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Volume.copy() drops channels, so match_geometry() fails on multichannel volumes with equal geometry #462

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Volume.copy() drops channels, so match_geometry() fails on multichannel volumes with equal geometry#462
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CPBridge

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@fedorov
fedorov
opened on Sep 25, 2026

Issue identified and summarized by Claude while working on ImagingDataCommons/idc-index-data#170

Volume.copy() does not pass channels to the constructor, so it fails for any volume with channel dimensions. match_geometry() calls copy() when the geometries already match, so a SEG volume that is already on its source image's grid cannot be matched to it.

import numpy as np
import highdicom as hd

vol = hd.Volume(
    array=np.zeros((2, 3, 3, 2), dtype=np.uint8),
    affine=np.eye(4),
    coordinate_system="PATIENT",
    channels={"SegmentNumber": [1, 2]},
)
vol.copy()
ValueError: Number of items in the 'channels' parameter (0) does not match the number of channel dimensions in the array (1).

highdicom 0.28.1. Workaround: skip match_geometry() when geometry_equal() is true.

Activity

  1. fedorov commented on Sep 25, 2026

    @fedorov
    fedorov
    on Sep 25, 2026
    MemberAuthor

    Real-data case from IDC (QIN-Breast PET and its BAMF SEG), public, no credentials needed:

    from pathlib import Path

import highdicom as hd
import pydicom
from idc_index import IDCClient

seg_uid = "1.2.276.0.7230010.3.1.3.17436516.294850.1696966650.448304"
pt_uid = "1.3.6.1.4.1.14519.5.2.1.8162.7003.717106612860546095602089628380"
IDCClient().download_from_selection(
    seriesInstanceUID=[seg_uid, pt_uid], downloadDir="data", dirTemplate="%SeriesInstanceUID"
)

pt = hd.get_volume_from_series(
    [pydicom.dcmread(f) for f in Path("data", pt_uid).glob("*.dcm")]
)
seg = hd.seg.segread(next(Path("data", seg_uid).glob("*.dcm"))).get_volume()
print(seg.geometry_equal(pt, tol=1e-3))  # True
seg.match_geometry(pt, tol=1e-3)  # ValueError
  2. CPBridge
    self-assigned this
    on Sep 25, 2026

  3. CPBridge commented on Oct 6, 2026

    @CPBridge
    CPBridge
    on Oct 6, 2026
    Collaborator

    Closed by #468

  4. CPBridge
    closed this as completedon Oct 6, 2026
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