if inArgs.verbose:
print
print "Image LPS World to CTF matrix"
print affine_ctf
print
util.save_itk_affine_matrix( affine_ctf, affine_out_wlps_to_wctf, inArgs.verbose )
#
# Save OUT Fiducials in LPS World space.
#
util.verify_outputs( stage1_output_files[0:3] )
cmd = [ "antsApplyTransformsToPoints", "-d", "3", "-i", fiducials_out_iras, "-o", fiducials_out_wlps, "-t", inArgs.iras_to_wras, inArgs.wras_to_wlps ]
util.iw_subprocess(cmd, inArgs.verbose, inArgs.verbose)
#
# Save OUT Fiducials in CTF World space.
#
util.verify_that_file_exists(fiducials_out_wlps)
cmd = [ "antsApplyTransformsToPoints", "-d", "3", "-i", fiducials_out_iras, "-o", fiducials_out_wctf, "-t", inArgs.iras_to_wras, inArgs.wras_to_wlps, inArgs.wlps_to_wctf ]
util.iw_subprocess(cmd, inArgs.verbose, inArgs.verbose)
util.verify_outputs( stage1_output_files )
rpa_wras = np.dot(img_affine_matrix_ras, np.concatenate( (rpa_iras, [1]) ))
lpa_wlps = np.dot(affine_wras_to_wlps, lpa_wras )
nas_wlps = np.dot(affine_wras_to_wlps, nas_wras )
rpa_wlps = np.dot(affine_wras_to_wlps, rpa_wras )
[ rotate_ctf, translate_ctf, origin_ctf ] = ctf_calc_rotate_translate_origin( nas_wlps, lpa_wlps, rpa_wlps, ctf_scale)
affine_ctf = ctf_calc_affine( rotate_ctf, translate_ctf, 0*origin_ctf)
if inArgs.verbose:
print
print "Image LPS World to CTF matrix"
print affine_ctf
print
iwUtilities.save_itk_affine_matrix( affine_ctf, inArgs.wlps_to_wctf )
#
# Save MEG Fiducials in LPS World space.
#
iwUtilities.verify_that_file_exists(inArgs.meg_iras)
iwUtilities.verify_that_file_exists(inArgs.iras_to_wras)
iwUtilities.verify_that_file_exists(inArgs.wras_to_wlps)
cmd = [ "antsApplyTransformsToPoints", "-d", "3", "-i", inArgs.meg_iras, "-o", inArgs.meg_wlps, "-t", inArgs.iras_to_wras, inArgs.wras_to_wlps ]
iwUtilities.iw_subprocess(cmd, inArgs.verbose, True )
print "inArgs.out_points = " + str(inArgs.out_points)
print "inArgs.ants_affine = " + str(inArgs.ants_affine)
print "inArgs.ants_warp = " + str(inArgs.ants_warp)
print "inArgs.wlps_to_wctf = " + str(inArgs.wlps_to_wctf)
print "inArgs.verbose = " + str(inArgs.verbose)
#
# Check inputs
#
input_files = [inArgs.in_ctf, inArgs.ants_affine, inArgs.ants_warp, inArgs.wlps_to_wctf];
for ii in input_files:
iwUtilities.verify_that_file_exists(ii)
#
# Transform CTF points to Native Space
#
cmd = [ "antsApplyTransformsToPoints", "-d", "3", "-i", inArgs.in_ctf, "-o", inArgs.out_native, "-t", "[", inArgs.wlps_to_wctf,",", "1", "]" ]
iwUtilities.iw_subprocess(cmd, inArgs.verbose)
clean_nan(inArgs.out_native)
#
# Transform CTF point to Template Space
#
cmd = [ "antsApplyTransformsToPoints", "-d", "3", "-i", inArgs.in_ctf, "-o", inArgs.out_template, "-t", "[", inArgs.wlps_to_wctf,",", "1", "]", inArgs.ants_affine, inArgs.ants_warp ]