def test_save_image_stack(self):
testdatadir = 'test_svimstack'
if os.path.exists(testdatadir):
shutil.rmtree(testdatadir, ignore_errors=True)
szx = 30
szy = 20
szz = 120
data3d = self.generate_waving_data(
szx, szy, szz, value=150, dtype=np.uint8)
# import sed3
# ed = sed3.sed3(data3d)
# ed.show()
#
dw = dwriter.DataWriter()
dw.save_image_stack(data3d, testdatadir + '/soubory.png')
dr = dreader.DataReader()
data3dnew, metadata = dr.Get3DData(
testdatadir, dataplus_format=False
# 'sample_data/volumetrie/'
)
# import sed3
# ed = sed3.sed3(data3dnew)
# ed.show()
self.assertEqual(
np.sum(np.abs(data3d - data3dnew)),
0
)
shutil.rmtree(testdatadir)
def test_write_and_read(self):
filename = 'test_file.dcm'
data = (np.random.random([30, 100, 120]) * 30).astype(np.int16)
data[0:5, 20:60, 60:70] += 30
metadata = {'voxelsize_mm': [1, 2, 3]}
dw = dwriter.DataWriter()
logger.debug(filename)
dw.Write3DData(data, filename, filetype='dcm', metadata=metadata)
dr = dreader.DataReader()
newdata, newmetadata = dr.Get3DData(filename, dataplus_format=False)
# print("meta ", metadata)
# print("new meta ", newmetadata)
# hack with -1024, because of wrong data reading
self.assertEqual(data[10, 10, 10], newdata[10, 10, 10])
self.assertEqual(data[2, 10, 1], newdata[2, 10, 1])
# print(metadata["voxelsize_mm"])
# print(newmetadata["voxelsize_mm"])
self.assertEqual(metadata['voxelsize_mm'][0],
newmetadata['voxelsize_mm'][0])
self. assertEqual(metadata['voxelsize_mm'][1],
newmetadata['voxelsize_mm'][1])
self.assertEqual(metadata['voxelsize_mm'][2],
newmetadata['voxelsize_mm'][2])
os.remove(filename)
def test_write_and_read(self):
filename = 'test_file.dcm'
data = (np.random.random([30, 100, 120]) * 30).astype(np.int16)
data[0:5, 20:60, 60:70, ] += 30
metadata = {'voxelsize_mm': [1, 2, 3]}
dw = dwriter.DataWriter()
dw.Write3DData(data, filename, filetype='dcm', metadata=metadata)
dr = dreader.DataReader()
newdata, newmetadata = dr.Get3DData(filename)
# print "meta ", metadata
# print "new meta ", newmetadata
# hack with -1024, because of wrong data reading
self. assertEqual(data[10, 10, 10], newdata[10, 10, 10])
self. assertEqual(data[2, 10, 1], newdata[2, 10, 1])
self. assertEqual(
metadata['voxelsize_mm'][0], newmetadata['voxelsize_mm'][0])
# @TODO there is a bug in SimpleITK. slice voxel size must be same
# self. assertEqual(metadata['voxelsize_mm'][1],
# newmetadata['voxelsize_mm'][1])
self. assertEqual(
metadata['voxelsize_mm'][2], newmetadata['voxelsize_mm'][2])
os.remove(filename)
def test_add_overlay_to_copied_dir(self):
"""
writes 3d label to copied dicom files
"""
filedir = 'test_outputs_dir'
n_files = 3
# number of tested overlay
i_overlay = 6
if not os.path.exists(filedir):
os.mkdir(filedir)
# open copied data to obtain dcmfilefilelist
dr = dreader.DataReader()
data3d, metadata = dr.Get3DData(
op.join(SAMPLE_DATA_DIR, 'jatra_5mm/'), dataplus_format=False
# 'sample_data/volumetrie/'
)
# for test we are working only with small number of files (n_files)
metadata['dcmfilelist'] = metadata['dcmfilelist'][:n_files]
# create overlay
overlay = np.zeros([n_files, 512, 512], dtype=np.uint8)
overlay[:, 450:500, 30:100] = 1
# if there is more slides, try more complicated overlay
overlay[0, 430:460, 20:110] = 1
overlay[-1:, 470:520, 10:120] = 1
overlays = {i_overlay: overlay}
dw = dwriter.DataWriter()
dw.DataCopyWithOverlay(metadata['dcmfilelist'], filedir, overlays)
# try read written data
dr = dreader.DataReader()
newdata, newmetadata = dr.Get3DData(filedir, dataplus_format=False)
# test old function
newoverlay = dr.GetOverlay()
newoverlay = dr.get_overlay()
self.assertTrue((newoverlay[i_overlay] == overlays[i_overlay]).all())
# os.remove(filename)
shutil.rmtree(filedir)
def test_write_dicom_from_scratch(self):
"""
Reads dicom data and from slices and stores into one Dicom file. This
file is then readed and compared with input data.
"""
filename = 'tests/output_dcm3d.dcm'
dr = dreader.DataReader()
path_to_data = op.join(SAMPLE_DATA_DIR, 'jatra_5mm')
logger.debug(SAMPLE_DATA_DIR)
logger.debug(path_to_data)
data3d, metadata = dr.Get3DData(
path_to_data, dataplus_format=False
# 'sample_data/volumetrie/'
)
dw = dwriter.DataWriter()
dw.Write3DData(data3d, filename, filetype='dcm', metadata=metadata)
data3d_n, metadata_n = dr.Get3DData(filename, dataplus_format=False)
self.assertEqual(data3d[10, 11, 12], data3d_n[10, 11, 12])
os.remove(filename)
def test_save_image_stack_with_writer(self):
testdatadir = 'test_svimstack_with_writer'
data3d = self.generate_waving_data(
szx=30, szy=20, szz=10, value=150, dtype=np.uint8)
dw = dwriter.DataWriter()
dw.Write3DData(data3d, testdatadir + '/soubory.png',
filetype='image_stack')
dr = dreader.DataReader()
data3dnew, metadata = dr.Get3DData(
testdatadir, dataplus_format=False
)
# import sed3
# ed = sed3.sed3(data3dnew)
# ed.show()
self.assertEqual(
np.sum(np.abs(data3d - data3dnew)),
0
)
shutil.rmtree(testdatadir)
def test_add_overlay_and_read_one_file_with_overlay(self):
filename = 'tests_outputs/test_file.dcm'
filedir = os.path.dirname(filename)
# number of tested overlay
i_overlay = 6
if not os.path.exists('tests_outputs'):
os.mkdir('tests_outputs')
data = (np.random.random([30, 100, 120]) * 30).astype(np.int16)
data[0:5, 20:60, 60:70] += 30
overlay = np.zeros([512, 512], dtype=np.uint8)
overlay[450:500, 30:100] = 1
# metadata = {'voxelsize_mm': [1, 2, 3]}
dw = dwriter.DataWriter()
dw.add_overlay_to_slice_file(
# 'sample_data/jatra_5mm/IM-0001-0019.dcm',
op.join(SAMPLE_DATA_DIR, 'volumetrie/volumetry_slice.DCM'),
overlay,
i_overlay,
filename
)
# import ipdb; ipdb.set_trace()
# print("asdfa")
dr = dreader.DataReader()
newdata, newmetadata = dr.Get3DData('tests_outputs', dataplus_format=False)
newoverlay = dr.get_overlay()
# print(newoverlay)
# ed = pyed.py3DSeedEditor(newoverlay[6])
# ed.show()
# print("oioiu")
self.assertTrue((newoverlay[i_overlay] == overlay).all())
# os.remove(filename)
shutil.rmtree(filedir)
def test_write_dcm_slices_datap(self):
# Z nějakého důvodu plošné snímky neukládají tloušťku řezu. Jinak by test měl fungovat.
datadir = "test_dcm"
filename = datadir + '/test_file{slice_position:07.3f}.dcm'
data = (np.random.random([30, 100, 120]) * 30).astype(np.int16)
data[0:5, 20:60, 60:70] += 30
datap = {'voxelsize_mm': [1, 2, 3], "data3d": data}
dw = dwriter.DataWriter()
dw.Write3DData(datap, filename, filetype='auto')
dr = dreader.DataReader()
newdata, newmetadata = dr.Get3DData(datadir, dataplus_format=False)
# print("meta ", metadata)
# print("new meta ", newmetadata)
# hack with -1024, because of wrong data reading
self.assertEqual(data[10, 10, 10], newdata[10, 10, 10])
self.assertEqual(data[2, 10, 1], newdata[2, 10, 1])
self.assertEqual(datap['voxelsize_mm'][0],
newmetadata['voxelsize_mm'][0])
# os.removedirs()
shutil.rmtree(datadir)
def test_add_overlay_and_read_one_file_with_overlay(self):
filename = 'tests_outputs/test_file.dcm'
filedir = os.path.dirname(filename)
# number of tested overlay
i_overlay = 6
if not os.path.exists('tests_outputs'):
os.mkdir('tests_outputs')
data = (np.random.random([30, 100, 120]) * 30).astype(np.int16)
data[0:5, 20:60, 60:70] += 30
overlay = np.zeros([512, 512], dtype=np.uint8)
overlay[450:500, 30:100] = 1
# metadata = {'voxelsize_mm': [1, 2, 3]}
dw = dwriter.DataWriter()
dw.add_overlay_to_slice_file(
# 'sample_data/jatra_5mm/IM-0001-0019.dcm',
lisa.dataset.join_sdp('volumetrie/volumetry_slice.DCM'),
overlay,
i_overlay,
filename
)
dr = dreader.DataReader()
newdata, newmetadata = dr.Get3DData('tests_outputs')
newoverlay = dr.GetOverlay()
# print overlay
# ed = pyed.sed3(newoverlay[6])
# ed.show()
self.assertTrue((newoverlay[i_overlay] == overlay).all())
# os.remove(filename)
shutil.rmtree(filedir)