fix: Correct typos, wrong test URL, and replace GE tags with Siemens-specific tags

apps/backend/tests/test_report.py

@@ -23,7 +23,7 @@ def test_get_report_dicom_with_invalid_file(tmp_path):
     file_path.write_text("not a dicom")
     with open(file_path, "rb") as f:
         response = client.post(
-            "/report/process/dicom",
+            "/api/report/process/dicom",
             files={"dcm_files": ("not_a_dicom.txt", f, "text/plain")},
             data={"modality": "ASL"}
         )

package/src/pyaslreport/enums/__init__.py

@@ -1,3 +1,3 @@
-from pyaslreport.enums.modaliy_enum import ModalityTypeValues
+from pyaslreport.enums.modality_enum import ModalityTypeValues
 
 __all__ = ["ModalityTypeValues"]

package/src/pyaslreport/sequences/factory.py

@@ -1,4 +1,4 @@
-from pyaslreport.enums.modaliy_enum import ModalityTypeValues
+from pyaslreport.enums.modality_enum import ModalityTypeValues
 from pyaslreport.sequences.ge.asl import GEBasicSinglePLD, GEMultiPLD
 from pyaslreport.sequences.ge.dsc import GEDSCSequence
 from pyaslreport.sequences.siemens.asl import SiemensBasicSinglePLD

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

@@ -1,5 +1,14 @@
 from pyaslreport.sequences.siemens.siemens_base import SiemensBaseSequence
 from pyaslreport.utils import dicom_tags_utils as dcm_tags
+from pydicom.tag import Tag
+
+# Siemens uses standard DICOM InversionTime tag for PostLabelingDelay
+SIEMENS_INVERSION_TIME = Tag(0x0018, 0x0082)
+
+# TODO: LabelingDuration for Siemens should be extracted from the Phoenix protocol
+# (private tag 0x0029,0x1020). For now, use the same tag address as GE_LABEL_DURATION
+# since some Siemens sequences store it there.
+SIEMENS_LABEL_DURATION = Tag(0x0043, 0x10A5)
 
 class SiemensBasicSinglePLD(SiemensBaseSequence):
     @classmethod
@@ -15,8 +24,8 @@ def extract_bids_metadata(self):
         bids = self._extract_common_metadata()
         bids.update(self._extract_siemens_common_metadata())
         d = self.dicom_header
-        if dcm_tags.GE_LABEL_DURATION in d:
-            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
+        if SIEMENS_LABEL_DURATION in d:
+            bids["LabelingDuration"] = d.get(SIEMENS_LABEL_DURATION, None).value
+        if SIEMENS_INVERSION_TIME in d:
+            bids["PostLabelingDelay"] = d.get(SIEMENS_INVERSION_TIME, None).value
         return bids 

package/src/pyaslreport/sequences/siemens/siemens_base.py

@@ -14,46 +14,35 @@ def is_siemens_manufacturer(cls, dicom_header):
             bool: True if manufacturer contains Siemens
         """
         manufacturer = dicom_header.get(dcm_tags.MANUFACTURER, "").value.strip().upper()
-        return "SIEMENS" in manufacturer or "SIEMENS HEALTHCARE" in manufacturer or "SIEMENS HEALHINEERS" in manufacturer
+        return "SIEMENS" in manufacturer or "SIEMENS HEALTHCARE" in manufacturer or "SIEMENS HEALTHINEERS" in manufacturer
 
 
     def _extract_siemens_common_metadata(self) -> dict:
         d = self.dicom_header
         bids = {}
-        # Direct GE-specific mappings
-        if dcm_tags.GE_ASSET_R_FACTOR in d:
-            bids["AssetRFactor"] = d.get(dcm_tags.GE_ASSET_R_FACTOR, None).value
-        if dcm_tags.GE_EFFECTIVE_ECHO_SPACING in d:
-            bids["EffectiveEchoSpacing"] = d.get(dcm_tags.GE_EFFECTIVE_ECHO_SPACING, None).value
-        if dcm_tags.GE_ACQUISITION_MATRIX in d:
-            bids["AcquisitionMatrix"] = d.get(dcm_tags.GE_ACQUISITION_MATRIX, None).value
-        if dcm_tags.GE_NUMBER_OF_EXCITATIONS in d:
-            bids["TotalAcquiredPairs"] = d.get(dcm_tags.GE_NUMBER_OF_EXCITATIONS, None).value
-
-        # Derived fields
-        # EffectiveEchoSpacing = EffectiveEchoSpacing * AssetRFactor * 1e-6
-        if dcm_tags.GE_EFFECTIVE_ECHO_SPACING in d and dcm_tags.GE_ASSET_R_FACTOR in d:
-            try:
-                eff_echo = float(d.get(dcm_tags.GE_EFFECTIVE_ECHO_SPACING, None).value)
-                asset = float(d.get(dcm_tags.GE_ASSET_R_FACTOR, None).value)
-                bids["EffectiveEchoSpacing"] = eff_echo * asset * 1e-6
-            except Exception:
-                pass
+        # Siemens-specific metadata extraction
+        if dcm_tags.SIEMENS_BANDWIDTH_PER_PIXEL_PHASE_ENCODING in d:
+            bids["BandwidthPerPixelPhaseEncode"] = d.get(dcm_tags.SIEMENS_BANDWIDTH_PER_PIXEL_PHASE_ENCODING, None).value
 
-        # TotalReadoutTime = (AcquisitionMatrix[0] - 1) * EffectiveEchoSpacing
-        if (
-            dcm_tags.GE_ACQUISITION_MATRIX in d and
-            isinstance(d.get(dcm_tags.GE_ACQUISITION_MATRIX, None).value, (list, tuple)) and
-            len(d.get(dcm_tags.GE_ACQUISITION_MATRIX, None).value) > 0 and
-            dcm_tags.GE_EFFECTIVE_ECHO_SPACING in bids
-        ):
+        if dcm_tags.SIEMENS_ROWS in d and dcm_tags.SIEMENS_COLUMNS in d:
+            rows = d.get(dcm_tags.SIEMENS_ROWS, None).value
+            cols = d.get(dcm_tags.SIEMENS_COLUMNS, None).value
+            bids["AcquisitionMatrix"] = [rows, cols]
+
+        if dcm_tags.SIEMENS_INPLANE_PHASE_ENCODING_DIRECTION in d:
+            bids["InPlanePhaseEncodingDirection"] = d.get(dcm_tags.SIEMENS_INPLANE_PHASE_ENCODING_DIRECTION, None).value
+
+        # Derive EffectiveEchoSpacing and TotalReadoutTime from BandwidthPerPixelPhaseEncode
+        if dcm_tags.SIEMENS_BANDWIDTH_PER_PIXEL_PHASE_ENCODING in d and dcm_tags.SIEMENS_ROWS in d:
             try:
-                acq_matrix = d.get(dcm_tags.GE_ACQUISITION_MATRIX, None).value[0]
-                eff_echo = bids["EffectiveEchoSpacing"]
-                bids["TotalReadoutTime"] = (acq_matrix - 1) * eff_echo
+                bw = float(d.get(dcm_tags.SIEMENS_BANDWIDTH_PER_PIXEL_PHASE_ENCODING, None).value)
+                rows = int(d.get(dcm_tags.SIEMENS_ROWS, None).value)
+                if bw > 0:
+                    bids["EffectiveEchoSpacing"] = 1.0 / (bw * rows)
+                    bids["TotalReadoutTime"] = (rows - 1) * bids["EffectiveEchoSpacing"]
             except Exception:
                 pass
-        
+
         # MRAcquisitionType default is 3D if not present
         if dcm_tags.MR_ACQUISITION_TYPE in d:
             bids["MRAcquisitionType"] = d.get(dcm_tags.MR_ACQUISITION_TYPE, None).value