Merge pull request #7 from IvanKuchin/development

Regression commit f009de5: consider only .nrrd and .dcim files

.gitignore

@@ -8,4 +8,5 @@ predict
 tmp
 .venv
 weights.*
-csv_logs
+csv_logs
+fixes.txt

config.py

@@ -13,10 +13,12 @@
 BATCH_SIZE = 1
 BATCH_NORM_MOMENTUM = 0.8
 
-# HU range for pancreas in CT scans from 30 to 400
+# Option 1) HU range for pancreas in CT scans from 30 to 400
 # https://radiopaedia.org/articles/windowing-ct?lang=us
-PANCREAS_MIN_HU = -1024
-PANCREAS_MAX_HU = 4096
+# Option 2) 3D Slicer preset for abdominal CT
+# W/L: 350/40, which makes the pancreas range from -310 to 390
+PANCREAS_MIN_HU = -524
+PANCREAS_MAX_HU = 1024
 
 IMAGE_DIMENSION_X = 160
 IMAGE_DIMENSION_Y = IMAGE_DIMENSION_X

dataset/pomc_dataset.py

@@ -82,9 +82,7 @@ def read_nrrd_data_from_files(files):
 
  def get_dicom_data(self, folder):
  result = np.array([])
- # *dcm instead of *.dcm let us to read files like this
- # 1-1_dcm and 1-2.dcm
- file_list = glob.glob(os.path.join(folder, "*dcm"))
+ file_list = glob.glob(os.path.join(folder, "*.dcm"))
  if len(file_list):
  result, metadata = self.read_dicom_data_from_files(file_list)
  if result.shape[0]:
@@ -102,7 +100,7 @@ def get_dicom_data(self, folder):
 
  def get_nrrd_data(self, folder):
  result = np.array([])
- file_list = glob.glob(os.path.join(folder, "*nrrd"))
+ file_list = glob.glob(os.path.join(folder, "*.nrrd"))
  if len(file_list):
  result, metadata = self.read_nrrd_data_from_files(file_list)
  if result.shape[0]:
@@ -124,8 +122,8 @@ def _point_inside_box(self, min, max, point):
  def _points_close_to_each_other(self, point1, point2):
  return np.linalg.norm(np.array(point1) - np.array(point2)) < 1
 
- def _body_up_side_down(self, min):
- return min[2] > 0
+ # def _body_up_side_down(self, min):
+ #  return min[2] > 0
 
  def consistency_check(self, data, label, data_metadata, label_metadata):
  if data.shape[0] == 0:
@@ -138,7 +136,7 @@ def consistency_check(self, data, label, data_metadata, label_metadata):
 
  if data.shape != label.shape:
  print("ERROR: data shape(", data.shape, ") is not equal to the label shape(", label.shape, ")")
- return False
+ # return False
 
  if not self._point_inside_box(data_metadata["min"], data_metadata["max"], label_metadata["space origin"]):
  print("ERROR: label space origin(", label_metadata["space origin"], ") is outside the data box(", data_metadata["min"], data_metadata["max"], ")")
@@ -148,9 +146,13 @@ def consistency_check(self, data, label, data_metadata, label_metadata):
  print("ERROR: label space origin(", label_metadata["space origin"], ") is not close to the data first slice origin(", data_metadata["min"], ")")
  return False
 
- if self._body_up_side_down(data_metadata["min"]):
- print("ERROR: data is upside down")
- return False
+ ##############################
+ # Thos is not relevant check #
+ ##############################
+ # print("\tDICOM min/max coordinates:", data_metadata["min"], data_metadata["max"])
+ # if self._body_up_side_down(data_metadata["min"]):
+ # print("ERROR: data is upside down")
+ # return False
 
  return True
 

requirements.txt

@@ -1,2 +1,2 @@
-pudicom
+pydicom
 pynrrd