class QTSeedEditor(QDialog):
"""
DICOM viewer.
"""
@staticmethod
def get_line(mode='h'):
line = QFrame()
if mode == 'h':
line.setFrameStyle(QFrame.HLine)
elif mode == 'v':
line.setFrameStyle(QFrame.VLine)
line.setSizePolicy(QSizePolicy.Minimum, QSizePolicy.Expanding)
return line
def initUI(self, shape, vscale, height=600,
mode='seed'):
"""
Initialize UI.
Parameters
----------
shape : (int, int, int)
Shape of data matrix.
vscale : (float, float, float)
Voxel scaling.
height : int
Maximal slice height in pixels.
mode : str
Editor mode.
"""
# picture
grid = height / float(shape[1] * vscale[1])
mgrid = (grid * vscale[0], grid * vscale[1])
self.slice_box = SliceBox(shape[:-1], mgrid,
mode)
self.slice_box.setScrollFun(self.scrollSlices)
self.connect(self.slice_box, SIGNAL('focus_slider'), self.focusSliceSlider)
# sliders
self.allow_select_slice = True
self.n_slices = shape[2]
self.slider = QSlider(Qt.Vertical)
self.slider.label = QLabel()
self.slider.label.setText('Slice: %d / %d' % (self.actual_slice,
self.n_slices))
self.slider.setRange(1, self.n_slices)
self.slider.valueChanged.connect(self.sliderSelectSlice)
self.slider.setValue(self.actual_slice)
self.slider_cw = {}
self.slider_cw['c'] = QSlider(Qt.Horizontal)
self.slider_cw['c'].valueChanged.connect(self.changeC)
self.slider_cw['c'].label = QLabel()
self.slider_cw['w'] = QSlider(Qt.Horizontal)
self.slider_cw['w'].valueChanged.connect(self.changeW)
self.slider_cw['w'].label = QLabel()
self.view_label = QLabel('View size: %d x %d' % self.img_aview.shape[:-1])
self.voxel_label = QLabel('Voxel size [mm]:\n %.2f x %.2f x %.2f'\
% tuple(self.voxel_size[np.array(self.act_transposition)]))
combo_view_options = VIEW_TABLE.keys()
combo_view = QComboBox(self)
combo_view.activated[str].connect(self.setView)
combo_view.addItems(combo_view_options)
# buttons
self.btn_quit = QPushButton("Return", self)
self.btn_quit.clicked.connect(self.quit)
combo_dmask = QComboBox(self)
combo_dmask.activated.connect(self.changeMask)
self.mask_points_tab, aux = self.init_draw_mask(DRAW_MASK, mgrid)
for icon, label in aux:
combo_dmask.addItem(icon, label)
self.slice_box.setMaskPoints(self.mask_points_tab[combo_dmask.currentIndex()])
self.status_bar = QStatusBar()
vopts = []
vmenu = []
appmenu = []
if mode == 'seed' and self.mode_fun is not None:
btn_recalc = QPushButton("Recalculate", self)
btn_recalc.clicked.connect(self.recalculate)
appmenu.append(QLabel('<b>Segmentation mode</b><br><br><br>' +
'Select the region of interest<br>' +
'using the mouse buttons:<br><br>' +
' <i>left</i> - inner region<br>' +
' <i>right</i> - outer region<br><br>'))
appmenu.append(btn_recalc)
appmenu.append(QLabel())
self.volume_label = QLabel('Volume:\n unknown')
appmenu.append(self.volume_label)
# Set middle pencil as default (M. Jirik)
combo_dmask.setCurrentIndex(1)
self.slice_box.setMaskPoints(
self.mask_points_tab[combo_dmask.currentIndex()])
# -----mjirik---end------
if mode == 'seed' or mode == 'crop'\
or mode == 'mask' or mode == 'draw':
btn_del = QPushButton("Delete Seeds", self)
btn_del.clicked.connect(self.deleteSliceSeeds)
vmenu.append(None)
vmenu.append(btn_del)
combo_contour_options = ['fill', 'contours', 'off']
combo_contour = QComboBox(self)
combo_contour.activated[str].connect(self.changeContourMode)
combo_contour.addItems(combo_contour_options)
self.changeContourMode(combo_contour_options[combo_contour.currentIndex()])
vopts.append(QLabel('Selection mode:'))
vopts.append(combo_contour)
if mode == 'mask':
btn_recalc_mask = QPushButton("Recalculate mask", self)
btn_recalc_mask.clicked.connect(self.updateMaskRegion_btn)
btn_all = QPushButton("Select all", self)
btn_all.clicked.connect(self.maskSelectAll)
btn_reset = QPushButton("Reset selection", self)
btn_reset.clicked.connect(self.resetSelection)
btn_reset_seads = QPushButton("Reset seads", self)
btn_reset_seads.clicked.connect(self.resetSeads)
btn_add = QPushButton("Add selection", self)
btn_add.clicked.connect(self.maskAddSelection)
btn_rem = QPushButton("Remove selection", self)
btn_rem.clicked.connect(self.maskRemoveSelection)
btn_mask = QPushButton("Mask region", self)
btn_mask.clicked.connect(self.maskRegion)
appmenu.append(QLabel('<b>Mask mode</b><br><br><br>' +
'Select the region to mask<br>' +
'using the left mouse button<br><br>'))
appmenu.append(self.get_line('h'))
appmenu.append(btn_recalc_mask)
appmenu.append(btn_all)
appmenu.append(btn_reset)
appmenu.append(btn_reset_seads)
appmenu.append(self.get_line('h'))
appmenu.append(btn_add)
appmenu.append(btn_rem)
appmenu.append(self.get_line('h'))
appmenu.append(btn_mask)
appmenu.append(self.get_line('h'))
self.mask_qhull = None
if mode == 'crop':
btn_crop = QPushButton("Crop", self)
btn_crop.clicked.connect(self.crop)
appmenu.append(QLabel('<b>Crop mode</b><br><br><br>' +
'Select the crop region<br>' +
'using the left mouse button<br><br>'))
appmenu.append(btn_crop)
if mode == 'draw':
appmenu.append(QLabel('<b>Manual segmentation<br> mode</b><br><br><br>' +
'Mark the region of interest<br>' +
'using the mouse buttons:<br><br>' +
' <i>left</i> - draw<br>' +
' <i>right</i> - erase<br>' +
' <i>middle</i> - vol. erase<br><br>'))
btn_reset = QPushButton("Reset", self)
btn_reset.clicked.connect(self.resetSliceDraw)
vmenu.append(None)
vmenu.append(btn_reset)
combo_erase_options = ['inside', 'outside']
combo_erase = QComboBox(self)
combo_erase.activated[str].connect(self.changeEraseMode)
combo_erase.addItems(combo_erase_options)
self.changeEraseMode(combo_erase_options[combo_erase.currentIndex()])
vopts.append(QLabel('Volume erase mode:'))
vopts.append(combo_erase)
hbox = QHBoxLayout()
vbox = QVBoxLayout()
vbox_left = QVBoxLayout()
vbox_app = QVBoxLayout()
hbox.addWidget(self.slice_box)
hbox.addWidget(self.slider)
vbox_left.addWidget(self.slider.label)
vbox_left.addWidget(self.view_label)
vbox_left.addWidget(self.voxel_label)
vbox_left.addWidget(QLabel())
vbox_left.addWidget(QLabel('View plane:'))
vbox_left.addWidget(combo_view)
vbox_left.addWidget(self.get_line())
vbox_left.addWidget(self.slider_cw['c'].label)
vbox_left.addWidget(self.slider_cw['c'])
vbox_left.addWidget(self.slider_cw['w'].label)
vbox_left.addWidget(self.slider_cw['w'])
vbox_left.addWidget(self.get_line())
vbox_left.addWidget(QLabel('Drawing mask:'))
vbox_left.addWidget(combo_dmask)
for ii in vopts:
vbox_left.addWidget(ii)
for ii in vmenu:
if ii is None:
vbox_left.addStretch(1)
else:
vbox_left.addWidget(ii)
for ii in appmenu:
if ii is None:
vbox_app.addStretch(1)
else:
vbox_app.addWidget(ii)
vbox_app.addStretch(1)
vbox_app.addWidget(self.btn_quit)
hbox.addLayout(vbox_left)
hbox.addWidget(self.get_line('v'))
hbox.addLayout(vbox_app)
vbox.addLayout(hbox)
vbox.addWidget(self.status_bar)
self.my_layout = vbox
self.setLayout(vbox)
self.setWindowTitle('Segmentation Editor')
self.show()
def __init__(self, img, viewPositions=None,
seeds=None, contours=None,
mode='seed', modeFun=None,
voxelSize=[1,1,1], volume_unit='mm3'):
"""
Initiate Editor
Parameters
----------
img : array
DICOM data matrix.
actualSlice : int
Index of actual slice.
seeds : array
Seeds, user defined regions of interest.
contours : array
Computed segmentation.
mode : str
Editor modes:
'seed' - seed editor
'crop' - manual crop
'draw' - drawing
'mask' - mask region
modeFun : fun
Mode function invoked by user button.
voxelSize : tuple of float
voxel size [mm]
volume_unit : allow select output volume in mililiters or mm3
[mm, ml]
"""
QDialog.__init__(self)
self.mode = mode
self.mode_fun = modeFun
self.actual_view = 'axial'
self.act_transposition = VIEW_TABLE[self.actual_view]
self.img = img
self.img_aview = self.img.transpose(self.act_transposition)
self.volume_unit = volume_unit
self.last_view_position = {}
for jj, ii in enumerate(VIEW_TABLE.iterkeys()):
if viewPositions is None:
viewpos = img.shape[VIEW_TABLE[ii][-1]] / 2
else:
viewpos = viewPositions[jj]
self.last_view_position[ii] =\
img.shape[VIEW_TABLE[ii][-1]] - viewpos - 1
self.actual_slice = self.last_view_position[self.actual_view]
# set contours
self.contours = contours
if self.contours is None:
self.contours_aview = None
else:
self.contours_aview = self.contours.transpose(self.act_transposition)
# masked data - has information about which data were removed
# 1 == enabled, 0 == deleted
# How to return:
# editorDialog.exec_()
# masked_data = editorDialog.masked
self.masked = np.ones(self.img.shape, np.int8)
self.voxel_size = np.squeeze(np.asarray(voxelSize))
self.voxel_scale = self.voxel_size / float(np.min(self.voxel_size))
self.voxel_volume = np.prod(voxelSize)
# set seeds
if seeds is None:
self.seeds = np.zeros(self.img.shape, np.int8)
else:
self.seeds = seeds
self.seeds_aview = self.seeds.transpose(self.act_transposition)
self.seeds_modified = False
self.initUI(self.img_aview.shape,
self.voxel_scale[np.array(self.act_transposition)],
600, mode)
if mode == 'draw':
self.seeds_orig = self.seeds.copy()
self.slice_box.setEraseFun(self.eraseVolume)
# set view window values C/W
lb = np.min(img)
self.img_min_val = lb
ub = np.max(img)
dul = np.double(ub) - np.double(lb)
self.cw_range = {'c': [lb, ub], 'w': [1, dul]}
self.slider_cw['c'].setRange(lb, ub)
self.slider_cw['w'].setRange(1, dul)
self.changeC(lb + dul / 2)
self.changeW(dul)
self.offset = np.zeros((3,), dtype=np.int16)
def showStatus(self, msg):
self.status_bar.showMessage(QString(msg))
QApplication.processEvents()
def init_draw_mask(self, draw_mask, grid):
mask_points = []
mask_iconlabel = []
for mask, label in draw_mask:
w, h = mask.shape
xx, yy = mask.nonzero()
mask_points.append((xx - w/2, yy - h/2))
img = QImage(w, h, QImage.Format_ARGB32)
img.fill(qRgba(255, 255, 255, 0))
for ii in range(xx.shape[0]):
img.setPixel(xx[ii], yy[ii], qRgba(0, 0, 0, 255))
img = img.scaled(QSize(w * grid[0], h * grid[1]))
icon = QIcon(QPixmap.fromImage(img))
mask_iconlabel.append((icon, label))
return mask_points, mask_iconlabel
def saveSliceSeeds(self):
aux = self.slice_box.getSliceSeeds()
if aux is not None:
self.seeds_aview[...,self.actual_slice] = aux
self.seeds_modified = True
else:
self.seeds_modified = False
def updateMaskRegion_btn(self):
self.saveSliceSeeds()
self.updateMaskRegion()
def updateMaskRegion(self):
crp = self.getCropBounds(return_nzs=True)
if crp is not None:
off, cri, nzs = crp
if nzs[0].shape[0] <=5:
self.showStatus("Not enough points (need >= 5)!")
else:
points = np.transpose(nzs)
hull = Delaunay(points)
X, Y, Z = np.mgrid[cri[0], cri[1], cri[2]]
grid = np.vstack([X.ravel(), Y.ravel(), Z.ravel()]).T
simplex = hull.find_simplex(grid)
fill = grid[simplex >=0,:]
fill = (fill[:,0], fill[:,1], fill[:,2])
if self.contours is None or self.contours_old is None:
self.contours = np.zeros(self.img.shape, np.int8)
self.contours_old = self.contours.copy()
else:
self.contours[self.contours != 2] = 0
self.contours[fill] = 1
self.contours_aview = self.contours.transpose(self.act_transposition)
self.selectSlice(self.actual_slice)
def maskRegion(self):
self.masked[self.contours == 0] = 0
self.img[self.contours != 2] = self.img_min_val
self.contours.fill(0)
self.contours_old = self.contours.copy()
self.seeds.fill(0)
self.selectSlice(self.actual_slice)
def maskAddSelection(self):
self.updateMaskRegion()
if self.contours is None:
return
self.contours[self.contours == 1] = 2
self.contours_old = self.contours.copy()
self.seeds.fill(0)
self.selectSlice(self.actual_slice)
def maskRemoveSelection(self):
self.updateMaskRegion()
if self.contours is None:
return
self.contours[self.contours == 1] = 0
self.contours_old = self.contours.copy()
self.seeds.fill(0)
self.selectSlice(self.actual_slice)
def maskSelectAll(self):
self.updateMaskRegion()
self.seeds[0][0][0] = 1
self.seeds[0][0][-1] = 1
self.seeds[0][-1][0] = 1
self.seeds[0][-1][-1] = 1
self.seeds[-1][0][0] = 1
self.seeds[-1][0][-1] = 1
self.seeds[-1][-1][0] = 1
self.seeds[-1][-1][-1] = 1
self.updateMaskRegion()
self.selectSlice(self.actual_slice)
def resetSelection(self):
self.updateMaskRegion()
if self.contours is None:
return
self.contours.fill(0)
self.contours_old = self.contours.copy()
self.seeds.fill(0)
self.selectSlice(self.actual_slice)
def resetSeads(self):
self.seeds.fill(0)
if self.contours is not None:
self.contours = self.contours_old.copy()
self.contours_aview = self.contours.transpose(self.act_transposition)
self.updateMaskRegion()
self.selectSlice(self.actual_slice)
def updateCropBounds(self):
crp = self.getCropBounds()
if crp is not None:
_, cri = crp
self.contours = np.zeros(self.img.shape, np.int8)
self.contours[cri].fill(1)
self.contours_aview = self.contours.transpose(self.act_transposition)
def focusSliceSlider(self):
self.slider.setFocus(True)
def sliderSelectSlice(self, value):
self.selectSlice(self.n_slices - value)
def scrollSlices(self, inc):
if abs(inc) > 0:
new = self.actual_slice + inc
self.selectSlice(new)
def selectSlice(self, value, force=False):
if not(self.allow_select_slice):
return
if (value < 0) or (value >= self.n_slices):
return
if (value != self.actual_slice) or force:
self.saveSliceSeeds()
if self.seeds_modified:
if self.mode == 'crop':
self.updateCropBounds()
elif self.mode == 'mask':
self.updateMaskRegion()
if self.contours is None:
contours = None
else:
contours = self.contours_aview[...,value]
slider_val = self.n_slices - value
self.slider.setValue(slider_val)
self.slider.label.setText('Slice: %d / %d' % (slider_val, self.n_slices))
self.slice_box.setSlice(self.img_aview[...,value],
self.seeds_aview[...,value],
contours)
self.actual_slice = value
def getSeeds(self):
return self.seeds
def getImg(self):
return self.img
def getOffset(self):
return self.offset * self.voxel_size
def getSeedsVal(self, label):
return self.img[self.seeds==label]
def getContours(self):
return self.contours
def setContours(self, contours):
self.contours = contours
self.contours_aview = self.contours.transpose(self.act_transposition)
self.selectSlice(self.actual_slice)
def changeCW(self, value, key):
rg = self.cw_range[key]
if (value < rg[0]) or (value > rg[1]):
return
if (value != self.slice_box.getCW()[key]):
self.slider_cw[key].setValue(value)
self.slider_cw[key].label.setText('%s: %d' % (key.upper(), value))
self.slice_box.setCW(value, key)
self.slice_box.updateSliceCW(self.img_aview[...,self.actual_slice])
def changeC(self, value):
self.changeCW(value, 'c')
def changeW(self, value):
self.changeCW(value, 'w')
def setView(self, value):
self.last_view_position[self.actual_view] = self.actual_slice
# save seeds
self.saveSliceSeeds()
if self.seeds_modified:
if self.mode == 'crop':
self.updateCropBounds()
elif self.mode == 'mask':
self.updateMaskRegion()
key = str(value)
self.actual_view = key
self.actual_slice = self.last_view_position[key]
self.act_transposition = VIEW_TABLE[key]
self.img_aview = self.img.transpose(self.act_transposition)
self.seeds_aview = self.seeds.transpose(self.act_transposition)
if self.contours is not None:
self.contours_aview = self.contours.transpose(self.act_transposition)
contours = self.contours_aview[...,self.actual_slice]
else:
contours = None
vscale = self.voxel_scale[np.array(self.act_transposition)]
height = self.slice_box.height()
grid = height / float(self.img_aview.shape[1] * vscale[1])
# width = (self.img_aview.shape[0] * vscale[0])[0]
# if width > 800:
# height = 400
# grid = height / float(self.img_aview.shape[1] * vscale[1])
mgrid = (grid * vscale[0], grid * vscale[1])
self.slice_box.resizeSlice(new_slice_size=self.img_aview.shape[:-1],
new_grid=mgrid)
self.slice_box.setSlice(self.img_aview[...,self.actual_slice],
self.seeds_aview[...,self.actual_slice],
contours)
self.allow_select_slice = False
self.n_slices = self.img_aview.shape[2]
slider_val = self.n_slices - self.actual_slice
self.slider.setRange(1, self.n_slices)
self.slider.setValue(slider_val)
self.allow_select_slice = True
self.slider.label.setText('Slice: %d / %d' % (slider_val,
self.n_slices))
self.view_label.setText('View size: %d x %d' % self.img_aview.shape[:-1])
self.adjustSize()
self.adjustSize()
def changeMask(self, val):
self.slice_box.setMaskPoints(self.mask_points_tab[val])
def changeContourMode(self, val):
self.slice_box.contour_mode = str(val)
self.slice_box.updateSlice()
def changeEraseMode(self, val):
self.slice_box.erase_mode = str(val)
def eraseVolume(self, pos, mode):
self.showStatus("Processing...")
xyz = np.array(pos + (self.actual_slice,))
p = np.zeros_like(xyz)
p[np.array(self.act_transposition)] = xyz
p = tuple(p)
if self.seeds[p] > 0:
if mode == 'inside':
erase_reg(self.seeds, p, val=0)
elif mode == 'outside':
erase_reg(self.seeds, p, val=-1)
idxs = np.where(self.seeds < 0)
self.seeds.fill(0)
self.seeds[idxs] = 1
if self.contours is None:
contours = None
else:
contours = self.contours_aview[...,self.actual_slice]
self.slice_box.setSlice(self.img_aview[...,self.actual_slice],
self.seeds_aview[...,self.actual_slice],
contours)
self.showStatus("Done")
def cropUpdate(self, img):
for ii in VIEW_TABLE.iterkeys():
self.last_view_position[ii] = 0
self.actual_slice = 0
self.img = img
self.img_aview = self.img.transpose(self.act_transposition)
self.contours = None
self.contours_aview = None
self.seeds = np.zeros(self.img.shape, np.int8)
self.seeds_aview = self.seeds.transpose(self.act_transposition)
self.seeds_modified = False
vscale = self.voxel_scale[np.array(self.act_transposition)]
height = self.slice_box.height()
grid = height / float(self.img_aview.shape[1] * vscale[1])
mgrid = (grid * vscale[0], grid * vscale[1])
self.slice_box.resizeSlice(new_slice_size=self.img_aview.shape[:-1],
new_grid=mgrid)
self.slice_box.setSlice(self.img_aview[...,self.actual_slice],
self.seeds_aview[...,self.actual_slice],
None)
self.allow_select_slice = False
self.n_slices = self.img_aview.shape[2]
self.slider.setValue(self.actual_slice + 1)
self.slider.setRange(1, self.n_slices)
self.allow_select_slice = True
self.slider.label.setText('Slice: %d / %d' % (self.actual_slice + 1,
self.n_slices))
self.view_label.setText('View size: %d x %d' % self.img_aview.shape[:-1])
def getCropBounds(self, return_nzs=False, flat=False):
nzs = self.seeds.nonzero()
cri = []
flag = True
for ii in range(3):
if nzs[ii].shape[0] == 0:
flag = False
break
smin, smax = np.min(nzs[ii]), np.max(nzs[ii])
if not(flat):
if smin == smax:
flag = False
break
cri.append((smin, smax))
if flag:
cri = np.array(cri)
out = []
offset = []
for jj, ii in enumerate(cri):
out.append(slice(ii[0], ii[1] + 1))
offset.append(ii[0])
if return_nzs:
return np.array(offset), tuple(out), nzs
else:
return np.array(offset), tuple(out)
else:
return None
def crop(self):
self.showStatus("Processing...")
crp = self.getCropBounds()
if crp is not None:
offset, cri = crp
crop = self.img[cri]
self.img = np.ascontiguousarray(crop)
self.offset += offset
self.showStatus('Done')
else:
self.showStatus('Region not selected!')
self.cropUpdate(self.img)
def recalculate(self, event):
self.saveSliceSeeds()
if np.abs(np.min(self.seeds) - np.max(self.seeds)) < 2:
self.showStatus('Inner and outer regions not defined!')
return
self.showStatus("Processing...")
self.mode_fun(self)
self.selectSlice(self.actual_slice)
self.updateVolume()
self.showStatus("Done")
def deleteSliceSeeds(self, event):
self.seeds_aview[...,self.actual_slice] = 0
self.slice_box.setSlice(seeds=self.seeds_aview[...,self.actual_slice])
self.slice_box.updateSlice()
def resetSliceDraw(self, event):
seeds_orig_aview = self.seeds_orig.transpose(self.act_transposition)
self.seeds_aview[...,self.actual_slice] = seeds_orig_aview[...,self.actual_slice]
self.slice_box.setSlice(seeds=self.seeds_aview[...,self.actual_slice])
self.slice_box.updateSlice()
def quit(self, event):
self.close()
def updateVolume(self):
text = 'Volume:\n unknown'
if self.voxel_volume is not None:
if self.mode == 'draw':
vd = self.seeds
else:
vd = self.contours
if vd is not None:
nzs = vd.nonzero()
nn = nzs[0].shape[0]
if self.volume_unit == 'ml':
text = 'Volume [ml]:\n %.2f' %\
(nn * self.voxel_volume / 1000)
else:
text = 'Volume [mm3]:\n %.2e' % (nn * self.voxel_volume)
self.volume_label.setText(text)
def getROI(self):
crp = self.getCropBounds()
if crp is not None:
_, cri = crp
else:
cri = []
for jj, ii in enumerate(self.img.shape):
off = self.offset[jj]
cri.append(slice(off, off + ii))
return cri
class QTSeedEditor(QDialog):
"""
DICOM viewer.
"""
@staticmethod
def get_line(mode='h'):
line = QFrame()
if mode == 'h':
line.setFrameStyle(QFrame.HLine)
elif mode == 'v':
line.setFrameStyle(QFrame.VLine)
line.setSizePolicy(QSizePolicy.Minimum, QSizePolicy.Expanding)
return line
def initUI(self, shape, vscale, height=600, mode='seed'):
"""
Initialize UI.
Parameters
----------
shape : (int, int, int)
Shape of data matrix.
vscale : (float, float, float)
Voxel scaling.
height : int
Maximal slice height in pixels.
mode : str
Editor mode.
"""
self.slab = {}
# picture
grid = height / float(shape[1] * vscale[1])
mgrid = (grid * vscale[0], grid * vscale[1])
self.slice_box = SliceBox(shape[:-1], mgrid, mode)
self.slice_box.setScrollFun(self.scrollSlices)
self.connect(self.slice_box, SIGNAL('focus_slider'),
self.focusSliceSlider)
# sliders
self.allow_select_slice = True
self.n_slices = shape[2]
self.slider = QSlider(Qt.Vertical)
self.slider.valueChanged.connect(self.sliderSelectSlice)
self.slider.label = QLabel()
self.slider.setRange(1, self.n_slices)
self.slider_cw = {}
self.slider_cw['c'] = QSlider(Qt.Horizontal)
self.slider_cw['c'].valueChanged.connect(self.changeC)
self.slider_cw['c'].label = QLabel()
self.slider_cw['w'] = QSlider(Qt.Horizontal)
self.slider_cw['w'].valueChanged.connect(self.changeW)
self.slider_cw['w'].label = QLabel()
self.view_label = QLabel('View size: %d x %d' %
self.img_aview.shape[:-1])
self.voxel_label = QLabel('Voxel size [mm]:\n %.2f x %.2f x %.2f'\
% tuple(self.voxel_size[np.array(self.act_transposition)]))
# combo_view_options = VIEW_TABLE.keys()
# combo_view = QComboBox(self)
# combo_view.activated[str].connect(self.setView)
# combo_view.addItems(combo_view_options)
#radio button group for choosing seed class ------------------------
self.current_class = 1
self.slice_box.seed_mark = self.current_class
number_group = QGroupBox(QString('Class markers'))
vbox_NG = QVBoxLayout()
r1 = QRadioButton('class 1')
r1.setStyleSheet('QRadioButton {color: red}')
r1.setChecked(True)
r2 = QRadioButton('class 2')
r2.setStyleSheet('QRadioButton {color: green}')
r3 = QRadioButton('class 3')
r3.setStyleSheet('QRadioButton {color: blue}')
r4 = QRadioButton('class 4')
r4.setStyleSheet('QRadioButton {color: cyan}')
r5 = QRadioButton('class 5')
r5.setStyleSheet('QRadioButton {color: magenta}')
vbox_NG.addWidget(r1)
vbox_NG.addWidget(r2)
vbox_NG.addWidget(r3)
vbox_NG.addWidget(r4)
vbox_NG.addWidget(r5)
number_group.setLayout(vbox_NG)
self.button_group = QButtonGroup()
self.button_group.addButton(r1, 1)
self.button_group.addButton(r2, 2)
self.button_group.addButton(r3, 3)
self.button_group.addButton(r4, 4)
self.button_group.addButton(r5, 5)
self.connect(self.button_group, SIGNAL("buttonClicked(int)"),
self.change_seed_class)
#-------------------------------------------------------------------
# buttons
# btn_save = QPushButton('Save', self)
# btn_save.clicked.connect(self.save)
btn_quit = QPushButton("Quit", self)
btn_quit.clicked.connect(self.quit)
# btn_crop = QPushButton('Crop', self)
# btn_crop.clicked.connect(self.crop)
combo_dmask = QComboBox(self)
combo_dmask.activated.connect(self.changeMask)
self.mask_points_tab, aux = self.init_draw_mask(DRAW_MASK, mgrid)
for icon, label in aux:
combo_dmask.addItem(icon, label)
self.slice_box.setMaskPoints(
self.mask_points_tab[combo_dmask.currentIndex()])
self.status_bar = QStatusBar()
vopts = []
vmenu = []
appmenu = []
# btn_recalc = QPushButton("Recalculate", self)
# btn_recalc.clicked.connect(self.recalculate)
# appmenu.append(QLabel('<b>Segmentation mode</b><br><br><br>' +
# 'Select the region of interest<br>' +
# 'using the mouse buttons.<br><br>'))
# appmenu.append(btn_recalc)
# appmenu.append(QLabel())
# self.volume_label = QLabel('Volume [mm3]:\n unknown')
# appmenu.append(self.volume_label)
# btn_crop = QPushButton("Crop", self)
# btn_crop.clicked.connect(self.crop)
# appmenu.append(btn_crop)
btn_save = QPushButton("Save Seeds", self)
btn_save.clicked.connect(self.saveSeeds)
appmenu.append(btn_save)
btn_del = QPushButton("Delete Seeds", self)
btn_del.clicked.connect(self.deleteSliceSeeds)
appmenu.append(btn_del)
# combo_contour_options = ['fill', 'contours', 'off']
# combo_contour = QComboBox(self)
# combo_contour.activated[str].connect(self.changeContourMode)
# combo_contour.addItems(combo_contour_options)
# self.changeContourMode(combo_contour_options[combo_contour.currentIndex()])
# vopts.append(QLabel('Selection mode:'))
# vopts.append(combo_contour)
# btn_reset = QPushButton("Reset Seeds", self)
# btn_reset.clicked.connect(self.resetSliceDraw)
# # appmenu.append(None)
# appmenu.append(btn_reset)
hbox = QHBoxLayout()
vbox = QVBoxLayout()
vbox_left = QVBoxLayout()
vbox_app = QVBoxLayout()
hbox.addWidget(self.slice_box)
hbox.addWidget(self.slider)
vbox_left.addWidget(self.slider.label)
vbox_left.addWidget(self.view_label)
vbox_left.addWidget(self.voxel_label)
# vbox_left.addWidget(QLabel())
# vbox_left.addWidget(QLabel('View plane:'))
# vbox_left.addWidget(combo_view)
vbox_left.addWidget(self.get_line())
vbox_left.addWidget(self.slider_cw['c'].label)
vbox_left.addWidget(self.slider_cw['c'])
vbox_left.addWidget(self.slider_cw['w'].label)
vbox_left.addWidget(self.slider_cw['w'])
vbox_left.addWidget(self.get_line())
vbox_left.addWidget(QLabel('Drawing mask:'))
vbox_left.addWidget(combo_dmask)
for ii in vopts:
vbox_left.addWidget(ii)
for ii in vmenu:
if ii is None:
vbox_left.addStretch(1)
else:
vbox_left.addWidget(ii)
for ii in appmenu:
if ii is None:
vbox_app.addStretch(1)
else:
vbox_app.addWidget(ii)
vbox_left.addWidget(self.get_line())
vbox_left.addWidget(number_group)
# vbox_app.addWidget(btn_crop)
vbox_app.addStretch(1)
# vbox_app.addWidget(btn_save)
vbox_app.addWidget(btn_quit)
hbox.addLayout(vbox_left)
hbox.addWidget(self.get_line('v'))
hbox.addLayout(vbox_app)
vbox.addLayout(hbox)
vbox.addWidget(self.status_bar)
self.setLayout(vbox)
self.setWindowTitle('Seed Editor')
self.show()
def __init__(self,
img,
seeds_fname='seeds.npy',
actualSlice=0,
seeds=None,
contours=None,
mode='seed',
modeFun=None,
voxelSize=[1, 1, 1]):
"""
Initiate Editor
Parameters
----------
img : array
DICOM data matrix.
actualSlice : int
Index of actual slice.
seeds : array
Seeds, user defined regions of interest.
contours : array
Computed segmentation.
mode : str
Editor modes:
'seed' - seed editor
'crop' - manual crop
'draw' - drawing
modeFun : fun
Mode function invoked by user button.
voxelSize : tuple of float
voxel size [mm]
"""
QDialog.__init__(self)
self.mode = mode
self.mode_fun = modeFun
self.seeds_fname = seeds_fname
# self.datapath = datapath
self.actual_view = 'axial'
self.act_transposition = VIEW_TABLE[self.actual_view]
self.last_view_position = {}
for ii in VIEW_TABLE.iterkeys():
self.last_view_position[ii] = img.shape[VIEW_TABLE[ii][-1]] - 1
self.img = img
self.img_aview = self.img.transpose(self.act_transposition)
self.actual_slice = self.img_aview.shape[-1] - actualSlice - 1
self.last_view_position[self.actual_view] = self.actual_slice
# set contours
self.contours = contours
if self.contours is None:
self.contours_aview = None
else:
self.contours_aview = self.contours.transpose(
self.act_transposition)
self.voxel_size = np.array(voxelSize)
self.voxel_scale = self.voxel_size / float(np.min(self.voxel_size))
self.voxel_volume = np.prod(voxelSize)
# set seeds
if seeds is None:
self.seeds = np.zeros(self.img.shape, np.int8)
else:
self.seeds = seeds
self.seeds_aview = self.seeds.transpose(self.act_transposition)
self.seeds_modified = False
self.initUI(self.img_aview.shape,
self.voxel_scale[np.array(self.act_transposition)], 600,
mode)
if mode == 'draw':
self.seeds_orig = self.seeds.copy()
self.slice_box.setEraseFun(self.eraseVolume)
# set view window values C/W
lb = np.min(img)
ub = np.max(img)
dul = ub - lb
self.cw_range = {'c': [lb, ub], 'w': [1, dul]}
self.slider_cw['c'].setRange(lb, ub)
self.slider_cw['w'].setRange(1, dul)
self.changeC(lb + dul / 2)
self.changeW(dul)
self.offset = np.zeros((3, ), dtype=np.int16)
def change_seed_class(self, id):
self.current_class = id
self.slice_box.seed_mark = self.current_class
# print 'Current seed class changed to ', id, '.'
def showStatus(self, msg):
self.status_bar.showMessage(QString(msg))
QApplication.processEvents()
def init_draw_mask(self, draw_mask, grid):
mask_points = []
mask_iconlabel = []
for mask, label in draw_mask:
w, h = mask.shape
xx, yy = mask.nonzero()
mask_points.append((xx - w / 2, yy - h / 2))
img = QImage(w, h, QImage.Format_ARGB32)
img.fill(qRgba(255, 255, 255, 0))
for ii in range(xx.shape[0]):
img.setPixel(xx[ii], yy[ii], qRgba(0, 0, 0, 255))
img = img.scaled(QSize(w * grid[0], h * grid[1]))
icon = QIcon(QPixmap.fromImage(img))
mask_iconlabel.append((icon, label))
return mask_points, mask_iconlabel
def saveSliceSeeds(self):
aux = self.slice_box.getSliceSeeds()
if aux is not None:
self.seeds_aview[..., self.actual_slice] = aux
self.seeds_modified = True
else:
self.seeds_modified = False
def saveSeeds(self):
print 'Saving seeds array ... ',
# aux = np.swapaxes(np.swapaxes(self.seeds_aview, 1, 2), 0, 1)
aux = np.swapaxes(self.seeds_aview, 0, 2)
np.save(self.seeds_fname, aux)
print 'done'
def updateCropBounds(self):
crp = self.getCropBounds()
if crp is not None:
_, cri = crp
self.contours = np.zeros(self.img.shape, np.int8)
self.contours[cri].fill(1)
self.contours_aview = self.contours.transpose(
self.act_transposition)
def focusSliceSlider(self):
self.slider.setFocus(True)
def sliderSelectSlice(self, value):
self.selectSlice(self.n_slices - value)
def scrollSlices(self, inc):
if abs(inc) > 0:
new = self.actual_slice + inc
self.selectSlice(new)
def selectSlice(self, value, force=False):
if not (self.allow_select_slice):
return
if (value < 0) or (value >= self.n_slices):
return
if (value != self.actual_slice) or force:
self.saveSliceSeeds()
if self.seeds_modified and (self.mode == 'crop'):
self.updateCropBounds()
if self.contours is None:
contours = None
else:
contours = self.contours_aview[..., value]
slider_val = self.n_slices - value
self.slider.setValue(slider_val)
self.slider.label.setText('Slice: %d / %d' %
(slider_val, self.n_slices))
self.slice_box.setSlice(self.img_aview[..., value],
self.seeds_aview[..., value], contours)
self.actual_slice = value
def getSeeds(self):
return self.seeds
def getImg(self):
return self.img
def getOffset(self):
return self.offset * self.voxel_size
def getSeedsVal(self, label):
return self.img[self.seeds == label]
def getContours(self):
return self.contours
def setContours(self, contours):
self.contours = contours
self.contours_aview = self.contours.transpose(self.act_transposition)
self.selectSlice(self.actual_slice)
def changeCW(self, value, key):
rg = self.cw_range[key]
if (value < rg[0]) or (value > rg[1]):
return
if (value != self.slice_box.getCW()[key]):
self.slider_cw[key].setValue(value)
self.slider_cw[key].label.setText('%s: %d' % (key.upper(), value))
self.slice_box.setCW(value, key)
self.slice_box.updateSliceCW(self.img_aview[...,
self.actual_slice])
def changeC(self, value):
self.changeCW(value, 'c')
def changeW(self, value):
self.changeCW(value, 'w')
def setView(self, value):
self.last_view_position[self.actual_view] = self.actual_slice
# save seeds
self.saveSliceSeeds()
if self.seeds_modified and (self.mode == 'crop'):
self.updateCropBounds(self.seeds_aview[..., self.actual_slice])
key = str(value)
self.actual_view = key
self.actual_slice = self.last_view_position[key]
self.act_transposition = VIEW_TABLE[key]
self.img_aview = self.img.transpose(self.act_transposition)
self.seeds_aview = self.seeds.transpose(self.act_transposition)
if self.contours is not None:
self.contours_aview = self.contours.transpose(
self.act_transposition)
contours = self.contours_aview[..., self.actual_slice]
else:
contours = None
vscale = self.voxel_scale[np.array(self.act_transposition)]
height = self.slice_box.height()
grid = height / float(self.img_aview.shape[1] * vscale[1])
mgrid = (grid * vscale[0], grid * vscale[1])
self.slice_box.resizeSlice(new_slice_size=self.img_aview.shape[:-1],
new_grid=mgrid)
self.slice_box.setSlice(self.img_aview[..., self.actual_slice],
self.seeds_aview[...,
self.actual_slice], contours)
self.allow_select_slice = False
self.n_slices = self.img_aview.shape[2]
slider_val = self.n_slices - self.actual_slice
self.slider.setValue(slider_val)
self.slider.setRange(1, self.n_slices)
self.allow_select_slice = True
self.slider.label.setText('Slice: %d / %d' %
(slider_val, self.n_slices))
self.view_label.setText('View size: %d x %d' %
self.img_aview.shape[:-1])
def changeMask(self, val):
self.slice_box.setMaskPoints(self.mask_points_tab[val])
def changeContourMode(self, val):
self.slice_box.contour_mode = str(val)
self.slice_box.updateSlice()
def changeEraseMode(self, val):
self.slice_box.erase_mode = str(val)
def eraseVolume(self, pos, mode):
self.showStatus("Processing...")
xyz = pos + (self.actual_slice, )
p = tuple(np.array(xyz)[np.array(self.act_transposition)])
if self.seeds[p] > 0:
if mode == 'inside':
erase_reg(self.seeds, p, val=0)
elif mode == 'outside':
erase_reg(self.seeds, p, val=-1)
idxs = np.where(self.seeds < 0)
self.seeds.fill(0)
self.seeds[idxs] = 1
if self.contours is None:
contours = None
else:
contours = self.contours_aview[..., self.actual_slice]
self.slice_box.setSlice(self.img_aview[..., self.actual_slice],
self.seeds_aview[...,
self.actual_slice], contours)
self.showStatus("Done")
def cropUpdate(self, img):
for ii in VIEW_TABLE.iterkeys():
self.last_view_position[ii] = 0
self.actual_slice = 0
self.img = img
self.img_aview = self.img.transpose(self.act_transposition)
self.contours = None
self.contours_aview = None
self.seeds = np.zeros(self.img.shape, np.int8)
self.seeds_aview = self.seeds.transpose(self.act_transposition)
self.seeds_modified = False
vscale = self.voxel_scale[np.array(self.act_transposition)]
height = self.slice_box.height()
grid = height / float(self.img_aview.shape[1] * vscale[1])
mgrid = (grid * vscale[0], grid * vscale[1])
self.slice_box.resizeSlice(new_slice_size=self.img_aview.shape[:-1],
new_grid=mgrid)
self.slice_box.setSlice(self.img_aview[..., self.actual_slice],
self.seeds_aview[..., self.actual_slice], None)
self.allow_select_slice = False
self.n_slices = self.img_aview.shape[2]
self.slider.setValue(self.actual_slice + 1)
self.slider.setRange(1, self.n_slices)
self.allow_select_slice = True
self.slider.label.setText('Slice: %d / %d' %
(self.actual_slice + 1, self.n_slices))
self.view_label.setText('View size: %d x %d' %
self.img_aview.shape[:-1])
def getCropBounds(self):
nzs = self.seeds.nonzero()
cri = []
flag = True
for ii in range(3):
if nzs[ii].shape[0] == 0:
flag = False
break
smin, smax = np.min(nzs[ii]), np.max(nzs[ii])
if smin == smax:
flag = False
break
cri.append((smin, smax))
if flag:
cri = np.array(cri)
out = []
offset = []
for jj, ii in enumerate(cri):
out.append(slice(ii[0], ii[1] + 1))
offset.append(ii[0])
return np.array(offset), tuple(out)
else:
return None
def crop(self):
self.showStatus("Processing...")
crp = self.getCropBounds()
if crp is not None:
offset, cri = crp
crop = self.img[cri]
self.img = np.ascontiguousarray(crop)
self.offset += offset
self.showStatus('Done')
else:
self.showStatus('Region not selected!')
self.cropUpdate(self.img)
def recalculate(self, event):
self.saveSliceSeeds()
if np.abs(np.min(self.seeds) - np.max(self.seeds)) < 2:
self.showStatus('At least two regions must be marked!')
return
self.showStatus("Processing...")
# idx = 3
# s = random_walker(self.img[idx,:,:], self.seeds[idx,:,:])#, mode='cg_mg')
# plt.figure()
# plt.imshow(mark_boundaries(self.img[idx,:,:], s))
# plt.show()
# self.segmentation = np.zeros(self.img.shape)
# self.segmentation[idx,:,:] = s
self.segmentation = random_walker(self.img, self.seeds, mode='cg_mg')
self.setContours(self.segmentation - 1)
self.selectSlice(self.actual_slice)
# self.updateVolume()
self.showStatus("Done")
def deleteSliceSeeds(self, event):
self.seeds_aview[..., self.actual_slice] = 0
self.slice_box.setSlice(seeds=self.seeds_aview[..., self.actual_slice])
self.slice_box.updateSlice()
def resetSliceDraw(self, event):
seeds_orig_aview = self.seeds_orig.transpose(self.act_transposition)
self.seeds_aview[..., self.actual_slice] = seeds_orig_aview[
..., self.actual_slice]
self.slice_box.setSlice(seeds=self.seeds_aview[..., self.actual_slice])
self.slice_box.updateSlice()
def quit(self, event):
self.close()
# def save(self, event):
# odp = os.path.expanduser("~/lisa_data")
# if not op.exists(odp):
# os.makedirs(odp)
#
# data = self.export()
# # data['version'] = self.version
# # data['experiment_caption'] = self.experiment_caption
# # data['lisa_operator_identifier'] = self.lisa_operator_identifier
# pth, filename = op.split(op.normpath(self.datapath))
# # filename += "-" + self.experiment_caption
# filepath = 'org-' + filename + '.pklz'
# filepath = op.join(odp, filepath)
# filepath = misc.suggest_filename(filepath)
# misc.obj_to_file(data, filepath, filetype='pklz')
#
# filepath = 'organ_last.pklz'
# filepath = op.join(odp, filepath)
# misc.obj_to_file(data, filepath, filetype='pklz')
# def export(self):
# slab = {}
# slab['none'] = 0
# slab['liver'] = 1
# slab['lesions'] = 6
# slab.update(self.slab)
#
# data = {}
# data['version'] = (1, 0, 1)
# data['data3d'] = self.img
# # data['crinfo'] = self.crinfo
# data['segmentation'] = self.segmentation
# data['slab'] = slab
# # data['voxelsize_mm'] = self.voxelsize_mm
# # data['orig_shape'] = self.orig_shape
# # data['processing_time'] = self.processing_time
# return data
def updateVolume(self):
text = 'Volume [mm3]:\n unknown'
if self.voxel_volume is not None:
if self.mode == 'draw':
vd = self.seeds
else:
vd = self.contours
if vd is not None:
nzs = vd.nonzero()
nn = nzs[0].shape[0]
text = 'Volume [mm3]:\n %.2e' % (nn * self.voxel_volume)
self.volume_label.setText(text)
def getROI(self):
crp = self.getCropBounds()
if crp is not None:
_, cri = crp
else:
cri = []
for jj, ii in enumerate(self.img.shape):
off = self.offset[jj]
cri.append(slice(off, off + ii))
return cri
class QTSeedEditor(QDialog):
"""
DICOM viewer.
"""
@staticmethod
def get_line(mode='h'):
line = QFrame()
if mode == 'h':
line.setFrameStyle(QFrame.HLine)
elif mode == 'v':
line.setFrameStyle(QFrame.VLine)
line.setSizePolicy(QSizePolicy.Minimum, QSizePolicy.Expanding)
return line
def initUI(self, shape, vscale, height=600, mode='seed'):
"""
Initialize UI.
Parameters
----------
shape : (int, int, int)
Shape of data matrix.
vscale : (float, float, float)
Voxel scaling.
height : int
Maximal slice height in pixels.
mode : str
Editor mode.
"""
# picture
grid = height / float(shape[1] * vscale[1])
mgrid = (grid * vscale[0], grid * vscale[1])
self.slice_box = SliceBox(shape[:-1], mgrid, mode)
self.slice_box.setScrollFun(self.scrollSlices)
self.connect(self.slice_box, SIGNAL('focus_slider'),
self.focusSliceSlider)
# sliders
self.allow_select_slice = True
self.n_slices = shape[2]
self.slider = QSlider(Qt.Vertical)
self.slider.label = QLabel()
self.slider.label.setText('Slice: %d / %d' %
(self.actual_slice, self.n_slices))
self.slider.setRange(1, self.n_slices)
self.slider.valueChanged.connect(self.sliderSelectSlice)
self.slider.setValue(self.actual_slice)
self.slider_cw = {}
self.slider_cw['c'] = QSlider(Qt.Horizontal)
self.slider_cw['c'].valueChanged.connect(self.changeC)
self.slider_cw['c'].label = QLabel()
self.slider_cw['w'] = QSlider(Qt.Horizontal)
self.slider_cw['w'].valueChanged.connect(self.changeW)
self.slider_cw['w'].label = QLabel()
self.view_label = QLabel('View size: %d x %d' %
self.img_aview.shape[:-1])
self.voxel_label = QLabel('Voxel size [mm]:\n %.2f x %.2f x %.2f'\
% tuple(self.voxel_size[np.array(self.act_transposition)]))
combo_view_options = VIEW_TABLE.keys()
combo_view = QComboBox(self)
combo_view.activated[str].connect(self.setView)
combo_view.addItems(combo_view_options)
# buttons
self.btn_quit = QPushButton("Return", self)
self.btn_quit.clicked.connect(self.quit)
combo_dmask = QComboBox(self)
combo_dmask.activated.connect(self.changeMask)
self.mask_points_tab, aux = self.init_draw_mask(DRAW_MASK, mgrid)
for icon, label in aux:
combo_dmask.addItem(icon, label)
self.slice_box.setMaskPoints(
self.mask_points_tab[combo_dmask.currentIndex()])
self.status_bar = QStatusBar()
self.seeds_copy = None
vopts = []
vmenu = []
appmenu = []
if mode == 'seed' and self.mode_fun is not None:
btn_recalc = QPushButton("Recalculate", self)
btn_recalc.clicked.connect(self.recalculate)
self.btn_save = QPushButton("Save seeds", self)
self.btn_save.clicked.connect(self.saveload_seeds)
btn_s2b = QPushButton("Seg. to bckgr.", self)
btn_s2b.clicked.connect(self.seg_to_background_seeds)
btn_s2f = QPushButton("Seg. to forgr.", self)
btn_s2f.clicked.connect(self.seg_to_foreground_seeds)
appmenu.append(
QLabel('<b>Segmentation mode</b><br><br><br>' +
'Select the region of interest<br>' +
'using the mouse buttons:<br><br>' +
' <i>left</i> - inner region<br>' +
' <i>right</i> - outer region<br><br>'))
appmenu.append(btn_recalc)
appmenu.append(self.btn_save)
appmenu.append(btn_s2f)
appmenu.append(btn_s2b)
appmenu.append(QLabel())
self.volume_label = QLabel('Volume:\n unknown')
appmenu.append(self.volume_label)
# Set middle pencil as default (M. Jirik)
combo_dmask.setCurrentIndex(1)
self.slice_box.setMaskPoints(
self.mask_points_tab[combo_dmask.currentIndex()])
# -----mjirik---end------
if mode == 'seed' or mode == 'crop'\
or mode == 'mask' or mode == 'draw':
combo_seed_label_options = ['all', '1', '2', '3', '4']
combo_seed_label = QComboBox(self)
combo_seed_label.activated[str].connect(self.changeFocusedLabel)
combo_seed_label.addItems(combo_seed_label_options)
self.changeFocusedLabel(
combo_seed_label_options[combo_seed_label.currentIndex()])
# vopts.append(QLabel('Label to delete:'))
# vopts.append(combo_seed_label)
vmenu.append(QLabel('Label to delete:'))
vmenu.append(combo_seed_label)
btn_del = QPushButton("Del Slice Seeds", self)
btn_del.clicked.connect(self.deleteSliceSeeds)
vmenu.append(None)
vmenu.append(btn_del)
btn_del = QPushButton("Del All Seeds", self)
btn_del.clicked.connect(self.deleteSeedsInAllImage)
vmenu.append(None)
vmenu.append(btn_del)
combo_contour_options = ['fill', 'contours', 'off']
combo_contour = QComboBox(self)
combo_contour.activated[str].connect(self.changeContourMode)
combo_contour.addItems(combo_contour_options)
self.changeContourMode(
combo_contour_options[combo_contour.currentIndex()])
vopts.append(QLabel('Selection mode:'))
vopts.append(combo_contour)
if mode == 'mask':
btn_recalc_mask = QPushButton("Recalculate mask", self)
btn_recalc_mask.clicked.connect(self.updateMaskRegion_btn)
btn_all = QPushButton("Select all", self)
btn_all.clicked.connect(self.maskSelectAll)
btn_reset = QPushButton("Reset selection", self)
btn_reset.clicked.connect(self.resetSelection)
btn_reset_seads = QPushButton("Reset seads", self)
btn_reset_seads.clicked.connect(self.resetSeads)
btn_add = QPushButton("Add selection", self)
btn_add.clicked.connect(self.maskAddSelection)
btn_rem = QPushButton("Remove selection", self)
btn_rem.clicked.connect(self.maskRemoveSelection)
btn_mask = QPushButton("Mask region", self)
btn_mask.clicked.connect(self.maskRegion)
appmenu.append(
QLabel('<b>Mask mode</b><br><br><br>' +
'Select the region to mask<br>' +
'using the left mouse button<br><br>'))
appmenu.append(self.get_line('h'))
appmenu.append(btn_recalc_mask)
appmenu.append(btn_all)
appmenu.append(btn_reset)
appmenu.append(btn_reset_seads)
appmenu.append(self.get_line('h'))
appmenu.append(btn_add)
appmenu.append(btn_rem)
appmenu.append(self.get_line('h'))
appmenu.append(btn_mask)
appmenu.append(self.get_line('h'))
self.mask_qhull = None
if mode == 'crop':
btn_crop = QPushButton("Crop", self)
btn_crop.clicked.connect(self.crop)
appmenu.append(
QLabel('<b>Crop mode</b><br><br><br>' +
'Select the crop region<br>' +
'using the left mouse button<br><br>'))
appmenu.append(btn_crop)
if mode == 'draw':
appmenu.append(
QLabel('<b>Manual segmentation<br> mode</b><br><br><br>' +
'Mark the region of interest<br>' +
'using the mouse buttons:<br><br>' +
' <i>left</i> - draw<br>' +
' <i>right</i> - erase<br>' +
' <i>middle</i> - vol. erase<br><br>'))
btn_reset = QPushButton("Reset", self)
btn_reset.clicked.connect(self.resetSliceDraw)
vmenu.append(None)
vmenu.append(btn_reset)
combo_erase_options = ['inside', 'outside']
combo_erase = QComboBox(self)
combo_erase.activated[str].connect(self.changeEraseMode)
combo_erase.addItems(combo_erase_options)
self.changeEraseMode(
combo_erase_options[combo_erase.currentIndex()])
vopts.append(QLabel('Volume erase mode:'))
vopts.append(combo_erase)
hbox = QHBoxLayout()
vbox = QVBoxLayout()
vbox_left = QVBoxLayout()
vbox_app = QVBoxLayout()
hbox.addWidget(self.slice_box)
hbox.addWidget(self.slider)
vbox_left.addWidget(self.slider.label)
vbox_left.addWidget(self.view_label)
vbox_left.addWidget(self.voxel_label)
vbox_left.addWidget(QLabel())
vbox_left.addWidget(QLabel('View plane:'))
vbox_left.addWidget(combo_view)
vbox_left.addWidget(self.get_line())
vbox_left.addWidget(self.slider_cw['c'].label)
vbox_left.addWidget(self.slider_cw['c'])
vbox_left.addWidget(self.slider_cw['w'].label)
vbox_left.addWidget(self.slider_cw['w'])
vbox_left.addWidget(self.get_line())
vbox_left.addWidget(QLabel('Drawing mask:'))
vbox_left.addWidget(combo_dmask)
for ii in vopts:
vbox_left.addWidget(ii)
for ii in vmenu:
if ii is None:
vbox_left.addStretch(1)
else:
vbox_left.addWidget(ii)
for ii in appmenu:
if ii is None:
vbox_app.addStretch(1)
else:
vbox_app.addWidget(ii)
vbox_app.addStretch(1)
vbox_app.addWidget(self.btn_quit)
hbox.addLayout(vbox_left)
hbox.addWidget(self.get_line('v'))
hbox.addLayout(vbox_app)
vbox.addLayout(hbox)
vbox.addWidget(self.status_bar)
self.my_layout = vbox
self.setLayout(vbox)
self.setWindowTitle('Segmentation Editor')
self.show()
def __init__(self,
img,
viewPositions=None,
seeds=None,
contours=None,
mode='seed',
modeFun=None,
voxelSize=[1, 1, 1],
volume_unit='mm3'):
"""
Initiate Editor
Parameters
----------
img : array
DICOM data matrix.
actualSlice : int
Index of actual slice.
seeds : array
Seeds, user defined regions of interest.
contours : array
Computed segmentation.
mode : str
Editor modes:
'seed' - seed editor
'crop' - manual crop
'draw' - drawing
'mask' - mask region
modeFun : fun
Mode function invoked by user button.
voxelSize : tuple of float
voxel size [mm]
volume_unit : allow select output volume in mililiters or mm3
[mm, ml]
"""
QDialog.__init__(self)
self.BACKGROUND_NOMODEL_SEED_LABEL = 4
self.FOREGROUND_NOMODEL_SEED_LABEL = 3
self.mode = mode
self.mode_fun = modeFun
self.actual_view = 'axial'
self.act_transposition = VIEW_TABLE[self.actual_view]
self.img = img
self.img_aview = self.img.transpose(self.act_transposition)
self.volume_unit = volume_unit
self.last_view_position = {}
for jj, ii in enumerate(VIEW_TABLE.keys()):
if viewPositions is None:
viewpos = img.shape[VIEW_TABLE[ii][-1]] / 2
else:
viewpos = viewPositions[jj]
self.last_view_position[ii] =\
img.shape[VIEW_TABLE[ii][-1]] - viewpos - 1
self.actual_slice = self.last_view_position[self.actual_view]
# set contours
self.contours = contours
if self.contours is None:
self.contours_aview = None
else:
self.contours_aview = self.contours.transpose(
self.act_transposition)
# masked data - has information about which data were removed
# 1 == enabled, 0 == deleted
# How to return:
# editorDialog.exec_()
# masked_data = editorDialog.masked
self.masked = np.ones(self.img.shape, np.int8)
self.voxel_size = np.squeeze(np.asarray(voxelSize))
self.voxel_scale = self.voxel_size / float(np.min(self.voxel_size))
self.voxel_volume = np.prod(voxelSize)
# set seeds
if seeds is None:
self.seeds = np.zeros(self.img.shape, np.int8)
else:
self.seeds = seeds
self.seeds_aview = self.seeds.transpose(self.act_transposition)
self.seeds_modified = False
self.initUI(self.img_aview.shape,
self.voxel_scale[np.array(self.act_transposition)], 600,
mode)
if mode == 'draw':
self.seeds_orig = self.seeds.copy()
self.slice_box.setEraseFun(self.eraseVolume)
# set view window values C/W
lb = np.min(img)
self.img_min_val = lb
ub = np.max(img)
dul = np.double(ub) - np.double(lb)
self.cw_range = {'c': [lb, ub], 'w': [1, dul]}
self.slider_cw['c'].setRange(lb, ub)
self.slider_cw['w'].setRange(1, dul)
self.changeC(lb + dul / 2)
self.changeW(dul)
self.offset = np.zeros((3, ), dtype=np.int16)
# set what labels will be deleted by 'delete seeds' button
self.textFocusedLabel = "all"
def showStatus(self, msg):
self.status_bar.showMessage(QString(msg))
QApplication.processEvents()
def init_draw_mask(self, draw_mask, grid):
mask_points = []
mask_iconlabel = []
for mask, label in draw_mask:
w, h = mask.shape
xx, yy = mask.nonzero()
mask_points.append((xx - w / 2, yy - h / 2))
img = QImage(w, h, QImage.Format_ARGB32)
img.fill(qRgba(255, 255, 255, 0))
for ii in range(xx.shape[0]):
img.setPixel(xx[ii], yy[ii], qRgba(0, 0, 0, 255))
img = img.scaled(QSize(w * grid[0], h * grid[1]))
icon = QIcon(QPixmap.fromImage(img))
mask_iconlabel.append((icon, label))
return mask_points, mask_iconlabel
def saveSliceSeeds(self):
aux = self.slice_box.getSliceSeeds()
if aux is not None:
self.seeds_aview[..., self.actual_slice] = aux
self.seeds_modified = True
else:
self.seeds_modified = False
def updateMaskRegion_btn(self):
self.saveSliceSeeds()
self.updateMaskRegion()
def updateMaskRegion(self):
crp = self.getCropBounds(return_nzs=True)
if crp is not None:
off, cri, nzs = crp
if nzs[0].shape[0] <= 5:
self.showStatus("Not enough points (need >= 5)!")
else:
points = np.transpose(nzs)
hull = Delaunay(points)
X, Y, Z = np.mgrid[cri[0], cri[1], cri[2]]
grid = np.vstack([X.ravel(), Y.ravel(), Z.ravel()]).T
simplex = hull.find_simplex(grid)
fill = grid[simplex >= 0, :]
fill = (fill[:, 0], fill[:, 1], fill[:, 2])
if self.contours is None or self.contours_old is None:
self.contours = np.zeros(self.img.shape, np.int8)
self.contours_old = self.contours.copy()
else:
self.contours[self.contours != 2] = 0
self.contours[fill] = 1
self.contours_aview = self.contours.transpose(
self.act_transposition)
self.selectSlice(self.actual_slice)
def maskRegion(self):
self.masked[self.contours == 0] = 0
self.img[self.contours != 2] = self.img_min_val
self.contours.fill(0)
self.contours_old = self.contours.copy()
self.seeds.fill(0)
self.selectSlice(self.actual_slice)
def maskAddSelection(self):
self.updateMaskRegion()
if self.contours is None:
return
self.contours[self.contours == 1] = 2
self.contours_old = self.contours.copy()
self.seeds.fill(0)
self.selectSlice(self.actual_slice)
def maskRemoveSelection(self):
self.updateMaskRegion()
if self.contours is None:
return
self.contours[self.contours == 1] = 0
self.contours_old = self.contours.copy()
self.seeds.fill(0)
self.selectSlice(self.actual_slice)
def maskSelectAll(self):
self.updateMaskRegion()
self.seeds[0][0][0] = 1
self.seeds[0][0][-1] = 1
self.seeds[0][-1][0] = 1
self.seeds[0][-1][-1] = 1
self.seeds[-1][0][0] = 1
self.seeds[-1][0][-1] = 1
self.seeds[-1][-1][0] = 1
self.seeds[-1][-1][-1] = 1
self.updateMaskRegion()
self.selectSlice(self.actual_slice)
def resetSelection(self):
self.updateMaskRegion()
if self.contours is None:
return
self.contours.fill(0)
self.contours_old = self.contours.copy()
self.seeds.fill(0)
self.selectSlice(self.actual_slice)
def resetSeads(self):
self.seeds.fill(0)
if self.contours is not None:
self.contours = self.contours_old.copy()
self.contours_aview = self.contours.transpose(
self.act_transposition)
self.updateMaskRegion()
self.selectSlice(self.actual_slice)
def updateCropBounds(self):
crp = self.getCropBounds()
if crp is not None:
_, cri = crp
self.contours = np.zeros(self.img.shape, np.int8)
self.contours[cri].fill(1)
self.contours_aview = self.contours.transpose(
self.act_transposition)
def focusSliceSlider(self):
self.slider.setFocus(True)
def sliderSelectSlice(self, value):
self.selectSlice(self.n_slices - value)
def scrollSlices(self, inc):
if abs(inc) > 0:
new = self.actual_slice + inc
self.selectSlice(new)
def selectSlice(self, value, force=False):
if not (self.allow_select_slice):
return
if (value < 0) or (value >= self.n_slices):
return
if (value != self.actual_slice) or force:
self.saveSliceSeeds()
if self.seeds_modified:
if self.mode == 'crop':
self.updateCropBounds()
elif self.mode == 'mask':
self.updateMaskRegion()
if self.contours is None:
contours = None
else:
contours = self.contours_aview[..., value]
slider_val = self.n_slices - value
self.slider.setValue(slider_val)
self.slider.label.setText('Slice: %d / %d' %
(slider_val, self.n_slices))
self.slice_box.setSlice(self.img_aview[..., value],
self.seeds_aview[..., value], contours)
self.actual_slice = value
def getSeeds(self):
return self.seeds
def getImg(self):
return self.img
def getOffset(self):
return self.offset * self.voxel_size
def getSeedsVal(self, label):
return self.img[self.seeds == label]
def getContours(self):
return self.contours
def setContours(self, contours):
"""
store segmentation
:param contours: segmentation
:return: Nothing
"""
"""
:param contours:
:return:
"""
self.contours = contours
self.contours_aview = self.contours.transpose(self.act_transposition)
self.selectSlice(self.actual_slice)
def changeCW(self, value, key):
rg = self.cw_range[key]
if (value < rg[0]) or (value > rg[1]):
return
if (value != self.slice_box.getCW()[key]):
self.slider_cw[key].setValue(value)
self.slider_cw[key].label.setText('%s: %d' % (key.upper(), value))
self.slice_box.setCW(value, key)
self.slice_box.updateSliceCW(self.img_aview[...,
self.actual_slice])
def changeC(self, value):
self.changeCW(value, 'c')
def changeW(self, value):
self.changeCW(value, 'w')
def setView(self, value):
self.last_view_position[self.actual_view] = self.actual_slice
# save seeds
self.saveSliceSeeds()
if self.seeds_modified:
if self.mode == 'crop':
self.updateCropBounds()
elif self.mode == 'mask':
self.updateMaskRegion()
key = str(value)
self.actual_view = key
self.actual_slice = self.last_view_position[key]
self.act_transposition = VIEW_TABLE[key]
self.img_aview = self.img.transpose(self.act_transposition)
self.seeds_aview = self.seeds.transpose(self.act_transposition)
if self.contours is not None:
self.contours_aview = self.contours.transpose(
self.act_transposition)
contours = self.contours_aview[..., self.actual_slice]
else:
contours = None
vscale = self.voxel_scale[np.array(self.act_transposition)]
height = self.slice_box.height()
grid = height / float(self.img_aview.shape[1] * vscale[1])
# width = (self.img_aview.shape[0] * vscale[0])[0]
# if width > 800:
# height = 400
# grid = height / float(self.img_aview.shape[1] * vscale[1])
mgrid = (grid * vscale[0], grid * vscale[1])
self.slice_box.resizeSlice(new_slice_size=self.img_aview.shape[:-1],
new_grid=mgrid)
self.slice_box.setSlice(self.img_aview[..., self.actual_slice],
self.seeds_aview[...,
self.actual_slice], contours)
self.allow_select_slice = False
self.n_slices = self.img_aview.shape[2]
slider_val = self.n_slices - self.actual_slice
self.slider.setRange(1, self.n_slices)
self.slider.setValue(slider_val)
self.allow_select_slice = True
self.slider.label.setText('Slice: %d / %d' %
(slider_val, self.n_slices))
self.view_label.setText('View size: %d x %d' %
self.img_aview.shape[:-1])
self.adjustSize()
self.adjustSize()
def changeMask(self, val):
self.slice_box.setMaskPoints(self.mask_points_tab[val])
def changeContourMode(self, val):
self.slice_box.contour_mode = str(val)
self.slice_box.updateSlice()
def changeEraseMode(self, val):
self.slice_box.erase_mode = str(val)
def eraseVolume(self, pos, mode):
self.showStatus("Processing...")
xyz = np.array(pos + (self.actual_slice, ))
p = np.zeros_like(xyz)
p[np.array(self.act_transposition)] = xyz
p = tuple(p)
if self.seeds[p] > 0:
if mode == 'inside':
erase_reg(self.seeds, p, val=0)
elif mode == 'outside':
erase_reg(self.seeds, p, val=-1)
idxs = np.where(self.seeds < 0)
self.seeds.fill(0)
self.seeds[idxs] = 1
if self.contours is None:
contours = None
else:
contours = self.contours_aview[..., self.actual_slice]
self.slice_box.setSlice(self.img_aview[..., self.actual_slice],
self.seeds_aview[...,
self.actual_slice], contours)
self.showStatus("Done")
def cropUpdate(self, img):
for ii in VIEW_TABLE.keys():
self.last_view_position[ii] = 0
self.actual_slice = 0
self.img = img
self.img_aview = self.img.transpose(self.act_transposition)
self.contours = None
self.contours_aview = None
self.seeds = np.zeros(self.img.shape, np.int8)
self.seeds_aview = self.seeds.transpose(self.act_transposition)
self.seeds_modified = False
vscale = self.voxel_scale[np.array(self.act_transposition)]
height = self.slice_box.height()
grid = height / float(self.img_aview.shape[1] * vscale[1])
mgrid = (grid * vscale[0], grid * vscale[1])
self.slice_box.resizeSlice(new_slice_size=self.img_aview.shape[:-1],
new_grid=mgrid)
self.slice_box.setSlice(self.img_aview[..., self.actual_slice],
self.seeds_aview[..., self.actual_slice], None)
self.allow_select_slice = False
self.n_slices = self.img_aview.shape[2]
self.slider.setValue(self.actual_slice + 1)
self.slider.setRange(1, self.n_slices)
self.allow_select_slice = True
self.slider.label.setText('Slice: %d / %d' %
(self.actual_slice + 1, self.n_slices))
self.view_label.setText('View size: %d x %d' %
self.img_aview.shape[:-1])
def getCropBounds(self, return_nzs=False, flat=False):
nzs = self.seeds.nonzero()
cri = []
flag = True
for ii in range(3):
if nzs[ii].shape[0] == 0:
flag = False
break
smin, smax = np.min(nzs[ii]), np.max(nzs[ii])
if not (flat):
if smin == smax:
flag = False
break
cri.append((smin, smax))
if flag:
cri = np.array(cri)
out = []
offset = []
for jj, ii in enumerate(cri):
out.append(slice(ii[0], ii[1] + 1))
offset.append(ii[0])
if return_nzs:
return np.array(offset), tuple(out), nzs
else:
return np.array(offset), tuple(out)
else:
return None
def crop(self):
self.showStatus("Processing...")
crp = self.getCropBounds()
if crp is not None:
offset, cri = crp
crop = self.img[cri]
self.img = np.ascontiguousarray(crop)
self.offset += offset
self.showStatus('Done')
else:
self.showStatus('Region not selected!')
self.cropUpdate(self.img)
def seg_to_background_seeds(self, event):
self.saveSliceSeeds()
self.seeds[self.seeds < 3] = 0
from PyQt4.QtCore import pyqtRemoveInputHook
# pyqtRemoveInputHook()
# import ipdb; ipdb.set_trace()
self.seeds[(self.contours == 1)
& (self.seeds < 3)] = self.BACKGROUND_NOMODEL_SEED_LABEL
self.contours[...] = 0
def seg_to_foreground_seeds(self, event):
self.saveSliceSeeds()
self.seeds[self.seeds < 3] = 0
# from PyQt4.QtCore import pyqtRemoveInputHook
# pyqtRemoveInputHook()
# import ipdb; ipdb.set_trace()
self.seeds[(self.contours == 1)
& (self.seeds < 3)] = self.FOREGROUND_NOMODEL_SEED_LABEL
self.contours[...] = 0
def saveload_seeds(self, event):
if self.seeds_copy is None:
self.seeds_copy = self.seeds.copy()
self.seeds[...] = 0
# print "save"
# from PyQt4.QtCore import pyqtRemoveInputHook
# pyqtRemoveInputHook()
# import ipdb; ipdb.set_trace()
self.btn_save.setText("Load seeds")
else:
# from PyQt4.QtCore import pyqtRemoveInputHook
# pyqtRemoveInputHook()
# import ipdb; ipdb.set_trace()
self.seeds[self.seeds_copy > 0] = self.seeds_copy[
self.seeds_copy > 0]
self.seeds_copy = None
self.btn_save.setText("Save seeds")
def recalculate(self, event):
self.saveSliceSeeds()
if np.abs(np.min(self.seeds) - np.max(self.seeds)) < 2:
self.showStatus('Inner and outer regions not defined!')
return
self.showStatus("Processing...")
self.mode_fun(self)
self.selectSlice(self.actual_slice)
self.updateVolume()
self.showStatus("Done")
def changeFocusedLabel(self, textlabel):
self.textFocusedLabel = textlabel
# logger
# print " lakjlfkj ", textlabel
logger.debug(self.textFocusedLabel)
def deleteSliceSeeds(self, event):
if self.textFocusedLabel == 'all':
self.seeds_aview[..., self.actual_slice] = 0
else:
# delete only seeds with specific label
self.seeds_aview[self.seeds_aview[..., self.actual_slice] ==
int(self.textFocusedLabel), self.actual_slice] = 0
self.slice_box.setSlice(seeds=self.seeds_aview[..., self.actual_slice])
self.slice_box.updateSlice()
def deleteSeedsInAllImage(self, event):
if self.textFocusedLabel == 'all':
self.seeds_aview[...] = 0
else:
# delete only seeds with specific label
self.seeds_aview[self.seeds_aview[...] == int(
self.textFocusedLabel)] = 0
self.slice_box.setSlice(seeds=self.seeds_aview[..., self.actual_slice])
self.slice_box.updateSlice()
def resetSliceDraw(self, event):
seeds_orig_aview = self.seeds_orig.transpose(self.act_transposition)
self.seeds_aview[..., self.actual_slice] = seeds_orig_aview[
..., self.actual_slice]
self.slice_box.setSlice(seeds=self.seeds_aview[..., self.actual_slice])
self.slice_box.updateSlice()
def quit(self, event):
self.close()
def updateVolume(self):
text = 'Volume:\n unknown'
if self.voxel_volume is not None:
if self.mode == 'draw':
vd = self.seeds
else:
vd = self.contours
if vd is not None:
nzs = vd.nonzero()
nn = nzs[0].shape[0]
if self.volume_unit == 'ml':
text = 'Volume [ml]:\n %.2f' %\
(nn * self.voxel_volume / 1000)
else:
text = 'Volume [mm3]:\n %.2e' % (nn * self.voxel_volume)
self.volume_label.setText(text)
def getROI(self):
crp = self.getCropBounds()
if crp is not None:
_, cri = crp
else:
cri = []
for jj, ii in enumerate(self.img.shape):
off = self.offset[jj]
cri.append(slice(off, off + ii))
return cri
class QTSeedEditor(QDialog):
"""
DICOM viewer.
"""
@staticmethod
def get_line(mode='h'):
line = QFrame()
if mode == 'h':
line.setFrameStyle(QFrame.HLine)
elif mode == 'v':
line.setFrameStyle(QFrame.VLine)
line.setSizePolicy(QSizePolicy.Minimum, QSizePolicy.Expanding)
return line
def initUI(self, shape, vscale, height=600,
mode='seed'):
"""
Initialize UI.
Parameters
----------
shape : (int, int, int)
Shape of data matrix.
vscale : (float, float, float)
Voxel scaling.
height : int
Maximal slice height in pixels.
mode : str
Editor mode.
"""
self.slab = {}
# picture
grid = height / float(shape[1] * vscale[1])
mgrid = (grid * vscale[0], grid * vscale[1])
self.slice_box = SliceBox(shape[:-1], mgrid, mode)
self.slice_box.setScrollFun(self.scrollSlices)
self.connect(self.slice_box, SIGNAL('focus_slider'), self.focusSliceSlider)
# sliders
self.allow_select_slice = True
self.n_slices = shape[2]
self.slider = QSlider(Qt.Vertical)
self.slider.valueChanged.connect(self.sliderSelectSlice)
self.slider.label = QLabel()
self.slider.setRange(1, self.n_slices)
self.slider_cw = {}
self.slider_cw['c'] = QSlider(Qt.Horizontal)
self.slider_cw['c'].valueChanged.connect(self.changeC)
self.slider_cw['c'].label = QLabel()
self.slider_cw['w'] = QSlider(Qt.Horizontal)
self.slider_cw['w'].valueChanged.connect(self.changeW)
self.slider_cw['w'].label = QLabel()
self.view_label = QLabel('View size: %d x %d' % self.img_aview.shape[:-1])
self.voxel_label = QLabel('Voxel size [mm]:\n %.2f x %.2f x %.2f'\
% tuple(self.voxel_size[np.array(self.act_transposition)]))
combo_view_options = VIEW_TABLE.keys()
combo_view = QComboBox(self)
combo_view.activated[str].connect(self.setView)
combo_view.addItems(combo_view_options)
#radio button group for choosing seed class ------------------------
self.current_class = 1
self.slice_box.seed_mark = self.current_class
number_group = QGroupBox(QString('Class markers'))
vbox_NG = QVBoxLayout()
r1 = QRadioButton('class 1')
r1.setStyleSheet('QRadioButton {color: red}')
r1.setChecked(True)
r2 = QRadioButton('class 2')
r2.setStyleSheet('QRadioButton {color: green}')
r3 = QRadioButton('class 3')
r3.setStyleSheet('QRadioButton {color: blue}')
r4 = QRadioButton('class 4')
r4.setStyleSheet('QRadioButton {color: cyan}')
r5 = QRadioButton('class 5')
r5.setStyleSheet('QRadioButton {color: magenta}')
vbox_NG.addWidget(r1)
vbox_NG.addWidget(r2)
vbox_NG.addWidget(r3)
vbox_NG.addWidget(r4)
vbox_NG.addWidget(r5)
number_group.setLayout(vbox_NG)
self.button_group = QButtonGroup()
self.button_group.addButton(r1, 1)
self.button_group.addButton(r2, 2)
self.button_group.addButton(r3, 3)
self.button_group.addButton(r4, 4)
self.button_group.addButton(r5, 5)
self.connect(self.button_group, SIGNAL("buttonClicked(int)"), self.change_seed_class)
#-------------------------------------------------------------------
# buttons
# btn_save = QPushButton('Save', self)
# btn_save.clicked.connect(self.save)
btn_quit = QPushButton("Quit", self)
btn_quit.clicked.connect(self.quit)
# btn_crop = QPushButton('Crop', self)
# btn_crop.clicked.connect(self.crop)
combo_dmask = QComboBox(self)
combo_dmask.activated.connect(self.changeMask)
self.mask_points_tab, aux = self.init_draw_mask(DRAW_MASK, mgrid)
for icon, label in aux:
combo_dmask.addItem(icon, label)
self.slice_box.setMaskPoints(self.mask_points_tab[combo_dmask.currentIndex()])
self.status_bar = QStatusBar()
vopts = []
vmenu = []
appmenu = []
if mode == 'seed':
btn_recalc = QPushButton("Recalculate", self)
btn_recalc.clicked.connect(self.recalculate)
appmenu.append(QLabel('<b>Segmentation mode</b><br><br><br>' +
'Select the region of interest<br>' +
'using the mouse buttons.<br><br>'))
appmenu.append(btn_recalc)
appmenu.append(QLabel())
self.volume_label = QLabel('Volume [mm3]:\n unknown')
appmenu.append(self.volume_label)
if mode == 'seed' or mode == 'crop':
btn_del = QPushButton("Delete Seeds", self)
btn_del.clicked.connect(self.deleteSliceSeeds)
vmenu.append(None)
vmenu.append(btn_del)
combo_contour_options = ['fill', 'contours', 'off']
combo_contour = QComboBox(self)
combo_contour.activated[str].connect(self.changeContourMode)
combo_contour.addItems(combo_contour_options)
self.changeContourMode(combo_contour_options[combo_contour.currentIndex()])
vopts.append(QLabel('Selection mode:'))
vopts.append(combo_contour)
if mode == 'crop':
btn_crop = QPushButton("Crop", self)
btn_crop.clicked.connect(self.crop)
appmenu.append(QLabel('<b>Crop mode</b><br><br><br>' +
'Select the crop region<br>' +
'using the left mouse button<br><br>'))
appmenu.append(btn_crop)
# if mode == 'draw':
# appmenu.append(QLabel('<b>Manual segmentation<br> mode</b><br><br><br>' +
# 'Mark the region of interest<br>' +
# 'using the mouse buttons:<br><br>' +
# ' <i>left</i> - draw<br>' +
# ' <i>right</i> - erase<br>' +
# ' <i>middle</i> - vol. erase<br><br>'))
#
# btn_reset = QPushButton("Reset", self)
# btn_reset.clicked.connect(self.resetSliceDraw)
# vmenu.append(None)
# vmenu.append(btn_reset)
#
# combo_erase_options = ['inside', 'outside']
# combo_erase = QComboBox(self)
# combo_erase.activated[str].connect(self.changeEraseMode)
# combo_erase.addItems(combo_erase_options)
# self.changeEraseMode(combo_erase_options[combo_erase.currentIndex()])
# vopts.append(QLabel('Volume erase mode:'))
# vopts.append(combo_erase)
hbox = QHBoxLayout()
vbox = QVBoxLayout()
vbox_left = QVBoxLayout()
vbox_app = QVBoxLayout()
hbox.addWidget(self.slice_box)
hbox.addWidget(self.slider)
vbox_left.addWidget(self.slider.label)
vbox_left.addWidget(self.view_label)
vbox_left.addWidget(self.voxel_label)
vbox_left.addWidget(QLabel())
vbox_left.addWidget(QLabel('View plane:'))
vbox_left.addWidget(combo_view)
vbox_left.addWidget(self.get_line())
vbox_left.addWidget(self.slider_cw['c'].label)
vbox_left.addWidget(self.slider_cw['c'])
vbox_left.addWidget(self.slider_cw['w'].label)
vbox_left.addWidget(self.slider_cw['w'])
vbox_left.addWidget(self.get_line())
vbox_left.addWidget(QLabel('Drawing mask:'))
vbox_left.addWidget(combo_dmask)
for ii in vopts:
vbox_left.addWidget(ii)
for ii in vmenu:
if ii is None:
vbox_left.addStretch(1)
else:
vbox_left.addWidget(ii)
for ii in appmenu:
if ii is None:
vbox_app.addStretch(1)
else:
vbox_app.addWidget(ii)
vbox_left.addWidget(self.get_line())
vbox_left.addWidget(number_group)
# vbox_app.addWidget(btn_crop)
vbox_app.addStretch(1)
# vbox_app.addWidget(btn_save)
vbox_app.addWidget(btn_quit)
hbox.addLayout(vbox_left)
hbox.addWidget(self.get_line('v'))
hbox.addLayout(vbox_app)
vbox.addLayout(hbox)
vbox.addWidget(self.status_bar)
self.setLayout(vbox)
self.setWindowTitle('Segmentation Editor')
self.show()
def __init__(self, img, actualSlice=0,
seeds=None, contours=None,
mode='seed', modeFun=None,
voxelSize=[1,1,1]):
"""
Initiate Editor
Parameters
----------
img : array
DICOM data matrix.
actualSlice : int
Index of actual slice.
seeds : array
Seeds, user defined regions of interest.
contours : array
Computed segmentation.
mode : str
Editor modes:
'seed' - seed editor
'crop' - manual crop
'draw' - drawing
modeFun : fun
Mode function invoked by user button.
voxelSize : tuple of float
voxel size [mm]
"""
QDialog.__init__(self)
self.mode = mode
self.mode_fun = modeFun
# self.datapath = datapath
self.actual_view = 'axial'
self.act_transposition = VIEW_TABLE[self.actual_view]
self.last_view_position = {}
for ii in VIEW_TABLE.iterkeys():
self.last_view_position[ii] = img.shape[VIEW_TABLE[ii][-1]] - 1
self.img = img
self.img_aview = self.img.transpose(self.act_transposition)
self.actual_slice = self.img_aview.shape[-1] - actualSlice - 1
self.last_view_position[self.actual_view] = self.actual_slice
# set contours
self.contours = contours
if self.contours is None:
self.contours_aview = None
else:
self.contours_aview = self.contours.transpose(self.act_transposition)
self.voxel_size = np.array(voxelSize)
self.voxel_scale = self.voxel_size / float(np.min(self.voxel_size))
self.voxel_volume = np.prod(voxelSize)
# set seeds
if seeds is None:
self.seeds = np.zeros(self.img.shape, np.int8)
else:
self.seeds = seeds
self.seeds_aview = self.seeds.transpose(self.act_transposition)
self.seeds_modified = False
self.initUI(self.img_aview.shape,
self.voxel_scale[np.array(self.act_transposition)],
600, mode)
if mode == 'draw':
self.seeds_orig = self.seeds.copy()
self.slice_box.setEraseFun(self.eraseVolume)
# set view window values C/W
lb = np.min(img)
ub = np.max(img)
dul = ub - lb
self.cw_range = {'c': [lb, ub], 'w': [1, dul]}
self.slider_cw['c'].setRange(lb, ub)
self.slider_cw['w'].setRange(1, dul)
self.changeC(lb + dul / 2)
self.changeW(dul)
self.offset = np.zeros((3,), dtype=np.int16)
def change_seed_class(self, id):
self.current_class = id
self.slice_box.seed_mark = self.current_class
# print 'Current seed class changed to ', id, '.'
def showStatus(self, msg):
self.status_bar.showMessage(QString(msg))
QApplication.processEvents()
def init_draw_mask(self, draw_mask, grid):
mask_points = []
mask_iconlabel = []
for mask, label in draw_mask:
w, h = mask.shape
xx, yy = mask.nonzero()
mask_points.append((xx - w/2, yy - h/2))
img = QImage(w, h, QImage.Format_ARGB32)
img.fill(qRgba(255, 255, 255, 0))
for ii in range(xx.shape[0]):
img.setPixel(xx[ii], yy[ii], qRgba(0, 0, 0, 255))
img = img.scaled(QSize(w * grid[0], h * grid[1]))
icon = QIcon(QPixmap.fromImage(img))
mask_iconlabel.append((icon, label))
return mask_points, mask_iconlabel
def saveSliceSeeds(self):
aux = self.slice_box.getSliceSeeds()
if aux is not None:
self.seeds_aview[...,self.actual_slice] = aux
self.seeds_modified = True
else:
self.seeds_modified = False
def updateCropBounds(self):
crp = self.getCropBounds()
if crp is not None:
_, cri = crp
self.contours = np.zeros(self.img.shape, np.int8)
self.contours[cri].fill(1)
self.contours_aview = self.contours.transpose(self.act_transposition)
def focusSliceSlider(self):
self.slider.setFocus(True)
def sliderSelectSlice(self, value):
self.selectSlice(self.n_slices - value)
def scrollSlices(self, inc):
if abs(inc) > 0:
new = self.actual_slice + inc
self.selectSlice(new)
def selectSlice(self, value, force=False):
if not(self.allow_select_slice):
return
if (value < 0) or (value >= self.n_slices):
return
if (value != self.actual_slice) or force:
self.saveSliceSeeds()
if self.seeds_modified and (self.mode == 'crop'):
self.updateCropBounds()
if self.contours is None:
contours = None
else:
contours = self.contours_aview[...,value]
slider_val = self.n_slices - value
self.slider.setValue(slider_val)
self.slider.label.setText('Slice: %d / %d' % (slider_val, self.n_slices))
self.slice_box.setSlice(self.img_aview[...,value],
self.seeds_aview[...,value],
contours)
self.actual_slice = value
def getSeeds(self):
return self.seeds
def getImg(self):
return self.img
def getOffset(self):
return self.offset * self.voxel_size
def getSeedsVal(self, label):
return self.img[self.seeds==label]
def getContours(self):
return self.contours
def setContours(self, contours):
self.contours = contours
self.contours_aview = self.contours.transpose(self.act_transposition)
self.selectSlice(self.actual_slice)
def changeCW(self, value, key):
rg = self.cw_range[key]
if (value < rg[0]) or (value > rg[1]):
return
if (value != self.slice_box.getCW()[key]):
self.slider_cw[key].setValue(value)
self.slider_cw[key].label.setText('%s: %d' % (key.upper(), value))
self.slice_box.setCW(value, key)
self.slice_box.updateSliceCW(self.img_aview[...,self.actual_slice])
def changeC(self, value):
self.changeCW(value, 'c')
def changeW(self, value):
self.changeCW(value, 'w')
def setView(self, value):
self.last_view_position[self.actual_view] = self.actual_slice
# save seeds
self.saveSliceSeeds()
if self.seeds_modified and (self.mode == 'crop'):
self.updateCropBounds(self.seeds_aview[...,self.actual_slice])
key = str(value)
self.actual_view = key
self.actual_slice = self.last_view_position[key]
self.act_transposition = VIEW_TABLE[key]
self.img_aview = self.img.transpose(self.act_transposition)
self.seeds_aview = self.seeds.transpose(self.act_transposition)
if self.contours is not None:
self.contours_aview = self.contours.transpose(self.act_transposition)
contours = self.contours_aview[...,self.actual_slice]
else:
contours = None
vscale = self.voxel_scale[np.array(self.act_transposition)]
height = self.slice_box.height()
grid = height / float(self.img_aview.shape[1] * vscale[1])
mgrid = (grid * vscale[0], grid * vscale[1])
self.slice_box.resizeSlice(new_slice_size=self.img_aview.shape[:-1],
new_grid=mgrid)
self.slice_box.setSlice(self.img_aview[...,self.actual_slice],
self.seeds_aview[...,self.actual_slice],
contours)
self.allow_select_slice = False
self.n_slices = self.img_aview.shape[2]
slider_val = self.n_slices - self.actual_slice
self.slider.setValue(slider_val)
self.slider.setRange(1, self.n_slices)
self.allow_select_slice = True
self.slider.label.setText('Slice: %d / %d' % (slider_val,
self.n_slices))
self.view_label.setText('View size: %d x %d' % self.img_aview.shape[:-1])
def changeMask(self, val):
self.slice_box.setMaskPoints(self.mask_points_tab[val])
def changeContourMode(self, val):
self.slice_box.contour_mode = str(val)
self.slice_box.updateSlice()
def changeEraseMode(self, val):
self.slice_box.erase_mode = str(val)
def eraseVolume(self, pos, mode):
self.showStatus("Processing...")
xyz = pos + (self.actual_slice,)
p = tuple(np.array(xyz)[np.array(self.act_transposition)])
if self.seeds[p] > 0:
if mode == 'inside':
erase_reg(self.seeds, p, val=0)
elif mode == 'outside':
erase_reg(self.seeds, p, val=-1)
idxs = np.where(self.seeds < 0)
self.seeds.fill(0)
self.seeds[idxs] = 1
if self.contours is None:
contours = None
else:
contours = self.contours_aview[...,self.actual_slice]
self.slice_box.setSlice(self.img_aview[...,self.actual_slice],
self.seeds_aview[...,self.actual_slice],
contours)
self.showStatus("Done")
def cropUpdate(self, img):
for ii in VIEW_TABLE.iterkeys():
self.last_view_position[ii] = 0
self.actual_slice = 0
self.img = img
self.img_aview = self.img.transpose(self.act_transposition)
self.contours = None
self.contours_aview = None
self.seeds = np.zeros(self.img.shape, np.int8)
self.seeds_aview = self.seeds.transpose(self.act_transposition)
self.seeds_modified = False
vscale = self.voxel_scale[np.array(self.act_transposition)]
height = self.slice_box.height()
grid = height / float(self.img_aview.shape[1] * vscale[1])
mgrid = (grid * vscale[0], grid * vscale[1])
self.slice_box.resizeSlice(new_slice_size=self.img_aview.shape[:-1],
new_grid=mgrid)
self.slice_box.setSlice(self.img_aview[...,self.actual_slice],
self.seeds_aview[...,self.actual_slice],
None)
self.allow_select_slice = False
self.n_slices = self.img_aview.shape[2]
self.slider.setValue(self.actual_slice + 1)
self.slider.setRange(1, self.n_slices)
self.allow_select_slice = True
self.slider.label.setText('Slice: %d / %d' % (self.actual_slice + 1,
self.n_slices))
self.view_label.setText('View size: %d x %d' % self.img_aview.shape[:-1])
def getCropBounds(self):
nzs = self.seeds.nonzero()
cri = []
flag = True
for ii in range(3):
if nzs[ii].shape[0] == 0:
flag = False
break
smin, smax = np.min(nzs[ii]), np.max(nzs[ii])
if smin == smax:
flag = False
break
cri.append((smin, smax))
if flag:
cri = np.array(cri)
out = []
offset = []
for jj, ii in enumerate(cri):
out.append(slice(ii[0], ii[1] + 1))
offset.append(ii[0])
return np.array(offset), tuple(out)
else:
return None
def crop(self):
self.showStatus("Processing...")
crp = self.getCropBounds()
if crp is not None:
offset, cri = crp
crop = self.img[cri]
self.img = np.ascontiguousarray(crop)
self.offset += offset
self.showStatus('Done')
else:
self.showStatus('Region not selected!')
self.cropUpdate(self.img)
def recalculate(self, event):
self.saveSliceSeeds()
if np.abs(np.min(self.seeds) - np.max(self.seeds)) < 2:
self.showStatus('At least two regions must be marked!')
return
self.showStatus("Processing...")
# idx = 3
# s = random_walker(self.img[idx,:,:], self.seeds[idx,:,:])#, mode='cg_mg')
# plt.figure()
# plt.imshow(mark_boundaries(self.img[idx,:,:], s))
# plt.show()
# self.segmentation = np.zeros(self.img.shape)
# self.segmentation[idx,:,:] = s
self.segmentation = random_walker(self.img, self.seeds, mode='cg_mg')
self.setContours(self.segmentation - 1)
self.selectSlice(self.actual_slice)
# self.updateVolume()
self.showStatus("Done")
def deleteSliceSeeds(self, event):
self.seeds_aview[...,self.actual_slice] = 0
self.slice_box.setSlice(seeds=self.seeds_aview[...,self.actual_slice])
self.slice_box.updateSlice()
def resetSliceDraw(self, event):
seeds_orig_aview = self.seeds_orig.transpose(self.act_transposition)
self.seeds_aview[...,self.actual_slice] = seeds_orig_aview[...,self.actual_slice]
self.slice_box.setSlice(seeds=self.seeds_aview[...,self.actual_slice])
self.slice_box.updateSlice()
def quit(self, event):
self.close()
# def save(self, event):
# odp = os.path.expanduser("~/lisa_data")
# if not op.exists(odp):
# os.makedirs(odp)
#
# data = self.export()
# # data['version'] = self.version
# # data['experiment_caption'] = self.experiment_caption
# # data['lisa_operator_identifier'] = self.lisa_operator_identifier
# pth, filename = op.split(op.normpath(self.datapath))
# # filename += "-" + self.experiment_caption
# filepath = 'org-' + filename + '.pklz'
# filepath = op.join(odp, filepath)
# filepath = misc.suggest_filename(filepath)
# misc.obj_to_file(data, filepath, filetype='pklz')
#
# filepath = 'organ_last.pklz'
# filepath = op.join(odp, filepath)
# misc.obj_to_file(data, filepath, filetype='pklz')
# def export(self):
# slab = {}
# slab['none'] = 0
# slab['liver'] = 1
# slab['lesions'] = 6
# slab.update(self.slab)
#
# data = {}
# data['version'] = (1, 0, 1)
# data['data3d'] = self.img
# # data['crinfo'] = self.crinfo
# data['segmentation'] = self.segmentation
# data['slab'] = slab
# # data['voxelsize_mm'] = self.voxelsize_mm
# # data['orig_shape'] = self.orig_shape
# # data['processing_time'] = self.processing_time
# return data
def updateVolume(self):
text = 'Volume [mm3]:\n unknown'
if self.voxel_volume is not None:
if self.mode == 'draw':
vd = self.seeds
else:
vd = self.contours
if vd is not None:
nzs = vd.nonzero()
nn = nzs[0].shape[0]
text = 'Volume [mm3]:\n %.2e' % (nn * self.voxel_volume)
self.volume_label.setText(text)
def getROI(self):
crp = self.getCropBounds()
if crp is not None:
_, cri = crp
else:
cri = []
for jj, ii in enumerate(self.img.shape):
off = self.offset[jj]
cri.append(slice(off, off + ii))
return cri