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#!/usr/bin/env python
# -*- coding: utf-8 -*-
#
# Project: Azimuthal integration
# https://github.com/kif/pyFAI
#
#
# Copyright (C) European Synchrotron Radiation Facility, Grenoble, France
#
# Principal author: Jérôme Kieffer (Jerome.Kieffer@ESRF.eu)
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with this program. If not, see <http://www.gnu.org/licenses/>.
#
__author__ = "Jérôme Kieffer"
__contact__ = "Jerome.Kieffer@ESRF.eu"
__license__ = "GPLv3+"
__copyright__ = "European Synchrotron Radiation Facility, Grenoble, France"
__date__ = "04/09/2013"
__status__ = "developement"
__docformat__ = 'restructuredtext'
import os
import logging
import types
from threading import Semaphore
import fabio
logger = logging.getLogger("pyFAI.processor")
from . import azimuthalIntegratory
from .detectors import detector_factory
AzimuthalIntegrator = azimuthalIntegrator.AzimuthalIntegrator
class Processor(object):
"""
This class can be set-up from a configuration file to define an azimuthal integrator
with all pre-processing and all post processing configured
"""
def __init__(self, config=None):
self.ai = AzimuthalIntegrator()
self.config = {}
self.config_file = "azimInt.json"
self.nbpt_azim = 0
if type(config) == dict:
self.config = config
elif type(config) in types.StringTypes:
if os.path.isfile(config):
self.config = json.load(open(config, "r"))
self.config_file(config)
else:
self.config = json.loads(config)
if self.config:
self.configure()
def __repr__(self):
"""
pretty print of myself
"""
lstout = ["Azimuthal Integrator:", self.ai.__repr__(),
"Input image shape: %s" % list(self.shapeIn),
"Number of points in radial direction: %s" % self.nbpt_rad,
"Number of points in azimuthal direction: %s" % self.nbpt_azim,
"Unit in radial dimension: %s" % self.unit.REPR,
"Correct for solid angle: %s" % self.correct_solid_angle,
"Polarization factor: %s" % self.polarization,
"Dark current image: %s" % self.dark_current_image,
"Flat field image: %s" % self.flat_field_image,
"Mask image: %s" % self.mask_image,
"Dummy: %s,\tDelta_Dummy: %s" % (self.dummy, self.delta_dummy),
"Directory: %s, \tExtension: %s" % (self.subdir, self.extension)]
return os.linesep.join(lstout)
def do_2D(self):
return self.nbpt_azim > 1
def reset(self):
"""
this is just to force the integrator to initialize
"""
logger.debug("did a reset")
self.ai.reset()
def configure(self, config=None):
if config is None:
config = self.config
if not config:
config = {}
if "poni" in config:
poni = config["poni"]
if poni and os.path.isfile(poni):
self.ai = AzimuthalIntegrator.loads(poni)
else:
self.ai = AzimuthalIntegrator()
detector = config.get("detector", "detector")
self.ai.detector = detector_factory(detector)
if "wavelength" in config:
wavelength = config["wavelength"]
try:
fwavelength = float(wavelength)
except ValueError:
logger.error("Unable to convert wavelength to float: %s" % wavelength)
else:
if fwavelength <= 0 or fwavelength > 1e-6:
logger.warning("Wavelength is in meter ... unlikely value %s" % fwavelength)
self.ai.wavelength = fwavelength
splineFile = config.get("splineFile")
if splineFile and os.path.isfile(splineFile):
self.ai.detector.splineFile = splineFile
self.ai.pixel1 = float(config.get("pixel1", 1))
self.ai.pixel2 = float(config.get("pixel2", 1))
self.ai.dist = config.get("dist", 1)
self.ai.poni1 = config.get("poni1", 0)
self.ai.poni2 = config.get("poni2", 0)
self.ai.rot1 = config.get("rot1", 0)
self.ai.rot2 = config.get("rot2", 0)
self.ai.rot3 = config.get("rot3", 0)
if config.get("chi_discontinuity_at_0"):
self.ai.setChiDiscAtZero()
else:
self.ai.setChiDiscAtPi()
mask_file = config.get("mask_file")
do_mask = config.get("do_mask")
if mask_file and os.path.exists(mask_file) and do_mask:
try:
mask = fabio.open(mask_file).data
except Exception as error:
logger.error("Unable to load mask file %s, error %s" % (mask_file, error))
else:
self.ai.mask = mask
self.mask_image = os.path.abspath(mask_file)
self.ai.set_darkfiles([i.strip() for i in config.get("dark_current", "").split(",")
if os.path.isfile(i.strip())])
self.ai.set_flatfiles([i.strip() for i in config.get("flat_field", "").split(",")
if os.path.isfile(i.strip())])
self.dark_current_image = self.ai.darkfiles
self.flat_field_image = self.ai.flatfiles
if config.get("do_2D"):
self.nbpt_azim = int(config.get("nbpt_azim"))
else:
self.nbpt_azim = 1
if config.get("nbpt_rad"):
self.nbpt_rad = int(config.get("nbpt_rad"))
self.unit = pyFAI.units.to_unit(config.get("unit", pyFAI.units.TTH_DEG))
self.do_poisson = config.get("do_poisson")
if config.get("do_polarization"):
self.polarization = config.get("polarization")
else:
self.polarization = None
logger.info(self.ai.__repr__())
self.reset()
# For now we do not calculate the LUT as the size of the input image is unknown
def get_config(self):
"""
retrieves the configuration
"""
to_save = { "poni": str(self.poni.text()).strip(),
"detector": str(self.detector.currentText()).lower(),
"wavelength":float_(self.wavelength.text()),
"splineFile":str(self.splineFile.text()).strip(),
"pixel1": float_(self.pixel1.text()),
"pixel2":float_(self.pixel2.text()),
"dist":float_(self.dist.text()),
"poni1":float_(self.poni1.text()),
"poni2":float_(self.poni2.text()),
"rot1":float_(self.rot1.text()),
"rot2":float_(self.rot2.text()),
"rot3":float_(self.rot3.text()),
"do_dummy": bool(self.do_dummy.isChecked()),
"do_mask": bool(self.do_mask.isChecked()),
"do_dark": bool(self.do_dark.isChecked()),
"do_flat": bool(self.do_flat.isChecked()),
"do_polarization":bool(self.do_polarization.isChecked()),
"val_dummy":float_(self.val_dummy.text()),
"delta_dummy":float_(self.delta_dummy.text()),
"mask_file":str(self.mask_file.text()).strip(),
"dark_current":str(self.dark_current.text()).strip(),
"flat_field":str(self.flat_field.text()).strip(),
"polarization_factor":float_(self.polarization_factor.value()),
"nbpt_rad":int_(self.rad_pt.text()),
"do_2D":bool(self.do_2D.isChecked()),
"nbpt_azim":int_(self.azim_pt.text()),
"chi_discontinuity_at_0": bool(self.chi_discontinuity_at_0.isChecked()),
"do_solid_angle": bool(self.do_solid_angle.isChecked()),
"do_radial_range": bool(self.do_radial_range.isChecked()),
"do_azimuthal_range": bool(self.do_azimuthal_range.isChecked()),
"do_poisson": bool(self.do_poisson.isChecked()),
"radial_range_min":float_(self.radial_range_min.text()),
"radial_range_max":float_(self.radial_range_max.text()),
"azimuth_range_min":float_(self.azimuth_range_min.text()),
"azimuth_range_max":float_(self.azimuth_range_max.text()),
}
if self.q_nm.isChecked():
to_save["unit"] = "q_nm^-1"
elif self.q_A.isChecked():
to_save["unit"] = "q_A^-1"
elif self.tth_deg.isChecked():
to_save["unit"] = "2th_deg"
elif self.tth_rad.isChecked():
to_save["unit"] = "2th_rad"
elif self.r_mm.isChecked():
to_save["unit"] = "r_mm"
try:
with open(filename, "w") as myFile:
json.dump(to_save, myFile, indent=4)
except IOError as error:
logger.error("Error while saving config: %s" % error)
else:
logger.debug("Saved")
def save_config(self, filename=None):
if not filename:
filename = self.config_file
def warmup(self):
"""
Reset and Process a dummy image to ensure eveything is initialized
"""
self.shapeIn
self.ai.reset()
if self.do_2D():
threading.Thread(target=self.ai.integrate2d,
name="init2d",
args=(numpy.zeros(self.shapeIn, dtype=numpy.float32),
self.nbpt_rad, self.nbpt_azim),
kwargs=dict(method="lut", unit=self.unit)
).start()
else:
threading.Thread(target=self.ai.integrate1d,
name="init1d",
args=(numpy.zeros(self.shapeIn, dtype=numpy.float32),
self.nbpt_rad),
kwargs=dict(method="lut", unit=self.unit)
).start()
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