def setup_gui(self):
"""
"""
self.glWidget = GLWidget(parent=self.gridWidget_4,
width=1508,
height=713,
bgcolor=(.5, .5, 0.9),
enable_light=False)
self.gridLayout_4.addWidget(self.glWidget)
# adding the editing items to ROI table
# double spinbox for x,y and z coordinates
self.dspbxcoord = QtGui.QDoubleSpinBox()
self.tblROI.setCellWidget(3, 1, self.dspbxcoord)
self.dspbycoord = QtGui.QDoubleSpinBox()
self.tblROI.setCellWidget(4, 1, self.dspbycoord)
self.dspbzcoord = QtGui.QDoubleSpinBox()
self.tblROI.setCellWidget(5, 1, self.dspbzcoord)
self.spbrad = QtGui.QSpinBox()
self.tblROI.setCellWidget(6, 1, self.spbrad)
# define method ROI
self.roimethod = 1 #tractome inside
# color button
self.colorlist = [
QtGui.QColor('red'),
QtGui.QColor('blue'),
QtGui.QColor('green'),
QtGui.QColor('yellow'),
QtGui.QColor('cyan'),
QtGui.QColor('black')
]
self.btncolor = QtGui.QPushButton()
self.tblROI.setCellWidget(2, 1, self.btncolor)
self.btncolor.setAutoFillBackground(True)
# connect button with QColorDialog
self.connect(self.btncolor, QtCore.SIGNAL("clicked()"),
self.on_btncolor_clicked)
# visibility checkbox
self.chkbvis = QtGui.QCheckBox()
self.chkbvis.setCheckState(QtCore.Qt.Checked)
self.connect(self.chkbvis, QtCore.SIGNAL("stateChanged(int)"),
self.on_chkbvis_stateChanged)
self.tblROI.setCellWidget(1, 1, self.chkbvis)
# self.show_hide_rows(True)
# creating the main Scene
self.tractome = Tractome()
self.add_scene(self.tractome.scene)
def setup_gui(self):
"""
"""
self.glWidget = GLWidget(parent = self.gridWidget_4,
width = 1508,
height = 713,
bgcolor = (.5, .5, 0.9),
enable_light = False)
self.gridLayout_4.addWidget(self.glWidget)
#for now, pbExtCluster will be invisible
self.pbExtCluster.setVisible(False)
# adding the editing items to ROI table
# double spinbox for x,y and z coordinates
self.dspbxcoord = QtGui.QDoubleSpinBox()
self.tblROI.setCellWidget(3, 1, self.dspbxcoord)
self.dspbycoord = QtGui.QDoubleSpinBox()
self.tblROI.setCellWidget(4, 1, self.dspbycoord)
self.dspbzcoord = QtGui.QDoubleSpinBox()
self.tblROI.setCellWidget(5, 1, self.dspbzcoord)
self.spbrad = QtGui.QSpinBox()
self.tblROI.setCellWidget(6, 1, self.spbrad)
# define method ROI
self.roimethod = 1 #tractome inside
# color button
self.colorlist = [QtGui.QColor('red'), QtGui.QColor('blue'), QtGui.QColor('green'), QtGui.QColor('yellow'), QtGui.QColor('cyan'), QtGui.QColor('black')]
self.btncolor = QtGui.QPushButton()
self.tblROI.setCellWidget(2, 1, self.btncolor)
self.btncolor.setAutoFillBackground(True)
# connect button with QColorDialog
self.connect(self.btncolor, QtCore.SIGNAL("clicked()"),
self.on_btncolor_clicked)
# visibility checkbox
self.chkbvis = QtGui.QCheckBox()
self.chkbvis.setCheckState(QtCore.Qt.Checked)
self.connect(self.chkbvis, QtCore.SIGNAL("stateChanged(int)"), self.on_chkbvis_stateChanged)
self.tblROI.setCellWidget(1, 1, self.chkbvis)
# self.show_hide_rows(True)
# creating the main Scene
self.tractome= Tractome()
self.add_scene(self.tractome.scene)
class MainWindow(QMainWindow, Ui_MainWindow):
"""
Class documentation goes here.
"""
def __init__(self, parent=None):
"""
Constructor
@param parent reference to the parent widget (QWidget)
"""
# calling base initializers
super(MainWindow, self).__init__(parent)
# calling base setupUi for ui configuration
self.setupUi(self)
# setting up the gui
self.setup_gui()
def setup_gui(self):
"""
"""
self.glWidget = GLWidget(parent = self.gridWidget_4,
width = 1508,
height = 713,
bgcolor = (.5, .5, 0.9),
enable_light = False)
self.gridLayout_4.addWidget(self.glWidget)
# adding the editing items to ROI table
# double spinbox for x,y and z coordinates
self.dspbxcoord = QtGui.QDoubleSpinBox()
self.tblROI.setCellWidget(3, 1, self.dspbxcoord)
self.dspbycoord = QtGui.QDoubleSpinBox()
self.tblROI.setCellWidget(4, 1, self.dspbycoord)
self.dspbzcoord = QtGui.QDoubleSpinBox()
self.tblROI.setCellWidget(5, 1, self.dspbzcoord)
self.spbrad = QtGui.QSpinBox()
self.tblROI.setCellWidget(6, 1, self.spbrad)
# define method ROI
self.roimethod = 1 #tractome inside
# color button
self.colorlist = [QtGui.QColor('red'), QtGui.QColor('blue'), QtGui.QColor('green'), QtGui.QColor('yellow'), QtGui.QColor('cyan'), QtGui.QColor('black')]
self.btncolor = QtGui.QPushButton()
self.tblROI.setCellWidget(2, 1, self.btncolor)
self.btncolor.setAutoFillBackground(True)
# connect button with QColorDialog
self.connect(self.btncolor, QtCore.SIGNAL("clicked()"),
self.on_btncolor_clicked)
# visibility checkbox
self.chkbvis = QtGui.QCheckBox()
self.chkbvis.setCheckState(QtCore.Qt.Checked)
self.connect(self.chkbvis, QtCore.SIGNAL("stateChanged(int)"), self.on_chkbvis_stateChanged)
self.tblROI.setCellWidget(1, 1, self.chkbvis)
# self.show_hide_rows(True)
# creating the main Scene
self.tractome= Tractome()
self.add_scene(self.tractome.scene)
def changenumstreamlines_handler(self, n_stream):
"""
"""
if (n_stream< 1e5) and (n_stream>= 50):
default = 50
else:
default = n_stream
self.spbRecluster.setValue(default)
self.spbRecluster.setRange(1, n_stream)
self.hSlReCluster.setValue(default)
self.hSlReCluster.setMinimum(1)
self.hSlReCluster.setMaximum(min(150, n_stream))
self.tblTract.item(1, 1).setText(str(n_stream))
def changenumrepresentatives_handler(self, n_rep):
"""
"""
self.tblTract.item(2, 1).setText(str(n_rep))
def on_dspbxcoord_valueChanged(self, value):
"""
"""
self.tractome.update_ROI(self.tblROI.item(0, 1).text(), coordx = value, rebuild = self.list_chkROIS[self.activeROI].isChecked())
self.glWidget.updateGL()
def on_dspbycoord_valueChanged(self, value):
"""
"""
self.tractome.update_ROI(self.tblROI.item(0, 1).text(), coordy = value, rebuild = self.list_chkROIS[self.activeROI].isChecked())
self.glWidget.updateGL()
def on_dspbzcoord_valueChanged(self, value):
self.tractome.update_ROI(self.tblROI.item(0, 1).text(), coordz = value, rebuild = self.list_chkROIS[self.activeROI].isChecked())
self.glWidget.updateGL()
def on_spbrad_valueChanged(self, value):
"""
"""
self.tractome.update_ROI(self.tblROI.item(0, 1).text(), radius=value, rebuild = self.list_chkROIS[self.activeROI].isChecked())
self.glWidget.updateGL()
def on_chkbvis_stateChanged(self, state):
"""
Shows or hides the ROI if the visibility checkbox is checked
or not correspondingly.
"""
self.tractome.show_hide_actor(self.tblROI.item(0, 1).text(), state)
self.glWidget.updateGL()
@Slot(QtGui.QTreeWidgetItem, int)
def on_treeObject_itemClicked(self, item, column):
"""
If the item selected is a ROI, the corresponding information
will be shown in the tableROI.
"""
name = str(item.text(0))
xcoord, ycoord, zcoord, radius, color= self.tractome.information_from_ROI(name)
index= self.treeObject.indexFromItem(item)
self.activeROI = index.row()
self.disconnect(self.tblROI, QtCore.SIGNAL("itemChanged(QtGui.QTableWidgetItem)"), self.on_tblROI_itemChanged)
self.updateROItable(name, xcoord, ycoord, zcoord, radius, color)
self.connect(self.tblROI, QtCore.SIGNAL("itemChanged(QtGui.QTableWidgetItem)"), self.on_tblROI_itemChanged)
def on_btncolor_clicked(self):
"""
"""
color = QtGui.QColorDialog().getColor()
self.btncolor.setStyleSheet( u'background-color:%s' % color.name())
self.tractome.update_ROI(self.tblROI.item(0, 1).text(), color = color.getRgbF())
@Slot(int)
def on_chkbShowTract_stateChanged(self, state):
"""
Shows or hides the tractography if the Checkbox is checked or
not correspondingly
"""
self.tractome.show_hide_actor('Bundle Picker', state)
self.glWidget.updateGL()
@Slot(int)
def on_chkbShowStruct_stateChanged(self, state):
"""
Shows or hides the structural image if the Checkbox is checked
or not correspondingly
"""
self.tractome.show_hide_actor('Volume Slicer', state)
self.glWidget.updateGL()
# @Slot(bool)
# def on_rdbInsSphere_toggled(self, checked):
# """
# Use method of Tractome inside sphere to compute the ROI
# """
# if checked:
# self.roimethod = 1
# self.tractome.update_ROI(self.tblROI.item(0, 1).text(), method = self.roimethod, rebuild= True)
# if len(self.list_chkROIS)>0:
# self.tractome.compute_streamlines_ROIS()
# @Slot(bool)
# def on_rdbtrackvis_toggled(self, checked):
# """
# Use method of Trackvis to compute the ROI
# """
# if checked:
# self.roimethod = 0
# self.tractome.update_ROI(self.tblROI.item(0, 1).text(), method = self.roimethod, rebuild= True)
# if len(self.list_chkROIS)>0:
# self.tractome.compute_streamlines_ROIS()
@Slot(int)
def on_spbRecluster_valueChanged(self, p0):
"""
Update slider Recluster
"""
self.hSlReCluster.setValue(p0)
@Slot(int)
def on_hSlReCluster_valueChanged(self, value):
"""
Update spbRecluster
"""
self.spbRecluster.setValue(value)
@Slot()
def on_pbRecluster_clicked(self):
"""
Call re-cluster function from tractome and update values of possible number of clusters for related objects.
"""
self.tractome.recluster(self.spbRecluster.value())
self.glWidget.updateGL()
@Slot()
def on_actionLoad_Structural_Image_triggered(self):
"""
Opens a dialog to allow the user to choose the structural
file.
"""
#Creating filedialog to search for the structural file
filedialog=QtGui.QFileDialog()
filedialog.setNameFilter(str("((*.gz *.nii *.img)"))
fileStruct, _= filedialog.getOpenFileName(self,"Open Structural file", os.getcwd(), str("(*.gz *.nii *.img)"))
if fileStruct != "":
struct_basename = os.path.basename(fileStruct)
self.create_update_Item('slicer')
self.tractome.loading_structural(fileStruct)
self.structnameitem.setText(0, struct_basename)
self.refocus_camera()
@Slot()
def on_actionLoad_MASk_triggered(self):
"""
Opens a dialog to allow the user to choose the mask file.
"""
#Creating filedialog to search for the structural file
filedialog=QtGui.QFileDialog()
filedialog.setNameFilter(str("((*.gz *.nii *.img)"))
fileMask, _= filedialog.getOpenFileName(self,"Open Mask file", os.getcwd(), str("(*.gz *.nii *.img)"))
if fileMask !="":
mask_basename = os.path.basename(fileMask)
self.prepare_interface_ROI('mask', nameroi = mask_basename)
self.tractome.loading_mask(fileMask, self.roi_color)
self.updateROItable(mask_basename, color = self.roi_color.name())
self.glWidget.updateGL()
@Slot()
def on_actionLoad_Tractography_triggered(self):
"""
Opens a dialog to allow the user to choose the tractography
file.
"""
filedialog=QtGui.QFileDialog()
filedialog.setNameFilter(str("(*.dpy *.trk)"))
fileTract, _= filedialog.getOpenFileName(self,"Open Tractography file", os.getcwd(), str("(*.dpy *.trk)"))
if fileTract !="":
tracks_basename = os.path.basename(fileTract)
self.create_update_Item('tractography')
self.tractome.loading_full_tractograpy(tracpath=fileTract)
self.set_clustering_values()
self.tractnameitem.setText(0, tracks_basename)
# connecting event that is fired when number of streamlines is changed after some action on the streamlinelabeler actor
self.tractome.streamlab.numstream_handler += self.changenumstreamlines_handler
self.tractome.streamlab.numrep_handler += self.changenumrepresentatives_handler
#add information to tab in Table
self.tblTract.item(0, 1).setText(tracks_basename)
trackcount = len(self.tractome.T)
self.tblTract.item(1, 1).setText(str(trackcount))
self.tblTract.item(2, 1).setText(str(len(self.tractome.streamlab.representative_ids)))
if hasattr(self.tractome, 'hdr'):
hdr = self.tractome.hdr
self.tblTract.item(3, 1).setText(str(hdr['voxel_size']))
self.tblTract.item(4, 1).setText(str(hdr['dim']))
self.tblTract.item(5, 1).setText(str(hdr['voxel_order']))
else:
self.tblTract.item(3, 1).setText('No info')
self.tblTract.item(4, 1).setText('No info')
self.tblTract.item(5, 1).setText('LAS')
self.grbCluster.setEnabled(True)
def create_update_Item(self, object):
"""
Creates or updates the specified item in the TreeObject and
the corresponding actor in the Scene (if neccesary).
"""
if object == 'tractography':
#checking if there is already a tractography open to substitute it
try:
self.tractnameitem
self.tractome.clear_actor('Bundle Picker')
self.clear_all_session()
#if there is no tractography open
except AttributeError:
self.tractnameitem = QtGui.QTreeWidgetItem(self.treeObject)
self.chkbShowTract.setEnabled(True)
self.tblTract.setEnabled(True)
self.actionSave_Segmentation.setEnabled(True)
self.actionSave_as_trackvis_file.setEnabled(True)
self.menuROI.setEnabled(True)
if object == 'slicer':
try:
self.structnameitem
self.treeObject.clear()
self.tractome.clear_all()
self.clear_all_session()
except AttributeError:
#If this is the first opening we create the tree item
self.chkbShowStruct.setEnabled(True)
self.actionLoad_Tractography.setEnabled(True)
self.structnameitem = QtGui.QTreeWidgetItem(self.treeObject)
@Slot()
def on_actionLoad_Saved_Segmentation_triggered(self):
"""
Opens a dialog to allow the user to choose a file of a
previously saved session.
"""
filedialog=QtGui.QFileDialog()
filedialog.setNameFilter(str("(*.seg)"))
fileSeg, _ = filedialog.getOpenFileName(self,"Open Segmentation file", os.getcwd(), str("(*.seg)"))
if fileSeg !="":
#checking if there is already a tractography open to substitute it
try:
self.structnameitem
self.tractnameitem
self.treeObject.clear()
self.tractome.clear_all()
self.clear_all_session()
#if there is no tractography open
except AttributeError:
self.chkbShowStruct.setEnabled(True)
self.chkbShowTract.setEnabled(True)
self.tblTract.setEnabled(True)
self.menuROI.setEnabled(True)
self.grbCluster.setEnabled(True)
self.actionLoad_Tractography.setEnabled(True)
self.actionSave_Segmentation.setEnabled(True)
self.actionSave_as_trackvis_file.setEnabled(True)
self.structnameitem = QtGui.QTreeWidgetItem(self.treeObject)
self.tractnameitem = QtGui.QTreeWidgetItem(self.treeObject)
self.tractome.load_segmentation(fileSeg)
#add structural and tractography file names to the treeview
struct_basename = os.path.basename(self.tractome.structpath)
self.structnameitem.setText(0, struct_basename)
tracks_basename = os.path.basename(self.tractome.tracpath)
self.set_clustering_values()
self.tractnameitem.setText(0, tracks_basename)
# connecting event that is fired when number of streamlines is changed after some action on the streamlinelabeler actor
self.tractome.streamlab.numstream_handler += self.changenumstreamlines_handler
self.tractome.streamlab.numrep_handler += self.changenumrepresentatives_handler
#add information to tab in Table
self.tblTract.item(0, 1).setText(tracks_basename)
trackcount = len(self.tractome.streamlab.streamline_ids)
self.tblTract.item(1, 1).setText(str(trackcount))
self.tblTract.item(2, 1).setText(str(len(self.tractome.streamlab.representative_ids)))
try:
hdr = self.tractome.hdr
self.tblTract.item(3, 1).setText(str(hdr['voxel_size']))
self.tblTract.item(4, 1).setText(str(hdr['dim']))
self.tblTract.item(5, 1).setText(str(hdr['voxel_order']))
except AttributeError:
self.tblTract.item(3, 1).setText('No info')
self.tblTract.item(4, 1).setText('No info')
self.tblTract.item(5, 1).setText('LAS')
self.refocus_camera()
def clear_all_session(self):
"""
Clear all the objects related to ROIs
"""
self.list_chkROIS = []
self.list_ands = []
self.list_ors = []
self.tblROISlist.clear()
self.tblROI.setEnabled(False)
self.tblROISlist.setEnabled(False)
self.tabProps_4.setCurrentIndex(0)
@Slot()
def on_actionSave_as_trackvis_file_triggered(self):
"""
Save streamlines of actual session in .trk file
"""
filename = QtGui.QFileDialog.getSaveFileName(self, 'Save Segmentation in .trk', os.getcwd(), str("(*.trk)"))
self.tractome.save_trk(filename)
@Slot()
def on_actionSave_Segmentation_triggered(self):
"""
Saves the current session.
"""
filename = QtGui.QFileDialog.getSaveFileName(self, 'Save Segmentation', os.getcwd(), str("(*.seg)"))
self.tractome.save_segmentation(filename)
@Slot()
def on_actionClose_triggered(self):
"""
Close application
"""
self.close()
def disconnect_signals(self):
"""
Disconnect signal of spinboxes in ROI tables. If they are
connected when updating min_max values of spinbox, the
valueChanged signal is unnecessarily called.
"""
self.disconnect(self.spbrad, QtCore.SIGNAL("valueChanged(int)"), self.on_spbrad_valueChanged)
self.disconnect(self.dspbxcoord, QtCore.SIGNAL("valueChanged(double)"), self.on_dspbxcoord_valueChanged)
self.disconnect(self.dspbycoord, QtCore.SIGNAL("valueChanged(double)"), self.on_dspbycoord_valueChanged)
self.disconnect(self.dspbzcoord, QtCore.SIGNAL("valueChanged(double)"), self.on_dspbzcoord_valueChanged)
def connect_signals(self):
"""
Reconnect signals of spinboxes in ROI tables, after min_max
values have been updated
"""
self.connect(self.spbrad, QtCore.SIGNAL("valueChanged(int)"), self.on_spbrad_valueChanged)
self.connect(self.dspbxcoord, QtCore.SIGNAL("valueChanged(double)"), self.on_dspbxcoord_valueChanged)
self.connect(self.dspbycoord, QtCore.SIGNAL("valueChanged(double)"), self.on_dspbycoord_valueChanged)
self.connect(self.dspbzcoord, QtCore.SIGNAL("valueChanged(double)"), self.on_dspbzcoord_valueChanged)
@Slot()
def on_actionCreate_Sphere_triggered(self):
"""
Create a ROI and plot sphere
"""
maxcoord = self.tractome.max_coordinates()
xmax = maxcoord[0]
ymax = maxcoord[1]
zmax = maxcoord[2]
self.grb_tractomeroi.setEnabled(True)
self.rdbInsSphere.toggle()
cantrois = 0
if hasattr(self, 'list_chkROIS'):
cantrois = len(self.list_chkROIS)
number =cantrois + 1 #to define the name of the ROI depending on the number of available ROIs
nameroi = 'ROI'+ str(number)
self.prepare_interface_ROI('sphere', coords=maxcoord, nameroi = nameroi)
self.tractome.create_ROI_sphere(nameroi, xmax/2, ymax/2, zmax/2, 2, self.roimethod, self.roi_color.getRgbF(), self.roi_color.name())
#add info of the ROI to ROI table
self.updateROItable(nameroi, xmax/2, ymax/2, zmax/2, 2, self.roi_color.name())
self.tabProps_4.setCurrentIndex(1)
self.glWidget.updateGL()
def prepare_interface_ROI(self, roi_type, coords=None, nameroi = None):
"""
Set values and status of all interface elementes related to
ROI.
"""
self.tblROI.setEnabled(True)
self.tblROISlist.setEnabled(True)
self.show_hide_rows(roi_type == 'mask')
try:
self.list_chkROIS
except AttributeError:
self.list_chkROIS = []
self.list_ands = []
self.list_ors = []
# add some fixed information to ROI table
if roi_type == 'sphere':
maxcoord = coords
self.radmax = np.amax(maxcoord)
# self.grbROImethod.setEnabled(True)
# setting some fixed values in the table
self.dspbxcoord.setRange(0, maxcoord[0])
self.dspbycoord.setRange(0,maxcoord[1])
self.dspbzcoord.setRange(0, maxcoord[2])
self.spbrad.setRange(1, self.radmax)
self.connect_signals()
cantrois = len(self.list_chkROIS)
self.activeROI = cantrois # to know which is the ROI shown in the table, in case some information needs to be changed
# define color
if cantrois < len(self.colorlist):
self.roi_color = self.colorlist[self.activeROI]
else:
poscolor = self.activeROI%len(self.colorlist)
self.roi_color = self.colorlist[poscolor]
# add item to tractography in tree
roinameitem = QtGui.QTreeWidgetItem(self.tractnameitem)
roinameitem.setText(0, nameroi) #should we add the whole file path?
# roinameitem.setSelected(True)
self.treeObject.expandAll()
# create checkbox for applying ROI, add to list and to table for applied ROIs
newchkroi = QtGui.QCheckBox()
newchkroi.setText(nameroi)
self.connect(newchkroi, QtCore.SIGNAL("stateChanged(int)"), self.on_chkroi_stateChanged)
self.list_chkROIS.append(newchkroi)
# create rdbuttons for operators and add checkbox for ROI
cantchk = cantrois
sizetblROIs = self.tblROISlist.geometry()
if cantchk==0:
self.tblROISlist.insertRow(0)
self.tblROISlist.setCellWidget(0, 0, newchkroi)
else:
self.tblROISlist.insertRow((2*cantchk)-1)
# create groupbox
grb_roi_operators= QtGui.QGroupBox()
# create radio buttons
rdband = QtGui.QRadioButton("AND")
rdbor = QtGui.QRadioButton("OR")
rdbor.setText('OR')
# add radio button to groupbox
horizontalLayout_roiop = QtGui.QHBoxLayout()
horizontalLayout_roiop.addWidget(rdband)
horizontalLayout_roiop.addWidget(rdbor)
horizontalLayout_roiop.addStretch(1)
grb_roi_operators.setLayout(horizontalLayout_roiop)
self.connect(rdband, QtCore.SIGNAL("clicked(bool)"), self.on_rdb_clicked)
self.connect(rdbor, QtCore.SIGNAL("clicked(bool)"), self.on_rdb_clicked)
#
self.tblROISlist.setCellWidget((2*cantchk)-1, 0, grb_roi_operators)
self.list_ands.append(rdband)
self.list_ors.append(rdbor)
self.tblROISlist.insertRow(2*cantchk)
self.tblROISlist.setCellWidget(2*cantchk, 0, newchkroi)
self.tblROISlist.resizeRowsToContents()
#resizing objects
sizeandrdb = rdband.geometry()
sizeorrdb = rdbor.geometry()
rdband.setGeometry(sizeandrdb.left(), sizeandrdb.top(), 5, sizeandrdb.height())
rdbor.setGeometry(sizeorrdb.left(), sizeorrdb.top(), 5, sizeorrdb.height())
#resizing checkbox
sizecheckbox = newchkroi.geometry()
newchkroi.setGeometry(sizecheckbox.left(), sizecheckbox.top(), sizetblROIs.width(), sizecheckbox.height())
def updateROItable(self, name,coordx=None, coordy=None, coordz=None, radius=None, color=None):
"""
Information of ROI is inserted in table when new ROI is
created or when ROI selection changes in treeview.
"""
#show info of ROI in the table
self.tblROI.item(0, 1).setText(name)
if coordx is not None:
self.disconnect_signals()
self.dspbxcoord.setValue(coordx)
self.dspbycoord.setValue(coordy)
self.dspbzcoord.setValue(coordz)
self.spbrad.setValue(radius)
self.connect_signals()
self.btncolor.setStyleSheet( u'background-color:%s' % color)
def show_hide_rows(self, hide):
"""
Hides or shows rows from TableROI, depending on the type of
ROI is selected on the tree.
"""
for i in range(3, self.tblROI.rowCount()):
self.tblROI.setRowHidden(i, hide)
self.tblROI.resizeRowsToContents()
def on_chkroi_stateChanged(self, checked):
"""
Computing streamlines to show according to ROIs that are
checked and their operators.
"""
last_chkd = 0
for pos in range(0, len(self.list_chkROIS)):
if self.list_chkROIS[pos].isChecked():
self.tractome.activation_ROIs(pos, True)
if pos!=(len(self.list_chkROIS)-1) and ((self.list_ands[pos].isChecked()==False) and (self.list_ors[pos].isChecked()==False)):
self.list_ands[pos].setChecked(True)
else:
self.tractome.activation_ROIs(pos, False, operator = 'and')
if pos!=(len(self.list_chkROIS)-1):
if self.list_ands[pos].isChecked():
self.list_ands[pos].setAutoExclusive(False)
self.list_ands[pos].setChecked(False)
self.list_ands[pos].setAutoExclusive(True)
if self.list_ors[pos].isChecked():
self.list_ors[pos].setAutoExclusive(False)
self.list_ors[pos].setChecked(False)
self.list_ors[pos].setAutoExclusive(True)
self.tractome.compute_streamlines_ROIS()
self.glWidget.updateGL()
def on_rdb_clicked(self, clicked):
"""
Computing streamlines to show according to ROIs that are
checked and their operators.
"""
for pos in range(0, len(self.list_ands)):
if self.list_ands[pos].isChecked():
self.tractome.activation_ROIs(pos, True, operator = 'and')
if self.list_ors[pos].isChecked():
self.tractome.activation_ROIs(pos, True, operator = 'or')
self.tractome.compute_streamlines_ROIS()
self.glWidget.updateGL()
@Slot(QtGui.QTableWidgetItem)
def on_tblROI_itemChanged(self, item):
"""
Will change name of ROI if this is edited in the table.
"""
treeitem = self.tractnameitem.child(self.activeROI)
if item is self.tblROI.item(0, 1):
prev_name_roi = str(treeitem.text(0))
index = self.treeObject.indexFromItem(treeitem, 0)
if index.isValid():
self.tractome.update_ROI(prev_name_roi, newname = item.text(), pos_activeroi = self.activeROI)
treeitem.setText(0, item.text())
@Slot()
def on_actionRe_Cluster_triggered(self):
"""
Re-cluster.
"""
self.spbRecluster.setEnabled(True)
self.hSlReCluster.setEnabled(True)
self.pbRecluster.setEnabled(True)
def set_clustering_values(self):
"""
"""
max, default = self.tractome.max_num_clusters()
self.spbRecluster. setValue(default)
self.spbRecluster.setRange(1, max)
self.hSlReCluster.setValue(default)
self.hSlReCluster.setMinimum(1)
self.hSlReCluster.setMaximum(min(150, max))
def initSpincamera(self, angle = 0.007 ):
"""
"""
if self._spinCameraTimerInit:
self.spinCameraTimer.timeout.disconnect()
def rotate_camera():
self.glWidget.world.camera.rotate_around_focal( angle, "yup" )
self.glWidget.updateGL()
self.spinCameraTimer.timeout.connect(rotate_camera)
self._spinCameraTimerInit = True
def spinCameraToggle(self):
"""
"""
if not self.spinCameraTimer.isActive():
self.spinCameraTimer.start()
else:
self.spinCameraTimer.stop()
def timerInit(self, interval = 30):
"""
"""
timer = QtCore.QTimer(self)
timer.setInterval( interval )
return timer
def add_scene(self, scene):
"""
"""
self.glWidget.world.add_scene(scene)
def set_camera(self, camera):
"""
"""
self.glWidget.world.camera = camera
def refocus_camera(self):
"""
"""
self.glWidget.world.refocus_camera()
def update_light_position(self, x, y, z):
"""
"""
if not self.glWidget.world.light is None:
self.glWidget.world.update_lightposition(x, y, z)
def screenshot(self, filename):
""" Store current OpenGL context as image.
"""
self.glWidget.updateGL()
self.glWidget.grabFrameBuffer().save( filename )
def keyPressEvent(self, event):
""" Handle all key press events.
"""
# print 'key pressed', event.key()
key = event.key()
# self.messages=empty_messages.copy()
# self.messages['key_pressed']=key
# self.glWidget.world.send_all_messages(self.messages)
# F1: fullscreen
# F2: next frame
# F3: previous frame
# F4: start rotating
# F12: reset camera
# Esc: close window
if key == QtCore.Qt.Key_F1:
if self.fullscreen:
self.showNormal()
else:
self.showFullScreen()
self.fullscreen = not self.fullscreen
elif key == QtCore.Qt.Key_F2:
self.glWidget.world.nextTimeFrame()
elif key == QtCore.Qt.Key_F3:
self.glWidget.world.previousTimeFrame()
elif key == QtCore.Qt.Key_F12:
self.glWidget.world.refocus_camera()
self.glWidget.world.camera.update()
self.glWidget.updateGL()
elif key == QtCore.Qt.Key_F4:
if (event.modifiers() & QtCore.Qt.ShiftModifier):
self.initSpincamera( angle = -0.01 )
self.spinCameraToggle()
else:
self.initSpincamera( angle = 0.01 )
self.spinCameraToggle()
elif key == QtCore.Qt.Key_Escape:
self.close()
else:
super(MainWindow, self).keyPressEvent( event )
self.glWidget.updateGL()
class MainWindow(QMainWindow, Ui_MainWindow):
"""
Class documentation goes here.
"""
def __init__(self, parent=None):
"""
Constructor
@param parent reference to the parent widget (QWidget)
"""
# calling base initializers
super(MainWindow, self).__init__(parent)
# calling base setupUi for ui configuration
self.setupUi(self)
# setting up the gui
self.setup_gui()
def setup_gui(self):
"""
"""
self.glWidget = GLWidget(parent = self.gridWidget_4,
width = 1508,
height = 713,
bgcolor = (.5, .5, 0.9),
enable_light = False)
self.gridLayout_4.addWidget(self.glWidget)
#for now, pbExtCluster will be invisible
self.pbExtCluster.setVisible(False)
# adding the editing items to ROI table
# double spinbox for x,y and z coordinates
self.dspbxcoord = QtGui.QDoubleSpinBox()
self.tblROI.setCellWidget(3, 1, self.dspbxcoord)
self.dspbycoord = QtGui.QDoubleSpinBox()
self.tblROI.setCellWidget(4, 1, self.dspbycoord)
self.dspbzcoord = QtGui.QDoubleSpinBox()
self.tblROI.setCellWidget(5, 1, self.dspbzcoord)
self.spbrad = QtGui.QSpinBox()
self.tblROI.setCellWidget(6, 1, self.spbrad)
# define method ROI
self.roimethod = 1 #tractome inside
# color button
self.colorlist = [QtGui.QColor('red'), QtGui.QColor('blue'), QtGui.QColor('green'), QtGui.QColor('yellow'), QtGui.QColor('cyan'), QtGui.QColor('black')]
self.btncolor = QtGui.QPushButton()
self.tblROI.setCellWidget(2, 1, self.btncolor)
self.btncolor.setAutoFillBackground(True)
# connect button with QColorDialog
self.connect(self.btncolor, QtCore.SIGNAL("clicked()"),
self.on_btncolor_clicked)
# visibility checkbox
self.chkbvis = QtGui.QCheckBox()
self.chkbvis.setCheckState(QtCore.Qt.Checked)
self.connect(self.chkbvis, QtCore.SIGNAL("stateChanged(int)"), self.on_chkbvis_stateChanged)
self.tblROI.setCellWidget(1, 1, self.chkbvis)
# self.show_hide_rows(True)
# creating the main Scene
self.tractome= Tractome()
self.add_scene(self.tractome.scene)
def changenumstreamlines_handler(self, n_stream):
"""
"""
if (n_stream< 1e5) and (n_stream>= 50):
default = 50
else:
default = n_stream
self.spbRecluster.setValue(default)
self.spbRecluster.setRange(1, n_stream)
self.hSlReCluster.setValue(default)
self.hSlReCluster.setMinimum(1)
self.hSlReCluster.setMaximum(min(150, n_stream))
self.tblTract.item(1, 1).setText(str(n_stream))
def changenumrepresentatives_handler(self, n_rep):
"""
"""
self.tblTract.item(2, 1).setText(str(n_rep))
def changenumknnextend_handler(self, changenn):
"""
"""
if changenn is True:
self.hSlExtclust.setValue(0)
def on_dspbxcoord_valueChanged(self, value):
"""
"""
self.tractome.update_ROI(self.tblROI.item(0, 1).text(), coordx = value, rebuild = self.list_chkROIS[self.activeROI].isChecked())
self.glWidget.updateGL()
def on_dspbycoord_valueChanged(self, value):
"""
"""
self.tractome.update_ROI(self.tblROI.item(0, 1).text(), coordy = value, rebuild = self.list_chkROIS[self.activeROI].isChecked())
self.glWidget.updateGL()
def on_dspbzcoord_valueChanged(self, value):
self.tractome.update_ROI(self.tblROI.item(0, 1).text(), coordz = value, rebuild = self.list_chkROIS[self.activeROI].isChecked())
self.glWidget.updateGL()
def on_spbrad_valueChanged(self, value):
"""
"""
self.tractome.update_ROI(self.tblROI.item(0, 1).text(), radius=value, rebuild = self.list_chkROIS[self.activeROI].isChecked())
self.glWidget.updateGL()
def on_chkbvis_stateChanged(self, state):
"""
Shows or hides the ROI if the visibility checkbox is checked
or not correspondingly.
"""
self.tractome.show_hide_actor(self.tblROI.item(0, 1).text(), state)
self.glWidget.updateGL()
@Slot(QtGui.QTreeWidgetItem, int)
def on_treeObject_itemClicked(self, item, column):
"""
If the item selected is a ROI, the corresponding information
will be shown in the tableROI.
"""
name = str(item.text(0))
xcoord, ycoord, zcoord, radius, color= self.tractome.information_from_ROI(name)
index= self.treeObject.indexFromItem(item)
self.activeROI = index.row()
self.disconnect(self.tblROI, QtCore.SIGNAL("itemChanged(QtGui.QTableWidgetItem)"), self.on_tblROI_itemChanged)
self.updateROItable(name, xcoord, ycoord, zcoord, radius, color)
self.connect(self.tblROI, QtCore.SIGNAL("itemChanged(QtGui.QTableWidgetItem)"), self.on_tblROI_itemChanged)
def on_btncolor_clicked(self):
"""
"""
color = QtGui.QColorDialog().getColor()
self.btncolor.setStyleSheet( u'background-color:%s' % color.name())
self.tractome.update_ROI(self.tblROI.item(0, 1).text(), color = color.getRgbF())
@Slot(int)
def on_chkbShowTract_stateChanged(self, state):
"""
Shows or hides the tractography if the Checkbox is checked or
not correspondingly
"""
self.tractome.show_hide_actor('Bundle Picker', state)
self.glWidget.updateGL()
@Slot(int)
def on_chkbShowStruct_stateChanged(self, state):
"""
Shows or hides the structural image if the Checkbox is checked
or not correspondingly
"""
self.tractome.show_hide_actor('Volume Slicer', state)
self.glWidget.updateGL()
# @Slot(bool)
# def on_rdbInsSphere_toggled(self, checked):
# """
# Use method of Tractome inside sphere to compute the ROI
# """
# if checked:
# self.roimethod = 1
# self.tractome.update_ROI(self.tblROI.item(0, 1).text(), method = self.roimethod, rebuild= True)
# if len(self.list_chkROIS)>0:
# self.tractome.compute_streamlines_ROIS()
# @Slot(bool)
# def on_rdbtrackvis_toggled(self, checked):
# """
# Use method of Trackvis to compute the ROI
# """
# if checked:
# self.roimethod = 0
# self.tractome.update_ROI(self.tblROI.item(0, 1).text(), method = self.roimethod, rebuild= True)
# if len(self.list_chkROIS)>0:
# self.tractome.compute_streamlines_ROIS()
@Slot(int)
def on_spbRecluster_valueChanged(self, p0):
"""
Update slider Recluster
"""
self.hSlReCluster.setValue(p0)
@Slot(int)
def on_hSlReCluster_valueChanged(self, value):
"""
Update spbRecluster
"""
self.spbRecluster.setValue(value)
@Slot()
def on_pbRecluster_clicked(self):
"""
Call re-cluster function from tractome and update values of possible number of clusters for related objects.
"""
self.tractome.recluster(self.spbRecluster.value())
self.hSlExtclust.setValue(0)
self.glWidget.updateGL()
@Slot(int)
def on_spbExtClust_valueChanged(self, p0):
"""
Update hSlExtclust and call method that computes kdtree-query.
"""
self.hSlExtclust.setValue(p0)
try:
self.tractome.compute_kqueries(p0)
self.glWidget.updateGL()
except TractomeError,e:
msgBox = QtGui.QMessageBox.critical(self, "Tractome Message", ''.join(e.args))
class MainWindow(QMainWindow, Ui_MainWindow):
"""
Class documentation goes here.
"""
def __init__(self, parent=None):
"""
Constructor
@param parent reference to the parent widget (QWidget)
"""
# calling base initializers
super(MainWindow, self).__init__(parent)
# calling base setupUi for ui configuration
self.setupUi(self)
# setting up the gui
self.setup_gui()
def setup_gui(self):
"""
"""
self.glWidget = GLWidget(parent = self.gridWidget_4,
width = 1508,
height = 713,
bgcolor = (.5, .5, 0.9),
enable_light = False)
self.gridLayout_4.addWidget(self.glWidget)
#for now, pbExtCluster will be invisible
self.pbExtCluster.setVisible(False)
# adding the editing items to ROI table
# double spinbox for x,y and z coordinates
self.dspbxcoord = QtGui.QDoubleSpinBox()
self.tblROI.setCellWidget(3, 1, self.dspbxcoord)
self.dspbycoord = QtGui.QDoubleSpinBox()
self.tblROI.setCellWidget(4, 1, self.dspbycoord)
self.dspbzcoord = QtGui.QDoubleSpinBox()
self.tblROI.setCellWidget(5, 1, self.dspbzcoord)
self.spbrad = QtGui.QSpinBox()
self.tblROI.setCellWidget(6, 1, self.spbrad)
# define method ROI
self.roimethod = 1 #tractome inside
# color button
self.colorlist = [QtGui.QColor('red'), QtGui.QColor('blue'), QtGui.QColor('green'), QtGui.QColor('yellow'), QtGui.QColor('cyan'), QtGui.QColor('black')]
self.btncolor = QtGui.QPushButton()
self.tblROI.setCellWidget(2, 1, self.btncolor)
self.btncolor.setAutoFillBackground(True)
# connect button with QColorDialog
self.connect(self.btncolor, QtCore.SIGNAL("clicked()"),
self.on_btncolor_clicked)
# visibility checkbox
self.chkbvis = QtGui.QCheckBox()
self.chkbvis.setCheckState(QtCore.Qt.Checked)
self.connect(self.chkbvis, QtCore.SIGNAL("stateChanged(int)"), self.on_chkbvis_stateChanged)
self.tblROI.setCellWidget(1, 1, self.chkbvis)
# self.show_hide_rows(True)
# creating the main Scene
self.tractome= Tractome()
self.add_scene(self.tractome.scene)
def changenumstreamlines_handler(self, n_stream):
"""
"""
if (n_stream< 1e5) and (n_stream>= 50):
default = 50
else:
default = n_stream
self.spbRecluster.setValue(default)
self.spbRecluster.setRange(1, n_stream)
self.hSlReCluster.setValue(default)
self.hSlReCluster.setMinimum(1)
self.hSlReCluster.setMaximum(min(150, n_stream))
self.tblTract.item(1, 1).setText(str(n_stream))
def changenumrepresentatives_handler(self, n_rep):
"""
"""
self.tblTract.item(2, 1).setText(str(n_rep))
def changenumknnextend_handler(self, changenn):
"""
"""
if changenn is True:
self.hSlExtclust.setValue(0)
def on_dspbxcoord_valueChanged(self, value):
"""
"""
self.tractome.update_ROI(self.tblROI.item(0, 1).text(), coordx = value, rebuild = self.list_chkROIS[self.activeROI].isChecked())
self.glWidget.updateGL()
def on_dspbycoord_valueChanged(self, value):
"""
"""
self.tractome.update_ROI(self.tblROI.item(0, 1).text(), coordy = value, rebuild = self.list_chkROIS[self.activeROI].isChecked())
self.glWidget.updateGL()
def on_dspbzcoord_valueChanged(self, value):
self.tractome.update_ROI(self.tblROI.item(0, 1).text(), coordz = value, rebuild = self.list_chkROIS[self.activeROI].isChecked())
self.glWidget.updateGL()
def on_spbrad_valueChanged(self, value):
"""
"""
self.tractome.update_ROI(self.tblROI.item(0, 1).text(), radius=value, rebuild = self.list_chkROIS[self.activeROI].isChecked())
self.glWidget.updateGL()
def on_chkbvis_stateChanged(self, state):
"""
Shows or hides the ROI if the visibility checkbox is checked
or not correspondingly.
"""
self.tractome.show_hide_actor(self.tblROI.item(0, 1).text(), state)
self.glWidget.updateGL()
@Slot(QtGui.QTreeWidgetItem, int)
def on_treeObject_itemClicked(self, item, column):
"""
If the item selected is a ROI, the corresponding information
will be shown in the tableROI.
"""
name = str(item.text(0))
xcoord, ycoord, zcoord, radius, color= self.tractome.information_from_ROI(name)
index= self.treeObject.indexFromItem(item)
self.activeROI = index.row()
self.disconnect(self.tblROI, QtCore.SIGNAL("itemChanged(QtGui.QTableWidgetItem)"), self.on_tblROI_itemChanged)
self.updateROItable(name, xcoord, ycoord, zcoord, radius, color)
self.connect(self.tblROI, QtCore.SIGNAL("itemChanged(QtGui.QTableWidgetItem)"), self.on_tblROI_itemChanged)
def on_btncolor_clicked(self):
"""
"""
color = QtGui.QColorDialog().getColor()
self.btncolor.setStyleSheet( u'background-color:%s' % color.name())
self.tractome.update_ROI(self.tblROI.item(0, 1).text(), color = color.getRgbF())
@Slot(int)
def on_chkbShowTract_stateChanged(self, state):
"""
Shows or hides the tractography if the Checkbox is checked or
not correspondingly
"""
self.tractome.show_hide_actor('Bundle Picker', state)
self.glWidget.updateGL()
@Slot(int)
def on_chkbShowStruct_stateChanged(self, state):
"""
Shows or hides the structural image if the Checkbox is checked
or not correspondingly
"""
self.tractome.show_hide_actor('Volume Slicer', state)
self.glWidget.updateGL()
# @Slot(bool)
# def on_rdbInsSphere_toggled(self, checked):
# """
# Use method of Tractome inside sphere to compute the ROI
# """
# if checked:
# self.roimethod = 1
# self.tractome.update_ROI(self.tblROI.item(0, 1).text(), method = self.roimethod, rebuild= True)
# if len(self.list_chkROIS)>0:
# self.tractome.compute_streamlines_ROIS()
# @Slot(bool)
# def on_rdbtrackvis_toggled(self, checked):
# """
# Use method of Trackvis to compute the ROI
# """
# if checked:
# self.roimethod = 0
# self.tractome.update_ROI(self.tblROI.item(0, 1).text(), method = self.roimethod, rebuild= True)
# if len(self.list_chkROIS)>0:
# self.tractome.compute_streamlines_ROIS()
@Slot(int)
def on_spbRecluster_valueChanged(self, p0):
"""
Update slider Recluster
"""
self.hSlReCluster.setValue(p0)
@Slot(int)
def on_hSlReCluster_valueChanged(self, value):
"""
Update spbRecluster
"""
self.spbRecluster.setValue(value)
@Slot()
def on_pbRecluster_clicked(self):
"""
Call re-cluster function from tractome and update values of possible number of clusters for related objects.
"""
self.tractome.recluster(self.spbRecluster.value())
self.hSlExtclust.setValue(0)
self.glWidget.updateGL()
@Slot(int)
def on_spbExtClust_valueChanged(self, p0):
"""
Update hSlExtclust and call method that computes kdtree-query.
"""
self.hSlExtclust.setValue(p0)
try:
self.tractome.compute_kqueries(p0)
self.glWidget.updateGL()
except TractomeError,e:
msgBox = QtGui.QMessageBox.critical(self, "Tractome Message", ''.join(e.args))
class MainWindow(QMainWindow, Ui_MainWindow):
"""
Class documentation goes here.
"""
def __init__(self, parent=None):
"""
Constructor
@param parent reference to the parent widget (QWidget)
"""
# calling base initializers
super(MainWindow, self).__init__(parent)
# calling base setupUi for ui configuration
self.setupUi(self)
# setting up the gui
self.setup_gui()
def setup_gui(self):
"""
"""
self.glWidget = GLWidget(parent=self.gridWidget_4,
width=1508,
height=713,
bgcolor=(.5, .5, 0.9),
enable_light=False)
self.gridLayout_4.addWidget(self.glWidget)
# adding the editing items to ROI table
# double spinbox for x,y and z coordinates
self.dspbxcoord = QtGui.QDoubleSpinBox()
self.tblROI.setCellWidget(3, 1, self.dspbxcoord)
self.dspbycoord = QtGui.QDoubleSpinBox()
self.tblROI.setCellWidget(4, 1, self.dspbycoord)
self.dspbzcoord = QtGui.QDoubleSpinBox()
self.tblROI.setCellWidget(5, 1, self.dspbzcoord)
self.spbrad = QtGui.QSpinBox()
self.tblROI.setCellWidget(6, 1, self.spbrad)
# define method ROI
self.roimethod = 1 #tractome inside
# color button
self.colorlist = [
QtGui.QColor('red'),
QtGui.QColor('blue'),
QtGui.QColor('green'),
QtGui.QColor('yellow'),
QtGui.QColor('cyan'),
QtGui.QColor('black')
]
self.btncolor = QtGui.QPushButton()
self.tblROI.setCellWidget(2, 1, self.btncolor)
self.btncolor.setAutoFillBackground(True)
# connect button with QColorDialog
self.connect(self.btncolor, QtCore.SIGNAL("clicked()"),
self.on_btncolor_clicked)
# visibility checkbox
self.chkbvis = QtGui.QCheckBox()
self.chkbvis.setCheckState(QtCore.Qt.Checked)
self.connect(self.chkbvis, QtCore.SIGNAL("stateChanged(int)"),
self.on_chkbvis_stateChanged)
self.tblROI.setCellWidget(1, 1, self.chkbvis)
# self.show_hide_rows(True)
# creating the main Scene
self.tractome = Tractome()
self.add_scene(self.tractome.scene)
def changenumstreamlines_handler(self, n_stream):
"""
"""
if (n_stream < 1e5) and (n_stream >= 50):
default = 50
else:
default = n_stream
self.spbRecluster.setValue(default)
self.spbRecluster.setRange(1, n_stream)
self.hSlReCluster.setValue(default)
self.hSlReCluster.setMinimum(1)
self.hSlReCluster.setMaximum(min(150, n_stream))
self.tblTract.item(1, 1).setText(str(n_stream))
def changenumrepresentatives_handler(self, n_rep):
"""
"""
self.tblTract.item(2, 1).setText(str(n_rep))
def on_dspbxcoord_valueChanged(self, value):
"""
"""
self.tractome.update_ROI(
self.tblROI.item(0, 1).text(),
coordx=value,
rebuild=self.list_chkROIS[self.activeROI].isChecked())
self.glWidget.updateGL()
def on_dspbycoord_valueChanged(self, value):
"""
"""
self.tractome.update_ROI(
self.tblROI.item(0, 1).text(),
coordy=value,
rebuild=self.list_chkROIS[self.activeROI].isChecked())
self.glWidget.updateGL()
def on_dspbzcoord_valueChanged(self, value):
self.tractome.update_ROI(
self.tblROI.item(0, 1).text(),
coordz=value,
rebuild=self.list_chkROIS[self.activeROI].isChecked())
self.glWidget.updateGL()
def on_spbrad_valueChanged(self, value):
"""
"""
self.tractome.update_ROI(
self.tblROI.item(0, 1).text(),
radius=value,
rebuild=self.list_chkROIS[self.activeROI].isChecked())
self.glWidget.updateGL()
def on_chkbvis_stateChanged(self, state):
"""
Shows or hides the ROI if the visibility checkbox is checked
or not correspondingly.
"""
self.tractome.show_hide_actor(self.tblROI.item(0, 1).text(), state)
self.glWidget.updateGL()
@Slot(QtGui.QTreeWidgetItem, int)
def on_treeObject_itemClicked(self, item, column):
"""
If the item selected is a ROI, the corresponding information
will be shown in the tableROI.
"""
name = str(item.text(0))
xcoord, ycoord, zcoord, radius, color = self.tractome.information_from_ROI(
name)
index = self.treeObject.indexFromItem(item)
self.activeROI = index.row()
self.disconnect(self.tblROI,
QtCore.SIGNAL("itemChanged(QtGui.QTableWidgetItem)"),
self.on_tblROI_itemChanged)
self.updateROItable(name, xcoord, ycoord, zcoord, radius, color)
self.connect(self.tblROI,
QtCore.SIGNAL("itemChanged(QtGui.QTableWidgetItem)"),
self.on_tblROI_itemChanged)
def on_btncolor_clicked(self):
"""
"""
color = QtGui.QColorDialog().getColor()
self.btncolor.setStyleSheet(u'background-color:%s' % color.name())
self.tractome.update_ROI(self.tblROI.item(0, 1).text(),
color=color.getRgbF())
@Slot(int)
def on_chkbShowTract_stateChanged(self, state):
"""
Shows or hides the tractography if the Checkbox is checked or
not correspondingly
"""
self.tractome.show_hide_actor('Bundle Picker', state)
self.glWidget.updateGL()
@Slot(int)
def on_chkbShowStruct_stateChanged(self, state):
"""
Shows or hides the structural image if the Checkbox is checked
or not correspondingly
"""
self.tractome.show_hide_actor('Volume Slicer', state)
self.glWidget.updateGL()
# @Slot(bool)
# def on_rdbInsSphere_toggled(self, checked):
# """
# Use method of Tractome inside sphere to compute the ROI
# """
# if checked:
# self.roimethod = 1
# self.tractome.update_ROI(self.tblROI.item(0, 1).text(), method = self.roimethod, rebuild= True)
# if len(self.list_chkROIS)>0:
# self.tractome.compute_streamlines_ROIS()
# @Slot(bool)
# def on_rdbtrackvis_toggled(self, checked):
# """
# Use method of Trackvis to compute the ROI
# """
# if checked:
# self.roimethod = 0
# self.tractome.update_ROI(self.tblROI.item(0, 1).text(), method = self.roimethod, rebuild= True)
# if len(self.list_chkROIS)>0:
# self.tractome.compute_streamlines_ROIS()
@Slot(int)
def on_spbRecluster_valueChanged(self, p0):
"""
Update slider Recluster
"""
self.hSlReCluster.setValue(p0)
@Slot(int)
def on_hSlReCluster_valueChanged(self, value):
"""
Update spbRecluster
"""
self.spbRecluster.setValue(value)
@Slot()
def on_pbRecluster_clicked(self):
"""
Call re-cluster function from tractome and update values of possible number of clusters for related objects.
"""
self.tractome.recluster(self.spbRecluster.value())
self.glWidget.updateGL()
@Slot()
def on_actionLoad_Structural_Image_triggered(self):
"""
Opens a dialog to allow the user to choose the structural
file.
"""
#Creating filedialog to search for the structural file
filedialog = QtGui.QFileDialog()
filedialog.setNameFilter(str("((*.gz *.nii *.img)"))
fileStruct, _ = filedialog.getOpenFileName(self,
"Open Structural file",
os.getcwd(),
str("(*.gz *.nii *.img)"))
if fileStruct != "":
struct_basename = os.path.basename(fileStruct)
self.create_update_Item('slicer')
self.tractome.loading_structural(fileStruct)
self.structnameitem.setText(0, struct_basename)
self.refocus_camera()
@Slot()
def on_actionLoad_MASk_triggered(self):
"""
Opens a dialog to allow the user to choose the mask file.
"""
#Creating filedialog to search for the structural file
filedialog = QtGui.QFileDialog()
filedialog.setNameFilter(str("((*.gz *.nii *.img)"))
fileMask, _ = filedialog.getOpenFileName(self, "Open Mask file",
os.getcwd(),
str("(*.gz *.nii *.img)"))
if fileMask != "":
mask_basename = os.path.basename(fileMask)
self.prepare_interface_ROI('mask', nameroi=mask_basename)
self.tractome.loading_mask(fileMask, self.roi_color)
self.updateROItable(mask_basename, color=self.roi_color.name())
self.glWidget.updateGL()
@Slot()
def on_actionLoad_Tractography_triggered(self):
"""
Opens a dialog to allow the user to choose the tractography
file.
"""
filedialog = QtGui.QFileDialog()
filedialog.setNameFilter(str("(*.dpy *.trk)"))
fileTract, _ = filedialog.getOpenFileName(self,
"Open Tractography file",
os.getcwd(),
str("(*.dpy *.trk)"))
if fileTract != "":
tracks_basename = os.path.basename(fileTract)
self.create_update_Item('tractography')
self.tractome.loading_full_tractograpy(tracpath=fileTract)
self.set_clustering_values()
self.tractnameitem.setText(0, tracks_basename)
# connecting event that is fired when number of streamlines is changed after some action on the streamlinelabeler actor
self.tractome.streamlab.numstream_handler += self.changenumstreamlines_handler
self.tractome.streamlab.numrep_handler += self.changenumrepresentatives_handler
#add information to tab in Table
self.tblTract.item(0, 1).setText(tracks_basename)
trackcount = len(self.tractome.T)
self.tblTract.item(1, 1).setText(str(trackcount))
self.tblTract.item(2, 1).setText(
str(len(self.tractome.streamlab.representative_ids)))
if hasattr(self.tractome, 'hdr'):
hdr = self.tractome.hdr
self.tblTract.item(3, 1).setText(str(hdr['voxel_size']))
self.tblTract.item(4, 1).setText(str(hdr['dim']))
self.tblTract.item(5, 1).setText(str(hdr['voxel_order']))
else:
self.tblTract.item(3, 1).setText('No info')
self.tblTract.item(4, 1).setText('No info')
self.tblTract.item(5, 1).setText('LAS')
self.grbCluster.setEnabled(True)
def create_update_Item(self, object):
"""
Creates or updates the specified item in the TreeObject and
the corresponding actor in the Scene (if neccesary).
"""
if object == 'tractography':
#checking if there is already a tractography open to substitute it
try:
self.tractnameitem
self.tractome.clear_actor('Bundle Picker')
self.clear_all_session()
#if there is no tractography open
except AttributeError:
self.tractnameitem = QtGui.QTreeWidgetItem(self.treeObject)
self.chkbShowTract.setEnabled(True)
self.tblTract.setEnabled(True)
self.actionSave_Segmentation.setEnabled(True)
self.actionSave_as_trackvis_file.setEnabled(True)
self.menuROI.setEnabled(True)
if object == 'slicer':
try:
self.structnameitem
self.treeObject.clear()
self.tractome.clear_all()
self.clear_all_session()
except AttributeError:
#If this is the first opening we create the tree item
self.chkbShowStruct.setEnabled(True)
self.actionLoad_Tractography.setEnabled(True)
self.structnameitem = QtGui.QTreeWidgetItem(self.treeObject)
@Slot()
def on_actionLoad_Saved_Segmentation_triggered(self):
"""
Opens a dialog to allow the user to choose a file of a
previously saved session.
"""
filedialog = QtGui.QFileDialog()
filedialog.setNameFilter(str("(*.seg)"))
fileSeg, _ = filedialog.getOpenFileName(self, "Open Segmentation file",
os.getcwd(), str("(*.seg)"))
if fileSeg != "":
#checking if there is already a tractography open to substitute it
try:
self.structnameitem
self.tractnameitem
self.treeObject.clear()
self.tractome.clear_all()
self.clear_all_session()
#if there is no tractography open
except AttributeError:
self.chkbShowStruct.setEnabled(True)
self.chkbShowTract.setEnabled(True)
self.tblTract.setEnabled(True)
self.menuROI.setEnabled(True)
self.grbCluster.setEnabled(True)
self.actionLoad_Tractography.setEnabled(True)
self.actionSave_Segmentation.setEnabled(True)
self.actionSave_as_trackvis_file.setEnabled(True)
self.structnameitem = QtGui.QTreeWidgetItem(self.treeObject)
self.tractnameitem = QtGui.QTreeWidgetItem(self.treeObject)
self.tractome.load_segmentation(fileSeg)
#add structural and tractography file names to the treeview
struct_basename = os.path.basename(self.tractome.structpath)
self.structnameitem.setText(0, struct_basename)
tracks_basename = os.path.basename(self.tractome.tracpath)
self.set_clustering_values()
self.tractnameitem.setText(0, tracks_basename)
# connecting event that is fired when number of streamlines is changed after some action on the streamlinelabeler actor
self.tractome.streamlab.numstream_handler += self.changenumstreamlines_handler
self.tractome.streamlab.numrep_handler += self.changenumrepresentatives_handler
#add information to tab in Table
self.tblTract.item(0, 1).setText(tracks_basename)
trackcount = len(self.tractome.streamlab.streamline_ids)
self.tblTract.item(1, 1).setText(str(trackcount))
self.tblTract.item(2, 1).setText(
str(len(self.tractome.streamlab.representative_ids)))
try:
hdr = self.tractome.hdr
self.tblTract.item(3, 1).setText(str(hdr['voxel_size']))
self.tblTract.item(4, 1).setText(str(hdr['dim']))
self.tblTract.item(5, 1).setText(str(hdr['voxel_order']))
except AttributeError:
self.tblTract.item(3, 1).setText('No info')
self.tblTract.item(4, 1).setText('No info')
self.tblTract.item(5, 1).setText('LAS')
self.refocus_camera()
def clear_all_session(self):
"""
Clear all the objects related to ROIs
"""
self.list_chkROIS = []
self.list_ands = []
self.list_ors = []
self.tblROISlist.clear()
self.tblROI.setEnabled(False)
self.tblROISlist.setEnabled(False)
self.tabProps_4.setCurrentIndex(0)
@Slot()
def on_actionSave_as_trackvis_file_triggered(self):
"""
Save streamlines of actual session in .trk file
"""
filename = QtGui.QFileDialog.getSaveFileName(
self, 'Save Segmentation in .trk', os.getcwd(), str("(*.trk)"))
self.tractome.save_trk(filename)
@Slot()
def on_actionSave_Segmentation_triggered(self):
"""
Saves the current session.
"""
filename = QtGui.QFileDialog.getSaveFileName(self, 'Save Segmentation',
os.getcwd(),
str("(*.seg)"))
self.tractome.save_segmentation(filename)
@Slot()
def on_actionClose_triggered(self):
"""
Close application
"""
self.close()
def disconnect_signals(self):
"""
Disconnect signal of spinboxes in ROI tables. If they are
connected when updating min_max values of spinbox, the
valueChanged signal is unnecessarily called.
"""
self.disconnect(self.spbrad, QtCore.SIGNAL("valueChanged(int)"),
self.on_spbrad_valueChanged)
self.disconnect(self.dspbxcoord, QtCore.SIGNAL("valueChanged(double)"),
self.on_dspbxcoord_valueChanged)
self.disconnect(self.dspbycoord, QtCore.SIGNAL("valueChanged(double)"),
self.on_dspbycoord_valueChanged)
self.disconnect(self.dspbzcoord, QtCore.SIGNAL("valueChanged(double)"),
self.on_dspbzcoord_valueChanged)
def connect_signals(self):
"""
Reconnect signals of spinboxes in ROI tables, after min_max
values have been updated
"""
self.connect(self.spbrad, QtCore.SIGNAL("valueChanged(int)"),
self.on_spbrad_valueChanged)
self.connect(self.dspbxcoord, QtCore.SIGNAL("valueChanged(double)"),
self.on_dspbxcoord_valueChanged)
self.connect(self.dspbycoord, QtCore.SIGNAL("valueChanged(double)"),
self.on_dspbycoord_valueChanged)
self.connect(self.dspbzcoord, QtCore.SIGNAL("valueChanged(double)"),
self.on_dspbzcoord_valueChanged)
@Slot()
def on_actionCreate_Sphere_triggered(self):
"""
Create a ROI and plot sphere
"""
maxcoord = self.tractome.max_coordinates()
xmax = maxcoord[0]
ymax = maxcoord[1]
zmax = maxcoord[2]
self.grb_tractomeroi.setEnabled(True)
self.rdbInsSphere.toggle()
cantrois = 0
if hasattr(self, 'list_chkROIS'):
cantrois = len(self.list_chkROIS)
number = cantrois + 1 #to define the name of the ROI depending on the number of available ROIs
nameroi = 'ROI' + str(number)
self.prepare_interface_ROI('sphere', coords=maxcoord, nameroi=nameroi)
self.tractome.create_ROI_sphere(nameroi, xmax / 2, ymax / 2, zmax / 2,
2, self.roimethod,
self.roi_color.getRgbF(),
self.roi_color.name())
#add info of the ROI to ROI table
self.updateROItable(nameroi, xmax / 2, ymax / 2, zmax / 2, 2,
self.roi_color.name())
self.tabProps_4.setCurrentIndex(1)
self.glWidget.updateGL()
def prepare_interface_ROI(self, roi_type, coords=None, nameroi=None):
"""
Set values and status of all interface elementes related to
ROI.
"""
self.tblROI.setEnabled(True)
self.tblROISlist.setEnabled(True)
self.show_hide_rows(roi_type == 'mask')
try:
self.list_chkROIS
except AttributeError:
self.list_chkROIS = []
self.list_ands = []
self.list_ors = []
# add some fixed information to ROI table
if roi_type == 'sphere':
maxcoord = coords
self.radmax = np.amax(maxcoord)
# self.grbROImethod.setEnabled(True)
# setting some fixed values in the table
self.dspbxcoord.setRange(0, maxcoord[0])
self.dspbycoord.setRange(0, maxcoord[1])
self.dspbzcoord.setRange(0, maxcoord[2])
self.spbrad.setRange(1, self.radmax)
self.connect_signals()
cantrois = len(self.list_chkROIS)
self.activeROI = cantrois # to know which is the ROI shown in the table, in case some information needs to be changed
# define color
if cantrois < len(self.colorlist):
self.roi_color = self.colorlist[self.activeROI]
else:
poscolor = self.activeROI % len(self.colorlist)
self.roi_color = self.colorlist[poscolor]
# add item to tractography in tree
roinameitem = QtGui.QTreeWidgetItem(self.tractnameitem)
roinameitem.setText(0, nameroi) #should we add the whole file path?
# roinameitem.setSelected(True)
self.treeObject.expandAll()
# create checkbox for applying ROI, add to list and to table for applied ROIs
newchkroi = QtGui.QCheckBox()
newchkroi.setText(nameroi)
self.connect(newchkroi, QtCore.SIGNAL("stateChanged(int)"),
self.on_chkroi_stateChanged)
self.list_chkROIS.append(newchkroi)
# create rdbuttons for operators and add checkbox for ROI
cantchk = cantrois
sizetblROIs = self.tblROISlist.geometry()
if cantchk == 0:
self.tblROISlist.insertRow(0)
self.tblROISlist.setCellWidget(0, 0, newchkroi)
else:
self.tblROISlist.insertRow((2 * cantchk) - 1)
# create groupbox
grb_roi_operators = QtGui.QGroupBox()
# create radio buttons
rdband = QtGui.QRadioButton("AND")
rdbor = QtGui.QRadioButton("OR")
rdbor.setText('OR')
# add radio button to groupbox
horizontalLayout_roiop = QtGui.QHBoxLayout()
horizontalLayout_roiop.addWidget(rdband)
horizontalLayout_roiop.addWidget(rdbor)
horizontalLayout_roiop.addStretch(1)
grb_roi_operators.setLayout(horizontalLayout_roiop)
self.connect(rdband, QtCore.SIGNAL("clicked(bool)"),
self.on_rdb_clicked)
self.connect(rdbor, QtCore.SIGNAL("clicked(bool)"),
self.on_rdb_clicked)
#
self.tblROISlist.setCellWidget((2 * cantchk) - 1, 0,
grb_roi_operators)
self.list_ands.append(rdband)
self.list_ors.append(rdbor)
self.tblROISlist.insertRow(2 * cantchk)
self.tblROISlist.setCellWidget(2 * cantchk, 0, newchkroi)
self.tblROISlist.resizeRowsToContents()
#resizing objects
sizeandrdb = rdband.geometry()
sizeorrdb = rdbor.geometry()
rdband.setGeometry(sizeandrdb.left(), sizeandrdb.top(), 5,
sizeandrdb.height())
rdbor.setGeometry(sizeorrdb.left(), sizeorrdb.top(), 5,
sizeorrdb.height())
#resizing checkbox
sizecheckbox = newchkroi.geometry()
newchkroi.setGeometry(sizecheckbox.left(), sizecheckbox.top(),
sizetblROIs.width(), sizecheckbox.height())
def updateROItable(self,
name,
coordx=None,
coordy=None,
coordz=None,
radius=None,
color=None):
"""
Information of ROI is inserted in table when new ROI is
created or when ROI selection changes in treeview.
"""
#show info of ROI in the table
self.tblROI.item(0, 1).setText(name)
if coordx is not None:
self.disconnect_signals()
self.dspbxcoord.setValue(coordx)
self.dspbycoord.setValue(coordy)
self.dspbzcoord.setValue(coordz)
self.spbrad.setValue(radius)
self.connect_signals()
self.btncolor.setStyleSheet(u'background-color:%s' % color)
def show_hide_rows(self, hide):
"""
Hides or shows rows from TableROI, depending on the type of
ROI is selected on the tree.
"""
for i in range(3, self.tblROI.rowCount()):
self.tblROI.setRowHidden(i, hide)
self.tblROI.resizeRowsToContents()
def on_chkroi_stateChanged(self, checked):
"""
Computing streamlines to show according to ROIs that are
checked and their operators.
"""
last_chkd = 0
for pos in range(0, len(self.list_chkROIS)):
if self.list_chkROIS[pos].isChecked():
self.tractome.activation_ROIs(pos, True)
if pos != (len(self.list_chkROIS) - 1) and (
(self.list_ands[pos].isChecked() == False) and
(self.list_ors[pos].isChecked() == False)):
self.list_ands[pos].setChecked(True)
else:
self.tractome.activation_ROIs(pos, False, operator='and')
if pos != (len(self.list_chkROIS) - 1):
if self.list_ands[pos].isChecked():
self.list_ands[pos].setAutoExclusive(False)
self.list_ands[pos].setChecked(False)
self.list_ands[pos].setAutoExclusive(True)
if self.list_ors[pos].isChecked():
self.list_ors[pos].setAutoExclusive(False)
self.list_ors[pos].setChecked(False)
self.list_ors[pos].setAutoExclusive(True)
self.tractome.compute_streamlines_ROIS()
self.glWidget.updateGL()
def on_rdb_clicked(self, clicked):
"""
Computing streamlines to show according to ROIs that are
checked and their operators.
"""
for pos in range(0, len(self.list_ands)):
if self.list_ands[pos].isChecked():
self.tractome.activation_ROIs(pos, True, operator='and')
if self.list_ors[pos].isChecked():
self.tractome.activation_ROIs(pos, True, operator='or')
self.tractome.compute_streamlines_ROIS()
self.glWidget.updateGL()
@Slot(QtGui.QTableWidgetItem)
def on_tblROI_itemChanged(self, item):
"""
Will change name of ROI if this is edited in the table.
"""
treeitem = self.tractnameitem.child(self.activeROI)
if item is self.tblROI.item(0, 1):
prev_name_roi = str(treeitem.text(0))
index = self.treeObject.indexFromItem(treeitem, 0)
if index.isValid():
self.tractome.update_ROI(prev_name_roi,
newname=item.text(),
pos_activeroi=self.activeROI)
treeitem.setText(0, item.text())
@Slot()
def on_actionRe_Cluster_triggered(self):
"""
Re-cluster.
"""
self.spbRecluster.setEnabled(True)
self.hSlReCluster.setEnabled(True)
self.pbRecluster.setEnabled(True)
def set_clustering_values(self):
"""
"""
max, default = self.tractome.max_num_clusters()
self.spbRecluster.setValue(default)
self.spbRecluster.setRange(1, max)
self.hSlReCluster.setValue(default)
self.hSlReCluster.setMinimum(1)
self.hSlReCluster.setMaximum(min(150, max))
def initSpincamera(self, angle=0.007):
"""
"""
if self._spinCameraTimerInit:
self.spinCameraTimer.timeout.disconnect()
def rotate_camera():
self.glWidget.world.camera.rotate_around_focal(angle, "yup")
self.glWidget.updateGL()
self.spinCameraTimer.timeout.connect(rotate_camera)
self._spinCameraTimerInit = True
def spinCameraToggle(self):
"""
"""
if not self.spinCameraTimer.isActive():
self.spinCameraTimer.start()
else:
self.spinCameraTimer.stop()
def timerInit(self, interval=30):
"""
"""
timer = QtCore.QTimer(self)
timer.setInterval(interval)
return timer
def add_scene(self, scene):
"""
"""
self.glWidget.world.add_scene(scene)
def set_camera(self, camera):
"""
"""
self.glWidget.world.camera = camera
def refocus_camera(self):
"""
"""
self.glWidget.world.refocus_camera()
def update_light_position(self, x, y, z):
"""
"""
if not self.glWidget.world.light is None:
self.glWidget.world.update_lightposition(x, y, z)
def screenshot(self, filename):
""" Store current OpenGL context as image.
"""
self.glWidget.updateGL()
self.glWidget.grabFrameBuffer().save(filename)
def keyPressEvent(self, event):
""" Handle all key press events.
"""
# print 'key pressed', event.key()
key = event.key()
# self.messages=empty_messages.copy()
# self.messages['key_pressed']=key
# self.glWidget.world.send_all_messages(self.messages)
# F1: fullscreen
# F2: next frame
# F3: previous frame
# F4: start rotating
# F12: reset camera
# Esc: close window
if key == QtCore.Qt.Key_F1:
if self.fullscreen:
self.showNormal()
else:
self.showFullScreen()
self.fullscreen = not self.fullscreen
elif key == QtCore.Qt.Key_F2:
self.glWidget.world.nextTimeFrame()
elif key == QtCore.Qt.Key_F3:
self.glWidget.world.previousTimeFrame()
elif key == QtCore.Qt.Key_F12:
self.glWidget.world.refocus_camera()
self.glWidget.world.camera.update()
self.glWidget.updateGL()
elif key == QtCore.Qt.Key_F4:
if (event.modifiers() & QtCore.Qt.ShiftModifier):
self.initSpincamera(angle=-0.01)
self.spinCameraToggle()
else:
self.initSpincamera(angle=0.01)
self.spinCameraToggle()
elif key == QtCore.Qt.Key_Escape:
self.close()
else:
super(MainWindow, self).keyPressEvent(event)
self.glWidget.updateGL()
