fix: copy dicom inputs before running dcm2niix

package/src/pyaslreport/converters/dicom_to_nifti_converter.py

@@ -1,6 +1,7 @@
 import json
 import os
 import re
+import shutil
 import subprocess
 import tempfile
 import pydicom
@@ -24,7 +25,9 @@ def convert(dcm_files, nifti_file=None, converted_files_location="/tmp/upload"):
         series_repetitions = {}
 
         with tempfile.TemporaryDirectory() as temp_dir:
-            for dcm_file in dcm_files:
+            for index, dcm_file in enumerate(dcm_files):
+                temp_file_path = os.path.join(temp_dir, f"{index}_{os.path.basename(dcm_file)}")
+                shutil.copy2(dcm_file, temp_file_path)
 
                 ds = pydicom.dcmread(dcm_file)
                 series_number_tag = ds.get((0x0020, 0x0011), None)

package/src/pyaslreport/tests/test_dicom_to_nifti_converter.py

@@ -0,0 +1,50 @@
+import json
+from pathlib import Path
+from types import SimpleNamespace
+from unittest.mock import patch
+
+from pyaslreport.converters.dicom_to_nifti_converter import DICOM2NiFTIConverter
+
+
+def test_convert_copies_files_to_temp_dir_and_runs_dcm2niix(tmp_path):
+    dicom_file = tmp_path / "input1.dcm"
+    dicom_file.write_bytes(b"fake dicom")
+    output_dir = tmp_path / "converted"
+    observed_temp_dir = {"path": None}
+
+    def fake_dcmread(_path):
+        def fake_get(tag, default=None):
+            if tag == (0x0020, 0x0011):
+                return SimpleNamespace(value=1)
+            if tag == (0x0029, 0x1020):
+                return SimpleNamespace(value=b"lRepetitions = 4")
+            return default
+
+        return SimpleNamespace(get=fake_get)
+
+    def fake_run(cmd, check, stdout, stderr):
+        temp_dir = Path(cmd[-1])
+        observed_temp_dir["path"] = temp_dir
+        assert any(temp_dir.iterdir())
+
+        output_dir.mkdir(exist_ok=True)
+        (output_dir / "series.nii.gz").write_bytes(b"fake nifti")
+        (output_dir / "series.json").write_text(json.dumps({"SeriesNumber": 1}))
+        return SimpleNamespace(stdout=b"", stderr=b"")
+
+    with patch("pyaslreport.converters.dicom_to_nifti_converter.pydicom.dcmread", side_effect=fake_dcmread), \
+         patch("pyaslreport.converters.dicom_to_nifti_converter.subprocess.run", side_effect=fake_run):
+        converted_files, converted_filenames, nifti_file, file_format, error = DICOM2NiFTIConverter.convert(
+            [str(dicom_file)],
+            converted_files_location=str(output_dir),
+        )
+
+    assert observed_temp_dir["path"] is not None
+    assert converted_filenames == ["series.json"]
+    assert converted_files == [str(output_dir / "series.json")]
+    assert nifti_file == str(output_dir / "series.nii.gz")
+    assert file_format == "dicom"
+    assert error is None
+
+    json_data = json.loads((output_dir / "series.json").read_text())
+    assert json_data["lRepetitions"] == "4"