319 standardize radiochemistry metadata caseorder (#325)

* set ModeOfAdministration to lower
* bump version

matlab/dcm2niix4pet.m

@@ -239,8 +239,6 @@ function dcm2niix4pet(FolderList,MetaList,varargin)
     end
 end
 
-
-
 %% convert
 % ----------
 for folder = 1:size(FolderList,1)
@@ -271,10 +269,8 @@ function dcm2niix4pet(FolderList,MetaList,varargin)
         telemetry_data.returncode = 1;
         telemetry(telemetry_data, folder);
         error('%s did not run properly',command)
-
     end
-
-
+
     % deal with dcm files
     dcmfiles = dir(fullfile(FolderList{folder},'*.dcm'));
     if isempty(dcmfiles) % since sometimes they have no ext :-(

matlab/telemetry.m

@@ -52,7 +52,7 @@ function telemetry(telemetry_data, input_path, output_path)
 
     % if running in CI don't run telemetry
     running_in_ci = strcmpi(getenv("CI"), 'true');
-    
+
     if disable_telemetry | disable_telemetry_env | running_in_ci
         e = false;
     else

matlab/updatejsonpetfile.m

@@ -289,6 +289,11 @@
     end
     filemetadata = update_arrays(filemetadata);
 
+    % set ModeOfAdministration to lower case
+    if isfield(filemetadata,'ModeOfAdministration')
+        filemetadata.ModeOfAdministration = lower(filemetadata.ModeOfAdministration);
+    end
+
     % clean-up
     fn_check = fieldnames(filemetadata);
     for f=1:size(fn_check,1)

pypet2bids/pypet2bids/dcm2niix4pet.py

@@ -690,6 +690,16 @@ def run_dcm2niix(self):
                     sidecar_json.update(self.spreadsheet_metadata.get("nifti_json", {}))
                     sidecar_json.update(self.additional_arguments)
 
+                    # set ModeOfAdministration to lower case
+                    if sidecar_json.get("ModeOfAdministration"):
+                        sidecar_json.update(
+                            {
+                                "ModeOfAdministration": sidecar_json.get(
+                                    "ModeOfAdministration"
+                                ).lower()
+                            }
+                        )
+
                     # this is mostly for ezBIDS, but it helps us to make better use of the series description that
                     # dcm2niix generates by default for PET imaging
                     collect_these_fields = {

pypet2bids/pypet2bids/ecat.py

@@ -453,6 +453,12 @@ def populate_sidecar(self, **kwargs):
         meta_radio_inputs = check_meta_radio_inputs(self.sidecar_template)
         self.sidecar_template.update(**meta_radio_inputs)
 
+        # set ModeOfAdministration to lower case
+        if self.sidecar_template.get("ModeOfAdministration", ""):
+            self.sidecar_template["ModeOfAdministration"] = self.sidecar_template[
+                "ModeOfAdministration"
+            ].lower()
+
     def prune_sidecar(self):
         """
         Eliminate unpopulated fields in sidecar while leaving in mandatory fields even if they are unpopulated.

pypet2bids/pypet2bids/telemetry.py

@@ -53,7 +53,10 @@ def telemetry_enabled(config_path=None):
         load_dotenv(dotenv_path=config_file)
 
     # check to see if telemetry is disabled
-    if os.getenv("PET2BIDS_TELEMETRY_ENABLED", "").lower() == "false" or os.getenv("CI", "false") == "true":
+    if (
+        os.getenv("PET2BIDS_TELEMETRY_ENABLED", "").lower() == "false"
+        or os.getenv("CI", "false") == "true"
+    ):
         return False
     else:
         return True

pypet2bids/pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "pypet2bids"
-version = "1.3.14"
+version = "1.3.15"
 description = "A python library for converting PET imaging and blood data to BIDS."
 authors = ["anthony galassi <[email protected]>"]
 license = "MIT"