Figure 5 added

figure_5.py

+import numpy as np
+import matplotlib.image as mpimg
+import matplotlib.pyplot as plt
+import matplotlib as mpl
+import os
+base_dir = os.path.abspath('')
+
+# printing individually #3C279E
+colors = ['#440053', 'orange', 'yellow', 'black']
+bounds = [0,49,99,149,199]
+
+cmap = mpl.colors.ListedColormap(colors)
+norm = mpl.colors.BoundaryNorm(bounds, cmap.N)
+
+# sample_c = mpimg.imread("/work1/s162377/Lua/mask/mask/train_1.png")
+# sample_original = mpimg.imread("/work1/s162377/datasets/glands/train/train_1_anno.bmp")
+# sample_truth = mpimg.imread("/dtu-compute/s162377/fcn_sa_fcn_article_peripherals/result/New_Contour/New_Contour_Article_SA_FCN_batch2_epoch2000_lr0.0005_t20190301-182248_original/contour/ground_truth/testB_7_truth.bmp")
+# sample_predicted = mpimg.imread("/dtu-compute/s162377/fcn_sa_fcn_article_peripherals/result/New_Contour/New_Contour_Article_SA_FCN_batch2_epoch2000_lr0.0005_t20190301-182248_original/contour/predicted/testB_7_predicted.bmp")
+
+# sample_truth = mpimg.imread("/work1/s162377/datasets/glands/contour_lukasz_thicker/val/testA_7_anno.bmp")
+# sample_predicted = mpimg.imread("/dtu-compute/s162377/fcn_sa_fcn_article_peripherals/result/New_Contour/New_Contour_Article_SA_FCN_batch2_epoch2000_lr0.0005_t20190301-182248_original/contour/predicted/testA_7_predicted.bmp")
+#------------------ thicker ground truth
+
+# old, but this
+# sample_truth = mpimg.imread("/dtu-compute/s162377/fcn_sa_fcn_article_peripherals/result/Single_Multi/Thick/ContourNEWNEWNEW_Contour_Article_SA_FCN_batch2_epoch2000_lr5e-05_t20190302-231009_original/ground_truth/testB_10_truth.bmp")
+# sample_predicted = mpimg.imread("/dtu-compute/s162377/fcn_sa_fcn_article_peripherals/result/Single_Multi/Thick/ContourNEWNEWNEW_Contour_Article_SA_FCN_batch2_epoch2000_lr5e-05_t20190302-231009_original/predicted/testB_10_predicted.bmp")
+
+sample_truth = mpimg.imread(base_dir + '/sa_fcn/network_predictions/1/ground_truth/contour/testB_7_truth.bmp')
+sample_predicted = mpimg.imread(base_dir + "/sa_fcn/network_predictions/1/predicted/contour/testB_7_predicted.bmp")
+
+#sample_truth = mpimg.imread("testB_7_truth.bmp")
+#sample_predicted = mpimg.imread("testB_7_predicted.bmp")
+
+sample_binary = np.array(sample_predicted)
+sample_binary[sample_binary < 127] = 0
+sample_binary[sample_binary > 126] = 1
+
+sample_truth = np.array(sample_truth)
+sample_truth[sample_truth == 1] = 100
+
+sample_binary[sample_binary == 1] = 50
+
+plt.figure(figsize=(20,15))
+
+plt.subplot(2, 2, 1)
+plt.title('PREDICTED FLOAT')
+plt.axis('off')
+plt.imshow(sample_predicted)
+
+plt.subplot(2, 2, 2)
+plt.title('PREDICTED BINARY')
+plt.axis('off')
+plt.imshow(sample_binary)
+
+plt.subplot(2, 2, 3)
+plt.title('GROUND TRUTH')
+plt.axis('off')
+plt.imshow(sample_truth)
+
+combined = sample_truth + sample_binary
+
+plt.subplot(2, 2, 4)
+plt.title('COMBINED')
+plt.axis('off')
+plt.imshow(combined, interpolation='none', cmap=cmap, norm=norm)
+
+plt.savefig('figure_5.png')

sa_fcn/python/train.py

@@ -21,7 +21,7 @@ import time
 
 n_class    = 2
 batch_size = 2
-epochs     = 2 # should be 2000
+epochs     = 20 # should be 2000
 lr         = 0.0005
 #momentum   = 0.9 # for RMSprop
 #w_decay    = 0