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changes after several weeks

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This commit is contained in:
Stefan
2022-09-05 11:16:50 +02:00
parent 03bd157664
commit e3b84db978
16 changed files with 1204 additions and 160 deletions
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15
scripts/7.Visualize_saliency.py
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@ -1,4 +1,5 @@
import argparse
from email.mime import image
import numpy as np
import matplotlib.pyplot as plt
import SimpleITK as sitk
@ -16,9 +17,10 @@ args = parser.parse_args()
SERIES = args.series
series_ = '_'.join(args.series)
EXPERIMENT = args.experiment
SALIENCY_DIR = f'./../train_output/{EXPERIMENT}_{series_}/saliency.npy'
IMAGES_DIR = f'./../train_output/{EXPERIMENT}_{series_}/images_list.npy'
SEGMENTATION_DIR = f'./../train_output/{EXPERIMENT}_{series_}/segmentations.npy'
fold = 0
SALIENCY_DIR = f'./../train_output/{EXPERIMENT}_{series_}_{fold}/saliency.npy'
IMAGES_DIR = f'./../train_output/{EXPERIMENT}_{series_}_{fold}/images_list.npy'
SEGMENTATION_DIR = f'./../train_output/{EXPERIMENT}_{series_}_{fold}/segmentations.npy'
SLIDE = 10
########## load saliency map ############
@ -44,8 +46,9 @@ min_value = np.amin(heatmap[:,:,SLIDE,:])
for indx in range(len(SERIES)):
print(indx)
axes[0,indx].imshow(np.transpose(images_list[:,:,SLIDE,indx]),cmap='gray')
im = axes[1,indx].imshow(np.transpose(np.squeeze(heatmap[:,:,SLIDE,indx])),vmin=min_value, vmax=max_value)
heatmap_i = np.transpose(np.squeeze(heatmap[:,:,SLIDE,indx]))
im = axes[0,indx].imshow(np.transpose(images_list[:,:,SLIDE,indx]),cmap='gray')
axes[0,indx].imshow(np.ma.masked_where(heatmap_i < 0.10, heatmap_i),vmin=min_value, vmax=max_value*0.5, alpha=0.25, cmap='jet')
axes[0,indx].set_title(SERIES[indx])
axes[0,indx].set_axis_off()
axes[1,indx].set_axis_off()
@ -54,4 +57,4 @@ cbar = fig.colorbar(im, ax=axes.ravel().tolist(), shrink=0.5, orientation='horiz
cbar.set_ticks([min_value,max_value])
cbar.set_ticklabels(['less important', 'important'])
fig.suptitle('Saliency map', fontsize=16)
plt.savefig(f'./../train_output/{EXPERIMENT}_{series_}/saliency_map.png', dpi=300)
plt.savefig(f'./../train_output/{EXPERIMENT}_{series_}_{fold}/saliency_map.png', dpi=300)