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walk-tomo-split.py
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walk-tomo-split.py
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import os
import sys
import argparse
import importlib
import ast
import logging
logger = logging.getLogger('walk-tomo-splitter')
hdlr = logging.FileHandler(os.path.join(os.path.dirname(os.path.realpath(__file__)),'walked-splitting.log'))
formatter = logging.Formatter('%(asctime)s %(levelname)s %(message)s')
hdlr.setFormatter(formatter)
logger.addHandler(hdlr)
logger.setLevel(logging.WARNING)
splitter = importlib.import_module('tomo-split')
#http://stackoverflow.com/questions/2859674/converting-python-list-of-strings-to-their-type
def _tryeval(val):
try:
val = ast.literal_eval(val)
except ValueError:
pass
return val
def _list_type(string):
lst = string.replace('[','')
lst = lst.replace(']','')
lst = lst.split(',')
lst = [k.replace("'", "").replace('"', '').replace(" ", "") for k in lst]
lst = [_tryeval(l) for l in lst]
return lst
def get_recon_path(path, root_folder, recon_folder='Recon', data_subpath=None):
comps = []
while True:
last, first = os.path.split(path)
if first == root_folder:
break
comps = [first] + comps
path = last
if data_subpath is not None:
for i,c in enumerate(comps):
if c in data_subpath:
comps.pop(i)
return os.path.split(os.path.join(last, first, recon_folder, *comps))[0]
def get_sample_paths(search_dir, sample_names, recon_folder, data_subpath=None):
out = []
for root, dirs, files in os.walk(search_dir):
if recon_folder not in root and os.path.split(root)[1] in sample_names:
if data_subpath is not None:
root = os.path.join(root, data_subpath)
out.append(root)
return out
def start_walking(input_dir, camera_type, sample_names, root_folder, \
recon_folder='Recon', window_size=80, margin=30, \
dimax_sep='@', andor_batch_size=100, profile_shrinkage_ratio=50, \
frac_grp_similarity_tolerance=0.1, frames_fraction_360deg=0.1, \
logs_path=None, data_subpath=None, multitiff=True, \
schema=None):
sample_paths = get_sample_paths(input_dir, sample_names, recon_folder, data_subpath=data_subpath)
output_paths = [get_recon_path(p, root_folder, recon_folder=recon_folder, data_subpath=data_subpath) \
for p in sample_paths]
for sample_path, output_path in zip(sample_paths, output_paths):
splitter.split_data(sample_path, \
camera_type, \
output_sample_dir=output_path, \
window_size=window_size, \
margin=margin, \
dimax_sep=dimax_sep, \
andor_batch_size=andor_batch_size, \
profile_shrinkage_ratio=profile_shrinkage_ratio, \
frac_grp_similarity_tolerance=frac_grp_similarity_tolerance, \
frames_fraction_360deg=frames_fraction_360deg, \
logs_path=logs_path, \
data_subpath=data_subpath, \
multitiff=multitiff, \
schema=schema)
def main():
parser = argparse.ArgumentParser('The tomo-splitter which walked away.')
parser.add_argument("-i", "--input_dir", \
help="Path to the folder where to start search", \
type=str, \
required=True)
parser.add_argument("-c", "--camera_type", \
help="The type of camera used for experiment", \
metavar=str([splitter.CAMERA_ANDOR, splitter.CAMERA_PCO_DIMAX]), \
type=splitter.check_camera_type, \
required=True)
parser.add_argument("-n", "--sample_names", \
help="List of sample names to process", \
type=_list_type, \
required=True)
parser.add_argument("-r", "--root_folder", \
help="The name of root folder", \
type=str, \
required=True)
parser.add_argument("-e", "--recon_folder", \
help="The name of reconstruction folder", \
type=str, \
default='Recon')
parser.add_argument("-b", "--data_subpath", \
help="The subpath to the data of the sample folder", \
type=str, \
default=None)
parser.add_argument("-k", "--no-multitiff", \
help="The data is a series of tif files", \
dest='multitiff', \
action='store_false')
parser.add_argument("-w", "--window_size", \
help="The window size of a patch to estimate the z-profile", \
type=int, \
default=80)
parser.add_argument("-m", "--margin", \
help="The amount of margin between the z-profile windows", \
type=int, \
default=30)
parser.add_argument("-d", "--dimax_sep", \
help="The separation symbol of pco dimax files (e.g. raw@00001.tif)", \
type=str, \
default='@')
parser.add_argument("-a", "--andor_batch_size", \
help="The number of projections to read in single run", \
type=int, \
default=100)
parser.add_argument("-s", "--profile_shrinkage_ratio", \
help="The ratio to find out whether the peak is significantly bigger than neighbours", \
type=int, \
default=50)
parser.add_argument("-t", "--similarity_tolerance", \
help="The tolerance coefficient to find almost similar image groups (e.g. flat1 and flat2)", \
type=float, \
min=0.01, \
max=1.0, \
action=splitter.Range, \
default=0.1)
parser.add_argument("-f", "--fact_frames_360deg", \
help="The fraction of projections to find an exact 360 degree projection", \
type=float, \
min=0.01, \
max=1.0, \
action=splitter.Range, \
default=0.1)
parser.add_argument("--schema", \
help="Manually specified splitting schema", \
type=_tryeval, \
default=None)
parser.add_argument("-l", "--logs_path", \
help="The the path to the logs", \
type=str, \
default=None)
args = parser.parse_args()
start_walking(args.input_dir, \
args.camera_type, \
args.sample_names, \
args.root_folder, \
recon_folder=args.recon_folder, \
window_size=args.window_size, \
margin=args.margin, \
dimax_sep=args.dimax_sep, \
andor_batch_size=args.andor_batch_size, \
profile_shrinkage_ratio=args.profile_shrinkage_ratio, \
frac_grp_similarity_tolerance=args.similarity_tolerance, \
frames_fraction_360deg=args.fact_frames_360deg, \
logs_path=args.logs_path, \
data_subpath=args.data_subpath, \
multitiff=args.multitiff, \
schema=args.schema)
if __name__ == "__main__":
sys.exit(main())