<reponame>vallsv/pyFAI<gh_stars>0
#!/usr/bin/env python
# -*- coding: utf-8 -*-
#
#    Project: Azimuthal integration
#             https://github.com/silx-kit/pyFAI
#
#    Copyright (C) 2015-2016 European Synchrotron Radiation Facility, Grenoble, France
#
#    Principal author:       <NAME> (<EMAIL>)
#
# 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.

"""This module contains the Worker class:

A tool able to perform azimuthal integration with:
additional saving capabilities like

- save as 2/3D structure in a HDF5 File
- read from HDF5 files

Aims at being integrated into a plugin like LImA or as model for the GUI

The configuration of this class is mainly done via a dictionary transmitted as a JSON string:
Here are the valid keys:

- "dist"
- "poni1"
- "poni2"
- "rot1"
- "rot3"
- "rot2"
- "pixel1"
- "pixel2"
- "splineFile"
- "wavelength"
- "poni" #path of the file
- "chi_discontinuity_at_0"
- "do_mask"
- "do_dark"
- "do_azimuthal_range"
- "do_flat"
- "do_2D"
- "azimuth_range_min"
- "azimuth_range_max"
- "polarization_factor"
- "nbpt_rad"
- "do_solid_angle"
- "do_radial_range"
- "do_poisson"
- "delta_dummy"
- "nbpt_azim"
- "flat_field"
- "radial_range_min"
- "dark_current"
- "do_polarization"
- "mask_file"
- "detector"
- "unit"
- "radial_range_max"
- "val_dummy"
- "do_dummy"
- "method"
"""


from __future__ import with_statement, print_function, division

__author__ = "<NAME>"
__contact__ = "<EMAIL>"
__license__ = "MIT"
__copyright__ = "European Synchrotron Radiation Facility, Grenoble, France"
__date__ = "10/01/2018"
__status__ = "development"

import threading
import os.path
import logging
import json

logger = logging.getLogger(__name__)

import numpy
import fabio
from .detectors import detector_factory
from .azimuthalIntegrator import AzimuthalIntegrator
from .distortion import Distortion
from . import units
try:
    from .ext.preproc import preproc
except ImportError as err:
    logger.warning("Unable to import preproc: %s", err)
    preproc = None
# from .io import h5py, HDF5Writer


def make_ai(config):
    """Create an Azimuthal integrator from the configuration
    stand alone function !

    :param config: dict with all parameters
    :return: configured (but uninitialized) AzimuthalIntgrator
    """
    poni = config.get("poni")
    if poni and os.path.isfile(poni):
        ai = AzimuthalIntegrator.sload(poni)
    else:
        ai = AzimuthalIntegrator()

    detector = config.get("detector", None)
    if detector:
        ai.detector = detector_factory(detector)

    wavelength = config.get("wavelength", 0)
    if wavelength:
        if wavelength <= 0 or wavelength > 1e-6:
            logger.warning("Wavelength is in meter ... unlikely value %s", wavelength)
        ai.wavelength = wavelength

    splinefile = config.get("splineFile")
    if splinefile and os.path.isfile(splinefile):
        ai.detector.splineFile = splinefile

    for key in ("pixel1", "pixel2", "dist", "poni1", "poni2", "rot1", "rot2", "rot3"):
        value = config.get(key)
        if value is not None:
            ai.__setattr__(key, value)
    if config.get("chi_discontinuity_at_0"):
        ai.setChiDiscAtZero()

    mask_file = config.get("mask_file")
    if mask_file and config.get("do_mask"):
        if os.path.exists(mask_file):
            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:
                ai.mask = mask

    dark_files = [i.strip() for i in config.get("dark_current", "").split(",")
                  if os.path.isfile(i.strip())]
    if dark_files and config.get("do_dark"):
        ai.set_darkfiles(dark_files)

    flat_files = [i.strip() for i in config.get("flat_field", "").split(",")
                  if os.path.isfile(i.strip())]
    if flat_files and config.get("do_flat"):
        ai.set_flatfiles(flat_files)

    return ai


class Worker(object):
    def __init__(self, azimuthalIntegrator=None,
                 shapeIn=(2048, 2048), shapeOut=(360, 500),
                 unit="r_mm", dummy=None, delta_dummy=None,
                 azimuthalIntgrator=None):
        """
        :param azimuthalIntegrator AzimuthalIntegrator: pyFAI.AzimuthalIntegrator instance
        :param azimuthalIntgrator AzimuthalIntegrator: pyFAI.AzimuthalIntegrator instance (deprecated)
        :param shapeIn: image size in input
        :param shapeOut: Integrated size: can be (1,2000) for 1D integration
        :param unit: can be "2th_deg, r_mm or q_nm^-1 ...
        """
        # TODO remove it in few month (added on 2016-08-04)
        if azimuthalIntgrator is not None:
            logger.warning("'Worker(azimuthalIntgrator=...)' parameter is deprecated cause it contains a typo. Please use 'azimuthalIntegrator='")
            azimuthalIntegrator = azimuthalIntgrator

        self._sem = threading.Semaphore()
        if azimuthalIntegrator is None:
            self.ai = AzimuthalIntegrator()
        else:
            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()
        self._normalization_factor = None  # Value of the monitor: divides the intensity by this value for normalization
        self.nbpt_azim, self.nbpt_rad = shapeOut
        self._unit = units.to_unit(unit)
        self.polarization_factor = None
        self.dummy = dummy
        self.delta_dummy = delta_dummy
        self.correct_solid_angle = True
        self.dark_current_image = None
        self.flat_field_image = None
        self.mask_image = None
        self.subdir = ""
        self.extension = None
        self.do_poisson = None
        self.needs_reset = True
        self.output = "numpy"  # exports as numpy array by default
        self.shape = shapeIn
        self.method = "csr"
        self.radial = None
        self.azimuthal = None
        self.radial_range = None
        self.azimuth_range = None
        self.safe = True

    def __repr__(self):
        """
        pretty print of myself
        """
        lstout = ["Azimuthal Integrator:", self.ai.__repr__(),
                  "Input image shape: %s" % list(self.shape),
                  "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,
                  "Correct for solid angle: %s" % self.correct_solid_angle,
                  "Polarization factor: %s" % self.polarization_factor,
                  "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),
                  "Radial range: %s" % self.radial_range,
                  "Azimuth range: %s" % self.azimuth_range]
        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
        """
        if self.needs_reset:
            with self._sem:
                if self.needs_reset:
                    self.ai.reset()
                    self.needs_reset = False
        # print self.__repr__()

    def reconfig(self, shape=(2048, 2048), sync=False):
        """
        This is just to force the integrator to initialize with a given input image shape

        :param shape: shape of the input image
        :param sync: return only when synchronized
        """
        self.shape = shape
        self.ai.reset()
        self.warmup(sync)

    def process(self, data, normalization_factor=1.0, writer=None, metadata=None):
        """
        Process a frame
        #TODO:
        dark, flat, sa are missing

        :param data: numpy array containing the input image
        :param writer: An open writer in which 'write' will be called with the result of the integration
        """

        with self._sem:
            monitor = self._normalization_factor * normalization_factor if self._normalization_factor else normalization_factor
        kwarg = {"unit": self.unit,
                 "dummy": self.dummy,
                 "delta_dummy": self.delta_dummy,
                 "method": self.method,
                 "polarization_factor": self.polarization_factor,
                 # "filename": None,
                 "safe": self.safe,
                 "data": data,
                 "correctSolidAngle": self.correct_solid_angle,
                 "safe": self.safe
                 }

        if metadata is not None:
            kwarg["metadata"] = metadata

        if monitor is not None:
            kwarg["normalization_factor"] = monitor

        if self.do_2D():
            kwarg["npt_rad"] = self.nbpt_rad
            kwarg["npt_azim"] = self.nbpt_azim
            # if "filename" in kwarg:
            #    if self.extension:
            #        kwarg["filename"] += self.extension
            #    else:
            #        kwarg["filename"] += ".azim"
        else:
            kwarg["npt"] = self.nbpt_rad
            # if "filename" in kwarg:
            #    if self.extension:
            #        kwarg["filename"] += self.extension
            #    else:
            #        kwarg["filename"] += ".xy"
        if self.do_poisson:
            kwarg["error_model"] = "poisson"
        else:
            kwarg["error_model"] = None

        if self.radial_range is not None:
            kwarg["radial_range"] = self.radial_range

        if self.azimuth_range is not None:
            kwarg["azimuth_range"] = self.azimuth_range

        try:
            if self.do_2D():
                integrated_result = self.ai.integrate2d(**kwarg)
                self.radial = integrated_result.radial
                self.azimuthal = integrated_result.azimuthal
                result = integrated_result.intensity
            else:
                integrated_result = self.ai.integrate1d(**kwarg)
                self.radial = integrated_result.radial
                self.azimuthal = None
                result = numpy.vstack(integrated_result).T

        except Exception as err:
            err2 = ["error in integration",
                    str(err),
                    "data.shape: %s" % (data.shape,),
                    "data.size: %s" % data.size,
                    "ai:",
                    str(self.ai),
                    "csr:",
                    # str(self.ai._csr_integrator),
                    # "csr size: %s" % self.ai._lut_integrator.size
                    ]
            logger.error("; ".join(err2))
            raise err

        if writer is not None:
            writer.write(integrated_result)

        if self.output == "numpy":
            return result

    def setSubdir(self, path):
        """
        Set the relative or absolute path for processed data
        """
        self.subdir = path

    def setExtension(self, ext):
        """
        enforce the extension of the processed data file written
        """
        if ext:
            self.extension = ext
        else:
            self.extension = None

    def setDarkcurrentFile(self, imagefile):
        self.ai.set_darkfiles(imagefile)
        self.dark_current_image = imagefile

    def setFlatfieldFile(self, imagefile):
        self.ai.set_flatfiles(imagefile)
        self.flat_field_image = imagefile

    def setJsonConfig(self, jsonconfig):
        print("start config ...")
        if os.path.isfile(jsonconfig):
            config = json.load(open(jsonconfig, "r"))
        else:
            config = json.loads(jsonconfig)
        if "poni" in config:
            poni = config["poni"]
            if poni and os.path.isfile(poni):
                self.ai = AzimuthalIntegrator.sload(poni)

        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["nbpt_rad"])
        self.unit = units.to_unit(config.get("unit", units.TTH_DEG))
        self.do_poisson = config.get("do_poisson")
        if config.get("do_polarization"):
            self.polarization_factor = config.get("polarization_factor")
        else:
            self.polarization_factor = None

        if config.get("do_OpenCL"):
            self.method = "csr_ocl"
        else:
            self.method = "csr"

        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 set_unit(self, value):
        self._unit = units.to_unit(value)

    def get_unit(self):
        return self._unit

    unit = property(get_unit, set_unit)

    def set_error_model(self, value):
        if value == "poisson":
            self.do_poisson = True
        elif value is None or value == "":
            self.do_poisson = False
        else:
            raise RuntimeError("Unsupported error model '%s'" % value)

    def get_error_model(self):
        if self.do_poisson:
            return "poisson"
        return None
    error_model = property(get_error_model, set_error_model)

    def get_config(self):
        """return configuration as a dictionary"""
        config = {"unit": str(self.unit)}
        for key in ["dist", "poni1", "poni2", "rot1", "rot3", "rot2", "pixel1", "pixel2", "splineFile", "wavelength"]:
            try:
                config[key] = self.ai.__getattribute__(key)
            except:
                pass
        for key in ["nbpt_azim", "nbpt_rad", "polarization_factor", "dummy", "delta_dummy",
                    "correct_solid_angle", "dark_current_image", "flat_field_image",
                    "mask_image", "do_poisson", "shape", "method"]:
            try:
                config[key] = self.__getattribute__(key)
            except:
                pass

        return config
#
#    "poni" #path of the file
#
#    "chi_discontinuity_at_0"
#    "do_mask"
#    "do_dark"
#    "do_azimuthal_range"
#    "do_flat"
#    "do_2D"
#    "azimuth_range_min"
#    "azimuth_range_max"
#
#    "polarization_factor"
#    "nbpt_rad"
#    "do_solid_angle"
#    "do_radial_range"
#    "do_poisson"
#    "delta_dummy"
#    "nbpt_azim"
#    "flat_field"
#    "radial_range_min"
#    "dark_current"
#    "do_polarization"
#    "mask_file"
#    "detector"
#    "unit"
#    "radial_range_max"
#    "val_dummy"
#    "do_dummy"
#    "method"
# }

    def get_json_config(self):
        """return configuration as a JSON string"""
        pass  # TODO

    def save_config(self, filename=None):
        if not filename:
            filename = self.config_file

    def warmup(self, sync=False):
        """
        Process a dummy image to ensure everything is initialized

        :param sync: wait for processing to be finished

        """
        t = threading.Thread(target=self.process,
                             name="init2d",
                             args=(numpy.zeros(self.shape, dtype=numpy.float32),))
        t.start()
        if sync:
            t.join()

    def get_normalization_factor(self):
        with self._sem:
            return self._normalization_factor

    def set_normalization_factor(self, value):
        with self._sem:
            self._normalization_factor = value
    normalization_factor = property(get_normalization_factor, set_normalization_factor)


class PixelwiseWorker(object):
    """
    Simple worker doing dark, flat, solid angle and polarization correction
    """
    def __init__(self, dark=None, flat=None, solidangle=None, polarization=None,
                 mask=None, dummy=None, delta_dummy=None, device=None):
        """Constructor of the worker

        :param dark: array
        :param flat: array
        :param solidangle: solid-angle array
        :param polarization: numpy array with 2D polarization corrections
        :param device: Used to influance OpenCL behavour: can be "cpu", "GPU", "Acc" or even an OpenCL context
        """
        self.ctx = None
        if dark is not None:
            self.dark = numpy.ascontiguousarray(dark, dtype=numpy.float32)
        else:
            self.dark = None
        if flat is not None:
            self.flat = numpy.ascontiguousarray(flat, dtype=numpy.float32)
        else:
            self.flat = None
        if solidangle is not None:
            self.solidangle = numpy.ascontiguousarray(solidangle, dtype=numpy.float32)
        else:
            self.solidangle = None
        if polarization is not None:
            self.polarization = numpy.ascontiguousarray(polarization, dtype=numpy.float32)
        else:
            self.polarization = None

        if mask is None:
            self.mask = False
        elif mask.min() < 0 and mask.max() == 0:  # 0 is valid, <0 is invalid
            self.mask = (mask < 0).astype(numpy.int8)
        else:
            self.mask = mask.astype(numpy.int8)

        self.dummy = dummy
        self.delta_dummy = delta_dummy
        if device is not None:
            logger.warning("GPU is not yet implemented")

    def process(self, data, normalization_factor=None):
        """
        Process the data and apply a normalization factor
        :param data: input data
        :param normalization: normalization factor
        :return: processed data
        """
        if preproc is not None:
            proc_data = preproc(data,
                                dark=self.dark,
                                flat=self.flat,
                                solidangle=self.solidangle,
                                polarization=self.polarization,
                                absorption=None,
                                mask=self.mask,
                                dummy=self.dummy,
                                delta_dummy=self.delta_dummy,
                                normalization_factor=normalization_factor,
                                empty=None)
        else:
            if self.dummy is not None:
                if self.delta_dummy is None:
                    self.mask = numpy.logical_or((data == self.dummy), self.mask)
                else:
                    self.mask = numpy.logical_or(abs(data - self.dummy) <= self.delta_dummy,
                                                 self.mask)
                do_mask = True
            else:
                do_mask = (self.mask is not False)
            # Explicitly make an copy !
            proc_data = numpy.array(data, dtype=numpy.float32)
            if self.dark is not None:
                proc_data -= self.dark
            if self.flat is not None:
                proc_data /= self.flat
            if self.solidangle is not None:
                proc_data /= self.solidangle
            if self.polarization is not None:
                proc_data /= self.polarization
            if normalization_factor is not None:
                proc_data /= normalization_factor
            if do_mask:
                proc_data[self.mask] = self.dummy or 0
        return proc_data


class DistortionWorker(object):
    """
    Simple worker doing dark, flat, solid angle and polarization correction
    """
    def __init__(self, detector=None, dark=None, flat=None, solidangle=None, polarization=None,
                 mask=None, dummy=None, delta_dummy=None, device=None):
        """Constructor of the worker
        :param dark: array
        :param flat: array
        :param solidangle: solid-angle array
        :param polarization: numpy array with 2D polarization corrections
        :param device: Used to influance OpenCL behavour: can be "cpu", "GPU", "Acc" or even an OpenCL context

        """

        self.ctx = None
        if dark is not None:
            self.dark = numpy.ascontiguousarray(dark, dtype=numpy.float32)
        else:
            self.dark = None
        if flat is not None:
            self.flat = numpy.ascontiguousarray(flat, dtype=numpy.float32)
        else:
            self.flat = None
        if solidangle is not None:
            self.solidangle = numpy.ascontiguousarray(solidangle, dtype=numpy.float32)
        else:
            self.solidangle = None
        if polarization is not None:
            self.polarization = numpy.ascontiguousarray(polarization, dtype=numpy.float32)
        else:
            self.polarization = None

        if mask is None:
            self.mask = False
        elif mask.min() < 0 and mask.max() == 0:  # 0 is valid, <0 is invalid
            self.mask = (mask < 0)
        else:
            self.mask = mask.astype(bool)

        self.dummy = dummy
        self.delta_dummy = delta_dummy
        if device is not None:
            logger.warning("GPU is not yet implemented")

        if detector is None:
            self.distortion = None
        else:
            self.distortion = Distortion(detector, method="LUT", device=device,
                                         mask=self.mask, empty=self.dummy or 0)

    def process(self, data, normalization_factor=1.0):
        """
        Process the data and apply a normalization factor
        :param data: input data
        :param normalization: normalization factor
        :return: processed data
        """
        if preproc is not None:
            proc_data = preproc(data,
                                dark=self.dark,
                                flat=self.flat,
                                solidangle=self.solidangle,
                                polarization=self.polarization,
                                absorption=None,
                                mask=self.mask,
                                dummy=self.dummy,
                                delta_dummy=self.delta_dummy,
                                normalization_factor=normalization_factor,
                                empty=None)
        else:
            if self.dummy is not None:
                if self.delta_dummy is None:
                    self.mask = numpy.logical_or((data == self.dummy), self.mask)
                else:
                    self.mask = numpy.logical_or(abs(data - self.dummy) <= self.delta_dummy,
                                                 self.mask)
                do_mask = True
            else:
                do_mask = (self.mask is not False)
            # Explicitly make an copy !
            proc_data = numpy.array(data, dtype=numpy.float32)
            if self.dark is not None:
                proc_data -= self.dark
            if self.flat is not None:
                proc_data /= self.flat
            if self.solidangle is not None:
                proc_data /= self.solidangle
            if self.polarization is not None:
                proc_data /= self.polarization
            if normalization_factor is not None:
                proc_data /= normalization_factor
            if do_mask:
                proc_data[self.mask] = self.dummy or 0

        if self.distortion is not None:
            return self.distortion.correct(proc_data, self.dummy, self.delta_dummy)
        else:
            return data

#!/usr/bin/env python
# -*- coding: utf-8 -*-
#
#    Project: Azimuthal integration
#             https://github.com/silx-kit/pyFAI
#
#    Copyright (C) 2015-2016 European Synchrotron Radiation Facility, Grenoble, France
#
#    Principal author:       <NAME> (<EMAIL>)
#
# 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.

"""This module contains the Worker class:

A tool able to perform azimuthal integration with:
additional saving capabilities like

- save as 2/3D structure in a HDF5 File
- read from HDF5 files

Aims at being integrated into a plugin like LImA or as model for the GUI

The configuration of this class is mainly done via a dictionary transmitted as a JSON string:
Here are the valid keys:

- "dist"
- "poni1"
- "poni2"
- "rot1"
- "rot3"
- "rot2"
- "pixel1"
- "pixel2"
- "splineFile"
- "wavelength"
- "poni" #path of the file
- "chi_discontinuity_at_0"
- "do_mask"
- "do_dark"
- "do_azimuthal_range"
- "do_flat"
- "do_2D"
- "azimuth_range_min"
- "azimuth_range_max"
- "polarization_factor"
- "nbpt_rad"
- "do_solid_angle"
- "do_radial_range"
- "do_poisson"
- "delta_dummy"
- "nbpt_azim"
- "flat_field"
- "radial_range_min"
- "dark_current"
- "do_polarization"
- "mask_file"
- "detector"
- "unit"
- "radial_range_max"
- "val_dummy"
- "do_dummy"
- "method"
"""


from __future__ import with_statement, print_function, division

__author__ = "<NAME>"
__contact__ = "<EMAIL>"
__license__ = "MIT"
__copyright__ = "European Synchrotron Radiation Facility, Grenoble, France"
__date__ = "10/01/2018"
__status__ = "development"

import threading
import os.path
import logging
import json

logger = logging.getLogger(__name__)

import numpy
import fabio
from .detectors import detector_factory
from .azimuthalIntegrator import AzimuthalIntegrator
from .distortion import Distortion
from . import units
try:
    from .ext.preproc import preproc
except ImportError as err:
    logger.warning("Unable to import preproc: %s", err)
    preproc = None
# from .io import h5py, HDF5Writer


def make_ai(config):
    """Create an Azimuthal integrator from the configuration
    stand alone function !

    :param config: dict with all parameters
    :return: configured (but uninitialized) AzimuthalIntgrator
    """
    poni = config.get("poni")
    if poni and os.path.isfile(poni):
        ai = AzimuthalIntegrator.sload(poni)
    else:
        ai = AzimuthalIntegrator()

    detector = config.get("detector", None)
    if detector:
        ai.detector = detector_factory(detector)

    wavelength = config.get("wavelength", 0)
    if wavelength:
        if wavelength <= 0 or wavelength > 1e-6:
            logger.warning("Wavelength is in meter ... unlikely value %s", wavelength)
        ai.wavelength = wavelength

    splinefile = config.get("splineFile")
    if splinefile and os.path.isfile(splinefile):
        ai.detector.splineFile = splinefile

    for key in ("pixel1", "pixel2", "dist", "poni1", "poni2", "rot1", "rot2", "rot3"):
        value = config.get(key)
        if value is not None:
            ai.__setattr__(key, value)
    if config.get("chi_discontinuity_at_0"):
        ai.setChiDiscAtZero()

    mask_file = config.get("mask_file")
    if mask_file and config.get("do_mask"):
        if os.path.exists(mask_file):
            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:
                ai.mask = mask

    dark_files = [i.strip() for i in config.get("dark_current", "").split(",")
                  if os.path.isfile(i.strip())]
    if dark_files and config.get("do_dark"):
        ai.set_darkfiles(dark_files)

    flat_files = [i.strip() for i in config.get("flat_field", "").split(",")
                  if os.path.isfile(i.strip())]
    if flat_files and config.get("do_flat"):
        ai.set_flatfiles(flat_files)

    return ai


class Worker(object):
    def __init__(self, azimuthalIntegrator=None,
                 shapeIn=(2048, 2048), shapeOut=(360, 500),
                 unit="r_mm", dummy=None, delta_dummy=None,
                 azimuthalIntgrator=None):
        """
        :param azimuthalIntegrator AzimuthalIntegrator: pyFAI.AzimuthalIntegrator instance
        :param azimuthalIntgrator AzimuthalIntegrator: pyFAI.AzimuthalIntegrator instance (deprecated)
        :param shapeIn: image size in input
        :param shapeOut: Integrated size: can be (1,2000) for 1D integration
        :param unit: can be "2th_deg, r_mm or q_nm^-1 ...
        """
        # TODO remove it in few month (added on 2016-08-04)
        if azimuthalIntgrator is not None:
            logger.warning("'Worker(azimuthalIntgrator=...)' parameter is deprecated cause it contains a typo. Please use 'azimuthalIntegrator='")
            azimuthalIntegrator = azimuthalIntgrator

        self._sem = threading.Semaphore()
        if azimuthalIntegrator is None:
            self.ai = AzimuthalIntegrator()
        else:
            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()
        self._normalization_factor = None  # Value of the monitor: divides the intensity by this value for normalization
        self.nbpt_azim, self.nbpt_rad = shapeOut
        self._unit = units.to_unit(unit)
        self.polarization_factor = None
        self.dummy = dummy
        self.delta_dummy = delta_dummy
        self.correct_solid_angle = True
        self.dark_current_image = None
        self.flat_field_image = None
        self.mask_image = None
        self.subdir = ""
        self.extension = None
        self.do_poisson = None
        self.needs_reset = True
        self.output = "numpy"  # exports as numpy array by default
        self.shape = shapeIn
        self.method = "csr"
        self.radial = None
        self.azimuthal = None
        self.radial_range = None
        self.azimuth_range = None
        self.safe = True

    def __repr__(self):
        """
        pretty print of myself
        """
        lstout = ["Azimuthal Integrator:", self.ai.__repr__(),
                  "Input image shape: %s" % list(self.shape),
                  "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,
                  "Correct for solid angle: %s" % self.correct_solid_angle,
                  "Polarization factor: %s" % self.polarization_factor,
                  "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),
                  "Radial range: %s" % self.radial_range,
                  "Azimuth range: %s" % self.azimuth_range]
        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
        """
        if self.needs_reset:
            with self._sem:
                if self.needs_reset:
                    self.ai.reset()
                    self.needs_reset = False
        # print self.__repr__()

    def reconfig(self, shape=(2048, 2048), sync=False):
        """
        This is just to force the integrator to initialize with a given input image shape

        :param shape: shape of the input image
        :param sync: return only when synchronized
        """
        self.shape = shape
        self.ai.reset()
        self.warmup(sync)

    def process(self, data, normalization_factor=1.0, writer=None, metadata=None):
        """
        Process a frame
        #TODO:
        dark, flat, sa are missing

        :param data: numpy array containing the input image
        :param writer: An open writer in which 'write' will be called with the result of the integration
        """

        with self._sem:
            monitor = self._normalization_factor * normalization_factor if self._normalization_factor else normalization_factor
        kwarg = {"unit": self.unit,
                 "dummy": self.dummy,
                 "delta_dummy": self.delta_dummy,
                 "method": self.method,
                 "polarization_factor": self.polarization_factor,
                 # "filename": None,
                 "safe": self.safe,
                 "data": data,
                 "correctSolidAngle": self.correct_solid_angle,
                 "safe": self.safe
                 }

        if metadata is not None:
            kwarg["metadata"] = metadata

        if monitor is not None:
            kwarg["normalization_factor"] = monitor

        if self.do_2D():
            kwarg["npt_rad"] = self.nbpt_rad
            kwarg["npt_azim"] = self.nbpt_azim
            # if "filename" in kwarg:
            #    if self.extension:
            #        kwarg["filename"] += self.extension
            #    else:
            #        kwarg["filename"] += ".azim"
        else:
            kwarg["npt"] = self.nbpt_rad
            # if "filename" in kwarg:
            #    if self.extension:
            #        kwarg["filename"] += self.extension
            #    else:
            #        kwarg["filename"] += ".xy"
        if self.do_poisson:
            kwarg["error_model"] = "poisson"
        else:
            kwarg["error_model"] = None

        if self.radial_range is not None:
            kwarg["radial_range"] = self.radial_range

        if self.azimuth_range is not None:
            kwarg["azimuth_range"] = self.azimuth_range

        try:
            if self.do_2D():
                integrated_result = self.ai.integrate2d(**kwarg)
                self.radial = integrated_result.radial
                self.azimuthal = integrated_result.azimuthal
                result = integrated_result.intensity
            else:
                integrated_result = self.ai.integrate1d(**kwarg)
                self.radial = integrated_result.radial
                self.azimuthal = None
                result = numpy.vstack(integrated_result).T

        except Exception as err:
            err2 = ["error in integration",
                    str(err),
                    "data.shape: %s" % (data.shape,),
                    "data.size: %s" % data.size,
                    "ai:",
                    str(self.ai),
                    "csr:",
                    # str(self.ai._csr_integrator),
                    # "csr size: %s" % self.ai._lut_integrator.size
                    ]
            logger.error("; ".join(err2))
            raise err

        if writer is not None:
            writer.write(integrated_result)

        if self.output == "numpy":
            return result

    def setSubdir(self, path):
        """
        Set the relative or absolute path for processed data
        """
        self.subdir = path

    def setExtension(self, ext):
        """
        enforce the extension of the processed data file written
        """
        if ext:
            self.extension = ext
        else:
            self.extension = None

    def setDarkcurrentFile(self, imagefile):
        self.ai.set_darkfiles(imagefile)
        self.dark_current_image = imagefile

    def setFlatfieldFile(self, imagefile):
        self.ai.set_flatfiles(imagefile)
        self.flat_field_image = imagefile

    def setJsonConfig(self, jsonconfig):
        print("start config ...")
        if os.path.isfile(jsonconfig):
            config = json.load(open(jsonconfig, "r"))
        else:
            config = json.loads(jsonconfig)
        if "poni" in config:
            poni = config["poni"]
            if poni and os.path.isfile(poni):
                self.ai = AzimuthalIntegrator.sload(poni)

        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["nbpt_rad"])
        self.unit = units.to_unit(config.get("unit", units.TTH_DEG))
        self.do_poisson = config.get("do_poisson")
        if config.get("do_polarization"):
            self.polarization_factor = config.get("polarization_factor")
        else:
            self.polarization_factor = None

        if config.get("do_OpenCL"):
            self.method = "csr_ocl"
        else:
            self.method = "csr"

        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 set_unit(self, value):
        self._unit = units.to_unit(value)

    def get_unit(self):
        return self._unit

    unit = property(get_unit, set_unit)

    def set_error_model(self, value):
        if value == "poisson":
            self.do_poisson = True
        elif value is None or value == "":
            self.do_poisson = False
        else:
            raise RuntimeError("Unsupported error model '%s'" % value)

    def get_error_model(self):
        if self.do_poisson:
            return "poisson"
        return None
    error_model = property(get_error_model, set_error_model)

    def get_config(self):
        """return configuration as a dictionary"""
        config = {"unit": str(self.unit)}
        for key in ["dist", "poni1", "poni2", "rot1", "rot3", "rot2", "pixel1", "pixel2", "splineFile", "wavelength"]:
            try:
                config[key] = self.ai.__getattribute__(key)
            except:
                pass
        for key in ["nbpt_azim", "nbpt_rad", "polarization_factor", "dummy", "delta_dummy",
                    "correct_solid_angle", "dark_current_image", "flat_field_image",
                    "mask_image", "do_poisson", "shape", "method"]:
            try:
                config[key] = self.__getattribute__(key)
            except:
                pass

        return config
#
#    "poni" #path of the file
#
#    "chi_discontinuity_at_0"
#    "do_mask"
#    "do_dark"
#    "do_azimuthal_range"
#    "do_flat"
#    "do_2D"
#    "azimuth_range_min"
#    "azimuth_range_max"
#
#    "polarization_factor"
#    "nbpt_rad"
#    "do_solid_angle"
#    "do_radial_range"
#    "do_poisson"
#    "delta_dummy"
#    "nbpt_azim"
#    "flat_field"
#    "radial_range_min"
#    "dark_current"
#    "do_polarization"
#    "mask_file"
#    "detector"
#    "unit"
#    "radial_range_max"
#    "val_dummy"
#    "do_dummy"
#    "method"
# }

    def get_json_config(self):
        """return configuration as a JSON string"""
        pass  # TODO

    def save_config(self, filename=None):
        if not filename:
            filename = self.config_file

    def warmup(self, sync=False):
        """
        Process a dummy image to ensure everything is initialized

        :param sync: wait for processing to be finished

        """
        t = threading.Thread(target=self.process,
                             name="init2d",
                             args=(numpy.zeros(self.shape, dtype=numpy.float32),))
        t.start()
        if sync:
            t.join()

    def get_normalization_factor(self):
        with self._sem:
            return self._normalization_factor

    def set_normalization_factor(self, value):
        with self._sem:
            self._normalization_factor = value
    normalization_factor = property(get_normalization_factor, set_normalization_factor)


class PixelwiseWorker(object):
    """
    Simple worker doing dark, flat, solid angle and polarization correction
    """
    def __init__(self, dark=None, flat=None, solidangle=None, polarization=None,
                 mask=None, dummy=None, delta_dummy=None, device=None):
        """Constructor of the worker

        :param dark: array
        :param flat: array
        :param solidangle: solid-angle array
        :param polarization: numpy array with 2D polarization corrections
        :param device: Used to influance OpenCL behavour: can be "cpu", "GPU", "Acc" or even an OpenCL context
        """
        self.ctx = None
        if dark is not None:
            self.dark = numpy.ascontiguousarray(dark, dtype=numpy.float32)
        else:
            self.dark = None
        if flat is not None:
            self.flat = numpy.ascontiguousarray(flat, dtype=numpy.float32)
        else:
            self.flat = None
        if solidangle is not None:
            self.solidangle = numpy.ascontiguousarray(solidangle, dtype=numpy.float32)
        else:
            self.solidangle = None
        if polarization is not None:
            self.polarization = numpy.ascontiguousarray(polarization, dtype=numpy.float32)
        else:
            self.polarization = None

        if mask is None:
            self.mask = False
        elif mask.min() < 0 and mask.max() == 0:  # 0 is valid, <0 is invalid
            self.mask = (mask < 0).astype(numpy.int8)
        else:
            self.mask = mask.astype(numpy.int8)

        self.dummy = dummy
        self.delta_dummy = delta_dummy
        if device is not None:
            logger.warning("GPU is not yet implemented")

    def process(self, data, normalization_factor=None):
        """
        Process the data and apply a normalization factor
        :param data: input data
        :param normalization: normalization factor
        :return: processed data
        """
        if preproc is not None:
            proc_data = preproc(data,
                                dark=self.dark,
                                flat=self.flat,
                                solidangle=self.solidangle,
                                polarization=self.polarization,
                                absorption=None,
                                mask=self.mask,
                                dummy=self.dummy,
                                delta_dummy=self.delta_dummy,
                                normalization_factor=normalization_factor,
                                empty=None)
        else:
            if self.dummy is not None:
                if self.delta_dummy is None:
                    self.mask = numpy.logical_or((data == self.dummy), self.mask)
                else:
                    self.mask = numpy.logical_or(abs(data - self.dummy) <= self.delta_dummy,
                                                 self.mask)
                do_mask = True
            else:
                do_mask = (self.mask is not False)
            # Explicitly make an copy !
            proc_data = numpy.array(data, dtype=numpy.float32)
            if self.dark is not None:
                proc_data -= self.dark
            if self.flat is not None:
                proc_data /= self.flat
            if self.solidangle is not None:
                proc_data /= self.solidangle
            if self.polarization is not None:
                proc_data /= self.polarization
            if normalization_factor is not None:
                proc_data /= normalization_factor
            if do_mask:
                proc_data[self.mask] = self.dummy or 0
        return proc_data


class DistortionWorker(object):
    """
    Simple worker doing dark, flat, solid angle and polarization correction
    """
    def __init__(self, detector=None, dark=None, flat=None, solidangle=None, polarization=None,
                 mask=None, dummy=None, delta_dummy=None, device=None):
        """Constructor of the worker
        :param dark: array
        :param flat: array
        :param solidangle: solid-angle array
        :param polarization: numpy array with 2D polarization corrections
        :param device: Used to influance OpenCL behavour: can be "cpu", "GPU", "Acc" or even an OpenCL context

        """

        self.ctx = None
        if dark is not None:
            self.dark = numpy.ascontiguousarray(dark, dtype=numpy.float32)
        else:
            self.dark = None
        if flat is not None:
            self.flat = numpy.ascontiguousarray(flat, dtype=numpy.float32)
        else:
            self.flat = None
        if solidangle is not None:
            self.solidangle = numpy.ascontiguousarray(solidangle, dtype=numpy.float32)
        else:
            self.solidangle = None
        if polarization is not None:
            self.polarization = numpy.ascontiguousarray(polarization, dtype=numpy.float32)
        else:
            self.polarization = None

        if mask is None:
            self.mask = False
        elif mask.min() < 0 and mask.max() == 0:  # 0 is valid, <0 is invalid
            self.mask = (mask < 0)
        else:
            self.mask = mask.astype(bool)

        self.dummy = dummy
        self.delta_dummy = delta_dummy
        if device is not None:
            logger.warning("GPU is not yet implemented")

        if detector is None:
            self.distortion = None
        else:
            self.distortion = Distortion(detector, method="LUT", device=device,
                                         mask=self.mask, empty=self.dummy or 0)

    def process(self, data, normalization_factor=1.0):
        """
        Process the data and apply a normalization factor
        :param data: input data
        :param normalization: normalization factor
        :return: processed data
        """
        if preproc is not None:
            proc_data = preproc(data,
                                dark=self.dark,
                                flat=self.flat,
                                solidangle=self.solidangle,
                                polarization=self.polarization,
                                absorption=None,
                                mask=self.mask,
                                dummy=self.dummy,
                                delta_dummy=self.delta_dummy,
                                normalization_factor=normalization_factor,
                                empty=None)
        else:
            if self.dummy is not None:
                if self.delta_dummy is None:
                    self.mask = numpy.logical_or((data == self.dummy), self.mask)
                else:
                    self.mask = numpy.logical_or(abs(data - self.dummy) <= self.delta_dummy,
                                                 self.mask)
                do_mask = True
            else:
                do_mask = (self.mask is not False)
            # Explicitly make an copy !
            proc_data = numpy.array(data, dtype=numpy.float32)
            if self.dark is not None:
                proc_data -= self.dark
            if self.flat is not None:
                proc_data /= self.flat
            if self.solidangle is not None:
                proc_data /= self.solidangle
            if self.polarization is not None:
                proc_data /= self.polarization
            if normalization_factor is not None:
                proc_data /= normalization_factor
            if do_mask:
                proc_data[self.mask] = self.dummy or 0

        if self.distortion is not None:
            return self.distortion.correct(proc_data, self.dummy, self.delta_dummy)
        else:
            return data
#!/usr/bin/env python # -*- coding: utf-8 -*- # #    Project: Azimuthal integration #             https://github.com/silx-kit/pyFAI # #    Copyright (C) 2015-2016 European Synchrotron Radiation Facility, Grenoble, France # #    Principal author:       <NAME> (<EMAIL>) # # 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. This module contains the Worker class:  A tool able to perform azimuthal integration with: additional saving capabilities like  - save as 2/3D structure in a HDF5 File - read from HDF5 files  Aims at being integrated into a plugin like LImA or as model for the GUI  The configuration of this class is mainly done via a dictionary transmitted as a JSON string: Here are the valid keys:  - "dist" - "poni1" - "poni2" - "rot1" - "rot3" - "rot2" - "pixel1" - "pixel2" - "splineFile" - "wavelength" - "poni" #path of the file - "chi_discontinuity_at_0" - "do_mask" - "do_dark" - "do_azimuthal_range" - "do_flat" - "do_2D" - "azimuth_range_min" - "azimuth_range_max" - "polarization_factor" - "nbpt_rad" - "do_solid_angle" - "do_radial_range" - "do_poisson" - "delta_dummy" - "nbpt_azim" - "flat_field" - "radial_range_min" - "dark_current" - "do_polarization" - "mask_file" - "detector" - "unit" - "radial_range_max" - "val_dummy" - "do_dummy" - "method" # from .io import h5py, HDF5Writer Create an Azimuthal integrator from the configuration     stand alone function !      :param config: dict with all parameters     :return: configured (but uninitialized) AzimuthalIntgrator :param azimuthalIntegrator AzimuthalIntegrator: pyFAI.AzimuthalIntegrator instance         :param azimuthalIntgrator AzimuthalIntegrator: pyFAI.AzimuthalIntegrator instance (deprecated)         :param shapeIn: image size in input         :param shapeOut: Integrated size: can be (1,2000) for 1D integration         :param unit: can be "2th_deg, r_mm or q_nm^-1 ... # TODO remove it in few month (added on 2016-08-04) #        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() # Value of the monitor: divides the intensity by this value for normalization # exports as numpy array by default pretty print of myself this is just to force the integrator to initialize # print self.__repr__() This is just to force the integrator to initialize with a given input image shape          :param shape: shape of the input image         :param sync: return only when synchronized Process a frame         #TODO:         dark, flat, sa are missing          :param data: numpy array containing the input image         :param writer: An open writer in which 'write' will be called with the result of the integration # "filename": None, # if "filename" in kwarg: #    if self.extension: #        kwarg["filename"] += self.extension #    else: #        kwarg["filename"] += ".azim" # if "filename" in kwarg: #    if self.extension: #        kwarg["filename"] += self.extension #    else: #        kwarg["filename"] += ".xy" # str(self.ai._csr_integrator), # "csr size: %s" % self.ai._lut_integrator.size Set the relative or absolute path for processed data enforce the extension of the processed data file written # For now we do not calculate the LUT as the size of the input image is unknown return configuration as a dictionary # #    "poni" #path of the file # #    "chi_discontinuity_at_0" #    "do_mask" #    "do_dark" #    "do_azimuthal_range" #    "do_flat" #    "do_2D" #    "azimuth_range_min" #    "azimuth_range_max" # #    "polarization_factor" #    "nbpt_rad" #    "do_solid_angle" #    "do_radial_range" #    "do_poisson" #    "delta_dummy" #    "nbpt_azim" #    "flat_field" #    "radial_range_min" #    "dark_current" #    "do_polarization" #    "mask_file" #    "detector" #    "unit" #    "radial_range_max" #    "val_dummy" #    "do_dummy" #    "method" # } return configuration as a JSON string # TODO Process a dummy image to ensure everything is initialized          :param sync: wait for processing to be finished Simple worker doing dark, flat, solid angle and polarization correction Constructor of the worker          :param dark: array         :param flat: array         :param solidangle: solid-angle array         :param polarization: numpy array with 2D polarization corrections         :param device: Used to influance OpenCL behavour: can be "cpu", "GPU", "Acc" or even an OpenCL context # 0 is valid, <0 is invalid Process the data and apply a normalization factor         :param data: input data         :param normalization: normalization factor         :return: processed data # Explicitly make an copy ! Simple worker doing dark, flat, solid angle and polarization correction Constructor of the worker         :param dark: array         :param flat: array         :param solidangle: solid-angle array         :param polarization: numpy array with 2D polarization corrections         :param device: Used to influance OpenCL behavour: can be "cpu", "GPU", "Acc" or even an OpenCL context # 0 is valid, <0 is invalid Process the data and apply a normalization factor         :param data: input data         :param normalization: normalization factor         :return: processed data # Explicitly make an copy !