torchio.visualization.make_gif() - Code Metrics - Inspection of "Add plot_volume indices parameter" - fepegar/torchio - Measure and Improve Code Quality continuously with Scrutinizer

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Pull Request — master (#682)

unknown

created 2021-10-06 22:10 UTC

torchio.visualization.make_gif() B

↳ Parent: torchio.visualization

Complexity

Conditions

Size

Total Lines	54
Code Lines	43

Duplication

Lines	0
Ratio	0 %

Importance

Changes

Metric	Value
eloc	43
dl	0
loc	54
rs	7.448
c	0
b	0
f	0
cc	7
nop	8

How to fix Long Method Many Parameters

import warnings

import torch
import numpy as np

from .typing import TypePath
from .data.subject import Subject
from .data.image import Image, LabelMap
from .transforms.preprocessing.spatial.to_canonical import ToCanonical
from .transforms.preprocessing.intensity.rescale import RescaleIntensity


def import_mpl_plt():
    try:
        import matplotlib as mpl
        import matplotlib.pyplot as plt
    except ImportError as e:
        raise ImportError('Install matplotlib for plotting support') from e
    return mpl, plt


def rotate(image, radiological=True, n=-1):
    # Rotate for visualization purposes
    image = np.rot90(image, n)
    if radiological:
        image = np.fliplr(image)
    return image


def plot_volume(
        image: Image,
        radiological=True,
        channel=-1,  # default to foreground for binary maps
        axes=None,
        cmap=None,
        output_path=None,
        show=True,
        xlabels=True,
        percentiles=(0.5, 99.5),
        figsize=None,
        reorient=True,
        indices=None,
        ):
    _, plt = import_mpl_plt()
    fig = None
    if axes is None:
        fig, axes = plt.subplots(1, 3, figsize=figsize)
    sag_axis, cor_axis, axi_axis = axes

    if reorient:
        image = ToCanonical()(image)
    data = image.data[channel]
    if indices is None:
        indices = np.array(data.shape) // 2
    i, j, k = indices
    slice_x = rotate(data[i, :, :], radiological=radiological)
    slice_y = rotate(data[:, j, :], radiological=radiological)
    slice_z = rotate(data[:, :, k], radiological=radiological)
    kwargs = {}
    is_label = isinstance(image, LabelMap)
    if isinstance(cmap, dict):
        slices = slice_x, slice_y, slice_z
        slice_x, slice_y, slice_z = color_labels(slices, cmap)
    else:
        if cmap is None:
            cmap = 'cubehelix' if is_label else 'gray'
        kwargs['cmap'] = cmap
    if is_label:
        kwargs['interpolation'] = 'none'

    sr, sa, ss = image.spacing
    kwargs['origin'] = 'lower'

    if percentiles is not None:
        p1, p2 = np.percentile(data, percentiles)
        kwargs['vmin'] = p1
        kwargs['vmax'] = p2

    sag_aspect = ss / sa
    sag_axis.imshow(slice_x, aspect=sag_aspect, **kwargs)
    if xlabels:
        sag_axis.set_xlabel('A')
    sag_axis.set_ylabel('S')
    sag_axis.invert_xaxis()
    #sag_axis.set_title('Sagittal')

    cor_aspect = ss / sr
    cor_axis.imshow(slice_y, aspect=cor_aspect, **kwargs)
    if xlabels:
        cor_axis.set_xlabel('R')
    cor_axis.set_ylabel('S')
    cor_axis.invert_xaxis()
    #cor_axis.set_title('Coronal')

    axi_aspect = sa / sr
    axi_axis.imshow(slice_z, **kwargs)
    if xlabels:
        axi_axis.set_xlabel('R')
    axi_axis.set_ylabel('A')
    axi_axis.invert_xaxis()
    #axi_axis.set_title('Axial')
    
    sag_axis.axis('off')
    cor_axis.axis('off')
    axi_axis.axis('off')

    #plt.tight_layout()

    if output_path is not None and fig is not None:
        fig.savefig(output_path, transparent=True)
    if show:
        plt.show()


def plot_subject(
        subject: Subject,
        cmap_dict=None,
        show=True,
        output_path=None,
        figsize=None,
        clear_axes=True,
        **kwargs,
        ):
    _, plt = import_mpl_plt()
    num_images = len(subject)
    many_images = num_images > 2
    subplots_kwargs = {'figsize': figsize}
    try:
        if clear_axes:
            subject.check_consistent_spatial_shape()
            subplots_kwargs['sharex'] = 'row' if many_images else 'col'
            subplots_kwargs['sharey'] = 'row' if many_images else 'col'
    except RuntimeError:  # different shapes in subject
        pass
    args = (3, num_images) if many_images else (num_images, 3)
    fig, axes = plt.subplots(*args, **subplots_kwargs)
    # The array of axes must be 2D so that it can be indexed correctly within
    # the plot_volume() function
    axes = axes.T if many_images else axes.reshape(-1, 3)
    iterable = enumerate(subject.get_images_dict(intensity_only=False).items())
    axes_names = 'sagittal', 'coronal', 'axial'
    for image_index, (name, image) in iterable:
        image_axes = axes[image_index]
        cmap = None
        if cmap_dict is not None and name in cmap_dict:
            cmap = cmap_dict[name]
        last_row = image_index == len(axes) - 1
        plot_volume(
            image,
            axes=image_axes,
            show=False,
            cmap=cmap,
            xlabels=last_row,
            **kwargs,
        )
        for axis, axis_name in zip(image_axes, axes_names):
            axis.set_title(f'{name} ({axis_name})')
    plt.tight_layout()
    if output_path is not None:
        fig.savefig(output_path)
    if show:
        plt.show()


def color_labels(arrays, cmap_dict):
    results = []
    for array in arrays:
        si, sj = array.shape
        rgb = np.zeros((si, sj, 3), dtype=np.uint8)
        for label, color in cmap_dict.items():
            if isinstance(color, str):
                mpl, _ = import_mpl_plt()
                color = mpl.colors.to_rgb(color)
                color = [255 * n for n in color]
            rgb[array == label] = color
        results.append(rgb)
    return results


def make_gif(
        tensor: torch.Tensor,
        axis: int,
        duration: float,  # of full gif
        output_path: TypePath,
        loop: int = 0,
        optimize: bool = True,
        rescale: bool = True,
        reverse: bool = False,
        ) -> None:
    try:
        from PIL import Image as ImagePIL
    except ModuleNotFoundError as e:
        message = (
            'Please install Pillow to use Image.to_gif():'
            ' pip install Pillow'
        )
        raise RuntimeError(message) from e
    tensor = RescaleIntensity((0, 255))(tensor) if rescale else tensor
    single_channel = len(tensor) == 1

    # Move channels dimension to the end and bring selected axis to 0
    axes = np.roll(range(1, 4), -axis)
    tensor = tensor.permute(*axes, 0)

    if single_channel:
        mode = 'P'
        tensor = tensor[..., 0]
    else:
        mode = 'RGB'
    array = tensor.byte().numpy()
    n = 2 if axis == 1 else 1
    images = [ImagePIL.fromarray(rotate(i, n=n)).convert(mode) for i in array]
    num_images = len(images)
    images = list(reversed(images)) if reverse else images
    frame_duration_ms = duration / num_images * 1000
    if frame_duration_ms < 10:
        fps = round(1000 / frame_duration_ms)
        frame_duration_ms = 10
        new_duration = frame_duration_ms * num_images / 1000
        message = (
            'The computed frame rate from the given duration is too high'
            f' ({fps} fps). The highest possible frame rate in the GIF'
            ' file format specification is 100 fps. The duration has been set'
            f' to {new_duration:.1f} seconds, instead of {duration:.1f}'
        )
        warnings.warn(message)
    images[0].save(
        output_path,
        save_all=True,
        append_images=images[1:],
        optimize=optimize,
        duration=frame_duration_ms,
        loop=loop,
    )


1			import warnings
2
3			import torch
4			import numpy as np
5
6			from .typing import TypePath
7			from .data.subject import Subject
8			from .data.image import Image, LabelMap
9			from .transforms.preprocessing.spatial.to_canonical import ToCanonical
10			from .transforms.preprocessing.intensity.rescale import RescaleIntensity
11
12
13			def import_mpl_plt():
14			try:
15			import matplotlib as mpl
16			import matplotlib.pyplot as plt
17			except ImportError as e:
18			raise ImportError('Install matplotlib for plotting support') from e
19			return mpl, plt
20
21
22			def rotate(image, radiological=True, n=-1):
23			# Rotate for visualization purposes
24			image = np.rot90(image, n)
25			if radiological:
26			image = np.fliplr(image)
27			return image
28
29
30			def plot_volume(
31			image: Image,
32			radiological=True,
33			channel=-1, # default to foreground for binary maps
34			axes=None,
35			cmap=None,
36			output_path=None,
37			show=True,
38			xlabels=True,
39			percentiles=(0.5, 99.5),
40			figsize=None,
41			reorient=True,
42			indices=None,
43			):
44			_, plt = import_mpl_plt()
45			fig = None
46			if axes is None:
47			fig, axes = plt.subplots(1, 3, figsize=figsize)
48			sag_axis, cor_axis, axi_axis = axes
49
50			if reorient:
51			image = ToCanonical()(image)
52			data = image.data[channel]
53			if indices is None:
54			indices = np.array(data.shape) // 2
55			i, j, k = indices
56			slice_x = rotate(data[i, :, :], radiological=radiological)
57			slice_y = rotate(data[:, j, :], radiological=radiological)
58			slice_z = rotate(data[:, :, k], radiological=radiological)
59			kwargs = {}
60			is_label = isinstance(image, LabelMap)
61			if isinstance(cmap, dict):
62			slices = slice_x, slice_y, slice_z
63			slice_x, slice_y, slice_z = color_labels(slices, cmap)
64			else:
65			if cmap is None:
66			cmap = 'cubehelix' if is_label else 'gray'
67			kwargs['cmap'] = cmap
68			if is_label:
69			kwargs['interpolation'] = 'none'
70
71			sr, sa, ss = image.spacing
72			kwargs['origin'] = 'lower'
73
74			if percentiles is not None:
75			p1, p2 = np.percentile(data, percentiles)
76			kwargs['vmin'] = p1
77			kwargs['vmax'] = p2
78
79			sag_aspect = ss / sa
80			sag_axis.imshow(slice_x, aspect=sag_aspect, **kwargs)
81			if xlabels:
82			sag_axis.set_xlabel('A')
83			sag_axis.set_ylabel('S')
84			sag_axis.invert_xaxis()
85			#sag_axis.set_title('Sagittal')
86
87			cor_aspect = ss / sr
88			cor_axis.imshow(slice_y, aspect=cor_aspect, **kwargs)
89			if xlabels:
90			cor_axis.set_xlabel('R')
91			cor_axis.set_ylabel('S')
92			cor_axis.invert_xaxis()
93			#cor_axis.set_title('Coronal')
94
95			axi_aspect = sa / sr
96			axi_axis.imshow(slice_z, **kwargs)
97			if xlabels:
98			axi_axis.set_xlabel('R')
99			axi_axis.set_ylabel('A')
100			axi_axis.invert_xaxis()
101			#axi_axis.set_title('Axial')
102
103			sag_axis.axis('off')
104			cor_axis.axis('off')
105			axi_axis.axis('off')
106
107			#plt.tight_layout()
108
109			if output_path is not None and fig is not None:
110			fig.savefig(output_path, transparent=True)
111			if show:
112			plt.show()
113
114
115			def plot_subject(
116			subject: Subject,
117			cmap_dict=None,
118			show=True,
119			output_path=None,
120			figsize=None,
121			clear_axes=True,
122			**kwargs,
123			):
124			_, plt = import_mpl_plt()
125			num_images = len(subject)
126			many_images = num_images > 2
127			subplots_kwargs = {'figsize': figsize}
128			try:
129			if clear_axes:
130			subject.check_consistent_spatial_shape()
131			subplots_kwargs['sharex'] = 'row' if many_images else 'col'
132			subplots_kwargs['sharey'] = 'row' if many_images else 'col'
133			except RuntimeError: # different shapes in subject
134			pass
135			args = (3, num_images) if many_images else (num_images, 3)
136			fig, axes = plt.subplots(args, *subplots_kwargs)
137			# The array of axes must be 2D so that it can be indexed correctly within
138			# the plot_volume() function
139			axes = axes.T if many_images else axes.reshape(-1, 3)
140			iterable = enumerate(subject.get_images_dict(intensity_only=False).items())
141			axes_names = 'sagittal', 'coronal', 'axial'
142			for image_index, (name, image) in iterable:
143			image_axes = axes[image_index]
144			cmap = None
145			if cmap_dict is not None and name in cmap_dict:
146			cmap = cmap_dict[name]
147			last_row = image_index == len(axes) - 1
148			plot_volume(
149			image,
150			axes=image_axes,
151			show=False,
152			cmap=cmap,
153			xlabels=last_row,
154			**kwargs,
155			)
156			for axis, axis_name in zip(image_axes, axes_names):
157			axis.set_title(f'{name} ({axis_name})')
158			plt.tight_layout()
159			if output_path is not None:
160			fig.savefig(output_path)
161			if show:
162			plt.show()
163
164
165			def color_labels(arrays, cmap_dict):
166			results = []
167			for array in arrays:
168			si, sj = array.shape
169			rgb = np.zeros((si, sj, 3), dtype=np.uint8)
170			for label, color in cmap_dict.items():
171			if isinstance(color, str):
172			mpl, _ = import_mpl_plt()
173			color = mpl.colors.to_rgb(color)
174			color = [255 * n for n in color]
175			rgb[array == label] = color
176			results.append(rgb)
177			return results
178
179
180			def make_gif(
181			tensor: torch.Tensor,
182			axis: int,
183			duration: float, # of full gif
184			output_path: TypePath,
185			loop: int = 0,
186			optimize: bool = True,
187			rescale: bool = True,
188			reverse: bool = False,
189			) -> None:
190			try:
191			from PIL import Image as ImagePIL
192			except ModuleNotFoundError as e:
193			message = (
194			'Please install Pillow to use Image.to_gif():'
195			' pip install Pillow'
196			)
197			raise RuntimeError(message) from e
198			tensor = RescaleIntensity((0, 255))(tensor) if rescale else tensor
199			single_channel = len(tensor) == 1
200
201			# Move channels dimension to the end and bring selected axis to 0
202			axes = np.roll(range(1, 4), -axis)
203			tensor = tensor.permute(*axes, 0)
204
205			if single_channel:
206			mode = 'P'
207			tensor = tensor[..., 0]
208			else:
209			mode = 'RGB'
210			array = tensor.byte().numpy()
211			n = 2 if axis == 1 else 1
212			images = [ImagePIL.fromarray(rotate(i, n=n)).convert(mode) for i in array]
213			num_images = len(images)
214			images = list(reversed(images)) if reverse else images
215			frame_duration_ms = duration / num_images * 1000
216			if frame_duration_ms < 10:
217			fps = round(1000 / frame_duration_ms)
218			frame_duration_ms = 10
219			new_duration = frame_duration_ms * num_images / 1000
220			message = (
221			'The computed frame rate from the given duration is too high'
222			f' ({fps} fps). The highest possible frame rate in the GIF'
223			' file format specification is 100 fps. The duration has been set'
224			f' to {new_duration:.1f} seconds, instead of {duration:.1f}'
225			)
226			warnings.warn(message)
227			images[0].save(
228			output_path,
229			save_all=True,
230			append_images=images[1:],
231			optimize=optimize,
232			duration=frame_duration_ms,
233			loop=loop,
234			)
235

fepegar / torchio

Pull Request — master (#682)

torchio.visualization.make_gif() B

Complexity

Size

Duplication

Importance

How to fix Long Method Many Parameters

Long Method

Many Parameters

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