示例#1
0
    def _parseSpectrum(self):
        """Parse spectrum data."""

        # get acquisition parames
        params = self._parseParams()
        if not params:
            return False

        # open spectrum
        try:
            document = file(self.path, 'rb')
            rawData = document.read()
            document.close()
        except IOError:
            return False

        # convert to list
        try:
            count = len(rawData) / struct.calcsize('i')
            start, end = 0, len(rawData)
            points = struct.unpack('i' * count, rawData[start:end])
        except:
            return False

        # check data length
        if len(points) != int(params['TD']):
            return False

        # shift X-axis
        if params['SPTYPE'] == 'psd':
            shift = float(params['ML1'])
            interval = float(params['DW'])
        else:
            shift = float(params['DELAY'])
            interval = float(params['DW'])

        buff = []
        for x in points:
            buff.append([shift, x])
            shift += interval
        points = buff

        # convert X-axis to m/z
        if params['SPTYPE'] == 'tof':
            points = self._convertTimeToMZ(points, float(params['ML1']),
                                           float(params['ML2']),
                                           float(params['ML3']))

        # convert to scan object
        spectrum = objects.scan(points)

        # set additional parameters
        spectrum.msLevel = 1
        if params['SPTYPE'] == 'psd':
            spectrum.msLevel = 2
            if 'Parent' in params:
                spectrum.precursorMZ = params['Parent']

        return spectrum
示例#2
0
 def _parseSpectrum(self):
     """Parse spectrum data."""
     
     # get acquisition parames
     params = self._parseParams()
     if not params:
         return False
     
     # open spectrum
     try:
         document = file(self.path, 'rb')
         rawData = document.read()
         document.close()
     except IOError:
         return False
     
     # convert to list
     try:
         count = len(rawData)/struct.calcsize('i')
         start, end = 0, len(rawData)
         points = struct.unpack('i' * count, rawData[start:end])
     except:
         return False
     
     # check data length
     if len(points) != int(params['TD']):
         return False
     
     # shift X-axis
     if params['SPTYPE'] == 'psd':
         shift = float(params['ML1'])
         interval = float(params['DW'])
     else:
         shift = float(params['DELAY'])
         interval = float(params['DW'])
     
     buff = []
     for x in points:
         buff.append([shift, x])
         shift += interval
     points = buff
     
     # convert X-axis to m/z
     if params['SPTYPE'] == 'tof':
         points = self._convertTimeToMZ(points, float(params['ML1']), float(params['ML2']), float(params['ML3']))
     
     # convert to scan object
     spectrum = objects.scan(points)
     
     # set additional parameters
     spectrum.msLevel = 1
     if params['SPTYPE'] == 'psd':
         spectrum.msLevel = 2
         if 'Parent' in params:
             spectrum.precursorMZ = params['Parent']
     
     return spectrum
示例#3
0
 def getSpectrum(self, discrete=False):
     """Get spectrum from document."""
     
     # parse data
     data = self._parseData()
     if not data:
         return False
     
     # parse data as peaklist (discrete points)
     if discrete:
         for x, p in enumerate(data):
             data[x] = objects.peak(p[0], p[1])
         spectrum = objects.scan(peaks=data)
     
     # parse data as spectrum (continuous line)
     else:
         spectrum = objects.scan(points=data)
     
     return spectrum
示例#4
0
文件: parser_xy.py 项目: mfitzp/toolz
    def getSpectrum(self, discrete=False):
        """Get spectrum from document."""

        # parse data
        data = self._parseData()
        if not data:
            return False

        # parse data as peaklist (discrete points)
        if discrete:
            for x, p in enumerate(data):
                data[x] = objects.peak(p[0], p[1])
            spectrum = objects.scan(peaks=data)

        # parse data as spectrum (continuous line)
        else:
            spectrum = objects.scan(points=data)

        return spectrum
示例#5
0
    def getSpectrum(self, scanNumber=None):
        """Get spectrum from document."""

        # init parser
        handler = scanHandler(scanNumber)
        parser = xml.sax.make_parser()
        parser.setContentHandler(handler)

        # parse document
        try:
            document = file(self.path)
            parser.parse(document)
            document.close()
            scan = handler.scan
        except stopParsing:
            scan = handler.scan
        except xml.sax.SAXException:
            return False

        # check data
        if not scan:
            return False

        # parse peaks
        try:
            points = self._parsePoints(scan)
        except:
            return False

        # parse data as peaklist (discrete points)
        if scan['spectrumType'] == 'discrete':
            for x, p in enumerate(points):
                points[x] = objects.peak(p[0], p[1])
            spectrum = objects.scan(peaks=points)

        # parse data as spectrum (continuous line)
        else:
            spectrum = objects.scan(points=points)

        # set metadata
        if scan['scanNumber']:
            spectrum.scanNumber = int(scan['scanNumber'])
        if scan['parentScanNumber']:
            spectrum.parentScanNumber = int(scan['parentScanNumber'])
        if scan['msLevel']:
            spectrum.msLevel = int(scan['msLevel'])
        if scan['polarity']:
            spectrum.polarity = scan['polarity']
        if scan['retentionTime']:
            spectrum.retentionTime = scan['retentionTime']
        if scan['totIonCurrent']:
            spectrum.totIonCurrent = float(scan['totIonCurrent'])
        if scan['basePeakMz']:
            spectrum.basePeakMZ = float(scan['basePeakMz'])
        if scan['basePeakIntensity']:
            spectrum.basePeakIntensity = float(scan['basePeakIntensity'])
        if scan['precursorMz']:
            spectrum.precursorMZ = float(scan['precursorMz'])
        if scan['precursorIntensity']:
            spectrum.precursorIntensity = float(scan['precursorIntensity'])

        return spectrum
示例#6
0
 def getSpectrum(self, scanNumber=None):
     """Get spectrum from document."""
     
     # init parser
     handler = scanHandler(scanNumber)
     parser = xml.sax.make_parser()
     parser.setContentHandler(handler)
     
     # parse document
     try:
         document = file(self.path)
         parser.parse(document)
         document.close()
         scan = handler.scan
     except stopParsing:
         scan = handler.scan
     except xml.sax.SAXException:
         return False
     
     # check data
     if not scan:
         return False
     
     # parse peaks
     try:
         points = self._parsePoints(scan)
     except:
         return False
     
     # parse data as peaklist (discrete points)
     if scan['spectrumType'] == 'discrete':
         for x, p in enumerate(points):
             points[x] = objects.peak(p[0], p[1])
         spectrum = objects.scan(peaks=points)
     
     # parse data as spectrum (continuous line)
     else:
         spectrum = objects.scan(points=points)
     
     # set metadata
     if scan['scanNumber']:
         spectrum.scanNumber = int(scan['scanNumber'])
     if scan['parentScanNumber']:
         spectrum.parentScanNumber = int(scan['parentScanNumber'])
     if scan['msLevel']:
         spectrum.msLevel = int(scan['msLevel'])
     if scan['polarity']:
         spectrum.polarity = scan['polarity']
     if scan['retentionTime']:
         spectrum.retentionTime = scan['retentionTime']
     if scan['totIonCurrent']:
         spectrum.totIonCurrent = float(scan['totIonCurrent'])
     if scan['basePeakMz']:
         spectrum.basePeakMZ = float(scan['basePeakMz'])
     if scan['basePeakIntensity']:
         spectrum.basePeakIntensity = float(scan['basePeakIntensity'])
     if scan['precursorMz']:
         spectrum.precursorMZ = float(scan['precursorMz'])
     if scan['precursorIntensity']:
         spectrum.precursorIntensity = float(scan['precursorIntensity'])
     
     return spectrum