def set_metadata(self, tag, value, force_vr=None):
# Do not update the metadata if no metadata is present.
if self.metadata is None:
return None
set_pydicom_meta_tag(dcm_seq=self.metadata, tag=tag, value=value, force_vr=force_vr)
def rename(self, new):
if self.metadata is not None:
# Obtain the old name
old = self.name
if not self.has_metadata(tag=(0x3006, 0x0020)):
raise ValueError(
f"The DICOM metaheader does not contain a Structure Set ROI sequence."
)
# Iterate over roi elements in the roi sequence
for ii, roi_element in enumerate(self.metadata[0x3006, 0x0020]):
# Find ROI name that matches the old name
if get_pydicom_meta_tag(dcm_seq=roi_element,
tag=(0x3006, 0x0026),
tag_type="str") == old:
set_pydicom_meta_tag(dcm_seq=roi_element,
tag=(0x3006, 0x0026),
value=new)
# Assign a new name
self.name = new
else:
# Assign a new name
self.name = new
def update_dicom_header(self, dcm):
# Update unit of pixel values
voxel_unit = "CM2ML" if self.suv_type == "BSA" else "GML"
set_pydicom_meta_tag(dcm_seq=dcm,
tag=(0x0054, 0x1001),
value=voxel_unit)
# Update the SUV type
set_pydicom_meta_tag(dcm_seq=dcm,
tag=(0x0054, 0x1006),
value=self.suv_type)
# Decay correction
set_pydicom_meta_tag(dcm_seq=dcm,
tag=(0x0054, 0x1102),
value=self.decay_correction)
# Add DECY to the image corrections, if this was not done previously.
image_corrections = get_pydicom_meta_tag(dcm_seq=dcm,
tag=(0x0028, 0x0051),
tag_type="mult_str",
default=[])
if "DECY" not in image_corrections:
image_corrections += ["DECY"]
set_pydicom_meta_tag(dcm_seq=dcm,
tag=(0x0028, 0x0051),
value=image_corrections)
# Update the image type
image_type = get_pydicom_meta_tag(dcm_seq=dcm,
tag=(0x0008, 0x0008),
tag_type="mult_str",
default=[])
if len(image_type) > 2:
image_type[0] = "DERIVED"
image_type[1] = "SECONDARY"
else:
image_type = ["DERIVED", "SECONDARY"]
set_pydicom_meta_tag(dcm_seq=dcm,
tag=(0x0008, 0x0008),
value=image_type)
return dcm
def _convert_to_parametric_map_iod(self):
if self.metadata is None:
return None
# Create a copy of the metadata.
old_dcm: FileDataset = copy.deepcopy(self.metadata)
# Update the SOP class to that of a parametric map image
self.set_metadata(tag=(0x0008, 0x0016), value="1.2.840.10008.5.1.4.1.1.30")
# Update the image type attribute
image_type = self.get_metadata(tag=(0x0008, 0x0008), tag_type="mult_str", default=[])
image_type = [image_type[ii] if ii < len(image_type) else "" for ii in range(4)]
image_type[0] = "DERIVED"
image_type[1] = "PRIMARY"
image_type[2] = image_type[2] if not image_type[2] == "" else "STATIC"
image_type[3] = "MIXED" if self.spat_transform == "base" else "FILTERED"
self.set_metadata(tag=(0x0008, 0x0008), value=image_type)
# Parametric Map Image module attributes that may be missing.
self.cond_set_metadata(tag=(0x2050, 0x0020), value="IDENTITY") # Presentation LUT shape
self.cond_set_metadata(tag=(0x0018, 0x9004), value="RESEARCH") # Content qualification
self.cond_set_metadata(tag=(0x0028, 0x0301), value="NO") # Burned-in Annotation
self.cond_set_metadata(tag=(0x0028, 0x0302), value="YES") # Recognisable facial features
self.cond_set_metadata(tag=(0x0070, 0x0080), value=self.get_export_descriptor().upper().strip()[:15]) # Content label
self.cond_set_metadata(tag=(0x0070, 0x0081), value=self.get_export_descriptor()[:63]) # Content description
self.cond_set_metadata(tag=(0x0070, 0x0084), value="Doe^John")
# Set the source instance sequence
source_instance_list = []
for reference_instance_sop_uid in self.slice_table.sop_instance_uid:
ref_inst = Dataset()
set_pydicom_meta_tag(dcm_seq=ref_inst, tag=(0x0008, 0x1150), value=get_pydicom_meta_tag(dcm_seq=old_dcm, tag=(0x0008, 0x0016), tag_type="str"))
set_pydicom_meta_tag(dcm_seq=ref_inst, tag=(0x0008, 0x1155), value=reference_instance_sop_uid)
source_instance_list += [ref_inst]
self.set_metadata(tag=(0x0008, 0x2112), value=Sequence(source_instance_list))
# Attributes from the enhanced general equipment module may be missing.
self.cond_set_metadata(tag=(0x0008, 0x0070), value="unknown") # Manufacturer
self.cond_set_metadata(tag=(0x0008, 0x1090), value="unknown") # Model name
self.cond_set_metadata(tag=(0x0018, 0x1000), value="unknown") # Device Serial Number
self.set_metadata(tag=(0x0018, 0x1020), value="MIRP " + get_version())
# Items from multi-frame function groups may be missing. We currently only use a single frame.
self.set_metadata(tag=(0x5200, 0x9229), value=Sequence()) # Shared functional groups sequence
self.set_metadata(tag=(0x5200, 0x9230), value=Sequence()) # Per-frame functional groups sequence
# Multi-frame Dimension module
# Dimension organisation sequence. We copy the frame of reference as UID.
dim_org_seq_elem = Dataset()
set_pydicom_meta_tag(dim_org_seq_elem, tag=(0x0020, 0x9164), value=self.get_metadata(tag=(0x0020, 0x0052), tag_type="str")) # Dimension organisation UID
self.set_metadata(tag=(0x0020, 0x9221), value=Sequence([dim_org_seq_elem]))
# Dimension Index sequence. We point to the instance number.
dim_index_seq_elem = Dataset()
set_pydicom_meta_tag(dim_index_seq_elem, tag=(0x0020, 0x9165), value=(0x0020, 0x0013)) # Dimension index pointer
set_pydicom_meta_tag(dim_index_seq_elem, tag=(0x0020, 0x9164), value=self.get_metadata(tag=(0x00200052), tag_type="str")) # Dimension organisation UID
self.set_metadata(tag=(0x0020, 0x9222), value=Sequence([dim_index_seq_elem]))
