#/*##########################################################################
#
# The PyMca X-Ray Fluorescence Toolkit
#
# Copyright (c) 2004-2015 European Synchrotron Radiation Facility
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# This file is part of the PyMca X-ray Fluorescence Toolkit developed at
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__author__ = "V.A. Sole - ESRF Data Analysis"
__contact__ = "sole@esrf.fr"
__license__ = "MIT"
__copyright__ = "European Synchrotron Radiation Facility, Grenoble, France"
__doc__= "Generate specfile from all EPL97 cross sections in keV and barn"
import os
import sys
import EADLSubshells
import EPDL97Parser as EPDLParser
Elements = EPDLParser.Elements
AVOGADRO_NUMBER = EPDLParser.AVOGADRO_NUMBER
import numpy
log = numpy.log
exp = numpy.exp
getTotalCoherentCrossSection = EPDLParser.getTotalCoherentCrossSection
getTotalIncoherentCrossSection = EPDLParser.getTotalIncoherentCrossSection
getTotalPhotoelectricCrossSection = EPDLParser.getTotalPhotoelectricCrossSection
getPartialPhotoelectricCrossSection = EPDLParser.getPartialPhotoelectricCrossSection
getTotalPairCrossSection = EPDLParser.getTotalPairCrossSection
getTotalTripletCrossSection = EPDLParser.getTotalTripletCrossSection

def getHeader(filename):
    text  = '#F %s\n' % filename
    text += '#U00 This file is a direct conversion to specfile format of \n'
    text += '#U01 the original EPDL97 photoelectric cross sections contained\n'
    text += '#U02 in the EPDL97.DAT file from the library.\n'
    text += '#U03 EPDL97 itself can be found at:\n'
    text += '#U04           http://www-nds.iaea.org/epdl97/libsall.htm\n'
    text += '#U05\n'
    text += '#U06 The command used to generate this file has been:\n'
    if len(sys.argv) > 3:
        text += '#U07 %s %s %s %s\n' % (os.path.basename(__file__),\
                                           sys.argv[1], sys.argv[2], sys.argv[3])
    else:
        text += '#U07 %s %s %s\n' % (os.path.basename(__file__),\
                                        sys.argv[1], sys.argv[2])
    text += '\n'
    return text

if __name__ == "__main__":
    if len(sys.argv) < 3:
        print("Usage:")
        print("python EPDL97GenerateCrossSections SPEC_output_filename barns_flag [short_output_flag]")
        sys.exit(0)

    SHORT_OUTPUT_FLAG = 0
    if len(sys.argv) > 3:
        SHORT_OUTPUT_FLAG = int(sys.argv[3])


    fname = sys.argv[1]
    if os.path.exists(fname):
        os.remove(fname)

    if int(sys.argv[2]):
        BARNS = True
    else:
        BARNS = False
    print("BARNS = %s" % BARNS)
    outfile = open(fname, 'wb')
    outfile.write(getHeader(fname))

    shells = EADLSubshells.SHELL_LIST
    bad_shells = ['L (', 'L23',
                  'M (', 'M23', 'M45',
                  'N (', 'N23', 'N45', 'N67',
                  'O (', 'O23', 'O45', 'O67', 'O89',
                  'P (', 'P23', 'P45', 'P67', 'P89', 'P101',
                  'Q (', 'Q23', 'Q45', 'Q67']
    LONG_LABELS = True

    #find the first element for which EPDL has N1 or P1 shell attenuation data
    if SHORT_OUTPUT_FLAG:
        testShell = "N1"
    else:
        testShell = "P1"
    z = 0
    i = 0
    while z == 0:
        i += 1
        try:
            dummy = getPartialPhotoelectricCrossSection(i, testShell, getmode=True)
            z = i
        except IOError:
            pass

    firstNonZeroPhotoelectric = z

    for i in range(1, 101):
        print("i = %d element = %s" % (i, Elements[i-1]))
        #coherent
        energy_cohe, value_cohe, mode_cohe = getTotalCoherentCrossSection(i,
                                                                getmode=True)
        #incoherent
        energy_incohe, value_incohe, mode_incohe = getTotalIncoherentCrossSection(i,
                                                                getmode=True)

        #photoelectric
        energy_photo, value_photo, mode_photo = getTotalPhotoelectricCrossSection(i,
                                                                getmode=True)

        #check to see the energies:
        #for j in range(10):
        #    print energy_cohe[j], energy_incohe[j], energy_photo[j]

        #to select an appropriate energy grid as close as possible to the original
        #while keeping in mind the PyMca goals, I use the coherent energy grid till
        #the non-zero first value of the photoelectric cross section. At that point,
        #I use the photoelectric energy grid.
        energy = numpy.concatenate((energy_cohe[energy_cohe<energy_photo[0]],
                                   energy_photo))

        #now perform a log-log interpolation when needed
        #lin-lin interpolation:
        #
        #              y0 (x1-x) + y1 (x-x0)
        #        y = -------------------------
        #                     x1 - x0
        #
        #log-log interpolation:
        #
        #                  log(y0) * log(x1/x) + log(y1) * log(x/x0)
        #        log(y) = ------------------------------------------
        #                                  log (x1/x0)
        #
        cohe    = numpy.zeros(len(energy), numpy.float64)
        incohe  = numpy.zeros(len(energy), numpy.float64)
        photo   = numpy.zeros(len(energy), numpy.float64)
        total   = numpy.zeros(len(energy), numpy.float64)

        #get the partial photoelectric cross sections
        photo_dict = {}
        photo_label_list = []
        photo_long_label_list = []
        END = False
        for shell in EADLSubshells.SHELL_LIST:
            if shell[0:3] in bad_shells:
                continue
            if shell[0:4] in bad_shells:
                continue
            # do not generate partial photoelectric cross sections for these shells
            if SHORT_OUTPUT_FLAG:
                if shell[0] in ['N', 'O', 'P', 'Q']:
                    continue
            else:
                if shell[0] in ['P', 'Q']:
                    continue
            photo_long_label_list.append(shell)
            actual_shell = shell.replace(' ','').split("(")[0]
            photo_label_list.append(actual_shell)
            photo_dict[actual_shell] = {}
            ene = energy * 1
            v   = photo * 0.0
            value = photo * 0.0
            if not END:
                try:
                    ene, v, mode = getPartialPhotoelectricCrossSection(i, actual_shell,
                                                                    getmode=True)
                    #log-log interpolate in the final energy grid
                    value = photo * 0.0
                    for n in range(len(energy)):
                        x = energy[n]
                        if (x == ene[0]) and (energy[n+1] == x):
                            #avoid entering twice the absorption edges
                            continue
                        if x == ene[0]:
                            value[n]=v[0]
                            continue
                        if x < ene[0]:
                            continue
                        j1 = 0
                        while ene[j1] < x:
                            j1 += 1
                        j0 = j1 - 1
                        x0 = ene[j0]
                        x1 = ene[j1]
                        y0 = v[j0]
                        y1 = v[j1]
                        value[n] = exp((log(y0) * log(x1/x) + log(y1) * log(x/x0))/log(x1/x0))
                except IOError:
                    END = True
                    #print sys.exc_info()
                    ene = energy * 1
                    v   = photo * 0.0
            photo_dict[actual_shell]['read_energy'] = ene
            photo_dict[actual_shell]['read_value']  = v
            photo_dict[actual_shell]['value']  = value

        #coherent needs to interpolate
        indices = numpy.nonzero(energy_cohe<energy_photo[0])
        cohe[indices]  = value_cohe[indices]
        for n in range(len(indices),len(energy)):
            x = energy[n]
            j1 = len(indices)
            if energy_cohe[j1] == x:
                cohe[n] = value_cohe[j1]
                continue
            while energy_cohe[j1] < x:
                j1 += 1
            j0 = j1 - 1
            if j0 < 0:
                print(x, energy_cohe[0])
                raise ValueError("coherent")
            x0 = energy_cohe[j0]
            x1 = energy_cohe[j1]
            y0 = value_cohe[j0]
            y1 = value_cohe[j1]
            cohe[n] = exp((log(y0) * log(x1/x) + log(y1) * log(x/x0))/log(x1/x0))

        #compton needs to interpolate everything
        for n in range(len(energy)):
            x = energy[n]
            j1 = 0
            if energy_incohe[j1] == x:
                incohe[n] = value_incohe[j1]
                continue
            while energy_incohe[j1] < x:
                j1 += 1
            j0 = j1 - 1
            if j0 < 0:
                print(x, energy_incohe[0])
                raise ValueError("compton")
            x0 = energy_incohe[j0]
            x1 = energy_incohe[j1]
            y0 = value_incohe[j0]
            y1 = value_incohe[j1]
            incohe[n] = exp((log(y0) * log(x1/x) + log(y1) * log(x/x0))/log(x1/x0))

        #photoelectric does not need to interpolate anything
        j1 = 0
        for n in range(len(energy)):
            x = energy[n]
            if x < energy_photo[0]:
                continue
            j1 = 0
            photo[n] = value_photo[j1]
            j1 += 1
        photo[energy>=energy_photo[0]] = value_photo[:]


        #convert to keV and cut at 500 keV
        energy *= 1000.
        indices = numpy.nonzero(energy<=500.)
        energy = energy[indices]
        photo  = photo[indices]
        cohe   = cohe[indices]
        incohe = incohe[indices]

        #I cut at 500 keV, I do not need to take the pair production
        total = photo + cohe + incohe

        #now I am ready to write a Specfile
        ele = Elements[i-1]
        text  = '#S %d %s\n' % (i, ele)
        text += '#N %d\n' % (7+len(photo_label_list))
        labels = '#L PhotonEnergy[keV]'
        labels += '  Rayleigh(coherent)[barn/atom]'
        labels += '  Compton(incoherent)[barn/atom]'
        labels += '  CoherentPlusIncoherent[barn/atom]'
        labels += '  Photoelectric[barn/atom]'
        if LONG_LABELS:
            for label in photo_long_label_list:
                labels += "  "+label.replace(" ","")+"[barn/atom]"
        else:
            for label in photo_label_list:
                labels += "  "+label+"[barn/atom]"
        labels += "  AllOthers[barn/atom]"
        labels += '  TotalCrossSection[barn/atom]\n'
        if not BARNS:
            labels = labels.replace("barn/atom", "cm2/g")
            factor = (1.0E-24*AVOGADRO_NUMBER)/EPDLParser.getAtomicWeights()[i-1]
        else:
            factor = 1.0
        text += labels
        if 0:
            fformat = "%g %g %g %g %g"
        else:
            fformat = "%.7E %.6E %.6E %.6E %.6E"
        outfile.write(text)
        cohe   *= factor
        incohe *= factor
        photo  *= factor
        total  *= factor
        for n in range(len(energy)):
            if energy[n] == (1000. * energy_photo[0]):
                # one additional line
                line = fformat % (energy[n],
                      cohe[n],
                      incohe[n],
                      cohe[n]+incohe[n],
                      0.0)
                for l in photo_label_list:
                    line += " 0."
                line += " 0.0 %.6E\n" % (cohe[n]+incohe[n])
                outfile.write(line)
            line = fformat % (energy[n],
                              cohe[n],
                              incohe[n],
                              cohe[n]+incohe[n],
                              photo[n])
            d = 0.0
            for l in photo_label_list:
                a = photo_dict[l]['value'][n] * factor
                #this tiny modification saves 20 Mbytes ...
                if a > 0.0:
                    line += " %.6E" % a
                else:
                    line += " 0."
                d += a
            restOfShells = photo[n]-d
            if (i < firstNonZeroPhotoelectric) or (restOfShells < 1.0E-7):
                line += " 0.0 %.6E\n" % (total[n])
            else:
                line += " %.6E %.6E\n" % (restOfShells, total[n])
            outfile.write(line)
        outfile.write('\n')
    outfile.close()
