def run(filenames, parent=None, proc=None, savepath=None):
''' uses filenames and processes fullSVD if no roi's specified '''
''' parent is from GUI '''
''' proc can be a saved ROI file from GUI '''
''' savepath is the folder in which to save _proc.npy '''
print('processing videos')
# grab files
Lys = []
Lxs = []
rois=None
if parent is not None:
filenames = parent.filenames
video = parent.video
containers = []
for fs in filenames:
cs = []
for f in fs:
cs.append(av.open(f))
cs[-1].streams.video[0].thread_type = 'AUTO'
containers.append(cs)
cumframes = parent.cumframes
nframes = parent.nframes
iframes = parent.iframes
sbin = parent.sbin
rois = utils.roi_to_dict(parent.ROIs, parent.rROI)
Ly = parent.Ly
Lx = parent.Lx
fullSVD = parent.checkBox.isChecked()
save_mat = parent.save_mat.isChecked()
sy = parent.sy
sx = parent.sx
else:
video=[]
containers = []
nframes = 0
iframes = []
cumframes = [0]
k=0
for fs in filenames:
vs = []
cs = []
for f in fs:
try:
vs.append(pims.Video(f))
except:
vs.append(pims.PyAVReaderIndexed(f))
cs.append(av.open(f))
cs[-1].streams.video[0].thread_type = 'AUTO'
video.append(vs)
containers.append(cs)
iframes.append(len(video[-1][0]))
cumframes.append(cumframes[-1] + len(video[-1][0]))
nframes += len(video[-1][0])
if k==0:
Ly = []
Lx = []
for vs in video[-1]:
fshape = vs.frame_shape
Ly.append(fshape[0])
Lx.append(fshape[1])
k+=1
iframes = np.array(iframes).astype(int)
cumframes = np.array(cumframes).astype(int)
if proc is None:
sbin = 4
fullSVD = True
save_mat = False
rois=None
else:
sbin = proc['sbin']
fullSVD = proc['fullSVD']
save_mat = proc['save_mat']
rois = proc['rois']
sy = proc['sy']
sx = proc['sx']
Lybin, Lxbin, iinds = binned_inds(Ly, Lx, sbin)
LYbin,LXbin,sybin,sxbin = utils.video_placement(Lybin, Lxbin)
nroi = 0
if rois is not None:
for r in rois:
if r['rind']==1:
r['yrange_bin'] = np.arange(np.floor(r['yrange'][0]/sbin),
np.floor(r['yrange'][-1]/sbin)).astype(int)
r['xrange_bin'] = np.arange(np.floor(r['xrange'][0]/sbin),
np.floor(r['xrange'][-1])/sbin).astype(int)
nroi+=1
isRGB = True
#if len(frame_shape) > 2:
# isRGB = True
tic = time.time()
# compute average frame and average motion across videos (binned by sbin)
avgframe, avgmotion = subsampled_mean(video, cumframes, Ly, Lx, sbin)
avgframe_reshape = utils.multivideo_reshape(np.hstack(avgframe)[:,np.newaxis],
LYbin,LXbin,sybin,sxbin,Lybin,Lxbin,iinds)
avgframe_reshape = np.squeeze(avgframe_reshape)
avgmotion_reshape = utils.multivideo_reshape(np.hstack(avgmotion)[:,np.newaxis],
LYbin,LXbin,sybin,sxbin,Lybin,Lxbin,iinds)
avgmotion_reshape = np.squeeze(avgmotion_reshape)
print('computed subsampled mean at %1.2fs'%(time.time() - tic))
ncomps = 500
if fullSVD or nroi>0:
# compute SVD from frames subsampled across videos and return spatial components
U = compute_SVD(video, cumframes, Ly, Lx, avgmotion, ncomps, sbin, rois, fullSVD)
print('computed subsampled SVD at %1.2fs'%(time.time() - tic))
U_reshape = U.copy()
if fullSVD:
U_reshape[0] = utils.multivideo_reshape(U_reshape[0], LYbin,LXbin,sybin,sxbin,Lybin,Lxbin,iinds)
if nroi>0:
k=1
for r in rois:
if r['rind']==1:
ly = r['yrange_bin'].size
lx = r['xrange_bin'].size
U_reshape[k] = np.reshape(U[k].copy(), (ly,lx,U[k].shape[-1]))
k+=1
else:
U = []
U_reshape = []
# project U onto all movie frames
# and compute pupil (if selected)
V, pups, blinks, runs = process_ROIs(containers, cumframes, Ly, Lx, avgmotion, U, sbin, tic, rois, fullSVD)
# smooth pupil and blinks and running
print('smoothing ...')
for p in pups:
if 'area' in p:
p['area_smooth'],_ = pupil.smooth(p['area'].copy())
p['com_smooth'] = p['com'].copy()
p['com_smooth'][:,0],_ = pupil.smooth(p['com_smooth'][:,0].copy())
p['com_smooth'][:,1],_ = pupil.smooth(p['com_smooth'][:,1].copy())
for b in blinks:
b,_ = pupil.smooth(b.copy())
#for r in runs:
# r[:,0],_ = pupil.smooth(r[:,0].copy())
# r[:,1],_ = pupil.smooth(r[:,1].copy())
#V_smooth = []
#for m in V:
# ms,ireplace = pupil.smooth(m[:,0].copy())#, win=50)
# ireplace[np.logical_or(ms>ms.std()*4, ms<ms.std()*-4)] = True
# print(ireplace.sum())
# inds = ireplace.nonzero()[0][:,np.newaxis] + np.arange(-50,51,1,int)[np.newaxis,:]
# inds[inds<0] = 0
# inds[inds>=m.shape[0]] = m.shape[0]-1
# m[ireplace,:] = np.nanmedian(m[inds,:], axis=1)
#V_smooth.append(m)
print('computed projection at %1.2fs'%(time.time() - tic))
proc = {
'filenames': filenames, 'save_path': savepath, 'iframes': iframes, 'Ly': Ly, 'Lx': Lx,
'sbin': sbin, 'fullSVD': fullSVD, 'save_mat': save_mat,
'Lybin': Lybin, 'Lxbin': Lxbin,
'sybin': sybin, 'sxbin': sxbin, 'LYbin': LYbin, 'LXbin': LXbin,
'avgframe': avgframe, 'avgmotion': avgmotion,
'avgframe_reshape': avgframe_reshape, 'avgmotion_reshape': avgmotion_reshape,
'motSVD': V, 'motMask': U, 'motMask_reshape': U_reshape,
'pupil': pups, 'running': runs, 'blink': blinks, 'rois': rois
}
# save processing
savename = save(proc, savepath)
return savename
def load_movies(self, filelist=None):
if filelist is not None:
self.filelist = filelist
try:
v = []
nframes = 0
iframes = []
cumframes = [0]
k=0
for fs in self.filelist:
vs = []
for f in fs:
try:
vs.append(pims.Video(f))
except:
print('pyavreaderindexed used - may be slower (try installing pims github version)')
vs.append(pims.PyAVReaderIndexed(f))
v.append(vs)
iframes.append(len(v[-1][0]))
cumframes.append(cumframes[-1] + len(v[-1][0]))
nframes += len(v[-1][0])
if k==0:
Ly = []
Lx = []
for vs in v[-1]:
fshape = vs.frame_shape
Ly.append(fshape[0])
Lx.append(fshape[1])
k+=1
good = True
except Exception as e:
print("ERROR: not a supported movie file")
print(e)
good = False
if good:
if len(self.rROI)>0:
for r in self.rROI:
if len(r) > 0:
for rr in r:
rr.remove(self)
if len(self.ROIs)>0:
for r in self.ROIs[::-1]:
r.remove(self)
self.ROIs = []
self.rROI=[]
self.reflectors=[]
self.saturation = []
self.iROI=0
self.nROIs=0
self.saturation=[]
# clear checkboxes
for k in range(len(self.lbls)):
self.lbls[k].setText('')
self.cbs1[k].setEnabled(False)
self.cbs2[k].setEnabled(False)
self.cbs1[k].setChecked(False)
self.cbs2[k].setChecked(False)
self.video = v
self.filenames = self.filelist
self.nframes = nframes
self.iframes = np.array(iframes).astype(int)
self.cumframes = np.array(cumframes).astype(int)
self.Ly = Ly
self.Lx = Lx
self.p1.clear()
self.p2.clear()
if len(self.Ly)<2:
self.LY = self.Ly[0]
self.LX = self.Lx[0]
self.sx = np.array([int(0)])
self.sy = np.array([int(0)])
self.vmap = np.zeros((self.LY,self.LX), np.int32)
else:
# make placement of movies
Ly = np.array(self.Ly.copy())
Lx = np.array(self.Lx.copy())
LY, LX, sy, sx = utils.video_placement(Ly, Lx)
print(LY, LX)
self.vmap = -1 * np.ones((LY,LX), np.int32)
for i in range(Ly.size):
self.vmap[sy[i]:sy[i]+Ly[i], sx[i]:sx[i]+Lx[i]] = i
self.sy = sy
self.sx = sx
self.LY = LY
self.LX = LX
self.fullimg = np.zeros((self.LY, self.LX, 3))
self.imgs = []
self.img = []
for i in range(len(self.Ly)):
self.imgs.append(np.zeros((self.Ly[i], self.Lx[i], 3, 3)))
self.img.append(np.zeros((self.Ly[i], self.Lx[i], 3)))
#self.srange = []
# get scaling from 100 random frames in the first video
#for n in range(len(self.Ly)):
# rperm = np.random.permutation(iframes[0])
# frames = np.zeros((self.Ly[n],self.Lx[n], min(40, iframes[0]-1)))
# for r in range(frames.shape[-1]):
# frames[:,:,r] = np.array(self.video[0][n][rperm[r]]).mean(axis=-1)
# self.srange.append(frames.mean() + frames.std()*np.array([-3,3]))
self.movieLabel.setText(os.path.dirname(self.filenames[0][0]))
self.frameDelta = int(np.maximum(5,self.nframes/200))
self.frameSlider.setSingleStep(self.frameDelta)
if self.nframes > 0:
self.updateFrameSlider()
self.updateButtons()
self.cframe = 1
self.loaded = True
self.processed = False
self.jump_to_frame()
return good