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from matplotlib import pyplot as plt |
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import math |
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import numpy as np |
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def visualize_results(img, mask, pred, n_slices: int=3, slices: list=None, title: str=""): |
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""" |
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img: tensor [C, H, W, Z] |
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mask: tensor [C, H, W, Z] |
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pred: tensor [C, H, W, Z] |
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n_slices: number of slices to visualize |
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slices: list of slices to visualize |
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title; title of the plot |
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""" |
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if slices is not None: |
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n_slices = len(slices) |
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fig, ax = plt.subplots(n_slices, 3, figsize=(14, 5*n_slices)) |
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inc = img.shape[-1] // n_slices |
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mask_masked = np.ma.masked_where(mask == 0, mask) |
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pred_masked = np.ma.masked_where(pred == 0, pred) |
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for i in range(n_slices): |
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slice_num = i*inc if slices is None else slices[i] |
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for c in range(3): |
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ax[i,c].imshow(img[0,:,:,slice_num], cmap="gray") |
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ax[i,c].axis("off") |
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ax[i,c].set_title(f'image') |
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ax[i,1].imshow(mask_masked[1,:,:,slice_num], cmap='jet', vmin=1, vmax=4, interpolation='none', alpha=0.5) |
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ax[i,1].imshow(mask_masked[2,:,:,slice_num], cmap='Reds', vmin=0, vmax=1.3, interpolation='none', alpha=0.8) |
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ax[i,1].set_title(f'ground truth') |
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ax[i,2].imshow(pred_masked[1,:,:,slice_num], cmap='jet', vmin=1, vmax=4, interpolation='none', alpha=0.5) |
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ax[i,2].imshow(pred_masked[2,:,:,slice_num], cmap='Reds', vmin=0, vmax=1.3, interpolation='none', alpha=0.8) |
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ax[i,2].set_title(f'predicted') |
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plt.suptitle(title, size=14) |
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plt.tight_layout() |
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plt.show() |
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def visualize_patient(img, mask=None, n_slices: int=3, slices: list=None, z_dim_last=True, mask_channel=0, title: str=""): |
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""" |
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img: tensor [C, H, W, Z] |
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mask: tensor [C, H, W, Z] |
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n: number of slices to visualize |
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""" |
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if slices is not None: |
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n_slices = len(slices) |
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fig, ax = plt.subplots(math.ceil(n_slices/3), 3, figsize=(14, 5*math.ceil(n_slices/3))) |
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if z_dim_last: inc = img.shape[-1] // n_slices |
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else: inc = img.shape[0] // n_slices |
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masked = np.ma.masked_where(mask == 0, mask) |
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for i in range(n_slices): |
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r, c = divmod(i, 3) |
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slice_num = i*inc if slices is None else slices[i] |
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if n_slices <= 3: |
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if z_dim_last: ax[c].imshow(img[0,:,:,slice_num], cmap="gray") |
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else: ax[c].imshow(img[slice_num,0,:,:], cmap="gray") |
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ax[c].axis("off") |
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ax[c].set_title(f'slice {slice_num}') |
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if mask is not None: |
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if z_dim_last: mask_overlay = ax[c].imshow(masked[mask_channel,:,:,slice_num], cmap='jet', vmin=1, vmax=4, interpolation='none', alpha=0.4) |
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else: mask_overlay = ax[c].imshow(masked[slice_num,mask_channel,:,:], cmap='jet', vmin=1, vmax=4, interpolation='none', alpha=0.4) |
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else: |
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if z_dim_last: ax[r][c].imshow(img[0,:,:,slice_num], cmap="gray") |
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else: ax[r][c].imshow(img[slice_num,0,:,:], cmap="gray") |
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ax[r][c].axis("off") |
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ax[r][c].set_title(f'slice {slice_num}') |
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if mask is not None: |
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if z_dim_last: mask_overlay = ax[r][c].imshow(masked[mask_channel,:,:,slice_num], cmap='jet', vmin=1, vmax=4, interpolation='none', alpha=0.4) |
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else: mask_overlay = ax[r][c].imshow(masked[slice_num,mask_channel,:,:], cmap='jet', vmin=1, vmax=4, interpolation='none', alpha=0.4) |
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plt.suptitle(title, size=14) |
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plt.tight_layout() |
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plt.show() |
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fig, ax = plt.subplots(math.ceil(n_slices/3), 3, figsize=(14, 5*math.ceil(n_slices/3))) |
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if z_dim_last: inc = img.shape[-1] // n_slices |
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else: inc = img.shape[0] // n_slices |
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for i in range(n_slices): |
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r, c = divmod(i, 3) |
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slice_num = i*inc if slices is None else slices[i] |
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if n_slices <= 3: |
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if z_dim_last: ax[c].imshow(img[0,:,:,slice_num], cmap="gray") |
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else: ax[c].imshow(img[slice_num,0,:,:], cmap="gray") |
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ax[c].axis("off") |
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ax[c].set_title(f'slice {slice_num}') |
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else: |
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if z_dim_last: ax[r][c].imshow(img[0,:,:,slice_num], cmap="gray") |
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else: ax[r][c].imshow(img[slice_num,0,:,:], cmap="gray") |
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ax[r][c].axis("off") |
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ax[r][c].set_title(f'slice {slice_num}') |
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plt.suptitle(title, size=14) |
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plt.tight_layout() |
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plt.show() |
