Brief release notes may be found on on Github. This page contains migration notes for major breaking changes to the library’s API.
Deprecation of add_segments method
Prior to highdicom 0.8.0, it was possible to add further segments to
highdicom.seg.Segmentation image after its construction using the
add_segments method. This was found to produce incorrect Dimension Index
Values if the empty frames did not match within all segments added.
To create the Dimension Index Values correctly, the constructor needs access to all segments in the image when it is first created. Therefore, the add_segments method was removed in highdicom 0.8.0. Instead, in highdicom 0.8.0 and later, multiple segments can be passed to the constructor by stacking their arrays along the fourth dimension.
Given code that adds segments like this, in highdicom 0.7.0 and earlier:
import numpy as np import highdicom as hd # Create initial segment mask and description mask_1 = np.array( # ... ) description_1 = hd.seg.SegmentDescription( # ... ) seg = hd.seg.Segmentation( # ... pixel_array=mask_1, segment_descriptions=[description_1], # ... ) # Create a second segment and add to the existing segmentation mask_2 = np.array( # ... ) description_2 = hd.seg.SegmentDescription( # ... ) seg.add_segments( # ... pixel_array=mask_2, segment_descriptions=[description_2], # ... )
This can be migrated to highdicom 0.8.0 and later by concatenating the arrays along the fourth dimension and calling the constructor at the end.
import numpy as np import highdicom as hd # Create initial segment mask and description mask_1 = np.array( # ... ) description_1 = hd.seg.SegmentDescription( # ... ) # Create a second segment and description mask_2 = np.array( # ... ) description_2 = hd.seg.SegmentDescription( # ... ) combined_segments = np.concatenate([mask_1, mask_2], axis=-1) combined_descriptions = [description_1, description_2] seg = hd.seg.Segmentation( # ... pixel_array=combined_segments, segment_descriptions=combined_descriptions, # ... )
Note that segments must always be stacked down the fourth dimension (with index
3) of the
pixel_array. In order to create a segmentation with multiple
segments for a single source frame, it is required to add a new dimension
(with length 1) as the first dimension (index 0) of the array.
Correct coordinate mapping
Prior to highdicom 0.14.1, mappings between image coordinates and reference coordinates did not take into account that there are two image coordinate systems, which are shifted by 0.5 pixels.
Pixel indices: (column, row) indices into the pixel matrix. The values are zero-based integers in the range [0, Columns - 1] and [0, Rows - 1]. Pixel indices are defined relative to the centers of pixels and the (0, 0) index is located at the center of the top left corner hand pixel of the total pixel matrix.
Image coordinates: (column, row) coordinates in the pixel matrix at sub-pixel resolution. The values are floating-point numbers in the range [0, Columns] and [0, Rows]. Image coordinates are defined relative to the top left corner of the pixels and the (0.0, 0.0) point is located at the top left corner of the top left corner hand pixel of the total pixel matrix.
To account for these differences, introduced two additional transformer classes
in highdicom 0.14.1. and made changes to the existing ones.
The existing transformer class now map between image coordinates and reference
While the new transformer classes map between pixel indices and reference
Note that you want to use the former classes for converting between spatial
coordinates (SCOORD) (
highdicom.sr.ScoordContentItem) and 3D spatial
coordinates (SCOORD3D) (
highdicom.sr.Scoord3DContentItem) and the
latter for determining the position of a pixel in the frame of reference or for
projecting a coordinate in the frame of reference onto the image plane.
To make the distinction between pixel indices and image coordinates as clear as
possible, we renamed the parameter of the
highdicom.spatial.map_pixel_into_coordinate_system() function from
index and enforce that the values that are provided via
the argument are integers rather than floats.
In addition, the return value of
highdicom.spatial.map_coordinate_into_pixel_matrix() is now a tuple of
Deprecation of processing_type parameter
In highdicom 0.15.0, the
processing_type parameter was removed from the
The parameter turned out to be superfluous, because the argument could be
derived from the type of the
Refactoring of SpecimenPreparationStep class
In highdicom 0.16.0 and later versions,
highdicom.content.SpecimenPreparationStep represents an item of the
Specimen Preparation Sequence rather than the Specimen Preparation Step Content
Item Sequence and the class is consequently derived from
pydicom.dataset.Dataset instead of
As a consequence, alternative construction of an instance of
highdicom.content.SpecimenPreparationStep needs to be performed using
from_dataset() instead of the
from_sequence() class method.
Deprecation of Big Endian Transfer Syntaxes
The use of “Big Endian” transfer syntaxes such as ExplicitVRBigEndian is
disallowed from highdicom 0.18.0 onwards. The use of Big Endian transfer
syntaxes has been retired in the standard for some time. To discourage the use
of retired transfer syntaxes and to simplify the logic when encoding and
decoding objects in which byte order is relevant, in version 0.17.0 and onwards
passing a big endian transfer syntax to the constructor of
highdicom.SOPClass or any of its subclasses will result in a value
Similarly, as of highdicom 0.18.0, it is no longer possible to pass datasets
with a Big Endian transfer syntax to the from_dataset methods of any of the
Change in MeasurementReport constructor for TID 1601 enhancement
A breaking change was made after highdicom 0.18.4 in the creation of Image
Library TID 1601 objects.
Previously the Imag Library was constructed by explicitly
passing a pydicom.sequence.Sequence of ImageLibraryEntryDescriptors
objects to the
highdicom.sr.MeasurementReport constructor in the image_library_groups
Now a pydicom.sequence.Sequence of pydicom.dataset.Dataset
objects is passed in the referenced_images argument and the
ImageLibrary components are created internally by highdicom.
This standardizes the content of the Image Library subcomponents.