def load_movie_chain(file_list,
fr=None,
start_time=0,
meta_data=None,
subindices=None,
bottom=0,
top=0,
left=0,
right=0):
''' load movies from list of file names
file_list: list of file names in string format
other parameters as in load_movie except
bottom, top, left, right to load only portion of the field of view
'''
mov = []
for f in tqdm(file_list):
m = load(f,
fr=fr,
start_time=start_time,
meta_data=meta_data,
subindices=subindices)
if m.ndim == 2:
m = m[np.newaxis, :, :]
tm, h, w = np.shape(m)
m = m[:, top:h - bottom, left:w - right]
mov.append(m)
return ts.concatenate(mov, axis=0)
def resize(self,fx=1,fy=1,fz=1,interpolation=cv2.INTER_AREA):
"""
resize movies along axis and interpolate or lowpass when necessary
it will not work without opencv
Parameters
-------------------
fx,fy,fz:fraction/multiple of dimension (.5 means the image will be half the size)
interpolation=cv2.INTER_AREA. Set to none if you do not want interpolation or lowpass
"""
T,d1,d2 =self.shape
d=d1*d2
elm=d*T
max_els=2**31-1
if elm > max_els:
chunk_size=(max_els)/d
new_m=[]
print('Resizing in chunks because of opencv bug')
for chunk in range(0,T,chunk_size):
print([chunk,np.minimum(chunk+chunk_size,T)])
m_tmp=self[chunk:np.minimum(chunk+chunk_size,T)].copy()
m_tmp=m_tmp.resize(fx=fx,fy=fy,fz=fz,interpolation=interpolation)
if len(new_m) == 0:
new_m=m_tmp
else:
new_m=timeseries.concatenate([new_m,m_tmp],axis=0)
return new_m
else:
if fx!=1 or fy!=1:
print "reshaping along x and y"
t,h,w=self.shape
newshape=(int(w*fy),int(h*fx))
mov=[];
print(newshape)
for frame in self:
mov.append(cv2.resize(frame,newshape,fx=fx,fy=fy,interpolation=interpolation))
self=movie(np.asarray(mov),**self.__dict__)
if fz!=1:
print "reshaping along z"
t,h,w=self.shape
self=np.reshape(self,(t,h*w))
mov=cv2.resize(self,(h*w,int(fz*t)),fx=1,fy=fz,interpolation=interpolation)
# self=cv2.resize(self,(h*w,int(fz*t)),fx=1,fy=fz,interpolation=interpolation)
mov=np.reshape(mov,(np.maximum(1,int(fz*t)),h,w))
self=movie(mov,**self.__dict__)
self.fr=self.fr*fz
return self
def load_movie_chain(file_list,fr=None,start_time=0,meta_data=None,subindices=None,bottom=0,top=0,left=0,right=0):
''' load movies from list of file names
file_list: list of file names in string format
other parameters as in load_movie except
bottom, top, left, right to load only portion of the field of view
'''
mov=[];
for f in file_list:
m=load(f,fr=fr,start_time=start_time,meta_data=meta_data,subindices=subindices);
tm,h,w=np.shape(m)
m=m[:,top:h-bottom,left:w-right]
mov.append(m)
return ts.concatenate(mov,axis=0)
def resize(self, fx=1, fy=1, fz=1, interpolation=cv2.INTER_AREA):
"""
resize movies along axis and interpolate or lowpass when necessary
it will not work without opencv
Parameters
-------------------
fx,fy,fz:fraction/multiple of dimension (.5 means the image will be half the size)
interpolation=cv2.INTER_AREA. Set to none if you do not want interpolation or lowpass
"""
T, d1, d2 = self.shape
d = d1 * d2
elm = d * T
max_els = 2**31 - 1
if elm > max_els:
chunk_size = (max_els) / d
new_m = []
print('Resizing in chunks because of opencv bug')
for chunk in range(0, T, chunk_size):
print([chunk, np.minimum(chunk + chunk_size, T)])
m_tmp = self[chunk:np.minimum(chunk + chunk_size, T)].copy()
m_tmp = m_tmp.resize(fx=fx,
fy=fy,
fz=fz,
interpolation=interpolation)
if len(new_m) == 0:
new_m = m_tmp
else:
new_m = timeseries.concatenate([new_m, m_tmp], axis=0)
return new_m
else:
if fx != 1 or fy != 1:
print "reshaping along x and y"
t, h, w = self.shape
newshape = (int(w * fy), int(h * fx))
mov = []
print(newshape)
for frame in self:
mov.append(
cv2.resize(frame,
newshape,
fx=fx,
fy=fy,
interpolation=interpolation))
self = movie(np.asarray(mov), **self.__dict__)
if fz != 1:
print "reshaping along z"
t, h, w = self.shape
self = np.reshape(self, (t, h * w))
mov = cv2.resize(self, (h * w, int(fz * t)),
fx=1,
fy=fz,
interpolation=interpolation)
# self=cv2.resize(self,(h*w,int(fz*t)),fx=1,fy=fz,interpolation=interpolation)
mov = np.reshape(mov, (np.maximum(1, int(fz * t)), h, w))
self = movie(mov, **self.__dict__)
self.fr = self.fr * fz
return self
def load_movie_chain(file_list,fr=None,start_time=0,meta_data=None,subindices=None):
mov=[];
for f in file_list:
mov.append(load(f,fr=fr,start_time=start_time,meta_data=meta_data,subindices=subindices))
return ts.concatenate(mov,axis=0)