def testExecute(self):
"""
"""
self.run()
# Checks that there are no error messages
plugin = self.getPlugin()
plugin.killAllWorkers()
if EDVerbose.isVerboseDebug():
plugin.cleanDispMat(plugin.getWorkingDirectory())
else:
plugin.cleanDispMat()
# Checking obtained results
xsDataResultSPD = plugin.getDataOutput()
EDVerbose.DEBUG("outfile = %s" % xsDataResultSPD.getCorrectedFile().getPath().getValue())
EDVerbose.DEBUG("reffile = %s" % os.path.join(self.getTestsDataImagesHome(), self.refOutput))
outputData = openimage(xsDataResultSPD.getCorrectedFile().getPath().getValue()).data
referenceData = openimage(os.path.join(self.getTestsDataImagesHome(), self.refOutput)).data
# res = 100 * (abs(outputData - referenceData).max() - referenceData.min()) / (referenceData.max() - referenceData.min())
# EDVerbose.screen("Maximum error = %.2f%%" % res)
# EDAssert.equal((res < 5), True)
EDAssert.arraySimilar(outputData, referenceData, "Simple comparison")
EDAssert.arraySimilar(outputData, referenceData, _fAbsMaxDelta=0.01, _fScaledMaxDelta=0.05, _strComment="Images comparison")
def testExecute(self):
"""
"""
self.run()
# Checks that there are no error messages
plugin = self.getPlugin()
plugin.killAllWorkers()
if EDVerbose.isVerboseDebug():
plugin.cleanDispMat(plugin.getWorkingDirectory())
else:
plugin.cleanDispMat()
# Checking obtained results
xsDataResultSPD = plugin.getDataOutput()
outputData = EDF(
xsDataResultSPD.getCakedFile().getPath().getValue()).GetData(0)
referenceData = EDF(
os.path.join(self.getTestsDataImagesHome(),
self.refOutput)).GetData(0)
relError = 100 * (abs(outputData - referenceData).max() -
referenceData.min()) / (referenceData.max() -
referenceData.min())
absError = abs(outputData - referenceData).max()
if relError > 5:
EDAssert.lowerThan(
relError, 5,
"Maximum relative error = %.2f%%, Maximum Absolute Error %.2f"
% (relError, absError))
else:
EDAssert.lowerThan(
absError, 5,
"Maximum relative error = %.2f%%, Maximum Absolute Error %.2f "
% (relError, absError))
def postProcess(self, _edObject=None):
"""
Calls the parent preProcess method
Checks that the installed 3rd party software is in the list of compatible versions
"""
EDPluginExecProcess.postProcess(self)
EDVerbose.DEBUG("EDPluginExecProcessScript.postProcess")
# Tests the compatibles executable versions
listCompatibleVersions = self.getListOfCompatibleVersions()
if(len(listCompatibleVersions) != 0):
bFound = False
for compatibleVersion in listCompatibleVersions:
bFound = self.findStringInLog(compatibleVersion)
if(bFound == True):
break
if(bFound == False):
strErrorMessage = "Plugin not compatible with %s, compatible versions are: %s" % (self.getStringVersion(), self.getCompatibleVersionsStringLine())
EDVerbose.error(strErrorMessage)
self.addErrorMessage(strErrorMessage)
self.setFailure()
if (EDVerbose.isVerboseDebug()):
raise RuntimeError, strErrorMessage
def testExecute(self):
"""
"""
self.run()
# Checks that there are no error messages
plugin = self.getPlugin()
plugin.killAllWorkers()
if EDVerbose.isVerboseDebug():
plugin.cleanDispMat(plugin.getWorkingDirectory())
else:
plugin.cleanDispMat()
# Checking obtained results
xsDataResultSPD = plugin.getDataOutput()
outputData = EDF(xsDataResultSPD.getCakedFile().getPath().getValue()).GetData(0)
referenceData = EDF(os.path.join(self.getTestsDataImagesHome(), self.refOutput)).GetData(0)
relError = 100 * (abs(outputData - referenceData).max() - referenceData.min()) / (referenceData.max() - referenceData.min())
absError = abs(outputData - referenceData).max()
if relError > 5:
EDAssert.lowerThan(relError, 5, "Maximum relative error = %.2f%%, Maximum Absolute Error %.2f" % (relError, absError))
else:
EDAssert.lowerThan(absError, 5, "Maximum relative error = %.2f%%, Maximum Absolute Error %.2f " % (relError, absError))
def rewriteAsciiHeader(self):
if EDVerbose.isVerboseDebug():
shutil.copy(self.integratedCurve, self.integratedCurve + ".bak")
lines = open(self.integratedCurve, "rb").readlines()
headerMarker = None
headers = []
firstData = None
for oneLine in lines:
stripedLine = oneLine.strip()
if headerMarker is None and len(stripedLine) > 0:
headerMarker = stripedLine[0]
if len(stripedLine) == 0:
continue
elif stripedLine.startswith(headerMarker):
headers.append(stripedLine[1:].strip())
else:
firstData = lines.index(oneLine)
break
outFile = open(self.integratedCurve, "wb")
outFile.write("# %s \r\n" % self.comments)
outFile.write(
"#Sample c= %s mg/ml \r\n# \r\n# Sample environment:\r\n" %
self.concentration)
if self.detector is not None:
outFile.write("# Detector: %s \r\n" % self.detector)
if self.detectorDistance is not None:
outFile.write("# DetectorDistance: %s \r\n" %
self.detectorDistance)
if self.pixelSize_1 is not None:
outFile.write("# PixelSize_1: %s \r\n" % self.pixelSize_1)
if self.pixelSize_2 is not None:
outFile.write("# PixelSize_2: %s \r\n" % self.pixelSize_2)
if self.beamCenter_1 is not None:
outFile.write("# BeamCenter_1: %s \r\n" % self.beamCenter_1)
if self.beamCenter_2 is not None:
outFile.write("# BeamCenter_2: %s \r\n" % self.beamCenter_2)
if self.beamStopDiode is not None:
outFile.write("# BeamStopDiode: %s \r\n" % self.beamStopDiode)
if self.wavelength is not None:
outFile.write("# Wavelength: %s \r\n" % self.wavelength)
if self.maskFile is not None:
outFile.write("# MaskFile: %s \r\n" % self.maskFile)
if self.normalizationFactor is not None:
outFile.write("# NormalizationFactor: %s \r\n" %
self.normalizationFactor)
if self.machineCurrent is not None:
outFile.write("# MachineCurrent: %s \r\n" % self.machineCurrent)
outFile.write("#\r\n")
for oneLine in headers:
outFile.write("# %s \r\n" % oneLine.strip())
outFile.write("# \r\n# Sample Information:\r\n")
outFile.write("# Concentration: %s\r\n" % self.concentration)
outFile.write("# Code: %s\r\n" % self.code)
outFile.write("\r\n".join([i.strip() for i in lines[firstData:]]))
outFile.close()
def testPopulateXSDataInputSPDCake(self):
edPluginControlID11 = self.createPlugin()
xsDataInputSPDCake = edPluginControlID11.populateXSDataInputSPDCake(self.dictID11Reference)
strDataPath = self.getPluginTestsDataHome()
strReferenceFile = "XSDataInputSPDCake_fromDict.xml"
strPath = os.path.join(strDataPath, strReferenceFile)
xsDataInputSPDCakeReference = XSDataInputSPDCake.parseString(self.readAndParseFile(strPath))
xsDataInputSPDCakeReference.setDeleteCorImg(XSDataBoolean(not (EDVerbose.isVerboseDebug())))
EDAssert.equal(xsDataInputSPDCakeReference.marshal(), xsDataInputSPDCake.marshal())
def testCleanDispMat(self):
edPluginSPD = self.createPlugin()
strXMLInput = EDUtilsFile.readFileAndParseVariables(self.strReferenceInputFileName, EDUtilsPath.getDictOfPaths())
xsDataInputSPDCake = XSDataInputSPDCake.parseString(strXMLInput)
edPluginSPD.setDataInput(xsDataInputSPDCake)
if EDVerbose.isVerboseDebug():
edPluginSPD.cleanDispMat(edPluginSPD.getWorkingDirectory())
else:
edPluginSPD.cleanDispMat()
def testCleanDispMat(self):
edPluginSPD = self.createPlugin()
strXMLInput = EDUtilsTest.readAndParseFile(self.strReferenceInputFileName)
xsDataInputSPDCake = XSDataInputSPDCake.parseString(strXMLInput)
edPluginSPD.setDataInput(xsDataInputSPDCake)
if EDVerbose.isVerboseDebug():
edPluginSPD.cleanDispMat(edPluginSPD.getWorkingDirectory())
else:
edPluginSPD.cleanDispMat()
def testCleanDispMat(self):
edPluginSPD = self.createPlugin()
strXMLInput = EDUtilsFile.readFileAndParseVariables(
self.strReferenceInputFileName, EDUtilsPath.getDictOfPaths())
xsDataInputSPDCake = XSDataInputSPDCake.parseString(strXMLInput)
edPluginSPD.setDataInput(xsDataInputSPDCake)
if EDVerbose.isVerboseDebug():
edPluginSPD.cleanDispMat(edPluginSPD.getWorkingDirectory())
else:
edPluginSPD.cleanDispMat()
def rewriteAsciiHeader(self):
if EDVerbose.isVerboseDebug():
shutil.copy(self.integratedCurve, self.integratedCurve + ".bak")
lines = open(self.integratedCurve, "rb").readlines()
headerMarker = None
headers = []
firstData = None
for oneLine in lines:
stripedLine = oneLine.strip()
if headerMarker is None and len(stripedLine) > 0:
headerMarker = stripedLine[0]
if len(stripedLine) == 0:
continue
elif stripedLine.startswith(headerMarker) :
headers.append(stripedLine[1:].strip())
else:
firstData = lines.index(oneLine)
break
outFile = open(self.integratedCurve, "wb")
outFile.write("# %s \r\n" % self.comments)
outFile.write("#Sample c= %s mg/ml \r\n# \r\n# Sample environment:\r\n" % self.concentration)
if self.detector is not None:
outFile.write("# Detector: %s \r\n" % self.detector)
if self.detectorDistance is not None:
outFile.write("# DetectorDistance: %s \r\n" % self.detectorDistance)
if self.pixelSize_1 is not None:
outFile.write("# PixelSize_1: %s \r\n" % self.pixelSize_1)
if self.pixelSize_2 is not None:
outFile.write("# PixelSize_2: %s \r\n" % self.pixelSize_2)
if self.beamCenter_1 is not None:
outFile.write("# BeamCenter_1: %s \r\n" % self.beamCenter_1)
if self.beamCenter_2 is not None:
outFile.write("# BeamCenter_2: %s \r\n" % self.beamCenter_2)
if self.beamStopDiode is not None:
outFile.write("# BeamStopDiode: %s \r\n" % self.beamStopDiode)
if self.wavelength is not None:
outFile.write("# Wavelength: %s \r\n" % self.wavelength)
if self.maskFile is not None:
outFile.write("# MaskFile: %s \r\n" % self.maskFile)
if self.normalizationFactor is not None:
outFile.write("# NormalizationFactor: %s \r\n" % self.normalizationFactor)
if self.machineCurrent is not None:
outFile.write("# MachineCurrent: %s \r\n" % self.machineCurrent)
outFile.write("#\r\n")
for oneLine in headers:
outFile.write("# %s \r\n" % oneLine.strip())
outFile.write("# \r\n# Sample Information:\r\n")
outFile.write("# Concentration: %s\r\n" % self.concentration)
outFile.write("# Code: %s\r\n" % self.code)
outFile.write("\r\n".join([i.strip() for i in lines[firstData:]]))
outFile.close()
def generateEdfheaderdelkey2DCommands(self):
"""
Generate the command line
"""
EDVerbose.DEBUG("*** EDPluginExecSaxsDelMetadatav1_0.generateEdfheaderdelkeyCommands")
if EDVerbose.isVerboseDebug():
strOptions = "0 2 1 1 '%s' '%s'" % (self.strKey, self.strImage)
else:
strOptions = "0 0 1 1 '%s' '%s'" % (self.strKey, self.strImage)
EDVerbose.DEBUG("edfheaderdelkey " + strOptions)
self.setScriptCommandline(strOptions)
def testPopulateXSDataInputSPDCake(self):
edPluginControlID11 = self.createPlugin()
xsDataInputSPDCake = edPluginControlID11.populateXSDataInputSPDCake(
self.dictID11Reference)
strDataPath = self.getPluginTestsDataHome()
strReferenceFile = "XSDataInputSPDCake_fromDict.xml"
strPath = os.path.join(strDataPath, strReferenceFile)
xsDataInputSPDCakeReference = XSDataInputSPDCake.parseString(
self.readAndParseFile(strPath))
xsDataInputSPDCakeReference.setDeleteCorImg(
XSDataBoolean(not (EDVerbose.isVerboseDebug())))
EDAssert.equal(xsDataInputSPDCakeReference.marshal(),
xsDataInputSPDCake.marshal())
def testGenerateSPDCommand(self):
edPluginSPD = self.createPlugin()
strXMLInput = EDUtilsFile.readFileAndParseVariables(self.strReferenceInputFileName, EDUtilsPath.getDictOfPaths())
xsDataInputSPDCake = XSDataInputSPDCake.parseString(strXMLInput)
edPluginSPD.setDataInput(xsDataInputSPDCake)
edPluginSPD.configure()
edPluginSPD.getInputParameter()
#edPluginSPD.preProcess()
edPluginSPD.generateSPDCommand()
EDVerbose.screen("SPD configuration:\n%s" % edPluginSPD.getSPDConfig())
if EDVerbose.isVerboseDebug():
expected = """off_1=0 off_2=0 verbose=2 src_ext=.edf cor_ext=.cor wvl=1.000000e-10 cen_1=1.050000e+03 cen_2=1.000000e+03 dis=1.000000e-01 pix_1=4.722440e-05 pix_2=4.683150e-05 do_distortion=0 do_dark=0"""
#"do_distortion=2 off_1=0 off_2=0 verbose=2 src_ext=.edf cor_ext=.cor wvl=1.000000e-10 cen_1=1.050000e+03 cen_2=1.000000e+03 dis=1.000000e-01 pix_1=4.722440e-05 pix_2=4.683150e-05 do_dark=0"
else:
expected = """off_1=0 off_2=0 verbose=0 src_ext=.edf cor_ext=.cor wvl=1.000000e-10 cen_1=1.050000e+03 cen_2=1.000000e+03 dis=1.000000e-01 pix_1=4.722440e-05 pix_2=4.683150e-05 do_distortion=0 do_dark=0"""
#do_distortion=2 off_1=0 off_2=0 verbose=0 src_ext=.edf cor_ext=.cor wvl=1.000000e-10 cen_1=1.050000e+03 cen_2=1.000000e+03 dis=1.000000e-01 pix_1=4.722440e-05 pix_2=4.683150e-05 do_dark=0"
EDAssert.equal(edPluginSPD.getSPDConfig(), expected)
def testGenerateSPDCommand(self):
edPluginSPD = self.createPlugin()
strXMLInput = EDUtilsFile.readFileAndParseVariables(
self.strReferenceInputFileName, EDUtilsPath.getDictOfPaths())
xsDataInputSPDCake = XSDataInputSPDCake.parseString(strXMLInput)
edPluginSPD.setDataInput(xsDataInputSPDCake)
edPluginSPD.configure()
edPluginSPD.getInputParameter()
#edPluginSPD.preProcess()
edPluginSPD.generateSPDCommand()
EDVerbose.screen("SPD configuration:\n%s" % edPluginSPD.getSPDConfig())
if EDVerbose.isVerboseDebug():
expected = """off_1=0 off_2=0 verbose=2 src_ext=.edf cor_ext=.cor wvl=1.000000e-10 cen_1=1.050000e+03 cen_2=1.000000e+03 dis=1.000000e-01 pix_1=4.722440e-05 pix_2=4.683150e-05 do_distortion=0 do_dark=0"""
#"do_distortion=2 off_1=0 off_2=0 verbose=2 src_ext=.edf cor_ext=.cor wvl=1.000000e-10 cen_1=1.050000e+03 cen_2=1.000000e+03 dis=1.000000e-01 pix_1=4.722440e-05 pix_2=4.683150e-05 do_dark=0"
else:
expected = """off_1=0 off_2=0 verbose=0 src_ext=.edf cor_ext=.cor wvl=1.000000e-10 cen_1=1.050000e+03 cen_2=1.000000e+03 dis=1.000000e-01 pix_1=4.722440e-05 pix_2=4.683150e-05 do_distortion=0 do_dark=0"""
#do_distortion=2 off_1=0 off_2=0 verbose=0 src_ext=.edf cor_ext=.cor wvl=1.000000e-10 cen_1=1.050000e+03 cen_2=1.000000e+03 dis=1.000000e-01 pix_1=4.722440e-05 pix_2=4.683150e-05 do_dark=0"
EDAssert.equal(edPluginSPD.getSPDConfig(), expected)
def testGenerateSPDCommand(self):
edPluginSPD = self.createPlugin()
edStringXMLInput = EDUtilsTest.readAndParseFile(self.m_edStringReferenceInputFileName)
xsDataInputSPDCake = XSDataInputSPDCake.parseString(edStringXMLInput)
edPluginSPD.setDataInput(xsDataInputSPDCake)
edPluginSPD.configure()
edPluginSPD.getInputParameter()
#edPluginSPD.preProcess()
edPluginSPD.generateSPDCommand()
EDVerbose.screen("SPD configuration:\n %s" % edPluginSPD.getSPDConfig())
if EDVerbose.isVerboseDebug():
expected = """off_1=0 off_2=0 verbose=2 src_ext=.edf wvl=1.000000e-10 cen_1=1.050000e+03 cen_2=1.000000e+03 dis=1.000000e-01 pix_1=4.722440e-05 pix_2=4.683150e-05 do_distortion=0 do_dark=0 cor_ext=.cor azim_int=1 azim_pass=0 azim_ext=.cor azim_r_num=1489"""
# """do_distortion=2 off_1=0 off_2=0 verbose=2 src_ext=.edf wvl=1.000000e-10 cen_1=1.050000e+03 cen_2=1.000000e+03 dis=1.000000e-01 pix_1=4.722440e-05 pix_2=4.683150e-05 do_dark=0 cor_ext=.cor azim_int=1 azim_pass=0 azim_ext=.cor azim_r_num=1489"""
else:
expected = """off_1=0 off_2=0 verbose=0 src_ext=.edf wvl=1.000000e-10 cen_1=1.050000e+03 cen_2=1.000000e+03 dis=1.000000e-01 pix_1=4.722440e-05 pix_2=4.683150e-05 do_distortion=0 do_dark=0 cor_ext=.cor azim_int=1 azim_pass=0 azim_ext=.cor azim_r_num=1489"""
# """do_distortion=2 off_1=0 off_2=0 verbose=0 src_ext=.edf wvl=1.000000e-10 cen_1=1.050000e+03 cen_2=1.000000e+03 dis=1.000000e-01 pix_1=4.722440e-05 pix_2=4.683150e-05 do_dark=0 cor_ext=.cor azim_int=1 azim_pass=0 azim_ext=.cor azim_r_num=1489"""
EDAssert.equal(edPluginSPD.getSPDConfig(), expected)
else:
ffx = FullFieldXas()
if os.path.isfile(".XSDataInputFullFieldXAS.xml"):
ffx.load(".XSDataInputFullFieldXAS.xml")
ffx.dontAlign = dontAlign
if dontAlign:
print ("*" * 80)
print ("*" + "Skipping image alignement part".center(78) + "*")
print ("*" * 80)
ffx.setup(_listInput=paths, _mode=mode)
if not isinstance(ffx.reference, int):
ffx.uploadReferenceFrame(ffx.reference)
ffx.save(".XSDataInputFullFieldXAS.xml")
ffx.dump("analysis-%s.json" % time.strftime("%Y%m%d-%Hh%Mm%Ss"))
edna = EDParallelExecute(
ffx.pluginName, ffx.makeXML, _functXMLerr=ffx.error, _bVerbose=True, _bDebug=debug, _iNbThreads=iNbCPU
)
edna.runEDNA(ffx.listInput, ffx.strMode, ffx.bNewerOnly)
EDVerbose.WARNING("Back to main !")
EDJob.synchronizeAll()
ffx.updateAttrRefImage()
EDPluginControlAlignStackv1_0.showData()
if keepShare:
EDShare.close()
elif (ffx.getNrErrors() == 0) and (not EDVerbose.isVerboseDebug()):
EDVerbose.WARNING("All processing finished successfully: Remove EDShare's big HDF5 file")
EDShare.close(remove=True)
else:
EDShare.close()
def process(self, _edObject=None):
EDPluginExec.process(self)
EDVerbose.DEBUG("EDPluginExportAsciiPowderv1_0.process")
if len(self.inputArray.shape) == 2:
iNbAzimBin, iLength = self.inputArray.shape
if iNbAzimBin == 1:
nplInt = self.inputArray[0, :]
else:
nonNull = ((abs(self.inputArray - self.fDummy) > self.fDeltaDummy)).astype("int").sum(axis=0)
nplInt = self.inputArray.sum(axis=0) / nonNull
elif len(self.inputArray.shape) == 1:
nplInt = self.inputArray
iLength = len(nplInt)
else:
EDVerbose.ERROR("EDPluginExportAsciiPowderv1_0.inputArray has a large dimension: %s " % (self.inputArray.shape))
nplTth = numpy.degrees(numpy.arctan((numpy.arange(iLength) + 0.5 + self.fRadOffset) * self.fPixelSize / self.fDistance))
if EDVerbose.isVerboseDebug():
open("raw.dat", "wb").write("\n".join(["%s\t%s" % (nplTth[i], nplInt[i]) for i in range(len(nplInt))]))
open("inputArray.xml", "wb").write(EDUtilsArray.arrayToXSData(nplInt, _bIncludeMd5sum=False).marshal())
XRPD = lambda tth: numpy.interp(tth, nplTth, nplInt, left=0, right=0)
tthMax = nplTth[-1]
tthMin = nplTth[0]
if (self.iNbBins is None):
self.iNbBins = iLength
pyfStep = (tthMax - tthMin) / (self.iNbBins - 1)
# # Create the output data
if "cif" in self.strFormat:
cif = CIF()
cif[ "_audit_creation_method" ] = 'EDNA'
cif[ "_pd_meas_2theta_range_inc" ] = str(pyfStep)
cif[ "_pd_meas_2theta_range_max" ] = str(tthMax)
cif[ "_pd_meas_2theta_range_min" ] = str(tthMin)
cif[ "_pd_meas_number_of_points" ] = str(self.iNbBins)
cif[ "_pd_meas_scan_method" ] = "fixed"
if "Title" in self.dHeader:
cif[ "_pd_spec_description"] = self.dHeader["Title"]
if self.fWavelength is not None:
cif["_diffrn_radiation_wavelength"] = str(self.fWavelength * 1.0e10) #in Angstrom acording to CIF dict
cif["_pd_instr_dist_spec/detc"] = str(self.fDistance * 1.0e3) #in mm acording to CIF dict
oneloop = []
for i in numpy.linspace(tthMin, tthMax, self.iNbBins):
oneloop.append({ "_pd_meas_intensity_total" : str(XRPD(i)) })
cif["loop_"] = [ [ ["_pd_meas_intensity_total"], oneloop ] ]
cif.saveCIF(self.outputFilename)
elif "chi" in self.strFormat :
f = open(self.outputFilename, "wb")
if "Title" in self.dHeader:
f.write(self.dHeader["Title"] + ": ")
f.write("Angular Profile\nTwo-Theta Angle (degrees)\nIntensity (normalised)\n%i\n" % self.iNbBins)
for i in numpy.linspace(tthMin, tthMax, self.iNbBins):
f.write("%f\t%f\n" % (i, XRPD(i)))
f.close()
elif "spr" in self.strFormat :
self.npaTwoTheta = numpy.linspace(tthMin, tthMax, self.iNbBins)
f = open(self.outputFilename, "wb")
f.write("# Generated by EDNA, Spread sheet with fortran order for fit2d compatibility" + os.linesep)
f.write("# dim0 (radial values in degrees): " + "\t".join(["%.2f" % i for i in self.npaTwoTheta]) + os.linesep)
f.write("# dim1 (azimuthal values in degrees): " + "\t".join(["%.2f" % i for i in numpy.degrees(self.fAzimSize * (numpy.arange(iNbAzimBin) + self.fAzimOffset))]) + os.linesep)
f.write("%i,%i\tStartPixel=(1,1)" % (self.iNbBins, iNbAzimBin) + os.linesep)
for i in xrange(iNbAzimBin):
XRPD = lambda tth: numpy.interp(tth, nplTth, self.inputArray[i, :], left=0, right=0)
f.write("\t".join(["%8.4f" % i for i in XRPD(self.npaTwoTheta)]) + os.linesep)
f.close()
else:
self.npaTwoTheta = numpy.linspace(tthMin, tthMax, self.iNbBins)
self.npaIntensities = XRPD(self.npaTwoTheta)
def process(self, _edObject=None):
EDPluginExec.process(self)
self.DEBUG("EDPluginExecStitchOffsetedImagev1_0.process")
shiftedImage = []
distanceSq = lambda t2f: (t2f[0] * t2f[0] + t2f[1] * t2f[1])
ref = self._lOffsets[0]
refOffset = distanceSq(ref)
shape = self._lImages[0].shape
if self._strMask:
mask = (1 - fabio.open(self._strMask).data).astype("bool")
else:
mask = 0
for img, offset, dummy in zip(self._lImages, self._lOffsets, self._lDummies):
shImg = scipy.ndimage.shift(img, offset, cval=dummy[0], order=0)
if dummy[1] == 0:
if self._strMask:
shImgMasked = numpy.ma.MaskedArray(shImg,
(shImg == dummy[0]) + scipy.ndimage.shift(mask, offset, cval=1, order=0))
else:
shImgMasked = numpy.ma.MaskedArray(shImg, (shImg == dummy[0]))
else:
if self._strMask:
shImgMasked = numpy.ma.MaskedArray(shImg,
(abs(shImg - dummy[0]) <= dummy[1]) + scipy.ndimage.shift(mask, offset, cval=1, order=0))
else:
shImgMasked = numpy.ma.MaskedArray(shImg, (abs(shImg - dummy[0]) <= dummy[1]))
shiftedImage.append(shImgMasked)
if (offset != ref) and (distanceSq(offset) < refOffset):
ref = offset
refOffset = distanceSq(offset)
refIdx = self._lOffsets.index(ref)
if EDVerbose.isVerboseDebug():
e = edfimage(data=shiftedImage[0].filled(self._fDummy),
header={"Dummy":str(self._fDummy), "Offset_1":str(self._lOffsets[0][0]), "Offset_2":str(self._lOffsets[0][1])})
for img, offset in zip(shiftedImage[1:], self._lOffsets[1:]):
e.appendFrame(data=img.filled(self._fDummy),
header={"Dummy":str(self._fDummy), "Offset_1":str(offset[0]), "Offset_2":str(offset[1])})
e.write("stack.edf")
ROI = False
if self.tCenter is None:
#the default center is the geometry center of the image ...
self.tCenter = [ i // 2 for i in shape ]
if self.tWidth is not None:
d0min = max(0, self.tCenter[0] - (self.tWidth[0] // 2))
d0max = min(shape[0], d0min + self.tWidth[0])
d1min = max(0, self.tCenter[1] - (self.tWidth[1] // 2))
d1max = min(shape[1], d1min + self.tWidth[1])
shape = (d0max - d0min, d1max - d1min)
else:
d0min = 0
d0max = shape[0]
d1min = 0
d1max = shape[1]
refImg = shiftedImage[refIdx]
stackMaskedImg = numpy.ma.zeros((len(self._lOffsets), refImg.shape[0], refImg.shape[1]))
self.screen("ROI[%s:%s, %s:%s]\t Autoscale: %s\tBlending method: %s" % (d0min, d0max, d1min, d1max, self._bAutoscale, self._strBlending))
if self._bAutoscale:
for idx, img in enumerate(shiftedImage):
ratio = (refImg[d0min:d0max, d1min:d1max] / img[d0min:d0max, d1min:d1max])
stackMaskedImg[idx] = ratio.mean() * img
else:
for idx, img in enumerate(shiftedImage):
stackMaskedImg[idx] = img
if self._strBlending.lower().startswith("naive"):
npaTempBool = numpy.cumsum((1 - stackMaskedImg.mask), axis=0) * (1 - stackMaskedImg.mask) == 1
result = numpy.ma.MaskedArray((npaTempBool * stackMaskedImg.data).sum(axis=0), stackMaskedImg.mask.prod(axis=0))
elif self._strBlending.lower().startswith("max"):
result = stackMaskedImg.max(axis=0)
elif self._strBlending.lower().startswith("min"):
result = stackMaskedImg.min(axis=0)
else: #self._strBlending.lower() == "mean":
result = stackMaskedImg.mean(axis=0)
self._ndaResult = result.filled(self._fDummy)
def postProcess(self, _edObject=None):
EDPluginExecProcessScript.postProcess(self)
EDVerbose.DEBUG("EDPluginSPDCakev1_1.postProcess")
xsDataInputSPDCake = self.getDataInput()
strOutputFileType = xsDataInputSPDCake.getOutputFileType().getValue()
# Determine the image file name without path and suffix
strInputImageFilePath = xsDataInputSPDCake.getInputFile().getPath(
).getValue()
strInputFileNameWithoutSuffix = os.path.splitext(
EDUtilsFile.getBaseName(strInputImageFilePath))[0]
self.strOutputFileSuffix = "data"
if (strOutputFileType == "PowderCIF"):
self.strOutputFileSuffix = "cif"
elif (strOutputFileType == "CHIPLOT"):
self.strOutputFileSuffix = "chi"
strOutputFileName = strInputFileNameWithoutSuffix + "." + self.strOutputFileSuffix
if self.outputDir is None:
self.m_strOutputFilePath = os.path.join(self.getWorkingDirectory(),
strOutputFileName)
else:
self.m_strOutputFilePath = os.path.join(self.outputDir,
strOutputFileName)
PyStrCakeFilePrefix = os.path.splitext(
os.path.split(strInputImageFilePath)[1])[0]
################################################################
#### Do some manipulation of the output image ##############
################################################################
EDFCakeFile = fabio.open(
os.path.join(self.getWorkingDirectory(),
PyStrCakeFilePrefix + ".azim.edf"))
npaData = EDFCakeFile.data
pydHeader = EDFCakeFile.header
pyfPixSize = float(pydHeader["PSize_1"].split()[0])
pyfDist = float(pydHeader["SampleDistance"].split()[0])
EDVerbose.DEBUG("Calculation done with PixSize=%s, distance= %s" %
(pydHeader["PSize_1"], pydHeader["SampleDistance"]))
pyiNbAzimBin, pyiLength = npaData.shape
nplInt = npaData.reshape((pyiLength))
nplTth = numpy.degrees(
numpy.arctan(
numpy.linspace(
0.5 * pyfPixSize / pyfDist,
(pyiLength - 0.5) * pyfPixSize / pyfDist,
pyiLength,
)))
#for the description of the +0.5 term, please refer to http://www.esrf.fr/computing/scientific/SAXS/doc/SaxsKeywords/SaxsKeywords.pdf page 23
######################################Debugging#######################
f = open(os.path.join(self.getWorkingDirectory(), "original.dat"), "w")
for i in range(pyiLength):
f.write("%f\t%f\n" % (nplTth[i], nplInt[i]))
f.close()
##############################end Debugging############################
XRPD = lambda tth: numpy.interp(tth, nplTth, nplInt, left=0, right=0)
pyfTthMin = nplTth[0]
pyfTthMax = nplTth[-1]
pyfStep = (pyfTthMax - pyfTthMin) / (pyiLength - 1)
########### Remove large files to prevent disk saturation when not in debug mode ###################
if not EDVerbose.isVerboseDebug():
os.remove(
os.path.join(self.getWorkingDirectory(),
PyStrCakeFilePrefix + ".cor.edf"))
os.remove(
os.path.join(self.getWorkingDirectory(),
PyStrCakeFilePrefix + ".azim.edf"))
# # Create the output data
xsDataResultSPDCake = XSDataResultSPDCake()
if (self.m_strOutputFilePath is not None):
if (strOutputFileType == "PowderCIF"):
import CIFfile
cif = CIFfile.CIF()
cif["_audit_creation_method"] = 'From 2-D detector using SPD and CIFfile'
cif["_pd_meas_2theta_range_inc"] = str(pyfStep)
cif["_pd_meas_2theta_range_max"] = str(pyfTthMax)
cif["_pd_meas_2theta_range_min"] = str(pyfTthMin)
cif["_pd_meas_number_of_points"] = str(pyiLength)
cif["_pd_meas_scan_method"] = "fixed"
cif["_pd_spec_description"] = pydHeader["title"]
cif["_diffrn_radiation_wavelength"] = str(
self.getDataInput().getWavelength().getValue())
cif["_pd_instr_dist_spec/detc"] = str(self.getDataInput(
).getSampleToDetectorDistance().getValue())
oneloop = []
#range( pyiLength ):
for i in numpy.linspace(pyfTthMin, pyfTthMax, pyiLength):
oneloop.append({"_pd_meas_intensity_total": str(XRPD(i))})
cif["loop_"] = [[["_pd_meas_intensity_total"], oneloop]]
cif.saveCIF(self.m_strOutputFilePath)
elif (strOutputFileType == "CHIPLOT"):
f = open(
os.path.join(self.getWorkingDirectory(),
self.m_strOutputFilePath), "w")
f.write(
pydHeader["title"] +
": Angular Profile\nTwo-Theta Angle (degrees)\nIntensity (normalised)\n%i\n"
% pyiLength)
for i in numpy.linspace(pyfTthMin, pyfTthMax, pyiLength):
f.write("%f\t%f\n" % (i, XRPD(i)))
f.close()
xsDataFile = XSDataFile()
xsDataFile.setPath(XSDataString(self.m_strOutputFilePath))
xsDataResultSPDCake.setCakedFile(xsDataFile)
self.setDataOutput(xsDataResultSPDCake)
def process(self, _edObject=None):
"""
This method starts the execution of the EDNA script using EDActionExecuteSystemCommand
In case of failure, an error message is added to the list and the plugin fails.
"""
EDPluginExecProcess.process(self)
EDVerbose.DEBUG("EDPluginExecProcessScript.process starting")
self.synchronizeOn()
if "TIMEOUT" in EDUtilsFile.readFile(self.__strPathToHostNamePidFile):
EDVerbose.error("Timeout message found in %s" % self.__strPathToHostNamePidFile)
self.hasTimedOut(True)
bTimeOut = self.isTimeOut()
if (bTimeOut == True):
EDVerbose.DEBUG("EDPluginExecProcessScript.process ========================================= ERROR! ================")
strErrorMessage = "%s execution timed out ( > %.1f s)!" % (self.__strScriptExecutable, float(self.getTimeOut()))
EDVerbose.error(strErrorMessage)
self.addErrorMessage(strErrorMessage)
self.setFailure()
strExecutionStatus = "timeout"
if (EDVerbose.isVerboseDebug()):
raise RuntimeError(strErrorMessage)
else:
strExecutionStatus = self.getExecutionStatus()
# Report an error if the result is not "0" and the result is not an empty string
if (not strExecutionStatus == "0" and not strExecutionStatus == ""):
EDVerbose.DEBUG("EDPluginExecProcessScript.process ========================================= ERROR! ================")
# Add any messages in the error log file (.err) to the list of error messages
strErrorLog = self.readProcessErrorLogFile()
if (strErrorLog is None):
strErrorMessage = "%s execution error - status : %s" % (self.getClassName(), strExecutionStatus)
EDVerbose.error(strErrorMessage)
self.addErrorMessage(strErrorMessage)
self.setFailure()
if (EDVerbose.isVerboseDebug()):
raise RuntimeError(strErrorMessage)
else:
strErrorMessage = "%s execution error : %s" % (self.getClassName(), strErrorLog)
EDVerbose.error(strErrorMessage)
self.addErrorMessage(strErrorMessage)
self.setFailure()
if (EDVerbose.isVerboseDebug()):
raise RuntimeError(strErrorMessage)
# Add any messages in the log file (.log) to the list of error messages
strLog = self.readProcessLogFile()
if strLog is not None:
# Cut down the log file to the last part if it's long
listLogLines = strLog.split("\n")
if len(listLogLines) > self.__iNumberOfLastLinesFromLogFileIfError:
strErrorMessage = "Last part of the %s log file:" % self.getScriptExecutable()
EDVerbose.ERROR(strErrorMessage)
self.addErrorMessage(strErrorMessage)
listLogLastLines = listLogLines[-self.__iNumberOfLastLinesFromLogFileIfError:]
strLogLastLines = ""
for strLine in listLogLastLines:
strLogLastLines += strLine + "\n"
EDVerbose.ERROR(strLogLastLines)
self.addErrorMessage(strLogLastLines)
strMessage = "Please inspect log file: %s" % os.path.join(self.getWorkingDirectory(), self.getScriptLogFileName())
EDVerbose.ERROR(strMessage)
self.addErrorMessage(strMessage)
else:
strMessage = "%s log file: \n%s" % (self.getScriptExecutable(), strLog)
EDVerbose.ERROR(strMessage)
self.addErrorMessage(strMessage)
# Save the return code of the external program in the PID file
open(self.__strPathToHostNamePidFile, "a").write(strExecutionStatus + os.linesep)
EDVerbose.DEBUG("EDPluginExecProcessScript.process finished ")
self.synchronizeOff()
def configure(self):
"""
Configures the plugin from the configuration file with the following parameters
- The shell that will execute the script
- Script executor
- Script executable to be invoked
- Path to CCP4 setup file if required
- The 3rd party executable installed version
"""
EDPluginExecProcess.configure(self)
EDVerbose.DEBUG("EDPluginExecProcessScript.configure")
xsPluginItem = self.getConfiguration()
if (xsPluginItem == None):
EDVerbose.warning("EDPluginExecProcessScript.configure: No plugin item defined.")
xsPluginItem = XSPluginItem()
strShell = EDConfiguration.getStringParamValue(xsPluginItem, EDPluginExecProcessScript.CONF_EXEC_PROCESS_SCRIPT_SHELL)
if(strShell == None):
EDVerbose.DEBUG("EDPluginExecProcessScript.configure: No configuration parameter found for: " + \
EDPluginExecProcessScript.CONF_EXEC_PROCESS_SCRIPT_SHELL + ", using default value: " + self.getScriptShell())
else:
self.setScriptShell(strShell)
strScriptExecutor = EDConfiguration.getStringParamValue(xsPluginItem, EDPluginExecProcessScript.CONF_EXEC_PROCESS_SCRIPT_EXECUTOR)
if(strScriptExecutor == None):
self.setScriptExecutor(self.getScriptShell())
EDVerbose.DEBUG("EDPluginExecProcessScript.configure: No configuration parameter found for: " + \
EDPluginExecProcessScript.CONF_EXEC_PROCESS_SCRIPT_EXECUTOR + ", using script shell: " + self.getScriptShell())
else:
self.setScriptExecutor(strScriptExecutor)
if (self.getScriptExecutable() is None):
strScriptExecutable = EDConfiguration.getStringParamValue(xsPluginItem, EDPluginExecProcessScript.CONF_EXEC_PROCESS_SCRIPT_EXECUTABLE)
if(strScriptExecutable == None):
strErrorMessage = "Configuration parameter missing: " + EDPluginExecProcessScript.CONF_EXEC_PROCESS_SCRIPT_EXECUTABLE
EDVerbose.error(strErrorMessage)
self.addErrorMessage(strErrorMessage)
self.setFailure()
if (EDVerbose.isVerboseDebug()):
raise RuntimeError, strErrorMessage
else:
# Check that the executable file exists
if (os.path.exists(strScriptExecutable) == False):
strErrorMessage = "Cannot find configured " + EDPluginExecProcessScript.CONF_EXEC_PROCESS_SCRIPT_EXECUTABLE + " : " + strScriptExecutable
EDVerbose.error(strErrorMessage)
self.addErrorMessage(strErrorMessage)
self.setFailure()
if (EDVerbose.isVerboseDebug()):
raise RuntimeError, strErrorMessage
else:
self.setScriptExecutable(strScriptExecutable)
strConfigSetupCCP4 = EDConfiguration.getStringParamValue(xsPluginItem, EDPluginExecProcessScript.CONF_EXEC_PROCESS_SCRIPT_SETUP_CCP4)
if(strConfigSetupCCP4 == None):
EDVerbose.DEBUG("EDPluginExecProcessScript.configure: No configuration parameter found for: " + \
EDPluginExecProcessScript.CONF_EXEC_PROCESS_SCRIPT_SETUP_CCP4 + ", NO default value!")
else:
self.setSetupCCP4(strConfigSetupCCP4)
strVersion = EDConfiguration.getStringParamValue(xsPluginItem, EDPluginExecProcessScript.CONF_EXEC_PROCESS_SCRIPT_VERSION_STRING)
if(strVersion == None):
EDVerbose.DEBUG("EDPluginExecProcessScript.configure: No configuration parameter found for: " + \
EDPluginExecProcessScript.CONF_EXEC_PROCESS_SCRIPT_VERSION_STRING + ", NO default value!")
else:
self.setStringVersion(strVersion)
if (self.__strScriptBaseName == None):
self.setScriptBaseName(self.getBaseName())
if (self.__strScriptFileName == None):
self.setScriptFileName(self.__strScriptBaseName + ".sh")
if (self.__strScriptLogFileName == None):
self.setScriptLogFileName(self.__strScriptBaseName + ".log")
if (self.__strScriptErrorLogFileName == None):
self.setScriptErrorLogFileName(self.__strScriptBaseName + ".err")
self.__strPathToHostNamePidFile = os.path.join(self.getWorkingDirectory(), os.path.basename(self.__strScriptExecutable) + "_hostNamePid.txt")
def postProcess(self, _edObject=None):
EDPluginExecProcessScript.postProcess(self)
EDVerbose.DEBUG("EDPluginSPDCakev1_1.postProcess")
xsDataInputSPDCake = self.getDataInput()
strOutputFileType = xsDataInputSPDCake.getOutputFileType().getValue()
# Determine the image file name without path and suffix
strInputImageFilePath = xsDataInputSPDCake.getInputFile().getPath().getValue()
strInputFileNameWithoutSuffix = os.path.splitext(EDUtilsFile.getBaseName(strInputImageFilePath))[0]
self.strOutputFileSuffix = "data"
if (strOutputFileType == "PowderCIF"):
self.strOutputFileSuffix = "cif"
elif (strOutputFileType == "CHIPLOT"):
self.strOutputFileSuffix = "chi"
strOutputFileName = strInputFileNameWithoutSuffix + "." + self.strOutputFileSuffix
if self.outputDir is None:
self.m_strOutputFilePath = os.path.join(self.getWorkingDirectory(), strOutputFileName)
else:
self.m_strOutputFilePath = os.path.join(self.outputDir, strOutputFileName)
PyStrCakeFilePrefix = os.path.splitext(os.path.split(strInputImageFilePath)[1])[0]
################################################################
#### Do some manipulation of the output image ##############
################################################################
EDFCakeFile = fabio.open(os.path.join(self.getWorkingDirectory(), PyStrCakeFilePrefix + ".azim.edf"))
npaData = EDFCakeFile.data
pydHeader = EDFCakeFile.header
pyfPixSize = float(pydHeader["PSize_1"].split()[0])
pyfDist = float(pydHeader["SampleDistance"].split()[0])
EDVerbose.DEBUG("Calculation done with PixSize=%s, distance= %s" % (pydHeader["PSize_1"], pydHeader["SampleDistance"]))
pyiNbAzimBin, pyiLength = npaData.shape
nplInt = npaData.reshape((pyiLength))
nplTth = numpy.degrees(numpy.arctan(numpy.linspace(0.5 * pyfPixSize / pyfDist, (pyiLength - 0.5) * pyfPixSize / pyfDist , pyiLength,)))
#for the description of the +0.5 term, please refer to http://www.esrf.fr/computing/scientific/SAXS/doc/SaxsKeywords/SaxsKeywords.pdf page 23
######################################Debugging#######################
f = open(os.path.join(self.getWorkingDirectory(), "original.dat"), "w")
for i in range(pyiLength):
f.write("%f\t%f\n" % (nplTth[i], nplInt[i]))
f.close()
##############################end Debugging############################
XRPD = lambda tth: numpy.interp(tth, nplTth, nplInt, left=0, right=0)
pyfTthMin = nplTth[0]
pyfTthMax = nplTth[-1]
pyfStep = (pyfTthMax - pyfTthMin) / (pyiLength - 1)
########### Remove large files to prevent disk saturation when not in debug mode ###################
if not EDVerbose.isVerboseDebug():
os.remove(os.path.join(self.getWorkingDirectory(), PyStrCakeFilePrefix + ".cor.edf"))
os.remove(os.path.join(self.getWorkingDirectory(), PyStrCakeFilePrefix + ".azim.edf"))
# # Create the output data
xsDataResultSPDCake = XSDataResultSPDCake()
if (self.m_strOutputFilePath is not None):
if (strOutputFileType == "PowderCIF"):
import CIFfile
cif = CIFfile.CIF()
cif[ "_audit_creation_method" ] = 'From 2-D detector using SPD and CIFfile'
cif[ "_pd_meas_2theta_range_inc" ] = str(pyfStep)
cif[ "_pd_meas_2theta_range_max" ] = str(pyfTthMax)
cif[ "_pd_meas_2theta_range_min" ] = str(pyfTthMin)
cif[ "_pd_meas_number_of_points" ] = str(pyiLength)
cif[ "_pd_meas_scan_method" ] = "fixed"
cif[ "_pd_spec_description" ] = pydHeader["title"]
cif["_diffrn_radiation_wavelength"] = str(self.getDataInput().getWavelength().getValue())
cif["_pd_instr_dist_spec/detc"] = str(self.getDataInput().getSampleToDetectorDistance().getValue())
oneloop = []
#range( pyiLength ):
for i in numpy.linspace(pyfTthMin, pyfTthMax, pyiLength):
oneloop.append({ "_pd_meas_intensity_total" : str(XRPD(i)) })
cif["loop_"] = [ [ ["_pd_meas_intensity_total"], oneloop ] ]
cif.saveCIF(self.m_strOutputFilePath)
elif (strOutputFileType == "CHIPLOT"):
f = open(os.path.join(self.getWorkingDirectory(), self.m_strOutputFilePath), "w")
f.write(pydHeader["title"] + ": Angular Profile\nTwo-Theta Angle (degrees)\nIntensity (normalised)\n%i\n" % pyiLength)
for i in numpy.linspace(pyfTthMin, pyfTthMax, pyiLength):
f.write("%f\t%f\n" % (i, XRPD(i)))
f.close()
xsDataFile = XSDataFile()
xsDataFile.setPath(XSDataString(self.m_strOutputFilePath))
xsDataResultSPDCake.setCakedFile(xsDataFile)
self.setDataOutput(xsDataResultSPDCake)
def process(self, _edObject=None):
EDPluginExec.process(self)
EDVerbose.DEBUG("EDPluginExportAsciiPowderv1_0.process")
if len(self.inputArray.shape) == 2:
iNbAzimBin, iLength = self.inputArray.shape
if iNbAzimBin == 1:
nplInt = self.inputArray[0, :]
else:
nonNull = ((abs(self.inputArray - self.fDummy) >
self.fDeltaDummy)).astype("int").sum(axis=0)
nplInt = self.inputArray.sum(axis=0) / nonNull
elif len(self.inputArray.shape) == 1:
nplInt = self.inputArray
iLength = len(nplInt)
else:
EDVerbose.ERROR(
"EDPluginExportAsciiPowderv1_0.inputArray has a large dimension: %s "
% (self.inputArray.shape))
nplTth = numpy.degrees(
numpy.arctan((numpy.arange(iLength) + 0.5 + self.fRadOffset) *
self.fPixelSize / self.fDistance))
if EDVerbose.isVerboseDebug():
open("raw.dat", "wb").write("\n".join([
"%s\t%s" % (nplTth[i], nplInt[i]) for i in range(len(nplInt))
]))
open("inputArray.xml", "wb").write(
EDUtilsArray.arrayToXSData(nplInt,
_bIncludeMd5sum=False).marshal())
XRPD = lambda tth: numpy.interp(tth, nplTth, nplInt, left=0, right=0)
tthMax = nplTth[-1]
tthMin = nplTth[0]
if (self.iNbBins is None):
self.iNbBins = iLength
pyfStep = (tthMax - tthMin) / (self.iNbBins - 1)
# # Create the output data
if "cif" in self.strFormat:
cif = CIF()
cif["_audit_creation_method"] = 'EDNA'
cif["_pd_meas_2theta_range_inc"] = str(pyfStep)
cif["_pd_meas_2theta_range_max"] = str(tthMax)
cif["_pd_meas_2theta_range_min"] = str(tthMin)
cif["_pd_meas_number_of_points"] = str(self.iNbBins)
cif["_pd_meas_scan_method"] = "fixed"
if "Title" in self.dHeader:
cif["_pd_spec_description"] = self.dHeader["Title"]
if self.fWavelength is not None:
cif["_diffrn_radiation_wavelength"] = str(
self.fWavelength *
1.0e10) #in Angstrom acording to CIF dict
cif["_pd_instr_dist_spec/detc"] = str(
self.fDistance * 1.0e3) #in mm acording to CIF dict
oneloop = []
for i in numpy.linspace(tthMin, tthMax, self.iNbBins):
oneloop.append({"_pd_meas_intensity_total": str(XRPD(i))})
cif["loop_"] = [[["_pd_meas_intensity_total"], oneloop]]
cif.saveCIF(self.outputFilename)
elif "chi" in self.strFormat:
f = open(self.outputFilename, "wb")
if "Title" in self.dHeader:
f.write(self.dHeader["Title"] + ": ")
f.write(
"Angular Profile\nTwo-Theta Angle (degrees)\nIntensity (normalised)\n%i\n"
% self.iNbBins)
for i in numpy.linspace(tthMin, tthMax, self.iNbBins):
f.write("%f\t%f\n" % (i, XRPD(i)))
f.close()
elif "spr" in self.strFormat:
self.npaTwoTheta = numpy.linspace(tthMin, tthMax, self.iNbBins)
f = open(self.outputFilename, "wb")
f.write(
"# Generated by EDNA, Spread sheet with fortran order for fit2d compatibility"
+ os.linesep)
f.write("# dim0 (radial values in degrees): " +
"\t".join(["%.2f" % i
for i in self.npaTwoTheta]) + os.linesep)
f.write("# dim1 (azimuthal values in degrees): " + "\t".join([
"%.2f" % i for i in numpy.degrees(self.fAzimSize *
(numpy.arange(iNbAzimBin) +
self.fAzimOffset))
]) + os.linesep)
f.write("%i,%i\tStartPixel=(1,1)" % (self.iNbBins, iNbAzimBin) +
os.linesep)
for i in xrange(iNbAzimBin):
XRPD = lambda tth: numpy.interp(
tth, nplTth, self.inputArray[i, :], left=0, right=0)
f.write(
"\t".join(["%8.4f" % i
for i in XRPD(self.npaTwoTheta)]) + os.linesep)
f.close()
else:
self.npaTwoTheta = numpy.linspace(tthMin, tthMax, self.iNbBins)
self.npaIntensities = XRPD(self.npaTwoTheta)
if ("EDNA_HOME" in os.environ):
if (os.environ["EDNA_HOME"] != strEdnaHome):
print("Warning: EDNA_HOME redefined to %s" % strEdnaHome)
os.environ["EDNA_HOME"] = strEdnaHome
else:
os.environ["EDNA_HOME"] = strEdnaHome
sys.path.append(os.path.join(os.environ["EDNA_HOME"], "kernel", "src"))
from EDUtilsLibraryInstaller import EDUtilsLibraryInstaller
from EDVerbose import EDVerbose
if __name__ == "__main__":
installDir = os.path.abspath(sys.argv[0]).split(os.sep)[-2]
EDVerbose.screen("Building %s" % installDir)
install = EDUtilsLibraryInstaller(installDir, strArchiveName)
install.checkPythonVersion()
install.downloadLibrary()
install.dependency("numpy", "20090405-Numpy-1.3")
install.unZipArchive()
try:
install.buildSources()
except Exception:
EDVerbose.ERROR("Error in the build")
install.installBuilt()
if not EDVerbose.isVerboseDebug():
install.cleanSources()
else:
EDVerbose.ERROR(
"This installer program is not made to be imported, please just run it"
)
def process(self, _edObject=None):
EDPluginExec.process(self)
self.DEBUG("EDPluginExecStitchOffsetedImagev1_0.process")
shiftedImage = []
distanceSq = lambda t2f: (t2f[0] * t2f[0] + t2f[1] * t2f[1])
ref = self._lOffsets[0]
refOffset = distanceSq(ref)
shape = self._lImages[0].shape
if self._strMask:
mask = (1 - fabio.open(self._strMask).data).astype("bool")
else:
mask = 0
for img, offset, dummy in zip(self._lImages, self._lOffsets,
self._lDummies):
shImg = scipy.ndimage.shift(img, offset, cval=dummy[0], order=0)
if dummy[1] == 0:
if self._strMask:
shImgMasked = numpy.ma.MaskedArray(
shImg, (shImg == dummy[0]) +
scipy.ndimage.shift(mask, offset, cval=1, order=0))
else:
shImgMasked = numpy.ma.MaskedArray(shImg,
(shImg == dummy[0]))
else:
if self._strMask:
shImgMasked = numpy.ma.MaskedArray(
shImg, (abs(shImg - dummy[0]) <= dummy[1]) +
scipy.ndimage.shift(mask, offset, cval=1, order=0))
else:
shImgMasked = numpy.ma.MaskedArray(
shImg, (abs(shImg - dummy[0]) <= dummy[1]))
shiftedImage.append(shImgMasked)
if (offset != ref) and (distanceSq(offset) < refOffset):
ref = offset
refOffset = distanceSq(offset)
refIdx = self._lOffsets.index(ref)
if EDVerbose.isVerboseDebug():
e = edfimage(data=shiftedImage[0].filled(self._fDummy),
header={
"Dummy": str(self._fDummy),
"Offset_1": str(self._lOffsets[0][0]),
"Offset_2": str(self._lOffsets[0][1])
})
for img, offset in zip(shiftedImage[1:], self._lOffsets[1:]):
e.appendFrame(data=img.filled(self._fDummy),
header={
"Dummy": str(self._fDummy),
"Offset_1": str(offset[0]),
"Offset_2": str(offset[1])
})
e.write("stack.edf")
ROI = False
if self.tCenter is None:
#the default center is the geometry center of the image ...
self.tCenter = [i // 2 for i in shape]
if self.tWidth is not None:
d0min = max(0, self.tCenter[0] - (self.tWidth[0] // 2))
d0max = min(shape[0], d0min + self.tWidth[0])
d1min = max(0, self.tCenter[1] - (self.tWidth[1] // 2))
d1max = min(shape[1], d1min + self.tWidth[1])
shape = (d0max - d0min, d1max - d1min)
else:
d0min = 0
d0max = shape[0]
d1min = 0
d1max = shape[1]
refImg = shiftedImage[refIdx]
stackMaskedImg = numpy.ma.zeros(
(len(self._lOffsets), refImg.shape[0], refImg.shape[1]))
self.screen(
"ROI[%s:%s, %s:%s]\t Autoscale: %s\tBlending method: %s" %
(d0min, d0max, d1min, d1max, self._bAutoscale, self._strBlending))
if self._bAutoscale:
for idx, img in enumerate(shiftedImage):
ratio = (refImg[d0min:d0max, d1min:d1max] /
img[d0min:d0max, d1min:d1max])
stackMaskedImg[idx] = ratio.mean() * img
else:
for idx, img in enumerate(shiftedImage):
stackMaskedImg[idx] = img
if self._strBlending.lower().startswith("naive"):
npaTempBool = numpy.cumsum((1 - stackMaskedImg.mask),
axis=0) * (1 - stackMaskedImg.mask) == 1
result = numpy.ma.MaskedArray(
(npaTempBool * stackMaskedImg.data).sum(axis=0),
stackMaskedImg.mask.prod(axis=0))
elif self._strBlending.lower().startswith("max"):
result = stackMaskedImg.max(axis=0)
elif self._strBlending.lower().startswith("min"):
result = stackMaskedImg.min(axis=0)
else: #self._strBlending.lower() == "mean":
result = stackMaskedImg.mean(axis=0)
self._ndaResult = result.filled(self._fDummy)
def configure(self):
"""
Configures the plugin from the configuration file with the following
parameters
- The shell that will execute the script
- Script executor
- Script executable to be invoked
- Path to CCP4 setup file if required
- The 3rd party executable installed version
"""
EDPluginExec.configure(self)
EDVerbose.DEBUG("EDPluginExecProcessXIA2CORE.configure")
xsPluginItem = self.getConfiguration()
if (xsPluginItem == None):
EDVerbose.warning(
"EDPluginExecProcessXIA2CORE.configure: No plugin item defined.")
xsPluginItem = XSPluginItem()
if (self.getExecutable() is None):
strExecutable = EDConfiguration.getStringParamValue(
xsPluginItem,
EDPluginExecProcessXIA2CORE.CONF_EXEC_PROCESS_EXECUTABLE)
if(strExecutable == None):
strErrorMessage = "Configuration parameter missing: " + \
EDPluginExecProcessXIA2CORE.CONF_EXEC_PROCESS_EXECUTABLE
EDVerbose.error(strErrorMessage)
self.addErrorMessage(strErrorMessage)
self.setFailure()
if (EDVerbose.isVerboseDebug()):
raise RuntimeError, strErrorMessage
else:
# Check that the executable file exists
if (os.path.exists(strExecutable) == False):
strErrorMessage = "Cannot find configured " + EDPluginExecProcessXIA2CORE.CONF_EXEC_PROCESS_EXECUTABLE + " : " + strExecutable
EDVerbose.error(strErrorMessage)
self.addErrorMessage(strErrorMessage)
self.setFailure()
if (EDVerbose.isVerboseDebug()):
raise RuntimeError, strErrorMessage
else:
self.setExecutable(strExecutable)
if (self.getConfigXIA2COREType() is None):
strXIA2COREType = EDConfiguration.getStringParamValue(
xsPluginItem,
EDPluginExecProcessXIA2CORE.CONF_EXEC_PROCESS_XIA2CORE_TYPE)
if(strXIA2COREType == None):
strErrorMessage = "Configuration parameter not set: " + \
EDPluginExecProcessXIA2CORE.CONF_EXEC_PROCESS_XIA2CORE_TYPE
EDVerbose.DEBUG(strErrorMessage)
else:
# FIXME test that this is a legal name
self.__strConfigXIA2COREType = strXIA2COREType
strVersion = EDConfiguration.getStringParamValue(xsPluginItem, EDPluginExecProcessXIA2CORE.CONF_EXEC_PROCESS_VERSION_STRING)
if(strVersion == None):
EDVerbose.DEBUG("EDPluginExecProcessXIA2CORE.configure: No configuration parameter found for: " + \
EDPluginExecProcessXIA2CORE.CONF_EXEC_PROCESS_VERSION_STRING + ", NO default value!")
else:
self.setStringVersion(strVersion)
if (self.__strLogFileName == None):
self.setLogFileName(self.getBaseName() + ".log")
if (self.__strErrorLogFileName == None):
self.setErrorLogFileName(self.getBaseName() + ".err")
if self.__strExecutable is None:
EDVerbose.ERROR("Executable not defined in configuration file")
# shall we raise an exception?
self.__strPathToHostNamePidFile = os.path.join(self.getWorkingDirectory(), os.path.basename(self.__strExecutable) + "_hostNamePid.txt")
return
if replay:
ffx = FullFieldXas.replay_from(replay)
else:
ffx = FullFieldXas()
if os.path.isfile(".XSDataInputFullFieldXAS.xml"):
ffx.load(".XSDataInputFullFieldXAS.xml")
ffx.dontAlign = dontAlign
if dontAlign:
print("*"*80)
print("*" + "Skipping image alignement part".center(78) + "*")
print("*"*80)
ffx.setup(_listInput=paths, _mode=mode)
if not isinstance(ffx.reference, int):
ffx.uploadReferenceFrame(ffx.reference)
ffx.save(".XSDataInputFullFieldXAS.xml")
ffx.dump("analysis-%s.json" % time.strftime("%Y%m%d-%Hh%Mm%Ss"))
edna = EDParallelExecute(ffx.pluginName, ffx.makeXML, _functXMLerr=ffx.error, _bVerbose=True, _bDebug=debug, _iNbThreads=iNbCPU)
edna.runEDNA(ffx.listInput, ffx.strMode , ffx.bNewerOnly)
EDVerbose.WARNING("Back to main !")
EDJob.synchronizeAll()
ffx.updateAttrRefImage()
EDPluginControlAlignStackv1_0.showData()
if keepShare:
EDShare.close()
elif (ffx.getNrErrors() == 0) and (not EDVerbose.isVerboseDebug()):
EDVerbose.WARNING("All processing finished successfully: Remove EDShare's big HDF5 file")
EDShare.close(remove=True)
else:
EDShare.close()
if "EDNA_HOME" in os.environ:
if os.environ["EDNA_HOME"] != strEdnaHome:
print("Warning: EDNA_HOME redefined to %s" % strEdnaHome)
os.environ["EDNA_HOME"] = strEdnaHome
else:
os.environ["EDNA_HOME"] = strEdnaHome
sys.path.append(os.path.join(os.environ["EDNA_HOME"], "kernel", "src"))
from EDUtilsLibraryInstaller import EDUtilsLibraryInstaller
from EDVerbose import EDVerbose
if __name__ == "__main__":
installDir = os.path.abspath(sys.argv[0]).split(os.sep)[-2]
EDVerbose.screen("Building %s" % installDir)
install = EDUtilsLibraryInstaller(installDir, strArchiveName)
install.checkPythonVersion()
install.downloadLibrary()
install.dependency("numpy", "20090405-Numpy-1.3")
install.unZipArchive()
try:
install.buildSources()
except Exception:
EDVerbose.ERROR("Error in the build")
install.installBuilt()
if not EDVerbose.isVerboseDebug():
install.cleanSources()
else:
EDVerbose.ERROR("This installer program is not made to be imported, please just run it")
def configure(self):
"""
Configures the plugin from the configuration file with the following
parameters
- The shell that will execute the script
- Script executor
- Script executable to be invoked
- Path to CCP4 setup file if required
- The 3rd party executable installed version
"""
EDPluginExec.configure(self)
EDVerbose.DEBUG("EDPluginExecProcessXIA2CORE.configure")
xsPluginItem = self.getConfiguration()
if (xsPluginItem == None):
EDVerbose.warning(
"EDPluginExecProcessXIA2CORE.configure: No plugin item defined."
)
xsPluginItem = XSPluginItem()
if (self.getExecutable() is None):
strExecutable = EDConfiguration.getStringParamValue(
xsPluginItem,
EDPluginExecProcessXIA2CORE.CONF_EXEC_PROCESS_EXECUTABLE)
if (strExecutable == None):
strErrorMessage = "Configuration parameter missing: " + \
EDPluginExecProcessXIA2CORE.CONF_EXEC_PROCESS_EXECUTABLE
EDVerbose.error(strErrorMessage)
self.addErrorMessage(strErrorMessage)
self.setFailure()
if (EDVerbose.isVerboseDebug()):
raise RuntimeError, strErrorMessage
else:
# Check that the executable file exists
if (os.path.exists(strExecutable) == False):
strErrorMessage = "Cannot find configured " + EDPluginExecProcessXIA2CORE.CONF_EXEC_PROCESS_EXECUTABLE + " : " + strExecutable
EDVerbose.error(strErrorMessage)
self.addErrorMessage(strErrorMessage)
self.setFailure()
if (EDVerbose.isVerboseDebug()):
raise RuntimeError, strErrorMessage
else:
self.setExecutable(strExecutable)
if (self.getConfigXIA2COREType() is None):
strXIA2COREType = EDConfiguration.getStringParamValue(
xsPluginItem,
EDPluginExecProcessXIA2CORE.CONF_EXEC_PROCESS_XIA2CORE_TYPE)
if (strXIA2COREType == None):
strErrorMessage = "Configuration parameter not set: " + \
EDPluginExecProcessXIA2CORE.CONF_EXEC_PROCESS_XIA2CORE_TYPE
EDVerbose.DEBUG(strErrorMessage)
else:
# FIXME test that this is a legal name
self.__strConfigXIA2COREType = strXIA2COREType
strVersion = EDConfiguration.getStringParamValue(
xsPluginItem,
EDPluginExecProcessXIA2CORE.CONF_EXEC_PROCESS_VERSION_STRING)
if (strVersion == None):
EDVerbose.DEBUG("EDPluginExecProcessXIA2CORE.configure: No configuration parameter found for: " + \
EDPluginExecProcessXIA2CORE.CONF_EXEC_PROCESS_VERSION_STRING + ", NO default value!")
else:
self.setStringVersion(strVersion)
if (self.__strLogFileName == None):
self.setLogFileName(self.getBaseName() + ".log")
if (self.__strErrorLogFileName == None):
self.setErrorLogFileName(self.getBaseName() + ".err")
if self.__strExecutable is None:
EDVerbose.ERROR("Executable not defined in configuration file")
# shall we raise an exception?
self.__strPathToHostNamePidFile = os.path.join(
self.getWorkingDirectory(),
os.path.basename(self.__strExecutable) + "_hostNamePid.txt")
return
