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Add default values for some DICOM fields #94

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Add default values for some DICOM fields #94

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ba60474
Add default values for some DICOM fields
jeffbaumes Aug 21, 2023
a923d00
Fix setup.py to work for local install
jeffbaumes Aug 21, 2023
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2 changes: 1 addition & 1 deletion rt_utils/ds_helper.py
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Original file line number Diff line number Diff line change
Expand Up @@ -81,7 +81,7 @@ def add_study_and_series_information(ds: FileDataset, series_data):
ds.SeriesDescription = getattr(reference_ds, "SeriesDescription", "")
ds.StudyInstanceUID = reference_ds.StudyInstanceUID
ds.SeriesInstanceUID = generate_uid() # TODO: find out if random generation is ok
ds.StudyID = reference_ds.StudyID
ds.StudyID = getattr(reference_ds, "StudyID", "")
ds.SeriesNumber = "1" # TODO: find out if we can just use 1 (Should be fine since its a new series)


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12 changes: 6 additions & 6 deletions rt_utils/image_helper.py
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Expand Up @@ -155,7 +155,7 @@ def get_pixel_to_patient_transformation_matrix(series_data):

first_slice = series_data[0]

offset = np.array(first_slice.ImagePositionPatient)
offset = np.array(getattr(first_slice, "ImagePositionPatient", [0, 0, 0]))
row_spacing, column_spacing = first_slice.PixelSpacing
slice_spacing = get_spacing_between_slices(series_data)
row_direction, column_direction, slice_direction = get_slice_directions(first_slice)
Expand All @@ -172,7 +172,7 @@ def get_pixel_to_patient_transformation_matrix(series_data):
def get_patient_to_pixel_transformation_matrix(series_data):
first_slice = series_data[0]

offset = np.array(first_slice.ImagePositionPatient)
offset = np.array(getattr(first_slice, "ImagePositionPatient", [0, 0, 0]))
row_spacing, column_spacing = first_slice.PixelSpacing
slice_spacing = get_spacing_between_slices(series_data)
row_direction, column_direction, slice_direction = get_slice_directions(first_slice)
Expand Down Expand Up @@ -209,11 +209,11 @@ def apply_transformation_to_3d_points(

def get_slice_position(series_slice: Dataset):
_, _, slice_direction = get_slice_directions(series_slice)
return np.dot(slice_direction, series_slice.ImagePositionPatient)
return np.dot(slice_direction, getattr(series_slice, "ImagePositionPatient", [0, 0, 0]))


def get_slice_directions(series_slice: Dataset):
orientation = series_slice.ImageOrientationPatient
orientation = getattr(series_slice, "ImageOrientationPatient", [1, 0, 0, 0, 1, 0])
row_direction = np.array(orientation[:3])
column_direction = np.array(orientation[3:])
slice_direction = np.cross(row_direction, column_direction)
Expand Down Expand Up @@ -265,8 +265,8 @@ def get_slice_contour_data(series_slice: Dataset, contour_sequence: Sequence):
def get_slice_mask_from_slice_contour_data(
series_slice: Dataset, slice_contour_data, transformation_matrix: np.ndarray
):
# Go through all contours in a slice, create polygons in correct space and with a correct format
# and append to polygons array (appropriate for fillPoly)
# Go through all contours in a slice, create polygons in correct space and with a correct format
# and append to polygons array (appropriate for fillPoly)
polygons = []
for contour_coords in slice_contour_data:
reshaped_contour_data = np.reshape(contour_coords, [len(contour_coords) // 3, 3])
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3 changes: 1 addition & 2 deletions setup.py
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Expand Up @@ -15,8 +15,7 @@
long_description=long_description,
long_description_content_type="text/markdown",
url="https://github.com/qurit/rtutils",
package_dir={'':"rt_utils"},
packages=setuptools.find_packages("rt_utils", exclude="tests"),
packages=setuptools.find_packages(exclude=["tests"]),
keywords=["RTStruct", "Dicom", "Pydicom"],
classifiers=[
"Operating System :: OS Independent",
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