def main():
# logger = logging.getLogger()
logger.setLevel(logging.WARNING)
ch = logging.StreamHandler()
logger.addHandler(ch)
# logger.debug('input params')
# input parser
parser = argparse.ArgumentParser(description='\
3D visualization of segmentation\n\
\npython show_segmentation.py\n\
\npython show_segmentation.py -i resection.pkl -l 2 3 4 -d 4')
parser.add_argument('-i',
'--inputfile',
default='organ.pkl',
help='input file')
parser.add_argument('-o',
'--outputfile',
default='~/lisa_data/mesh_geom.vtk',
help='output file')
parser.add_argument('-d',
'--degrad',
type=int,
default=4,
help='data degradation, default 4')
parser.add_argument(
'-r',
'--resize',
type=float,
default=None,
help='resize voxel to defined size in milimeters, default is None')
parser.add_argument('-l',
'--label',
type=int,
metavar='N',
nargs='+',
default=[1],
help='segmentation labels, default 1')
args = parser.parse_args()
# data = misc.obj_from_file(args.inputfile, filetype='pickle')
import io3d
data = io3d.read(args.inputfile, dataplus_format=True)
# args.label = np.array(eval(args.label))
# print args.label
# import pdb; pdb.set_trace()
ds = np.zeros(data['segmentation'].shape, np.bool)
for i in range(0, len(args.label)):
ds = ds | (data['segmentation'] == args.label[i])
outputfile = os.path.expanduser(args.outputfile)
showSegmentation(ds,
degrad=args.degrad,
voxelsize_mm=data['voxelsize_mm'],
vtk_file=outputfile,
resize_mm=args.resize)
def main():
parser = argparse.ArgumentParser(
description='data3dviewer - Viewer for 3d data (mostly from CT)')
parser.add_argument('path', help='Path to directory with 3d data')
parser.add_argument('-d',
'--debug',
action='store_true',
help='Debug mode')
args = parser.parse_args()
logging.basicConfig(stream=sys.stdout)
logger = logging.getLogger()
logger.setLevel(logging.WARNING)
if args.debug:
logger.setLevel(logging.DEBUG)
# load dicom data
logger.info("Loading 3d data from: %s" % os.path.abspath(args.path))
datap = io3d.read(os.path.abspath(args.path), dataplus_format=True)
data3d = datap["data3d"]
logger.info("voxelsize: %s" % str(datap["voxelsize_mm"]))
# temporary fix for io3d <-512;511> value range bug
# this is caused by hardcoded slope 0.5 in dcmreader
if np.min(data3d) >= -512: data3d = data3d * 2
# display data
ed = sed3.sed3(data3d)
ed.show()
def add_data_file(self, filename):
import io3d
datap = io3d.read(filename, dataplus_format=True)
if not 'segmentation' in datap.keys():
datap['segmentation'] = datap['data3d']
self.add_data(**datap)
def get_old(dataset_label, data_id, destination_dir=None):
"""Get the 3D data from specified dataset with specified id.
Download data if necessary.
:param dataset_label:
:param data_id: integer or wildcards file pattern
:param destination_dir:
:return:
"""
# TODO implement
if destination_dir is None:
destination_dir = op.join(dataset_path(get_root=True), "medical", "orig")
destination_dir = op.expanduser(destination_dir)
data_url, url, expected_hash, hash_path, relative_output_path = get_dataset_meta(
dataset_label
)
paths = glob.glob(os.path.join(destination_dir, hash_path))
paths.sort()
import fnmatch
print(paths)
print(data_id)
pathsf = fnmatch.filter(paths, data_id)
print(pathsf)
datap = io3d.read(pathsf[0], dataplus_format=True)
return datap
def setUpClass(cls):
datap = io3d.read(
io3d.datasets.join_path(TEST_DATA_DIR, "PATIENT_DICOM"),
dataplus_format=True)
cls.obj = bodynavigation.BodyNavigation(datap["data3d"], datap["voxelsize_mm"])
cls.data3d = datap["data3d"]
cls.shape = datap["data3d"].shape
def main():
import io3d
logger = logging.getLogger()
logger.setLevel(logging.DEBUG)
ch = logging.StreamHandler()
logger.addHandler(ch)
# create file handler which logs even debug messages
# fh = logging.FileHandler('log.txt')
# fh.setLevel(logging.DEBUG)
# formatter = logging.Formatter(
# '%(asctime)s - %(name)s - %(levelname)s - %(message)s')
# fh.setFormatter(formatter)
# logger.addHandler(fh)
# logger.debug('start')
# input parser
parser = argparse.ArgumentParser(description=__doc__)
parser.add_argument(
'-i',
'--inputfile',
default=None,
# required=True,
help='input file')
parser.add_argument(
'--dict',
default="{'jatra':2, 'ledviny':7}",
# required=True,
help='input dict')
parser.add_argument('-d',
'--debug',
action='store_true',
help='Debug mode')
args = parser.parse_args()
if args.debug:
ch.setLevel(logging.DEBUG)
app = QtGui.QApplication(sys.argv)
# w = QtGui.QWidget()
# w = DictEdit(dictionary={'jatra':2, 'ledviny':7})
if args.inputfile is None:
datap = {'segmentation': None}
else:
datap = io3d.read(args.inputfile, dataplus_format=True)
if not 'segmentation' in datap.keys():
datap['segmentation'] = datap['data3d']
# import ipdb; ipdb.set_trace()
w = ShowSegmentationWidget(show_load_button=True, **datap)
# w = SelectLabelWidget(segmentation=datap["segmentation"])
w.resize(250, 150)
w.move(300, 300)
w.setWindowTitle('Simple')
w.show()
sys.exit(app.exec_())
def setUpClass(cls):
datap = io3d.read(io3d.datasets.join_path(TEST_DATA_DIR,
"PATIENT_DICOM"),
dataplus_format=True)
cls.obj = bodynavigation.BodyNavigation(datap["data3d"],
datap["voxelsize_mm"])
cls.data3d = datap["data3d"]
cls.shape = datap["data3d"].shape
def test_read_dataset_where_is_voxelsize_equal_zero(self):
"""
voxelsize_mm[0] should be grater than zero
"""
dcmdir = r"E:\data\medical\orig\ct_porcine_liver\P03\23-9-13_23913\Makro\VEN_ABDOMEN_5_0_B31S_0002"
# dcmdir = r"E:\data\medical\orig\ct porctine liver\P01\29-8-12-a\Nejlep_rozli_nevycistene"
datap = io3d.read(dcmdir)
self.assertGreater(datap["voxelsize_mm"][0], 0)
def test_read_dataset_where_is_voxelsize_equal_zero(self):
"""
voxelsize_mm[0] should be grater than zero
"""
dcmdir = r"E:\data\medical\orig\ct_porcine_liver\P03\23-9-13_23913\Makro\VEN_ABDOMEN_5_0_B31S_0002"
# dcmdir = r"E:\data\medical\orig\ct porctine liver\P01\29-8-12-a\Nejlep_rozli_nevycistene"
datap = io3d.read(dcmdir)
self.assertGreater(datap["voxelsize_mm"][0], 0)
def test_read_mhd_and_write_pklz(self):
"""
test data on sliver dataset
:return:
"""
infn = op.join(op.expanduser(io3d.datasets.local_dir), "sliver07/training/liver-orig001.mhd")
datap = io3d.read(infn, dataplus_format=True)
datap["segmentation"] = np.zeros_like(datap["data3d"], dtype=np.uint8)
io3d.write(datap, path="test_mhd.pklz")
def setUpClass(cls):
# hide io3d logger
logging.getLogger("io3d").setLevel(logging.WARNING)
# init dataset information
cls.dataset = loadDatasetsInfo()[DATASET_NAME]
cls.dataset = joinDatasetPaths(cls.dataset, ROOT_PATH)
# init OrganDetection object
datap = io3d.read(cls.dataset["CT_DATA_PATH"], dataplus_format=True)
cls.obj = OrganDetection(datap["data3d"], datap["voxelsize_mm"])
def test_read_mhd_and_write_pklz(self):
"""
test data on sliver dataset
:return:
"""
# infn = op.join(op.expanduser(io3d.datasets.local_dir), "sliver07/training/liver-orig001.mhd")
infn = io3d.datasets.join_path("liver-orig001.mhd")
datap = io3d.read(infn, dataplus_format=True)
datap["segmentation"] = np.zeros_like(datap["data3d"], dtype=np.uint8)
io3d.write(datap, path="test_mhd.pklz")
def setUpClass(cls):
# hide io3d logger
logging.getLogger("io3d").setLevel(logging.WARNING)
# init dataset information
cls.dataset = loadDatasetsInfo()[DATASET_NAME]
cls.dataset = joinDatasetPaths(cls.dataset, ROOT_PATH)
# init OrganDetection object
datap = io3d.read(cls.dataset["CT_DATA_PATH"], dataplus_format=True)
cls.obj = OrganDetection(datap["data3d"], datap["voxelsize_mm"])
def test_read_and_write_dataset_to_fix_problem_with_out_of_memory(self):
"""
voxelsize_mm[0] should be grater than zero
"""
dcmdir = r"E:\data\medical\orig\ct_porcine_liver\P01\29-8-12-a\MIkroCT-nejhrubsi_rozliseni\DICOM_liver-1st-important_Macro_pixel-size53.0585um"
# dcmdir = r"E:\tmp\data\medical\orig\ct_porcine_liver\P01\29-8-12-a\MIkroCT-nejhrubší rozlišení\DICOM_liver-1st-important_Macro_pixel-size53.0585um"
# dcmdir = r"E:\data\medical\orig\ct porctine liver\P01\29-8-12-a\Nejlep_rozli_nevycistene"
datap = io3d.read(dcmdir)
io3d.write(datap, "~/tmp/nejhrubsi.mhd")
self.assertGreater(datap["voxelsize_mm"][0], 0)
def test_read_and_write_dataset_to_fix_problem_with_out_of_memory(self):
"""
voxelsize_mm[0] should be grater than zero
"""
dcmdir = r"E:\data\medical\orig\ct_porcine_liver\P01\29-8-12-a\MIkroCT-nejhrubsi_rozliseni\DICOM_liver-1st-important_Macro_pixel-size53.0585um"
# dcmdir = r"E:\tmp\data\medical\orig\ct_porcine_liver\P01\29-8-12-a\MIkroCT-nejhrubší rozlišení\DICOM_liver-1st-important_Macro_pixel-size53.0585um"
# dcmdir = r"E:\data\medical\orig\ct porctine liver\P01\29-8-12-a\Nejlep_rozli_nevycistene"
datap = io3d.read(dcmdir)
io3d.write(datap, "~/tmp/nejhrubsi.mhd")
self.assertGreater(datap["voxelsize_mm"][0], 0)
def get(dataset_label, series_number=None, *args, **kwargs):
"""
:param dataset_label: label from data_urls
:param series_number: Series identification in study.
:param args:
:param kwargs:
:return:
"""
# relative path in the datasets
relative_path_extracted_from_data_urls = ""
datapath = join_path(
relative_path_extracted_from_data_urls, "medical", "data", get_root=True
)
# read 3D data from datapath
datap = io3d.read(
datapath, series_number=series_number, dataplus_format=True, *args, **kwargs
)
return datap
def loadscan2(scannum):
'''
Load a scan along with its labels (from second dataset).
Parameters
scannum - id of the loaded scan
----
returns [[slice, label], [slice, label], ...]
'''
datap = io3d.read(
f'data/medical/orig/sliver07/training/liver-orig0{str(scannum).zfill(2)}.mhd'
)
data3d = datap['data3d']
scan = []
i = 1
for slice in data3d:
id = getsliceid2(scannum, i)
scan.append([slice, id])
i += 1
return scan
def loadscan(scannum):
'''
Load a scan along with its labels (from Ircad dataset).
Parameters
scannum - id of the loaded scan
----
returns [[slice, label], [slice, label], ...]
'''
pth = io3d.datasets.join_path(
'medical/orig/3Dircadb1.{}/PATIENT_DICOM/'.format(scannum),
get_root=True)
datap = io3d.read(pth)
data3d = datap['data3d']
scan = []
i = 1
for slice in data3d:
id = getsliceid(scannum, i)
scan.append([slice, id])
i += 1
return scan
def main():
logger = logging.getLogger()
logger.setLevel(logging.WARNING)
ch = logging.StreamHandler()
logger.addHandler(ch)
# logger.debug('input params')
# input parser
parser = argparse.ArgumentParser(description='\
3D visualization of segmentation\n\
\npython show_segmentation.py\n\
\npython show_segmentation.py -i resection.pkl -l 2 3 4 -d 4')
parser.add_argument('-i',
'--inputfile',
default="organ.pklz",
help='input file')
parser.add_argument('-o',
'--outputfile',
default='~/lisa_data/mesh_geom.vtk',
help='output file')
parser.add_argument('-d',
'--degrad',
type=int,
default=4,
help='data degradation, default 4')
parser.add_argument(
'-r',
'--resize',
type=float,
default=None,
help='resize voxel to defined size in milimeters, default is None')
parser.add_argument(
'-rvn',
'--resize-voxel-number',
type=float,
default=None,
help='resize voxel to defined number of voxels, default is None')
parser.add_argument('-l',
'--label',
type=int,
metavar='N',
nargs='+',
default=[1],
help='segmentation labels, default 1')
args = parser.parse_args()
# data = misc.obj_from_file(args.inputfile, filetype='pickle')
# if args.inputfile is None:
# ds = None
# data = {
# "voxelsize_mm": [1, 1, 1]
# }
# else:
import io3d
data = io3d.read(args.inputfile, dataplus_format=True)
# args.label = np.array(eval(args.label))
# print args.label
if "segmentation" in data.keys() and np.sum(data["segmentation"] > 0):
segmentation_key = "segmentation"
else:
segmentation_key = "data3d"
# import pdb; pdb.set_trace()
_stats(data[segmentation_key])
ds = select_labels(data[segmentation_key], args.label)
# ds = ds.astype("uint8")
# tonzero_voxels_number = np.sum(ds != 0)
# if nonzero_voxels_number == 0:
# ds = data["data3d"] > 0
outputfile = os.path.expanduser(args.outputfile)
showSegmentation(ds,
degrad=args.degrad,
voxelsize_mm=data['voxelsize_mm'],
vtk_file=outputfile,
resize_mm=args.resize,
resize_voxel_number=args.resize_voxel_number)
def test_idx_data(self):
io3d.read("/home/mjirik/data/medical/orig/cvd-matrm3/microscopy_data/MM358-001-uint8.idx")
parser = argparse.ArgumentParser(description='Registration data from different files')
parser.add_argument('-d', '--debug', action='store_true',
help='run in debug mode')
parser.add_argument('-i', '--inputfile', default=None, nargs="N",
help='input file or directory with data')
parser.add_argument('-o', '--outpufile', default=None,
help='output file or directory with data')
args = parser.parse_args()
if args.debug:
logger.setLevel(logging.DEBUG)
for fn in args.inputfile:
datap = io3d.read(fn)
# pyed = sed3.sed3(datap['data3d'], contour=datap['segmentation'] == datap['slab']['porta'])
# pyed.show()
#pyed = sed3.sed3(data['segmentation'])
#pyed.show()
# Uvolneni pameti
if args.outputfile == None:
io3d.write(datap_out, args.outpufile)
def test_read_python27_pickle(self):
import io3d
datap = io3d.read(io3d.datasets.join_path("exp_small", "seeds", "org-liver-orig003-seeds.pklz"), dataplus_format=True)
self.assertTrue("segmentation" in datap)
parser.add_argument('-d',
'--debug',
action='store_true',
help='run in debug mode')
parser.add_argument('-i',
'--inputfile',
default=None,
nargs="N",
help='input file or directory with data')
parser.add_argument('-o',
'--outpufile',
default=None,
help='output file or directory with data')
args = parser.parse_args()
if args.debug:
logger.setLevel(logging.DEBUG)
for fn in args.inputfile:
datap = io3d.read(fn)
# pyed = sed3.sed3(datap['data3d'], contour=datap['segmentation'] == datap['slab']['porta'])
# pyed.show()
#pyed = sed3.sed3(data['segmentation'])
#pyed.show()
# Uvolneni pameti
if args.outputfile == None:
io3d.write(datap_out, args.outpufile)
def load3DData(path):
return io3d.read(path)[0]
def test_idx_data(self):
io3d.read(
"/home/mjirik/data/medical/orig/cvd-matrm3/microscopy_data/MM358-001-uint8.idx"
)
def test_read_python27_pickle(self):
import io3d
datap = io3d.read(io3d.datasets.join_path(
"exp_small", "seeds", "org-liver-orig003-seeds.pklz"),
dataplus_format=True)
self.assertTrue("segmentation" in datap)
def test_read_big_big_data(self):
"""
files in nejlepsi_rozli_nevycistene
"""
dcmdir = r"E:\data\medical\orig\ct_porcine_liver\P01\29-8-12-a\Nejlep_rozli_nevycistene"
io3d.read(dcmdir)
'-i', '--inputfile',
default='organ.pkl',
help='input file')
parser.add_argument(
'-o', '--outputfile',
default='~/lisa_data/mesh_geom.vtk',
help='output file')
parser.add_argument(
'-d', '--degrad', type=int,
default=4,
help='data degradation, default 4')
parser.add_argument(
'-l', '--label', type=int, metavar='N', nargs='+',
default=[1],
help='segmentation labels, default 1')
args = parser.parse_args()
# data = misc.obj_from_file(args.inputfile, filetype='pickle')
import io3d
data = io3d.read(args.inputfile, dataplus_format=True)
# args.label = np.array(eval(args.label))
# print args.label
# import pdb; pdb.set_trace()
ds = np.zeros(data['segmentation'].shape, np.bool)
for i in range(0, len(args.label)):
ds = ds | (data['segmentation'] == args.label[i])
outputfile = os.path.expanduser(args.outputfile)
showSegmentation(ds, degrad=args.degrad, voxelsize_mm=data['voxelsize_mm'], vtk_file=outputfile)
def test_read_big_big_data(self):
"""
files in nejlepsi_rozli_nevycistene
"""
dcmdir = r"E:\data\medical\orig\ct_porcine_liver\P01\29-8-12-a\Nejlep_rozli_nevycistene"
io3d.read(dcmdir)
'--inputfile',
default=None,
help='input file or directory with data')
args = parser.parse_args()
if args.debug:
logger.setLevel(logging.DEBUG)
defaultoutputfile = "vessels.pkl"
if args.defaultoutputfile:
args.outputfile = defaultoutputfile
#else:
#dcm_read_from_dir('/home/mjirik/data/medical/data_orig/46328096/')
#data3d, metadata = dcmreaddata.dcm_read_from_dir()
datap = io3d.read(args.inputfile)
import sed3
# pyed = sed3.sed3(oseg.orig_scale_segmentation)
#pyed.show()
# information about crop
#cri = oseg.crinfo
#oseg.data3d = oseg.data3d[cri[0][0]:cri[0][1],cri[1][0]:cri[1][1],cri[2][0]:cri[2][1]]
#pyed = sed3.sed3(oseg.data3d, contour = oseg.orig_scale_segmentation)
print('slab', datap['slab'])
#import ipdb; ipdb.set_trace() # BREAKPOINT
#pyed = sed3.sed3(data['data3d'], contour = data['segmentation'])
#pyed.show()
#import pdb; pdb.set_trace()
