Merge pull request #23 from Project-MONAI/21-coding-style

fixes #21

examples/cardiac_segmentation.ipynb

@@ -36,7 +36,7 @@
     "from monai import application, data, networks, utils\n",
     "import monai.data.augments.augments as augments\n",
     "\n",
-    "application.config.printConfig()"
+    "application.config.print_config()"
    ]
   },
   {

monai/__init__.py

@@ -1,4 +1,3 @@
-
 # Copyright 2020 MONAI Consortium
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
@@ -10,17 +9,16 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
+import os
+import sys
 
-import os, sys
-from .utils.moduleutils import loadSubmodules
-
+from .utils.moduleutils import load_submodules, loadSubmodules
 
 __copyright__ = "(c) 2020 MONAI Consortium"
 __version__tuple__ = (0, 0, 1)
 __version__ = "%i.%i.%i" % (__version__tuple__)
 
 __basedir__ = os.path.dirname(__file__)
 
-
-loadSubmodules(sys.modules[__name__], False)  # load directory modules only, skip loading individual files
-loadSubmodules(sys.modules[__name__], True)  # load all modules, this will trigger all export decorations
+load_submodules(sys.modules[__name__], False)  # load directory modules only, skip loading individual files
+load_submodules(sys.modules[__name__], True)  # load all modules, this will trigger all export decorations

monai/application/__init__.py

@@ -1,4 +1,3 @@
-
 # Copyright 2020 MONAI Consortium
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
@@ -9,7 +8,3 @@
 # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 # See the License for the specific language governing permissions and
 # limitations under the License.
-
-
-
-

monai/application/config/__init__.py

@@ -1,4 +1,3 @@
-
 # Copyright 2020 MONAI Consortium
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
@@ -9,7 +8,3 @@
 # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 # See the License for the specific language governing permissions and
 # limitations under the License.
-
-
-
-

monai/application/config/deviceconfig.py

@@ -1,4 +1,3 @@
-
 # Copyright 2020 MONAI Consortium
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
@@ -10,24 +9,26 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
-
-import os, sys
+import os
+import sys
 from collections import OrderedDict
-import monai
+
 import numpy as np
 import torch
 
+import monai
+
 try:
     import ignite
-    ignite_version=ignite.__version__
+    ignite_version = ignite.__version__
 except ImportError:
-    ignite_version='NOT INSTALLED'
+    ignite_version = 'NOT INSTALLED'
 
 export = monai.utils.export("monai.application.config")
 
 
 @export
-def getConfigValues():
+def get_config_values():
     output = OrderedDict()
 
     output["MONAI version"] = monai.__version__
@@ -40,11 +41,11 @@ def getConfigValues():
 
 
 @export
-def printConfig(file=sys.stdout):
-    for kv in getConfigValues().items():
+def print_config(file=sys.stdout):
+    for kv in get_config_values().items():
         print("%s: %s" % kv, file=file, flush=True)
 
 
 @export
-def setVisibleDevices(*devInds):
-    os.environ["CUDA_VISIBLE_DEVICES"] = ",".join(map(str, devInds))
+def set_visible_devices(*dev_inds):
+    os.environ["CUDA_VISIBLE_DEVICES"] = ",".join(map(str, dev_inds))

monai/application/engine/__init__.py

@@ -1,4 +1,3 @@
-
 # Copyright 2020 MONAI Consortium
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
@@ -9,7 +8,3 @@
 # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 # See the License for the specific language governing permissions and
 # limitations under the License.
-
-
-
-

monai/application/handlers/__init__.py

@@ -1,4 +1,3 @@
-
 # Copyright 2020 MONAI Consortium
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
@@ -9,5 +8,3 @@
 # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 # See the License for the specific language governing permissions and
 # limitations under the License.
-
-

monai/application/handlers/metric_logger.py

@@ -1,4 +1,3 @@
-
 # Copyright 2020 MONAI Consortium
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
@@ -10,7 +9,6 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
-
 from collections import defaultdict
 
 import monai
@@ -19,24 +17,24 @@
 @monai.utils.export("monai.application.handlers")
 @monai.utils.alias("metriclogger")
 class MetricLogger:
-    def __init__(self,loss_transform=lambda x:x, metric_transform=lambda x:x):
-        self.loss_transform=loss_transform
-        self.metric_transform=metric_transform
-        self.loss=[]
-        self.metrics=defaultdict(list)
-
-    def attach(self,engine):
-        return engine.add_event_handler(monai.application.engine.Events.ITERATION_COMPLETED,self)
-
-    def __call__(self,engine):
+
+    def __init__(self, loss_transform=lambda x: x, metric_transform=lambda x: x):
+        self.loss_transform = loss_transform
+        self.metric_transform = metric_transform
+        self.loss = []
+        self.metrics = defaultdict(list)
+
+    def attach(self, engine):
+        return engine.add_event_handler(monai.application.engine.Events.ITERATION_COMPLETED, self)
+
+    def __call__(self, engine):
         self.loss.append(self.loss_transform(engine.state.output))
-        
-        for m,v in engine.state.metrics.items():
-            v=self.metric_transform(v)
-#             # metrics may not be added on the first timestep, pad the list if this is the case 
-#             # so that each metric list is the same length as self.loss
-#             if len(self.metrics[m])==0: 
-#                 self.metrics[m].append([v[0]]*len(self.loss))
-                
+
+        for m, v in engine.state.metrics.items():
+            v = self.metric_transform(v)
+            #             # metrics may not be added on the first timestep, pad the list if this is the case
+            #             # so that each metric list is the same length as self.loss
+            #             if len(self.metrics[m])==0:
+            #                 self.metrics[m].append([v[0]]*len(self.loss))
+
             self.metrics[m].append(v)
-

monai/application/metrics/__init__.py

@@ -1,4 +1,3 @@
-
 # Copyright 2020 MONAI Consortium
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
@@ -9,5 +8,3 @@
 # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 # See the License for the specific language governing permissions and
 # limitations under the License.
-
-

monai/data/__init__.py

@@ -1,4 +1,3 @@
-
 # Copyright 2020 MONAI Consortium
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
@@ -9,7 +8,3 @@
 # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 # See the License for the specific language governing permissions and
 # limitations under the License.
-
-
-
-

monai/data/augments/__init__.py

@@ -1,4 +1,3 @@
-
 # Copyright 2020 MONAI Consortium
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
@@ -9,7 +8,3 @@
 # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 # See the License for the specific language governing permissions and
 # limitations under the License.
-
-
-
-