def __init__(self, datap1=None, datap2=None):
QtGui.QWidget.__init__(self, parent=None)
# self.ui = Ui_MainWindow()
self.setStyleSheet("""QToolTip {
background-color: black;
color: white;
border: black solid 1px
}""")
self.ui = SegViewerGUI()
self.ui.setupUi(self)
# uprava stylu pro lepsi vizualizaci splitteru
QtGui.QApplication.setStyle(QtGui.QStyleFactory.create('Cleanlooks'))
# self.im = im
# self.labels = labels
self.mode = MODE_VIEWING
self.show_view_L = True
self.show_view_R = False
self.view_L = data_view_widget.SliceBox(self)
self.view_R = data_view_widget.SliceBox(self)
self.data_1 = Data.Data()
self.data_2 = Data.Data()
self.data_L = None
self.data_R = None
self.show_mode_L = SHOW_IM
self.show_mode_R = SHOW_IM
# load parameters
self.params = {
'win_l': 50,
'win_w': 350,
'alpha': 4,
'beta': 1,
'zoom': 0,
'scale': 0.25,
'perc': 30,
'k_std_h': 3,
'healthy_simple_estim': 0,
'prob_w': 0.0001,
'unaries_as_cdf': 0,
'bgd_label': 0,
'hypo_label': 1,
'healthy_label': 2,
'hyper_label': 3,
'data_dir': '/home/tomas/Data/liver_segmentation'
# 'voxel_size': (1, 1, 1)
}
self.params.update(self.load_parameters())
self.actual_slice_L = 0
self.actual_slice_R = 0
self.selected_objects_labels = None # list of objects' labels selected in tableview
# self.voxel_size = self.params['voxel_size']
self.view_widget_width = 50
self.two_views = False
if datap1 is not None or datap2 is not None:
self.setup_data(datap1, datap2)
# combo boxes - for figure views
self.ui.figure_L_CB.currentIndexChanged.connect(
self.figure_L_CB_callback)
self.ui.figure_R_CB.currentIndexChanged.connect(
self.figure_R_CB_callback)
data_viewer_layout = QtGui.QHBoxLayout()
# data_viewer_layout.addWidget(self.form_widget)
data_viewer_layout.addWidget(self.view_L)
data_viewer_layout.addWidget(self.view_R)
self.ui.viewer_F.setLayout(data_viewer_layout)
# connecting callbacks ----------------------------------
self.ui.view_L_BTN.clicked.connect(self.view_L_callback)
self.ui.view_R_BTN.clicked.connect(self.view_R_callback)
# show image data
self.ui.show_im_L_BTN.clicked.connect(self.show_im_L_callback)
self.ui.show_im_R_BTN.clicked.connect(self.show_im_R_callback)
# show label data
self.ui.show_labels_L_BTN.clicked.connect(self.show_labels_L_callback)
self.ui.show_labels_R_BTN.clicked.connect(self.show_labels_R_callback)
# show contours data
self.ui.show_contours_L_BTN.clicked.connect(
self.show_contours_L_callback)
self.ui.show_contours_R_BTN.clicked.connect(
self.show_contours_R_callback)
# connecting scrollbars
self.ui.slice_C_SB.valueChanged.connect(self.slider_C_changed)
self.ui.slice_L_SB.valueChanged.connect(self.slider_L_changed)
self.ui.slice_R_SB.valueChanged.connect(self.slider_R_changed)
# to be able to capture key press events immediately
self.setFocus()
def __init__(self, datap1=None, datap2=None):
QtGui.QWidget.__init__(self, parent=None)
# self.ui = Ui_MainWindow()
self.setStyleSheet("""QToolTip {
background-color: black;
color: white;
border: black solid 1px
}""")
self.ui = SegViewerGUI()
self.ui.setupUi(self)
# uprava stylu pro lepsi vizualizaci splitteru
QtGui.QApplication.setStyle(QtGui.QStyleFactory.create('Cleanlooks'))
# self.im = im
# self.labels = labels
self.mode = MODE_VIEWING
self.show_view_L = True
self.show_view_R = False
self.view_L = data_view_widget.SliceBox(self)
self.view_R = data_view_widget.SliceBox(self)
self.data_1 = Data.Data()
self.data_2 = Data.Data()
self.data_L = None
self.data_R = None
self.show_mode_L = SHOW_IM
self.show_mode_R = SHOW_IM
# load parameters
self.params = {
'win_l': 50,
'win_w': 350,
'alpha': 4,
'beta': 1,
'zoom': 0,
'scale': 0.25,
'perc': 30,
'k_std_h': 3,
'healthy_simple_estim': 0,
'prob_w': 0.0001,
'unaries_as_cdf': 0,
'bgd_label': 0,
'hypo_label': 1,
'healthy_label': 2,
'hyper_label': 3,
'data_dir': '/home/tomas/Data/liver_segmentation'
# 'voxel_size': (1, 1, 1)
}
self.params.update(self.load_parameters())
self.actual_slice_L = 0
self.actual_slice_R = 0
self.selected_objects_labels = None # list of objects' labels selected in tableview
# self.voxel_size = self.params['voxel_size']
self.view_widget_width = 50
self.two_views = False
if datap1 is not None or datap2 is not None:
self.setup_data(datap1, datap2)
# combo boxes - for figure views
self.ui.figure_L_CB.currentIndexChanged.connect(self.figure_L_CB_callback)
self.ui.figure_R_CB.currentIndexChanged.connect(self.figure_R_CB_callback)
data_viewer_layout = QtGui.QHBoxLayout()
# data_viewer_layout.addWidget(self.form_widget)
data_viewer_layout.addWidget(self.view_L)
data_viewer_layout.addWidget(self.view_R)
self.ui.viewer_F.setLayout(data_viewer_layout)
# connecting callbacks ----------------------------------
self.ui.view_L_BTN.clicked.connect(self.view_L_callback)
self.ui.view_R_BTN.clicked.connect(self.view_R_callback)
# show image data
self.ui.show_im_L_BTN.clicked.connect(self.show_im_L_callback)
self.ui.show_im_R_BTN.clicked.connect(self.show_im_R_callback)
# show label data
self.ui.show_labels_L_BTN.clicked.connect(self.show_labels_L_callback)
self.ui.show_labels_R_BTN.clicked.connect(self.show_labels_R_callback)
# show contours data
self.ui.show_contours_L_BTN.clicked.connect(self.show_contours_L_callback)
self.ui.show_contours_R_BTN.clicked.connect(self.show_contours_R_callback)
# connecting scrollbars
self.ui.slice_C_SB.valueChanged.connect(self.slider_C_changed)
self.ui.slice_L_SB.valueChanged.connect(self.slider_L_changed)
self.ui.slice_R_SB.valueChanged.connect(self.slider_R_changed)
# to be able to capture key press events immediately
self.setFocus()
class SegViewer(QtGui.QMainWindow):
"""Main class of the programm."""
# def __init__(self, datap_1=None, datap_2=None, fname_1=None, fname_2=None, disp_smoothed=False, parent=None):
def __init__(self, datap1=None, datap2=None):
QtGui.QWidget.__init__(self, parent=None)
# self.ui = Ui_MainWindow()
self.setStyleSheet("""QToolTip {
background-color: black;
color: white;
border: black solid 1px
}""")
self.ui = SegViewerGUI()
self.ui.setupUi(self)
# uprava stylu pro lepsi vizualizaci splitteru
QtGui.QApplication.setStyle(QtGui.QStyleFactory.create('Cleanlooks'))
# self.im = im
# self.labels = labels
self.mode = MODE_VIEWING
self.show_view_L = True
self.show_view_R = False
self.view_L = data_view_widget.SliceBox(self)
self.view_R = data_view_widget.SliceBox(self)
self.data_1 = Data.Data()
self.data_2 = Data.Data()
self.data_L = None
self.data_R = None
self.show_mode_L = SHOW_IM
self.show_mode_R = SHOW_IM
# load parameters
self.params = {
'win_l': 50,
'win_w': 350,
'alpha': 4,
'beta': 1,
'zoom': 0,
'scale': 0.25,
'perc': 30,
'k_std_h': 3,
'healthy_simple_estim': 0,
'prob_w': 0.0001,
'unaries_as_cdf': 0,
'bgd_label': 0,
'hypo_label': 1,
'healthy_label': 2,
'hyper_label': 3,
'data_dir': '/home/tomas/Data/liver_segmentation'
# 'voxel_size': (1, 1, 1)
}
self.params.update(self.load_parameters())
self.actual_slice_L = 0
self.actual_slice_R = 0
self.selected_objects_labels = None # list of objects' labels selected in tableview
# self.voxel_size = self.params['voxel_size']
self.view_widget_width = 50
self.two_views = False
if datap1 is not None or datap2 is not None:
self.setup_data(datap1, datap2)
# combo boxes - for figure views
self.ui.figure_L_CB.currentIndexChanged.connect(
self.figure_L_CB_callback)
self.ui.figure_R_CB.currentIndexChanged.connect(
self.figure_R_CB_callback)
data_viewer_layout = QtGui.QHBoxLayout()
# data_viewer_layout.addWidget(self.form_widget)
data_viewer_layout.addWidget(self.view_L)
data_viewer_layout.addWidget(self.view_R)
self.ui.viewer_F.setLayout(data_viewer_layout)
# connecting callbacks ----------------------------------
self.ui.view_L_BTN.clicked.connect(self.view_L_callback)
self.ui.view_R_BTN.clicked.connect(self.view_R_callback)
# show image data
self.ui.show_im_L_BTN.clicked.connect(self.show_im_L_callback)
self.ui.show_im_R_BTN.clicked.connect(self.show_im_R_callback)
# show label data
self.ui.show_labels_L_BTN.clicked.connect(self.show_labels_L_callback)
self.ui.show_labels_R_BTN.clicked.connect(self.show_labels_R_callback)
# show contours data
self.ui.show_contours_L_BTN.clicked.connect(
self.show_contours_L_callback)
self.ui.show_contours_R_BTN.clicked.connect(
self.show_contours_R_callback)
# connecting scrollbars
self.ui.slice_C_SB.valueChanged.connect(self.slider_C_changed)
self.ui.slice_L_SB.valueChanged.connect(self.slider_L_changed)
self.ui.slice_R_SB.valueChanged.connect(self.slider_R_changed)
# to be able to capture key press events immediately
self.setFocus()
def setup_data(self, datap1=None, datap2=None):
# DATA ---------------------------------------------
if datap1 is not None:
self.data_1 = Data.Data()
self.data_1.create_data(datap1, 'datap1', self.params)
self.params['voxel_size'] = datap1['voxelsize_mm']
self.params['voxels2ml_k'] = np.prod(
self.params['voxel_size']) * 0.001
if datap2 is not None:
self.data_2 = Data.Data()
self.data_2.create_data(datap2, 'datap2', self.params)
if self.data_1.loaded:
#seting up figure and data_L, data_R
self.ui.figure_L_CB.addItem(self.data_1.filename.split('/')[-1])
self.ui.figure_R_CB.addItem(self.data_1.filename.split('/')[-1])
self.data_L = self.data_1
self.active_data_idx = 1
self.active_data = self.data_1
if not self.data_2.loaded:
self.data_R = self.data_1
self.ui.slice_R_SB.setMaximum(self.data_1.n_slices - 1)
self.ui.slice_C_SB.setMaximum(self.data_1.n_slices - 1)
self.ui.slice_L_SB.setMaximum(self.data_1.n_slices - 1)
self.ui.show_labels_L_BTN.setEnabled(True)
self.ui.show_contours_L_BTN.setEnabled(True)
if self.data_2.loaded:
self.ui.figure_L_CB.addItem(self.data_2.filename.split('/')[-1])
self.ui.figure_R_CB.addItem(self.data_2.filename.split('/')[-1])
self.data_R = self.data_2
self.ui.figure_R_CB.setCurrentIndex(1)
if not self.data_1.loaded:
self.data_L = self.data_2
self.active_data = self.data_2
self.active_data_idx = 2
self.ui.slice_C_SB.setMaximum(self.data_2.n_slices - 1)
self.ui.slice_L_SB.setMaximum(self.data_2.n_slices - 1)
self.ui.show_labels_L_BTN.setEnabled(True)
self.ui.show_contours_L_BTN.setEnabled(True)
self.ui.slice_R_SB.setMaximum(self.data_2.n_slices - 1)
if self.data_L is not None:
self.view_L.setup_widget(self.data_L.data_aview.shape[:-1],
self.params['voxel_size'][1:])
self.view_L.setCW(self.params['win_l'], 'c')
self.view_L.setCW(self.params['win_w'], 'w')
self.view_L.setSlice(self.data_L.data_aview[..., 0])
# mouse click signal
# self.view_L.mouseClickSignal.connect(self.mouse_click_event)
# self.view_L.mousePressEvent = self.view_L.myMousePressEvent
if self.data_R is not None:
self.view_R.setup_widget(self.data_R.data_aview.shape[:-1],
self.params['voxel_size'][1:])
self.view_R.setCW(self.params['win_l'], 'c')
self.view_R.setCW(self.params['win_w'], 'w')
self.view_R.setSlice(self.data_R.data_aview[..., 0])
if not self.show_view_L:
self.view_L.setVisible(False)
if not self.show_view_R:
self.view_R.setVisible(False)
def keyPressEvent(self, QKeyEvent):
print 'key event: ',
key = QKeyEvent.key()
if key == QtCore.Qt.Key_Escape:
print 'Escape'
self.close()
else:
print key, ' - unrecognized hot key.'
def load_parameters(self, config_path='config.ini'):
config = ConfigParser.ConfigParser()
config.read(config_path)
params = dict()
# an automatic way
for section in config.sections():
for option in config.options(section):
try:
params[option] = config.getint(section, option)
except ValueError:
try:
params[option] = config.getfloat(section, option)
except ValueError:
if option == 'voxel_size':
str = config.get(section, option)
params[option] = np.array(map(
int, str.split(', ')))
else:
params[option] = config.get(section, option)
return params
def scroll_event(self, value, who):
if who == 0: # left viewer
new = self.actual_slice_L + value
if (new < 0) or (new >= self.data_L.n_slices):
return
elif who == 1: # right viewer
new = self.actual_slice_R + value
if (new < 0) or (new >= self.data_R.n_slices):
return
def slider_C_changed(self, val):
if val == self.actual_slice_L:
return
if (val >= 0) and (val < self.data_L.n_slices):
diff = val - self.actual_slice_L
self.actual_slice_L = val
else:
return
new_slice_R = self.actual_slice_R + diff
if new_slice_R < 0:
new_slice_R = 0
elif new_slice_R >= self.data_R.n_slices:
new_slice_R = self.data_R.n_slices - 1
self.actual_slice_R = new_slice_R
self.ui.slice_L_SB.setValue(self.actual_slice_L)
self.ui.slice_R_SB.setValue(self.actual_slice_R)
im_L = self.get_image('L')
im_R = self.get_image('R')
if self.show_mode_L == SHOW_CONTOURS:
labels_L = self.data_L.labels_filt[self.actual_slice_L, :, :]
# obj_centers_L = self.data_L.object_centers_filt[self.actual_slice_L, ...]
else:
labels_L = None
# obj_centers_L = None
if self.show_mode_R == SHOW_CONTOURS:
labels_R = self.data_R.labels_filt[self.actual_slice_R, :, :]
# obj_centers_R = self.data_R.object_centers_filt[self.actual_slice_R, ...]
else:
labels_R = None
# obj_centers_R = None
# self.view_L.setSlice(im_L, contours=labels_L, centers=obj_centers_L)
# self.view_R.setSlice(im_R, contours=labels_R, centers=obj_centers_R)
self.view_L.setSlice(im_L, contours=labels_L)
self.view_R.setSlice(im_R, contours=labels_R)
self.ui.slice_number_L_LBL.setText(
'%i/%i' % (self.actual_slice_L + 1, self.data_L.n_slices))
# self.ui.slice_number_C_LBL.setText('slice # = %i/%i' % (self.actual_slice_L + 1, self.data_L.n_slices))
def slider_L_changed(self, val):
if val == self.actual_slice_L:
return
if (val >= 0) and (val < self.data_L.n_slices):
self.actual_slice_L = val
else:
return
self.ui.slice_C_SB.setValue(self.actual_slice_L)
im_L = self.get_image('L')
if self.show_mode_L == SHOW_CONTOURS:
labels_L = self.data_L.labels_filt[self.actual_slice_L, :, :]
# obj_centers = self.data_L.object_centers_filt[self.actual_slice_L, ...]
obj_centers = None
else:
labels_L = None
obj_centers = None
# self.view_L.setSlice(im_L, contours=labels_L, centers=obj_centers)
self.view_L.setSlice(im_L, contours=labels_L)
self.ui.slice_number_L_LBL.setText(
'%i/%i' % (self.actual_slice_L + 1, self.data_L.n_slices))
# self.ui.slice_number_C_LBL.setText('slice # = %i/%i' % (self.actual_slice_L + 1, self.data_L.n_slices))
def slider_R_changed(self, val):
if (val >= 0) and (val < self.data_R.n_slices):
self.actual_slice_R = val
else:
return
self.ui.slice_number_R_LBL.setText(
'%i/%i' % (self.actual_slice_R + 1, self.data_R.n_slices))
im_R = self.get_image('R')
if self.show_mode_R == SHOW_CONTOURS:
labels_R = self.data_R.labels_filt[self.actual_slice_R, :, :]
# obj_centers = self.data_R.object_centers_filt[self.actual_slice_R, ...]
obj_centers = None
else:
labels_R = None
obj_centers = None
# self.view_R.setSlice(im_R, contours=labels_R, centers=obj_centers)
self.view_R.setSlice(im_R, contours=labels_R)
def view_L_callback(self):
if self.show_view_L != self.show_view_R: # logical XOR
self.one_view_size = self.size()
self.show_view_L = not self.show_view_L
self.view_L.setVisible(self.show_view_L)
# enabling and disabling other toolbar icons
self.ui.show_im_L_BTN.setEnabled(self.show_view_L)
# if self.show_view_L and self.data_L.labels is not None:
if self.show_view_L and self.data_L.processed:
self.ui.show_labels_L_BTN.setEnabled(True)
self.ui.show_contours_L_BTN.setEnabled(True)
else:
self.ui.show_labels_L_BTN.setEnabled(False)
self.ui.show_contours_L_BTN.setEnabled(False)
# self.statusBar().showMessage('Left view set to %s' % self.show_view_L)
# print 'view_1 set to', self.show_view_1
self.view_L.update()
# resizing back to one view size
if self.show_view_L != self.show_view_R: # logical XOR
self.setMinimumSize(self.one_view_size)
self.resize(self.one_view_size)
self.setMinimumSize(QtCore.QSize(0, 0))
def view_R_callback(self):
if self.show_view_L != self.show_view_R: # logical XOR
self.one_view_size = self.size()
self.show_view_R = not self.show_view_R
self.view_R.setVisible(self.show_view_R)
# enabling and disabling other toolbar icons
self.ui.show_im_R_BTN.setEnabled(not self.ui.show_im_R_BTN.isEnabled())
if self.show_view_R and self.data_R.processed:
self.ui.show_labels_R_BTN.setEnabled(True)
self.ui.show_contours_R_BTN.setEnabled(True)
else:
self.ui.show_labels_R_BTN.setEnabled(False)
self.ui.show_contours_R_BTN.setEnabled(False)
self.view_R.update()
# resizing back to one view size
if self.show_view_L != self.show_view_R: # logical XOR
self.setMinimumSize(self.one_view_size)
self.resize(self.one_view_size)
self.setMinimumSize(QtCore.QSize(0, 0))
def show_im_L_callback(self):
self.show_mode_L = SHOW_IM
self.view_L.show_mode = self.view_L.SHOW_IM
im = self.get_image('L')
self.view_L.setSlice(im)
def show_im_R_callback(self):
self.show_mode_R = SHOW_IM
self.view_R.show_mode = self.view_R.SHOW_IM
im = self.get_image('R')
self.view_R.setSlice(im)
def show_labels_L_callback(self):
self.show_mode_L = SHOW_LABELS
self.view_L.show_mode = self.view_L.SHOW_LABELS
im = self.get_image('L')
self.view_L.setSlice(im)
def show_labels_R_callback(self):
self.show_mode_R = SHOW_LABELS
self.view_R.show_mode = self.view_R.SHOW_LABELS
im = self.get_image('R')
self.view_R.setSlice(im)
def show_contours_L_callback(self):
if self.show_mode_L == SHOW_CONTOURS:
self.view_L.contours_mode_is_fill = not self.view_L.contours_mode_is_fill
self.show_contours_L()
def show_contours_L(self):
self.show_mode_L = SHOW_CONTOURS
self.view_L.show_mode = self.view_L.SHOW_CONTOURS
im = self.get_image('L')
labels = self.data_L.labels_filt[self.actual_slice_L, :, :]
self.view_L.setSlice(im, contours=labels)
def show_contours_R_callback(self):
if self.show_mode_R == SHOW_CONTOURS:
self.view_R.contours_mode_is_fill = not self.view_R.contours_mode_is_fill
self.show_contours_R()
def show_contours_R(self):
self.show_mode_R = SHOW_CONTOURS
self.view_R.show_mode = self.view_R.SHOW_CONTOURS
im = self.get_image('R')
labels = self.data_R.labels_filt[self.actual_slice_R, :, :]
self.view_R.setSlice(im, contours=labels)
def update_view_L(self):
if self.show_view_L:
if self.view_L.show_mode == self.view_L.SHOW_LABELS:
self.show_labels_L_callback()
elif self.view_L.show_mode == self.view_L.SHOW_CONTOURS:
self.show_contours_L()
def update_view_R(self):
if self.show_view_R:
if self.view_R.show_mode == self.view_R.SHOW_LABELS:
self.show_labels_R_callback()
elif self.view_R.show_mode == self.view_R.SHOW_CONTOURS:
self.show_contours_R()
def figure_L_CB_callback(self):
if self.ui.figure_L_CB.currentIndex() == 0:
self.data_L = self.data_1
elif self.ui.figure_L_CB.currentIndex() == 1:
self.data_L = self.data_2
if self.actual_slice_L >= self.data_L.n_slices:
self.actual_slice_L = self.data_L.n_slices - 1
self.ui.slice_L_SB.setMaximum(self.data_L.n_slices - 1)
self.ui.slice_C_SB.setMaximum(self.data_L.n_slices - 1)
if (self.data_L.labels is not None) and self.show_view_L:
self.ui.show_labels_L_BTN.setEnabled(True)
self.ui.show_contours_L_BTN.setEnabled(True)
else:
self.ui.show_labels_L_BTN.setEnabled(False)
self.ui.show_contours_L_BTN.setEnabled(False)
self.view_L.reinit((self.data_L.shape[2], self.data_L.shape[1]))
self.show_im_L_callback()
def figure_R_CB_callback(self):
if self.ui.figure_R_CB.currentIndex() == 0:
self.data_R = self.data_1
elif self.ui.figure_R_CB.currentIndex() == 1:
self.data_R = self.data_2
if self.actual_slice_R >= self.data_R.n_slices:
self.actual_slice_R = self.data_R.n_slices - 1
self.ui.slice_R_SB.setMaximum(self.data_R.n_slices - 1)
if (self.data_R.labels is not None) and self.show_view_R:
self.ui.show_labels_R_BTN.setEnabled(True)
self.ui.show_contours_R_BTN.setEnabled(True)
else:
self.ui.show_labels_R_BTN.setEnabled(False)
self.ui.show_contours_R_BTN.setEnabled(False)
# self.view_R.reinit(self.data_R.shape[2:0:-1])
self.view_R.reinit((self.data_R.shape[2], self.data_R.shape[1]))
self.show_im_R_callback()
def get_image(self, site):
im = None
if site == 'L':
if self.show_mode_L == SHOW_IM or self.show_mode_L == SHOW_CONTOURS:
im = self.data_L.data_aview[..., self.actual_slice_L]
elif self.show_mode_L == SHOW_LABELS:
# im = self.data_L.labels_aview[...,self.actual_slice_L]
im = self.data_L.labels_filt_aview[..., self.actual_slice_L]
# elif self.show_mode_L == SHOW_FILTERED_LABELS:
# im = self.data_L.labels_filt_aview[...,self.actual_slice_L]
elif site == 'R':
if self.show_mode_R == SHOW_IM or self.show_mode_R == SHOW_CONTOURS:
im = self.data_R.data_aview[..., self.actual_slice_R]
elif self.show_mode_R == SHOW_LABELS:
# im = self.data_R.labels_aview[...,self.actual_slice_R]
im = self.data_R.labels_filt_aview[..., self.actual_slice_R]
# elif self.show_mode_R == SHOW_FILTERED_LABELS:
# im = self.data_R.labels_filt_aview[...,self.actual_slice_R]
return im
class SegViewer(QtGui.QMainWindow):
"""Main class of the programm."""
# def __init__(self, datap_1=None, datap_2=None, fname_1=None, fname_2=None, disp_smoothed=False, parent=None):
def __init__(self, datap1=None, datap2=None):
QtGui.QWidget.__init__(self, parent=None)
# self.ui = Ui_MainWindow()
self.setStyleSheet("""QToolTip {
background-color: black;
color: white;
border: black solid 1px
}""")
self.ui = SegViewerGUI()
self.ui.setupUi(self)
# uprava stylu pro lepsi vizualizaci splitteru
QtGui.QApplication.setStyle(QtGui.QStyleFactory.create('Cleanlooks'))
# self.im = im
# self.labels = labels
self.mode = MODE_VIEWING
self.show_view_L = True
self.show_view_R = False
self.view_L = data_view_widget.SliceBox(self)
self.view_R = data_view_widget.SliceBox(self)
self.data_1 = Data.Data()
self.data_2 = Data.Data()
self.data_L = None
self.data_R = None
self.show_mode_L = SHOW_IM
self.show_mode_R = SHOW_IM
# load parameters
self.params = {
'win_l': 50,
'win_w': 350,
'alpha': 4,
'beta': 1,
'zoom': 0,
'scale': 0.25,
'perc': 30,
'k_std_h': 3,
'healthy_simple_estim': 0,
'prob_w': 0.0001,
'unaries_as_cdf': 0,
'bgd_label': 0,
'hypo_label': 1,
'healthy_label': 2,
'hyper_label': 3,
'data_dir': '/home/tomas/Data/liver_segmentation'
# 'voxel_size': (1, 1, 1)
}
self.params.update(self.load_parameters())
self.actual_slice_L = 0
self.actual_slice_R = 0
self.selected_objects_labels = None # list of objects' labels selected in tableview
# self.voxel_size = self.params['voxel_size']
self.view_widget_width = 50
self.two_views = False
if datap1 is not None or datap2 is not None:
self.setup_data(datap1, datap2)
# combo boxes - for figure views
self.ui.figure_L_CB.currentIndexChanged.connect(self.figure_L_CB_callback)
self.ui.figure_R_CB.currentIndexChanged.connect(self.figure_R_CB_callback)
data_viewer_layout = QtGui.QHBoxLayout()
# data_viewer_layout.addWidget(self.form_widget)
data_viewer_layout.addWidget(self.view_L)
data_viewer_layout.addWidget(self.view_R)
self.ui.viewer_F.setLayout(data_viewer_layout)
# connecting callbacks ----------------------------------
self.ui.view_L_BTN.clicked.connect(self.view_L_callback)
self.ui.view_R_BTN.clicked.connect(self.view_R_callback)
# show image data
self.ui.show_im_L_BTN.clicked.connect(self.show_im_L_callback)
self.ui.show_im_R_BTN.clicked.connect(self.show_im_R_callback)
# show label data
self.ui.show_labels_L_BTN.clicked.connect(self.show_labels_L_callback)
self.ui.show_labels_R_BTN.clicked.connect(self.show_labels_R_callback)
# show contours data
self.ui.show_contours_L_BTN.clicked.connect(self.show_contours_L_callback)
self.ui.show_contours_R_BTN.clicked.connect(self.show_contours_R_callback)
# connecting scrollbars
self.ui.slice_C_SB.valueChanged.connect(self.slider_C_changed)
self.ui.slice_L_SB.valueChanged.connect(self.slider_L_changed)
self.ui.slice_R_SB.valueChanged.connect(self.slider_R_changed)
# to be able to capture key press events immediately
self.setFocus()
def setup_data(self, datap1=None, datap2=None):
# DATA ---------------------------------------------
if datap1 is not None:
self.data_1 = Data.Data()
self.data_1.create_data(datap1, 'datap1', self.params)
self.params['voxel_size'] = datap1['voxelsize_mm']
self.params['voxels2ml_k'] = np.prod(self.params['voxel_size']) * 0.001
if datap2 is not None:
self.data_2 = Data.Data()
self.data_2.create_data(datap2, 'datap2', self.params)
if self.data_1.loaded:
#seting up figure and data_L, data_R
self.ui.figure_L_CB.addItem(self.data_1.filename.split('/')[-1])
self.ui.figure_R_CB.addItem(self.data_1.filename.split('/')[-1])
self.data_L = self.data_1
self.active_data_idx = 1
self.active_data = self.data_1
if not self.data_2.loaded:
self.data_R = self.data_1
self.ui.slice_R_SB.setMaximum(self.data_1.n_slices - 1)
self.ui.slice_C_SB.setMaximum(self.data_1.n_slices - 1)
self.ui.slice_L_SB.setMaximum(self.data_1.n_slices - 1)
self.ui.show_labels_L_BTN.setEnabled(True)
self.ui.show_contours_L_BTN.setEnabled(True)
if self.data_2.loaded:
self.ui.figure_L_CB.addItem(self.data_2.filename.split('/')[-1])
self.ui.figure_R_CB.addItem(self.data_2.filename.split('/')[-1])
self.data_R = self.data_2
self.ui.figure_R_CB.setCurrentIndex(1)
if not self.data_1.loaded:
self.data_L = self.data_2
self.active_data = self.data_2
self.active_data_idx = 2
self.ui.slice_C_SB.setMaximum(self.data_2.n_slices - 1)
self.ui.slice_L_SB.setMaximum(self.data_2.n_slices - 1)
self.ui.show_labels_L_BTN.setEnabled(True)
self.ui.show_contours_L_BTN.setEnabled(True)
self.ui.slice_R_SB.setMaximum(self.data_2.n_slices - 1)
if self.data_L is not None:
self.view_L.setup_widget(self.data_L.data_aview.shape[:-1], self.params['voxel_size'][1:])
self.view_L.setCW(self.params['win_l'], 'c')
self.view_L.setCW(self.params['win_w'], 'w')
self.view_L.setSlice(self.data_L.data_aview[...,0])
# mouse click signal
# self.view_L.mouseClickSignal.connect(self.mouse_click_event)
# self.view_L.mousePressEvent = self.view_L.myMousePressEvent
if self.data_R is not None:
self.view_R.setup_widget(self.data_R.data_aview.shape[:-1], self.params['voxel_size'][1:])
self.view_R.setCW(self.params['win_l'], 'c')
self.view_R.setCW(self.params['win_w'], 'w')
self.view_R.setSlice(self.data_R.data_aview[...,0])
if not self.show_view_L:
self.view_L.setVisible(False)
if not self.show_view_R:
self.view_R.setVisible(False)
def keyPressEvent(self, QKeyEvent):
print 'key event: ',
key = QKeyEvent.key()
if key == QtCore.Qt.Key_Escape:
print 'Escape'
self.close()
else:
print key, ' - unrecognized hot key.'
def load_parameters(self, config_path='config.ini'):
config = ConfigParser.ConfigParser()
config.read(config_path)
params = dict()
# an automatic way
for section in config.sections():
for option in config.options(section):
try:
params[option] = config.getint(section, option)
except ValueError:
try:
params[option] = config.getfloat(section, option)
except ValueError:
if option == 'voxel_size':
str = config.get(section, option)
params[option] = np.array(map(int, str.split(', ')))
else:
params[option] = config.get(section, option)
return params
def scroll_event(self, value, who):
if who == 0: # left viewer
new = self.actual_slice_L + value
if (new < 0) or (new >= self.data_L.n_slices):
return
elif who == 1: # right viewer
new = self.actual_slice_R + value
if (new < 0) or (new >= self.data_R.n_slices):
return
def slider_C_changed(self, val):
if val == self.actual_slice_L:
return
if (val >= 0) and (val < self.data_L.n_slices):
diff = val - self.actual_slice_L
self.actual_slice_L = val
else:
return
new_slice_R = self.actual_slice_R + diff
if new_slice_R < 0:
new_slice_R = 0
elif new_slice_R >= self.data_R.n_slices:
new_slice_R = self.data_R.n_slices - 1
self.actual_slice_R = new_slice_R
self.ui.slice_L_SB.setValue(self.actual_slice_L)
self.ui.slice_R_SB.setValue(self.actual_slice_R)
im_L = self.get_image('L')
im_R = self.get_image('R')
if self.show_mode_L == SHOW_CONTOURS:
labels_L = self.data_L.labels_filt[self.actual_slice_L, :, :]
# obj_centers_L = self.data_L.object_centers_filt[self.actual_slice_L, ...]
else:
labels_L = None
# obj_centers_L = None
if self.show_mode_R == SHOW_CONTOURS:
labels_R = self.data_R.labels_filt[self.actual_slice_R, :, :]
# obj_centers_R = self.data_R.object_centers_filt[self.actual_slice_R, ...]
else:
labels_R = None
# obj_centers_R = None
# self.view_L.setSlice(im_L, contours=labels_L, centers=obj_centers_L)
# self.view_R.setSlice(im_R, contours=labels_R, centers=obj_centers_R)
self.view_L.setSlice(im_L, contours=labels_L)
self.view_R.setSlice(im_R, contours=labels_R)
self.ui.slice_number_L_LBL.setText('%i/%i' % (self.actual_slice_L + 1, self.data_L.n_slices))
# self.ui.slice_number_C_LBL.setText('slice # = %i/%i' % (self.actual_slice_L + 1, self.data_L.n_slices))
def slider_L_changed(self, val):
if val == self.actual_slice_L:
return
if (val >= 0) and (val < self.data_L.n_slices):
self.actual_slice_L = val
else:
return
self.ui.slice_C_SB.setValue(self.actual_slice_L)
im_L = self.get_image('L')
if self.show_mode_L == SHOW_CONTOURS:
labels_L = self.data_L.labels_filt[self.actual_slice_L, :, :]
# obj_centers = self.data_L.object_centers_filt[self.actual_slice_L, ...]
obj_centers = None
else:
labels_L = None
obj_centers = None
# self.view_L.setSlice(im_L, contours=labels_L, centers=obj_centers)
self.view_L.setSlice(im_L, contours=labels_L)
self.ui.slice_number_L_LBL.setText('%i/%i' % (self.actual_slice_L + 1, self.data_L.n_slices))
# self.ui.slice_number_C_LBL.setText('slice # = %i/%i' % (self.actual_slice_L + 1, self.data_L.n_slices))
def slider_R_changed(self, val):
if (val >= 0) and (val < self.data_R.n_slices):
self.actual_slice_R = val
else:
return
self.ui.slice_number_R_LBL.setText('%i/%i' % (self.actual_slice_R + 1, self.data_R.n_slices))
im_R = self.get_image('R')
if self.show_mode_R == SHOW_CONTOURS:
labels_R = self.data_R.labels_filt[self.actual_slice_R, :, :]
# obj_centers = self.data_R.object_centers_filt[self.actual_slice_R, ...]
obj_centers = None
else:
labels_R = None
obj_centers = None
# self.view_R.setSlice(im_R, contours=labels_R, centers=obj_centers)
self.view_R.setSlice(im_R, contours=labels_R)
def view_L_callback(self):
if self.show_view_L != self.show_view_R: # logical XOR
self.one_view_size = self.size()
self.show_view_L = not self.show_view_L
self.view_L.setVisible(self.show_view_L)
# enabling and disabling other toolbar icons
self.ui.show_im_L_BTN.setEnabled(self.show_view_L)
# if self.show_view_L and self.data_L.labels is not None:
if self.show_view_L and self.data_L.processed:
self.ui.show_labels_L_BTN.setEnabled(True)
self.ui.show_contours_L_BTN.setEnabled(True)
else:
self.ui.show_labels_L_BTN.setEnabled(False)
self.ui.show_contours_L_BTN.setEnabled(False)
# self.statusBar().showMessage('Left view set to %s' % self.show_view_L)
# print 'view_1 set to', self.show_view_1
self.view_L.update()
# resizing back to one view size
if self.show_view_L != self.show_view_R: # logical XOR
self.setMinimumSize(self.one_view_size)
self.resize(self.one_view_size)
self.setMinimumSize(QtCore.QSize(0, 0))
def view_R_callback(self):
if self.show_view_L != self.show_view_R: # logical XOR
self.one_view_size = self.size()
self.show_view_R = not self.show_view_R
self.view_R.setVisible(self.show_view_R)
# enabling and disabling other toolbar icons
self.ui.show_im_R_BTN.setEnabled(not self.ui.show_im_R_BTN.isEnabled())
if self.show_view_R and self.data_R.processed:
self.ui.show_labels_R_BTN.setEnabled(True)
self.ui.show_contours_R_BTN.setEnabled(True)
else:
self.ui.show_labels_R_BTN.setEnabled(False)
self.ui.show_contours_R_BTN.setEnabled(False)
self.view_R.update()
# resizing back to one view size
if self.show_view_L != self.show_view_R: # logical XOR
self.setMinimumSize(self.one_view_size)
self.resize(self.one_view_size)
self.setMinimumSize(QtCore.QSize(0, 0))
def show_im_L_callback(self):
self.show_mode_L = SHOW_IM
self.view_L.show_mode = self.view_L.SHOW_IM
im = self.get_image('L')
self.view_L.setSlice(im)
def show_im_R_callback(self):
self.show_mode_R = SHOW_IM
self.view_R.show_mode = self.view_R.SHOW_IM
im = self.get_image('R')
self.view_R.setSlice(im)
def show_labels_L_callback(self):
self.show_mode_L = SHOW_LABELS
self.view_L.show_mode = self.view_L.SHOW_LABELS
im = self.get_image('L')
self.view_L.setSlice(im)
def show_labels_R_callback(self):
self.show_mode_R = SHOW_LABELS
self.view_R.show_mode = self.view_R.SHOW_LABELS
im = self.get_image('R')
self.view_R.setSlice(im)
def show_contours_L_callback(self):
if self.show_mode_L == SHOW_CONTOURS:
self.view_L.contours_mode_is_fill = not self.view_L.contours_mode_is_fill
self.show_contours_L()
def show_contours_L(self):
self.show_mode_L = SHOW_CONTOURS
self.view_L.show_mode = self.view_L.SHOW_CONTOURS
im = self.get_image('L')
labels = self.data_L.labels_filt[self.actual_slice_L, :, :]
self.view_L.setSlice(im, contours=labels)
def show_contours_R_callback(self):
if self.show_mode_R == SHOW_CONTOURS:
self.view_R.contours_mode_is_fill = not self.view_R.contours_mode_is_fill
self.show_contours_R()
def show_contours_R(self):
self.show_mode_R = SHOW_CONTOURS
self.view_R.show_mode = self.view_R.SHOW_CONTOURS
im = self.get_image('R')
labels = self.data_R.labels_filt[self.actual_slice_R, :, :]
self.view_R.setSlice(im, contours=labels)
def update_view_L(self):
if self.show_view_L:
if self.view_L.show_mode == self.view_L.SHOW_LABELS:
self.show_labels_L_callback()
elif self.view_L.show_mode == self.view_L.SHOW_CONTOURS:
self.show_contours_L()
def update_view_R(self):
if self.show_view_R:
if self.view_R.show_mode == self.view_R.SHOW_LABELS:
self.show_labels_R_callback()
elif self.view_R.show_mode == self.view_R.SHOW_CONTOURS:
self.show_contours_R()
def figure_L_CB_callback(self):
if self.ui.figure_L_CB.currentIndex() == 0:
self.data_L = self.data_1
elif self.ui.figure_L_CB.currentIndex() == 1:
self.data_L = self.data_2
if self.actual_slice_L >= self.data_L.n_slices:
self.actual_slice_L = self.data_L.n_slices - 1
self.ui.slice_L_SB.setMaximum(self.data_L.n_slices - 1)
self.ui.slice_C_SB.setMaximum(self.data_L.n_slices - 1)
if (self.data_L.labels is not None) and self.show_view_L:
self.ui.show_labels_L_BTN.setEnabled(True)
self.ui.show_contours_L_BTN.setEnabled(True)
else:
self.ui.show_labels_L_BTN.setEnabled(False)
self.ui.show_contours_L_BTN.setEnabled(False)
self.view_L.reinit((self.data_L.shape[2], self.data_L.shape[1]))
self.show_im_L_callback()
def figure_R_CB_callback(self):
if self.ui.figure_R_CB.currentIndex() == 0:
self.data_R = self.data_1
elif self.ui.figure_R_CB.currentIndex() == 1:
self.data_R = self.data_2
if self.actual_slice_R >= self.data_R.n_slices:
self.actual_slice_R = self.data_R.n_slices - 1
self.ui.slice_R_SB.setMaximum(self.data_R.n_slices - 1)
if (self.data_R.labels is not None) and self.show_view_R:
self.ui.show_labels_R_BTN.setEnabled(True)
self.ui.show_contours_R_BTN.setEnabled(True)
else:
self.ui.show_labels_R_BTN.setEnabled(False)
self.ui.show_contours_R_BTN.setEnabled(False)
# self.view_R.reinit(self.data_R.shape[2:0:-1])
self.view_R.reinit((self.data_R.shape[2], self.data_R.shape[1]))
self.show_im_R_callback()
def get_image(self, site):
im = None
if site == 'L':
if self.show_mode_L == SHOW_IM or self.show_mode_L == SHOW_CONTOURS:
im = self.data_L.data_aview[..., self.actual_slice_L]
elif self.show_mode_L == SHOW_LABELS:
# im = self.data_L.labels_aview[...,self.actual_slice_L]
im = self.data_L.labels_filt_aview[..., self.actual_slice_L]
# elif self.show_mode_L == SHOW_FILTERED_LABELS:
# im = self.data_L.labels_filt_aview[...,self.actual_slice_L]
elif site == 'R':
if self.show_mode_R == SHOW_IM or self.show_mode_R == SHOW_CONTOURS:
im = self.data_R.data_aview[..., self.actual_slice_R]
elif self.show_mode_R == SHOW_LABELS:
# im = self.data_R.labels_aview[...,self.actual_slice_R]
im = self.data_R.labels_filt_aview[..., self.actual_slice_R]
# elif self.show_mode_R == SHOW_FILTERED_LABELS:
# im = self.data_R.labels_filt_aview[...,self.actual_slice_R]
return im
