コード例 #1
0
 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)
コード例 #2
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)