def mode_change(self, i):
self.activityMode = i
if self.loaded:
# activity used for correlations
self.bin = int(self.binedit.text())
nb = int(np.floor(float(self.Fcell.shape[1]) / float(self.bin)))
if i == 0:
f = self.Fcell
elif i == 1:
f = self.Fneu
elif i == 2:
f = self.Fcell - 0.7 * self.Fneu
else:
f = self.Spks
ncells = len(self.stat)
self.Fbin = f[:, :nb * self.bin].reshape(
(ncells, nb, self.bin)).mean(axis=2)
self.Fbin = self.Fbin - self.Fbin.mean(axis=1)[:, np.newaxis]
self.Fstd = (self.Fbin**2).sum(axis=1)
self.trange = np.arange(0, self.Fcell.shape[1])
# if in correlation-view, recompute
if self.ops_plot[2] == self.ops_plot[3].shape[1]:
fig.corr_masks(self)
elif self.ops_plot[2] == self.ops_plot[3].shape[1] + 1:
fig.beh_masks(self)
fig.plot_colorbar(self, self.ops_plot[2])
M = fig.draw_masks(self)
fig.plot_masks(self, M)
fig.plot_trace(self)
self.show()
def press(self, parent, bid):
for b in range(len(parent.colors)+2):
if parent.colorbtns.button(b).isEnabled():
parent.colorbtns.button(b).setStyleSheet(parent.styleUnpressed)
self.setStyleSheet(parent.stylePressed)
parent.ops_plot[2] = bid
if not parent.sizebtns.button(1).isChecked():
if bid==0:
for b in [1,2]:
parent.topbtns.button(b).setEnabled(False)
parent.topbtns.button(b).setStyleSheet(parent.styleInactive)
else:
for b in [1,2]:
parent.topbtns.button(b).setEnabled(True)
parent.topbtns.button(b).setStyleSheet(parent.styleUnpressed)
else:
for b in range(3):
parent.topbtns.button(b).setEnabled(False)
parent.topbtns.button(b).setStyleSheet(parent.styleInactive)
if bid==6:
fig.corr_masks(parent)
#elif bid==7:
# fig.beh_masks(parent)
M = fig.draw_masks(parent)
fig.plot_masks(parent,M)
fig.plot_colorbar(parent,bid)
def make_masks_and_buttons(self):
self.loadBeh.setEnabled(True)
self.bloaded = False
self.ROI_remove()
self.isROI = False
self.ops_plot[1] = 0
self.ops_plot[2] = 0
self.ops_plot[3] = []
self.ops_plot[4] = []
self.setWindowTitle(self.fname)
# set bin size to be 0.5s by default
self.bin = int(self.ops['tau'] * self.ops['fs'] / 2)
self.binedit.setText(str(self.bin))
# add boundaries to stat for ROI overlays
ncells = len(self.stat)
for n in range(0, ncells):
ypix = self.stat[n]['ypix'].flatten()
xpix = self.stat[n]['xpix'].flatten()
iext = fig.boundary(ypix, xpix)
self.stat[n]['yext'] = ypix[iext]
self.stat[n]['xext'] = xpix[iext]
ycirc, xcirc = fig.circle(self.stat[n]['med'],
self.stat[n]['radius'])
goodi = (ycirc >= 0) & (xcirc >= 0) & (ycirc < self.ops['Ly']) & (
xcirc < self.ops['Lx'])
self.stat[n]['ycirc'] = ycirc[goodi]
self.stat[n]['xcirc'] = xcirc[goodi]
# enable buttons
self.enable_views_and_classifier()
# make color arrays for various views
fig.make_colors(self)
self.ichosen = int(0)
self.imerge = [int(0)]
self.iflip = int(0)
self.ichosen_stats()
self.comboBox.setCurrentIndex(2)
# colorbar
self.colormat = fig.make_colorbar()
fig.plot_colorbar(self, self.ops_plot[2])
tic = time.time()
fig.init_masks(self)
print(time.time() - tic)
M = fig.draw_masks(self)
fig.plot_masks(self, M)
self.lcell1.setText('%d' % (ncells - self.iscell.sum()))
self.lcell0.setText('%d' % (self.iscell.sum()))
fig.init_range(self)
fig.plot_trace(self)
if (type(self.ops['diameter'])
is not int) and (len(self.ops['diameter']) > 1):
self.xyrat = self.ops['diameter'][0] / self.ops['diameter'][1]
else:
self.xyrat = 1.0
self.p1.setAspectLocked(lock=True, ratio=self.xyrat)
self.p2.setAspectLocked(lock=True, ratio=self.xyrat)
self.loaded = True
self.mode_change(2)
self.show()
# no classifier loaded
classifier.activate(self, False)
def suggest_merge(self, parent):
parent.ichosen = self.merge_list[self.n][0]
parent.imerge = list(self.merge_list[self.n])
if self.unmerged[self.n]:
self.iMerge.setText('suggested ROIs to merge: %s'%parent.imerge)
self.doMerge.setEnabled(True)
self.p0.clear()
cell0 = parent.imerge[0]
sstring = ''
for i in parent.imerge[1:]:
rgb = hsv_to_rgb([parent.ops_plot[3][i,0],1,1])*255
pen = pg.mkPen(rgb, width=3)
scatter=pg.ScatterPlotItem(parent.Fbin[cell0], parent.Fbin[i], pen=pen)
self.p0.addItem(scatter)
sstring += ' %d '%i
self.p0.setLabel('left', sstring)
self.p0.setLabel('bottom', str(cell0))
else:
# set to the merged ROI index
parent.ichosen = parent.stat[parent.ichosen]['inmerge']
parent.imerge = [parent.ichosen]
self.iMerge.setText('ROIs merged: %s'%list(parent.stat[parent.ichosen]['imerge']))
self.doMerge.setEnabled(False)
self.p0.clear()
self.n+=1
if self.n > len(self.merge_list)-1:
self.n = 0
parent.ichosen_stats()
M = fig.draw_masks(parent)
fig.plot_masks(parent, M)
fig.plot_trace(parent)
parent.zoom_to_cell()
parent.win.show()
parent.show()
def do_merge(self, parent):
merge_ROIs(parent)
for ilist in self.merge_list:
for n in range(ilist.size):
if parent.stat[ilist[n]]['inmerge'] > 0:
ilist[n] = parent.stat[ilist[n]]['inmerge']
ilist = np.unique(ilist)
self.unmerged[self.n-1] = False
self.cc_row = np.matmul(parent.Fbin[parent.iscell], parent.Fbin[-1].T) / parent.Fbin.shape[-1]
self.cc_row /= parent.Fstd[parent.iscell] * parent.Fstd[-1] + 1e-3
self.cc_row[-1] = 0
self.CC = np.concatenate((self.CC, self.cc_row[np.newaxis, :-1]), axis=0)
self.CC = np.concatenate((self.CC, self.cc_row[:,np.newaxis]), axis=1)
parent.ichosen = parent.stat.size-1
parent.imerge = [parent.ichosen]
self.iMerge.setText('ROIs merged: %s'%parent.stat[parent.ichosen]['imerge'])
self.doMerge.setEnabled(False)
parent.ichosen_stats()
M = fig.draw_masks(parent)
fig.plot_masks(parent, M)
fig.plot_trace(parent)
parent.win.show()
parent.show()
def ROIs_on(self, state):
if state == QtCore.Qt.Checked:
self.ops_plot[0] = True
else:
self.ops_plot[0] = False
if self.loaded:
M = fig.draw_masks(self)
fig.plot_masks(self, M)
def press(self, parent, bid):
for b in parent.viewbtns.buttons():
b.setStyleSheet(parent.styleUnpressed)
self.setStyleSheet(parent.stylePressed)
parent.ops_plot[1] = bid
if parent.ops_plot[2] == parent.ops_plot[3].shape[1]:
fig.draw_corr(parent)
M = fig.draw_masks(parent)
fig.plot_masks(parent, M)
def press(self, parent, bid):
for b in range(len(parent.views)):
if parent.viewbtns.button(b).isEnabled():
parent.viewbtns.button(b).setStyleSheet(parent.styleUnpressed)
self.setStyleSheet(parent.stylePressed)
parent.ops_plot[1] = bid
if parent.ops_plot[2] == parent.ops_plot[3].shape[1]:
fig.draw_corr(parent)
M = fig.draw_masks(parent)
fig.plot_masks(parent,M)
def merge_ROIs(parent):
merge_activity_masks(parent)
n = parent.iscell.size-1
redraw_masks(parent, n)
parent.ichosen = n
parent.imerge = [n]
M = fig.draw_masks(parent)
fig.plot_masks(parent, M)
fig.plot_trace(parent)
parent.win.show()
parent.show()
def apply(parent):
classval = parent.probedit.value()
iscell = parent.probcell > classval
fig.flip_for_class(parent, iscell)
M = fig.draw_masks(parent)
fig.plot_masks(parent,M)
np.save(parent.basename+'/iscell.npy',
np.concatenate((np.expand_dims(parent.iscell,axis=1),
np.expand_dims(parent.probcell,axis=1)), axis=1))
parent.lcell0.setText(' %d'%parent.iscell.sum())
parent.lcell1.setText(' %d'%(parent.iscell.size-parent.iscell.sum()))
def top_selection(self, bid):
self.ROI_remove()
draw = False
ncells = len(self.stat)
icells = np.minimum(ncells, self.ntop)
if bid == 1:
top = True
elif bid == 2:
top = False
if self.sizebtns.button(0).isChecked():
wplot = 0
draw = True
elif self.sizebtns.button(2).isChecked():
wplot = 1
draw = True
if draw:
if self.ops_plot[2] != 0:
# correlation view
if self.ops_plot[2] == self.ops_plot[3].shape[1]:
istat = self.ops_plot[4]
elif self.ops_plot[2] == self.ops_plot[3].shape[1] + 1:
istat = self.ops_plot[5]
elif self.ops_plot[2] == self.ops_plot[3].shape[1] + 2:
istat = self.ops_plot[6]
# statistics view
else:
istat = self.ops_plot[3][:, self.ops_plot[2]]
if wplot == 0:
icell = np.array(self.iscell.nonzero()).flatten()
istat = istat[self.iscell]
else:
icell = np.array((~self.iscell).nonzero()).flatten()
istat = istat[~self.iscell]
inds = istat.argsort()
if top:
inds = inds[:icells]
self.ichosen = icell[inds[-1]]
else:
inds = inds[-icells:]
self.ichosen = icell[inds[0]]
self.imerge = []
for n in inds:
self.imerge.append(icell[n])
# draw choices
if self.ops_plot[2] == self.ops_plot[3].shape[1]:
fig.corr_masks(self)
fig.plot_colorbar(self, self.ops_plot[2])
self.ichosen_stats()
M = fig.draw_masks(self)
fig.plot_masks(self, M)
fig.plot_trace(self)
self.show()
def select_cells(self,parent):
parent.imerge = []
if self.selected.size < 5000:
for n in self.selected:
parent.imerge.append(self.cells[self.isort[n]])
parent.ichosen = parent.imerge[0]
parent.ichosen_stats()
M = fig.draw_masks(parent)
fig.plot_masks(parent,M)
fig.plot_trace(parent)
parent.show()
else:
print('too many cells selected')
def number_chosen(self):
if self.loaded:
self.ichosen = int(self.ROIedit.text())
if self.ichosen >= len(self.stat):
self.ichosen = len(self.stat) - 1
self.imerge = [self.ichosen]
if self.ops_plot[2] == self.ops_plot[3].shape[1]:
fig.corr_masks(self)
fig.plot_colorbar(self, self.ops_plot[2])
self.ichosen_stats()
M = fig.draw_masks(self)
fig.plot_masks(self, M)
fig.plot_trace(self)
self.show()
def activate(parent, inactive):
if inactive:
parent.probcell = parent.model.apply(parent.stat)
istat = parent.probcell
parent.clabels[-2] = [istat.min(), (istat.max()-istat.min())/2, istat.max()]
istat = istat - istat.min()
istat = istat / istat.max()
istat = istat / 1.3
istat = istat + 0.1
icols = 1 - istat
parent.ops_plot[3][:,-1] = icols
fig.class_masks(parent)
M = fig.draw_masks(parent)
fig.plot_masks(parent,M)
def select_cells(self, ypix, xpix):
i = self.ROIplot
iROI0 = self.iROI[i, 0, ypix, xpix]
icells = np.unique(iROI0[iROI0 >= 0])
self.imerge = []
for n in icells:
if (self.iROI[i, :, ypix, xpix]
== n).sum() > 0.6 * self.stat[n]['npix']:
self.imerge.append(n)
if len(self.imerge) > 0:
self.ichosen = self.imerge[0]
if self.ops_plot[2] == self.ops_plot[3].shape[1]:
fig.corr_masks(self)
fig.plot_colorbar(self, self.ops_plot[2])
self.ichosen_stats()
M = fig.draw_masks(self)
fig.plot_masks(self, M)
fig.plot_trace(self)
self.show()
def plot_clicked(self, event):
'''left-click chooses a cell, right-click flips cell to other view'''
flip = False
choose = False
zoom = False
replot = False
items = self.win.scene().items(event.scenePos())
posx = 0
posy = 0
iplot = 0
if self.loaded:
#print(event.modifiers() == QtCore.Qt.ControlModifier)
for x in items:
if x == self.img1:
pos = self.p1.mapSceneToView(event.scenePos())
posy = pos.x()
posx = pos.y()
iplot = 1
elif x == self.img2:
pos = self.p2.mapSceneToView(event.scenePos())
posy = pos.x()
posx = pos.y()
iplot = 2
elif x == self.p3:
iplot = 3
elif (x == self.p1
or x == self.p2) and x != self.img1 and x != self.img2:
iplot = 4
if event.double():
zoom = True
if iplot == 1 or iplot == 2:
if event.button() == 2:
flip = True
elif event.button() == 1:
if event.double():
zoom = True
else:
choose = True
if iplot == 3 and event.double():
zoom = True
posy = int(posy)
posx = int(posx)
if zoom:
self.zoom_plot(iplot)
if (choose or flip) and (iplot == 1 or iplot == 2):
ichosen = int(self.iROI[iplot - 1, 0, posx, posy])
if ichosen < 0:
choose = False
flip = False
if choose:
merged = False
if event.modifiers() == QtCore.Qt.ControlModifier:
if self.iscell[self.imerge[0]] == self.iscell[ichosen]:
if ichosen not in self.imerge:
self.imerge.append(ichosen)
self.ichosen = ichosen
merged = True
elif ichosen in self.imerge and len(
self.imerge) > 1:
self.imerge.remove(ichosen)
self.ichosen = self.imerge[0]
merged = True
if not merged:
self.imerge = [ichosen]
self.ichosen = ichosen
if flip:
if ichosen not in self.imerge:
self.imerge = [ichosen]
self.ichosen = ichosen
self.flip_plot(iplot)
if choose or flip or replot:
if self.isROI:
self.ROI_remove()
if not self.sizebtns.button(1).isChecked():
for btn in self.topbtns.buttons():
if btn.isChecked():
btn.setStyleSheet(self.styleUnpressed)
if self.ops_plot[2] == self.ops_plot[3].shape[1]:
fig.corr_masks(self)
fig.plot_colorbar(self, self.ops_plot[2])
self.ichosen_stats()
M = fig.draw_masks(self)
fig.plot_masks(self, M)
fig.plot_trace(self)
self.show()