def interactivity(self, min_val=None, max_val=None, qt_app=None):
"""
Interactive seed setting with 3d seed editor
"""
from seed_editor_qt import QTSeedEditor
from PyQt4.QtGui import QApplication
if min_val is None:
min_val = np.min(self.img)
if max_val is None:
max_val = np.max(self.img)
window_c = ((max_val + min_val) / 2) # .astype(np.int16)
window_w = (max_val - min_val) # .astype(np.int16)
if qt_app is None:
qt_app = QApplication(sys.argv)
pyed = QTSeedEditor(self.img,
modeFun=self.interactivity_loop,
voxelSize=self.voxelsize,
seeds=self.seeds,
volume_unit=self.volume_unit
)
pyed.changeC(window_c)
pyed.changeW(window_w)
qt_app.exec_()
def remove_area(self):
if not self.nogui:
app = QApplication(sys.argv)
pyed = QTSeedEditor(
self.data3d, mode='mask'
)
pyed.exec_()
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 cropDcm(self):
oseg = self.oseg
if oseg.data3d is None:
self.statusBar().showMessage('No DICOM data!')
return
self.statusBar().showMessage('Cropping DICOM data...')
QApplication.processEvents()
pyed = QTSeedEditor(oseg.data3d, mode='crop',
voxelSize=oseg.voxelsize_mm)
# @TODO
mx = self.oseg.viewermax
mn = self.oseg.viewermin
width = mx - mn
# enter = (float(mx)-float(mn))
center = np.average([mx, mn])
logger.debug("window params max %f min %f width, %f center %f" %
(mx, mn, width, center))
pyed.changeC(center)
pyed.changeW(width)
pyed.exec_()
crinfo = pyed.getROI()
if crinfo is not None:
tmpcrinfo = []
for ii in crinfo:
tmpcrinfo.append([ii.start, ii.stop])
# seg.data3d = qmisc.crop(oseg.data3d, oseg.crinfo)
oseg.crop(tmpcrinfo)
self.setLabelText(self.text_dcm_data, self.getDcmInfo())
self.statusBar().showMessage('Ready')
def maskRegion(self):
if self.dcm_3Ddata is None:
self.statusBar().showMessage('No DICOM data!')
return
self.statusBar().showMessage('Mask region...')
QApplication.processEvents()
pyed = QTSeedEditor(self.dcm_3Ddata, mode='mask',
voxelSize=self.voxel_sizemm)
pyed.exec_()
self.statusBar().showMessage('Ready')
def maskRegion(self):
if self.dcm_3Ddata is None:
self.statusBar().showMessage('No DICOM data!')
return
self.statusBar().showMessage('Mask region...')
QApplication.processEvents()
pyed = QTSeedEditor(self.dcm_3Ddata,
mode='mask',
voxelSize=self.voxel_sizemm)
pyed.exec_()
self.statusBar().showMessage('Ready')
def showRemoveDialog(self, data3d=None):
if data3d is None:
data3d=self.ha.data3d
helpW = QLabel('Remove unneeded data')
self.changeHelpWidget(widget=helpW)
newapp = QTSeedEditor(data3d, mode='mask')
newapp.status_bar.hide()
self.embedWidget(newapp)
newapp.exec_()
self.changeHelpWidget(widget=None) # removes help
self.fixWindow()
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 showCropDialog(self,data3d=None):
if data3d is None:
data3d=self.data3d
helpW = QLabel('Crop data')
self.changeHelpWidget(widget=helpW)
newapp = QTSeedEditor(data3d, mode='crop')
newapp.status_bar.hide()
self.embedWidget(newapp)
newapp.exec_()
self.changeHelpWidget(widget=None) # removes help
self.fixWindow()
return newapp.img
def interactivity(self, min_val=None, max_val=None):
from seed_editor_qt import QTSeedEditor
import_gui()
logger.debug('interactivity')
# if self.edit_data:
# self.data3d = self.data_editor(self.data3d)
igc = self._interactivity_begin()
pyed = QTSeedEditor(igc.img,
seeds=igc.seeds,
modeFun=igc.interactivity_loop,
voxelSize=igc.voxelsize,
volume_unit='ml')
# set window
if min_val is None:
min_val = np.min(self.data3d)
if max_val is None:
max_val = np.max(self.data3d)
window_c = ((max_val + min_val) / 2)
window_w = (max_val - min_val)
pyed.changeC(window_c)
pyed.changeW(window_w)
pyed.exec_()
# @TODO někde v igc.interactivity() dochází k přehození nul za jedničy,
# tady se to řeší hackem
if igc.segmentation is not None:
self.segmentation = (igc.segmentation == 0).astype(np.int8)
self._interactivity_end(igc)
def cropDcm(self):
if self.dcm_3Ddata is None:
self.statusBar().showMessage('No DICOM data!')
return
self.statusBar().showMessage('Cropping DICOM data...')
QApplication.processEvents()
pyed = QTSeedEditor(self.dcm_3Ddata, mode='crop',
voxelSize=self.voxel_sizemm)
pyed.exec_()
self.dcm_3Ddata = pyed.getImg()
self.dcm_offsetmm = pyed.getOffset()
self.setLabelText(self.text_dcm_data, self.getDcmInfo())
self.statusBar().showMessage('Ready')
self.statusBar().showMessage('Ready')
def show_output(self):
""" Run viewer with output data3d and segmentation. """
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(self.data3d, contours=self.segmentation)
pyed.exec_()
#import pdb; pdb.set_trace()
#pyed = QTSeedEditor(deletemask, mode='draw')
#pyed.exec_()
app.exit()
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 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 visualization(self):
"""
Run viewer with output data3d and segmentation
"""
from seed_editor_qt import QTSeedEditor
from PyQt4.QtGui import QApplication
import numpy as np
#, QMainWindow
app = QApplication(sys.argv)
#pyed = QTSeedEditor(self.data3d, contours=(self.segmentation>0))
pyed = QTSeedEditor(self.segmentation)
pyed.exec_()
#import pdb; pdb.set_trace()
#pyed = QTSeedEditor(deletemask, mode='draw')
#pyed.exec_()
app.exit()
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 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 cropDcm(self):
if self.dcm_3Ddata is None:
self.statusBar().showMessage('No DICOM data!')
return
self.statusBar().showMessage('Cropping DICOM data...')
QApplication.processEvents()
pyed = QTSeedEditor(self.dcm_3Ddata,
mode='crop',
voxelSize=self.voxel_sizemm)
pyed.exec_()
self.dcm_3Ddata = pyed.getImg()
self.dcm_offsetmm = pyed.getOffset()
self.setLabelText(self.text_dcm_data, self.getDcmInfo())
self.statusBar().showMessage('Ready')
self.statusBar().showMessage('Ready')
def maskRegion(self):
if self.oseg.data3d is None:
self.statusBar().showMessage('No DICOM data!')
return
self.statusBar().showMessage('Mask region...')
QApplication.processEvents()
pyed = QTSeedEditor(self.oseg.data3d, mode='mask',
voxelSize=self.oseg.voxelsize_mm)
mx = self.oseg.viewermax
mn = self.oseg.viewermin
width = mx - mn
# enter = (float(mx)-float(mn))
center = np.average([mx, mn])
logger.debug("window params max %f min %f width, %f center %f" %
(mx, mn, width, center))
pyed.changeC(center)
pyed.changeW(width)
pyed.exec_()
self.statusBar().showMessage('Ready')
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!')