def run_aligner(args):
# Make a list of all the relevant sections
with open(args.sections_list_file, 'rt') as in_f:
secs_ts_fnames = in_f.readlines()
secs_ts_fnames = [fname.strip() for fname in secs_ts_fnames]
# Make sure the tilespecs exist
all_files_exist = True
for sec_ts_fname in secs_ts_fnames:
if not os.path.exists(sec_ts_fname):
print("Cannot find tilespec file: {}".format(sec_ts_fname))
all_files_exist = False
if not all_files_exist:
print("One or more tilespecs could not be found, exiting!")
return
out_folder = './output_aligned_ECS_test9_cropped'
conf_fname = '../../conf/conf_example.yaml'
conf = StackAligner.load_conf_from_file(args.conf_fname)
logger.report_event("Loading sections", log_level=logging.INFO)
sections = []
# TODO - Should be done in a parallel fashion
for ts_fname in secs_ts_fnames:
with open(ts_fname, 'rt') as in_f:
tilespec = ujson.load(in_f)
wafer_num = int(os.path.basename(ts_fname).split('_')[0].split('W')[1])
sec_num = int(
os.path.basename(ts_fname).split('.')[0].split('_')[1].split('Sec')
[1])
sections.append(
Section.create_from_tilespec(tilespec,
wafer_section=(wafer_num, sec_num)))
logger.report_event("Initializing aligner", log_level=logging.INFO)
aligner = StackAligner(conf)
logger.report_event("Aligning sections", log_level=logging.INFO)
aligner.align_sections(
sections) # will align and update the section tiles' transformations
del aligner
logger.end_process('main ending', rh_logger.ExitCode(0))
with in_fs.open(fs.path.basename(in_ts_fname), 'rt') as in_f:
in_ts = ujson.load(in_f)
wafer_num = int(
fs.path.basename(in_ts_fname).split('_')[0].split('W')[1])
sec_num = int(
fs.path.basename(in_ts_fname).split('.')[0].split('_')[1].split(
'Sec')[1])
section = Section.create_from_tilespec(in_ts,
wafer_section=(wafer_num,
sec_num))
stitcher.stitch_section(section)
# Save the tilespec
section.save_as_json(out_ts_fname)
# out_tilespec = section.tilespec
# import json
# with open(out_ts_fname, 'wt') as out_f:
# json.dump(out_tilespec, out_f, sort_keys=True, indent=4)
del stitcher
if __name__ == '__main__':
args = parse_args()
logger.start_process('main', '2d_stitcher_driver.py', [args])
run_stitcher(args)
logger.end_process('main ending', rh_logger.ExitCode(0))
'tile_files_or_dirs',
metavar='tile_files_or_dirs',
type=str,
nargs='+',
help=
'a list of json files that need to be normalized or a directories of json files'
)
parser.add_argument('-o',
'--output_dir',
type=str,
help='an output directory (default: ./after_norm)',
default='./after_norm')
parser.add_argument('-p',
'--processes_num',
type=int,
help='number of processes (default: 1)',
default=1)
args = parser.parse_args()
logger.start_process('normalize_coordinates', 'normalize_coordinates.py',
[args.tile_files_or_dirs, args.output_dir])
pool = mp.Pool(processes=args.processes_num)
normalize_coordinates(args.tile_files_or_dirs, args.output_dir, pool)
pool.close()
pool.join()
logger.end_process('normalize_coordinates', rh_logger.ExitCode(0))
return aligner.align_imgs(imgs)
if __name__ == '__main__':
imgs_dir = '/n/coxfs01/paragt/Adi/R0/images_margin'
conf_fname = '../conf_example.yaml'
out_path = './output_imgs'
processes_num = 8
logger.start_process('main', 'aligner.py',
[imgs_dir, conf_fname, out_path, processes_num])
conf = StackAligner.load_conf_from_file(conf_fname)
transforms = StackAligner.align_img_files(imgs_dir, conf, processes_num)
# Save the transforms to a temp output folder
if not os.path.exists(out_path):
os.makedirs(out_path)
print('Writing output to: {}'.format(out_path))
img_fnames, imgs = StackAligner.read_imgs(imgs_dir)
for img_fname, img, transform in zip(img_fnames, imgs, transforms):
# assumption: the output image shape will be the same as the input image
out_fname = os.path.join(out_path, os.path.basename(img_fname))
img_transformed = cv2.warpAffine(img,
transform[:2, :],
(img.shape[1], img.shape[0]),
flags=cv2.INTER_AREA)
cv2.imwrite(out_fname, img_transformed)
logger.end_process('align_imgs ending', rh_logger.ExitCode(0))