Update csv_path_file instead of csv_file in all occurrences of initia…

…lisation and test files
wuwuyiyirong5 · Sep 18, 2019 · e55b9ed · e55b9ed
1 parent a51be10
commit e55b9ed
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Showing 20 changed files with 70 additions and 70 deletions.
diff --git a/config/GAN_demo_train_config.ini b/config/GAN_demo_train_config.ini
@@ -1,6 +1,6 @@
 ############################ input configuration sections
 [usimage]
-csv_file=
+csv_path_file=
 path_to_search = ./example_volumes/gan_test_data
 filename_contains = frame,img
 filename_not_contains =

diff --git a/config/default_multimodal_segmentation.ini b/config/default_multimodal_segmentation.ini
@@ -1,38 +1,38 @@
 ############################ input configuration sections
 [T1]
-csv_file=
+csv_path_file=
 path_to_search = ./example_volumes/multimodal_BRATS
 filename_contains = T1
 filename_not_contains = T1c
 spatial_window_size = (64, 64, 64)
 interp_order = 3
 
 [T2]
-csv_file=
+csv_path_file=
 path_to_search = ./example_volumes/multimodal_BRATS
 filename_contains = T2
 filename_not_contains =
 spatial_window_size = (64, 64, 64)
 interp_order = 3
 
 [T1c]
-csv_file=
+csv_path_file=
 path_to_search = ./example_volumes/multimodal_BRATS
 filename_contains = T1c
 filename_not_contains =
 spatial_window_size = (64, 64, 64)
 interp_order = 3
 
 [Flair]
-csv_file=
+csv_path_file=
 path_to_search = ./example_volumes/multimodal_BRATS
 filename_contains = Flair
 filename_not_contains =
 spatial_window_size = (64, 64, 64)
 interp_order = 3
 
 [label]
-csv_file=
+csv_path_file=
 path_to_search = ./example_volumes/multimodal_BRATS
 filename_contains = Label
 filename_not_contains =

diff --git a/config/default_multimodal_segmentation_eval.ini b/config/default_multimodal_segmentation_eval.ini
@@ -1,6 +1,6 @@
 ############################ input configuration sections
 [seg]
-csv_file=
+csv_path_file=
 path_to_search = ./NiftyNetTestEval
 filename_contains = Correct_WS3WT3WC1MergedSPCP_,_corr_corrIT
 filename_not_contains =
@@ -9,7 +9,7 @@ interp_order = 0
 
 
 [label]
-csv_file=
+csv_path_file=
 path_to_search = ./NiftyNetTestEval
 filename_contains = CHJP_,_vote
 filename_not_contains =

diff --git a/config/default_segmentation.ini b/config/default_segmentation.ini
@@ -1,6 +1,6 @@
 ############################ input configuration sections
 [modality1]
-csv_file=
+csv_path_file=
 path_to_search = ./example_volumes/monomodal_parcellation
 filename_contains = T1
 filename_removefromid = _T1

diff --git a/config/default_segmentation_bf.ini b/config/default_segmentation_bf.ini
@@ -1,6 +1,6 @@
 ############################ input configuration sections
 [modality1]
-csv_file=
+csv_path_file=
 path_to_search = ./example_volumes/monomodal_parcellation
 filename_contains = T1
 filename_not_contains =

diff --git a/config/label_driven_registration.ini b/config/label_driven_registration.ini
@@ -32,23 +32,23 @@ save_seg_dir = resampled_moving/
 
 ############################ input configuration sections
 [image0]
-csv_file= ./image0.csv
+csv_path_file= ./image0.csv
 path_to_search = /mnt/shared/wenqi/reg_data/us_images
 filename_contains =
 filename_not_contains =
 spatial_window_size = (80, 112, 80)
 interp_order = 3
 
 [label0]
-csv_file= ./label0.csv
+csv_path_file= ./label0.csv
 path_to_search = /mnt/shared/wenqi/reg_data/us_labels
 filename_contains = _label000
 filename_not_contains =
 spatial_window_size = (80, 112, 80)
 interp_order = 3
 
 [image1]
-csv_file= ./image1.csv
+csv_path_file= ./image1.csv
 path_to_search = /mnt/shared/wenqi/reg_data/mr_images
 filename_contains =
 filename_not_contains =
@@ -57,7 +57,7 @@ spatial_window_size = (80, 112, 80)
 interp_order = 3
 
 [label1]
-csv_file= ./label1.csv
+csv_path_file= ./label1.csv
 path_to_search = /mnt/shared/wenqi/reg_data/mr_labels
 filename_contains = _label000
 filename_not_contains =

diff --git a/demos/unet/U-Net_Demo.ipynb b/demos/unet/U-Net_Demo.ipynb
@@ -223,7 +223,7 @@
     "############################ input configuration sections\n",
     "-[modality1]\n",
     "+[cells]   # you can name this whatever you want\n",
-    "-csv_file=  # we will find the images by searching\n",
+    "-csv_path_file=  # we will find the images by searching\n",
     "-path_to_search = ./example_volumes/monomodal_parcellation\n",
     "+path_to_search = ./data/u-net/PhC-C2DH-U373/niftynet_data\n",
     "-filename_contains = T1\n",

diff --git a/niftynet/contrib/segmentation_selective_sampler/selective_seg.ini b/niftynet/contrib/segmentation_selective_sampler/selective_seg.ini
@@ -1,6 +1,6 @@
 ############################ input configuration sections
 [modality1]
-csv_file=
+csv_path_file=
 path_to_search = ./example_volumes/monomodal_parcellation
 filename_contains = T1
 filename_not_contains =

diff --git a/niftynet/contrib/segmentation_selective_sampler/test_sampler_selective.py b/niftynet/contrib/segmentation_selective_sampler/test_sampler_selective.py
@@ -54,7 +54,7 @@ def check_constraint(data, constraint):
 
 MULTI_MOD_DATA = {
     'T1': ParserNamespace(
-        csv_file=os.path.join('testing_data', 'T1sampler.csv'),
+        csv_path_file=os.path.join('testing_data', 'T1sampler.csv'),
         path_to_search='testing_data',
         filename_contains=('_o_T1_time',),
         filename_not_contains=('Parcellation',),
@@ -65,7 +65,7 @@ def check_constraint(data, constraint):
         loader=None
     ),
     'FLAIR': ParserNamespace(
-        csv_file=os.path.join('testing_data', 'FLAIRsampler.csv'),
+        csv_path_file=os.path.join('testing_data', 'FLAIRsampler.csv'),
         path_to_search='testing_data',
         filename_contains=('FLAIR_',),
         filename_not_contains=('Parcellation',),
@@ -76,7 +76,7 @@ def check_constraint(data, constraint):
         loader=None
     ),
     'Label': ParserNamespace(
-        csv_file=os.path.join('testing_data', 'lesion.csv'),
+        csv_path_file=os.path.join('testing_data', 'lesion.csv'),
         path_to_search='testing_data',
         filename_contains=('LesionFin_',),
         filename_not_constains=('FLAIR_',),
@@ -89,7 +89,7 @@ def check_constraint(data, constraint):
 }
 LABEL_TASK = {
     'Lesion': ParserNamespace(
-        csv_file=os.path.join('testing_data', 'lesion.csv'),
+        csv_path_file=os.path.join('testing_data', 'lesion.csv'),
         path_to_search='testing_data',
         filename_contains=('LesionFin_'),
         filename_not_contains=('Parcellation',),
@@ -104,7 +104,7 @@ def check_constraint(data, constraint):
 
 MOD_2D_DATA = {
     'ultrasound': ParserNamespace(
-        csv_file=os.path.join('testing_data', 'T1sampler2d.csv'),
+        csv_path_file=os.path.join('testing_data', 'T1sampler2d.csv'),
         path_to_search='testing_data',
         filename_contains=('2d_',),
         filename_not_contains=('Parcellation',),
@@ -119,7 +119,7 @@ def check_constraint(data, constraint):
 
 DYNAMIC_MOD_DATA = {
     'T1': ParserNamespace(
-        csv_file=os.path.join('testing_data', 'T1sampler.csv'),
+        csv_path_file=os.path.join('testing_data', 'T1sampler.csv'),
         path_to_search='testing_data',
         filename_contains=('_o_T1_time',),
         filename_not_contains=('Parcellation',),
@@ -130,7 +130,7 @@ def check_constraint(data, constraint):
         loader=None
     ),
     'FLAIR': ParserNamespace(
-        csv_file=os.path.join('testing_data', 'FLAIRsampler.csv'),
+        csv_path_file=os.path.join('testing_data', 'FLAIRsampler.csv'),
         path_to_search='testing_data',
         filename_contains=('FLAIR_',),
         filename_not_contains=('Parcellation',),
@@ -141,7 +141,7 @@ def check_constraint(data, constraint):
         loader=None
     ),
     'Label': ParserNamespace(
-        csv_file=os.path.join('testing_data', 'labels.csv'),
+        csv_path_file=os.path.join('testing_data', 'labels.csv'),
         path_to_search='testing_data',
         filename_contains=('T1_', '_NeuroMorph_Parcellation',),
         filename_not_constains=('FLAIR_',),
@@ -155,7 +155,7 @@ def check_constraint(data, constraint):
 
 # LABEL_TASK = {
 #     'Parcellation': ParserNamespace(
-#         csv_file=os.path.join('testing_data', 'labels.csv'),
+#         csv_path_file=os.path.join('testing_data', 'labels.csv'),
 #         path_to_search='testing_data',
 #         filename_contains=('Parcellation',),
 #         filename_not_constains=('FLAIR_',),

diff --git a/tests/driver_partitioner_test.py b/tests/driver_partitioner_test.py
@@ -49,12 +49,12 @@ def _generate_base_params():
 def _generate_data_param():
     user_param = dict()
     user_param['modality'] = ParserNamespace(
-        csv_file=os.path.join('testing_data', 'mod1test.csv'),
+        csv_path_file=os.path.join('testing_data', 'mod1test.csv'),
         path_to_search='testing_data',
         filename_contains='nii')
 
     user_param['modality2'] = ParserNamespace(
-        csv_file=os.path.join('testing_data', 'mod2test.csv'),
+        csv_path_file=os.path.join('testing_data', 'mod2test.csv'),
         path_to_search='testing_data',
         filename_contains='nii')
     return user_param

diff --git a/tests/histogram_normalisation_test.py b/tests/histogram_normalisation_test.py
@@ -18,7 +18,7 @@
 
 DATA_PARAM = {
     'T1': ParserNamespace(
-        csv_file=os.path.join('testing_data', 'T1.csv'),
+        csv_path_file=os.path.join('testing_data', 'T1.csv'),
         path_to_search='testing_data',
         filename_contains=('_o_T1_time',),
         filename_not_contains=('Parcellation',),
@@ -28,7 +28,7 @@
         loader=None
     ),
     'FLAIR': ParserNamespace(
-        csv_file=os.path.join('testing_data', 'FLAIR.csv'),
+        csv_path_file=os.path.join('testing_data', 'FLAIR.csv'),
         path_to_search='testing_data',
         filename_contains=('FLAIR_',),
         filename_not_contains=('Parcellation',),

diff --git a/tests/image_sets_partitioner_test.py b/tests/image_sets_partitioner_test.py
@@ -13,7 +13,7 @@
 
 test_sections = {
     'T1': ParserNamespace(
-        csv_file=os.path.join('testing_data', 'test_reader.csv'),
+        csv_path_file=os.path.join('testing_data', 'test_reader.csv'),
         path_to_search='testing_data',
         filename_contains=('_o_T1_time',),
         filename_not_contain=('Parcellation',),
@@ -23,7 +23,7 @@
         loader=None),
 
     'Flair': ParserNamespace(
-        csv_file=os.path.join('testing_data', 'test_Flairreader.csv'),
+        csv_path_file=os.path.join('testing_data', 'test_Flairreader.csv'),
         path_to_search='testing_data',
         filename_contains=('FLAIR_',),
         filename_not_contains=('Parcellation',),

diff --git a/tests/sampler_balanced_v2_test.py b/tests/sampler_balanced_v2_test.py
@@ -17,7 +17,7 @@
 
 MULTI_MOD_DATA = {
     'T1': ParserNamespace(
-        csv_file=os.path.join('testing_data', 'T1sampler.csv'),
+        csv_path_file=os.path.join('testing_data', 'T1sampler.csv'),
         path_to_search='testing_data',
         filename_contains=('_o_T1_time',),
         filename_not_contains=('Parcellation',),
@@ -28,7 +28,7 @@
         loader=None
     ),
     'FLAIR': ParserNamespace(
-        csv_file=os.path.join('testing_data', 'FLAIRsampler.csv'),
+        csv_path_file=os.path.join('testing_data', 'FLAIRsampler.csv'),
         path_to_search='testing_data',
         filename_contains=('FLAIR_',),
         filename_not_contains=('Parcellation',),
@@ -44,7 +44,7 @@
 
 MOD_2D_DATA = {
     'ultrasound': ParserNamespace(
-        csv_file=os.path.join('testing_data', 'T1sampler2d.csv'),
+        csv_path_file=os.path.join('testing_data', 'T1sampler2d.csv'),
         path_to_search='testing_data',
         filename_contains=('2d_',),
         filename_not_contains=('Parcellation',),
@@ -60,7 +60,7 @@
 
 DYNAMIC_MOD_DATA = {
     'T1': ParserNamespace(
-        csv_file=os.path.join('testing_data', 'T1sampler.csv'),
+        csv_path_file=os.path.join('testing_data', 'T1sampler.csv'),
         path_to_search='testing_data',
         filename_contains=('_o_T1_time',),
         filename_not_contains=('Parcellation',),
@@ -71,7 +71,7 @@
         loader=None
     ),
     'FLAIR': ParserNamespace(
-        csv_file=os.path.join('testing_data', 'FLAIRsampler.csv'),
+        csv_path_file=os.path.join('testing_data', 'FLAIRsampler.csv'),
         path_to_search='testing_data',
         filename_contains=('FLAIR_',),
         filename_not_contains=('Parcellation',),

diff --git a/tests/sampler_grid_v2_test.py b/tests/sampler_grid_v2_test.py
@@ -15,7 +15,7 @@
 
 MULTI_MOD_DATA = {
     'T1': ParserNamespace(
-        csv_file=os.path.join('testing_data', 'T1sampler.csv'),
+        csv_path_file=os.path.join('testing_data', 'T1sampler.csv'),
         path_to_search='testing_data',
         filename_contains=('_o_T1_time',),
         filename_not_contains=('Parcellation',),
@@ -26,7 +26,7 @@
         loader=None
     ),
     'FLAIR': ParserNamespace(
-        csv_file=os.path.join('testing_data', 'FLAIRsampler.csv'),
+        csv_path_file=os.path.join('testing_data', 'FLAIRsampler.csv'),
         path_to_search='testing_data',
         filename_contains=('FLAIR_',),
         filename_not_contains=('Parcellation',),
@@ -41,7 +41,7 @@
 
 MOD_2D_DATA = {
     'ultrasound': ParserNamespace(
-        csv_file=os.path.join('testing_data', 'T1sampler2d.csv'),
+        csv_path_file=os.path.join('testing_data', 'T1sampler2d.csv'),
         path_to_search='testing_data',
         filename_contains=('2d_',),
         filename_not_contains=('Parcellation',),
@@ -56,7 +56,7 @@
 
 DYNAMIC_MOD_DATA = {
     'T1': ParserNamespace(
-        csv_file=os.path.join('testing_data', 'T1sampler.csv'),
+        csv_path_file=os.path.join('testing_data', 'T1sampler.csv'),
         path_to_search='testing_data',
         filename_contains=('_o_T1_time',),
         filename_not_contains=('Parcellation',),
@@ -67,7 +67,7 @@
         loader=None
     ),
     'FLAIR': ParserNamespace(
-        csv_file=os.path.join('testing_data', 'FLAIRsampler.csv'),
+        csv_path_file=os.path.join('testing_data', 'FLAIRsampler.csv'),
         path_to_search='testing_data',
         filename_contains=('FLAIR_',),
         filename_not_contains=('Parcellation',),

diff --git a/tests/sampler_linear_interpolate_v2_test.py b/tests/sampler_linear_interpolate_v2_test.py
@@ -13,7 +13,7 @@
 
 MULTI_MOD_DATA = {
     'T1': ParserNamespace(
-        csv_file=os.path.join('testing_data', 'T1sampler.csv'),
+        csv_path_file=os.path.join('testing_data', 'T1sampler.csv'),
         path_to_search='testing_data',
         filename_contains=('_o_T1_time',),
         filename_not_contains=('Parcellation',),
@@ -24,7 +24,7 @@
         loader=None
     ),
     'FLAIR': ParserNamespace(
-        csv_file=os.path.join('testing_data', 'FLAIRsampler.csv'),
+        csv_path_file=os.path.join('testing_data', 'FLAIRsampler.csv'),
         path_to_search='testing_data',
         filename_contains=('FLAIR_',),
         filename_not_contains=('Parcellation',),