calculation.py

#!/usr/bin/env python
##############################################################################
#
# PDFgui            by DANSE Diffraction group
#                   Simon J. L. Billinge
#                   (c) 2006 trustees of the Michigan State University.
#                   All rights reserved.
#
# File coded by:    Pavol Juhas, Jiwu Liu
#
# See AUTHORS.txt for a list of people who contributed.
# See LICENSE.txt for license information.
#
##############################################################################

"""class Calculation for performing PDF simulation from model structure.
"""

import copy
import math

from diffpy.pdfgui.control.controlerrors import ControlConfigError, ControlKeyError, ControlValueError
from diffpy.pdfgui.control.pdfcomponent import PDFComponent
from diffpy.pdfgui.utils import pickle_loads, safeCPickleDumps


class Calculation(PDFComponent):
    """Perform a theoretical computation of PDF from model structure.

    Data members:

    rmin   -- read-only lower boundary of rcalc, change with setRGrid()
    rstep  -- read-only r-grid step, use setRGrid() to change it
    rmax   -- read-only upper boundary of rcalc, change with setRGrid()
    rlen   -- read-only number of r points, set by setRGrid().
              To be used in PdfFit.alloc()
    rcalc  -- list of r values, this is set after calculation is finished
    Gcalc  -- list of calculated G values
    stype  -- scattering type, 'X' or 'N'
    qmax   -- maximum value of Q in inverse Angstroms.  Termination ripples
              are ignored for qmax=0.
    qdamp  -- specifies width of Gaussian damping factor in pdf_obs due
              to imperfect Q resolution
    qbroad -- quadratic peak broadening factor related to dataset
    spdiameter -- particle diameter for shape damping function.
              Note: this attribute has been moved to FitStructure and is
              maintained only for backward compatible reading of PDFgui
              project files.
    dscale -- total scale factor
    """

    def __init__(self, name):
        """initialize Calculation

        name -- calculation name
        """
        PDFComponent.__init__(self, name)

        # rmin, rstep, rmax, rlen, rcalc
        self.setRGrid(rmin=0.1, rstep=0.01, rmax=10.0)
        self.rcalc = []
        self.Gcalc = []
        self.stype = "X"
        # user must specify qmax to get termination ripples
        self.qmax = 0.0
        self.qdamp = 0.001
        self.qbroad = 0.0
        self.spdiameter = None
        self.dscale = 1.0
        return

    def _getStrId(self):
        """make a string identifier

        return value: string id
        """
        return "c_" + self.name

    def setRGrid(self, rmin=None, rstep=None, rmax=None):
        """Change specified r-grid parameters (rmin, rstep, rmax).
        Adjust rmax for integer number of steps.

        rmin  -- new low rcalc boundary
        rstep -- new r-grid step
        rmax  -- new maximum rcalc, slightly adjusted to accommodate rstep

        No return value.
        Raise ControlValueError for invalid range specification.
        """
        if rmin is None:
            rmin = self.rmin
        if rstep is None:
            rstep = self.rstep
        if rmax is None:
            rmax = self.rmax
        rstep = float(rstep)
        # check if arguments are valid
        if not rmin > 0:
            emsg = "Low range boundary must be positive."
            raise ControlValueError(emsg)
        if not rmin < rmax:
            emsg = "Invalid range boundaries."
            raise ControlValueError(emsg)
        if rstep <= 0.0:
            emsg = "Invalid value of rstep, rstep must be positive."
            raise ControlValueError(emsg)
        # find number of r bins
        nbins = int(math.ceil((rmax - rmin) / rstep))
        # check for overshot due to round-off
        epsilonr = 1.0e-8 * rstep
        deltarmax = abs(rmin + (nbins - 1) * rstep - rmax)
        if nbins > 1 and deltarmax < epsilonr:
            nbins -= 1
        # All went well, let us go ahead and set the attributes.
        self.rmin = rmin
        self.rstep = rstep
        self.rmax = rmin + nbins * rstep
        self.rlen = nbins + 1
        return

    def start(self):
        """entry function for calculation"""
        from diffpy.pdfgui.control.fitting import getEngineExceptions, handleEngineException

        try:
            self.calculate()
        except getEngineExceptions() as error:
            gui = self.owner.controlCenter.gui
            handleEngineException(error, gui)

        # inform gui of change ( when engine calculation fails, it will update gui as well )
        gui = self.owner.controlCenter.gui
        if gui:
            gui.postEvent(gui.OUTPUT, None)
            gui.postEvent(gui.PLOTNOW, self)
        return

    def calculate(self):
        """do the real calculation"""
        # clean up old results
        self.rcalc = []
        self.Gcalc = []

        # do the job
        if len(self.owner.strucs) == 0:
            raise ControlConfigError("No structure is given for calculation")

        # make sure parameters are initialized
        self.owner.updateParameters()
        from diffpy.pdffit2 import PdfFit

        server = PdfFit()

        # structure needs to be read before dataset allocation
        for struc in self.owner.strucs:
            server.read_struct_string(struc.writeStr("pdffit"))
            for key, var in struc.constraints.items():
                server.constrain(key, var.formula)

        # set up dataset
        server.alloc(self.stype, self.qmax, self.qdamp, self.rmin, self.rmax, self.rlen)
        server.setvar("qbroad", self.qbroad)
        server.setvar("dscale", self.dscale)

        # phase related variables
        # pair selection applies to current dataset,
        # therefore it has to be done after alloc
        for phaseidx0, struc in enumerate(self.owner.strucs):
            phaseidx1 = phaseidx0 + 1
            server.setphase(phaseidx1)
            server.setvar("pscale", struc.getvar("pscale"))
            server.setvar("spdiameter", struc.getvar("spdiameter"))
            struc.applyPairSelection(server, phaseidx1)

        # set up parameters
        for index, par in self.owner.parameters.items():
            server.setpar(index, par.initialValue())  # info[0] = init value
            # fix if fixed.  Note: all parameters are free after server.reset().
            if par.fixed:
                server.fixpar(index)

        # all ready here
        server.calc()

        # get results
        self.rcalc = server.getR()
        self.Gcalc = server.getpdf_fit()

    def write(self, filename):
        """write this calculated PDF to a file

        filename -- name of file to write to

        No return value.
        """
        txt = self.writeStr()
        f = open(filename, "w")
        f.write(txt)
        f.close()
        return

    def writeStr(self):
        """String representation of calculated PDF.

        Returns data string
        """
        import time
        from getpass import getuser

        lines = []
        # write metadata
        lines.extend(
            [
                "History written: " + time.ctime(),
                "produced by " + getuser(),
                "##### PDFgui calculation",
            ]
        )
        # stype
        if self.stype == "X":
            lines.append("stype=X  x-ray scattering")
        elif self.stype == "N":
            lines.append("stype=N  neutron scattering")
        # dscale
        if self.dscale:
            lines.append("dscale=%g" % self.dscale)
        # qmax
        if self.qmax == 0:
            qmax_line = "qmax=0   correction not applied"
        else:
            qmax_line = "qmax=%.2f" % self.qmax
        lines.append(qmax_line)
        # qdamp
        if isinstance(self.qdamp, float):
            lines.append("qdamp=%g" % self.qdamp)
        # qbroad
        if self.qbroad:
            lines.append("qbroad=%g" % self.qbroad)
        # write data:
        lines.append("##### start data")
        lines.append("#L r(A) G(r)")
        for i in range(len(self.rcalc)):
            lines.append("%g %g" % (self.rcalc[i], self.Gcalc[i]))
        # lines are ready here
        datastring = "\n".join(lines) + "\n"
        return datastring

    def load(self, z, subpath):
        """load data from a zipped project file

        z       -- zipped project file
        subpath -- path to its own storage within project file

        returns a tree of internal hierachy
        """
        config = pickle_loads(z.read(subpath + "config"))
        self.rmin = config["rmin"]
        self.rstep = config["rstep"]
        self.rmax = config["rmax"]
        self.rlen = config["rlen"]
        self.rcalc = config["rcalc"]
        self.Gcalc = config["Gcalc"]
        self.stype = config["stype"]
        self.qmax = config["qmax"]
        self.qdamp = config.get("qdamp", config.get("qsig"))
        self.qbroad = config.get("qbroad", config.get("qalp", 0.0))
        self.spdiameter = config.get("spdiameter")
        self.dscale = config["dscale"]
        return

    def save(self, z, subpath):
        """save data from a zipped project file

        z       -- zipped project file
        subpath -- path to its own storage within project file
        """
        config = {
            "rmin": self.rmin,
            "rstep": self.rstep,
            "rmax": self.rmax,
            "rlen": self.rlen,
            "rcalc": self.rcalc,
            "Gcalc": self.Gcalc,
            "stype": self.stype,
            "qmax": self.qmax,
            "qdamp": self.qdamp,
            "qbroad": self.qbroad,
            "dscale": self.dscale,
        }
        z.writestr(subpath + "config", safeCPickleDumps(config))
        return

    def copy(self, other=None):
        """copy self to other. if other is None, create new instance

        other -- reference to other object

        returns reference to copied object
        """
        if other is None:
            other = Calculation(self.name)

        # rcalc and Gcalc may be assigned, they get replaced by new lists
        # after every calculation
        assign_attributes = (
            "rmin",
            "rstep",
            "rmax",
            "rlen",
            "rcalc",
            "Gcalc",
            "stype",
            "qmax",
            "qdamp",
            "qbroad",
            "dscale",
        )
        copy_attributes = ()
        for a in assign_attributes:
            setattr(other, a, getattr(self, a))
        for a in copy_attributes:
            setattr(other, a, copy.copy(getattr(self, a)))
        return other

    def getYNames(self):
        """get names of data item which can be plotted as y

        returns a name str list
        """
        return [
            "Gcalc",
        ]

    def getXNames(self):
        """get names of data item which can be plotted as x

        returns a name str list
        """
        return [
            "r",
        ]

    def getData(self, dataname, step=None):
        """get Calculation data member

        name -- data item name
        step -- ignored, just for compatibility with Organizer.getData()

        returns data object, be it a single number, a list, or a list of list
        """
        if dataname not in ["rcalc", "Gcalc"]:
            emsg = "%s is not valid dataname" % dataname
            raise ControlKeyError(emsg)
        return self.__dict__[dataname]

    def getMetaDataNames(self):
        """return all applicable meta data names"""
        # FIXME: Currently we haven't thought about this
        return []

    def getMetaData(self, name):
        """get meta data value

        name -- meta data name
        returns meta data value
        """
        return None


# End of class Calculation

# simple test code
if __name__ == "__main__":
    Calculation("name")

# End of file