FormatSEReBICpedestal.py

#!/usr/bin/env python
# FormatSEReBICpedestal.py

from __future__ import annotations

# Experimental format for TIA .ser files used by FEI microscope at eBIC. This
# version adds a pedestal level to the image data as determined by the
# environment variable ADD_PEDESTAL. A warning will be issued to counter
# against the use of this format by mistake
import logging
import os

from dxtbx.format.FormatSEReBIC import FormatSEReBIC

logger = logging.getLogger("dials")


class FormatSEReBICpedestal(FormatSEReBIC):
    def __init__(self, image_file, **kwargs):
        from dxtbx import IncorrectFormatError

        if not self.understand(image_file):
            raise IncorrectFormatError(self, image_file)
        FormatSEReBIC.__init__(self, image_file, **kwargs)
        self.pedestal = os.environ.get("ADD_PEDESTAL", 0)
        self.pedestal = float(self.pedestal)
        logger.info(
            "WARNING: Using FormatSEReBICpedestal. The value {0} will "
            "be added to all pixels".format(self.pedestal)
        )

    def get_raw_data(self, index):
        raw_data = super(FormatSEReBICpedestal, self).get_raw_data(index).as_double()
        raw_data += self.pedestal
        return raw_data


if __name__ == "__main__":
    import sys

    for arg in sys.argv[1:]:
        print(FormatSEReBICpedestal.understand(arg))