def test_save_image_stack_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)
# import sed3
# ed = sed3.sed3(data3d)
# ed.show()
#
io3d.write(data3d, testdatadir + "/soubory{:04d}.tiff")
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_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_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)
# import sed3
# ed = sed3.sed3(data3d)
# ed.show()
#
io3d.write(data3d, testdatadir + "/soubory{:04d}.tiff")
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_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_write_single_dicom(self):
filename = 'tests_outputs/single_test_file.dcm'
filedir = os.path.dirname(filename)
data3d = np.zeros([10,10,10], dtype=np.uint8)
data3d [1:, 5, 3:9] = 124
data3d [3:, 2:7, 4] = 60
io3d.write(data3d, filename)
os.remove(filename)
def test_write_single_dicom(self):
filename = 'tests_outputs/single_test_file.dcm'
filedir = os.path.dirname(filename)
data3d = np.zeros([10,10,10], dtype=np.uint8)
data3d [1:, 5, 3:9] = 124
data3d [3:, 2:7, 4] = 60
io3d.write(data3d, filename)
os.remove(filename)
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 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_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 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_io3d(self):
import io3d
data3d = np.zeros([10, 10, 10])
segmentation = np.zeros([10, 10, 10])
data3d[2:7, :3:5, :6] = 100
datap = {
"data3d": data3d,
# "segmentation": segmentation,
"voxelsize_mm": [1, 1, 1]
}
io3d.write(datap, "file1.pklz")
def test_save_big_data(self):
output_filename = "~/tmp/big_data.mhd"
if op.exists(op.expanduser(output_filename)):
os.remove(op.expanduser(output_filename))
data3d = np.zeros([1024, 1024, 1024], dtype=np.uint16)
voxelsize_mm = [0.5, 0.5, 0.5]
datap = dict(data3d=data3d, voxelsize_mm=voxelsize_mm)
io3d.write(datap, output_filename)
self.assertTrue(op.exists(op.expanduser(output_filename)))
# clean
if op.exists(op.expanduser(output_filename)):
os.remove(op.expanduser(output_filename))
def test_save_big_data(self):
output_filename = "~/tmp/big_data.mhd"
if op.exists(op.expanduser(output_filename)):
os.remove(op.expanduser(output_filename))
data3d = np.zeros([1024, 1024, 1024], dtype=np.uint16)
voxelsize_mm = [0.5, 0.5, 0.5]
datap = dict(data3d=data3d, voxelsize_mm=voxelsize_mm)
io3d.write(datap, output_filename)
self.assertTrue(op.exists(op.expanduser(output_filename)))
# clean
if op.exists(op.expanduser(output_filename)):
os.remove(op.expanduser(output_filename))
def saveVolumeToFile(self, filename="output{:06d}.jpg"):
if self.data3d is None:
self.generate_volume()
# self.tvgvol.saveToFile(filename)
import io3d
import io3d.misc
import numpy as np
data = {
'data3d': self.data3d.astype(np.uint8), #* self.output_intensity,
'voxelsize_mm': self.voxelsize_mm,
# 'segmentation': np.zeros_like(self.data3d, dtype=np.int8)
}
io3d.write(data, filename)
def test_synthetic_volumetric_data_generation():
"""
Generovani umeleho stromu do 3D a jeho evaluace.
V testu dochazi ke kontrole predpokladaneho objemu a deky cev
"""
# from skelet3d.tree import TreeGenerator
# from fibrous.tree import TubeSkeletonBuilder as TreeGenerator
# from fibrous.tree import TreeBuilder as TreeGenerator
from fibrous.tb_volume import TBVolume as TreeGenerator
# print("zacatek podezreleho testu")
# import segmentation
# import misc
# generate 3d data from yaml for testing
tvg = TreeGenerator()
yaml_path = os.path.join(path_to_script, "./hist_stats_test.yaml")
tvg.importFromYaml(yaml_path)
tvg.set_area_sampling(voxelsize_mm=[1, 1, 1], shape=[100, 101, 102])
# tvg.voxelsize_mm = [1, 1, 1]
# tvg.shape = [100, 100, 100]
# data3d = tvg.generateTree()
data3d = tvg.buildTree()
assert data3d.shape[0] == 100
assert data3d.shape[1] == 101
assert data3d.shape[2] == 102
# plt.imshow(data3d[:,:,50])
# plt.colorbar()
# plt.show()
io3d.write(data3d.astype(np.uint8), path="./slice{:04d}.jpg")
# self.assertEqual(data3d.shape[0], 100)
# self.assertEqual(data3d.shape[1], 101)
# self.assertEqual(data3d.shape[2], 102)
tvg = TreeGenerator()
yaml_path = os.path.join(path_to_script, "./hist_stats_test.yaml")
tvg.importFromYaml(yaml_path)
tvg.set_area_sampling(voxelsize_mm=[0.5, 0.5, 0.5], shape=[100, 101, 102])
io3d.write(data3d.astype(np.uint8), path="./ssslice{:04d}.jpg")
def save(self, outputfile, filetype='pklz'):
import io3d
import io3d.misc
import numpy as np
data = {
'data3d': self.data3d.astype(np.uint8), # * self.output_intensity,
'voxelsize_mm': self.voxelsize_mm,
# 'segmentation': np.zeros_like(self.data3d, dtype=np.int8)
}
# data3d = np.zeros([10,10,10])
# segmentation = np.zeros([10,10,10])
#
# data3d [2:7,:3:5, :6] = 100
# datap = {
# "data3d": data3d,
# "segmentation": segmentation,
# "voxelsize_mm": [1,1,1]
# }
# io3d.write(datap, "file1.pklz")
# import ipdb; ipdb.set_trace()
io3d.write(data, outputfile)
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 main():
#logger = logging.getLogger(__name__)
logger = logging.getLogger()
logger.setLevel(logging.WARNING)
ch = logging.StreamHandler()
logger.addHandler(ch)
#logger.debug('input params')
# input parser
parser = argparse.ArgumentParser(description=
'Segmentation of bones, lungs and heart.')
parser.add_argument('-i','--datadir',
default=None,
help='path to data dir')
parser.add_argument('-o','--output',
default=None,
help='output file')
parser.add_argument('-d', '--debug', action='store_true',
help='run in debug mode')
parser.add_argument('-ss', '--segspine', action='store_true',
help='run spine segmentaiton')
parser.add_argument('-sb', '--segbody', action='store_true',
help='run body segmentaiton')
parser.add_argument('-exd', '--exampledata', action='store_true',
help='run unittest')
parser.add_argument('-so', '--show_output', action='store_true',
help='Show output data in viewer')
args = parser.parse_args()
if args.debug:
logger.setLevel(logging.DEBUG)
if args.exampledata:
args.dcmdir = '../sample_data/liver-orig001.raw'
# if dcmdir == None:
#else:
#dcm_read_from_dir('/home/mjirik/data/medical/data_orig/46328096/')
#data3d, metadata = dcmr.dcm_read_from_dir(args.dcmdir)
import io3d
data3d , metadata = io3d.datareader.read(args.datadir)
bn = BodyNavigation(data3d = data3d,
voxelsize_mm = metadata['voxelsize_mm'],
)
seg = np.zeros(data3d.shape, dtype=np.int8)
#sseg.orientation()
if args.segspine:
seg += bn.get_spine()
if args.segspine:
seg += bn.get_body()
#print ("Data size: " + str(data3d.nbytes) + ', shape: ' + str(data3d.shape) )
#igc = pycut.ImageGraphCut(data3d, zoom = 0.5)
#igc.interactivity()
#igc.make_gc()
#igc.show_segmentation()
# volume
#volume_mm3 = np.sum(oseg.segmentation > 0) * np.prod(oseg.voxelsize_mm)
#pyed = sed3.sed3(oseg.data3d, contour = oseg.segmentation)
#pyed.show()
if args.show_output:
import sed3
sed3.show_slices(data3d, contour=seg)
#savestring = raw_input ('Save output data? (y/n): ')
#sn = int(snstring)
if args.output is not None: # savestring in ['Y','y']:
md = {
'voxelsize_mm': metadata['voxelsize_mm'],
'segmentation': seg, }
io3d.write(data3d, args.output, metadata=md)
nObj=1,
biggestObjects=args.biggest,
# dataFiltering = True,
interactivity=True,
binaryClosingIterations=2,
binaryOpeningIterations=0)
datap['slab']['none'] = 0
datap['slab']['liver'] = 1
datap['slab']['porta'] = 2
#print np.max(output)
#import pdb; pdb.set_trace()
#data = {}
#data['data3d'] = oseg.data3d
#data['crinfo'] = oseg.crinfo
#data['segmentation'] = oseg.segmentation
datap['segmentation'][output] = datap['slab']['porta']
#data['slab'] = slab
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, args.outpufile)