def run(self):
self.checkParameterValues()
self.numpyRandomSeed = random.randint(0,2**32)
self._numpyRandom = np.random.RandomState(self.numpyRandomSeed)
# create checkerboard background
self._squareSizePix = round(self.squareSize*self.pixelsPerDeg)
leftOffset = rightOffset = topOffset = bottomOffset = self._squareSizePix
bckgnd = self.makeCheckerboard((math.ceil(self.imageSize[1]/self._squareSizePix),math.ceil(self.imageSize[0]/self._squareSizePix)))
if self.moveLikeOpticFlow:
centerOffset = (self.imageSize[0]/2)%self._squareSizePix
if centerOffset>0:
self.shiftBckgnd(bckgnd[:,::-1],centerOffset,centerOffset)
rightOffset = centerOffset
checkerboardImage = np.copy(bckgnd[:self.imageSize[1],:self.imageSize[0]])
# get trialTypes
trialTypes = list(itertools.product(self.bckgndSpeed,[dir for dir in self.bckgndDir if dir in (0,180)],self.patchSize,self.patchSpeed,[dir for dir in self.patchDir if dir in (0,180)],self.patchElevation))
trialTypes.extend(itertools.product(self.bckgndSpeed,[dir for dir in self.bckgndDir if dir in (90,270)],self.patchSize,self.patchSpeed,[dir for dir in self.patchDir if dir in (90,270)],self.patchAzimuth))
for params in trialTypes[:]:
# don't need all bckgnd directions for bckgndSpeed=0
# or all patch sizes, directions, and positions for patchSpeed=0
# or patch speed and direction = bckgnd speed and direction when both speeds > 0
if ((params[0]==0 and params[1]!=self.bckgndDir[0])
or (params[3]==0 and (params[2]!=self.patchSize[0] or params[3]!=self.patchSpeed[0] or params[4]!=self.patchDir[0] or (params[5]!=self.patchElevation[0] if params[4] in (0,180) else params[5]!=self.patchAzimuth[0])))
or (params[0]>0 and params[3]>0 and params[0]==params[3] and params[1]==params[4])):
if params in trialTypes:
trialTypes.remove(params)
# run
frame = 0
trial = -1
trialFrame = -1
self.trialStartFrame = []
self.trialNumFrames = []
self.trialBckgndSpeed = []
self.trialBckgndDir = []
self.trialPatchSize = []
self.trialPatchSpeed = []
self.trialPatchDir = []
self.trialPatchPos = []
while trial<=len(trialTypes)-1: #This used to be just <, which I think omits one of the stimulus conditions...
try:
if trialFrame==-1:
trial += 1
print('starting trial: ' + str(trial))
trialFrame = 0
self.trialBckgndSpeed.append(trialTypes[trial][0])
self.trialBckgndDir.append(trialTypes[trial][1])
self.trialPatchSize.append(trialTypes[trial][2])
self.trialPatchSpeed.append(trialTypes[trial][3])
self.trialPatchDir.append(trialTypes[trial][4])
self.trialPatchPos.append(trialTypes[trial][5])
if self.trialBckgndDir[-1]==0:
bckgndOffset = leftOffset
elif self.trialBckgndDir[-1]==180:
bckgndOffset = rightOffset
elif self.trialBckgndDir[-1]==90:
bckgndOffset = bottomOffset
else:
bckgndOffset = topOffset
bckgndMovPerFrame = int(round(self.trialBckgndSpeed[-1]*self.pixelsPerDeg/self.frameRate))
patchMovPerFrame = int(round(self.trialPatchSpeed[-1]*self.pixelsPerDeg/self.frameRate))
patchSizePix = int(round(self.trialPatchSize[-1]*self.pixelsPerDeg))
if patchMovPerFrame>0:
patchSquares = round(self.trialPatchSize[-1]/self.squareSize)
patch = self.makeCheckerboard((patchSquares,)*2)
if self.trialPatchDir[-1] in [0,180]:
y = self._squareSizePix*round((self.imageSize[1]/2-self.imagePosition[1]+self.trialPatchPos[-1]*self.pixelsPerDeg)/self._squareSizePix-patchSquares/2)
if topOffset<self._squareSizePix:
y -= topOffset
if self.trialPatchDir[-1]==0:
patchPos = [self.imageSize[0]/2-patchSizePix,y]
else:
patchPos = [self.imageSize[0],y]
self.trialNumFrames.append(int(round((self.imageSize[0]/2+patchSizePix)/patchMovPerFrame)))
else:
x = self._squareSizePix*round((self.imageSize[0]/2-self.imagePosition[0]+self.trialPatchPos[-1]*self.pixelsPerDeg)/self._squareSizePix)-int(patchSizePix/2)
if leftOffset<self._squareSizePix:
x -= leftOffset
if self.trialPatchDir[-1]==90:
patchPos = [x,self.imageSize[1]]
else:
patchPos = [x,-patchSizePix]
self.trialNumFrames.append(int(round((self.imageSize[1]+patchSizePix)/patchMovPerFrame)))
else:
if bckgndMovPerFrame>0:
if self.trialBckgndDir[-1] in [0,180]:
self.trialNumFrames.append(int(round(self.imageSize[0]/2/bckgndMovPerFrame)))
else:
self.trialNumFrames.append(int(round(self.imageSize[1]/bckgndMovPerFrame)))
else:
self.trialNumFrames.append(int(round(2*self.frameRate)))
trialMovie = []
else:
if trialFrame==0:
self.trialStartFrame.append(frame)
print('starting movie for trial: ' + str(trial))
if bckgndMovPerFrame>0:
if bckgndOffset==0:
bckgndOffset = self._squareSizePix
bckgndOffset += bckgndMovPerFrame
if bckgndOffset>self._squareSizePix:
newSqOffset = int(bckgndOffset-self._squareSizePix)
bckgndOffset %= self._squareSizePix
else:
newSqOffset = 0
if self.trialBckgndDir[-1]==0:
if self.moveLikeOpticFlow:
self.shiftBckgnd(bckgnd[:,self.imageSize[0]/2+1:],bckgndMovPerFrame,newSqOffset)
self.shiftBckgnd(bckgnd[:,self.imageSize[0]/2::-1],bckgndMovPerFrame,newSqOffset)
else:
self.shiftBckgnd(bckgnd,bckgndMovPerFrame,newSqOffset)
elif self.trialBckgndDir[-1]==180:
if self.moveLikeOpticFlow:
self.shiftBckgnd(bckgnd[:,-1:self.imageSize[0]/2:-1],bckgndMovPerFrame,newSqOffset)
self.shiftBckgnd(bckgnd[:,:self.imageSize[0]/2+1],bckgndMovPerFrame,newSqOffset)
else:
self.shiftBckgnd(bckgnd[:,::-1],bckgndMovPerFrame,newSqOffset)
elif self.trialBckgndDir[-1]==90:
self.shiftBckgnd(bckgnd[:,::-1].T,bckgndMovPerFrame,newSqOffset)
else:
self.shiftBckgnd(bckgnd.T,bckgndMovPerFrame,newSqOffset)
checkerboardImage = np.copy(bckgnd[:self.imageSize[1],:self.imageSize[0]])
if patchMovPerFrame>0:
if self.trialPatchDir[-1]==0:
patchPos[0] += patchMovPerFrame
elif self.trialPatchDir[-1]==180:
patchPos[0] -= patchMovPerFrame
elif self.trialPatchDir[-1]==90:
patchPos[1] -= patchMovPerFrame
else:
patchPos[1] += patchMovPerFrame
if patchPos[0]<=self.imageSize[0] and patchPos[1]<=self.imageSize[1]:
patchImagePos = copy.copy(patchPos)
patchImage = patch
if patchPos[0]<self.imageSize[0]/2:
patchImage = patch[:,int(self.imageSize[0]/2-patchPos[0]):]
patchImagePos[0] = self.imageSize[0]/2
if patchPos[1]<0:
patchImage = patch[-patchPos[1]:,:]
patchImagePos[1] = 0
if patchPos[0]+patch.shape[1]>self.imageSize[0]:
patchImage = patch[:,:int(self.imageSize[0]-patchPos[0])]
if patchPos[1]+patch.shape[0]>self.imageSize[1]:
patchImage = patch[:self.imageSize[1]-patchPos[1],:]
checkerboardImage[int(patchImagePos[1]):int(patchImagePos[1]+patchImage.shape[0]),int(patchImagePos[0]):int(patchImagePos[0]+patchImage.shape[1])] = patchImage
if trialFrame==self.trialNumFrames[-1]-1:
if self.trialBckgndDir[-1]==0:
leftOffset = bckgndOffset
rightOffset = self._squareSizePix-bckgndOffset
if self.moveLikeOpticFlow:
rightOffset += centerOffset
if rightOffset>self._squareSizePix:
rightOffset -= self._squareSizePix
elif self.trialBckgndDir[-1]==180:
rightOffset = bckgndOffset
leftOffset = self._squareSizePix-bckgndOffset
if self.moveLikeOpticFlow:
leftOffset -= centerOffset
if leftOffset<0:
leftOffset += self._squareSizePix
elif self.trialBckgndDir[-1]==90:
bottomOffset = bckgndOffset
topOffset = self._squareSizePix-bckgndOffset
else:
topOffset = bckgndOffset
bottomOffset = self._squareSizePix-bckgndOffset
trialMovie.append(checkerboardImage[:,self.imageSize[0]/2:])
frame += 1
trialFrame += 1
if trialFrame==self.trialNumFrames[-1]:
print('saving trial:' + str(trial))
np.save(os.path.join(self.savePath,'trial'+str(trial)+ '_duration_' + str(self.trialNumFrames[-1]/self.frameRate) + '.npy'),np.stack(trialMovie))
trialFrame = -1
except:
print('Failed to render trial: ' + str(trial))
continue
fileIO.objToHDF5(self,os.path.join(self.savePath,'params.hdf5'))
def saveHDF5(self,filePath=None):
fileIO.objToHDF5(self,filePath)
}
for u in units[goodUnits]:
spikes = nwb['processing'][probe]['UnitTimes'][str(u)]['times'][:]
data[mouse]['spikeTimes'][probe][str(u)] = spikes
for epoch, times in zip(('preChange', 'change'),
(preChangeTimes, changeTimes)):
data[mouse]['sdfs'][probe][epoch].append(
analysis_utils.getSDF(spikes,
times - 0.25,
1,
sampInt=0.001,
filt='exp',
sigma=0.005,
avg=False)[0])
fileIO.objToHDF5(obj=None,
saveDict=data,
filePath=os.path.join(dirPath, 'naiveMiceData2.hdf5'))
nwb.close()
# make population data hdf5 from experiment nwb files
#for mouse in mouseIDs:
# print(mouse)
# nwb = h5py.File(os.path.join(dirPath,'mouse'+mouse+'.spikes.nwb'))
# data = {mouse:{}}
# data[mouse]['runTime'] = nwb['acquisition']['timeseries']['RunningSpeed']['timestamps'][:]
# data[mouse]['runSpeed'] = nwb['acquisition']['timeseries']['RunningSpeed']['data'][:]
# data[mouse]['flashTimes'] = nwb['stimulus']['presentation']['change_detection_2']['timestamps'][:,0]
# data[mouse]['flashImages'] = nwb['stimulus']['presentation']['change_detection_2']['data'][:,0].astype(int)
# changeIndex = np.where(np.diff(data[mouse]['flashImages'])!=0)[0]+1
# data[mouse]['changeTimes'] = data[mouse]['flashTimes'][changeIndex]
# data[mouse]['changeImages']= data[mouse]['flashImages'][changeIndex]