def test_dcmread_get_dcmdir_qt(self):
dirpath = dcmr.get_dcmdir_qt()
#self.data3d, self.metadata = dcmr.dcm_read_from_dir(self.dcmdir)
reader = dcmr.DicomReader(dirpath)
self.data3d = reader.get_3Ddata()
self.metadata = reader.get_metaData()
def setUp(self):
# self.dcmdir = os.path.join(
# path_to_script, '../sample_data/jatra_06mm_jenjatraplus/')
self.dcmdir = os.path.join(path_to_script, '../sample_data/jatra_5mm')
# self.data3d, self.metadata = dcmr.dcm_read_from_dir(self.dcmdir)
reader = dcmr.DicomReader(self.dcmdir)
self.data3d = reader.get_3Ddata()
self.metadata = reader.get_metaData()
def test_dcmread_select_series(self):
#dirpath = dcmr.get_dcmdir_qt()
dirpath = '/home/mjirik/data/medical/data_orig/46328096/'
#dirpath = dcmr.get_dcmdir_qt()
#app = QMainWindow()
reader = dcmr.DicomReader(dirpath,
series_number=55555) #, #qt_app =app)
#app.exit()
self.data3d = reader.get_3Ddata()
self.metadata = reader.get_metaData()
def test_dcmread_series_number(self):
dcmdir = lisa.dataset.join_sdp('jatra_5mm')
#dcmdir = '/home/mjirik/data/medical/data_orig/jatra-kma/jatra_5mm/'
#self.data3d, self.metadata = dcmr.dcm_read_from_dir(self.dcmdir)
# spravne cislo serie je 7
reader = dcmr.DicomReader(dcmdir, series_number=7)
data3d = reader.get_3Ddata()
metadata = reader.get_metaData()
self.assertEqual(data3d.shape[2], 512)
self.assertEqual(metadata['voxelsize_mm'][0], 5)
def test_dcmread(self):
dcmdir = lisa.dataset.join_sdp('jatra_5mm')
#dcmdir = '/home/mjirik/data/medical/data_orig/jatra-kma/jatra_5mm/'
#self.data3d, self.metadata = dcmr.dcm_read_from_dir(self.dcmdir)
reader = dcmr.DicomReader(dcmdir)
data3d = reader.get_3Ddata()
metadata = reader.get_metaData()
#slice size is 512x512
self.assertEqual(data3d.shape[2], 512)
# voxelsize depth = 5 mm
self.assertEqual(metadata['voxelsize_mm'][0], 5)
def test_DicomReader_overlay(self):
#import matplotlib.pyplot as plt
dcmdir = lisa.dataset.join_sdp('volumetrie/')
#dcmdir = '/home/mjirik/data/medical/data_orig/jatra-kma/jatra_5mm/'
#self.data3d, self.metadata = dcmr.dcm_read_from_dir(self.dcmdir)
reader = dcmr.DicomReader(dcmdir)
overlay = reader.get_overlay()
#import pdb; pdb.set_trace()
#plt.imshow(overlay[1][:,:,0])
#plt.show()
self.assertEqual(overlay[1][0, 200, 200], 1)
self.assertEqual(overlay[1][0, 100, 100], 0)
def test_texture_features(self):
"""
Interactivity is stored to file
"""
try:
from pysegbase.seed_editor_qt import QTSeedEditor
except:
logger.warning("Deprecated of pyseg_base as submodule")
from seed_editor_qt import QTSeedEditor
from PyQt4.QtGui import QApplication
from skimage.feature import greycomatrix, greycoprops
import misc
dcmdir = os.path.join(path_to_script, './../sample_data/jatra_5mm')
#gcparams = {'pairwiseAlpha':10, 'use_boundary_penalties':True}
#segparams = {'pairwise_alpha_per':3, 'use_boundary_penalties':True,'boundary_penalties_sigma':200}
#oseg = organ_segmentation.OrganSegmentation(dcmdir, working_voxelsize_mm = 4, segparams=segparams)
#oseg.add_seeds_mm([120],[120],[70], label=1, radius=30)
#oseg.add_seeds_mm([170,220,250],[250,280,200],[70], label=2, radius=30)
reader = dcmr.DicomReader(dcmdir) # , qt_app=qt_app)
data3d = reader.get_3Ddata()
# normalizace na čísla od nuly do 255
data3d = data3d / (2**4)
metadata = reader.get_metaData()
iparams = {}
iparams['series_number'] = reader.series_number
iparams['datadir'] = dcmdir
working_voxelsize_mm = 2
voxelsize_mm = np.array(metadata['voxelsize_mm'])
zoom = voxelsize_mm / working_voxelsize_mm
PATCH_SIZE = 21
PATCH_DIST = 15
shp = data3d.shape
vx, vy, vz = np.mgrid[0:shp[0] - PATCH_SIZE:PATCH_DIST,
0:shp[1] - PATCH_SIZE:PATCH_DIST,
0:shp[2] - PATCH_SIZE:8]
import pdb
pdb.set_trace()
feat = np.zeros(vx.shape)
feat2 = np.zeros(vx.shape)
#vx = vx.reshape(-1)
#vy = vy.reshape(-1)
#vz = vz.reshape(-1)
#for i in range(0,len(vx)):
it = np.nditer(vx, flags=['multi_index'])
while not it.finished:
vxi = vx[it.multi_index]
vyi = vy[it.multi_index]
vzi = vz[it.multi_index]
patch = data3d[vxi:vxi + PATCH_SIZE, vyi:vyi + PATCH_SIZE, vzi]
patch = np.squeeze(patch)
print(it.iterindex, ' - ', vxi, ' ', vyi, ' ', vzi, ' - ',
it.multi_index)
#import pdb; pdb.set_trace()
glcm = greycomatrix(patch, [5], [0],
256,
symmetric=True,
normed=True)
dissimilarity = greycoprops(glcm, 'dissimilarity')
feat[it.multi_index] = dissimilarity
feat2[it.multi_index] = greycoprops(glcm, 'correlation')
it.iternext()
locations = [(474, 291), (440, 433), (466, 18), (462, 236)]
qt_app = QApplication(sys.argv)
pyed = QTSeedEditor(feat)
qt_app.exec_()
pyed = QTSeedEditor(feat2)
qt_app.exec_()
pdb