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""" Test DICOM functionality.
"""
from zipfile import ZipFile
import numpy as np
import pytest
import imageio.v2 as iio
import imageio.v3 as iio3
from imageio import core
import imageio.plugins.dicom
from conftest import deprecated_test
@pytest.fixture(scope="module")
def examples(test_images, tmp_path_factory):
"""Create two dirs, one with one dataset and one with two datasets"""
workdir = tmp_path_factory.getbasetemp() / "test_dicom"
# Prepare sources
fname1 = test_images / "dicom_sample1.zip"
fname2 = test_images / "dicom_sample2.zip"
dname1 = workdir / "dicom_sample1"
dname2 = workdir / "dicom_sample2"
# folder 1
ZipFile(fname1).extractall(dname1)
# folder 2
ZipFile(fname1).extractall(dname2)
ZipFile(fname2).extractall(dname2)
# a file from each folder
# tests expect this to be a string
fname1 = str(next(dname1.iterdir()))
fname2 = str(next(dname2.iterdir()))
yield dname1, dname2, fname1, fname2
@deprecated_test
def test_read_empty_dir(tmp_path):
# Test that no format is found, but no error is raised
request = core.Request(tmp_path, "ri")
assert iio.formats.search_read_format(request) is None
def test_dcmtk():
# This should not crach, we make no assumptions on whether its
# available or not
imageio.plugins.dicom.get_dcmdjpeg_exe()
@deprecated_test
def test_selection(test_images, tmp_path, examples):
dname1, dname2, fname1, fname2 = examples
# Test that DICOM can examine file
F = iio.formats.search_read_format(core.Request(fname1, "ri"))
assert F.name == "DICOM"
assert isinstance(F, type(iio.formats["DICOM"]))
# Test that we cannot save
request = core.Request(tmp_path / "test.dcm", "wi")
assert not F.can_write(request)
# Test fail on wrong file
fname2 = fname1 + ".fake"
bb = open(fname1, "rb").read()
bb = bb[:128] + b"XXXX" + bb[132:]
open(fname2, "wb").write(bb)
with pytest.raises(Exception):
F.get_reader(core.Request(fname2, "ri"))
# Test special files with other formats
im = iio.imread(test_images / "dicom_file01.dcm")
assert im.shape == (512, 512)
im = iio.imread(test_images / "dicom_file03.dcm")
assert im.shape == (512, 512)
im = iio.imread(test_images / "dicom_file04.dcm")
assert im.shape == (512, 512)
# Expected fails
fname = test_images / "dicom_file90.dcm"
with pytest.raises(RuntimeError):
iio.imread(fname) # 1.2.840.10008.1.2.4.91
fname = test_images / "dicom_file91.dcm"
with pytest.raises(RuntimeError):
iio.imread(fname) # not pixel data
# This one *should* work, but does not, see issue #18
try:
iio.imread(test_images / "dicom_file02.dcm")
except Exception:
pass
def test_progress(examples):
dname1, dname2, fname1, fname2 = examples
iio.imread(fname1, progress=True)
iio.imread(fname1, progress=core.StdoutProgressIndicator("test"))
iio.imread(fname1, progress=None)
with pytest.raises(ValueError):
iio.imread(fname1, progress=3)
def test_different_read_modes(examples):
dname1, dname2, fname1, fname2 = examples
for fname, dname, n in [(fname1, dname1, 1), (fname2, dname2, 2)]:
# Test imread()
im = iio.imread(fname)
assert isinstance(im, np.ndarray)
assert im.shape == (512, 512)
# Test mimread()
ims = iio.mimread(fname)
assert isinstance(ims, list)
assert ims[0].shape == im.shape
assert len(ims) > 1
#
ims2 = iio.mimread(dname, format="DICOM")
assert len(ims) == len(ims2)
# Test volread()
vol = iio.volread(dname, format="DICOM")
assert vol.ndim == 3
assert vol.shape[0] > 10
assert vol.shape[1:] == (512, 512)
#
vol2 = iio.volread(fname) # fname works as well
assert (vol == vol2).all()
# Test mvolread()
vols = iio.mvolread(dname, format="DICOM")
assert isinstance(vols, list)
assert len(vols) == n
assert vols[0].shape == vol.shape
assert sum([v.shape[0] for v in vols]) == len(ims)
def test_different_read_modes_with_readers(examples):
dname1, dname2, fname1, fname2 = examples
for fname, dname, n in [(fname1, dname1, 1), (fname2, dname2, 2)]:
# Test imread()
R = iio.read(fname, "DICOM", "i")
assert len(R) == 1
assert isinstance(R.get_meta_data(), dict)
assert isinstance(R.get_meta_data(0), dict)
# Test mimread()
R = iio.read(fname, "DICOM", "I")
if n == 1:
assert len(R) > 10
else:
assert len(R) == 20 + 25
assert isinstance(R.get_meta_data(), dict)
assert isinstance(R.get_meta_data(0), dict)
# Test volread()
R = iio.read(fname, "DICOM", "v")
assert len(R) == n # we ask for one, but get an honest number
assert isinstance(R.get_meta_data(), dict)
assert isinstance(R.get_meta_data(0), dict)
# Test mvolread()
R = iio.read(fname, "DICOM", "V")
assert len(R) == n
assert isinstance(R.get_meta_data(), dict)
assert isinstance(R.get_meta_data(0), dict)
# Touch DicomSeries objects
assert repr(R._series[0])
assert R._series[0].description
assert len(R._series[0].sampling) == 3
R = iio.read(fname, "DICOM", "?")
with pytest.raises(RuntimeError):
R.get_length()
def test_v3_reading(test_images):
# this is a regression test for
# https://github.com/imageio/imageio/issues/862
expected = iio.imread(test_images / "dicom_file01.dcm")
actual = iio3.imread(test_images / "dicom_file01.dcm")
assert np.allclose(actual, expected)
def test_contiguous_dicom_series(test_images, tmp_path):
# this is a regression test for
# https://github.com/imageio/imageio/issues/1067
fname = test_images / "dicom_issue_1067.zip"
with ZipFile(fname) as zip_ref:
zip_ref.extractall(tmp_path)
dname = tmp_path / "modified_dicom_sample1"
ims = iio.volread(dname, "DICOM")
assert ims.shape == (25, 512, 512)
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