11463837481

Committed 22 Oct 2024 03:49PM CUT coverage: 85.341%. Remained the same

Build # 11463837481

Build Type

Pull #722

github

Committed by

web-flow

Commit Message

Merge 37286119b into 6074d8529

Pull Request Pull Request #722: COMP: version bump

Run Details

4512 of 5287 relevant lines covered (85.34%)

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38.1

ants/plotting/plot_directory.py

"""
Functions for plotting ants images
"""


__all__ = [
    "plot_directory"
]

import fnmatch
import math
import os
import warnings

from matplotlib import gridspec
import matplotlib.pyplot as plt
import matplotlib.patheffects as path_effects
import matplotlib.lines as mlines
import matplotlib.patches as patches
import matplotlib.mlab as mlab
import matplotlib.animation as animation
from mpl_toolkits.axes_grid1.inset_locator import inset_axes


import numpy as np

import ants


def plot_directory(
    directory,
    recursive=False,
    regex="*",
    save_prefix="",
    save_suffix="",
    axis=None,
    **kwargs
):
    """
    Create and save an ANTsPy plot for every image matching a given regular
    expression in a directory, optionally recursively. This is a good function
    for quick visualize exploration of all of images in a directory

    ANTsR function: N/A

    Arguments
    ---------
    directory : string
        directory in which to search for images and plot them

    recursive : boolean
        If true, this function will search through all directories under
        the given directory recursively to make plots.
        If false, this function will only create plots for images in the
        given directory

    regex : string
        regular expression used to filter out certain filenames or suffixes

    save_prefix : string
        sub-string that will be appended to the beginning of all saved plot filenames.
        Default is to add nothing.

    save_suffix : string
        sub-string that will be appended to the end of all saved plot filenames.
        Default is add nothing.

    kwargs : keyword arguments
        any additional arguments to pass onto the `ants.plot` function.
        e.g. overlay, alpha, cmap, etc. See `ants.plot` for more options.

    Example
    -------
    >>> import ants
    >>> ants.plot_directory(directory='~/desktop/testdir',
                            recursive=False, regex='*')
    """

    def has_acceptable_suffix(fname):
        suffixes = {".nii.gz"}
        return sum([fname.endswith(sx) for sx in suffixes]) > 0

    if directory.startswith("~"):
        directory = os.path.expanduser(directory)

    if not os.path.isdir(directory):
        raise ValueError("directory %s does not exist!" % directory)

    for root, dirnames, fnames in os.walk(directory):
        for fname in fnames:
            if fnmatch.fnmatch(fname, regex) and has_acceptable_suffix(fname):
                load_fname = os.path.join(root, fname)
                fname = fname.replace(".".join(fname.split(".")[1:]), "png")
                fname = fname.replace(".png", "%s.png" % save_suffix)
                fname = "%s%s" % (save_prefix, fname)
                save_fname = os.path.join(root, fname)
                img = ants.image_read(load_fname)

                if axis is None:
                    axis_range = [i for i in range(img.dimension)]
                else:
                    axis_range = axis if isinstance(axis, (list, tuple)) else [axis]

                if img.dimension > 2:
                    for axis_idx in axis_range:
                        filename = save_fname.replace(".png", "_axis%i.png" % axis_idx)
                        ncol = int(math.sqrt(img.shape[axis_idx]))
                        ants.plot(
                            img,
                            axis=axis_idx,
                            nslices=img.shape[axis_idx],
                            ncol=ncol,
                            filename=filename,
                            **kwargs
                        )
                else:
                    filename = save_fname
                    ants.plot(img, filename=filename, **kwargs)

1	"""
2	Functions for plotting ants images
3	"""
4
5
6	__all__ = [	1✔
7	"plot_directory"
8	]
9
10	import fnmatch	1✔
11	import math	1✔
12	import os	1✔
13	import warnings	1✔
14
15	from matplotlib import gridspec	1✔
16	import matplotlib.pyplot as plt	1✔
17	import matplotlib.patheffects as path_effects	1✔
18	import matplotlib.lines as mlines	1✔
19	import matplotlib.patches as patches	1✔
20	import matplotlib.mlab as mlab	1✔
21	import matplotlib.animation as animation	1✔
22	from mpl_toolkits.axes_grid1.inset_locator import inset_axes	1✔
23
24
25	import numpy as np	1✔
26
27	import ants	1✔
28
29
30	def plot_directory(	1✔
31	directory,
32	recursive=False,
33	regex="*",
34	save_prefix="",
35	save_suffix="",
36	axis=None,
37	**kwargs
38	):
39	"""
40	Create and save an ANTsPy plot for every image matching a given regular
41	expression in a directory, optionally recursively. This is a good function
42	for quick visualize exploration of all of images in a directory
43
44	ANTsR function: N/A
45
46	Arguments
47	---------
48	directory : string
49	directory in which to search for images and plot them
50
51	recursive : boolean
52	If true, this function will search through all directories under
53	the given directory recursively to make plots.
54	If false, this function will only create plots for images in the
55	given directory
56
57	regex : string
58	regular expression used to filter out certain filenames or suffixes
59
60	save_prefix : string
61	sub-string that will be appended to the beginning of all saved plot filenames.
62	Default is to add nothing.
63
64	save_suffix : string
65	sub-string that will be appended to the end of all saved plot filenames.
66	Default is add nothing.
67
68	kwargs : keyword arguments
69	any additional arguments to pass onto the `ants.plot` function.
70	e.g. overlay, alpha, cmap, etc. See `ants.plot` for more options.
71
72	Example
73	-------
74	>>> import ants
75	>>> ants.plot_directory(directory='~/desktop/testdir',
76	recursive=False, regex='*')
77	"""
78
79	def has_acceptable_suffix(fname):	×
80	suffixes = {".nii.gz"}	×
81	return sum([fname.endswith(sx) for sx in suffixes]) > 0	×
82
83	if directory.startswith("~"):	×
84	directory = os.path.expanduser(directory)	×
85
86	if not os.path.isdir(directory):	×
87	raise ValueError("directory %s does not exist!" % directory)	×
88
89	for root, dirnames, fnames in os.walk(directory):	×
90	for fname in fnames:	×
91	if fnmatch.fnmatch(fname, regex) and has_acceptable_suffix(fname):	×
92	load_fname = os.path.join(root, fname)	×
93	fname = fname.replace(".".join(fname.split(".")[1:]), "png")	×
94	fname = fname.replace(".png", "%s.png" % save_suffix)	×
95	fname = "%s%s" % (save_prefix, fname)	×
96	save_fname = os.path.join(root, fname)	×
97	img = ants.image_read(load_fname)	×
98
99	if axis is None:	×
100	axis_range = [i for i in range(img.dimension)]	×
101	else:
102	axis_range = axis if isinstance(axis, (list, tuple)) else [axis]	×
103
104	if img.dimension > 2:	×
105	for axis_idx in axis_range:	×
106	filename = save_fname.replace(".png", "_axis%i.png" % axis_idx)	×
107	ncol = int(math.sqrt(img.shape[axis_idx]))	×
108	ants.plot(	×
109	img,
110	axis=axis_idx,
111	nslices=img.shape[axis_idx],
112	ncol=ncol,
113	filename=filename,
114	**kwargs
115	)
116	else:
117	filename = save_fname	×
118	ants.plot(img, filename=filename, **kwargs)	×

ANTsX / ANTsPy / 11463837481

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