inArgs = parser.parse_args()
#
#
#
input_directory = os.path.abspath(inArgs.in_dir)
output_directory = util.path_relative_to( input_directory, inArgs.out_dir)
#
#
#
util.print_stage("Displaying inputs to wbi_swi_rigid_to_inia.py", inArgs.verbose )
if inArgs.verbose:
print
print "input_directory = " + input_directory
print "output_directory = " + output_directory
print
print "inArgs.image = " + str(inArgs.image)
print "inArgs.in_icsa = " + str(inArgs.in_icsa)
print "inArgs.out_iras = " + str(inArgs.out_iras)
print "inArgs.out_wlps = " + str(inArgs.out_wlps)
print "inArgs.iras_to_wras = " + str(inArgs.iras_to_wras)
print "inArgs.wras_to_wlps = " + str(inArgs.wras_to_wlps)
print "inArgs.wlps_to_wctf = " + str(inArgs.wlps_to_wctf)
print "inArgs.verbose = " + str(inArgs.verbose)
default=False)
inArgs = parser.parse_args()
#
#
#
input_directory = os.path.abspath(inArgs.in_dir)
output_directory = util.path_relative_to(input_directory, inArgs.out_dir)
#
#
#
util.print_stage("Displaying inputs to wbi_swi_rigid_to_inia.py",
inArgs.verbose)
if inArgs.verbose:
print
print "input_directory = " + input_directory
print "output_directory = " + output_directory
print
print "inArgs.image = " + str(inArgs.image)
print "inArgs.in_fiducials = " + str(inArgs.in_fiducials)
print
print "inArgs.verbose = " + str(inArgs.verbose)
#
#
#
reference_ctf = image_native
reference_template = util.path_relative_to( input_directory, inArgs.reference_template )
fiducials_native_icsa = 'fiducials_native_icsa.csv'
stage_directory = [ os.path.abspath( os.path.join( output_directory, '00-rename' )),
os.path.abspath( os.path.join( output_directory, '01-transform_fiducials' )),
os.path.abspath( os.path.join( output_directory, '02-transform_images' ))
]
#
#
#
util.print_stage("Displaying inputs to wbi_swi_rigid_to_inia.py", inArgs.verbose )
if inArgs.verbose:
print
print "input_directory = " + input_directory
print "output_directory = " + output_directory
print
print "inArgs.image = " + str(inArgs.in_image)
print "inArgs.in_icsa = " + str(inArgs.in_fiducials)
print
print "inArgs.iras_to_wras = " + inArgs.iras_to_wras
print "inArgs.wras_to_wlps = " + inArgs.wras_to_wlps
print "inArgs.wlps_to_wctf = " + inArgs.wlps_to_wctf
print
print "inArgs.verbose = " + str(inArgs.verbose)
"--verbose",
help="Verbose flag",
action="store_true",
default=False)
parser.add_argument("--debug",
help="Debug flag",
action="store_true",
default=False)
inArgs = parser.parse_args()
#
#
#
util.print_stage("Displaying inputs to iwCtf_transform_points",
inArgs.debug)
if inArgs.debug:
print
print "inArgs.in_fiducials = " + str(inArgs.in_fiducials)
print "inArgs.out_fiducials = " + str(inArgs.out_fiducials)
print
print "inArgs.native_to_ctf = " + inArgs.native_to_ctf
print
print "inArgs.verbose = " + str(inArgs.verbose)
in_coordinate_system = inArgs.in_coordinate_system.lower()
out_coordinate_system = inArgs.out_coordinate_system.lower()
template_to_native = inArgs.template_to_native
native_to_template = inArgs.native_to_template