7/4 Fix aaa pipeline

[iv-lop]

(1) was hitting permission error when overwriting ~/../segmentations/converted_dcm.nii.gz
added this to spine.py:

if self.save:
# Save spine segmentation
seg_path = os.path.join(
inference_pipeline.output_dir, "segmentations", "spine.nii.gz"
)
# remove stale file & ensure directory exists
if os.path.exists(seg_path):
os.remove(seg_path)
os.makedirs(os.path.dirname(seg_path), exist_ok=True)
nib.save(segmentation, seg_path)

  # Save converted DICOM volume
  converted_path = os.path.join(
      inference_pipeline.output_dir, "segmentations", "converted_dcm.nii.gz"
  )
  if os.path.exists(converted_path):
      os.remove(converted_path)
  os.makedirs(os.path.dirname(converted_path), exist_ok=True)
  nib.save(medical_volume, converted_path)

(2)
in aaa.py:
In class AortaSegmentation.call
added line: inference_pipeline.dicom_series_path = inference_pipeline.input_path
also added: print("DICOM series path is:", inference_pipeline.input_path) for debug

in inference_pipeline.py:
added: def call(self, inference_pipeline=None, input_path: str = None, **kwargs):
and added:
# pick whether we're writing onto self or the wrapped pipeline
target = inference_pipeline or self

  # 1) stash input_path if provided
  if input_path is not None:
      target.input_path = input_path

  # 2) stash everything else (output_dir, model_dir, etc.)
  for key, value in kwargs.items():
      setattr(target, key, value)

in process.py:
added: pipeline(input_path=path, output_dir=output_dir, model_dir=model_dir)

(3)
changed C2C AAA-pipeline builder code to:

def AAAPipelineBuilder(path, args):
# build the "crop" pipeline and pull out its step‐classes
crop_pipeline = AxialCropperPipelineBuilder(path, args)
# now concatenate its classes with the AAA steps
classes = crop_pipeline.inference_classes + [
aaa.AortaSegmentation(),
aaa.AortaDiameter(),
aaa.AortaMetricsSaver(),
]
return InferencePipeline(classes)

(4)
made this change in aaa.py:

if os.path.isdir(DICOM_PATH):
    # classic DICOM‐series folder
    first_file = sorted(os.listdir(DICOM_PATH))[0]
    dicom = pydicom.dcmread(os.path.join(DICOM_PATH, first_file))
    dicom.PhotometricInterpretation = "YBR_FULL"
    pixel_conversion = dicom.PixelSpacing
    print("Pixel conversion:", pixel_conversion)
    RATIO_PIXEL_TO_MM = pixel_conversion[0]

    # get slice count from the DICOM metadata
    SLICE_COUNT = dicom.InstanceNumber
    print("Slice count from DICOM header:", SLICE_COUNT)
else:
    # NIfTI file → grab spacing from the header
    nii = nib.load(DICOM_PATH)
    zooms = nii.header.get_zooms()  # e.g. (0.7, 0.7, 1.0)
    RATIO_PIXEL_TO_MM = float(zooms[0])

    # get slice count from the loaded volume
    SLICE_COUNT = len(ct_img)
    print("Slice count from NIfTI shape:", SLICE_COUNT)