def test_data_editor(self):
"""
Funkce provádí změnu vstupních dat - data3d
"""
#pyed = py3DSeedEditor.py3DSeedEditor(self.data3d, contour = oseg.segmentation)
#pyed.show()
from seed_editor_qt import QTSeedEditor
from PyQt4.QtGui import QApplication
import numpy as np
im3d = np.random.rand(15,15,15)
print ("Select pixels for deletion (it will be setted to 0)")
#, QMainWindow
app = QApplication(sys.argv)
pyed = QTSeedEditor(im3d, mode='draw')
pyed.exec_()
deletemask = pyed.getSeeds()
print ("If it is ok, press 'Return'. If it is wrong, click into image and press 'Return'")
# rewrite input data
im3d [deletemask != 0] = 0
pyed = QTSeedEditor(im3d)
app.exec_()
sds = pyed.getSeeds()
# if usere select pixel, there will be 1 or 2 in sds
self.assertLess(np.max(sds), 1)
def manualSeg(self):
if self.dcm_3Ddata is None:
self.statusBar().showMessage('No DICOM data!')
return
pyed = QTSeedEditor(self.dcm_3Ddata,
seeds=self.segmentation_data,
mode='draw',
voxelVolume=self.voxel_volume)
pyed.exec_()
self.segmentation_data = pyed.getSeeds()
self.checkSegData()
def autoSeg(self):
if self.dcm_3Ddata is None:
self.statusBar().showMessage('No DICOM data!')
return
igc = pycut.ImageGraphCut(self.dcm_3Ddata, voxelsize=self.voxel_sizemm)
pyed = QTSeedEditor(self.dcm_3Ddata,
seeds=self.segmentation_seeds,
modeFun=igc.interactivity_loop,
voxelSize=self.voxel_sizemm)
pyed.exec_()
self.segmentation_data = pyed.getContours()
self.segmentation_seeds = pyed.getSeeds()
self.checkSegData()
def autoSeg(self):
if self.dcm_3Ddata is None:
self.statusBar().showMessage('No DICOM data!')
return
igc = pycat.ImageGraphCut(self.dcm_3Ddata,
voxelsize=self.voxel_sizemm)
pyed = QTSeedEditor(self.dcm_3Ddata,
seeds=self.segmentation_seeds,
modeFun=igc.interactivity_loop,
voxelVolume=self.voxel_volume)
pyed.exec_()
self.segmentation_data = pyed.getContours()
self.segmentation_seeds = pyed.getSeeds()
self.checkSegData()
def manualSeg(self):
oseg = self.oseg
# rint 'ms d3d ', oseg.data3d.shape
# rint 'ms seg ', oseg.segmentation.shape
# rint 'crinfo ', oseg.crinfo
if oseg.data3d is None:
self.statusBar().showMessage('No DICOM data!')
return
sgm = oseg.segmentation.astype(np.uint8)
pyed = QTSeedEditor(oseg.data3d,
seeds=sgm,
mode='draw',
voxelSize=oseg.voxelsize_mm, volume_unit='ml')
pyed.exec_()
oseg.segmentation = pyed.getSeeds()
self.oseg.processing_time = time.time() - self.oseg.time_start
self.checkSegData('manual seg., ')
def data_editor(self, im3d, cval=0):
"""
Function changes input data - data3d.
cval: value is set to deleted data
"""
from seed_editor_qt import QTSeedEditor
from PyQt4.QtGui import QApplication
#import numpy as np
#, QMainWindow
print ("Select voxels for deletion")
app = QApplication(sys.argv)
pyed = QTSeedEditor(im3d, mode='draw')
pyed.exec_()
deletemask = pyed.getSeeds()
#import pdb; pdb.set_trace()
#pyed = QTSeedEditor(deletemask, mode='draw')
#pyed.exec_()
app.exit()
#pyed.exit()
del app
del pyed
im3d[deletemask != 0] = cval
#print ("Check output")
# rewrite input data
#pyed = QTSeedEditor(im3d)
#pyed.exec_()
#el pyed
#import pdb; pdb.set_trace()
return im3d
def test_viewer_seeds(self):
from seed_editor_qt import QTSeedEditor
from PyQt4.QtGui import QApplication
import numpy as np
img3d = (np.random.rand(30,30,30)*10).astype(np.int16)
seeds = (np.zeros(img3d.shape)).astype(np.int8)
seeds[3:6, 12:18,9:16] = 1
seeds[3:6,19:22,21:27 ] = 2
#, QMainWindow
app = QApplication(sys.argv)
pyed = QTSeedEditor(img3d, seeds=seeds)
pyed.exec_()
deletemask = pyed.getSeeds()
#import pdb; pdb.set_trace()
#pyed = QTSeedEditor(deletemask, mode='draw')
#pyed.exec_()
app.exit()
def cropDcm(self):
if self.dcm_3Ddata is None:
self.statusBar().showMessage('No DICOM data!')
return
self.statusBar().showMessage('Cropping DICOM data...')
QApplication.processEvents()
is_reduced = False
shape = self.dcm_3Ddata.shape
max12 = np.max(shape[:2])
if max12 > 128:
is_reduced = True
czoom = [128.0 / max12] * 2
if shape[2] > 32:
czoom.append(32.0 / shape[2])
else:
czoom.append(1.0)
czoom = np.array(czoom)
reduced_3Ddata = ndimage.zoom(self.dcm_3Ddata, czoom,
prefilter=False, mode='nearest')
else:
reduced_3Ddata = self.dcm_3Ddata
pyed = QTSeedEditor(reduced_3Ddata, mode='crop')
pyed.exec_()
nzs = pyed.getSeeds().nonzero()
if nzs is not None:
cri = []
for ii in range(3):
if nzs[ii].shape[0] == 0:
nzs = None
break
smin, smax = np.min(nzs[ii]), np.max(nzs[ii])
if smin == smax:
nzs = None
break
cri.append((smin, smax))
cri = np.array(cri)
if is_reduced and nzs is not None:
aux = (cri.T * (1.0 / czoom)).T
cri[:,0] = np.floor(aux[:,0])
cri[:,1] = np.ceil(aux[:,1])
if nzs is not None:
crop = self.dcm_3Ddata[cri[0][0]:(cri[0][1] + 1),
cri[1][0]:(cri[1][1] + 1),
cri[2][0]:(cri[2][1] + 1)]
self.dcm_3Ddata = np.ascontiguousarray(crop)
self.dcm_offsetmm = cri[:,0] * self.voxel_sizemm
self.setLabelText(self.text_dcm_data, self.getDcmInfo())
self.statusBar().showMessage('Ready')
else:
self.statusBar().showMessage('No crop information!')
