#######DO NOT NEED TO TOUCH BELOW
makedir(out)
#load src, concatenate and make sure appropriate bitdepth
vol = np.asarray([
tifffile.imread(xx).astype('uint8') for xx in listdirfull(src)
]) #need to do the uint8 thing
nsrc = src + '.tif'
if resize_scale:
vol = resize(
vol,
[xx * resize_scale for xx in tifffile.imread(atlas_path).shape])
tifffile.imsave(nsrc, vol.astype('uint16')) #needs to be 16 bit!
#now run elastix:
elastix_command_line_call(fx=atlas_path,
mv=nsrc,
out=out,
parameters=parameters)
if False:
#elastix parameter file to use for alignment typically both Order1_Par0000affine.txt follwed by Order2_Par0000bspline.txt
parameters = [
'/media/tpisano/FAT32/volumetric/elastix_bsplineopt/Order2_Par0000bspline.txt'
]
#Path to Atlas, note that this must be oriented in the same way as your dataset, see FIJI/ImageJ for ways to reorient
atlas_path = '/media/tpisano/FAT32/volumetric/average_template_25_coronal.tif'
#location of aligned files from serial_section_processing.py
src = '/media/tpisano/FAT32/volumetric/elastix_bsplineopt/affine.tif'
#location to save elastix output into
cell = str(sys.argv[4]) #folder for cell channel e.g. Ex_642_Em_2
param_fld = "/jukebox/wang/zahra/python/BrainPipe/parameterfolder" #change if using rat
#registration vol to atlas
# cell = True #no separate cell/registration volume
# src = "/jukebox/LightSheetTransfer/tp/20200701_12_55_28_20170207_db_bl6_crii_rpv_01/"
if stepid == 0:
reg = os.path.join(src, reg)
mv = os.path.join(reg, "downsized_for_atlas.tif")
fx = "/jukebox/LightSheetTransfer/atlas/sagittal_atlas_20um_iso.tif"
out = os.path.join(os.path.dirname(src), "elastix")
if not os.path.exists(out): os.mkdir(out)
params = [os.path.join(param_fld, xx) for xx in os.listdir(param_fld)]
#run
e_out, transformfiles = elastix_command_line_call(fx, mv, out, params)
if cell:
#cell vol to registration vol
mv = os.path.join(src, cell+"/downsized_for_atlas.tif")
fx = os.path.join(src, reg+"/downsized_for_atlas.tif")
out = os.path.join(src, "elastix/%s_to_%s" % (cell, reg))
if not os.path.exists(out): os.mkdir(out)
params = [os.path.join(param_fld, xx) for xx in os.listdir(param_fld)]
#run
e_out, transformfiles = elastix_command_line_call(fx, mv, out, params)
elif stepid == 1:
#atlas to registration vol
#inverse transform
print("Doing inverse transform atlas -> reg")
#atlas to registration vol
#inverse transform
fx1 = os.path.join(src, "Ex_488_Em_0_downsized",
"downsized_for_atlas_ch488.tif")
mv1 = atl
assert os.path.exists(fx1)
assert os.path.exists(mv1)
print("\nPath to downsized vol for inverse registration to atlas: %s" %
fx1)
print("\nPath to atlas: %s" % mv1)
params = [os.path.join(param_fld, xx) for xx in os.listdir(param_fld)]
#run
e_out, transformfiles = elastix_command_line_call(
fx1, mv1, out1, params)
elif array_id == 1:
#registration vol to cell vol
#inverse transform
print("Doing inverse transform reg -> cell")
mv2 = os.path.join(src, "Ex_488_Em_0_downsized",
"downsized_for_atlas_ch488.tif")
fx2 = os.path.join(src, "Ex_642_Em_2_downsized",
"downsized_for_atlas_ch642.tif")
assert os.path.exists(fx2)
assert os.path.exists(mv2)
out2 = os.path.join(out1, "488_to_642")