def save_compare_tifs():
if verbose:print('####save some stacks for comparison (img and membrane contour')
filehandler.d_load_info['load_dir']= 'base'
filehandler.d_load_info['f_name'] = '4D_membrane_contour'
filehandler.d_save_info['f_name'] = 'Compare_3D_membrane_contour' + '_ST' + str(nb_stack)
slice_tif(ix_slice_time=[nb_stack-1,nb_stack],filehandler=filehandler,verbose=False)
filehandler.d_load_info['f_name'] = 'raw4D'
filehandler.d_save_info['f_name'] = 'Compare_raw3D' + '_ST' + str(nb_stack)
slice_tif(ix_slice_time=[nb_stack-1,nb_stack],filehandler=filehandler,verbose=False)
return
def make_image_sequence():
print(' - making image sequence', flush=True)
# fh.d_load_info['load_dir'] = IMG_RAW_DIR
fh.d_load_info['f_name'] = str(
param_xml.get_file_info(
field='img_raw_file')) # prm['img_raw_file']
a_raw = fh.load_tif(verbose=False)
if len(a_raw.shape) == 3:
z, _, _ = a_raw.shape
t = 1
else:
t, z, _, _ = a_raw.shape
fh.extend_save_info(extra_dir_1='Image_Sequence',
reset_to_snapshot=True)
for t_i in range(t):
for z_i in range(z):
a_slice = slice_tif(a_raw,
ix_slice_time=[t_i, t_i + 1],
ix_slice_z=[z_i, z_i + 1],
verbose=False)
fh.d_save_info['f_name'] = param_xml.get_file_info(
field='img_raw_file').stem + '_t' + str(t_i + 1).zfill(
3) + '_z' + str(z_i + 1).zfill(3)
fh.save_data(a_slice, verbose=False)
#print('|',end='')
fh.reset_save_info()
return
def create_stack():
if prm['verbose']:print("##create a stack ----------------------------------------------------------------------------timestep{0}".format(nb_stack))
img = slice_tif(na_tif=a_4D_membrane,ix_slice_time=[nb_stack-1 + prm['offset_input_img'] ,nb_stack + prm['offset_input_img'] ],verbose=False)
img_bin = np.zeros(img.shape,'bool')
img_bin[img > 0] = True
stack = Stack(img = img_bin,timestep=nb_stack,feat_tracker=feat_tracker,name=fh.d_load_info['f_name'])
return stack
def create_stack():
if verbose:print("##create a stack ----------------------------------------------------------------------------timestep{0}".format(nb_stack))
img = slice_tif(na_tif=a_4D_membrane,ix_slice_time=[nb_stack-1,nb_stack],verbose=False)
img_bin = np.zeros(img.shape,'bool')
img_bin[img > 0] = True
stack = Stack(img = img_bin,timestep=nb_stack,feat_tracker=feat_tracker,name=filehandler.d_load_info['f_name'])
return stack
def load_extra_channel():
if not DIR_EXTRA_CHANNEL:
return None
filehandler.d_load_info['load_dir'] = DIR_EXTRA_CHANNEL
filehandler.d_load_info['f_name'] = FILE_EXTRA_CHANNEL
filehandler.d_save_info['pre_f_name'] = ''
return slice_tif(ix_slice_time= [lnb_stack[0] - 1, lnb_stack[-1]], filehandler=filehandler,verbose=False,RGB=True,trim_1D=False)
def add_exterior_mask():
if not USE_EXTERIOR_OVERLAY:return
if verbose:print("###add a mask to shield off the exterior")
filehandler.d_load_info['load_dir'] = DIR_EXTERIOR_MASK if DIR_EXTERIOR_MASK else os.path.join(filehandler.get_root_save_location(),'002_preprocessing')
filehandler.d_load_info['f_name'] = FILE_EXTERIOR_MASK if FILE_EXTERIOR_MASK else 'exterior_mask.tif'
stack.add_exterior_mask(slice_tif(filehandler=filehandler,ix_slice_time=[nb_stack-1,nb_stack],verbose=False),mask=True)
return
def get_extra_channel(): fh.d_load_info['f_name'] = str(param_xml.get_file_info(field='img_raw_file')) fh.d_save_info['pre_f_name'] = '' try: a_extra_channel = convert_16bit_to_RGB(fh.load_tif(),clip_not_scale=True) except: return None if len(a_extra_channel.shape)==4: #turn stack into timelapse z, y, x, rgba = a_extra_channel.shape a_extra_channel = a_extra_channel.reshape((1, z, y, x, rgba)) if len(prm['l_stack_raw']) == 0: a_slice_tif = slice_tif(na_tif=a_extra_channel,ix_slice_time= [prm['l_stack_nb'][0] - 1, prm['l_stack_nb'][-1]],verbose=False,RGB=True,trim_1D=False) else: a_slice_tif = slice_tif(na_tif=a_extra_channel,ix_slice_time= [i-1 for i in prm['l_stack_raw']],verbose=False,RGB=True,trim_1D=False) make_brighter=True #causes memory crash for big timelapses,so go stack by stack if make_brighter: for ix, i in enumerate(a_slice_tif): a_slice_tif[ix, :] = adjust_gamma(i, gamma=0.5) return a_slice_tif
def add_exterior_mask():
if not prm['use_exterior_overlay']:return
if prm['verbose']:print("###add a mask to shield off the exterior")
# fh.d_load_info['load_dir'] = prm['DIR_EXTERIOR_MASK'] if prm['DIR_EXTERIOR_MASK'] else os.path.join(fh.get_root_save_location(),'002_preprocessing')
if prm['exterior_mask_file']:
fh.d_load_info['f_name'] = prm['exterior_mask_file']
else:
fh.d_load_info['f_name'] = os.path.join(fh.get_root_save_location(),'002_preprocessing','exterior_mask.tif')
if os.path.exists(fh.d_load_info['f_name']):
stack.add_exterior_mask(slice_tif(filehandler=fh,ix_slice_time=[nb_stack-1 + prm['offset_exterior_mask'] ,nb_stack + prm['offset_exterior_mask'] ],verbose=False),mask=True)
else:
print('No exterior mask used. File does not exist: ',fh.d_load_info['f_name'])
return
def get_extra_channel():
if DIR_EXTRA_CHANNEL:
filehandler.d_load_info['load_dir'] = DIR_EXTRA_CHANNEL
filehandler.d_load_info['f_name'] = FILE_EXTRA_CHANNEL
filehandler.d_save_info['pre_f_name'] = ''
a_extra_channel = filehandler.load_tif()
else:
filehandler.d_load_info['load_dir'] = IMG_RAW_DIR
filehandler.d_load_info['f_name'] = IMG_RAW_FILE
filehandler.d_save_info['pre_f_name'] = ''
a_extra_channel = convert_16bit_to_RGB(filehandler.load_tif(storage_name='IMG_RAW_FILE'),clip_not_scale=True)
if len(a_extra_channel.shape)==4: #turn stack into timelapse
z,y,x,rgba = a_extra_channel.shape
a_extra_channel = a_extra_channel.reshape((1,z,y,x,rgba))
return slice_tif(na_tif=a_extra_channel,ix_slice_time= [lnb_stack[0] - 1, lnb_stack[-1]],verbose=False,RGB=True,trim_1D=False)
def make_image_sequence():
print(' - making image sequence')
# filehandler.d_load_info['load_dir'] = IMG_RAW_DIR
filehandler.d_load_info['f_name'] = str(img_raw_file)
a_raw = filehandler.load_tif()
if len(a_raw.shape)==3:
z,_,_ = a_raw.shape
t=1
else:
t,z,_,_ = a_raw.shape
filehandler.extend_save_info(extra_dir_1='Image_Sequence',reset_to_snapshot=True)
for t_i in range(t):
for z_i in range(z):
a_slice = slice_tif(a_raw,ix_slice_time=[t_i,t_i+1],ix_slice_z=[z_i,z_i+1],verbose=False)
filehandler.d_save_info['f_name'] = img_raw_file.stem + '_t' + str(t_i+1).zfill(3) + '_z' + str(z_i+1).zfill(3)
filehandler.save_data(a_slice,verbose=False)
print('|',end='')
filehandler.reset_save_info()
return