trying to sort out import issue

medimages4tests/dummy/raw/pet/siemens/biograph_vision/vr20b/pet_calibration/__init__.py

@@ -0,0 +1,3 @@
+from .data import get_data
+
+__all__ = ["get_data"]

medimages4tests/dummy/raw/pet/siemens/biograph_vision/vr20b/pet_calibration/data.py

@@ -0,0 +1,16 @@
+import typing as ty
+from pathlib import Path
+import tempfile
+from .header import get_image_header
+from ..base import generate_raw_data
+
+
+def get_data(out_dir: Path = None, **kwargs) -> ty.List[Path]:
+    tmp_dir = Path(tempfile.mkdtemp())
+    dicom_hdr_fspath = next(get_image_header(tmp_dir, **kwargs).iterdir())
+    return generate_raw_data(
+        dicom_hdr_fspath=dicom_hdr_fspath,
+        out_dir=out_dir,
+    )
+
+

medimages4tests/dummy/raw/pet/siemens/biograph_vision/vr20b/pet_calibration/header.py

@@ -0,0 +1,91 @@
+from medimages4tests.dummy.dicom.base import (
+    generate_dicom,
+    default_dicom_dir,
+    evolve_header,
+)
+
+
+def get_image_header(out_dir, **kwargs):
+    hdr = evolve_header(constant_hdr, **kwargs)
+    return generate_dicom(out_dir, num_vols, hdr, collated_data, {})
+
+
+num_vols = 1
+
+
+constant_hdr = {
+    "00080005": {"vr": "CS", "Value": ["ISO_IR 100"]},
+    "00080008": {"vr": "CS", "Value": ["ORIGINAL", "PRIMARY", "PET_CALIBRATION"]},
+    "00080012": {"vr": "DA", "Value": ["20230725"]},
+    "00080013": {"vr": "TM", "Value": ["071306.000000"]},
+    "00080016": {"vr": "UI", "Value": ["1.3.12.2.1107.5.9.1"]},
+    "00080018": {
+        "vr": "UI",
+        "Value": ["1.3.12.2.1107.5.1.4.10016.30000023072501543220300000001"],
+    },
+    "00080020": {"vr": "DA", "Value": ["20230725"]},
+    "00080021": {"vr": "DA", "Value": ["20230725"]},
+    "00080022": {"vr": "DA", "Value": ["20230725"]},
+    "00080030": {"vr": "TM", "Value": ["114938.720000"]},
+    "00080031": {"vr": "TM", "Value": ["115432.206000"]},
+    "00080032": {"vr": "TM", "Value": ["071306.000000"]},
+    "00080050": {"vr": "SH"},
+    "00080060": {"vr": "CS", "Value": ["PT"]},
+    "00080070": {"vr": "LO", "Value": ["SIEMENS"]},
+    "00080080": {"vr": "LO", "Value": ["An institute"]},
+    "00080081": {"vr": "ST", "Value": ["Address of said institute"]},
+    "00080090": {"vr": "PN"},
+    "00081010": {"vr": "SH", "Value": ["QUADRA10016"]},
+    "00081030": {"vr": "LO", "Value": ["Researcher^Project"]},
+    "0008103E": {"vr": "LO", "Value": ["PET Raw Data"]},
+    "00081040": {"vr": "LO", "Value": ["PET"]},
+    "00081090": {"vr": "LO", "Value": ["Biograph128_Vision Quadra Edge-1232"]},
+    "00082111": {"vr": "ST", "Value": ["PETCT"]},
+    "00100010": {"vr": "PN", "Value": ["FirstName^LastName"]},
+    "00100020": {"vr": "LO", "Value": ["Session Label"]},
+    "00100030": {"vr": "DA", "Value": ["19700101"]},
+    "00100040": {"vr": "CS", "Value": ["O"]},
+    "00101010": {"vr": "AS", "Value": ["053Y"]},
+    "00101030": {"vr": "DS", "Value": [1.27]},
+    "00181000": {"vr": "LO", "Value": ["10016"]},
+    "00181020": {"vr": "LO", "Value": ["VR20B"]},
+    "00181030": {"vr": "LO", "Value": ["Onco (Adult)"]},
+    "00181200": {"vr": "DA", "Value": ["20230725", "20230611"]},
+    "00181201": {"vr": "TM", "Value": ["071306.000000", "134228.000000"]},
+    "00185100": {"vr": "CS", "Value": ["HFS"]},
+    "0020000D": {
+        "vr": "UI",
+        "Value": ["1.3.12.2.1107.5.1.4.10016.30000023072501493873200000001"],
+    },
+    "0020000E": {
+        "vr": "UI",
+        "Value": ["1.3.12.2.1107.5.1.4.10016.30000023072501543220300000002"],
+    },
+    "00200010": {"vr": "SH", "Value": ["PROJECT_ID"]},
+    "00200011": {"vr": "IS", "Value": [602]},
+    "00200012": {"vr": "IS", "Value": [1]},
+    "00200013": {"vr": "IS", "Value": [1]},
+    "00200052": {
+        "vr": "UI",
+        "Value": ["1.3.12.2.1107.5.1.4.10016.30000023072501494590400000000"],
+    },
+    "00204000": {"vr": "LT", "Value": ["PET Normalization"]},
+    "00290010": {"vr": "LO", "Value": ["SIEMENS CSA NON-IMAGE"]},
+    "00290011": {"vr": "LO", "Value": ["SIEMENS CSA HEADER"]},
+    "00290012": {"vr": "LO", "Value": ["SIEMENS MEDCOM HEADER"]},
+    "00291008": {"vr": "CS", "Value": ["PET_CALIB_T"]},
+    "00291009": {"vr": "LO", "Value": ["1.3"]},
+    "00291108": {"vr": "CS", "Value": ["PET_HDR_QC"]},
+    "00291109": {"vr": "LO", "Value": ["1.3"]},
+    "7FE10010": {"vr": "LO", "Value": ["SIEMENS CSA NON-IMAGE"]},
+    "00104000": {"vr": "LT", "Value": ["Patient comments string"]},
+    "00081048": {"vr": "PN", "Value": [{"Alphabetic": "Some Phenotype"}]},
+}
+
+
+collated_data = {
+    "00291010": {"vr": "OB", "BinaryLength": 3168},
+    "00291110": {"vr": "OB", "BinaryLength": 1220},
+    "00291220": {"vr": "OB", "BinaryLength": 80},
+    "7FE11010": {"vr": "OB", "BinaryLength": 352},
+}

medimages4tests/import_tools.py

@@ -119,7 +119,7 @@ def raw_pet_to_gen_code(fspath: Path, out_dir: Path):
             num_vols=1,
             constant_hdr=json.dumps(constant_hdr, indent="    "),
             varying_hdr=json.dumps(varying_hdr),
-            collated_data=json.dumps([data]),
+            collated_data=json.dumps(data),
         )
     )
     init_fspath = out_dir / "__init__.py"

tests/test_raw_pet.py

@@ -33,4 +33,4 @@ def test_siemens_raw_pet_data_creation(siemens_raw_pet_data: ModuleType):
     out_dir = Path(tempfile.mkdtemp())
 
     # Generate raw PET data files
-    siemens_raw_pet_data.get_image(out_dir)
+    siemens_raw_pet_data.get_data(out_dir)