def testCheckParameters(self):
xsDataInput = XSDataInputBioSaxsSingleSamplev1_0()
xsDataInput.directory1D = XSDataFile()
xsDataInput.directory2D = XSDataFile()
xsDataInput.directoryMisc = XSDataFile()
xsDataInput.bufferSeries = [XSDataFileSeries()]
xsDataInput.sampleSeries = [XSDataFileSeries()]
edPluginExecBioSaxsSingleSamplev1_0 = self.createPlugin()
edPluginExecBioSaxsSingleSamplev1_0.setDataInput(xsDataInput)
edPluginExecBioSaxsSingleSamplev1_0.checkParameters()
def testCheckParameters(self):
xsDataInput = XSDataInputBioSaxsReduceFileSeriev1_0()
xsDataInput.fileSerie = XSDataFileSeries()
xsDataInput.sample = XSDataBioSaxsSample()
xsDataInput.experimentSetup = XSDataBioSaxsExperimentSetup()
xsDataInput.directory1D = XSDataFile()
xsDataInput.directory2D = XSDataFile()
xsDataInput.directoryMisc = XSDataFile()
edPluginExecBioSaxsReduceFileSerie = self.createPlugin()
edPluginExecBioSaxsReduceFileSerie.setDataInput(xsDataInput)
edPluginExecBioSaxsReduceFileSerie.checkParameters()
def testCheckParameters(self):
"""
complex type XSDataInputBioSaxsSmartMergev1_0 extends XSDataInput {
inputFile: XSDataFile []
absoluteFidelity: XSDataDouble optional
relativeFidelity: XSDataDouble optional
mergedCurve: XSDataFile
"""
xsDataInput = XSDataInputBioSaxsSmartMergev1_0()
xsDataInput.inputCurves = [XSDataFile()]
xsDataInput.absoluteFidelity = XSDataDouble()
xsDataInput.relativeFidelity = XSDataDouble()
xsDataInput.mergedCurve = XSDataFile()
edPluginExecBioSaxsSmartMerge = self.createPlugin()
edPluginExecBioSaxsSmartMerge.setDataInput(xsDataInput)
edPluginExecBioSaxsSmartMerge.checkParameters()
def testCheckParameters(self):
"""
complex type XSDataInputBioSaxsToSAS extends XSDataInput {
inputFile: XSDataFile []
absoluteFidelity: XSDataDouble optional
relativeFidelity: XSDataDouble optional
mergedCurve: XSDataFile
"""
xsDataInput = XSDataInputBioSaxsToSASv1_0()
xsDataInput.subtractedCurve = XSDataFile()
edPlugin = self.createPlugin()
edPlugin.setDataInput(xsDataInput)
edPlugin.checkParameters()
def fileName2xml(filename):
"""Here we create the XML string to be passed to the EDNA plugin from the input filename
This can / should be modified by the final user
@param filename: full path of the input file
@type filename: python string representing the path
@rtype: XML string
@return: python string
"""
if not filename.endswith(".edf"):
return
xsd = XSDataInputBioSaxsAsciiExportv1_0()
xsd.integratedImage = XSDataImage(XSDataString(filename))
xsd.integratedCurve = XSDataFile(XSDataString(os.path.splitext(filename)[0] + ".dat"))
return xsd.marshal()
def toXml(self, filename):
"""Here we create the XML string to be passed to the EDNA plugin from the input filename
This can / should be modified by the final user
@param filename: full path of the input file
@type filename: python string representing the path
@rtype: XML string
@return: python string
"""
# Is the file to process?
dirname, basename = os.path.split(filename)
rootDir, dirname = os.path.split(dirname)
basename, ext = os.path.splitext(basename)
if not ((dirname.lower() == "raw") and (ext.lower() == ".edf")):
self.DEBUG("Not processing %s" % filename)
return
existing2DImage = os .path.join(rootDir, "2d", basename + ".edf")
if os.path.isfile(existing2DImage):
# print existing2DImage
title = None
for line in open(existing2DImage):
if len(line) > 512:
break
else:
line = line.strip()
if line.startswith("title"):
title = line.split("=", 1)[-1]
if line.startswith("Center_1")and (self.beamCenter_1 is None):
try:
self.experimentSetup.beamCenter_1 = XSDataDouble(float(line.split("=", 1)[-1].split()[0]))
except Exception:
self.ERROR("Reading from header: not a float " + line)
elif line.startswith("Center_2")and (self.beamCenter_2 is None):
try:
self.experimentSetup.beamCenter_2 = XSDataDouble(float(line.split("=", 1)[-1].split()[0]))
except Exception:
self.ERROR("Reading from header: not a float " + line)
elif line.startswith("PSize_1")and (self.pixelSize_1 is None):
try:
self.experimentSetup.pixelSize_1 = XSDataLength(float(line.split("=", 1)[-1].split()[0]))
except Exception:
self.ERROR("Reading from header: not a float " + line)
elif line.startswith("PSize_2") and (self.pixelSize_2 is None):
try:
self.experimentSetup.pixelSize_2 = XSDataLength(float(line.split("=", 1)[-1].split()[0]))
except Exception:
self.ERROR("Reading from header: not a float " + line)
elif line.startswith("SampleDistance") and (self.detectorDistance is None) :
try:
self.experimentSetup.detectorDistance = XSDataLength(float(line.split("=", 1)[-1].split()[0]))
except Exception:
self.ERROR("Reading from header: not a float " + line)
elif line.startswith("WaveLength")and (self.wavelength is None):
try:
self.experimentSetup.wavelength = XSDataWavelength(float(line.split("=", 1)[-1].split()[0]))
except Exception:
self.ERROR("Reading from header: not a float " + line)
if title:
for block in title.split(","):
if "=" in block:
key, value = block.split("=", 1)
elif ":" in block:
key, value = block.split(":", 1)
else:
key = None
if key:
key = key.strip()
value = value.strip()
# print key, value
if key == "DiodeCurr":
try:
self.experimentSetup.beamStopDiode = XSDataDouble(float(value))
except Exception:
self.ERROR("Unable to convert %s to float" % block)
elif key == "MachCurr":
try:
self.experimentSetup.machineCurrent = XSDataDouble(float(value.split()[0]))
except Exception:
self.ERROR("Unable to convert %s to float" % block)
elif key == "Concentration":
try:
self.sample.concentration = XSDataDouble(float(value.split()[0]))
except Exception:
self.ERROR("Unable to convert %s to float" % block)
elif (key == "Comments") and (self.comment is None):
self.sample.comments = XSDataString(value.strip())
elif (key == "Code") and (self.code is None) :
self.sample.code = XSDataString(value.strip())
elif (key == "Mask") and (self.maskFile is None):
self.experimentSetup.maskFile = XSDataImage(XSDataString(value.strip()))
elif (key == "Normalisation") and (self.normalization is None):
try:
self.experimentSetup.normalizationFactor = XSDataDouble(float(value.split()[0]))
except Exception:
self.ERROR("Unable to convert %s to float" % block)
xsd = XSDataInputBioSaxsProcessOneFilev1_0()
xsd.rawImage = XSDataImage(XSDataString(filename))
xsd.rawImageSize = XSDataInteger(self.imageSize)
xsd.experimentSetup = self.experimentSetup
xsd.sample = self.sample
dir1d = os.path.join(rootDir, self.dest1D)
dir2d = os.path.join(rootDir, self.dest2D)
dirMisc = os.path.join(rootDir, self.destMisc)
if not os.path.exists(dir1d):
os.makedirs(dir1d)
if not os.path.exists(dir2d):
os.makedirs(dir2d)
if not os.path.exists(dirMisc):
os.makedirs(dirMisc)
xsd.normalizedImage = XSDataImage(XSDataString(os.path.join(dir2d, basename + ".edf")))
xsd.integratedImage = XSDataImage(XSDataString(os.path.join(dirMisc, basename + ".ang")))
xsd.integratedCurve = XSDataFile(XSDataString(os.path.join(dir1d, basename + ".dat")))
# print xsd.marshal()
return xsd.marshal()
def cliReadParam(self):
print("Welcome to the Reprocessing of BioSaxs data. Enter '-' to re-use data from headers")
raw = raw_input(("Sample code [%s]: " % self.code).ljust(LEN_INPUT_STR)).strip()
if raw != "":
self.code = raw
raw = raw_input(("Sample comments [%s]: " % self.comment).ljust(LEN_INPUT_STR)).strip()
if raw != "":
self.comment = raw
ok = False
while not ok:
raw = raw_input(("Wavelength (in meter) [%s]: " % self.wavelength).ljust(LEN_INPUT_STR)).strip()
if raw == "-":
ok = True
elif raw != "":
try:
self.wavelenth = float(raw)
ok = True
except Exception:
self.ERROR("Unable to convert to float: %s" % raw)
ok = False
raw = raw_input(("Detector used [%s]:" % self.detector).ljust(LEN_INPUT_STR)).strip()
if raw != "":
self.detector = raw.lower()
ok = False
while not ok:
raw = raw_input(("Detector image size in bytes [%s]: " % self.imageSize).ljust(LEN_INPUT_STR)).strip()
if raw != "":
try:
self.imageSize = float(raw)
ok = True
except Exception:
self.ERROR("Unable to convert to float: %s" % raw)
ok = False
else:
ok = bool(self.imageSize)
ok = False
while not ok:
raw = raw_input(("Mask file [%s]: " % self.maskFile).ljust(LEN_INPUT_STR)).strip()
if raw == "-":
ok = True
elif raw != "":
self.maskFile = raw
ok = True
if raw != "-" and ((self.maskFile is None) or (os.path.isfile(self.maskFile) is False)):
ok = False
ok = False
while not ok:
raw = raw_input(("Sample - Detector distance in meter [%s]: " % self.detectorDistance).ljust(LEN_INPUT_STR)).strip()
if raw == "-":
ok = True
elif raw != "":
try:
self.detectorDistance = float(raw)
ok = True
except Exception:
self.ERROR("Unable to convert to float: %s" % raw)
ok = False
ok = False
while not ok:
raw = raw_input(("Normalization factor [%s]: " % self.normalization).ljust(LEN_INPUT_STR)).strip()
if raw == "-":
ok = True
elif raw != "":
try:
self.normalization = float(raw)
ok = True
except Exception:
self.ERROR("Unable to convert to float: %s" % raw)
ok = False
ok = False
while not ok:
raw = raw_input(("Pixel size [%s %s]: " % (self.pixelSize_1, self.pixelSize_2)).ljust(LEN_INPUT_STR)).strip()
if raw == "-":
ok = True
elif raw != "":
lpx = raw.split()
if len(lpx) == 1:
try:
self.pixelSize_1 = float(lpx[0])
self.pixelSize_2 = float(lpx[0])
ok = True
except Exception:
self.ERROR("Unable to convert to float: %s" % raw)
ok = False
else:
try:
self.pixelSize_1 = float(lpx[0])
self.pixelSize_2 = float(lpx[1])
ok = True
except Exception:
self.ERROR("Unable to convert to float: %s" % raw)
ok = False
else:
if isinstance(self.pixelSize_1, (float, int)) and isinstance(self.pixelSize_2, (float, int)):
ok = True
ok = False
while not ok:
raw = raw_input(("Beam Center position [%s %s]: " % (self.beamCenter_1, self.beamCenter_2)).ljust(LEN_INPUT_STR)).strip()
if raw == "-":
ok = True
elif raw != "":
lpx = raw.split()
if len(lpx) == 1:
try:
self.beamCenter_1 = float(lpx[0])
self.beamCenter_2 = float(lpx[0])
ok = True
except Exception:
self.ERROR("Unable to convert to float: %s" % raw)
ok = False
else:
try:
self.beamCenter_1 = float(lpx[0])
self.beamCenter_2 = float(lpx[1])
ok = True
except Exception:
self.ERROR("Unable to convert to float: %s" % raw)
ok = False
else:
if isinstance(self.beamCenter_1, (float, int)) and isinstance(self.beamCenter_2, (float, int)):
ok = True
###########################################
if self.code is not None:
self.sample.code = XSDataString(self.code)
if self.comment is not None:
self.sample.comment = XSDataString(self.comment)
if self.detector is not None:
self.experimentSetup.detector = XSDataString(self.detector)
if self.detectorDistance is not None:
self.experimentSetup.detectorDistance = XSDataLength(self.detectorDistance)
if self.pixelSize_1 is not None:
self.experimentSetup.pixelSize_1 = XSDataLength(self.pixelSize_1)
if self.pixelSize_2 is not None:
self.experimentSetup.pixelSize_2 = XSDataLength(self.pixelSize_2)
if self.beamCenter_1 is not None:
self.experimentSetup.beamCenter_1 = XSDataDouble(self.beamCenter_1)
if self.beamCenter_2 is not None:
self.experimentSetup.beamCenter_2 = XSDataDouble(self.beamCenter_2)
if self.maskFile is not None:
self.experimentSetup.maskFile = XSDataFile(XSDataString(self.maskFile))