def extractOut(self, sasCIFdict, sasCIFfile, data_block_id=''):
sasCIFfile = os.path.split(sasCIFfile)[-1]
if data_block_id:
data_block_list = [data_block_id]
else:
data_block_list = sasCIFdict.keys()
for data_block_id in data_block_list:
if '_sas_p_of_R' in sasCIFdict[data_block_id]:
outfile = open(sasCIFfile[0:-7] + '.out', 'w')
intensityTable = [sasCIFdict[data_block_id]['_sas_p_of_R_extrapolated_intensity']['momentum_transfer'],
sasCIFdict[data_block_id]['_sas_p_of_R_extrapolated_intensity']['intensity_reg']]
intensityHeader = ['S', 'I REG']
# Alignment of experimental and extrapolated intensities
if '_sas_scan_intensity' in sasCIFdict[data_block_id]:
qmin = float(sasCIFdict[data_block_id]['_sas_p_of_R_details']['qmin'])
qmax = float(sasCIFdict[data_block_id]['_sas_p_of_R_details']['qmax'])
sIntensity = \
[float(x) for x in sasCIFdict[data_block_id]['_sas_scan_intensity']['momentum_transfer']]
firstPointIntensity = min(range(len(sIntensity)), key=lambda i: abs(sIntensity[i] - qmin))
lastPointIntensity = min(range(len(sIntensity)), key=lambda i: abs(sIntensity[i] - qmax)) + 1
sExtrapolated = [float(x) for x in intensityTable[0]]
firstPointExtrapolated = \
min(range(len(sExtrapolated)), key=lambda i: abs(sExtrapolated[i] - qmin))
lastPointExtrapolated = \
min(range(len(sExtrapolated)), key=lambda i: abs(sExtrapolated[i] - qmax)) + 1
# If the number of points were reduced by GNOM, then regrid
# the curve with DATREGRID
if not (lastPointIntensity - firstPointIntensity) \
== (lastPointExtrapolated - firstPointExtrapolated):
datFileInt = open('int.dat', 'w')
table = [sasCIFdict[data_block_id]['_sas_scan_intensity']['momentum_transfer'],
sasCIFdict[data_block_id]['_sas_scan_intensity']['intensity'],
sasCIFdict[data_block_id]['_sas_scan_intensity']['intensity_su_counting']]
writeDatFile = wsd.saxsdocout()
writeDatFile.writeCurves(table, datFileInt)
datFileInt.close()
datFileExt = open('ext.dat', 'w')
writeDatFile = wsd.saxsdocout()
writeDatFile.writeCurves(intensityTable, datFileExt)
datFileExt.close()
call(['datregrid', '-t', 'ext.dat', 'int.dat', '-o', 'intExt.dat'])
datFileIntExt = saxsdocument.read('intExt.dat').curve
call(['rm', 'ext.dat', 'int.dat', 'intExt.dat'])
scatVect = [float('%14E' % value)
for value in list(zip(*datFileIntExt[0])[0])]
intensity = [str('%14E' % value)
for value in list(zip(*datFileIntExt[0])[1])]
error = [str('%14E' % value)
for value in list(zip(*datFileIntExt[0])[2])]
firstPointIntensity = \
min(range(len(scatVect)), key=lambda i: abs(scatVect[i] - qmin))
lastPointIntensity = \
min(range(len(scatVect)), key=lambda i: abs(scatVect[i] - qmax)) + 1
else:
intensity = sasCIFdict[data_block_id][
'_sas_scan_intensity']['intensity']
error = sasCIFdict[data_block_id][
'_sas_scan_intensity']['intensity_su_counting']
tailPoints = (lastPointExtrapolated - firstPointExtrapolated) - \
len(intensity[firstPointIntensity:lastPointIntensity])
Jexp = [' '] * firstPointExtrapolated + \
intensity[firstPointIntensity:lastPointIntensity] + [' '] * tailPoints
Error = [' '] * firstPointExtrapolated + \
error[firstPointIntensity:lastPointIntensity] + [' '] * tailPoints
Jreg = [' '] * firstPointExtrapolated + \
sasCIFdict[data_block_id]['_sas_p_of_R_extrapolated_intensity'][
'intensity_reg'][firstPointExtrapolated:]
intensityTable.insert(1, Jexp)
intensityTable.insert(2, Error)
intensityTable.insert(3, Jreg)
intensityHeader = ['S', 'J EXP', 'ERROR', 'J REG', 'I REG']
pRTable = [sasCIFdict[data_block_id]['_sas_p_of_R']['r'],
sasCIFdict[data_block_id]['_sas_p_of_R']['P'],
sasCIFdict[data_block_id]['_sas_p_of_R']['P_error']]
writeoutfile = wsd.saxsdocout()
# Write creator&version
creator, version = sasCIFdict[data_block_id]['_sas_p_of_R_details']['software_p_of_R'].split()
writeoutfile.writeText(' '.join(creator) + ' Version ' + version + '\n', outfile)
# Write curves
writeoutfile.writeCurves(
intensityTable, outfile, intensityHeader)
writeoutfile.writeText(' Distance distribution function of particle \n', outfile)
writeoutfile.writeCurves(
pRTable, outfile, ['R', 'P(R)', 'ERROR'])
# Write properties
propList = [
'Rg_from_Guinier', 'I0_from_Guinier', 'Rg_from_PR', 'I0_from_PR']
propDict = collections.OrderedDict()
for prop in propList:
if prop in sasCIFdict[data_block_id]['_sas_result'].keys():
propDict[prop] = sasCIFdict[data_block_id]['_sas_result'][prop]
writeoutfile.writeProperties(propDict, outfile)
outfile.close()
def __init__(self, filename, sasCIFdict):
self.sasfile = saxsdocument.read(filename)
self.filename = filename
self.sasCIFdict = sasCIFdict
