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#!/usr/bin/env python
# coding: utf-8
#
# Project: X-ray image reader
# https://github.com/silx-kit/fabio
#
#
# Copyright (C) European Synchrotron Radiation Facility, Grenoble, France
#
# Principal author: Jérôme Kieffer (Jerome.Kieffer@ESRF.eu)
#
# Permission is hereby granted, free of charge, to any person
# obtaining a copy of this software and associated documentation files
# (the "Software"), to deal in the Software without restriction,
# including without limitation the rights to use, copy, modify, merge,
# publish, distribute, sublicense, and/or sell copies of the Software,
# and to permit persons to whom the Software is furnished to do so,
# subject to the following conditions:
#
# The above copyright notice and this permission notice shall be
# included in all copies or substantial portions of the Software.
#
# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
# EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
# OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
# NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
# HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
# WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
# FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
# OTHER DEALINGS IN THE SOFTWARE.
"""Portable image converter based on FabIO library
to export Eiger frames (including te one from LImA)
to a set of esperanto frames which can be imported
into CrysalisPro.
"""
__author__ = "Jerome Kieffer"
__copyright__ = "European Synchrotron Radiation Facility, Grenoble, France"
__licence__ = "MIT"
__date__ = "23/04/2021"
__status__ = "production"
FOOTER = """To import your files as a project:
* Start CrysalisPro and open any project
* press "F5" to open the console
* Type `esperanto createrunlist` and select your first and last frame
"""
import logging
logging.basicConfig()
logger = logging.getLogger("eiger2crysalis")
import sys
import os
import shutil
from .. import esperantoimage, eigerimage, limaimage, sparseimage
from ..openimage import openimage as fabio_open
from .._version import version as fabio_version
from ..nexus import get_isotime
from ..utils.cli import ProgressBar, expand_args
import numpy
import argparse
try:
import hdf5plugin
except ImportError:
pass
try:
import numexpr
except ImportError:
logger.error("Numexpr is needed to interpret formula ...")
EXIT_SUCCESS = 0
EXIT_FAILURE = 1
EXIT_ARGUMENT_FAILURE = 2
try:
from scipy import constants
except ImportError:
# Updated with scipy 1.4
CONST_hc = 12.398419843320026
else:
CONST_hc = constants.c * constants.h / constants.e * 1e7
def as_str(smth):
"Transform to string"
if isinstance(any, bytes):
return smth.decode()
else:
return str(smth)
class Converter:
def __init__(self, options):
self.options = options
self.mask = None
if not self.options.verbose:
self.progress = ProgressBar("HDF5 --> Esperanto", len(options.images), 30)
self.succeeded = True
prefix = os.path.commonprefix([os.path.abspath(i) for i in self.options.images])
if "{dirname}" in self.options.output:
self.dirname = os.path.dirname(prefix)
else:
self.dirname = os.path.dirname(os.path.abspath(self.options.output))
if "{prefix}" in self.options.output:
self.prefix = os.path.basename(prefix)
else:
self.prefix = os.path.basename(os.path.abspath(self.options.output)).split("{")[0]
self.headers = None
def geometry_transform(self, image):
"Transforms an image according to the requested command line options"
if self.options.rotation:
image = numpy.rot90(image, k=self.options.rotation // 90)
if self.options.transpose:
image = image.T
if self.options.flip_ud:
image = numpy.flipud(image)
if self.options.flip_lr:
image = numpy.fliplr(image)
return image
def new_beam_center(self, x, y, shape):
"""Calculate the position of the beam after all transformations:
:param x, y: position in the initial image
:shape: shape of the input image
:return: x, y, coordinated of the new beam center within the esperanto frame.
"""
dummy = 123
m = numpy.zeros(shape, dtype=numpy.int32)
m[int(y + 0.5), int(x + 0.5)] = dummy
f = esperantoimage.EsperantoImage(data=m)
n = self.geometry_transform(f.data)
w = numpy.argmin(abs(n.ravel() - dummy))
return w % n.shape[-1], w // n.shape[-1]
def convert_all(self):
self.succeeded = True
start_at = 0
self.headers = self.common_headers()
for filename in self.options.images:
finish_at = self.convert_one(filename, start_at)
self.succeeded = self.succeeded and (finish_at > 0)
start_at += finish_at
def finish(self):
if not self.succeeded:
if not self.options.verbose:
self.progress.clear()
print("Conversion or part of it failed. You can try with --debug to have more output information.")
return EXIT_FAILURE
else:
if not self.options.verbose:
self.progress.clear()
print(FOOTER)
return EXIT_SUCCESS
def common_headers(self):
headers = {
# SPECIAL_CCD_1
"delectronsperadu": 1,
"ldarkcorrectionswitch": 0,
"lfloodfieldcorrectionswitch/mode": 0,
"dsystemdcdb2gain": 1.0,
"ddarksignal": 0,
"dreadnoiserms": 0,
# SPECIAL_CCD_2
"ioverflowflag":0 ,
"ioverflowafterremeasureflag":0,
"inumofdarkcurrentimages":0,
"inumofmultipleimages":0,
"loverflowthreshold": 1000000,
# SPECIAL_CCD_3
# SPECIAL_CCD_4
# SPECIAL_CCD_5
# TIME
# "dexposuretimeinsec": 0.2,
"doverflowtimeinsec": 0 ,
"doverflowfilter":0,
# MONITOR
# PIXELSIZE
# "drealpixelsizex": 0.075,
# "drealpixelsizey": 0.075,
"dsithicknessmmforpixeldetector": 1,
# TIMESTAMP
"timestampstring": get_isotime(),
# GRIDPATTERN
# STARTANGLESINDEG
# "dom_s":-180 + i,
# "dth_s":0,
# "dka_s":0,
# "dph_s":0,
# ENDANGLESINDEG
# "dom_e":-179 + i,
# "dth_e": 0,
# "dka_e": 0,
# "dph_e": 0,
# GONIOMODEL_1
"dbeam2indeg":0,
"dbeam3indeg":0,
"detectorrotindeg_x":0,
"detectorrotindeg_y":0,
"detectorrotindeg_z":0,
# "dxorigininpix": img.data.shape[1] - (img.data.shape[1] - data.shape[1]) / 2 - center_x,
# "dyorigininpix": img.data.shape[0] - center_y,
"dalphaindeg": 50,
"dbetaindeg": 0,
# "ddistanceinmm": 117,
# GONIOMODEL_2
# WAVELENGTH
# "dalpha1": wl,
# "dalpha2": wl,
# "dalpha12": wl,
# "dbeta1": wl,
# MONOCHROMATOR
"ddvalue-prepolfac": 0.98,
"orientation-type": "SYNCHROTRON",
# ABSTORUN
}
with fabio_open(self.options.images[0]) as source:
shape = source.data.shape
dtype = source.data.dtype
if self.progress is not None:
self.progress.max_value = source.nframes * len(self.options.images)
if isinstance(source, limaimage.LimaImage):
# Populate the Pilatus header from the Lima
entry_name = source.h5.attrs.get("default")
if entry_name:
entry = source.h5.get(entry_name)
if entry:
data_name = entry.attrs["default"]
if data_name:
data_grp = entry.get(data_name)
if data_grp:
nxdetector = data_grp.parent
try:
headers["drealpixelsizex"] = nxdetector["detector_information/pixel_size/xsize"][()] * 1e3
headers["drealpixelsizey"] = nxdetector["detector_information/pixel_size/ysize"][()] * 1e3
except Exception as e:
logger.warning("Error in searching for pixel size (%s): %s", type(e), e)
try:
t1 = nxdetector["acquisition/exposure_time"][()]
headers["dexposuretimeinsec"] = t1
except Exception as e:
logger.warning("Error in searching for exposure time (%s): %s", type(e), e)
elif isinstance(source, sparseimage.SparseImage):
entry_name = source.h5.attrs.get("default")
if entry_name:
entry = source.h5.get(entry_name)
if entry:
instruments = [i for i in entry.values() if as_str(i.attrs.get("NX_class", "")) == "NXinstrument"]
if instruments:
instrument = instruments[0]
detectors = [i for i in instrument.values() if as_str(i.attrs.get("NX_class", "")) == "NXdetector"]
if detectors:
detector = detectors[0]
headers["drealpixelsizex"] = detector["x_pixel_size"][()] * 1e3
headers["drealpixelsizey"] = detector["y_pixel_size"][()] * 1e3
headers["dxorigininpix"] = detector["beam_center_x"][()]
headers["dyorigininpix"] = detector["beam_center_y"][()]
headers["ddistanceinmm"] = detector["distance"][()] * 1e3
monchromators = [i for i in instrument.values() if as_str(i.attrs.get("NX_class", "")) == "NXmonochromator"]
if monchromators:
wavelength = monchromators[0]["wavelength"][()]
self.mask = numpy.logical_not(numpy.isfinite(source.mask))
headers["dexposuretimeinsec"] = 1 # meaningfull value.
elif isinstance(source, eigerimage.EigerImage):
raise NotImplementedError("Please implement Eiger detector data format parsing or at least open an issue")
else:
raise NotImplementedError("Unsupported format: %s" % source.__class__.__name__)
if self.mask is None:
self.mask = numpy.zeros(shape, dtype=dtype)
# Parse option for headers
if self.options.energy:
wavelength = CONST_hc / self.options.energy
elif self.options.wavelength:
wavelength = self.options.wavelength
headers["dalpha1"] = headers["dalpha2"] = headers["dalpha12"] = headers["dbeta1"] = wavelength
if self.options.distance:
headers["ddistanceinmm"] = self.options.distance
if self.options.beam:
x, y = self.options.beam
x, y = self.new_beam_center(x, y, shape)
headers["dxorigininpix"] = x
headers["dyorigininpix"] = y
if self.options.alpha:
headers["dalphaindeg"] = self.options.alpha
if self.options.kappa is not None:
try:
value = float(self.options.kappa)
except ValueError: # Handle the string
value = numexpr.NumExpr(self.options.kappa)
headers["dka_s"] = headers["dka_e"] = value
if self.options.theta is not None:
try:
value = float(self.options.theta)
except ValueError: # Handle the string
value = numexpr.NumExpr(self.options.theta)
headers["dth_s"] = headers["dth_e"] = value
if self.options.phi is not None:
try:
value = float(self.options.phi)
except ValueError: # Handle the string
value = numexpr.NumExpr(self.options.phi)
headers["dph_s"] = headers["dph_e"] = value
if self.options.omega is not None:
try:
value = float(self.options.omega)
except ValueError:
# Handle the string
value = numexpr.NumExpr(self.options.omega)
headers["dom_s"] = headers["dom_e"] = value
return headers
def convert_one(self, input_filename, start_at=0):
"""
Convert a single file using options
:param str input_filename: The input filename
:param object options: List of options provided from the command line
:param start_at: index to start at for given file
:rtype: int
:returns: the number of frames processed
"""
self.progress.update(start_at + 0.5, input_filename)
input_filename = os.path.abspath(input_filename)
input_exists = os.path.exists(input_filename)
if self.options.verbose:
print("Converting file '%s'" % (input_filename))
if not input_exists:
logger.error("Input file '%s' do not exists. Conversion skipped.", input_filename)
return -1
try:
logger.debug("Load '%s'", input_filename)
source = fabio_open(input_filename)
except KeyboardInterrupt:
raise
except Exception as e:
logger.error("Loading input file '%s' failed cause: \"%s\". Conversion skipped.", input_filename, e.message)
logger.debug("Backtrace", exc_info=True)
return -1
for i, frame in enumerate(source):
idx = i + start_at
self.progress.update(idx + 0.5, input_filename + " - " + str(idx))
input_data = frame.data
numpy.maximum(self.mask, input_data, out=self.mask)
input_data = input_data.astype(numpy.int32)
input_data[input_data == numpy.iinfo(frame.data.dtype).max] = self.options.dummy
converted = esperantoimage.EsperantoImage(data=input_data) # This changes the shape
converted.data = self.geometry_transform(converted.data)
for k, v in self.headers.items():
if callable(v):
if k.endswith("s"):
converted.header[k] = v(idx)
else: # k.endswith("e"):
converted.header[k] = v(idx + 1)
else:
converted.header[k] = v
output_filename = self.options.output.format(index=((idx + self.options.offset)),
prefix=self.prefix,
dirname=self.dirname)
os.makedirs(os.path.dirname(output_filename), exist_ok=True)
try:
logger.debug("Write '%s'", output_filename)
if not self.options.dry_run:
converted.write(output_filename)
except KeyboardInterrupt:
raise
except Exception as e:
logger.error("Saving output file '%s' failed cause: \"%s: %s\". Conversion skipped.", output_filename, type(e), e)
logger.debug("Backtrace", exc_info=True)
return -1
return source.nframes
def treat_mask(self):
if self.progress:
self.progress.update(self.progress.max_value - 1, "Generate mask")
try:
from pyFAI.ext import dynamic_rectangle
except ImportError:
print("A recent version of pyFAI is needed to export the mask in a format compatible wit CrysalisPro")
else:
mask = self.mask == numpy.iinfo(self.mask.dtype).max
esperantoimage.EsperantoImage.DUMMY = 1
new_mask = self.geometry_transform(esperantoimage.EsperantoImage(data=self.mask).data)
esperantoimage.EsperantoImage.DUMMY = -1
rectangles = dynamic_rectangle.decompose_mask(new_mask.astype(numpy.int8))
self.progress.update(self.progress.max_value - 0.5, f"Exporting {len(rectangles)} rectangles as mask")
dummy_filename = self.options.output.format(index=self.options.offset,
prefix=self.prefix,
dirname=self.dirname)
dirname = os.path.dirname(dummy_filename)
numpy.save(os.path.join(dirname, self.prefix + "_mask.npy"), self.mask)
with open(os.path.join(dirname, self.prefix + ".set"), mode="wb") as maskfile:
maskfile.write(b'#XCALIBUR SYSTEM\r\n')
maskfile.write(b'#XCALIBUR SETUP FILE\r\n')
maskfile.write(b'#*******************************************************************************************************\r\n')
maskfile.write(b'# CHIP CHARACTERISTICS e_19_020609.ccd D A T E Wed-Sep-16-10-00-59-2009\r\n')
maskfile.write(b'# This program produces version 1.9\r\n')
maskfile.write(b'#******************************************************************************************************\r\n')
maskfile.write(b'#THIS FILE IS USER READABLE - BUT SHOULD NOT BE TOUCHED BY THE USER\r\n')
maskfile.write(b'#ANY CHANGES TO THIS FILE WILL RESULT IN LOSS OF WARRANTY!\r\n')
maskfile.write(b'#CHIP IDCODE producer type serial\r\n')
maskfile.write(b'CHIP IDCODE "n/a" "n/a" "n/a\r\n')
maskfile.write(b'#CHIP TAPER producer type serial\r\n')
maskfile.write(b'CHIP TAPER "" "" ""\r\n')
maskfile.write(b'#ALL COORDINATES GO FROM 0 TO N-1\r\n')
maskfile.write(b'#CHIP BADPOINT treatment options: IGNORE,REPLACE,AVERAGE\r\n')
maskfile.write(b'#CHIP BADPOINT x1x1 y1x1 treatment r1x1x1 r1y1x1 r2x1x1 r2y1x1\r\n')
maskfile.write(b'#CHIP BADPOINT 630 422 REPLACE 632 422 0 0\r\n')
maskfile.write(b'#CHIP BADRECTANGLE xl xr yb yt\r\n')
for r in rectangles:
if r.area == 1:
maskfile.write(f"CHIP BADPOINT {r.col} {r.row} IGNORE {r.col} {r.row} {r.col} {r.row}\r\n".encode())
else:
maskfile.write(f"CHIP BADRECTANGLE {r.col} {r.col+r.width} {r.row} {r.row+r.height}\r\n".encode())
maskfile.write(b'#END OF XCALIBUR CHIP CHARACTERISTICS FILE\r\n')
# Make a backup as the original could be overwritten by Crysalis at import
shutil.copyfile(os.path.join(dirname, self.prefix + ".set"), os.path.join(dirname, self.prefix + ".set.orig"))
def main():
epilog = """return codes: 0 means a success. 1 means the conversion
contains a failure, 2 means there was an error in the
arguments"""
parser = argparse.ArgumentParser(prog="eiger2crysalis",
description=__doc__,
epilog=epilog)
parser.add_argument("IMAGE", nargs="*",
help="File with input images")
parser.add_argument("-V", "--version", action='version', version=fabio_version,
help="output version and exit")
parser.add_argument("-v", "--verbose", action='store_true', dest="verbose", default=False,
help="show information for each conversions")
parser.add_argument("--debug", action='store_true', dest="debug", default=False,
help="show debug information")
group = parser.add_argument_group("main arguments")
group.add_argument("-l", "--list", action="store_true", dest="list", default=None,
help="show the list of available formats and exit")
group.add_argument("-o", "--output", default='{dirname}/{prefix}/{prefix}_1_{index}.esperanto', type=str,
help="output directory and filename template")
group.add_argument("-O", "--offset", type=int, default=1,
help="index offset, CrysalisPro likes indexes to start at 1, Python starts at 0")
group.add_argument("-D", "--dummy", type=int, default=-1,
help="Set masked values to this dummy value")
group = parser.add_argument_group("optional behaviour arguments")
# group.add_argument("-f", "--force", dest="force", action="store_true", default=False,
# help="if an existing destination file cannot be" +
# " opened, remove it and try again (this option" +
# " is ignored when the -n option is also used)")
# group.add_argument("-n", "--no-clobber", dest="no_clobber", action="store_true", default=False,
# help="do not overwrite an existing file (this option" +
# " is ignored when the -i option is also used)")
# group.add_argument("--remove-destination", dest="remove_destination", action="store_true", default=False,
# help="remove each existing destination file before" +
# " attempting to open it (contrast with --force)")
# group.add_argument("-u", "--update", dest="update", action="store_true", default=False,
# help="copy only when the SOURCE file is newer" +
# " than the destination file or when the" +
# " destination file is missing")
# group.add_argument("-i", "--interactive", dest="interactive", action="store_true", default=False,
# help="prompt before overwrite (overrides a previous -n" +
# " option)")
group.add_argument("--dry-run", dest="dry_run", action="store_true", default=False,
help="do everything except modifying the file system")
group.add_argument("--calc-mask", dest="calc_mask", default=False, action="store_true",
help="Generate a mask from pixels marked as invalid. Off by default since it takes time")
group = parser.add_argument_group("Experimental setup options")
group.add_argument("-e", "--energy", type=float, default=None,
help="Energy of the incident beam in keV")
group.add_argument("-w", "--wavelength", type=float, default=None,
help="Wavelength of the incident beam in Å")
group.add_argument("-d", "--distance", type=float, default=None,
help="Detector distance in millimeters")
group.add_argument("-b", "--beam", nargs=2, type=float, default=None,
help="Direct beam in pixels x, y")
group = parser.add_argument_group("Goniometer setup")
# group.add_argument("--axis", type=str, default=None,
# help="Goniometer angle used for scanning: 'omega', 'phi' or 'kappa'")
group.add_argument("--alpha", type=float, default=50,
help="Goniometer angle alpha value in deg. Constant, angle between kappa/omega.")
group.add_argument("--kappa", type=str, default=0,
help="Goniometer angle kappa value in deg or formula f(index).")
# group.add_argument("--chi", type=str, default=0,
# help="Goniometer angle chi value in deg. or formula f(index).")
group.add_argument("--phi", type=str, default=0,
help="Goniometer angle phi value in deg. or formula f(index). Inner-most rotation.")
group.add_argument("--omega", type=str, default=0,
help="Goniometer angle omega value in deg. or formula f(index). Outer-most rotation.")
group.add_argument("--theta", type=str, default=0,
help="Goniometer angle theta value in deg. or formula f(index). Tilt angle of the detector.")
group = parser.add_argument_group("Image preprocessing (Important: applied in this order!)")
group.add_argument("--rotation", type=int, default=180,
help="Rotate the initial image by this value in degrees. Must be a multiple of 90°. By default 180 deg (flip_up with origin=lower and flip_lr because the image is seen from the sample).")
group.add_argument("--transpose", default=False, action="store_true",
help="Flip the x/y axis")
group.add_argument("--flip-ud", dest="flip_ud", default=False, action="store_true",
help="Flip the image upside-down")
group.add_argument("--flip-lr", dest="flip_lr", default=False, action="store_true",
help="Flip the image left-right")
try:
args = parser.parse_args()
if args.debug:
logger.setLevel(logging.DEBUG)
if args.list:
print("Supported formats: LimaImage, EigerImage, SparseImage")
return
if len(args.IMAGE) == 0:
raise argparse.ArgumentError(None, "No input file specified.")
# the upper case IMAGE is used for the --help auto-documentation
args.images = expand_args(args.IMAGE)
args.images.sort()
except argparse.ArgumentError as e:
logger.error(e.message)
logger.debug("Backtrace", exc_info=True)
return EXIT_ARGUMENT_FAILURE
esperantoimage.EsperantoImage.DUMMY = args.dummy
converter = Converter(args)
converter.convert_all()
if args.calc_mask:
converter.treat_mask()
return converter.finish()
if __name__ == "__main__":
result = main()
sys.exit(result)
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