def visualization(self):
"""
Run viewer with output data3d and segmentation
"""
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
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 visualization(self):
"""
Run viewer with output data3d and segmentation
"""
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
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 test_viewer_seeds(self):
try:
from pysegbase.seed_editor_qt import QTSeedEditor
except:
print("Deprecated of pyseg_base as submodule")
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 test_viewer_seeds(self):
app = QApplication(sys.argv)
dcmdir = QFileDialog.getExistingDirectory(caption='Select DICOM Folder',
options=QFileDialog.ShowDirsOnly)
print ('ahoj')
#app.exec_()
#app.exit(0)
#del(app)
#import pdb; pdb.set_trace()
img = np.random.rand(30,30,30)
print '1'
app = QApplication(sys.argv)
print '2'
pyed = QTSeedEditor(img)
print '3'
app.exec_()
del(app)
app = QApplication(sys.argv)
print '2'
pyed = QTSeedEditor(img)
print '3'
app.exec_()
del(app)
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 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',
voxelSize=self.voxel_sizemm)
pyed.exec_()
self.segmentation_data = pyed.getSeeds()
self.checkSegData()
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.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 test_data_editor(self):
"""
Funkce provádí změnu vstupních dat - data3d
"""
#pyed = sed3.sed3(self.data3d, contour = oseg.segmentation)
#pyed.show()
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
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):
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 = datetime.datetime.now() - self.oseg.time_start
self.checkSegData("manual seg., ")
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 btnManualSeg(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 = \
datetime.datetime.now() - self.oseg.time_start
self.checkSegData('manual seg., ')
def test_data_editor(self):
"""
Funkce provádí změnu vstupních dat - data3d
"""
#pyed = sed3.sed3(self.data3d, contour = oseg.segmentation)
#pyed.show()
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
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 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")
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
