fix: Standardize BaseSequence to separate metadata extraction and ASL context generation

package/src/pyaslreport/main.py

@@ -34,7 +34,10 @@ def get_bids_metadata(data):
     if sequence is None:
         raise ValueError(f"No matching sequence found for modality '{modality}' with the provided DICOM header")
 
-    return sequence.extract_bids_metadata()
+    metadata = sequence.extract_bids_metadata()
+    asl_context = sequence.generate_asl_context(data.get("nifti_file"))
+
+    return metadata, asl_context
 
 
 def get_dicom_header(dicom_dir: str):

package/src/pyaslreport/sequences/base_sequence.py

@@ -30,6 +30,11 @@ def extract_bids_metadata(self) -> dict:
         """Extract and convert DICOM metadata to BIDS fields."""
         pass
 
+    @abstractmethod
+    def generate_asl_context(self, nifti_path: str = None) -> list:
+        """Generate the ASL context array."""
+        pass
+
     def _extract_common_metadata(self) -> dict:
         """Extract and convert common DICOM metadata fields to BIDS fields, including ms->s conversion where needed."""
         dataset = self.dicom_header

package/src/pyaslreport/sequences/ge/asl/ge_basic_single_pld.py

@@ -23,7 +23,8 @@ def extract_bids_metadata(self):
             bids["PostLabelingDelay"] = dicom_header.get(dcm_tags.GE_INVERSION_TIME, None).value
 
 
-        asl_context = self._generate_asl_context(1)
+        return bids
 
-        return bids, asl_context
+    def generate_asl_context(self, nifti_path: str = None) -> list:
+        return self._generate_asl_context(1)
 

package/src/pyaslreport/sequences/ge/asl/ge_easl_multi_pld.py

@@ -95,7 +95,9 @@ def extract_bids_metadata(self):
                 bids["LabelingDuration"] = LD_lin
                 bids["PostLabelingDelay"] = PLD_lin
 
-        # ASLcontext: all deltaM, last one is m0scan
-        asl_context = self._generate_asl_context(npld if npld else 2)
+        return bids
 
-        return bids, asl_context
+    def generate_asl_context(self, nifti_path: str = None) -> list:
+        dataset = self.dicom_header
+        npld = dataset.get(dcm_tags.GE_PRIVATE_CV6, None).value if dcm_tags.GE_PRIVATE_CV6 in dataset else None
+        return self._generate_asl_context(npld if npld else 2)

package/src/pyaslreport/sequences/siemens/asl/siemens_basic_single_pld.py

@@ -19,4 +19,7 @@ def extract_bids_metadata(self):
             bids["LabelingDuration"] = d.get(dcm_tags.GE_LABEL_DURATION, None).value
         if dcm_tags.GE_INVERSION_TIME in d:
             bids["PostLabelingDelay"] = d.get(dcm_tags.GE_INVERSION_TIME, None).value
-        return bids 
+        return bids 
+
+    def generate_asl_context(self, nifti_path: str = None) -> list:
+        return ["m0scan", "control", "label"]