_label_indices(dataarray)	1✔
96	n_labels = len(label_indices)	1✔
97	if add_colorbar and n_labels > max_n_labels:	1✔
98	msg = f"""The array currently contains {n_labels} labels and 'max_n_labels'	1✔
99	is set to {max_n_labels}. The colorbar is not displayed!"""
100	print(msg)	1✔
101	add_colorbar = False	1✔
102
103	# Redefine label array to have consecutive integers starting from 1
104	# dataarray = redefine_label_array(dataarray, label_indices=label_indices)
105
106	# Replace 0 with nan
107	dataarray = dataarray.where(dataarray > 0)	1✔
108
109	# Define appropriate colormap
110	plot_kwargs, cbar_kwargs = get_label_colorbar_settings(label_indices, cmap=cmap)	1✔
111
112	# Plot image
113	ticklabels = cbar_kwargs.pop("ticklabels", None)	1✔
114	if not add_colorbar:	1✔
115	cbar_kwargs = {}	1✔
116	if use_imshow:	1✔
117	p = dataarray.plot.imshow(	1✔
118	x=x,
119	y=y,
120	ax=ax,
121	add_colorbar=add_colorbar,
122	cbar_kwargs=cbar_kwargs,
123	**plot_kwargs,
124	)
125	else:
126	p = dataarray.plot.pcolormesh(	1✔
127	x=x,
128	y=y,
129	ax=ax,
130	add_colorbar=add_colorbar,
131	cbar_kwargs=cbar_kwargs,
132	**plot_kwargs,
133	)
134	plt.title(dataarray.name)	1✔
135	if add_colorbar and ticklabels is not None:	1✔
136	p.colorbar.ax.set_yticklabels(ticklabels)	1✔
137	return p	1✔

ghiggi / ximage / 23169211772

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