deepreg.vis.main() - Code Metrics - DeepRegNet/DeepReg - Measure and Improve Code Quality continuously with Scrutinizer

deepreg.vis.main() C
last analyzed 2022-05-18 21:56 UTC

↳ Parent: deepreg.vis

Complexity

Conditions

Size

Total Lines	125
Code Lines	85

Duplication

Lines	0
Ratio	0 %

Importance

Changes

Metric	Value
eloc	85
dl	0
loc	125
rs	6.0909
c	0
b	0
f	0
cc	7
nop	1

How to fix Long Method

"""
Module to generate visualisations of data
at command line interface.
Requires ffmpeg writer to write gif files
"""

import argparse
import os
from typing import List

import matplotlib.animation as animation
import matplotlib.pyplot as plt
import numpy as np
import numpy.matlib

from deepreg import log
from deepreg.dataset.loader.nifti_loader import load_nifti_file
from deepreg.model.layer import Warping

logger = log.get(__name__)


def string_to_list(string: str) -> List[str]:
    """
    Converts a comma separated string to a list of strings
    also removes leading or trailing spaces from each element in list.

    :param string: string which is to be converted to list
    :return: list of strings
    """
    return [elem.strip() for elem in string.split(",")]


def gif_slices(img_paths, save_path="", interval=50):
    """
    Generates and saves gif of slices of image
    supports multiple images to generate multiple gif files.

    :param img_paths: list or comma separated string of image paths
    :param save_path: path to directory where visualisation/s is/are to be saved
    :param interval: time in miliseconds between frames of gif
    """
    if type(img_paths) is str:
        img_paths = string_to_list(img_paths)
    img = load_nifti_file(img_paths[0])
    img_shape = np.shape(img)
    for img_path in img_paths:
        fig = plt.figure()
        ax = plt.Axes(fig, [0.0, 0.0, 1.0, 1.0])
        ax.set_axis_off()
        fig.add_axes(ax)

        img = load_nifti_file(img_path)

        frames = []
        for index in range(img_shape[-1]):
            frame = plt.imshow(img[:, :, index], aspect="auto", animated=True)
            # plt.axis('off')
            frames.append([frame])

        anim = animation.ArtistAnimation(fig, frames, interval=interval)

        path_to_anim_save = os.path.join(
            save_path, os.path.split(img_path)[-1].split(".")[0] + ".gif"
        )

        anim.save(path_to_anim_save)
        logger.info("Animation saved to: %s.", path_to_anim_save)


def tile_slices(img_paths, save_path="", fname=None, slice_inds=None, col_titles=None):
    """
    Generate a tiled plot of multiple images for multiple slices in the image.
    Rows are different slices, columns are different images.

    :param img_paths: list or comma separated string of image paths
    :param save_path: path to directory where visualisation/s is/are to be saved
    :param fname: file name with extension to save visualisation to
    :param slice_inds: list of slice indices to plot for each image
    :param col_titles: titles for each column, if None then inferred from file names
    """
    if type(img_paths) is str:
        img_paths = string_to_list(img_paths)
    img = load_nifti_file(img_paths[0])
    img_shape = np.shape(img)

    if slice_inds is None:
        slice_inds = [round(np.random.rand() * (img_shape[-1]) - 1)]

    if col_titles is None:
        col_titles = [
            os.path.split(img_path)[-1].split(".")[0] for img_path in img_paths
        ]

    num_inds = len(slice_inds)
    num_imgs = len(img_paths)

    subplot_mat = np.array(np.arange(num_inds * num_imgs) + 1).reshape(
        num_inds, num_imgs
    )

    plt.figure(figsize=(num_imgs * 2, num_inds * 2))

    imgs = [load_nifti_file(p) for p in img_paths]

    for col_num, img in enumerate(imgs):
        for row_num, index in enumerate(slice_inds):
            plt.subplot(num_inds, num_imgs, subplot_mat[row_num, col_num])
            plt.imshow(img[:, :, index])
            plt.axis("off")
            if row_num - 0 < 1e-3:
                plt.title(col_titles[col_num])

    if fname is None:
        fname = "visualisation.png"
    save_fig_to = os.path.join(save_path, fname)
    plt.savefig(save_fig_to)
    logger.info("Plot saved to: %s", save_fig_to)


def gif_warp(
    img_paths, ddf_path, slice_inds=None, num_interval=100, interval=50, save_path=""
):
    """
    Apply ddf to image slice/s to generate gif.

    :param img_paths: list or comma separated string of image paths
    :param ddf_path: path to ddf to use for warping
    :param slice_inds: list of slice indices to use for each image
    :param num_interval: number of intervals in which to apply ddf
    :param interval: time in miliseconds between frames of gif
    :param save_path: path to directory where visualisation/s is/are to be saved
    """
    if type(img_paths) is str:
        img_paths = string_to_list(img_paths)

    image = load_nifti_file(img_paths[0])
    img_shape = np.shape(image)

    if slice_inds is None:
        slice_inds = [round(np.random.rand() * (img_shape[-1]) - 1)]

    for img_path in img_paths:
        for slice_ind in slice_inds:

            fig = plt.figure()
            ax = plt.Axes(fig, [0.0, 0.0, 1.0, 1.0])
            ax.set_axis_off()
            fig.add_axes(ax)

            ddf_scalers = np.linspace(0, 1, num=num_interval)

            frames = []
            for ddf_scaler in ddf_scalers:
                image = load_nifti_file(img_path)
                ddf = load_nifti_file(ddf_path)
                fixed_image_shape = ddf.shape[:3]
                image = np.expand_dims(image, axis=0)
                ddf = np.expand_dims(ddf, axis=0) * ddf_scaler

                warped_image = Warping(fixed_image_size=fixed_image_shape)([ddf, image])
                warped_image = np.squeeze(warped_image.numpy())

                frame = plt.imshow(
                    warped_image[:, :, slice_ind], aspect="auto", animated=True
                )

                frames.append([frame])

            anim = animation.ArtistAnimation(fig, frames, interval=interval)
            path_to_anim_save = os.path.join(
                save_path,
                os.path.split(img_path)[-1].split(".")[0]
                + "_slice_"
                + str(slice_ind)
                + ".gif",
            )

            anim.save(path_to_anim_save)
            logger.info("Animation saved to: %s", path_to_anim_save)


def gif_tile_slices(img_paths, save_path=None, size=(2, 2), fname=None, interval=50):
    """
    Creates tiled gif over slices of multiple images.

    :param img_paths: list or comma separated string of image paths
    :param save_path: path to directory where visualisation/s is/are to be saved
    :param interval: time in miliseconds between frames of gif
    :param size: number of columns and rows of images for the tiled gif
        (tuple e.g. (2,2))
    :param fname: filename to save visualisation to
    """
    if type(img_paths) is str:
        img_paths = string_to_list(img_paths)

    num_images = np.prod(size)
    if int(len(img_paths)) != int(num_images):
        raise ValueError(
            "The number of images supplied is "
            + str(len(img_paths))
            + " whereas the number required is "
            + str(np.prod(size))
            + " as size specified is "
            + str(size)
        )

    img = load_nifti_file(img_paths[0])
    img_shape = np.shape(img)

    imgs = []
    for img_path in img_paths:
        img = load_nifti_file(img_path)
        shape = np.shape(img)
        if shape != img_shape:
            raise ValueError("all images do not have equal shapes")
        imgs.append(img)

    frames = []

    fig = plt.figure()
    ax = plt.Axes(fig, [0.0, 0.0, 1.0, 1.0])
    ax.set_axis_off()
    fig.add_axes(ax)

    for index in range(img_shape[-1]):

        temp_tiles = []
        frame = np.matlib.repmat(
            np.ones((img_shape[0], img_shape[1])), size[0], size[1]
        )

        for img in imgs:
            temp_tile = img[:, :, index]
            temp_tiles.append(temp_tile)

        tile_count = 0
        for i in range(size[0]):
            for j in range(size[1]):
                tile = temp_tiles[tile_count]
                tile_count += 1
                frame[
                    i * img_shape[0] : (i + 1) * img_shape[0],
                    j * img_shape[0] : (j + 1) * img_shape[0],
                ] = tile

        frame = plt.imshow(frame, aspect="auto", animated=True)

        frames.append([frame])

    if fname is None:
        fname = "visualisation.gif"

    anim = animation.ArtistAnimation(fig, frames, interval=interval)
    path_to_anim_save = os.path.join(save_path, fname)

    anim.save(path_to_anim_save)
    logger.info("Animation saved to: %s", path_to_anim_save)


def main(args=None):
    """
    CLI for deepreg_vis tool.

    Requires ffmpeg wirter to write gif files.

    :param args:
    """
    parser = argparse.ArgumentParser(
        description="deepreg_vis", formatter_class=argparse.RawTextHelpFormatter
    )

    parser.add_argument(
        "--mode",
        "-m",
        help="Mode of visualisation \n"
        "0 for animtion over image slices, \n"
        "1 for warp animation, \n"
        "2 for tile plot",
        type=int,
        required=True,
    )
    parser.add_argument(
        "--image-paths",
        "-i",
        help="File path for image file "
        "(can specify multiple paths using a comma separated string)",
        type=str,
        required=True,
    )
    parser.add_argument(
        "--save-path",
        "-s",
        help="Path to directory where resulting visualisation is saved",
        default="",
    )

    parser.add_argument(
        "--interval",
        help="Interval between frames of animation (in miliseconds)\n"
        "Applicable only if --mode 0 or --mode 1 or --mode 3",
        type=int,
        default=50,
    )
    parser.add_argument(
        "--ddf-path",
        help="Path to ddf used for warping images\n"
        "Applicable only and required if --mode 1",
        type=str,
        default=None,
    )
    parser.add_argument(
        "--num-interval",
        help="Number of intervals to use for warping\n" "Applicable only if --mode 1",
        type=int,
        default=100,
    )
    parser.add_argument(
        "--slice-inds",
        help="Comma separated string of indexes of slices"
        " to be used for the visualisation\n"
        "Applicable only if --mode 1 or --mode 2",
        type=str,
        default=None,
    )
    parser.add_argument(
        "--fname",
        help="File name (with extension like .png, .jpeg, .gif, ...)"
        " to save visualisation to\n"
        "Applicable only if --mode 2 or --mode 3",
        type=str,
        default=None,
    )
    parser.add_argument(
        "--col-titles",
        help="Comma separated string of column titles to use "
        "(inferred from file names if not provided)\n"
        "Applicable only if --mode 2",
        default=None,
    )
    parser.add_argument(
        "--size",
        help="Comma separated string of number of columns and rows (e.g. '2,2')\n"
        "Applicable only if --mode 3",
        default="2,2",
    )

    # init arguments
    args = parser.parse_args(args)

    if args.slice_inds is not None:
        args.slice_inds = string_to_list(args.slice_inds)
        args.slice_inds = [int(elem) for elem in args.slice_inds]

    if args.mode == 0:
        gif_slices(
            img_paths=args.image_paths, save_path=args.save_path, interval=args.interval
        )
    elif args.mode == 1:
        if args.ddf_path is None:
            raise Exception("--ddf-path is required when using --mode 1")
        gif_warp(
            img_paths=args.image_paths,
            ddf_path=args.ddf_path,
            slice_inds=args.slice_inds,
            num_interval=args.num_interval,
            interval=args.interval,
            save_path=args.save_path,
        )
    elif args.mode == 2:
        tile_slices(
            img_paths=args.image_paths,
            save_path=args.save_path,
            fname=args.fname,
            slice_inds=args.slice_inds,
            col_titles=args.col_titles,
        )
    elif args.mode == 3:
        size = tuple([int(elem) for elem in string_to_list(args.size)])
        gif_tile_slices(
            img_paths=args.image_paths,
            save_path=args.save_path,
            fname=args.fname,
            interval=args.interval,
            size=size,
        )


if __name__ == "__main__":
    main()  # pragma: no cover


1			"""
2			Module to generate visualisations of data
3			at command line interface.
4			Requires ffmpeg writer to write gif files
5			"""
6
7			import argparse
8			import os
9			from typing import List
10
11			import matplotlib.animation as animation
12			import matplotlib.pyplot as plt
13			import numpy as np
14			import numpy.matlib
15
16			from deepreg import log
17			from deepreg.dataset.loader.nifti_loader import load_nifti_file
18			from deepreg.model.layer import Warping
19
20			logger = log.get(__name__)
21
22
23			def string_to_list(string: str) -> List[str]:
24			"""
25			Converts a comma separated string to a list of strings
26			also removes leading or trailing spaces from each element in list.
27
28			:param string: string which is to be converted to list
29			:return: list of strings
30			"""
31			return [elem.strip() for elem in string.split(",")]
32
33
34			def gif_slices(img_paths, save_path="", interval=50):
35			"""
36			Generates and saves gif of slices of image
37			supports multiple images to generate multiple gif files.
38
39			:param img_paths: list or comma separated string of image paths
40			:param save_path: path to directory where visualisation/s is/are to be saved
41			:param interval: time in miliseconds between frames of gif
42			"""
43			if type(img_paths) is str:
44			img_paths = string_to_list(img_paths)
45			img = load_nifti_file(img_paths[0])
46			img_shape = np.shape(img)
47			for img_path in img_paths:
48			fig = plt.figure()
49			ax = plt.Axes(fig, [0.0, 0.0, 1.0, 1.0])
50			ax.set_axis_off()
51			fig.add_axes(ax)
52
53			img = load_nifti_file(img_path)
54
55			frames = []
56			for index in range(img_shape[-1]):
57			frame = plt.imshow(img[:, :, index], aspect="auto", animated=True)
58			# plt.axis('off')
59			frames.append([frame])
60
61			anim = animation.ArtistAnimation(fig, frames, interval=interval)
62
63			path_to_anim_save = os.path.join(
64			save_path, os.path.split(img_path)[-1].split(".")[0] + ".gif"
65			)
66
67			anim.save(path_to_anim_save)
68			logger.info("Animation saved to: %s.", path_to_anim_save)
69
70
71			def tile_slices(img_paths, save_path="", fname=None, slice_inds=None, col_titles=None):
72			"""
73			Generate a tiled plot of multiple images for multiple slices in the image.
74			Rows are different slices, columns are different images.
75
76			:param img_paths: list or comma separated string of image paths
77			:param save_path: path to directory where visualisation/s is/are to be saved
78			:param fname: file name with extension to save visualisation to
79			:param slice_inds: list of slice indices to plot for each image
80			:param col_titles: titles for each column, if None then inferred from file names
81			"""
82			if type(img_paths) is str:
83			img_paths = string_to_list(img_paths)
84			img = load_nifti_file(img_paths[0])
85			img_shape = np.shape(img)
86
87			if slice_inds is None:
88			slice_inds = [round(np.random.rand() * (img_shape[-1]) - 1)]
89
90			if col_titles is None:
91			col_titles = [
92			os.path.split(img_path)[-1].split(".")[0] for img_path in img_paths
93			]
94
95			num_inds = len(slice_inds)
96			num_imgs = len(img_paths)
97
98			subplot_mat = np.array(np.arange(num_inds * num_imgs) + 1).reshape(
99			num_inds, num_imgs
100			)
101
102			plt.figure(figsize=(num_imgs * 2, num_inds * 2))
103
104			imgs = [load_nifti_file(p) for p in img_paths]
105
106			for col_num, img in enumerate(imgs):
107			for row_num, index in enumerate(slice_inds):
108			plt.subplot(num_inds, num_imgs, subplot_mat[row_num, col_num])
109			plt.imshow(img[:, :, index])
110			plt.axis("off")
111			if row_num - 0 < 1e-3:
112			plt.title(col_titles[col_num])
113
114			if fname is None:
115			fname = "visualisation.png"
116			save_fig_to = os.path.join(save_path, fname)
117			plt.savefig(save_fig_to)
118			logger.info("Plot saved to: %s", save_fig_to)
119
120
121			def gif_warp(
122			img_paths, ddf_path, slice_inds=None, num_interval=100, interval=50, save_path=""
123			):
124			"""
125			Apply ddf to image slice/s to generate gif.
126
127			:param img_paths: list or comma separated string of image paths
128			:param ddf_path: path to ddf to use for warping
129			:param slice_inds: list of slice indices to use for each image
130			:param num_interval: number of intervals in which to apply ddf
131			:param interval: time in miliseconds between frames of gif
132			:param save_path: path to directory where visualisation/s is/are to be saved
133			"""
134			if type(img_paths) is str:
135			img_paths = string_to_list(img_paths)
136
137			image = load_nifti_file(img_paths[0])
138			img_shape = np.shape(image)
139
140			if slice_inds is None:
141			slice_inds = [round(np.random.rand() * (img_shape[-1]) - 1)]
142
143			for img_path in img_paths:
144			for slice_ind in slice_inds:
145
146			fig = plt.figure()
147			ax = plt.Axes(fig, [0.0, 0.0, 1.0, 1.0])
148			ax.set_axis_off()
149			fig.add_axes(ax)
150
151			ddf_scalers = np.linspace(0, 1, num=num_interval)
152
153			frames = []
154			for ddf_scaler in ddf_scalers:
155			image = load_nifti_file(img_path)
156			ddf = load_nifti_file(ddf_path)
157			fixed_image_shape = ddf.shape[:3]
158			image = np.expand_dims(image, axis=0)
159			ddf = np.expand_dims(ddf, axis=0) * ddf_scaler
160
161			warped_image = Warping(fixed_image_size=fixed_image_shape)([ddf, image])
162			warped_image = np.squeeze(warped_image.numpy())
163
164			frame = plt.imshow(
165			warped_image[:, :, slice_ind], aspect="auto", animated=True
166			)
167
168			frames.append([frame])
169
170			anim = animation.ArtistAnimation(fig, frames, interval=interval)
171			path_to_anim_save = os.path.join(
172			save_path,
173			os.path.split(img_path)[-1].split(".")[0]
174			+ "_slice_"
175			+ str(slice_ind)
176			+ ".gif",
177			)
178
179			anim.save(path_to_anim_save)
180			logger.info("Animation saved to: %s", path_to_anim_save)
181
182
183			def gif_tile_slices(img_paths, save_path=None, size=(2, 2), fname=None, interval=50):
184			"""
185			Creates tiled gif over slices of multiple images.
186
187			:param img_paths: list or comma separated string of image paths
188			:param save_path: path to directory where visualisation/s is/are to be saved
189			:param interval: time in miliseconds between frames of gif
190			:param size: number of columns and rows of images for the tiled gif
191			(tuple e.g. (2,2))
192			:param fname: filename to save visualisation to
193			"""
194			if type(img_paths) is str:
195			img_paths = string_to_list(img_paths)
196
197			num_images = np.prod(size)
198			if int(len(img_paths)) != int(num_images):
199			raise ValueError(
200			"The number of images supplied is "
201			+ str(len(img_paths))
202			+ " whereas the number required is "
203			+ str(np.prod(size))
204			+ " as size specified is "
205			+ str(size)
206			)
207
208			img = load_nifti_file(img_paths[0])
209			img_shape = np.shape(img)
210
211			imgs = []
212			for img_path in img_paths:
213			img = load_nifti_file(img_path)
214			shape = np.shape(img)
215			if shape != img_shape:
216			raise ValueError("all images do not have equal shapes")
217			imgs.append(img)
218
219			frames = []
220
221			fig = plt.figure()
222			ax = plt.Axes(fig, [0.0, 0.0, 1.0, 1.0])
223			ax.set_axis_off()
224			fig.add_axes(ax)
225
226			for index in range(img_shape[-1]):
227
228			temp_tiles = []
229			frame = np.matlib.repmat(
230			np.ones((img_shape[0], img_shape[1])), size[0], size[1]
231			)
232
233			for img in imgs:
234			temp_tile = img[:, :, index]
235			temp_tiles.append(temp_tile)
236
237			tile_count = 0
238			for i in range(size[0]):
239			for j in range(size[1]):
240			tile = temp_tiles[tile_count]
241			tile_count += 1
242			frame[
243			i * img_shape[0] : (i + 1) * img_shape[0],
244			j * img_shape[0] : (j + 1) * img_shape[0],
245			] = tile
246
247			frame = plt.imshow(frame, aspect="auto", animated=True)
248
249			frames.append([frame])
250
251			if fname is None:
252			fname = "visualisation.gif"
253
254			anim = animation.ArtistAnimation(fig, frames, interval=interval)
255			path_to_anim_save = os.path.join(save_path, fname)
256
257			anim.save(path_to_anim_save)
258			logger.info("Animation saved to: %s", path_to_anim_save)
259
260
261			def main(args=None):
262			"""
263			CLI for deepreg_vis tool.
264
265			Requires ffmpeg wirter to write gif files.
266
267			:param args:
268			"""
269			parser = argparse.ArgumentParser(
270			description="deepreg_vis", formatter_class=argparse.RawTextHelpFormatter
271			)
272
273			parser.add_argument(
274			"--mode",
275			"-m",
276			help="Mode of visualisation \n"
277			"0 for animtion over image slices, \n"
278			"1 for warp animation, \n"
279			"2 for tile plot",
280			type=int,
281			required=True,
282			)
283			parser.add_argument(
284			"--image-paths",
285			"-i",
286			help="File path for image file "
287			"(can specify multiple paths using a comma separated string)",
288			type=str,
289			required=True,
290			)
291			parser.add_argument(
292			"--save-path",
293			"-s",
294			help="Path to directory where resulting visualisation is saved",
295			default="",
296			)
297
298			parser.add_argument(
299			"--interval",
300			help="Interval between frames of animation (in miliseconds)\n"
301			"Applicable only if --mode 0 or --mode 1 or --mode 3",
302			type=int,
303			default=50,
304			)
305			parser.add_argument(
306			"--ddf-path",
307			help="Path to ddf used for warping images\n"
308			"Applicable only and required if --mode 1",
309			type=str,
310			default=None,
311			)
312			parser.add_argument(
313			"--num-interval",
314			help="Number of intervals to use for warping\n" "Applicable only if --mode 1",
315			type=int,
316			default=100,
317			)
318			parser.add_argument(
319			"--slice-inds",
320			help="Comma separated string of indexes of slices"
321			" to be used for the visualisation\n"
322			"Applicable only if --mode 1 or --mode 2",
323			type=str,
324			default=None,
325			)
326			parser.add_argument(
327			"--fname",
328			help="File name (with extension like .png, .jpeg, .gif, ...)"
329			" to save visualisation to\n"
330			"Applicable only if --mode 2 or --mode 3",
331			type=str,
332			default=None,
333			)
334			parser.add_argument(
335			"--col-titles",
336			help="Comma separated string of column titles to use "
337			"(inferred from file names if not provided)\n"
338			"Applicable only if --mode 2",
339			default=None,
340			)
341			parser.add_argument(
342			"--size",
343			help="Comma separated string of number of columns and rows (e.g. '2,2')\n"
344			"Applicable only if --mode 3",
345			default="2,2",
346			)
347
348			# init arguments
349			args = parser.parse_args(args)
350
351			if args.slice_inds is not None:
352			args.slice_inds = string_to_list(args.slice_inds)
353			args.slice_inds = [int(elem) for elem in args.slice_inds]
354
355			if args.mode == 0:
356			gif_slices(
357			img_paths=args.image_paths, save_path=args.save_path, interval=args.interval
358			)
359			elif args.mode == 1:
360			if args.ddf_path is None:
361			raise Exception("--ddf-path is required when using --mode 1")
362			gif_warp(
363			img_paths=args.image_paths,
364			ddf_path=args.ddf_path,
365			slice_inds=args.slice_inds,
366			num_interval=args.num_interval,
367			interval=args.interval,
368			save_path=args.save_path,
369			)
370			elif args.mode == 2:
371			tile_slices(
372			img_paths=args.image_paths,
373			save_path=args.save_path,
374			fname=args.fname,
375			slice_inds=args.slice_inds,
376			col_titles=args.col_titles,
377			)
378			elif args.mode == 3:
379			size = tuple([int(elem) for elem in string_to_list(args.size)])
380			gif_tile_slices(
381			img_paths=args.image_paths,
382			save_path=args.save_path,
383			fname=args.fname,
384			interval=args.interval,
385			size=size,
386			)
387
388
389			if __name__ == "__main__":
390			main() # pragma: no cover
391

DeepRegNet / DeepReg

deepreg.vis.main() C last analyzed 2022-05-18 21:56 UTC

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deepreg.vis.main() C
last analyzed 2022-05-18 21:56 UTC