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,
contours=((self.oseg.segmentation == 0).astype(np.int8)*2)
)
pyed.contours_old = pyed.contours.copy()
# initial mask set
# pyed.masked = np.ones(self.oseg.data3d.shape, np.int8)
# pyed.masked = (self.oseg.segmentation == 0).astype(np.int8)
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):
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.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,
contours=((self.oseg.segmentation == 0).astype(np.int8)*2)
)
pyed.contours_old = pyed.contours.copy()
# initial mask set
# pyed.masked = np.ones(self.oseg.data3d.shape, np.int8)
# pyed.masked = (self.oseg.segmentation == 0).astype(np.int8)
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):
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 interactivity(self, min_val=None, max_val=None):
try:
from pysegbase.seed_editor_qt import QTSeedEditor
except:
logger.warning("Deprecated of pyseg_base as submodule")
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()
# from PyQt4.QtCore import pyqtRemoveInputHook
# pyqtRemoveInputHook()
# import ipdb; ipdb.set_trace() # noqa BREAKPOINT
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 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")
