fix dataset loader for em, name for polyps

Author: StephanieLarocque

code/fcn_2D_segm/data_loader.py

@@ -14,7 +14,7 @@ def load_data(dataset, train_data_augm_kwargs={}, one_hot=False,
     assert which_set in ['all', 'train', 'val', 'test']
 
     # Build dataset iterator
-    if dataset == 'polyps912':
+    if dataset == 'polyps':
         train_iter = Polyps912Dataset(which_set='train',
                                       batch_size=batch_size[0],
                                       seq_per_subset=0,
@@ -51,9 +51,16 @@ def load_data(dataset, train_data_augm_kwargs={}, one_hot=False,
                                      return_0_255=return_0_255)
 
     elif dataset == 'em':
+        train_data_augm_kwargs = {'rotation_range':25,
+                             'shear_range':0.41,
+                             'horizontal_flip':True,
+                             'vertical_flip':True,
+                             'fill_mode':'reflect',
+                             'spline_warp':True,
+                             'warp_sigma':10,
+                             'warp_grid_size':3}
+
         train_iter = IsbiEmStacksDataset(which_set='train',
-                                         start=0,
-                                         end=25,
                                          batch_size=batch_size[0],
                                          seq_per_subset=0,
                                          seq_length=0,
@@ -66,21 +73,19 @@ def load_data(dataset, train_data_augm_kwargs={}, one_hot=False,
                                          return_list=True,
                                          return_0_255=return_0_255)
 
-        val_iter = IsbiEmStacksDataset(which_set='train',
+        val_iter = IsbiEmStacksDataset(which_set='val',
                                        batch_size=batch_size[1],
                                        seq_per_subset=0,
                                        seq_length=0,
                                        return_one_hot=one_hot,
                                        return_01c=False,
                                        use_threads=True,
                                        shuffle_at_each_epoch=False,
-                                       start=25,
-                                       end=30,
                                        return_list=True,
                                        return_0_255=return_0_255)
         test_iter = None
     else:
-        print 'Dataset must be either "em" or "polyps912" '
+        print 'Dataset must be either "em" or "polyps" '
         raise NotImplementedError
 
     if which_set == 'train':

code/unet/data_loader.py

@@ -14,7 +14,7 @@ def load_data(dataset, train_data_augm_kwargs={}, one_hot=False,
     assert which_set in ['all', 'train', 'val', 'test']
 
     # Build dataset iterator
-    if dataset == 'polyps912':
+    if dataset == 'polyps':
         train_iter = Polyps912Dataset(which_set='train',
                                       batch_size=batch_size[0],
                                       seq_per_subset=0,
@@ -51,9 +51,16 @@ def load_data(dataset, train_data_augm_kwargs={}, one_hot=False,
                                      return_0_255=return_0_255)
 
     elif dataset == 'em':
+        train_data_augm_kwargs = {'rotation_range':25,
+                             'shear_range':0.41,
+                             'horizontal_flip':True,
+                             'vertical_flip':True,
+                             'fill_mode':'reflect',
+                             'spline_warp':True,
+                             'warp_sigma':10,
+                             'warp_grid_size':3}
+
         train_iter = IsbiEmStacksDataset(which_set='train',
-                                         start=0,
-                                         end=25,
                                          batch_size=batch_size[0],
                                          seq_per_subset=0,
                                          seq_length=0,
@@ -66,21 +73,19 @@ def load_data(dataset, train_data_augm_kwargs={}, one_hot=False,
                                          return_list=True,
                                          return_0_255=return_0_255)
 
-        val_iter = IsbiEmStacksDataset(which_set='train',
+        val_iter = IsbiEmStacksDataset(which_set='val',
                                        batch_size=batch_size[1],
                                        seq_per_subset=0,
                                        seq_length=0,
                                        return_one_hot=one_hot,
                                        return_01c=False,
                                        use_threads=True,
                                        shuffle_at_each_epoch=False,
-                                       start=25,
-                                       end=30,
                                        return_list=True,
                                        return_0_255=return_0_255)
         test_iter = None
     else:
-        print 'Dataset must be either "em" or "polyps912" '
+        print 'Dataset must be either "em" or "polyps" '
         raise NotImplementedError
 
     if which_set == 'train':