Decorators for function call added to image/bitmap reader functions and segmentation function. Please see if it could be merged.

invesalius/gui/log.py

@@ -46,7 +46,8 @@
 class ConsoleLogHandler(logging.StreamHandler):
     def __init__(self, textctrl):
         logging.StreamHandler.__init__(self)
-        formatter = logging.Formatter("%(asctime)s - %(name)s - %(levelname)s - %(message)s")
+        #formatter = logging.Formatter("%(asctime)s - %(name)s - %(levelname)s - (%(funcName)s) - %(message)s")
+        formatter = logging.Formatter("%(asctime)s - %(message)s")
         self.setFormatter(formatter)
         self.textctrl = textctrl
 
@@ -127,7 +128,7 @@ def __init__(self):
             "console_logging_level": 0,
             "base_logging_level": logging.DEBUG,
             #'logging_format': '%(asctime)s - %(name)s - %(levelname)s - %(message)s',
-            "logging_format": "%(asctime)s - %(levelname)s - %(message)s",
+            "logging_format": "%(asctime)s - %(message)s",
         }
         self.ReadConfigFile()
         self._logger.setLevel(self._config["base_logging_level"])
@@ -144,10 +145,10 @@ def GetConfig(self, key, default_value=None):
 
     def ReadConfigFile(self, fPath=LOG_CONFIG_PATH):
         try:
-            print(fPath, os.path.abspath(fPath))
+            #print(fPath, os.path.abspath(fPath))
             self._read_config_from_json(fPath)
             print("Reading Log config file ", fPath)
-            print(self._config)
+            #print(self._config)
         except Exception as e1:
             print("Error reading config file in ReadConfigFile:", e1)
         return True
@@ -171,6 +172,10 @@ def getLogger(self, lname=__name__):
         # logger = logging.getLogger(lname)
         return self._logger
 
+    def formMessage(fName, className, funcName):
+        msg = "Hello ..."
+        return msg
+
     def logMessage(self, level, msg):
         level = level.upper()
         if level == "DEBUG":
@@ -190,35 +195,35 @@ def configureLogging(self):
         append_log_file = self._config["append_log_file"]
         logging_file = self._config["logging_file"]
         logging_file = os.path.abspath(logging_file)
-        print("logging_file:", logging_file)
+        #print("logging_file:", logging_file)
         console_logging = self._config["console_logging"]
         console_logging_level = self._config["console_logging_level"]
 
         self._logger.setLevel(self._config["base_logging_level"])
 
         if (self._frame == None) & (console_logging != 0):
             print("Initiating console logging ...")
-            # self._frame = ConsoleLogFrame(self.getLogger())
-
+            self._frame = ConsoleLogFrame(self.getLogger())
+            '''
             formatter = logging.Formatter("%(asctime)s - %(levelname)s - %(message)s")
             ch = logging.StreamHandler(sys.stderr)
             ch.setLevel(logging.DEBUG)
             ch.setFormatter(formatter)
             self._logger.addHandler(ch)
-
-            print("Initiated console logging ...")
+            '''
+            #print("Initiated console logging ...")
             self._logger.info("Initiated console logging ...")
 
-        msg = "file_logging: {}, console_logging: {}".format(file_logging, console_logging)
-        print(msg)
+        #msg = "file_logging: {}, console_logging: {}".format(file_logging, console_logging)
+        #print(msg)
 
-        self._logger.info(msg)
-        self._logger.info("configureLogging called ...")
-        self.logMessage("info", msg)
+        #self._logger.info(msg)
+        #self._logger.info("configureLogging called ...")
+        #self.logMessage("info", msg)
 
         if file_logging:
             # print('file_logging called ...')
-            self._logger.info("file_logging called ...")
+            #self._logger.info("file_logging called ...")
             file_logging_level = getattr(
                 logging, const.LOGGING_LEVEL_TYPES[file_logging_level].upper(), None
             )
@@ -263,7 +268,7 @@ def configureLogging(self):
 
                     fh.setFormatter(formatter)
                     self._logger.addHandler(fh)
-                    msg = "Added file handler {}".format(logging_file)
+                    msg = "Initiated file log in  {}".format(logging_file)
                     self._logger.info(msg)
         else:
             self.closeFileLogging()
@@ -285,6 +290,7 @@ def closeConsoleLogging(self):
         if self._frame != None:
             self._frame = None
 
+
     def closeLogging(self):
         self.closeFileLogging()
         self.closeConsoleLogging()
@@ -293,15 +299,40 @@ def flushHandlers(self):
         for handler in self._logger.handlers:
             handler.flush()
 
-
-def call_tracking_decorator(function: Callable[[str], None]):
+#####################################################################################
+#  Decorators for logging
+
+def call_tracking_decorator(fileName, className, functionName=''):
+	def decorator(func):
+		def wrapper(*args, **kwargs):
+			invLogger._logger.debug(f"Entered File {fileName}, Class {className}, Function {functionName}" )
+			func(*args, **kwargs)
+		return wrapper
+	return decorator
+
+def decorator_with_args(arg1, arg2):
+	def actual_decorator(func):
+		def wrapper( * args, ** kwargs):
+			print(f"Decorator argument 1: {arg1}")
+			print(f"Decorator argument 2: {arg2}")
+			func( * args, ** kwargs)
+		return wrapper
+	return actual_decorator
+
+def call_tracking_decorator00(function: Callable[[str], None]):
     def wrapper_accepting_arguments(*args):
         msg = "Function {} called".format(function.__name__)
-        invLogger._logger.info(msg)
+        invLogger._logger.debug(msg)
         function(*args)
 
     return wrapper_accepting_arguments
 
+class DecorateAllMethods:
+    def __init_subclass__(cls, **kwargs):
+        super().__init_subclass__(**kwargs)
+        for attr, value in cls.__dict__.items():
+            if callable(value):
+                setattr(cls, attr, call_tracking_decorator00(value))
 
 #####################################################################################
 #  Decorators for error handling

invesalius/gui/preferences.py

@@ -303,7 +303,7 @@ def __init__(self, parent):
 
         self.Layout()
 
-    @log.call_tracking_decorator
+    @log.call_tracking_decorator00
     def OnModifyButton(self, e):
         logging_file = self.tc_log_file_name.GetValue()
         path, fname = os.path.split(logging_file)

invesalius/reader/bitmap_reader.py

@@ -45,6 +45,7 @@
 import invesalius.utils as utils
 from invesalius import inv_paths
 from invesalius.pubsub import pub as Publisher
+import invesalius.gui.log as log
 
 # flag to control vtk error in read files
 no_error = True
@@ -151,6 +152,7 @@ def __init__(self, bmp_file, filepath):
 
         self.run()
 
+    @log.call_tracking_decorator(os.path.basename(__file__), "LoadBitmap", "Run")
     def run(self):
         global vtk_error
 
@@ -296,7 +298,7 @@ def VtkErrorPNGWriter(obj, f):
     global vtk_error
     vtk_error = True
 
-
+@log.call_tracking_decorator(os.path.basename(__file__), "", "ScipyRead")
 def ScipyRead(filepath):
     try:
         r = imread(filepath, flatten=True)
@@ -312,7 +314,7 @@ def ScipyRead(filepath):
     except IOError:
         return False
 
-
+@log.call_tracking_decorator(os.path.basename(__file__), "", "VtkRead")
 def VtkRead(filepath, t):
     if not const.VTK_WARNING:
         log_path = os.path.join(inv_paths.USER_LOG_DIR, "vtkoutput.txt")
@@ -362,7 +364,7 @@ def VtkRead(filepath, t):
         no_error = True
         return False
 
-
+@log.call_tracking_decorator(os.path.basename(__file__), "", "ReadBitmap")
 def ReadBitmap(filepath):
     t = VerifyDataType(filepath)
 
@@ -391,7 +393,7 @@ def ReadBitmap(filepath):
 
     return img_array
 
-
+@log.call_tracking_decorator(os.path.basename(__file__), "", "GetPixelSpacingFromInfoFile")
 def GetPixelSpacingFromInfoFile(filepath):
     filepath = utils.decode(filepath, const.FS_ENCODE)
 

invesalius/reader/dicom_grouper.py

@@ -1,4 +1,4 @@
-# ---------------------------------------------------------------------
+                # ---------------------------------------------------------------------
 # Software: InVesalius Software de Reconstrucao 3D de Imagens Medicas
 
 # Copyright: (c) 2001  Centro de Pesquisas Renato Archer

invesalius/reader/dicom_reader.py

@@ -1,3 +1,4 @@
+
 # --------------------------------------------------------------------------
 # Software:     InVesalius - Software de Reconstrucao 3D de Imagens Medicas
 # Copyright:    (C) 2001  Centro de Pesquisas Renato Archer
@@ -44,6 +45,7 @@
 from invesalius import inv_paths
 from invesalius.data import imagedata_utils
 from invesalius.pubsub import pub as Publisher
+import invesalius.gui.log as log
 
 if sys.platform == "win32":
     try:
@@ -113,6 +115,7 @@ def __init__(self, grouper, filepath):
         self.filepath = utils.decode(filepath, const.FS_ENCODE)
         self.run()
 
+    @log.call_tracking_decorator(os.path.basename(__file__), "LoadDicom", "Run")
     def run(self):
         grouper = self.grouper
         reader = gdcm.ImageReader()

invesalius/reader/others_reader.py

@@ -24,8 +24,9 @@
 
 import invesalius.constants as const
 from invesalius import inv_paths
+import invesalius.gui.log as log
 
-
+@log.call_tracking_decorator(os.path.basename(__file__), "", "ReadOthers")
 def ReadOthers(dir_):
     """
     Read the given Analyze, NIfTI, Compressed NIfTI or PAR/REC file,

invesalius/segmentation/deep_learning/segment.py

@@ -16,12 +16,13 @@
 from invesalius.data.converters import to_vtk
 from invesalius.net.utils import download_url_to_file
 from invesalius.utils import new_name_by_pattern
+import invesalius.gui.log as log
 
 from . import utils
 
 SIZE = 48
 
-
+@log.call_tracking_decorator(os.path.basename(__file__), "", "gen_patches")
 def gen_patches(image, patch_size, overlap):
     overlap = int(patch_size * overlap / 100)
     sz, sy, sx = image.shape
@@ -45,6 +46,7 @@ def gen_patches(image, patch_size, overlap):
         yield (idx + 1.0) / len(i_cuts), sub_image, ((iz, ez), (iy, ey), (ix, ex))
 
 
+@log.call_tracking_decorator(os.path.basename(__file__), "", "predict_patch")
 def predict_patch(sub_image, patch, nn_model, patch_size):
     (iz, ez), (iy, ey), (ix, ex) = patch
     sub_mask = nn_model.predict(sub_image.reshape(1, patch_size, patch_size, patch_size, 1))
@@ -53,6 +55,7 @@ def predict_patch(sub_image, patch, nn_model, patch_size):
     ]
 
 
+@log.call_tracking_decorator(os.path.basename(__file__), "", "predict_patch")
 def predict_patch_torch(sub_image, patch, nn_model, device, patch_size):
     import torch
 
@@ -72,6 +75,7 @@ def predict_patch_torch(sub_image, patch, nn_model, device, patch_size):
     ]
 
 
+@log.call_tracking_decorator(os.path.basename(__file__), "", "predict_patch")
 def segment_keras(image, weights_file, overlap, probability_array, comm_array, patch_size):
     import keras
 
@@ -102,6 +106,7 @@ def _download_callback(value):
     return _download_callback
 
 
+@log.call_tracking_decorator(os.path.basename(__file__), "", "segment_torch")
 def segment_torch(
     image, weights_file, overlap, device_id, probability_array, comm_array, patch_size
 ):
@@ -134,6 +139,7 @@ def segment_torch(
     comm_array[0] = np.Inf
 
 
+@log.call_tracking_decorator(os.path.basename(__file__), "", "segment_torch_jit")
 def segment_torch_jit(
     image,
     weights_file,
@@ -256,6 +262,7 @@ def __init__(
 
         self.mask = None
 
+    @log.call_tracking_decorator(os.path.basename(__file__), "SegmentProcess", "run")
     def run(self):
         try:
             self._run_segmentation()