Merge pull request #57 from Hendrik-code/dicom_extreaction

Dicom extraction, Segmentation via TPTBox, new tutorial

Author: Hendrik-code

TPTBox/core/bids_files.py

@@ -73,31 +73,31 @@ def validate_entities(key: str, value: str, name: str, verbose: bool):
         if key in entity_left_right and value not in ["L", "R"]:
             print(f"[!] value for {key} must be in {['L', 'R']}. This name '{name}' is invalid, with value {value}")
             return False
-        parts = [
-            "mag",
-            "phase",
-            "real",
-            "imag",
-            "inphase",
-            "outphase",
-            "fat",
-            "water",
-            "eco0-opp1",
-            "eco0-opp1",
-            "eco1-pip1",
-            "eco2-opp2",
-            "eco3-in1",
-            "eco4-pop1",
-            "eco5-arb1",
-            "fat-outphase",
-            "water-outphase",
-            "water-fraction",
-            "fat-fraction",
-            "r2s",
-        ]
-        if key in entity_parts and value not in parts:
-            print(f'[!] value for {key} must be in {parts}. This name "{name}" is invalid, with value {value}')
-            return False
+        # parts = [
+        #    "mag",
+        #    "phase",
+        #    "real",
+        #    "imag",
+        #    "inphase",
+        #    "outphase",
+        #    "fat",
+        #    "water",
+        #    "eco0-opp1",
+        #    "eco0-opp1",
+        #    "eco1-pip1",
+        #    "eco2-opp2",
+        #    "eco3-in1",
+        #    "eco4-pop1",
+        #    "eco5-arb1",
+        #    "fat-outphase",
+        #    "water-outphase",
+        #    "water-fraction",
+        #    "fat-fraction",
+        #    "r2s",
+        # ]
+        # if key in entity_parts and value not in parts:
+        #    print(f'[!] value for {key} must be in {parts}. This name "{name}" is invalid, with value {value}')
+        #    return False
         else:
             return True
     except Exception as e:
@@ -942,15 +942,15 @@ def open_nii(self):
             raise ValueError(f"nii.gz not present. Found only {self.file.keys()}\t{self.file}\n\n{self}") from e
 
     def get_grid_info(self):
-        from TPTBox.core.dicom.dicom_extract import add_grid_info_to_json
+        from TPTBox.core.dicom.dicom_extract import _add_grid_info_to_json
         from TPTBox.core.nii_poi_abstract import Grid
 
         nii_file = self.get_nii_file()
         if nii_file is None:
             return None
         if not self.has_json():
             self.file["json"] = Path(str(nii_file).split(".")[0] + ".json")
-        return Grid(**add_grid_info_to_json(nii_file, self.file["json"])["Grid"])
+        return Grid(**_add_grid_info_to_json(nii_file, self.file["json"])["grid"])
 
     def get_nii_file(self):
         for key in _supported_nii_files:

TPTBox/core/dicom/dicom2nii_utils.py

@@ -42,19 +42,9 @@
     },
     "pd": {"rule": "acq", "iso": "PD_FS_SPC_COR"},
 }
-# [
-#
-#
-#
-#    "PD_FS_SPC_COR",
-#    "3D_GRE_TRA_F",
-#
-#
-#
-# ]
-
-
-def test_nii(path: Path | str | BIDS_FILE):
+
+
+def __test_nii(path: Path | str | BIDS_FILE):
     if isinstance(path, str):
         path = Path(path)
     if path.exists():
@@ -82,7 +72,7 @@ def find_all_broken(path: str = "/DATA/NAS/datasets_processed/NAKO/dataset-nako/
         q = subj.new_query(flatten=True)
         q.filter_filetype("nii.gz")
         for f in q.loop_list():
-            if not test_nii(f):
+            if not __test_nii(f):
                 print("BROKEN:", f)
                 brocken.append(f)
                 with open("broken.pkl", "wb") as w:
@@ -97,8 +87,8 @@ def find_all_broken(path: str = "/DATA/NAS/datasets_processed/NAKO/dataset-nako/
 )
 
 
-def test_and_replace(out_folder="/media/data/NAKO/dataset-nako2"):
-    from TPTBox.core.dicom.dicom_extract import extract_folder
+def __test_and_replace(out_folder="/media/data/NAKO/dataset-nako2"):
+    from TPTBox.core.dicom.dicom_extract import extract_dicom_folder
 
     with open("/run/user/1000/gvfs/smb-share:server=172.21.251.64,share=nas/tools/TPTBox/broken.pkl", "rb") as w:
         brocken = pickle.load(w)
@@ -127,7 +117,7 @@ def test_and_replace(out_folder="/media/data/NAKO/dataset-nako2"):
                     except StopIteration:
                         continue
                 if f2.exists():
-                    out_files.update(extract_folder(f2, Path(out_folder), make_subject_chunks=3, verbose=False))
+                    out_files.update(extract_dicom_folder(f2, Path(out_folder), make_subject_chunks=3, verbose=False))
                 else:
                     print(f, f.exists())
         else:
@@ -140,11 +130,11 @@ def test_and_replace(out_folder="/media/data/NAKO/dataset-nako2"):
                     print((source_folder_encrypted / source_folders[mod][sub_key]) / (f"{subj}*.zip"))
                     continue
             ## Call the extraction
-            out_files = extract_folder(zip_file, Path(out_folder), make_subject_chunks=3, verbose=False)
+            out_files = extract_dicom_folder(zip_file, Path(out_folder), make_subject_chunks=3, verbose=False)
         ## -- Testing ---
         # Save over brocken...
         for o in out_files.values():
-            if o is not None and not test_nii(o):
+            if o is not None and not __test_nii(o):
                 Print_Logger().on_fail("Still Broken ", out_files)
 
 
@@ -156,7 +146,6 @@ def clean_dicom_data(dcm_data) -> dict:
         # raise NoImageError()
     else:
         del py_dataset.PixelData
-    print(type(py_dataset))
     py_dict = py_dataset.to_json_dict(suppress_invalid_tags=True)
     for tag in ["00291010", "00291020"]:
         if tag in py_dict and "InlineBinary" in py_dict[tag]:
@@ -204,7 +193,7 @@ def test_name_conflict(json_ob, file):
     return False
 
 
-def save_json(json_ob, file):
+def save_json(json_ob, file, check_exist=False):
     """
     recieves a json object and a path and saves the object as a json file
     """
@@ -214,7 +203,7 @@ def convert(obj):
             return int(obj)
         raise TypeError
 
-    if test_name_conflict(json_ob, file):
+    if check_exist and test_name_conflict(json_ob, file):
         raise FileExistsError(file)
     if Path(file).exists():
         return True
@@ -229,7 +218,7 @@ def load_json(file):
 
 
 if __name__ == "__main__":
-    test_and_replace()
+    __test_and_replace()
     # find_all_broken()
     # test_and_replace(
     #    "/DATA/NAS/datasets_processed/NAKO/dataset-nako/rawdata/101/101776/mevibe/sub-101776_sequ-94_acq-ax_part-eco0-opp1_mevibe.nii.gz",