"""Application to concatenate a serie of scan with different z to a single NXtomo"""
import argparse
import logging
import os
import re
import numpy as np
from tomoscan.framereducer.method import ReduceMethod
from nxtomomill.converter import from_h5_to_nx
from nxtomomill.io.config import TomoHDF5Config
from ..utils.flat_reducer import flat_reducer
from ..utils.utils import strip_extension
logging.basicConfig(level=logging.INFO)
_logger = logging.getLogger(__name__)
[docs]def str2bool(v):
if isinstance(v, bool):
return v
if v.lower() in ("yes", "true", "t", "y", "1"):
return True
elif v.lower() in ("no", "false", "f", "n", "0"):
return False
else:
raise argparse.ArgumentTypeError("Boolean value expected.")
[docs]def get_arguments(user_args):
parser = argparse.ArgumentParser(
description="""
creates all the target nxs for all the stages.
If the postfixes for reference scans are give (the one before and another after the measurements) the reduced flats dark are also created.
The references scans are expected to contains projections to be 'interpreted' as flats
"""
)
parser.add_argument(
"--filename_template",
required=False,
default=None,
help="""The filename template. To be used for multiples zstages it must contain one or more segments equal to "X"*ndigits which will be replaced by the stage number, for the scans, and, for the reference scans, by the begin/end prefixes""",
)
parser.add_argument(
"--filename",
required=False,
default=None,
help="""The filename. To be used for a single scan""",
)
parser.add_argument(
"--output_filename_template",
required=False,
default=None,
help="""Optional, default to a name deduced from filename_template. The output filename template. It must contain one or more segments equal to "X"*ndigits which will be replaced by the stage number""",
)
parser.add_argument(
"--entry_name", required=False, help="entry_name", default="entry0000"
)
parser.add_argument(
"--total_nstages",
type=int,
default=None,
required=True,
help="How many stages. Example: from 0 to 43 -> --total_nstages 44. ",
)
parser.add_argument(
"--first_stage",
type=int,
default=0,
required=False,
help="Optional. Defaults to zero. The number of the first considered stage. Use this to do a smaller sequence",
)
parser.add_argument(
"--last_stage",
type=int,
default=-1,
required=False,
help="Optional. Defaults to total_nstages-1. The number of the last considered stage. Use this to do a smaller sequence",
)
parser.add_argument(
"--do_references",
type=str2bool,
default=False,
required=False,
help="Optional. If given the reference scans are used for the extraction of the flats/dark. The reference scans are obtained using the ref postfixes",
)
parser.add_argument(
"--extracted_reference_target_dir",
type=str,
default=None,
required=None,
help="Optional. By default the extracted reference will be written in the same directory as the nexus scan. As the extraction procedure is time consuming they can be written instead to a common directory",
)
parser.add_argument(
"--ref_scan_begin",
type=str,
default=None,
required=False,
help="""used when "do_reference" is True. It is optional. It is the reference scan. """,
)
parser.add_argument(
"--ref_scan_end",
type=str,
default=None,
required=False,
help="""used when "do_reference" is True. It is optional. It is the end for the reference scan . """,
)
parser.add_argument(
"--target_directory",
type=str,
default="./",
required=False,
help="""Where files are written. Optional, defaults to current directory""",
)
parser.add_argument(
"--median_or_mean",
type=str,
choices=[ReduceMethod.MEAN.value, ReduceMethod.MEDIAN.value],
default=ReduceMethod.MEAN.value,
required=False,
help="""Choose betwen median or mean. Optional. Default is mean""",
)
parser.add_argument(
"--voxel_size",
type=float,
default=None,
required=False,
help="""Defaults to zero. If set to a different value the bliss generated nexus files will be corrected. Units are micron""",
)
parser.add_argument(
"--dark_default_value",
type=float,
default=300,
required=False,
help="""The dark value that is used for scans without dark""",
)
args = parser.parse_args(user_args)
if args.last_stage == -1:
args.last_stage = args.total_nstages - 1
return args
def _convert_bliss2nx(bliss_ref_name, nexus_name, corrections_dict={}):
config = TomoHDF5Config()
config.overwrite = True
config.input_file = bliss_ref_name
config.output_file = nexus_name
config.load_extra_params_section(corrections_dict)
from_h5_to_nx(config)
[docs]def main(argv):
args = get_arguments(argv[1:])
if args.filename_template is not None:
name_template_for_numeric = template_to_format_string(args.filename_template)
else:
name_template_for_numeric = args.filename
if name_template_for_numeric is None:
raise ValueError(
" Either filename_template of filename must be given as arguments"
)
if args.output_filename_template is not None:
args.output_refname_template = None
if args.filename is None:
if args.extracted_reference_target_dir is None:
args.output_refname_template = template_to_format_string(
args.output_filename_template, literal=True
)
else:
args.output_refname_template = None
args.output_filename_template = template_to_format_string(
args.output_filename_template, literal=False
)
else:
# will be deduced at output time
args.output_refname_template = None
extra_dict = {}
if args.voxel_size:
extra_dict.update(
{
"x_pixel_size": args.voxel_size * 1.0e-6,
"y_pixel_size": args.voxel_size * 1.0e-6,
}
)
if args.do_references:
refs_nexus_names = []
for bliss_ref_name, what in (
(args.ref_scan_begin, "begin"),
(args.ref_scan_end, "end"),
):
if args.output_refname_template is None:
if args.extracted_reference_target_dir is None:
extraction_target_dir = args.target_directory
else:
extraction_target_dir = args.extracted_reference_target_dir
nexus_name = os.path.join(
extraction_target_dir,
strip_extension(os.path.basename(bliss_ref_name), _logger) + ".nx",
)
else:
nexus_name = args.output_refname_template.format(what=what)
_convert_bliss2nx(bliss_ref_name, nexus_name, extra_dict)
refs_nexus_names.append(nexus_name)
for iz in range(args.first_stage, args.last_stage + 1):
bliss_name = name_template_for_numeric.format(i_stage=iz)
if args.output_filename_template is None:
nexus_name = os.path.join(
args.target_directory,
strip_extension(os.path.basename(bliss_name), _logger) + ".nx",
)
else:
nexus_name = args.output_filename_template.format(i_stage=iz)
_convert_bliss2nx(bliss_name, nexus_name, extra_dict)
if args.do_references:
factor = (iz + 1) / (args.total_nstages)
flat_reducer(
nexus_name,
ref_start_filename=refs_nexus_names[0],
ref_end_filename=refs_nexus_names[1],
mixing_factor=factor,
entry_name=args.entry_name,
median_or_mean=args.median_or_mean,
save_intermediated=False,
reuse_intermediated=True,
dark_default_value=args.dark_default_value,
)
return 0
