def _read_footer(file):
"""
Loads and parses the source file's xml footer metadata to an 'untangle' object.
"""
footer_pos = read_at(file, 678, 8, np.uint64)[0]
file.seek(footer_pos)
xmltext = file.read()
parser = untangle.make_parser()
sax_handler = untangle.Handler()
parser.setContentHandler(sax_handler)
parser.parse(StringIO(xmltext))
loaded_footer = sax_handler.root
return loaded_footer
def quick_loader_with_stats(snippet, spec):
'''snippet is either bkg or counts'''
spe = spec[snippet]['spe']
frames = spec['frames_to_save']
reps = spec['reps']
sensor_width = spec['sensor_width']
frames_per_rep = spec['frames_per_rep']
with open(os.path.join(spe['dir'], spe['fname'])) as file:
# load frames, and compute statistics
file.seek(4100)
dtype = [('', np.uint16)
for i in range(sensor_width)] + [('', np.uint64),
('', np.uint64),
('', np.uint64)]
data = np.fromfile(file, dtype, count=frames)
counts = np.array([
np.mean((data['f%d' % i]).reshape(reps, frames_per_rep), axis=0)
for i in range(sensor_width)
]).T
counts_std = np.array([
np.std((data['f%d' % i]).reshape(reps, frames_per_rep), axis=0)
for i in range(sensor_width)
]).T / np.sqrt(spec['reps'])
timetags = np.array(
[data['f%d' % i] for i in range(sensor_width, sensor_width + 2)]).T
# fullframes = np.array([(data['f%d'%i]).reshape(reps,frames_per_rep) for i in range(sensor_width)]).T
# load wavelength info from footer
file.seek(678)
footer_pos = np.fromfile(file, np.uint64,
8)[0] #read_at(file, 678, 8, np.uint64)[0]
file.seek(footer_pos)
xmltext = file.read()
parser = untangle.make_parser()
sax_handler = untangle.Handler()
parser.setContentHandler(sax_handler)
parser.parse(StringIO(xmltext))
loaded_footer = sax_handler.root
wavelength_string = StringIO(loaded_footer.SpeFormat.Calibrations.
WavelengthMapping.Wavelength.cdata)
wavelength = np.loadtxt(wavelength_string, delimiter=',')
return counts, timetags, wavelength, counts_std
def parse_file(file):
parser = untangle.make_parser()
sax_handler = untangle.Handler()
parser.setContentHandler(sax_handler)
parser.parse(file)
return sax_handler.root
def test_cdata(self):
h = untangle.Handler()
h.startElement('foo', {})
h.characters('baz')
self.assertEquals('baz', h.root.children[0].cdata)
def test_handler(self):
h = untangle.Handler()
h.startElement('foo', {})
h.endElement('foo')
self.assertEquals('foo', h.root.children[0]._name)
def test_empty_handler(self):
h = untangle.Handler()
self.assertRaises(IndexError, h.endElement, 'foo')
self.assertRaises(IndexError, h.characters, 'bar')
def test_cdata(self):
h = untangle.Handler()
h.startElement("foo", {})
h.characters("baz")
self.assertEqual("baz", h.root.children[0].cdata)