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test_dicom.py
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test_dicom.py
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""" Test DICOM functionality.
"""
import os
from zipfile import ZipFile
import numpy as np
from pytest import raises
from imageio.testing import run_tests_if_main, get_test_dir, need_internet
import imageio
from imageio import core
from imageio.core import get_remote_file
test_dir = get_test_dir()
_prepared = None
def _prepare():
""" Create two dirs, one with one dataset and one with two datasets
"""
need_internet()
global _prepared
if _prepared and os.path.isfile(_prepared[2]):
return _prepared
# Prepare sources
fname1 = get_remote_file('images/dicom_sample1.zip')
fname2 = get_remote_file('images/dicom_sample2.zip')
dname1 = os.path.join(test_dir, 'dicom_sample1')
dname2 = os.path.join(test_dir, 'dicom_sample2')
# Extract zipfiles
z = ZipFile(fname1)
z.extractall(dname1)
z.extractall(dname2)
z = ZipFile(fname2)
z.extractall(dname2)
# Get arbitrary file names
fname1 = os.path.join(dname1, os.listdir(dname1)[0])
fname2 = os.path.join(dname2, os.listdir(dname2)[0])
# Cache and return
_prepared = dname1, dname2, fname1, fname2
return dname1, dname2, fname1, fname2
def test_read_empty_dir():
# Create an empty dir
empty = os.path.join(test_dir, 'empty_dir')
if not os.path.isdir(empty):
os.mkdir(empty)
# Test that no format is found, but no error is raised
request = core.Request(empty, 'ri')
assert imageio.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()
def test_selection():
dname1, dname2, fname1, fname2 = _prepare()
# Test that DICOM can examine file
F = imageio.formats.search_read_format(core.Request(fname1, 'ri'))
assert F.name == 'DICOM'
assert F is imageio.formats['DICOM']
# Test that we cannot save
request = core.Request(os.path.join(test_dir, '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)
raises(Exception, F.get_reader, core.Request(fname2, 'ri'))
# Test special files with other formats
im = imageio.imread(get_remote_file('images/dicom_file01.dcm'))
assert im.shape == (512, 512)
im = imageio.imread(get_remote_file('images/dicom_file03.dcm'))
assert im.shape == (512, 512)
im = imageio.imread(get_remote_file('images/dicom_file04.dcm'))
assert im.shape == (512, 512)
# Expected fails
fname = get_remote_file('images/dicom_file90.dcm')
raises(RuntimeError, imageio.imread, fname) # 1.2.840.10008.1.2.4.91
fname = get_remote_file('images/dicom_file91.dcm')
raises(RuntimeError, imageio.imread, fname) # not pixel data
# This one *should* work, but does not, see issue #18
try:
imageio.imread(get_remote_file('images/dicom_file02.dcm'))
except Exception:
pass
def test_progress():
dname1, dname2, fname1, fname2 = _prepare()
imageio.imread(fname1, progress=True)
imageio.imread(fname1, progress=core.StdoutProgressIndicator('test'))
imageio.imread(fname1, progress=None)
raises(ValueError, imageio.imread, fname1, progress=3)
def test_different_read_modes():
dname1, dname2, fname1, fname2 = _prepare()
for fname, dname, n in [(fname1, dname1, 1), (fname2, dname2, 2)]:
# Test imread()
im = imageio.imread(fname)
assert isinstance(im, np.ndarray)
assert im.shape == (512, 512)
# Test mimread()
ims = imageio.mimread(fname)
assert isinstance(ims, list)
assert ims[0].shape == im.shape
assert len(ims) > 1
#
ims2 = imageio.mimread(dname)
assert len(ims) == len(ims2)
# Test volread()
vol = imageio.volread(dname)
assert vol.ndim == 3
assert vol.shape[0] > 10
assert vol.shape[1:] == (512, 512)
#
vol2 = imageio.volread(fname) # fname works as well
assert (vol == vol2).all()
# Test mvolread()
vols = imageio.mvolread(dname)
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():
dname1, dname2, fname1, fname2 = _prepare()
for fname, dname, n in [(fname1, dname1, 1), (fname2, dname2, 2)]:
# Test imread()
R = imageio.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 = imageio.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 = imageio.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 = imageio.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 = imageio.read(fname, 'DICOM', '?')
raises(RuntimeError, R.get_length)
run_tests_if_main()