Merge pull request #1 from jomasator2/MIDS36

Mids36

xnat2mids/__main__.py

@@ -39,23 +39,7 @@
     This application allow the user to download one project on XNAT and
     transform this project in MIDS format
 
-    There are 2 functions in this code:
-        download one project from xnat application:
-        arguments:
-            Prefix  -w --web PAGE_WEB        1) The URL page where XNAT is.
-            Prefix  -p --project [PROJECTS]  2) The project name to download
-            Prefix  -i --input PATH          3) the directory where the files
-                                                will be downloaded
-            Prefix  -u --user [USER]         4) The username to login in XNAT
-                                                If not write a username, It
-                                                loggin as guest.
-
-        Convert the xnat directories of the project in MIDS format:
-        arguments:
-            Prefix      -i --input      PATH   1) the directory where the files will
-                                        be downloaded
-            Prefix      -o --output     PATH   2) Directory where the MIDS model
-                                        is applied.
+    
 """
 ###############################################################################
 # Imports
@@ -93,49 +77,9 @@ def main():
     This sorfware allows the user to Download one project into XNAT platform
     and convert the XNAT images directory in MIDS directory.
 
-    The aplication execution needs Python --version >= 3.5.
-
-    there are 2 functions in this code:
-
-      Download temporary projects from xnat application:
-
-         arguments:
-          + Prefix    -w --web PAGE_WEB         1) The URL page where XNAT is.
-
-          + Prefix    -u --user [USER]          2) The username to login in XNAT
-                                                If not write a username, It logins
-                                                as guest.
-
-          + Prefix    -i --input INPUT          4) The directory where the
-                                                files will be downloaded.
-
-          + Prefix    -t --types [sdnbr]         5) Download types of MRI images
-                                                   included in xnat
-                                                   - d = dicom + dicom metadata in
-                                                         folder NIFTI
-                                                   - n = nifti or png if image is
-                                                         one slide (2D) + roi
-                                                   - b = BIDS (only in CENTRAL XNAT)
-                                                   - r = Structural report
-                                                   default = nr
+    The aplication execution needs Python --version >= 3.6.7
 
-
-          + Prefix    --overwrite                5) Overwrite download files
-
-
-      Convert the xnat directories of the project in MIDS format:
-
-        arguments:
-
-          + Prefix    -i --input INPUT          1) The directory where the files
-                                                will be downloaded.
-
-          + Prefix    -o --output OUTPUT        2) Directory where the MIDS model
-                                                is applied.
-          + Prefix    -bp --body-part           3) Specify which part of the body are 
-                                                    in the dataset(A clear dataset with
-                                                    only one part are needed)
-        """
+    """
     )
     parser.add_argument('-w', '--web', type=str, default=None,
                         help='The URL page where XNAT is.')

xnat2mids/conversion/io_json.py

@@ -15,14 +15,10 @@
 """
 
 
-def add_tag_dicom(tag, description, value, json_file_path):
+def add_tags_dicom(tag_dict, json_file_path):
     json_file = load_json(json_file_path)
-    for i in range(len(json_file["ResultSet"]["Result"])):
-        if json_file["ResultSet"]["Result"][i]["tag1"] == tag:
-            json_file["ResultSet"]["Result"][i]["value"] = value
-            break
-    else:
-        json_file["ResultSet"]["Result"].append({"tag1":tag, "tag2":"", "desc":description, "value":value})
+    for tag, value in tag_dict.items():
+        json_file[tag] = value
     save_json(json_file, json_file_path)
 
 

xnat2mids/mids_conversion.py

@@ -6,6 +6,7 @@
 import pandas
 
 from xnat2mids.conversion.io_json import load_json
+from xnat2mids.conversion.io_json import add_tags_dicom
 from xnat2mids.procedures.magnetic_resonance_procedures import ProceduresMR
 from xnat2mids.procedures.light_procedures import LightProcedure
 from xnat2mids.protocols.scans_tagger import Tagger
@@ -115,7 +116,7 @@ def create_directory_mids_v1(xnat_data_path, mids_data_path, body_part):
 
             mids_session_path = mids_data_path.joinpath(subject_name, session_name)
             xml_session_rois = list(sessions_xnat_path.rglob('*.xml'))
-            #print(f"1: {mids_session_path=}")
+            #print(f"1: {mids_session_path}")
             tagger = Tagger()
             tagger.load_table_protocol(
                 './xnat2mids/protocols/protocol_RM_prostate.tsv'
@@ -133,7 +134,6 @@ def create_directory_mids_v1(xnat_data_path, mids_data_path, body_part):
                         path_dicoms= list(scans_path.joinpath("resources").rglob("*.dcm"))[0].parent
                         folder_conversion = dicom2niix(path_dicoms, options_dcm2niix) #.joinpath("resources")
                     else:
-
                         path_dicoms= list(scans_path.joinpath("resources").rglob("*.dcm"))[0].parent
                         folder_conversion = dicom2png(path_dicoms, options_dcm2niix) #.joinpath("resources")
 
@@ -165,8 +165,8 @@ def create_directory_mids_v1(xnat_data_path, mids_data_path, body_part):
 "
                     # print()
                     # print(modality, study_description, ProtocolName, image_type)
-                    print(f"{study_description=}")
-                    print(f"{Protocol_name=}")
+                    print(f"{study_description}")
+                    print(f"{Protocol_name}")
                     if modality == "MR":
                         # via BIDS protocols
                         searched_prost = prostate_pattern_comp.search(study_description)
@@ -184,7 +184,7 @@ def create_directory_mids_v1(xnat_data_path, mids_data_path, body_part):
                                 folder_conversion, mids_session_path, session_name, protocol, acq, dir_, folder_BIDS, body_part
                             )
 
-                    if modality == "OP":
+                    if modality in ["OP", "SC", "XC", "OT"]:
                         laterality = dict_json.get("Laterality")
                         acq = "" if "ORIGINAL" in image_type else "opacitysubstract"
                         # print(laterality, acq)

xnat2mids/procedures/light_procedures.py

@@ -34,7 +34,7 @@ def copy_sessions(self, subject_name):
             df_aux.index = numpy.arange(1, len(df_aux) + 1)
             print(len(df_aux))
             activate_run = True if len(df_aux) > 1 else False
-            print(f"{activate_run=}")
+            print(f"{activate_run}")
             for index, row in df_aux.iterrows():
                 activate_acq_partioned = True if len(row['run']) > 1 else False
                 for acq, file_ in enumerate(sorted(row['run'])):
@@ -64,7 +64,7 @@ def calculate_name(self, subject_name, key, num_run, num_part, activate_run, act
         rec = f"{key_list[1] if key_list[1] else ''}"
         chunk = f"{num_part+1 if activate_acq_partioned else ''}"
         run = f"{num_run if activate_run else ''}"
-        print(f"{run=}")
+        print(f"{run}")
         # print(f"{key=}")
         return "_".join([
             part for part in [

xnat2mids/procedures/magnetic_resonance_procedures.py

@@ -103,7 +103,7 @@ def calculate_name(self, subject_name, keys, num_run, num_part, activate_run, ac
         print(num_part, activate_acq_partioned)
         acq = f"{keys[1] if keys[1] else ''}"
         chunk = f"{num_part if activate_acq_partioned else ''}"
-        print(f"{keys=}")
+        print(f"{keys}")
         return "_".join([
             part for part in [
                 subject_name,