def process(self, _edObject=None):
EDPluginExec.process(self)
EDVerbose.DEBUG("*** EDPluginEDFReadHeaderv1_0.process")
# Read the header contents and put it into an dictionary
edStringPathToInputFile = self.getDataInput().getEdfFile().getPath(
).getValue()
pyFileDescriptor = open(edStringPathToInputFile, "r")
edfFile = EdfFile(pyFileDescriptor)
pyFileDescriptor.close()
iNumberOfImages = edfFile.GetNumImages()
if (iNumberOfImages == 0):
edStringErrorMessage = EDMessage.ERROR_UNEXPECTED_01 % (
self.getPluginName() + ".preProcess: No images in file " +
edStringPathToInputFile)
EDVerbose.error(edStringErrorMessage)
self.addErrorMessage(edStringErrorMessage)
raise RuntimeError, edStringErrorMessage
#if ( iNumberOfImages > 1 ):
# pass
#EDVerbose.warning( "Warning! More than one image in file " + edStringPathToInputFile ", reading header from first image" )
self.m_edDictionaryHeader = edfFile.GetHeader(0)
def process(self, _edObject=None):
EDPluginControl.process(self)
EDVerbose.DEBUG("EDPluginBioSaxsMetadatav1_0.process")
if not os.path.isfile(self.strInputImage):
EDVerbose.WARNING("The given input file does not exist !!!")
header = {}
else:
header = EdfFile(self.strInputImage).GetHeader(0)
for key in EDUtilsBioSaxs.TRANSLATION:
if key in dir(self) and self.__getattribute__(key) is None:
if EDUtilsBioSaxs.TRANSLATION[key] in header:
if key in EDUtilsBioSaxs.FLOAT_KEYS:
setattr(
self, key,
float(header[EDUtilsBioSaxs.TRANSLATION[key]]))
else:
setattr(self, key,
header[EDUtilsBioSaxs.TRANSLATION[key]])
if self.strOutputImage is not None:
if os.path.abspath(self.strOutputImage) != os.path.abspath(
self.strInputImage):
shutil.copy(self.strInputImage, self.strOutputImage)
keyToUpgrade = []
for key in EDUtilsBioSaxs.TRANSLATION:
if key in dir(self) and self.__getattribute__(key) is None:
if EDUtilsBioSaxs.TRANSLATION[key] not in header:
keyToUpgrade.append(key)
else:
if key in EDUtilsBioSaxs.FLOAT_KEYS:
oneHeader = float(
header[EDUtilsBioSaxs.TRANSLATION[key]])
else:
oneHeader = header[EDUtilsBioSaxs.TRANSLATION[key]]
oneValue = eval("self.%s" % key)
EDVerbose.DEBUG(
"key: %s value_header=%s(%s) value_extra=%s(%s)" %
(key, oneHeader, oneHeader.__class__,
eval("self.%s" % key), eval(
"self.%s" % key).__class__))
if oneHeader != oneValue:
keyToUpgrade.append(key)
for key in keyToUpgrade:
if not self.__bSaxsMetadataFailed:
xsdi = XSDataInputSaxsAddMetadatav1_0()
xsdi.setInputImage(self.xsdInputData.getOutputImage())
xsdi.setKey(XSDataString(EDUtilsBioSaxs.TRANSLATION[key]))
xsdi.setValue(XSDataString("%s" % eval("self.%s" % key)))
edPlugin = self.loadPlugin(
self.__strControlledPluginMetadata)
edPlugin.setDataInput(xsdi)
edPlugin.connectSUCCESS(self.doSuccessMetadata)
edPlugin.connectFAILURE(self.doFailureMetadata)
edPlugin.executeSynchronous()
if self.__bSaxsMetadataFailed:
EDVerbose.screen(
"EDPluginBioSaxsMetadatav1_0.process: writeMetadata using EdfFile "
)
edf = EdfFile(self.strOutputImage)
headers = [
edf.GetHeader(i) for i in xrange(edf.GetNumImages())
]
data = [edf.GetData(i) for i in xrange(edf.GetNumImages())]
del edf
for key in EDUtilsBioSaxs.TRANSLATION:
if key in dir(self) and self.__getattribute__(key) is None:
header[EDUtilsBioSaxs.TRANSLATION[key]] = eval(
"self.%s" % key)
edf = EdfFile(self.strOutputImage)
if len(data) == 1:
edf.WriteImage(header, data[0], Append=0)
elif len(data) > 1:
edf.WriteImage(header, data[0], Append=0)
for datum in data[1:]:
edf.WriteImage({}, datum, Append=1)
else:
EDVerbose.WARNING("There are not data in %s !!!" %
self.strInputImage)
