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_save_image_stack_with_unique_series_number_based_on_filename(self):
testdatadir = 'test_svimstack2'
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)
io3d.write(data3d, testdatadir + "/{series_number:03d}/soubory{slice_position:07.3f}.tiff")
# second time there should be directory 002/
io3d.write(data3d, testdatadir + "/{series_number:03d}/soubory{slice_position:07.3f}.tiff")
dr = dreader.DataReader()
data3dnew, metadata = dr.Get3DData(
testdatadir + "/002/", 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_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_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_read_data_without_slice_thickness(self):
""" data without SliceThickness
:return:
"""
dr = dreader.DataReader()
data3dnew, metadata = dr.Get3DData(
"~/data/medical/orig/dicom_test_claudio", dataplus_format=False
)
metadata
def runComputation(imageDx, imageDy, imageDz, coloridx, calculateout, V, FV,
input_pkl_file, BORDER_FILE, DIR_O, label):
dr = datareader.DataReader()
datap = dr.Get3DData(input_pkl_file,
qt_app=None,
dataplus_format=True,
gui=False)
if 'segmentation' not in datap.keys():
datap = segmentation_from_data3d(datap, label)
segmentation = datap['segmentation'].astype(np.uint8)
# segmentation = datap['segmentation'][::5,::5,::5]
# segmentation = datap['segmentation'][300:330,300:350,300:350]
# datap['segmentation'] = (segmentation == 1).astype(np.uint8)
# import ipdb; ipdb.set_trace() # noqa BREAKPOINT
# hack kvuli barvam
segmentation[0, 0, 0] = 0
segmentation[0, 0, 1] = 1
datap['segmentation'] = segmentation
logger.debug("unique %s " % (str(np.unique(datap['segmentation']))))
imageHeight, imageWidth = datap['segmentation'][:, :, :].shape[1:3]
# getImageData(INPUT_DIR+str(BEST_IMAGE)+PNG_EXTENSION)
# imageDepth = countFilesInADir(INPUT_DIR)
imageDepth = datap['segmentation'].shape[0]
Nx, Ny, Nz = imageHeight / imageDx, imageWidth / imageDx, imageDepth / imageDz
returnValue = 2
try:
# pixelCalc, centroidsCalc = centroidcalc(INPUT_DIR, BEST_IMAGE, colors)
# centroidsCalc = np.array([0, 1])
centroidsCalc = np.unique(datap['segmentation'])
returnValue = startComputeChains(imageHeight, imageWidth, imageDepth,
imageDx, imageDy, imageDz, Nx, Ny, Nz,
calculateout, BORDER_FILE,
centroidsCalc, coloridx, datap, DIR_O)
except:
exc_type, exc_value, exc_traceback = sys.exc_info()
lines = traceback.format_exception(exc_type, exc_value, exc_traceback)
log(1, ["Error: " + ''.join('!! ' + line for line in lines)
]) # Log it or whatever here
returnValue = 2
tracert.print_exc()
return returnValue
def readData3d(dcmdir):
qt_app = None
if dcmdir is None:
from PyQt5 import QtGui, QtWidgets
#QApplication
qt_app = QtWidgets.QApplication(sys.argv)
# same as data_reader_get_dcmdir_qt
# from PyQt4.QtGui import QFileDialog, QApplication
# dcmdir = QFileDialog.getExistingDirectory(
# caption='Select DICOM Folder',
# options=QFileDialog.ShowDirsOnly)
# dcmdir = "%s" %(dcmdir)
# dcmdir = dcmdir.encode("utf8")
dcmdir = datareader.get_dcmdir_qt(qt_app)
reader = datareader.DataReader()
data3d, metadata = reader.Get3DData(dcmdir, qt_app=None, dataplus_format=False)
return data3d, metadata, qt_app
def read_data_orig_and_seg(inputdata, i):
""" Loads data_orig and data_seg from yaml file
"""
reader = datareader.DataReader()
data3d_a_path = os.path.join(inputdata['basedir'],
inputdata['data'][i]['sliverseg'])
data3d_a, metadata_a = reader.Get3DData(data3d_a_path)
data3d_b_path = os.path.join(inputdata['basedir'],
inputdata['data'][i]['sliverorig'])
data3d_b, metadata_b = reader.Get3DData(data3d_b_path)
# import pdb; pdb.set_trace()
data3d_seg = (data3d_a > 0).astype(np.int8)
data3d_orig = data3d_b
return data3d_orig, data3d_seg, metadata_a['voxelsize_mm']
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 importDataWithGui(self):
oseg = self.oseg
reader = datareader.DataReader()
# seg.data3d, metadata =
datap = reader.Get3DData(oseg.datapath, dataplus_format=True)
# rint datap.keys()
# self.iparams['series_number'] = self.metadata['series_number']
# self.iparams['datapath'] = self.datapath
oseg.import_dataplus(datap)
self.statusBar().showMessage('Ready')
#### SET BUTTONS/MENU ####
#self.btnLoad.show()
#self.btnBackLoad.hide()
self.btnSave.setDisabled(False)
#self.btnSeg.setDisabled(False)
self.btnSegmentation.setDisabled(False)
self.btnCompare.setDisabled(False)
def main():
#logger = logging.getLogger(__name__)
logger = logging.getLogger()
logger.setLevel(logging.WARNING)
ch = logging.StreamHandler()
logger.addHandler(ch)
#logger.debug('input params')
## read confguraton from file, use default values from OrganSegmentation
# input parser
parser = argparse.ArgumentParser(
description=' Show dicom data with overlay')
parser.add_argument('-i',
'--inputdatapath',
default='',
help='path to data dir')
args_obj = parser.parse_args()
args = vars(args_obj)
#print args["arg"]
reader = datareader.DataReader()
data3d, metadata = reader.Get3DData(args['inputdatapath'], qt_app=None)
overlays = reader.GetOverlay()
overlay = np.zeros(data3d.shape, dtype=np.int8)
print "overlays ", overlays.keys()
for key in overlays:
overlay += overlays[key]
#import ipdb; ipdb.set_trace() # BREAKPOINT
pyed = sed3.sed3(data3d, contour=overlay)
pyed.show()
#print savestring
# import pdb; pdb.set_trace()
return
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)
def eval_all_from_dataset_metadata(inputdata, visualization=False,
special_evaluation_function=None):
"""
set metadata
"""
evaluation_all = {
'file1': [],
'file2': [],
'volume1_mm3': [],
'volume2_mm3': [],
'err1_mm3': [],
'err2_mm3': [],
'err1_percent': [],
'err2_percent': [],
'voe': [],
'vd': [],
'avgd': [],
'rmsd': [],
'processing_time': [],
'organ_interactivity_counter': [],
'maxd': []
}
for i in range(0, len(inputdata['data'])):
reader = datareader.DataReader()
data3d_a_path = os.path.join(inputdata['basedir'],
inputdata['data'][i]['sliverseg'])
data3d_a, metadata_a = reader.Get3DData(data3d_a_path, dataplus_format=False)
print("inputdata ", list(inputdata['data'][i].values()))
try:
# if there is defined overlay
data3d_a = reader.get_overlay()[inputdata['data'][i][
'overlay_number']]
logger.info('overlay loaded')
print('overlay loaded')
except:
logger.debug("overlay not loaded")
pass
logger.debug('data A shape ' + str(data3d_a.shape))
data3d_b_path = os.path.join(inputdata['basedir'],
inputdata['data'][i]['ourseg'])
obj_b = misc.obj_from_file(data3d_b_path, filetype='pickle')
# data_b, metadata_b = reader.Get3DData(data3d_b_path)
if 'crinfo' in obj_b.keys():
data3d_b = qmisc.uncrop(obj_b['segmentation'],
obj_b['crinfo'], data3d_a.shape)
else:
data3d_b = obj_b['segmentation']
# import pdb; pdb.set_trace()
# data3d_a = (data3d_a > 1024).astype(np.int8)
data3d_a = (data3d_a > 0).astype(np.int8)
data3d_b = (data3d_b > 0).astype(np.int8)
if visualization:
pyed = sed3.sed3(data3d_a, # + (4 * data3d_b)
contour=data3d_b)
pyed.show()
evaluation_one = compare_volumes(data3d_a, data3d_b,
metadata_a['voxelsize_mm'])
if special_evaluation_function is not None:
evaluation_one.update(
special_evaluation_function(
data3d_a, data3d_b, metadata_a['voxelsize_mm']
))
evaluation_all['file1'].append(data3d_a_path)
evaluation_all['file2'].append(data3d_b_path)
for key in evaluation_one.keys():
if key not in evaluation_all.keys():
evaluation_all[key] = []
evaluation_all[key].append(evaluation_one[key])
# evaluation_all['volume1_mm3'].append(evaluation_one['volume1_mm3'])
# evaluation_all['volume2_mm3'].append(evaluation_one['volume2_mm3'])
# evaluation_all['err1_mm3'].append(evaluation_one['err1_mm3'])
# evaluation_all['err2_mm3'].append(evaluation_one['err2_mm3'])
# evaluation_all['err1_percent'].append(evaluation_one['err1_percent'])
# evaluation_all['err2_percent'].append(evaluation_one['err2_percent'])
# evaluation_all['voe'].append(evaluation_one['voe'])
# evaluation_all['vd'].append(evaluation_one['vd'])
# evaluation_all['avgd'].append(evaluation_one['avgd'])
# evaluation_all['rmsd'].append(evaluation_one['rmsd'])
# evaluation_all['maxd'].append(evaluation_one['maxd'])
if 'processing_time' in obj_b.keys():
# this is only for compatibility with march2014 data
processing_time = obj_b['processing_time']
organ_interactivity_counter = obj_b['organ_interactivity_counter']
else:
try:
processing_time = obj_b['processing_information']['organ_segmentation']['processing_time'] # noqa
organ_interactivity_counter = obj_b['processing_information']['organ_segmentation'][
'organ_interactivity_counter'] # noqa
except:
processing_time = 0
organ_interactivity_counter = 0
evaluation_all['processing_time'].append(processing_time)
evaluation_all['organ_interactivity_counter'].append(
organ_interactivity_counter)
return evaluation_all
