def onROIfromImg(self):
stim = []
for item in self.items:
idx = self.items.index(item)
if item.checkState(2) == Qt.Checked:
stim.append(self.pngs[idx])
self.control = TmsROI(stim, self)
self.MDI.addSubWindow(self.control)
self.control.ROISignal.connect(self.onROIchanged)
self.control.show()
def onROIfromImg(self):
stim = []
for item in self.items:
idx = self.items.index(item)
if item.checkState(2) == Qt.Checked:
stim.append(self.pngs[idx])
self.control = TmsROI(stim, self)
self.MDI.addSubWindow(self.control)
self.control.ROISignal.connect(self.onROIchanged)
self.control.show()
class TMSControl(QMainWindow):
imageChanged = pyqtSignal(str)
def __init__(self, ROIs=None, parent=None):
QMainWindow.__init__(self, parent)
self.setWindowTitle('TMS Parameter Control')
self.imgfile = None
self.ROInames = []
if ROIs != None:
self.ROIs = []
for i in range(len(ROIs)):
self.ROIs.append(ROIs[i].ROI)
self.ROInames.append('ROI_%d'%(i+1))
else:
self.ROIs = []
self.createMainFrame()
self.createImgView()
self.createMenu()
def createMainFrame(self):
self.mainFrame = QWidget()
self.MDI = QMdiArea()
self.view = QTreeWidget()
self.view.setColumnCount(4)
self.view.setHeaderLabels(['Filename', 'Condition', 'TMS', 'Baseline'])
listLabel = QLabel('Check frames with stimulation:')
self.showBarPlot = QPushButton('Show Results')
self.view.itemDoubleClicked.connect(self.onSelect)
self.showBarPlot.clicked.connect(self.onPlot)
vbox = QVBoxLayout()
vbox.addWidget(listLabel)
vbox.addWidget(self.view)
vbox.addWidget(self.showBarPlot)
hbox = QHBoxLayout()
hbox.addLayout(vbox)
hbox.addWidget(self.MDI)
self.mainFrame.setLayout(hbox)
self.setCentralWidget(self.mainFrame)
def createImgView(self):
self.imgView = ImageView(self)
self.MDI.addSubWindow(self.imgView)
self.imgView.show()
def createMenu(self):
'''
Creates the file menu
'''
self.file_menu = self.menuBar().addMenu("&File")
load_action = self.create_action("&Open Images",
shortcut="Ctrl+O", slot=self.onOpen,
tip="Open a set of image directories")
save_ROI_action = self.create_action("&Save ROIs", slot=self.onSaveROIs,
shortcut="Ctrl+R", tip="Save each ROI to a .npy file")
load_ROI_action = self.create_action("&Load ROI",
shortcut="Ctrl+L", slot=self.onLoadROI,
tip="Load ROIs from files")
export_action = self.create_action("&Export Results", slot=self.onExport,
shortcut="Ctrl+S", tip="Export results to file")
colormap_action = self.create_action("Export &Activations", slot=self.onExportActivations,
shortcut="Ctrl+C", tip="Export activation images to csv files")
quit_action = self.create_action("&Quit", slot=self.close,
shortcut="Ctrl+Q", tip="Close the application")
roi_from_img_action = self.create_action("&ROI from images", slot=self.onROIfromImg,
tip="Use TMS images to define an ROI")
self.settings_menu = self.menuBar().addMenu("&Settings")
save_settings_action = self.create_action("Save Se&ttings",
slot=self.onSaveSettings, tip="Save check settings")
load_settings_action = self.create_action("&Load Settings",
slot=self.onLoadSettings, tip="Load a settings file")
self.add_actions(self.file_menu, (load_action, save_ROI_action, load_ROI_action, roi_from_img_action,
None, export_action, colormap_action, None, quit_action))
self.add_actions(self.settings_menu, (save_settings_action, load_settings_action))
def add_actions(self, target, actions):
'''
Adds the actions to the file menu
'''
for action in actions:
if action is None:
target.addSeparator()
else:
target.addAction(action)
def create_action( self, text, slot=None, shortcut=None,
icon=None, tip=None, checkable=False,
signal="triggered()"):
'''
Creates actions for the file menu
'''
action = QAction(text, self)
if icon is not None:
action.setIcon(QIcon(":/%s.png" % icon))
if shortcut is not None:
action.setShortcut(shortcut)
if tip is not None:
action.setToolTip(tip)
action.setStatusTip(tip)
if slot is not None:
self.connect(action, SIGNAL(signal), slot)
if checkable:
action.setCheckable(True)
return action
def getResults(self, stim, nostim):
if self.ROIs == []:
warn = QMessageBox.warning(self, "No ROI specified", "Warning: No ROI specified")
else:
thread = WorkThread(stim, nostim, self.ROIs)
prog = ProgressWidget(thread)
prog.show()
thread.run()
self.stimval, self.nostimval, self.conditions, self.stimfiles, self.nostimfiles, \
self.stimpx, self.nostimpx, self.stimcenter, self.nostimcenter = thread.getVals()
def onExportActivations(self):
dirname = QFileDialog.getExistingDirectory(parent=self, caption="Choose a directory for export")
dirname = str(dirname)
if dirname != '':
self.onCalculate()
for n in range(len(self.stimfiles)):
for i in range(len(self.stimfiles[n])):
filename = (os.path.basename(self.stimfiles[n][i]))[:-3] + 'csv'
np.savetxt(os.path.join(dirname, filename), self.stimpx[n][i], fmt='%d', delimiter=',')
def onROIfromImg(self):
stim = []
for item in self.items:
idx = self.items.index(item)
if item.checkState(2) == Qt.Checked:
stim.append(self.pngs[idx])
self.control = TmsROI(stim, self)
self.MDI.addSubWindow(self.control)
self.control.ROISignal.connect(self.onROIchanged)
self.control.show()
def onROIchanged(self):
self.ROIs = []
for i in range(len(self.control.ROIs)):
self.ROIs.append(self.control.ROIs[i].ROI)
self.ROInames.append('ROI_%d'%(i+1))
self.imageChanged.emit(self.imgfile)
def onSaveSettings(self):
filename = QFileDialog.getSaveFileName(parent=self, caption="Choose a settings filename", filter='*.txt')
f = open(filename, 'w')
for item in self.items:
idx = self.items.index(item)
if item.checkState(2) == Qt.Checked:
f.write('%s,True,'%self.pngs[idx])
else:
f.write('%s,False,'%self.pngs[idx])
if item.checkState(3) == Qt.Checked:
f.write('True\n')
else:
f.write('False\n')
f.close()
def onLoadSettings(self):
filename = QFileDialog.getOpenFileName(parent=self, caption="Open a settings file", filter='*.txt')
f = open(filename, 'r').readlines()
basepngs = []
for i in range(len(self.pngs)):
basepngs.append(os.path.basename(self.pngs[i]))
for i in range(len(f)):
l = f[i][:-1].split(',')
png = l[0]
TMS = l[1]
try:
baseline = l[2]
except IndexError:
baseline = 'False'
if TMS == 'True':
try:
idx = basepngs.index(os.path.basename(png))
self.items[idx].setCheckState(2, Qt.Checked)
except ValueError:
pass
if baseline == 'True':
try:
idx = basepngs.index(os.path.basename(png))
self.items[idx].setCheckState(3, Qt.Checked)
except ValueError:
pass
def onLoadROI(self):
files = QFileDialog.getOpenFileNamesAndFilter(parent=self, caption="Choose ROI files", filter='*.npy')
self.ROIs = []
self.ROInames = []
for f in list(files[0]):
ROI = np.load(str(f))
self.ROIs.append(ROI)
self.ROInames.append(f[:-4])
self.imageChanged.emit(self.imgfile)
def onSaveROIs(self):
for roi in self.ROIs:
filename = QFileDialog.getSaveFileNameAndFilter(parent=self, caption="Choose a save file name",
filter="*.npy")
np.save(str(filename[0]), roi)
np.savetxt(str(filename[0][:-3]+'csv'), roi, fmt='%d', delimiter=',')
def onOpen(self):
fd = MultiDirectoryFileDialog()
fd.exec_()
dirs = fd.filesSelected()
self.view.clear()
parent = self.view.invisibleRootItem()
try:
self.pngs = []
self.items = []
for d in dirs:
files = sorted(os.listdir(d))
dname = os.path.basename(d)
condition = dname.split('_')[1]
topitem = QTreeWidgetItem(parent, [dname])
topitem.setText(0, dname)
topitem.setChildIndicatorPolicy(QTreeWidgetItem.ShowIndicator)
topitem.setExpanded(True)
for f in files:
if f[-3:] == 'png':
self.pngs.append(os.path.join(d, f))
item = QTreeWidgetItem(topitem, [f, condition])
item.setText(0, f)
item.setText(1, condition)
item.setCheckState(2, Qt.Unchecked)
item.setCheckState(3, Qt.Unchecked)
self.items.append(item)
self.view.setColumnWidth(0, 200)
self.view.setColumnWidth(1, 75)
self.view.setColumnWidth(2, 50)
self.view.setColumnWidth(3, 50)
except TypeError:
pass
def onExport(self):
filename = QFileDialog.getSaveFileName(parent=self, caption="Choose a save file name")
self.onCalculate()
f = open(filename, 'w')
f.write('filename,condition,stim,center_x,center_y,')
for i in range(0, self.stimval[0].shape[1], 2):
f.write('ROI_%d_pos,ROI_%d_neg,'%((i/2)+1,(i/2)+1))
f.write('\n')
for n in range(len(self.stimval)):
for i in range(self.stimval[n].shape[0]):
f.write('%s,%s,stim,%0.6f,%0.6f,'%(self.stimfiles[n][i], str(self.conditions[n][0]),
self.stimcenter[n][i][0],self.stimcenter[n][i][1]))
for j in range(0, self.stimval[n].shape[1], 2):
f.write('%0.6f,%0.6f,'%(self.stimval[n][i,j], self.stimval[n][i,j+1]))
f.write('\n')
for n in range(len(self.nostimval)):
for i in range(self.nostimval[n].shape[0]):
f.write('%s,%s,no_stim,%0.6f,%0.6f,'%(self.nostimfiles[n][i], str(self.conditions[n][0]),
self.nostimcenter[n][i][0],self.nostimcenter[n][i][1]))
for j in range(0, self.nostimval[n].shape[1], 2):
f.write('%0.6f,%0.6f,'%(self.nostimval[n][i,j], self.nostimval[n][i,j+1]))
f.write('\n')
f.close()
def onSelect(self, item):
try:
idx = self.items.index(item)
self.imgfile = self.pngs[idx]
self.imageChanged.emit(str(self.imgfile))
except ValueError:
pass
def onCalculate(self):
stim = []
nostim = []
for item in self.items:
idx = self.items.index(item)
if item.checkState(2) == Qt.Checked:
stim.append([self.pngs[idx], item.text(1)])
if item.checkState(3) == Qt.Checked:
nostim.append([self.pngs[idx], item.text(1)])
self.getResults(stim, nostim)
def onPlot(self):
self.onCalculate()
bp = BarPlot(self)
self.MDI.addSubWindow(bp)
bp.show()
av = ActivationView(control=self)
self.MDI.addSubWindow(av)
av.show()
class TMSControl(QMainWindow):
imageChanged = pyqtSignal(str)
def __init__(self, ROIs=None, parent=None):
QMainWindow.__init__(self, parent)
self.setWindowTitle('TMS Parameter Control')
self.imgfile = None
self.ROInames = []
if ROIs != None:
self.ROIs = []
for i in range(len(ROIs)):
self.ROIs.append(ROIs[i].ROI)
self.ROInames.append('ROI_%d' % (i + 1))
else:
self.ROIs = []
self.createMainFrame()
self.createImgView()
self.createMenu()
def createMainFrame(self):
self.mainFrame = QWidget()
self.MDI = QMdiArea()
self.view = QTreeWidget()
self.view.setColumnCount(4)
self.view.setHeaderLabels(['Filename', 'Condition', 'TMS', 'Baseline'])
listLabel = QLabel('Check frames with stimulation:')
self.showBarPlot = QPushButton('Show Results')
self.view.itemDoubleClicked.connect(self.onSelect)
self.showBarPlot.clicked.connect(self.onPlot)
vbox = QVBoxLayout()
vbox.addWidget(listLabel)
vbox.addWidget(self.view)
vbox.addWidget(self.showBarPlot)
hbox = QHBoxLayout()
hbox.addLayout(vbox)
hbox.addWidget(self.MDI)
self.mainFrame.setLayout(hbox)
self.setCentralWidget(self.mainFrame)
def createImgView(self):
self.imgView = ImageView(self)
self.MDI.addSubWindow(self.imgView)
self.imgView.show()
def createMenu(self):
'''
Creates the file menu
'''
self.file_menu = self.menuBar().addMenu("&File")
load_action = self.create_action("&Open Images",
shortcut="Ctrl+O",
slot=self.onOpen,
tip="Open a set of image directories")
save_ROI_action = self.create_action(
"&Save ROIs",
slot=self.onSaveROIs,
shortcut="Ctrl+R",
tip="Save each ROI to a .npy file")
load_ROI_action = self.create_action("&Load ROI",
shortcut="Ctrl+L",
slot=self.onLoadROI,
tip="Load ROIs from files")
export_action = self.create_action("&Export Results",
slot=self.onExport,
shortcut="Ctrl+S",
tip="Export results to file")
colormap_action = self.create_action(
"Export &Activations",
slot=self.onExportActivations,
shortcut="Ctrl+C",
tip="Export activation images to csv files")
quit_action = self.create_action("&Quit",
slot=self.close,
shortcut="Ctrl+Q",
tip="Close the application")
roi_from_img_action = self.create_action(
"&ROI from images",
slot=self.onROIfromImg,
tip="Use TMS images to define an ROI")
self.settings_menu = self.menuBar().addMenu("&Settings")
save_settings_action = self.create_action("Save Se&ttings",
slot=self.onSaveSettings,
tip="Save check settings")
load_settings_action = self.create_action("&Load Settings",
slot=self.onLoadSettings,
tip="Load a settings file")
self.add_actions(self.file_menu,
(load_action, save_ROI_action, load_ROI_action,
roi_from_img_action, None, export_action,
colormap_action, None, quit_action))
self.add_actions(self.settings_menu,
(save_settings_action, load_settings_action))
def add_actions(self, target, actions):
'''
Adds the actions to the file menu
'''
for action in actions:
if action is None:
target.addSeparator()
else:
target.addAction(action)
def create_action(self,
text,
slot=None,
shortcut=None,
icon=None,
tip=None,
checkable=False,
signal="triggered()"):
'''
Creates actions for the file menu
'''
action = QAction(text, self)
if icon is not None:
action.setIcon(QIcon(":/%s.png" % icon))
if shortcut is not None:
action.setShortcut(shortcut)
if tip is not None:
action.setToolTip(tip)
action.setStatusTip(tip)
if slot is not None:
self.connect(action, SIGNAL(signal), slot)
if checkable:
action.setCheckable(True)
return action
def getResults(self, stim, nostim):
if self.ROIs == []:
warn = QMessageBox.warning(self, "No ROI specified",
"Warning: No ROI specified")
else:
thread = WorkThread(stim, nostim, self.ROIs)
prog = ProgressWidget(thread)
prog.show()
thread.run()
self.stimval, self.nostimval, self.conditions, self.stimfiles, self.nostimfiles, \
self.stimpx, self.nostimpx, self.stimcenter, self.nostimcenter = thread.getVals()
def onExportActivations(self):
dirname = QFileDialog.getExistingDirectory(
parent=self, caption="Choose a directory for export")
dirname = str(dirname)
if dirname != '':
self.onCalculate()
for n in range(len(self.stimfiles)):
for i in range(len(self.stimfiles[n])):
filename = (os.path.basename(
self.stimfiles[n][i]))[:-3] + 'csv'
np.savetxt(os.path.join(dirname, filename),
self.stimpx[n][i],
fmt='%d',
delimiter=',')
def onROIfromImg(self):
stim = []
for item in self.items:
idx = self.items.index(item)
if item.checkState(2) == Qt.Checked:
stim.append(self.pngs[idx])
self.control = TmsROI(stim, self)
self.MDI.addSubWindow(self.control)
self.control.ROISignal.connect(self.onROIchanged)
self.control.show()
def onROIchanged(self):
self.ROIs = []
for i in range(len(self.control.ROIs)):
self.ROIs.append(self.control.ROIs[i].ROI)
self.ROInames.append('ROI_%d' % (i + 1))
self.imageChanged.emit(self.imgfile)
def onSaveSettings(self):
filename = QFileDialog.getSaveFileName(
parent=self, caption="Choose a settings filename", filter='*.txt')
f = open(filename, 'w')
for item in self.items:
idx = self.items.index(item)
if item.checkState(2) == Qt.Checked:
f.write('%s,True,' % self.pngs[idx])
else:
f.write('%s,False,' % self.pngs[idx])
if item.checkState(3) == Qt.Checked:
f.write('True\n')
else:
f.write('False\n')
f.close()
def onLoadSettings(self):
filename = QFileDialog.getOpenFileName(parent=self,
caption="Open a settings file",
filter='*.txt')
f = open(filename, 'r').readlines()
basepngs = []
for i in range(len(self.pngs)):
basepngs.append(os.path.basename(self.pngs[i]))
for i in range(len(f)):
l = f[i][:-1].split(',')
png = l[0]
TMS = l[1]
try:
baseline = l[2]
except IndexError:
baseline = 'False'
if TMS == 'True':
try:
idx = basepngs.index(os.path.basename(png))
self.items[idx].setCheckState(2, Qt.Checked)
except ValueError:
pass
if baseline == 'True':
try:
idx = basepngs.index(os.path.basename(png))
self.items[idx].setCheckState(3, Qt.Checked)
except ValueError:
pass
def onLoadROI(self):
files = QFileDialog.getOpenFileNamesAndFilter(
parent=self, caption="Choose ROI files", filter='*.npy')
self.ROIs = []
self.ROInames = []
for f in list(files[0]):
ROI = np.load(str(f))
self.ROIs.append(ROI)
self.ROInames.append(f[:-4])
self.imageChanged.emit(self.imgfile)
def onSaveROIs(self):
for roi in self.ROIs:
filename = QFileDialog.getSaveFileNameAndFilter(
parent=self, caption="Choose a save file name", filter="*.npy")
np.save(str(filename[0]), roi)
np.savetxt(str(filename[0][:-3] + 'csv'),
roi,
fmt='%d',
delimiter=',')
def onOpen(self):
fd = MultiDirectoryFileDialog()
fd.exec_()
dirs = fd.filesSelected()
self.view.clear()
parent = self.view.invisibleRootItem()
try:
self.pngs = []
self.items = []
for d in dirs:
files = sorted(os.listdir(d))
dname = os.path.basename(d)
condition = dname.split('_')[1]
topitem = QTreeWidgetItem(parent, [dname])
topitem.setText(0, dname)
topitem.setChildIndicatorPolicy(QTreeWidgetItem.ShowIndicator)
topitem.setExpanded(True)
for f in files:
if f[-3:] == 'png':
self.pngs.append(os.path.join(d, f))
item = QTreeWidgetItem(topitem, [f, condition])
item.setText(0, f)
item.setText(1, condition)
item.setCheckState(2, Qt.Unchecked)
item.setCheckState(3, Qt.Unchecked)
self.items.append(item)
self.view.setColumnWidth(0, 200)
self.view.setColumnWidth(1, 75)
self.view.setColumnWidth(2, 50)
self.view.setColumnWidth(3, 50)
except TypeError:
pass
def onExport(self):
filename = QFileDialog.getSaveFileName(
parent=self, caption="Choose a save file name")
self.onCalculate()
f = open(filename, 'w')
f.write('filename,condition,stim,center_x,center_y,')
for i in range(0, self.stimval[0].shape[1], 2):
f.write('ROI_%d_pos,ROI_%d_neg,' % ((i / 2) + 1, (i / 2) + 1))
f.write('\n')
for n in range(len(self.stimval)):
for i in range(self.stimval[n].shape[0]):
f.write('%s,%s,stim,%0.6f,%0.6f,' %
(self.stimfiles[n][i], str(self.conditions[n][0]),
self.stimcenter[n][i][0], self.stimcenter[n][i][1]))
for j in range(0, self.stimval[n].shape[1], 2):
f.write('%0.6f,%0.6f,' %
(self.stimval[n][i, j], self.stimval[n][i, j + 1]))
f.write('\n')
for n in range(len(self.nostimval)):
for i in range(self.nostimval[n].shape[0]):
f.write(
'%s,%s,no_stim,%0.6f,%0.6f,' %
(self.nostimfiles[n][i], str(self.conditions[n][0]),
self.nostimcenter[n][i][0], self.nostimcenter[n][i][1]))
for j in range(0, self.nostimval[n].shape[1], 2):
f.write(
'%0.6f,%0.6f,' %
(self.nostimval[n][i, j], self.nostimval[n][i, j + 1]))
f.write('\n')
f.close()
def onSelect(self, item):
try:
idx = self.items.index(item)
self.imgfile = self.pngs[idx]
self.imageChanged.emit(str(self.imgfile))
except ValueError:
pass
def onCalculate(self):
stim = []
nostim = []
for item in self.items:
idx = self.items.index(item)
if item.checkState(2) == Qt.Checked:
stim.append([self.pngs[idx], item.text(1)])
if item.checkState(3) == Qt.Checked:
nostim.append([self.pngs[idx], item.text(1)])
self.getResults(stim, nostim)
def onPlot(self):
self.onCalculate()
bp = BarPlot(self)
self.MDI.addSubWindow(bp)
bp.show()
av = ActivationView(control=self)
self.MDI.addSubWindow(av)
av.show()