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"""
Application to patch a NXtomo entry. invalidating some frame or adding some.
.. code-block:: bash
usage: nxtomomill patch-nx [-h] [--darks-at-start DARKS_AT_START] [--darks-at-end DARKS_AT_END] [--flats-at-start FLATS_AT_START] [--flats-at-end FLATS_AT_END] [--invalid-frames INVALID_FRAMES]
[--update-to-projection UPDATE_TO_PROJECTION] [--update-to-dark UPDATE_TO_DARK] [--update-to-flat UPDATE_TO_FLAT] [--update-to-alignment UPDATE_TO_ALIGNMENT] [--embed-data]
file_path entry
Insert dark and / or flat frames and metadata into anexisting NXTomo file from url(s).
positional arguments:
file_path NXTomo file to patch
entry entry in the provided file
optional arguments:
-h, --help show this help message and exit
--darks-at-start DARKS_AT_START, --darks-start DARKS_AT_START
url to the dataset containing darks to be store atthe beginning. url should be providing the "default?silx way": silx:///data/image.edf?path=/scan_0/detector/data (see
www.silx.org/doc/silx/latest/modules/io/url.html?highlight=dataurl#silx.io.url.DataUrl)of just by giving dataset_path@file_path
--darks-at-end DARKS_AT_END, --darks-end DARKS_AT_END
url to the dataset containing darks to be store atthe end.url should be providing the "default?silx way": silx:///data/image.edf?path=/scan_0/detector/data (see
www.silx.org/doc/silx/latest/modules/io/url.html?highlight=dataurl#silx.io.url.DataUrl)of just by giving dataset_path@file_path
--flats-at-start FLATS_AT_START, --flats-start FLATS_AT_START
url to the dataset containing flats to be store atthe beginning of the acquisition sequence (made before projections acquisition). url should be providing the "default?silx way":
silx:///data/image.edf?path=/scan_0/detector/data (see www.silx.org/doc/silx/latest/modules/io/url.html?highlight=dataurl#silx.io.url.DataUrl)of just by giving dataset_path@file_path
--flats-at-end FLATS_AT_END, --flats-end FLATS_AT_END
url to the dataset containing flats to be store atthe beginning of end of the sequence (made before projections acquisition). url should be providing the "default?silx way":
silx:///data/image.edf?path=/scan_0/detector/data (see www.silx.org/doc/silx/latest/modules/io/url.html?highlight=dataurl#silx.io.url.DataUrl)of just by giving dataset_path@file_path
--invalid-frames INVALID_FRAMES
Define the set of frames to be mark as invalid. Frames can be provided two ways: - has a list: frame_index_1,frame_index_2 - has a python slice: from:to:steps
--update-to-projection UPDATE_TO_PROJECTION, --update-to-proj UPDATE_TO_PROJECTION
Define the set of frames to be mark as projection. Frames can be provided two ways: - has a list: frame_index_1,frame_index_2 - has a python slice: from:to:steps
--update-to-dark UPDATE_TO_DARK
Define the set of frames to be mark as dark. Frames can be provided two ways: - has a list: frame_index_1,frame_index_2 - has a python slice: from:to:steps
--update-to-flat UPDATE_TO_FLAT
Define the set of frames to be mark as flat. Frames can be provided two ways: - has a list: frame_index_1,frame_index_2 - has a python slice: from:to:steps
--update-to-alignment UPDATE_TO_ALIGNMENT
Define the set of frames to be mark as alignment. Frames can be provided two ways: - has a list: frame_index_1,frame_index_2 - has a python slice: from:to:steps
--embed-data Embed data from url in the file if not already inside
"""
__authors__ = ["H. Payno"]
__license__ = "MIT"
__date__ = "12/10/2020"
import argparse
import logging
import os
from silx.io.url import DataUrl
from silx.utils.enum import Enum as _Enum
from tomoscan.esrf.scan.nxtomoscan import NXtomoScan
from nxtomomill import utils
from nxtomo.nxobject.nxdetector import ImageKey
logging.basicConfig(level=logging.DEBUG)
_logger = logging.getLogger(__name__)
_SILX_DATA_URL = "www.silx.org/doc/silx/latest/modules/io/url.html?highlight=dataurl#silx.io.url.DataUrl"
_INFO_URL = (
'url should be providing the "default?silx way": '
"silx:///data/image.edf?path=/scan_0/detector/data "
f"(see {_SILX_DATA_URL})"
"of just by giving dataset_path@file_path"
)
class _ImageKeyName(_Enum):
ALIGNMENT = "alignment"
PROJECTION = "projection"
FLAT_FIELD = "flat"
DARK_FIELD = "dark"
INVALID = "invalid"
@staticmethod
def to_image_key(image_key) -> ImageKey:
image_key = _ImageKeyName.from_value(image_key.lower())
if image_key is _ImageKeyName.ALIGNMENT:
return ImageKey.ALIGNMENT
elif image_key is _ImageKeyName.PROJECTION:
return ImageKey.PROJECTION
elif image_key is _ImageKeyName.DARK_FIELD:
return ImageKey.DARK_FIELD
elif image_key is _ImageKeyName.FLAT_FIELD:
return ImageKey.FLAT_FIELD
elif image_key is _ImageKeyName.INVALID:
return ImageKey.INVALID
else:
raise ValueError(f"{image_key} not handled")
_INFO_FRAME_INPUT = (
"Frames can be provided three ways: \n"
"- has a list: frame_index_1,frame_index_2\n"
"- has a python slice: from:to:steps\n"
f"- has an image key value. Valid values are {_ImageKeyName.values()}\n"
)
def _extract_data_url(url_as_a_str):
"""
Extract url from a string
"""
if url_as_a_str is None:
return None
elif "@" in url_as_a_str:
try:
entry, file_path = url_as_a_str.split("@")
except Exception:
_logger.error(f"Fail to create an url from {url_as_a_str}. {_INFO_URL}")
return None
else:
url = DataUrl(file_path=file_path, data_path=entry, scheme="silx")
return url
else:
try:
url = DataUrl(path=url_as_a_str)
except Exception as e:
_logger.error(
f"Fail to create an url from {url_as_a_str}."
f"Reason is {e}. For more information see {_SILX_DATA_URL}"
)
return None
else:
return url
def _get_slice_to_modify(slice_as_str, master_file, entry):
"""
Return a list of int or a `slice` from slice_as_str
:param slice_as_str:
:return: slice to be modify on the image_key and image_key_control dataset
:rtype: Union[None, slice, list]
"""
if slice_as_str is None:
return None
elif slice_as_str.lower() in _ImageKeyName.values():
image_key = _ImageKeyName.to_image_key(slice_as_str)
scan = NXtomoScan(master_file, entry)
frames = scan.frames
slices = []
for frame in frames:
if frame.image_key is image_key:
slices.append(frame.index)
return slices
elif ":" in slice_as_str:
elmts = slice_as_str.split(":")
def get_value(index):
if index >= len(elmts):
return None
elif elmts[index] == "":
return None
else:
return int(elmts[index])
from_ = get_value(0)
to_ = get_value(1)
step = get_value(2)
return slice(from_, to_, step)
else:
return [int(index) for index in slice_as_str.split(",")]
[docs]def main(argv):
""" """
parser = argparse.ArgumentParser(
description="Insert dark and / or flat frames and metadata into an"
"existing NXTomo file from url(s)."
)
parser.add_argument("file_path", help="NXTomo file to patch")
parser.add_argument("entry", help="entry in the provided file")
# dark and flat options
parser.add_argument(
"--darks-at-start",
"--darks-start",
default=None,
help="url to the dataset containing darks to be store at"
"the beginning. " + _INFO_URL,
)
parser.add_argument(
"--darks-at-end",
"--darks-end",
default=None,
help="url to the dataset containing darks to be store at"
"the end." + _INFO_URL,
)
parser.add_argument(
"--flats-at-start",
"--flats-start",
default=None,
help="url to the dataset containing flats to be store at"
"the beginning of the acquisition sequence (made before "
"projections acquisition). " + _INFO_URL,
)
parser.add_argument(
"--flats-at-end",
"--flats-end",
default=None,
help="url to the dataset containing flats to be store at"
"the beginning of end of the sequence (made before "
"projections acquisition). " + _INFO_URL,
)
# modify frame type option
parser.add_argument(
"--invalid-frames",
default=None,
help="Define the set of frames to be mark as invalid. " + _INFO_FRAME_INPUT,
)
parser.add_argument(
"--update-to-projection",
"--update-to-proj",
default=None,
help="Define the set of frames to be mark as projection. "
"" + _INFO_FRAME_INPUT,
)
parser.add_argument(
"--update-to-dark",
default=None,
help="Define the set of frames to be mark as dark. " + _INFO_FRAME_INPUT,
)
parser.add_argument(
"--update-to-flat",
default=None,
help="Define the set of frames to be mark as flat. " + _INFO_FRAME_INPUT,
)
parser.add_argument(
"--update-to-alignment",
default=None,
help="Define the set of frames to be mark as alignment. "
"" + _INFO_FRAME_INPUT,
)
parser.add_argument(
"--embed-data",
default=False,
action="store_true",
help="Embed data from url in the file if not already inside",
)
options = parser.parse_args(argv[1:])
# get information for adding dark / flat
darks_start_url = _extract_data_url(options.darks_at_start)
darks_end_url = _extract_data_url(options.darks_at_end)
flat_start_url = _extract_data_url(options.flats_at_start)
flat_end_url = _extract_data_url(options.flats_at_end)
patch_det_data = darks_start_url or flat_start_url or flat_end_url or darks_end_url
# get information for modifying image_key
slice_to_update_to_dark = _get_slice_to_modify(
options.update_to_dark, master_file=options.file_path, entry=options.entry
)
slice_to_update_to_flat = _get_slice_to_modify(
options.update_to_flat, master_file=options.file_path, entry=options.entry
)
slice_to_update_to_projection = _get_slice_to_modify(
options.update_to_projection, master_file=options.file_path, entry=options.entry
)
slice_to_update_to_alignment = _get_slice_to_modify(
options.update_to_alignment, master_file=options.file_path, entry=options.entry
)
slice_to_invalid = _get_slice_to_modify(
options.invalid_frames, master_file=options.file_path, entry=options.entry
)
patch_image_key = (
slice_to_update_to_dark
or slice_to_update_to_flat
or slice_to_update_to_projection
or slice_to_update_to_alignment
or slice_to_invalid
)
if patch_det_data and patch_image_key:
_logger.info(
"Both adding dark / flat and modifying `image_key` / "
"`image_key_control` are requested. Will first add "
"dark / flat then modify `image_key` / "
"`image_key_control`."
)
elif not (patch_det_data or patch_image_key):
_logger.warning(
"No url provided for dark or flats or frame type to "
"modify. Nothing to be done."
)
elif not utils.is_nx_tomo_entry(file_path=options.file_path, entry=options.entry):
_logger.error(
f"{options.entry}@{options.file_path} is not recognized as a valid NXTomo entry."
)
elif not os.access(options.file_path, os.W_OK):
_logger.error(f"You don't have rights to write on {options.file_path}.")
else:
slices_patch = {
ImageKey.ALIGNMENT: slice_to_update_to_alignment,
ImageKey.PROJECTION: slice_to_update_to_projection,
ImageKey.FLAT_FIELD: slice_to_update_to_flat,
ImageKey.DARK_FIELD: slice_to_update_to_dark,
ImageKey.INVALID: slice_to_invalid,
}
if patch_image_key:
_logger.info("start updating frames")
for image_key_type, frames_to_update in slices_patch.items():
if frames_to_update is None:
continue
utils.change_image_key_control(
file_path=options.file_path,
entry=options.entry,
frames_indexes=frames_to_update,
image_key_control_value=image_key_type,
logger=_logger,
)
if patch_det_data:
_logger.info("start adding dark and flat field")
utils.add_dark_flat_nx_file(
file_path=options.file_path,
entry=options.entry,
darks_start=darks_start_url,
flats_start=flat_start_url,
darks_end=darks_end_url,
flats_end=flat_end_url,
embed_data=True,
logger=_logger,
)
