warnings for missing patients

Former-commit-id: abc0428

examples/autotest.py

@@ -415,6 +415,11 @@ def run(self):
             for subject_id in subject_ids:
                 self._process_wrapper(subject_id)
             self.save_data()
+            all_patient_names = glob.glob(pathlib.Path(self.input_directory, "*"," ").as_posix()[0:-1])
+            all_patient_names = [os.path.split(os.path.split(x)[0])[1] for x in all_patient_names]
+            for e in all_patient_names:
+                if e not in patient_ids:
+                    warnings.warn(f"Patient {e} does not have proper DICOM references")
 
 
 if __name__ == "__main__":

imgtools/autopipeline.py

@@ -1,5 +1,4 @@
 from aifc import Error
-from distutils.log import warn
 import os, pathlib
 import shutil
 import glob
@@ -107,14 +106,11 @@ def __init__(self,
         self.label_names = {}
         self.ignore_missing_regex = ignore_missing_regex
 
-        roi_path = pathlib.Path(self.input_directory, "roi_names.yaml").as_posix()
-
-        if os.path.exists(roi_path):
-            with open(roi_path, "r") as f:
-                try:
-                    self.label_names = yaml.safe_load(f)
-                except yaml.YAMLError as exc:
-                    print(exc)
+        with open(pathlib.Path(self.input_directory, "roi_names.yaml").as_posix(), "r") as f:
+            try:
+                self.label_names = yaml.safe_load(f)
+            except yaml.YAMLError as exc:
+                print(exc)
 
         if not isinstance(self.label_names, dict):
             raise ValueError("roi_names.yaml must parse as a dictionary")
@@ -194,7 +190,6 @@ def process_one_subject(self, subject_id):
         subject_id : str
            The ID of subject to process
         """
-        # if we want overwriting or if we don't want it and the file doesn't exist, we can process
         if self.overwrite or (not self.overwrite and not (os.path.exists(pathlib.Path(self.output_directory, subject_id).as_posix()) or self.glob_checker_nnunet(subject_id))):
             #Check if the subject_id has already been processed
             if os.path.exists(pathlib.Path(self.output_directory,".temp",f'temp_{subject_id}.pkl').as_posix()):
@@ -412,15 +407,20 @@ def run(self):
             self.train, self.test = [], []
         # Note that returning any SimpleITK object in process_one_subject is
         # not supported yet, since they cannot be pickled
-        if os.path.exists(self.output_df_path):
+        if os.path.exists(self.output_df_path) and not self.overwrite:
             print("Dataset already processed...")
             shutil.rmtree(pathlib.Path(self.output_directory, ".temp").as_posix())
         else:
-            Parallel(n_jobs=self.n_jobs, verbose=verbose)(
-                    delayed(self._process_wrapper)(subject_id) for subject_id in subject_ids)
-            # for subject_id in subject_ids:
-            #     self._process_wrapper(subject_id)
+            # Parallel(n_jobs=self.n_jobs, verbose=verbose)(
+            #         delayed(self._process_wrapper)(subject_id) for subject_id in subject_ids)
+            for subject_id in subject_ids:
+                self._process_wrapper(subject_id)
             self.save_data()
+            all_patient_names = glob.glob(pathlib.Path(self.input_directory, "*"," ").as_posix()[0:-1])
+            all_patient_names = [os.path.split(os.path.split(x)[0])[1] for x in all_patient_names]
+            for e in all_patient_names:
+                if e not in patient_ids:
+                    warnings.warn(f"Patient {e} does not have proper DICOM references")
 
 def main():
     args = parser()