def edit_histogram_gui(hist):
items = []
binSlider = SliderLabel(0)
binSlider.setMinimum(1)
binSlider.setMaximum(len(hist.plot_data))
binSlider.setValue(hist.n_bins)
items.append({'name': 'Bins', 'string': 'Bins', 'object': binSlider})
bd = BaseDialog(items, "Histogram options", 'Set the number of bins in the histogram')
bd.accepted.connect(lambda : hist.setData(n_bins=binSlider.value()))
bd.rejected.connect(hist.reset)
bd.changeSignal.connect(lambda : hist.preview(n_bins=binSlider.value()))
bd.show()
g.m.dialog = bd
def edit_histogram_gui(hist):
items = []
binSlider = SliderLabel(0)
binSlider.setMinimum(1)
binSlider.setMaximum(len(hist.plot_data))
binSlider.setValue(hist.n_bins)
items.append({'name': 'Bins', 'string': 'Bins', 'object': binSlider})
bd = BaseDialog(items, "Histogram options",
'Set the number of bins in the histogram')
bd.accepted.connect(lambda: hist.setData(n_bins=binSlider.value()))
bd.rejected.connect(hist.reset)
bd.changeSignal.connect(lambda: hist.preview(n_bins=binSlider.value()))
bd.show()
g.m.dialog = bd
class Volume_Viewer(QWidget):
closeSignal=Signal()
def show_wo_focus(self):
self.show()
self.window.activateWindow() # for Windows
self.window.raise_() # for MacOS
def __init__(self,window=None,parent=None):
super(Volume_Viewer,self).__init__(parent) ## Create window with ImageView widget
g.m.volume_viewer=self
window.lostFocusSignal.connect(self.hide)
window.gainedFocusSignal.connect(self.show_wo_focus)
self.window=window
self.setWindowTitle('Light Sheet Volume View Controller')
self.setWindowIcon(QIcon('images/favicon.png'))
self.setGeometry(QRect(422, 35, 222, 86))
self.layout = QVBoxLayout()
self.vol_shape=window.volume.shape
mv,mz,mx,my=window.volume.shape
self.currentAxisOrder=[0,1,2,3]
self.current_v_Index=0
self.current_z_Index=0
self.current_x_Index=0
self.current_y_Index=0
self.formlayout=QFormLayout()
self.formlayout.setLabelAlignment(Qt.AlignRight)
self.xzy_position_label=QLabel('Z position')
self.zSlider=SliderLabel(0)
self.zSlider.setRange(0,mz-1)
self.zSlider.label.valueChanged.connect(self.zSlider_updated)
self.zSlider.slider.mouseReleaseEvent=self.zSlider_release_event
self.sideViewOn=CheckBox()
self.sideViewOn.setChecked(False)
self.sideViewOn.stateChanged.connect(self.sideViewOnClicked)
self.sideViewSide = QComboBox(self)
self.sideViewSide.addItem("X")
self.sideViewSide.addItem("Y")
self.MaxProjButton = QPushButton('Max Intenstiy Projection')
self.MaxProjButton.pressed.connect(self.make_maxintensity)
self.exportVolButton = QPushButton('Export Volume')
self.exportVolButton.pressed.connect(self.export_volume)
self.formlayout.addRow(self.xzy_position_label,self.zSlider)
self.formlayout.addRow('Side View On',self.sideViewOn)
self.formlayout.addRow('Side View Side',self.sideViewSide)
self.formlayout.addRow('', self.MaxProjButton)
self.formlayout.addRow('', self.exportVolButton)
self.layout.addWidget(self.zSlider)
self.layout.addLayout(self.formlayout)
self.setLayout(self.layout)
self.setGeometry(QRect(381, 43, 416, 110))
self.show()
def closeEvent(self, event):
event.accept() # let the window close
def zSlider_updated(self,z_val):
self.current_v_Index=self.window.currentIndex
vol=self.window.volume
testimage=np.squeeze(vol[self.current_v_Index,z_val,:,:])
viewRect = self.window.imageview.view.targetRect()
self.window.imageview.setImage(testimage,autoLevels=False)
self.window.imageview.view.setRange(viewRect, padding = 0)
self.window.image = testimage
def zSlider_release_event(self,ev):
vol=self.window.volume
if self.currentAxisOrder[1]==1: # 'z'
self.current_z_Index=self.zSlider.value()
image=np.squeeze(vol[:,self.current_z_Index,:,:])
elif self.currentAxisOrder[1]==2: # 'x'
self.current_x_Index=self.zSlider.value()
image=np.squeeze(vol[:,self.current_x_Index,:,:])
elif self.currentAxisOrder[1]==3: # 'y'
self.current_y_Index=self.zSlider.value()
image=np.squeeze(vol[:,self.current_y_Index,:,:])
viewRect = self.window.imageview.view.viewRect()
self.window.imageview.setImage(image,autoLevels=False)
self.window.imageview.view.setRange(viewRect, padding=0)
self.window.image = image
self.window.imageview.setCurrentIndex(self.current_v_Index)
self.window.activateWindow() # for Windows
self.window.raise_() # for MacOS
QSlider.mouseReleaseEvent(self.zSlider.slider, ev)
def sideViewOnClicked(self, checked):
self.current_v_Index=self.window.currentIndex
vol=self.window.volume
if checked==2: #checked=True
assert self.currentAxisOrder==[0,1,2,3]
side = self.sideViewSide.currentText()
if side=='X':
vol=vol.swapaxes(1,2)
self.currentAxisOrder=[0,2,1,3]
vol=vol.swapaxes(2,3)
self.currentAxisOrder=[0,2,3,1]
elif side=='Y':
vol=vol.swapaxes(1,3)
self.currentAxisOrder=[0,3,2,1]
else: #checked=False
if self.currentAxisOrder == [0,3,2,1]:
vol=vol.swapaxes(1,3)
self.currentAxisOrder=[0,1,2,3]
elif self.currentAxisOrder == [0,2,3,1]:
vol=vol.swapaxes(2,3)
vol=vol.swapaxes(1,2)
self.currentAxisOrder=[0,1,2,3]
if self.currentAxisOrder[1]==1: # 'z'
idx=self.current_z_Index
self.xzy_position_label.setText('Z position')
self.zSlider.setRange(0,self.vol_shape[1]-1)
elif self.currentAxisOrder[1]==2: # 'x'
idx=self.current_x_Index
self.xzy_position_label.setText('X position')
self.zSlider.setRange(0,self.vol_shape[2]-1)
elif self.currentAxisOrder[1]==3: # 'y'
idx=self.current_y_Index
self.xzy_position_label.setText('Y position')
self.zSlider.setRange(0,self.vol_shape[3]-1)
image=np.squeeze(vol[:,idx,:,:])
self.window.imageview.setImage(image,autoLevels=False)
self.window.volume=vol
self.window.imageview.setCurrentIndex(self.current_v_Index)
self.zSlider.setValue(idx)
def make_maxintensity(self):
vol=self.window.volume
new_vol=np.max(vol,1)
if self.currentAxisOrder[1]==1: # 'z'
name='Max Z projection'
elif self.currentAxisOrder[1]==2: # 'x'
name = 'Max X projection'
elif self.currentAxisOrder[1]==3: # 'y'
name = 'Max Y projection'
Window(new_vol, name=name)
def export_volume(self):
vol=self.window.volume
export_path = QFileDialog.getExistingDirectory(g.m, "Select a parent folder to save into.", expanduser("~"), QFileDialog.ShowDirsOnly)
export_path = os.path.join(export_path, 'light_sheet_vols')
i=0
while os.path.isdir(export_path+str(i)):
i+=1
export_path=export_path+str(i)
os.mkdir(export_path)
for v in np.arange(len(vol)):
A=vol[v]
filename=os.path.join(export_path,str(v)+'.tiff')
if len(A.shape)==3:
A=np.transpose(A,(0,2,1)) # This keeps the x and the y the same as in FIJI
elif len(A.shape)==2:
A=np.transpose(A,(1,0))
tifffile.imsave(filename, A)
class Drift_Correction(BaseProcess):
'''Draw rectangular ROIs around tracer locations to track movement over time. Locate the center coordinates and correct the image for drift
'''
def __init__(self):
super().__init__()
findButton = QPushButton("Find Centers")
findButton.pressed.connect(self.find_centers)
self.slider = SliderLabel()
self.slider.setRange(0, 10)
self.slider.valueChanged.connect(self.plotCenters)
self.items.append({
'name': 'findButton',
'string': 'Locate centroids',
'object': findButton
})
self.items.append({
'name': 'smoothness',
'string': 'Drift Smoothness',
'object': self.slider
})
# Enable antialiasing for prettier plots
pg.setConfigOptions(antialias=True)
self.scatter = pg.ScatterPlotItem()
self.p1 = pg.PlotWidget(title="X Shift")
self.p2 = pg.PlotWidget(title="Y Shift")
def gui(self):
super().gui()
self.ui.layout.insertWidget(0, self.p1)
self.ui.layout.insertWidget(1, self.p2)
self.ui.resize(1000, 600)
def plotCenters(self):
self.p1.clear()
self.p2.clear()
for r in self.rois:
centers = np.copy(r['centers'])
#self.p1.plot(y=centers[:, 0] / np.average(centers[:, 0]), pen=r['roi'].pen)
#self.p2.plot(y=centers[:, 1] / np.average(centers[:, 1]), pen=r['roi'].pen)
self.p1.plot(y=gf(centers[:, 0], self.slider.value()),
pen=r['roi'].pen)
self.p2.plot(y=gf(centers[:, 1], self.slider.value()),
pen=r['roi'].pen)
def __call__(self, keepSourceWindow=False):
xx, yy = [], []
for i in range(len(self.p1.plotItem.items)):
xx.append(self.p1.plotItem.items[i].getData()[1])
yy.append(self.p2.plotItem.items[i].getData()[1])
diffs = np.mean([xx, yy], 1).T
diffs = -1 * diffs + diffs[0]
im = np.copy(g.m.currentWindow.image)
for i, sh in enumerate(diffs):
g.m.statusBar().showMessage("shifting frame %d of %d" %
(i, len(diffs)))
im[i] = shift(im[i], sh)
QApplication.instance().processEvents()
return Window(im)
def find_centers(self):
win = g.m.currentWindow
im = win.image
mx, my = win.imageDimensions()
self.rois = []
g.centers = []
for roi in g.m.currentWindow.rois:
mask = roi.mask
mask = mask[(mask[:, 0] >= 0) * (mask[:, 0] < mx) *
(mask[:, 1] >= 0) * (mask[:, 1] < my)]
xx = mask[:, 0]
yy = mask[:, 1]
centers = []
for frame in im:
gframe = gf(frame, 1)
x0, y0 = np.unravel_index(gframe.argmax(), gframe.shape)
#centers.append([x0, y0])
#vals = fitGaussian(frame, (x0, y0, 1, 3))
#x1, y1, a, b = vals[0]
centers.append([x0, y0])
self.rois.append({'roi': roi, 'centers': centers})
self.plotCenters()
class Drift_Correction(BaseProcess):
'''Draw rectangular ROIs around tracer locations to track movement over time. Locate the center coordinates and correct the image for drift
'''
def __init__(self):
super().__init__()
findButton = QPushButton("Find Centers")
findButton.pressed.connect(self.find_centers)
self.slider = SliderLabel()
self.slider.setRange(0, 10)
self.slider.valueChanged.connect(self.plotCenters)
self.items.append({'name':'findButton','string':'Locate centroids','object':findButton})
self.items.append({'name':'smoothness', 'string': 'Drift Smoothness', 'object':self.slider})
# Enable antialiasing for prettier plots
pg.setConfigOptions(antialias=True)
self.scatter = pg.ScatterPlotItem()
self.p1 = pg.PlotWidget(title="X Shift")
self.p2 = pg.PlotWidget(title="Y Shift")
def gui(self):
super().gui()
self.ui.layout.insertWidget(0, self.p1)
self.ui.layout.insertWidget(1, self.p2)
self.ui.resize(1000, 600)
def plotCenters(self):
self.p1.clear()
self.p2.clear()
for r in self.rois:
centers = np.copy(r['centers'])
#self.p1.plot(y=centers[:, 0] / np.average(centers[:, 0]), pen=r['roi'].pen)
#self.p2.plot(y=centers[:, 1] / np.average(centers[:, 1]), pen=r['roi'].pen)
self.p1.plot(y=gf(centers[:, 0], self.slider.value()), pen=r['roi'].pen)
self.p2.plot(y=gf(centers[:, 1], self.slider.value()), pen=r['roi'].pen)
def __call__(self, keepSourceWindow=False):
xx, yy = [], []
for i in range(len(self.p1.plotItem.items)):
xx.append(self.p1.plotItem.items[i].getData()[1])
yy.append(self.p2.plotItem.items[i].getData()[1])
diffs = np.mean([xx, yy], 1).T
diffs = -1 * diffs + diffs[0]
im = np.copy(g.m.currentWindow.image)
for i, sh in enumerate(diffs):
g.m.statusBar().showMessage("shifting frame %d of %d" % (i, len(diffs)))
im[i] = shift(im[i], sh)
QApplication.instance().processEvents()
return Window(im)
def find_centers(self):
win = g.m.currentWindow
im = win.image
mx,my=win.imageDimensions()
self.rois = []
g.centers = []
for roi in g.m.currentWindow.rois:
mask = roi.mask
mask=mask[(mask[:,0]>=0)*(mask[:,0]<mx)*(mask[:,1]>=0)*(mask[:,1]<my)]
xx=mask[:,0]; yy=mask[:,1]
centers = []
for frame in im:
gframe = gf(frame, 1)
x0, y0 = np.unravel_index(gframe.argmax(), gframe.shape)
#centers.append([x0, y0])
#vals = fitGaussian(frame, (x0, y0, 1, 3))
#x1, y1, a, b = vals[0]
centers.append([x0, y0])
self.rois.append({'roi': roi, 'centers': centers})
self.plotCenters()
