def _parse_xml(filename):
tree = ET.parse(filename)
om = convert_xml_to_dict(tree.getroot())
info = {
'raw_filename': om.root.raw_file.filename,
'width': 128,
'height': 128,
'raw_height': 130,
'record-by': 'image'
}
if om.has_item('root.count'):
# Stack of images
info.update(
{'series_count': int(om.root.scan_parameters.series_count)})
elif om.has_item('root.pix_x') and om.has_item('root.pix_y'):
# 2D x 2D
info.update({
'scan_x': int(om.root.pix_x),
'scan_y': int(om.root.pix_y)
})
else:
raise IOError("Unsupported Empad file: the scan parameters cannot "
"be imported.")
return om, info
def _axes_jeol_sightx(tiff, op, shape, names):
# convert xml text to dictionary of tiff op['ImageDescription']
# convert_xml_to_dict need to remove white spaces before decoding XML
scales, offsets, units = _axes_defaults()
jeol_xml = ''.join([line.strip(" \r\n\t\x01\x00") for line in op['ImageDescription'].split('\n')])
from hyperspy.misc.io.tools import convert_xml_to_dict
jeol_dict = convert_xml_to_dict(jeol_xml)
op['ImageDescription'] = jeol_dict['TemReporter']
eos = op["ImageDescription"]["Eos"]["EosMode"]
illumi = op["ImageDescription"]["IlluminationSystem"]
imaging = op["ImageDescription"]["ImageFormingSystem"]
# TEM/STEM
is_STEM = eos == "modeASID"
mode_strs = []
mode_strs.append("STEM" if is_STEM else "TEM")
mode_strs.append(illumi["ImageField"][4:]) # Bright Fiels?
if is_STEM:
mode_strs.append(imaging["ScanningImageFormingMode"][4:])
else:
mode_strs.append(imaging["ImageFormingMode"][4:])
mode_strs.append(imaging["SelectorString"]) # Mag / Camera Length
op["SightX_Notes"] = ", ".join(mode_strs)
res_unit_tag = op['ResolutionUnit']
if res_unit_tag == TIFF.RESUNIT.INCH:
scale = 0.0254 # inch/m
else:
scale = 0.01 # tiff scaling, cm/m
# TEM - MAG
if (eos == "eosTEM") and (imaging["ModeString"] == "MAG"):
mag = float(imaging["SelectorValue"])
scales['x'], scales['y'] = _get_scales_from_x_y_resolution(op, factor=scale / mag * 1e9)
units = {"x": "nm", "y": "nm", "z": "nm"}
# TEM - DIFF
elif (eos == "eosTEM") and (imaging["ModeString"] == "DIFF"):
def wave_len(ht):
import scipy.constants as constants
momentum = 2 * constants.m_e * constants.elementary_charge * ht * \
(1 + constants.elementary_charge * ht / (2 * constants.m_e * constants.c ** 2))
return constants.h / np.sqrt(momentum)
camera_len = float(imaging["SelectorValue"])
ht = float(op["ImageDescription"]["ElectronGun"]["AccelerationVoltage"])
if imaging["SelectorUnitString"] == "mm": # convert to "m"
camera_len /= 1000
elif imaging["SelectorUnitString"] == "cm": # convert to "m"
camera_len /= 100
scale /= camera_len * wave_len(ht) * 1e9 # in nm
scales['x'], scales['y'] = _get_scales_from_x_y_resolution(op, factor=scale)
units = {"x": "1 / nm", "y": "1 / nm", "z": t.Undefined}
scales, offsets, units = _order_axes_by_name(names, scales, offsets, units)
axes = _build_axes_dictionaries(shape, names, scales, offsets, units)
return axes