Source code for GSASIIfiles

# -*- coding: utf-8 -*-
########### SVN repository information ###################
# $Date: 2021-08-05 12:43:13 +0000 (Thu, 05 Aug 2021) $
# $Author: vondreele $
# $Revision: 5008 $
# $URL: https://subversion.xray.aps.anl.gov/pyGSAS/trunk/GSASIIfiles.py $
# $Id: GSASIIfiles.py 5008 2021-08-05 12:43:13Z vondreele $
########### SVN repository information ###################
'''
*GSASIIfiles: data (non-GUI) I/O routines*
==========================================

Module with miscellaneous routines for input and output from files.

This module should not contain any references to wxPython so that it
can be imported for scriptable use or potentially on clients where
wx is not installed.

Future refactoring: This module and GSASIIIO.py needs some work to
move non-wx routines here. It may will likely make sense to rename the module(s)
at that point.
'''
from __future__ import division, print_function
import platform
import os
import sys
import glob
import inspect
import numpy as np

import GSASIIpath
GSASIIpath.SetVersionNumber("$Revision: 5008 $")

# N.B. This is duplicated in G2IO
[docs]def sfloat(S): 'Convert a string to float. An empty field or a unconvertable value is treated as zero' if S.strip(): try: return float(S) except ValueError: pass return 0.0
G2printLevel = 'all' '''This defines the level of output from calls to :func:`G2Print`, which should be used in place of print() within this module. Settings for this are 'all', 'warn', 'error' or 'none'. Also see: :func:`G2Print` and :func:`G2SetPrintLevel`. '''
[docs]def G2SetPrintLevel(level): '''Set the level of output from calls to :func:`G2Print`, which should be used in place of print() within GSASII. Settings for the mode are 'all', 'warn', 'error' or 'none' :param str level: a string used to set the print level, which may be 'all', 'warn', 'error' or 'none'. Note that capitalization and extra letters in level are ignored, so 'Warn', 'warnings', etc. will all set the mode to 'warn' ''' global G2printLevel for mode in 'all', 'warn', 'error', 'none': if mode in level.lower(): G2printLevel = mode return else: G2Print('G2SetPrintLevel Error: level={} cannot be interpreted.', 'Use all, warn, error or none.')
[docs]def find(name, path): '''find 1st occurance of file in path ''' for root, dirs, files in os.walk(path): if name in files: return os.path.join(root, name)
[docs]def G2Print(*args,**kwargs): '''Print with filtering based level of output (see :func:`G2SetPrintLevel`). Use G2Print() as replacement for print(). :param str mode: if specified, this should contain the mode for printing ('error', 'warn' or anything else). If not specified, the first argument of the print command (args[0]) should contain the string 'error' for error messages and 'warn' for warning messages (capitalization and additional letters ignored.) ''' if G2printLevel == 'none': return if kwargs.get('mode') is None: testStr = str(args[0]).lower() else: testStr = kwargs['mode'][:].lower() del kwargs['mode'] level = 2 for i,mode in enumerate(('error', 'warn')): if mode in testStr: level = i break if G2printLevel == 'error' and level > 0: return if G2printLevel == 'warn' and level > 1: return print(*args,**kwargs)
def get_python_versions(packagelist): versions = [['Python', sys.version.split()[0]]] for pack in packagelist: try: versions.append([pack.__name__, pack.__version__]) except: pass versions.append(['Platform', sys.platform + ' ' + platform.architecture()[0] + ' ' + platform.machine()]) return versions def makeInstDict(names,data,codes): inst = dict(zip(names,zip(data,data,codes))) for item in inst: inst[item] = list(inst[item]) return inst
[docs]def SetPowderInstParms(Iparm, rd): '''extracts values from instrument parameters in rd.instdict or in array Iparm. Create and return the contents of the instrument parameter tree entry. ''' Irads = {0:' ',1:'CrKa',2:'FeKa',3:'CuKa',4:'MoKa',5:'AgKa',6:'TiKa',7:'CoKa'} DataType = Iparm['INS HTYPE '].strip()[:3] # take 1st 3 chars # override inst values with values read from data file Bank = rd.powderentry[2] #should be used in multibank iparm files if rd.instdict.get('type'): DataType = rd.instdict.get('type') data = [DataType,] instname = Iparm.get('INS 1INAME ') irad = int(Iparm.get('INS 1 IRAD ','0')) if instname: rd.Sample['InstrName'] = instname.strip() if 'C' in DataType: wave1 = None wave2 = 0.0 if rd.instdict.get('wave'): wl = rd.instdict.get('wave') wave1 = wl[0] if len(wl) > 1: wave2 = wl[1] s = Iparm['INS 1 ICONS'] if not wave1: wave1 = sfloat(s[:10]) wave2 = sfloat(s[10:20]) v = (wave1,wave2, sfloat(s[20:30])/100.,sfloat(s[55:65]),sfloat(s[40:50])) #get lam1, lam2, zero, pola & ratio if not v[1]: names = ['Type','Lam','Zero','Polariz.','U','V','W','X','Y','Z','SH/L','Azimuth'] v = (v[0],v[2],v[4]) codes = [0,0,0,0,0] rd.Sample.update({'Type':'Debye-Scherrer','Absorption':[0.,False],'DisplaceX':[0.,False],'DisplaceY':[0.,False]}) else: names = ['Type','Lam1','Lam2','Zero','I(L2)/I(L1)','Polariz.','U','V','W','X','Y','Z','SH/L','Azimuth'] codes = [0,0,0,0,0,0,0] rd.Sample.update({'Type':'Bragg-Brentano','Shift':[0.,False],'Transparency':[0.,False], 'SurfRoughA':[0.,False],'SurfRoughB':[0.,False]}) data.extend(v) if 'INS 1PRCF ' in Iparm: v1 = Iparm['INS 1PRCF '].split() v = Iparm['INS 1PRCF 1'].split() data.extend([float(v[0]),float(v[1]),float(v[2])]) #get GU, GV & GW - always here azm = float(Iparm.get('INS 1DETAZM','0.0')) v = Iparm['INS 1PRCF 2'].split() if v1[0] == 3: data.extend([float(v[0]),float(v[1]),0.0,float(v[2])+float(v[3],azm)]) #get LX, LY, Z, S+H/L & azimuth else: data.extend([0.0,0.0,0.0,0.002,azm]) #OK defaults if fxn #3 not 1st in iprm file else: v1 = Iparm['INS 1PRCF1 '].split() v = Iparm['INS 1PRCF11'].split() data.extend([float(v[0]),float(v[1]),float(v[2])]) #get GU, GV & GW - always here azm = float(Iparm.get('INS 1DETAZM','0.0')) v = Iparm['INS 1PRCF12'].split() if v1[0] == 3: data.extend([float(v[0]),float(v[1]),0.0,float(v[2])+float(v[3],azm)]) #get LX, LY, Z, S+H/L & azimuth else: data.extend([0.0,0.0,0.0,0.002,azm]) #OK defaults if fxn #3 not 1st in iprm file codes.extend([0,0,0,0,0,0,0]) Iparm1 = makeInstDict(names,data,codes) Iparm1['Source'] = [Irads[irad],Irads[irad]] Iparm1['Bank'] = [Bank,Bank,0] return [Iparm1,{}] elif 'T' in DataType: names = ['Type','fltPath','2-theta','difC','difA', 'difB','Zero','alpha','beta-0','beta-1', 'beta-q','sig-0','sig-1','sig-2','sig-q', 'X','Y','Z','Azimuth',] codes = [0,0,0,0,0, 0,0,0,0,0, 0,0,0,0,0, 0,0,0,0,] azm = 0. if 'INS 1DETAZM' in Iparm: azm = float(Iparm['INS 1DETAZM']) rd.Sample['Azimuth'] = azm fltPath0 = 20. #arbitrary if 'INS FPATH1' in Iparm: s = Iparm['INS FPATH1'].split() fltPath0 = sfloat(s[0]) if 'INS 1BNKPAR' not in Iparm: #bank missing from Iparm file return [] s = Iparm['INS 1BNKPAR'].split() fltPath1 = sfloat(s[0]) data.extend([fltPath0+fltPath1,]) #Flight path source-sample-detector data.extend([sfloat(s[1]),]) #2-theta for bank s = Iparm['INS 1 ICONS'].split() data.extend([sfloat(s[0]),sfloat(s[1]),0.0,sfloat(s[2])]) #difC,difA,difB,Zero if 'INS 1PRCF ' in Iparm: s = Iparm['INS 1PRCF '].split() pfType = int(s[0]) s = Iparm['INS 1PRCF 1'].split() if abs(pfType) == 1: data.extend([sfloat(s[1]),sfloat(s[2]),sfloat(s[3])]) #alpha, beta-0, beta-1 s = Iparm['INS 1PRCF 2'].split() data.extend([0.0,0.0,sfloat(s[1]),sfloat(s[2]),0.0,0.0,0.0,0.0,azm]) #beta-q, sig-0, sig-1, sig-2, sig-q, X, Y, Z elif abs(pfType) in [3,4,5]: data.extend([sfloat(s[0]),sfloat(s[1]),sfloat(s[2])]) #alpha, beta-0, beta-1 if abs(pfType) == 4: data.extend([0.0,0.0,sfloat(s[3]),0.0,0.0,0.0,0.0,0.0,azm]) #beta-q, sig-0, sig-1, sig-2, sig-q, X, Y, Z else: s = Iparm['INS 1PRCF 2'].split() data.extend([0.0,0.0,sfloat(s[0]),sfloat(s[1]),0.0,0.0,0.0,0.0,azm]) #beta-q, sig-0, sig-1, sig-2, sig-q, X, Y, Z elif abs(pfType) == 2: print('''***WARNING gsas profile function #2 does not give valid GSAS-II diffractometer/profile coefficients *** you should request GSAS-II instparm file from Instrument responsible''') data.extend([sfloat(s[1]),0.0,1./sfloat(s[3])]) #alpha, beta-0, beta-1 data.extend([0.0,0.0,sfloat(s[1]),0.0,0.0,0.0,0.0,0.0,azm]) #beta-q, sig-0, sig-1, sig-2, sig-q, X, Y, Z else: s = Iparm['INS 1PRCF1 '].split() pfType = int(s[0]) s = Iparm['INS 1PRCF11'].split() if abs(pfType) == 1: data.extend([sfloat(s[1]),sfloat(s[2]),sfloat(s[3])]) #alpha, beta-0, beta-1 s = Iparm['INS 1PRCF12'].split() data.extend([0.0,0.0,sfloat(s[1]),sfloat(s[2]),0.0,0.0,0.0,0.0,0.0,azm]) #beta-q, sig-0, sig-1, sig-2, sig-q, X, Y, Z elif abs(pfType) in [3,4,5]: data.extend([sfloat(s[0]),sfloat(s[1]),sfloat(s[2])]) #alpha, beta-0, beta-1 if abs(pfType) == 4: data.extend([0.0,0.0,sfloat(s[3]),0.0,0.0,0.0,0.0,0.0,azm]) #beta-q, sig-0, sig-1, sig-2, sig-q, X, Y, Z else: s = Iparm['INS 1PRCF12'].split() data.extend([0.0,0.0,sfloat(s[0]),sfloat(s[1]),0.0,0.0,0.0,0.0,azm]) #beta-q, sig-0, sig-1, sig-2, sig-q, X, Y, Z Inst1 = makeInstDict(names,data,codes) Inst1['Bank'] = [Bank,Bank,0] Inst2 = {} if pfType < 0: Ipab = 'INS 1PAB'+str(-pfType) Npab = int(Iparm[Ipab+' '].strip()) Inst2['Pdabc'] = [] for i in range(Npab): k = Ipab+str(i+1).rjust(2) s = Iparm[k].split() Inst2['Pdabc'].append([float(t) for t in s]) Inst2['Pdabc'] = np.array(Inst2['Pdabc']) Inst2['Pdabc'].T[3] += Inst2['Pdabc'].T[0]*Inst1['difC'][0] #turn 3rd col into TOF if 'INS 1I ITYP' in Iparm: s = Iparm['INS 1I ITYP'].split() Ityp = int(s[0]) Tminmax = [float(s[1])*1000.,float(s[2])*1000.] Itypes = ['Exponential','Maxwell/Exponential','','Maxwell/Chebyschev',''] if Ityp in [1,2,4]: Inst2['Itype'] = Itypes[Ityp-1] Inst2['Tminmax'] = Tminmax Icoeff = [] Iesd = [] Icovar = [] for i in range(3): s = Iparm['INS 1ICOFF'+str(i+1)].split() Icoeff += [float(S) for S in s] s = Iparm['INS 1IECOF'+str(i+1)].split() Iesd += [float(S) for S in s] NT = 10 for i in range(8): s = Iparm['INS 1IECOR'+str(i+1)] if i == 7: NT = 8 Icovar += [float(s[6*j:6*j+6]) for j in range(NT)] Inst2['Icoeff'] = Icoeff Inst2['Iesd'] = Iesd Inst2['Icovar'] = Icovar return [Inst1,Inst2]
[docs]def ReadPowderInstprm(instLines, bank, databanks, rd): '''Read lines from a GSAS-II (new) instrument parameter file similar to G2pwdGUI.OnLoad If instprm file has multiple banks each with header #Bank n: ..., this finds matching bank no. to load - problem with nonmatches? Note that this routine performs a similar role to :meth:`GSASIIdataGUI.GSASII.ReadPowderInstprm`, but that will call a GUI routine for selection when needed. This routine will raise exceptions on errors and will select the first bank when a choice might be appropriate. TODO: refactor to combine the two routines. :param list instLines: strings from GSAS-II parameter file; can be concatenated with ';' :param int bank: bank number to check when instprm file has '#BANK n:...' strings when bank = n then use parameters; otherwise skip that set. Ignored if BANK n: not present. NB: this kind of instprm file made by a Save all profile command in Instrument Par ameters :return dict: Inst instrument parameter dict if OK, or str: Error message if failed (transliterated from GSASIIdataGUI.py:1235 (rev 3008), function of the same name) ''' if 'GSAS-II' not in instLines[0]: raise ValueError("Not a valid GSAS-II instprm file") newItems = [] newVals = [] Found = False il = 0 if bank is None: banklist = set() for S in instLines: if S[0] == '#' and 'Bank' in S: banklist.add(int(S.split(':')[0].split()[1])) # Picks the first bank by default if len(banklist) > 1: bank = sorted(banklist)[0] else: bank = 1 rd.powderentry[2] = bank while il < len(instLines): S = instLines[il] if S[0] == '#': if Found: break if 'Bank' in S: if bank == int(S.split(':')[0].split()[1]): il += 1 S = instLines[il] else: il += 1 S = instLines[il] while il < len(instLines) and '#Bank' not in S: il += 1 if il == len(instLines): raise ValueError("Bank {} not found in instprm file".format(bank)) S = instLines[il] continue else: il += 1 S = instLines[il] Found = True if '"""' in S: delim = '"""' elif "'''" in S: delim = "'''" else: S = S.replace(' ', '') SS = S.strip().split(';') for s in SS: item, val = s.split(':', 1) newItems.append(item) try: newVals.append(float(val)) except ValueError: newVals.append(val) il += 1 continue # read multiline values, delimited by ''' or """ item, val = S.strip().split(':', 1) val = val.replace(delim, '').rstrip() val += '\n' while True: il += 1 if il >= len(instLines): break S = instLines[il] if delim in S: val += S.replace(delim, '').rstrip() val += '\n' break else: val += S.rstrip() val += '\n' newItems.append(item) newVals.append(val) il += 1 if 'Lam1' in newItems: rd.Sample.update({'Type':'Bragg-Brentano','Shift':[0.,False],'Transparency':[0.,False], 'SurfRoughA':[0.,False],'SurfRoughB':[0.,False]}) else: rd.Sample.update({'Type':'Debye-Scherrer','Absorption':[0.,False],'DisplaceX':[0.,False],'DisplaceY':[0.,False]}) return [makeInstDict(newItems, newVals, len(newVals)*[False]), {}]
[docs]def LoadImportRoutines(prefix, errprefix=None, traceback=False): '''Routine to locate GSASII importers matching a prefix string ''' if errprefix is None: errprefix = prefix readerlist = [] import_files = {} if '.' not in sys.path: sys.path.append('.') for path in sys.path: for filename in glob.iglob(os.path.join(path, 'G2'+prefix+'*.py')): pkg = os.path.splitext(os.path.split(filename)[1])[0] if pkg in import_files: G2Print('Warning: file {} hidden by {}' .format(os.path.abspath(filename),import_files[pkg])) else: import_files[pkg] = filename for pkg in sorted(import_files.keys()): try: exec('import '+pkg) for name, value in inspect.getmembers(eval(pkg)): if name.startswith('_'): continue if inspect.isclass(value): for method in 'Reader', 'ExtensionValidator', 'ContentsValidator': if not hasattr(value, method): break if not callable(getattr(value, method)): break else: reader = value() if reader.UseReader: readerlist.append(reader) except AttributeError: G2Print ('Import_' + errprefix + ': Attribute Error ' + import_files[pkg]) if traceback: traceback.print_exc(file=sys.stdout) except Exception as exc: G2Print ('\nImport_' + errprefix + ': Error importing file ' + import_files[pkg]) G2Print (u'Error message: {}\n'.format(exc)) if traceback: traceback.print_exc(file=sys.stdout) return readerlist
[docs]def LoadExportRoutines(parent, traceback=False): '''Routine to locate GSASII exporters ''' exporterlist = [] import_files = {} if '.' not in sys.path: sys.path.append('.') for path in sys.path: for filename in glob.iglob(os.path.join(path,"G2export*.py")): pkg = os.path.splitext(os.path.split(filename)[1])[0] if pkg in import_files: G2Print('Warning: file {} hidden by {}' .format(os.path.abspath(filename),import_files[pkg])) else: import_files[pkg] = filename # go through the routines and import them, saving objects that # have export routines (method Exporter) for pkg in sorted(import_files.keys()): try: exec('import '+pkg) for clss in inspect.getmembers(eval(pkg)): # find classes defined in package if clss[0].startswith('_'): continue if not inspect.isclass(clss[1]): continue # check if we have the required methods if not hasattr(clss[1],'Exporter'): continue if not callable(getattr(clss[1],'Exporter')): continue if parent is None: if not hasattr(clss[1],'Writer'): continue else: if not hasattr(clss[1],'loadParmDict'): continue if not callable(getattr(clss[1],'loadParmDict')): continue try: exporter = clss[1](parent) # create an export instance except AttributeError: pass except Exception as exc: G2Print ('\nExport init: Error substantiating class ' + clss[0]) G2Print (u'Error message: {}\n'.format(exc)) if traceback: traceback.print_exc(file=sys.stdout) continue exporterlist.append(exporter) except AttributeError: G2Print ('Export Attribute Error ' + import_files[pkg]) if traceback: traceback.print_exc(file=sys.stdout) except Exception as exc: G2Print ('\nExport init: Error importing file ' + import_files[pkg]) G2Print (u'Error message: {}\n'.format(exc)) if traceback: traceback.print_exc(file=sys.stdout) return exporterlist
[docs]def readColMetadata(imagefile): '''Reads image metadata from a column-oriented metadata table (1-ID style .par file). Called by :func:`GetColumnMetadata` The .par file has any number of columns separated by spaces. The directory for the file must be specified in Config variable :data:`config_example.Column_Metadata_directory`. As an index to the .par file a second "label file" must be specified with the same file root name as the .par file but the extension must be .XXX_lbls (where .XXX is the extension of the image) or if that is not present extension .lbls. :param str imagefile: the full name of the image file (with extension, directory optional) :returns: a dict with parameter values. Named parameters will have the type based on the specified Python function, named columns will be character strings The contents of the label file will look like this:: # define keywords filename:lambda x,y: "{}_{:0>6}".format(x,y)|33,34 distance: float | 75 wavelength:lambda keV: 12.398425/float(keV)|9 pixelSize:lambda x: [74.8, 74.8]|0 ISOlikeDate: lambda dow,m,d,t,y:"{}-{}-{}T{} ({})".format(y,m,d,t,dow)|0,1,2,3,4 Temperature: float|53 FreePrm2: int | 34 | Free Parm2 Label # define other variables 0:day 1:month 2:date 3:time 4:year 7:I_ring This file contains three types of lines in any order. * Named parameters are evaluated with user-supplied Python code (see subsequent information). Specific named parameters are used to determine values that are used for image interpretation (see table, below). Any others are copied to the Comments subsection of the Image tree item. * Column labels are defined with a column number (integer) followed by a colon (:) and a label to be assigned to that column. All labeled columns are copied to the Image's Comments subsection. * Comments are any line that does not contain a colon. Note that columns are numbered starting at zero. Any named parameter may be defined provided it is not a valid integer, but the named parameters in the table have special meanings, as descibed. The parameter name is followed by a colon. After the colon, specify Python code that defines or specifies a function that will be called to generate a value for that parameter. Note that several keywords, if defined in the Comments, will be found and placed in the appropriate section of the powder histogram(s)'s Sample Parameters after an integration: ``Temperature``, ``Pressure``, ``Time``, ``FreePrm1``, ``FreePrm2``, ``FreePrm3``, ``Omega``, ``Chi``, and ``Phi``. After the Python code, supply a vertical bar (|) and then a list of one more more columns that will be supplied as arguments to that function. Note that the labels for the three FreePrm items can be changed by including that label as a third item with an additional vertical bar. Labels will be ignored for any other named parameters. The examples above are discussed here: ``filename:lambda x,y: "{}_{:0>6}".format(x,y)|33,34`` Here the function to be used is defined with a lambda statement:: lambda x,y: "{}_{:0>6}".format(x,y) This function will use the format function to create a file name from the contents of columns 33 and 34. The first parameter (x, col. 33) is inserted directly into the file name, followed by a underscore (_), followed by the second parameter (y, col. 34), which will be left-padded with zeros to six characters (format directive ``:0>6``). When there will be more than one image generated per line in the .par file, an alternate way to generate list of file names takes into account the number of images generated:: lambda x,y,z: ["{}_{:0>6}".format(x,int(y)+i) for i in range(int(z))] Here a third parameter is used to specify the number of images generated, where the image number is incremented for each image. ``distance: float | 75`` Here the contents of column 75 will be converted to a floating point number by calling float on it. Note that the spaces here are ignored. ``wavelength:lambda keV: 12.398425/float(keV)|9`` Here we define an algebraic expression to convert an energy in keV to a wavelength and pass the contents of column 9 as that input energy ``pixelSize:lambda x: [74.8, 74.8]|0`` In this case the pixel size is a constant (a list of two numbers). The first column is passed as an argument as at least one argument is required, but that value is not used in the expression. ``ISOlikeDate: lambda dow,m,d,t,y:"{}-{}-{}T{} ({})".format(y,m,d,t,dow)|0,1,2,3,4`` This example defines a parameter that takes items in the first five columns and formats them in a different way. This parameter is not one of the pre-defined parameter names below. Some external code could be used to change the month string (argument ``m``) to a integer from 1 to 12. ``FreePrm2: int | 34 | Free Parm2 Label`` In this example, the contents of column 34 will be converted to an integer and placed as the second free-named parameter in the Sample Parameters after an integration. The label for this parameter will be changed to "Free Parm2 Label". **Pre-defined parameter names** ============= ========= ======== ===================================================== keyword required type Description ============= ========= ======== ===================================================== filename yes str or generates the file name prefix for the matching image list file (MyImage001 for file /tmp/MyImage001.tif) or a list of file names. polarization no float generates the polarization expected based on the monochromator angle, defaults to 0.99. center no list of generates the approximate beam center on the detector 2 floats in mm, such as [204.8, 204.8]. distance yes float generates the distance from the sample to the detector in mm pixelSize no list of generates the size of the pixels in microns such as 2 floats [200.0, 200.0]. wavelength yes float generates the wavelength in Angstroms ============= ========= ======== ===================================================== ''' dir,fil = os.path.split(os.path.abspath(imagefile)) imageName,ext = os.path.splitext(fil) if not GSASIIpath.GetConfigValue('Column_Metadata_directory'): return parfiles = glob.glob(os.path.join(GSASIIpath.GetConfigValue('Column_Metadata_directory'),'*.par')) if len(parfiles) == 0: G2Print('Sorry, No Column metadata (.par) file found in '+ GSASIIpath.GetConfigValue('Column_Metadata_directory')) return {} for parFil in parfiles: # loop over all .par files (hope just 1) in image dir until image is found parRoot = os.path.splitext(parFil)[0] for e in (ext+'_lbls','.lbls'): if os.path.exists(parRoot+e): lblFil = parRoot+e break else: G2Print('Warning: No labels definitions found for '+parFil) continue labels,lbldict,keyCols,keyExp,errors = readColMetadataLabels(lblFil) if errors: print('Errors in labels file '+lblFil) for i in errors: print(' '+i) continue else: G2Print('Read '+lblFil) # scan through each line in this .par file, looking for the matching image rootname fp = open(parFil,'r') for iline,line in enumerate(fp): items = line.strip().split(' ') nameList = keyExp['filename'](*[items[j] for j in keyCols['filename']]) if type(nameList) is str: if nameList != imageName: continue name = nameList else: for name in nameList: if name == imageName: break # got a match else: continue # parse the line and finish metadata = evalColMetadataDicts(items,labels,lbldict,keyCols,keyExp) metadata['par file'] = parFil metadata['lbls file'] = lblFil G2Print("Metadata read from {} line {}".format(parFil,iline+1)) fp.close() return metadata else: G2Print("Image {} not found in {}".format(imageName,parFil)) fp.close() continue fp.close() else: G2Print("Warning: No .par metadata for image {}".format(imageName)) return {}
[docs]def readColMetadataLabels(lblFil): '''Read the .*lbls file and setup for metadata assignments ''' lbldict = {} keyExp = {} keyCols = {} labels = {} errors = [] fp = open(lblFil,'r') # read column labels for iline,line in enumerate(fp): # read label definitions line = line.strip() if not line or line[0] == '#': continue # comments items = line.split(':') if len(items) < 2: continue # lines with no colon are also comments # does this line a definition for a named parameter? key = items[0] try: int(key) except ValueError: # try as named parameter since not a valid number items = line.split(':',1)[1].split('|') try: f = eval(items[0]) # compile the expression if not callable(f): errors += ['Expression "{}" for key {} is not a function (line {})'. format(items[0],key,iline)] continue keyExp[key] = f except Exception as msg: errors += ['Expression "{}" for key {} is not valid (line {})'. format(items[0],key,iline)] errors += [str(msg)] continue keyCols[key] = [int(i) for i in items[1].strip().split(',')] if key.lower().startswith('freeprm') and len(items) > 2: labels[key] = items[2] continue if len(items) == 2: # simple column definition lbldict[int(items[0])] = items[1] fp.close() if 'filename' not in keyExp: errors += ["File {} is invalid. No valid filename expression.".format(lblFil)] return labels,lbldict,keyCols,keyExp,errors
[docs]def evalColMetadataDicts(items,labels,lbldict,keyCols,keyExp,ShowError=False): '''Evaluate the metadata for a line in the .par file ''' metadata = {lbldict[j]:items[j] for j in lbldict} named = {} for key in keyExp: try: res = keyExp[key](*[items[j] for j in keyCols[key]]) except: if ShowError: res = "*** error ***" else: continue named[key] = res metadata.update(named) for lbl in labels: # add labels for FreePrm's metadata['label_'+lbl[4:].lower()] = labels[lbl] return metadata
[docs]def GetColumnMetadata(reader): '''Add metadata to an image from a column-type metadata file using :func:`readColMetadata` :param reader: a reader object from reading an image ''' if not GSASIIpath.GetConfigValue('Column_Metadata_directory'): return parParms = readColMetadata(reader.readfilename) if not parParms: return # check for read failure specialKeys = ('filename',"polarization", "center", "distance", "pixelSize", "wavelength",) reader.Comments = ['Metadata from {} assigned by {}'.format(parParms['par file'],parParms['lbls file'])] for key in parParms: if key in specialKeys+('par file','lbls file'): continue reader.Comments += ["{} = {}".format(key,parParms[key])] if "polarization" in parParms: reader.Data['PolaVal'][0] = parParms["polarization"] else: reader.Data['PolaVal'][0] = 0.99 if "center" in parParms: reader.Data['center'] = parParms["center"] if "pixelSize" in parParms: reader.Data['pixelSize'] = parParms["pixelSize"] if "wavelength" in parParms: reader.Data['wavelength'] = parParms['wavelength'] else: G2Print('Error: wavelength not defined in {}'.format(parParms['lbls file'])) if "distance" in parParms: reader.Data['distance'] = parParms['distance'] reader.Data['setdist'] = parParms['distance'] else: G2Print('Error: distance not defined in {}'.format(parParms['lbls file']))
[docs]def LoadControls(Slines,data): 'Read values from a .imctrl (Image Controls) file' cntlList = ['color','wavelength','distance','tilt','invert_x','invert_y','type','Oblique', 'fullIntegrate','outChannels','outAzimuths','LRazimuth','IOtth','azmthOff','DetDepth', 'calibskip','pixLimit','cutoff','calibdmin','Flat Bkg','varyList','setdist', 'PolaVal','SampleAbs','dark image','background image','twoth'] save = {} for S in Slines: if S[0] == '#': continue [key,val] = S.strip().split(':',1) if key in ['type','calibrant','binType','SampleShape','color',]: #strings save[key] = val elif key in ['varyList',]: save[key] = eval(val) #dictionary elif key in ['rotation']: save[key] = float(val) elif key in ['center',]: if ',' in val: save[key] = eval(val) else: vals = val.strip('[] ').split() save[key] = [float(vals[0]),float(vals[1])] elif key in cntlList: save[key] = eval(val) data.update(save)
[docs]def WriteControls(filename,data): 'Write current values to a .imctrl (Image Controls) file' File = open(filename,'w') keys = ['type','color','wavelength','calibrant','distance','center','Oblique', 'tilt','rotation','azmthOff','fullIntegrate','LRazimuth','setdist', 'IOtth','outChannels','outAzimuths','invert_x','invert_y','DetDepth', 'calibskip','pixLimit','cutoff','calibdmin','Flat Bkg','varyList', 'binType','SampleShape','PolaVal','SampleAbs','dark image','background image', 'twoth'] for key in keys: if key not in data: #uncalibrated! continue File.write(key+':'+str(data[key])+'\n') File.close()
[docs]def RereadImageData(ImageReaderlist,imagefile,ImageTag=None,FormatName=''): '''Read a single image with an image importer. This is called to reread an image after it has already been imported, so it is not necessary to reload metadata. Based on :func:`GetImageData.GetImageData` which this can replace where imageOnly=True :param list ImageReaderlist: list of Reader objects for images :param str imagefile: name of image file :param int/str ImageTag: specifies a particular image to be read from a file. First image is read if None (default). :param str formatName: the image reader formatName :returns: an image as a numpy array ''' # determine which formats are compatible with this file primaryReaders = [] secondaryReaders = [] for rd in ImageReaderlist: flag = rd.ExtensionValidator(imagefile) if flag is None: secondaryReaders.append(rd) elif flag: if not FormatName: primaryReaders.append(rd) elif FormatName == rd.formatName: primaryReaders.append(rd) if len(secondaryReaders) + len(primaryReaders) == 0: G2Print('Error: No matching format for file '+imagefile) raise Exception('No image read') errorReport = '' if not imagefile: return for rd in primaryReaders+secondaryReaders: rd.ReInitialize() # purge anything from a previous read rd.errors = "" # clear out any old errors if not rd.ContentsValidator(imagefile): # rejected on cursory check errorReport += "\n "+rd.formatName + ' validator error' if rd.errors: errorReport += ': '+rd.errors continue flag = rd.Reader(imagefile,None,blocknum=ImageTag) if flag: # this read succeeded if rd.Image is None: raise Exception('No image read. Strange!') if GSASIIpath.GetConfigValue('Transpose'): G2Print ('Warning: Transposing Image!') rd.Image = rd.Image.T #rd.readfilename = imagefile return rd.Image else: G2Print('Error reading file '+imagefile) G2Print('Error messages(s)\n'+errorReport) raise Exception('No image read')
[docs]def readMasks(filename,masks,ignoreThreshold): '''Read a GSAS-II masks file''' File = open(filename,'r') save = {} oldThreshold = masks['Thresholds'][0] S = File.readline() while S: if S[0] == '#': S = File.readline() continue [key,val] = S.strip().split(':',1) if key in ['Points','Rings','Arcs','Polygons','Frames','Thresholds']: if ignoreThreshold and key == 'Thresholds': S = File.readline() continue save[key] = eval(val) if key == 'Thresholds': save[key][0] = oldThreshold save[key][1][1] = min(oldThreshold[1],save[key][1][1]) S = File.readline() File.close() masks.update(save) # CleanupMasks for key in ['Points','Rings','Arcs','Polygons']: masks[key] = masks.get(key,[]) masks[key] = [i for i in masks[key] if len(i)]
[docs]def PDFWrite(PDFentry,fileroot,PDFsaves,PDFControls,Inst={},Limits=[]): '''Write PDF-related data (G(r), S(Q),...) into files, as selected. :param str PDFentry: name of the PDF entry in the tree. This is used for comments in the file specifying where it came from; it can be arbitrary :param str fileroot: name of file(s) to be written. The extension will be ignored. :param list PDFsaves: flags that determine what type of file will be written: PDFsaves[0], if True writes a I(Q) file with a .iq extension PDFsaves[1], if True writes a S(Q) file with a .sq extension PDFsaves[2], if True writes a F(Q) file with a .fq extension PDFsaves[3], if True writes a G(r) file with a .gr extension PDFsaves[4], if True writes G(r) in a pdfGUI input file with a .gr extension. Note that if PDFsaves[3] and PDFsaves[4] are both True, the pdfGUI overwrites the G(r) file. PDFsaves[5], if True writes F(Q) & g(R) with .fq & .gr extensions overwrites these if selected by option 2, 3 or 4 :param dict PDFControls: The PDF parameters and computed results :param dict Inst: Instrument parameters from the PDWR entry used to compute the PDF. Needed only when PDFsaves[4] is True. :param list Limits: Computation limits from the PDWR entry used to compute the PDF. Needed only when PDFsaves[4] is True. ''' import scipy.interpolate as scintp fileroot = os.path.splitext(fileroot)[0] if PDFsaves[0]: #I(Q) iqfilename = fileroot+'.iq' iqdata = PDFControls['I(Q)'][1] iqfxn = scintp.interp1d(iqdata[0],iqdata[1],kind='linear') iqfile = open(iqfilename,'w') iqfile.write('#T I(Q) %s\n'%(PDFentry)) iqfile.write('#L Q I(Q)\n') qnew = np.arange(iqdata[0][0],iqdata[0][-1],0.005) iqnew = zip(qnew,iqfxn(qnew)) for q,iq in iqnew: iqfile.write("%15.6g %15.6g\n" % (q,iq)) iqfile.close() G2Print (' I(Q) saved to: '+iqfilename) if PDFsaves[1]: #S(Q) sqfilename = fileroot+'.sq' sqdata = PDFControls['S(Q)'][1] sqfxn = scintp.interp1d(sqdata[0],sqdata[1],kind='linear') sqfile = open(sqfilename,'w') sqfile.write('#T S(Q) %s\n'%(PDFentry)) sqfile.write('#L Q S(Q)\n') qnew = np.arange(sqdata[0][0],sqdata[0][-1],0.005) sqnew = zip(qnew,sqfxn(qnew)) for q,sq in sqnew: sqfile.write("%15.6g %15.6g\n" % (q,sq)) sqfile.close() G2Print (' S(Q) saved to: '+sqfilename) if PDFsaves[2]: #F(Q) fqfilename = fileroot+'.fq' fqdata = PDFControls['F(Q)'][1] fqfxn = scintp.interp1d(fqdata[0],fqdata[1],kind='linear') fqfile = open(fqfilename,'w') fqfile.write('#T F(Q) %s\n'%(PDFentry)) fqfile.write('#L Q F(Q)\n') qnew = np.arange(fqdata[0][0],fqdata[0][-1],0.005) fqnew = zip(qnew,fqfxn(qnew)) for q,fq in fqnew: fqfile.write("%15.6g %15.6g\n" % (q,fq)) fqfile.close() G2Print (' F(Q) saved to: '+fqfilename) if PDFsaves[3]: #G(R) grfilename = fileroot+'.gr' grdata = PDFControls['G(R)'][1] grfxn = scintp.interp1d(grdata[0],grdata[1],kind='linear') grfile = open(grfilename,'w') grfile.write('#T G(R) %s\n'%(PDFentry)) grfile.write('#L R G(R)\n') rnew = np.arange(grdata[0][0],grdata[0][-1],0.010) grnew = zip(rnew,grfxn(rnew)) for r,gr in grnew: grfile.write("%15.6g %15.6g\n" % (r,gr)) grfile.close() G2Print (' G(R) saved to: '+grfilename) if PDFsaves[4]: #pdfGUI file for G(R) import GSASIImath as G2mth import GSASIIlattice as G2lat grfilename = fileroot+'.gr' grdata = PDFControls['G(R)'][1] qdata = PDFControls['I(Q)'][1][0] grfxn = scintp.interp1d(grdata[0],grdata[1],kind='linear') grfile = open(grfilename,'w') rnew = np.arange(grdata[0][0],grdata[0][-1],0.010) grnew = zip(rnew,grfxn(rnew)) grfile.write('[DEFAULT]\n') grfile.write('\n') grfile.write('version = GSAS-II-v'+str(GSASIIpath.GetVersionNumber())+'\n') grfile.write('\n') grfile.write('# input and output specifications\n') grfile.write('dataformat = Qnm\n') grfile.write('inputfile = %s\n'%(PDFControls['Sample']['Name'])) grfile.write('backgroundfile = %s\n'%(PDFControls['Sample Bkg.']['Name'])) grfile.write('outputtype = gr\n') grfile.write('\n') grfile.write('# PDF calculation setup\n') if 'x' in Inst['Type']: grfile.write('mode = %s\n'%('xray')) elif 'N' in Inst['Type']: grfile.write('mode = %s\n'%('neutron')) wave = G2mth.getMeanWave(Inst) grfile.write('wavelength = %.5f\n'%(wave)) formula = '' for el in PDFControls['ElList']: formula += el num = PDFControls['ElList'][el]['FormulaNo'] if num == round(num): formula += '%d'%(int(num)) else: formula += '%.2f'%(num) grfile.write('composition = %s\n'%(formula)) grfile.write('bgscale = %.3f\n'%(-PDFControls['Sample Bkg.']['Mult'])) highQ = 2.*np.pi/G2lat.Pos2dsp(Inst,Limits[1][1]) grfile.write('qmaxinst = %.2f\n'%(highQ)) grfile.write('qmin = %.5f\n'%(qdata[0])) grfile.write('qmax = %.4f\n'%(qdata[-1])) grfile.write('rmin = %.2f\n'%(PDFControls['Rmin'])) grfile.write('rmax = %.2f\n'%(PDFControls['Rmax'])) grfile.write('rstep = 0.01\n') grfile.write('\n') grfile.write('# End of config '+63*'-') grfile.write('\n') grfile.write('#### start data\n') grfile.write('#S 1\n') grfile.write('#L r($\\AA$) G($\\AA^{-2}$)\n') for r,gr in grnew: grfile.write("%15.2F %15.6F\n" % (r,gr)) grfile.close() G2Print (' G(R) saved to: '+grfilename) if len(PDFsaves) > 5 and PDFsaves[5]: #RMCProfile files for F(Q) & g(r) overwrites any above fqfilename = fileroot+'.fq' fqdata = PDFControls['F(Q)'][1] fqfxn = scintp.interp1d(fqdata[0],fqdata[1],kind='linear') fqfile = open(fqfilename,'w') qnew = np.arange(fqdata[0][0],fqdata[0][-1],0.005) nq = qnew.shape[0] fqfile.write('%20d\n'%nq-1) fqfile.write(fqfilename+'\n') fqnew = zip(qnew,fqfxn(qnew)) for q,fq in fqnew[1:]: fqfile.write("%15.6g %15.6g\n" % (q,fq)) fqfile.close() G2Print (' F(Q) saved to: '+fqfilename) grfilename = fileroot+'.gr' grdata = PDFControls['g(r)'][1] grfxn = scintp.interp1d(grdata[0],grdata[1],kind='linear') grfile = open(grfilename,'w') rnew = np.arange(grdata[0][0],grdata[0][-1],0.010) nr = rnew.shape[0] grfile.write('%20d\n'%nr-1) grfile.write(grfilename+'\n') grnew = zip(rnew,grfxn(rnew)) for r,gr in grnew[1:]: grfile.write("%15.6g %15.6g\n" % (r,gr)) grfile.close() G2Print (' G(R) saved to: '+grfilename)