def map_keys(term_mapping, base, metadata):
"""
Given a term mapping dictionary and a metadata dictionary, translate
the input keys within the "raw" metadata into a parsed value in the
"nx_meta" metadata structure.
Parameters
----------
term_mapping : dict
Dictionary where keys are tuples of strings (the input terms),
and values are either a single string or a list of strings (the
output terms).
base : list
The 'root' path within the metadata dictionary of where to start
applying the input terms
metadata : dict
A metadata dictionary as returned by :py:meth:`get_ser_metadata`
Returns
-------
metadata : dict
The same metadata dictionary with some values added under the
root-level ``nx_meta`` key, as specified by ``term_mapping``
Notes
-----
The ``term_mapping`` parameter should be a dictionary of the form:
.. code-block:: python
{
('val1_1', 'val1_2') : 'output_val_1',
('val1_1', 'val2_2') : 'output_val_2',
etc.
}
Assuming ``base`` is ``['ObjectInfo', 'AcquireInfo']``, this would map
the term present at ``ObjectInfo.AcquireInfo.val1_1.val1_2`` into
``nx_meta.output_val_1``, and ``ObjectInfo.AcquireInfo.val1_1.val2_2`` into
``nx_meta.output_val_2``, and so on. If one of the output terms is a list,
the resulting metadata will be nested. `e.g.` ``['output_val_1',
'output_val_2']`` would get mapped to ``nx_meta.output_val_1.output_val_2``.
"""
for in_term in term_mapping.keys():
out_term = term_mapping[in_term]
if isinstance(in_term, tuple):
in_term = list(in_term)
if isinstance(out_term, str):
out_term = [out_term]
val = _try_get_dict_val(metadata, base + in_term)
# only add the value to this list if we found it
if val != 'not found':
_set_nest_dict_val(metadata, ['nx_meta'] + out_term,
_convert_to_numeric(val))
return metadata
def parse_det_info(mdict, det_name):
"""
Parses the `Detector` portion of the metadata dictionary from the Quanta to
get values such as brightness, contrast, signal, etc.
Parameters
----------
mdict : dict
A metadata dictionary as returned by :py:meth:`get_quanta_metadata`
det_name : str
The "detector name" read from the root-level ``Beam`` node of the
metadata dictionary
Returns
-------
mdict : dict
The same metadata dictionary with some values added under the
root-level ``nx_meta`` key
"""
to_parse = [([det_name, 'Brightness'], ['Detector Brightness Setting']),
([det_name, 'Contrast'], ['Detector Contrast Setting']),
([det_name, 'EnhancedContrast'],
['Detector Enhanced Contrast '
'Setting']), ([det_name, 'Signal'], ['Detector Signal']),
([det_name, 'Grid'], ['Detector Grid Voltage (V)']),
([det_name, 'Setting'], ['Detector Setting'])]
for m_in, m_out in to_parse:
val = _try_get_dict_val(mdict, m_in)
if val != 'not found':
try:
val = _Decimal(val)
if m_in == [det_name, 'Setting']:
# if "Setting" value is numeric, it's just the Grid
# voltage so skip it
continue
except (ValueError, _invalidOp):
pass
_set_nest_dict_val(
mdict, ['nx_meta'] + m_out,
float(val) if isinstance(val, _Decimal) else val)
_set_nest_dict_val(mdict, ['nx_meta'] + ['Detector Name'], det_name)
return mdict
def parse_scan_info(mdict, scan_name):
"""
Parses the `Scan` portion of the metadata dictionary (on a Quanta this is
always `"EScan"`) to get values such as dwell time, field width, and pixel
size
Parameters
----------
mdict : dict
A metadata dictionary as returned by :py:meth:`get_quanta_metadata`
scan_name : str
The "scan name" read from the root-level ``Beam`` node of the
metadata dictionary
Returns
-------
mdict : dict
The same metadata dictionary with some values added under the
root-level ``nx_meta`` key
"""
# Values are in SI units, but we want easy to display, so include the
# exponential factor that will get us from input unit (such as seconds)
# to output unit (such as μs -- meaning factor = 6)
to_parse = [
([scan_name, 'Dwell'], ['Pixel Dwell Time (μs)'], 6),
([scan_name, 'FrameTime'], ['Total Frame Time (s)'], 0),
([scan_name, 'HorFieldsize'], ['Horizontal Field Width (μm)'], 6),
([scan_name, 'VerFieldsize'], ['Vertical Field Width (μm)'], 6),
([scan_name, 'PixelHeight'], ['Pixel Width (nm)'], 9),
([scan_name, 'PixelWidth'], ['Pixel Height (nm)'], 9),
]
for m_in, m_out, factor in to_parse:
val = _try_get_dict_val(mdict, m_in)
if val != 'not found' and val != '':
val = _Decimal(val) * _Decimal(str(10**factor))
_set_nest_dict_val(
mdict, ['nx_meta'] + m_out,
float(val) if isinstance(val, _Decimal) else val)
return mdict
def _process_thickness_metadata(mdict, base):
abs_thick = _try_get_dict_val(
mdict, base + ['Thickness', 'Absolute', 'Measurement'])
abs_units = _try_get_dict_val(mdict,
base + ['Thickness', 'Absolute', 'Units'])
abs_mfp = _try_get_dict_val(
mdict, base + ['Thickness', 'Absolute', 'Mean Free Path'])
rel_thick = _try_get_dict_val(
mdict, base + ['Thickness', 'Relative', 'Measurement'])
if abs_thick != 'not found':
_set_nest_dict_val(
mdict,
['nx_meta', 'EELS', f'Thickness (absolute) ['
f'{abs_units}]'], abs_thick)
if abs_mfp != 'not found':
_set_nest_dict_val(
mdict,
['nx_meta', 'EELS', 'Thickness (absolute) mean '
'free path'], abs_mfp[0])
if rel_thick != 'not found':
_set_nest_dict_val(mdict,
['nx_meta', 'EELS', 'Thickness (relative) [t/λ]'],
rel_thick)
return mdict
def parse_system_info(mdict):
"""
Parses the `System` portion of the metadata dictionary from the Quanta to
get values such as software version, chamber config, etc.
Parameters
----------
mdict : dict
A metadata dictionary as returned by :py:meth:`get_quanta_metadata`
Returns
-------
mdict : dict
The same metadata dictionary with some values added under the
root-level ``nx_meta`` key
"""
to_parse = [(['System', 'Chamber'], ['Chamber ID']),
(['System', 'Pump'], ['Vacuum Pump']),
(['System', 'SystemType'], ['System Type']),
(['System', 'Stage'], ['Stage Description'])]
for m_in, m_out in to_parse:
val = _try_get_dict_val(mdict, m_in)
if val != 'not found':
_set_nest_dict_val(mdict, ['nx_meta'] + m_out, val)
# Parse software info into one output tag:
output_vals = []
val = _try_get_dict_val(mdict, ['System', 'Software'])
if val != 'not found':
output_vals.append(val)
val = _try_get_dict_val(mdict, ['System', 'BuildNr'])
if val != 'not found':
output_vals.append(f'(build {val})')
if len(output_vals) > 0:
_set_nest_dict_val(mdict, ['nx_meta'] + ['Software Version'],
' '.join(output_vals))
# parse column and type into one output tag:
output_vals = []
val = _try_get_dict_val(mdict, ['System', 'Column'])
if val != 'not found':
output_vals.append(val)
val = _try_get_dict_val(mdict, ['System', 'Type'])
if val != 'not found':
output_vals.append(val)
if len(output_vals) > 0:
_set_nest_dict_val(mdict, ['nx_meta'] + ['Column Type'],
' '.join(output_vals))
return mdict
def parse_dm3_spectrum_image_info(mdict):
"""
Parses metadata from the DigitalMicrograph tag structure that concerns any
spectrum imaging information (from the "SI" tag) and places it in a
"Spectrum Imaging" dictionary underneath the root-level ``nx_meta`` node.
Metadata values that are commonly incorrect or may be placeholders are
specified in a list under the ``nx_meta.warnings`` node.
Parameters
----------
mdict : dict
A metadata dictionary as returned by :py:meth:`get_dm3_metadata`
Returns
-------
mdict : dict
The metadata dictionary with all the "EDS-specific" metadata
added as sub-node under the ``nx_meta`` root level dictionary
"""
pre_path = get_pre_path(mdict)
# Spectrum imaging .dm3 tags of interest:
base = pre_path + ['SI']
for m_in, m_out in \
[(['Acquisition', 'Pixel time (s)'], ['Pixel time (s)']),
(['Acquisition', 'SI Application Mode', 'Name'], ['Scan Mode']),
(['Acquisition', 'Spatial Sampling', 'Height (pixels)'],
['Spatial Sampling (Vertical)']),
(['Acquisition', 'Spatial Sampling', 'Width (pixels)'],
['Spatial Sampling (Horizontal)']),
(['Acquisition', 'Scan Options', 'Sub-pixel sampling'],
['Sub-pixel Sampling Factor'])]:
val = _try_get_dict_val(mdict, base + m_in)
# only add the value to this list if we found it, and it's not
# one of the "facility-wide" set values that do not have any meaning:
if val != 'not found':
# add last value of each parameter to the "EDS" sub-tree of nx_meta
_set_nest_dict_val(mdict, ['nx_meta', 'Spectrum Imaging'] + m_out,
val)
# Check spatial drift correction separately:
drift_per_val = _try_get_dict_val(
mdict, base +
['Acquisition', 'Artefact Correction', 'Spatial Drift', 'Periodicity'])
drift_unit_val = _try_get_dict_val(
mdict, base +
['Acquisition', 'Artefact Correction', 'Spatial Drift', 'Units'])
if drift_per_val != 'not found' and drift_unit_val != 'not found':
val_to_set = f"Spatial drift correction every {drift_per_val} " \
f"{drift_unit_val}"
# make sure statement looks gramatically correct
if drift_per_val == 1:
val_to_set = val_to_set.replace('(s)', '')
else:
val_to_set = val_to_set.replace('(s)', 's')
# fix for "seconds(s)" (stupid DM...)
if val_to_set[-2:] == 'ss':
val_to_set = val_to_set[:-1]
_set_nest_dict_val(
mdict, ['nx_meta', 'Spectrum Imaging', 'Artefact Correction'],
val_to_set)
# Calculate acquisition duration:
start_val = _try_get_dict_val(mdict, base + ['Acquisition', 'Start time'])
end_val = _try_get_dict_val(mdict, base + ['Acquisition', 'End time'])
if start_val != 'not found' and end_val != 'not found':
start_dt = _dt.strptime(start_val, '%I:%M:%S %p')
end_dt = _dt.strptime(end_val, '%I:%M:%S %p')
duration = (end_dt - start_dt).seconds
_set_nest_dict_val(
mdict, ['nx_meta', 'Spectrum Imaging', 'Acquisition Duration (s)'],
duration)
# Set the dataset type to SpectrumImage if it is already a Spectrum (
# otherwise it's just a STEM image) and any Spectrum Imaging tags were
# added
if 'Spectrum Imaging' in mdict['nx_meta']:
if mdict['nx_meta']['DatasetType'] == 'Spectrum':
_logger.info('Detected file as SpectrumImage type based on '
'presence of spectral metadata and spectrum imaging '
'info')
mdict['nx_meta']['DatasetType'] = 'SpectrumImage'
mdict['nx_meta']['Data Type'] = 'Spectrum_Imaging'
if 'EELS' in mdict['nx_meta']:
mdict['nx_meta']['Data Type'] = 'EELS_Spectrum_Imaging'
if 'EDS' in mdict['nx_meta']:
mdict['nx_meta']['Data Type'] = 'EDS_Spectrum_Imaging'
return mdict
def parse_dm3_eds_info(mdict):
"""
Parses metadata from the DigitalMicrograph tag structure that concerns any
EDS acquisition or spectrometer settings, placing it in an ``EDS``
dictionary underneath the root-level ``nx_meta`` node. Metadata values
that are commonly incorrect or may be placeholders are specified in a
list under the ``nx_meta.warnings`` node.
Parameters
----------
mdict : dict
A metadata dictionary as returned by :py:meth:`get_dm3_metadata`
Returns
-------
mdict : dict
The metadata dictionary with all the "EDS-specific" metadata
added as sub-node under the ``nx_meta`` root level dictionary
"""
pre_path = get_pre_path(mdict)
# EELS .dm3 tags of interest:
base = pre_path + ['EDS']
for m in [['Acquisition', 'Continuous Mode'],
['Acquisition', 'Count Rate Unit'],
['Acquisition', 'Dispersion (eV)'],
['Acquisition', 'Energy Cutoff (V)'],
['Acquisition', 'Exposure (s)'], ['Count rate'],
['Detector Info', 'Active layer'],
['Detector Info', 'Azimuthal angle'],
['Detector Info', 'Dead layer'],
['Detector Info', 'Detector type'],
['Detector Info', 'Elevation angle'], ['Detector Info', 'Fano'],
['Detector Info', 'Gold layer'],
['Detector Info', 'Incidence angle'],
['Detector Info', 'Solid angle'],
['Detector Info', 'Stage tilt'],
['Detector Info', 'Window thickness'],
['Detector Info', 'Window type'], ['Detector Info', 'Zero fwhm'],
['Live time'], ['Real time']]:
val = _try_get_dict_val(mdict, base + m)
# only add the value to this list if we found it, and it's not
# one of the "facility-wide" set values that do not have any meaning:
if val != 'not found':
# add last value of each parameter to the "EDS" sub-tree of nx_meta
_set_nest_dict_val(mdict, ['nx_meta', 'EDS'] +
[m[-1] if len(m) > 1 else m[0]], val)
# test to see if the SI attribute is present in the metadata dictionary.
# If so, then some of the relevant EDS values are located there, rather
# than in the root-level EDS tag (all of the EDS.Acquisition tags from
# above)
if _try_get_dict_val(mdict, pre_path + ['SI']) != 'not found':
for m in [['Acquisition', 'Continuous Mode'],
['Acquisition', 'Count Rate Unit'],
['Acquisition', 'Dispersion (eV)'],
['Acquisition', 'Energy Cutoff (V)'],
['Acquisition', 'Exposure (s)']]:
val = _try_get_dict_val(mdict, pre_path + ['SI'] + m)
if val != 'not found':
# add last value of each parameter to the "EDS" sub-tree of
# nx_meta
_set_nest_dict_val(mdict, ['nx_meta', 'EDS'] + [m[-1]], val)
# for an SI EDS dataset, set "Live time", "Real time" and "Count rate"
# to the averages stored in the ImageList.TagGroup0.ImageTags.EDS.Images
# values
im_dict = _try_get_dict_val(mdict, pre_path + ['EDS', 'Images'])
if isinstance(im_dict, dict):
for k, v in im_dict.items():
if k in mdict['nx_meta']['EDS']:
del mdict['nx_meta']['EDS'][k]
# this should work for 2D (spectrum image) as well as 1D
# (linescan) datasets since DM saves this information as a 1D
# list regardless of original data shape
avg_val = _np.array(v).mean()
_set_nest_dict_val(mdict,
['nx_meta', 'EDS'] + [f'{k} (SI Average)'],
avg_val)
# Add the .dm3 EDS values to the warnings list, since they might not be
# accurate
for m in [['Count rate'], ['Detector Info', 'Active layer'],
['Detector Info', 'Azimuthal angle'],
['Detector Info', 'Dead layer'],
['Detector Info', 'Detector type'],
['Detector Info', 'Elevation angle'], ['Detector Info', 'Fano'],
['Detector Info', 'Gold layer'],
['Detector Info', 'Incidence angle'],
['Detector Info', 'Solid angle'],
['Detector Info', 'Stage tilt'],
['Detector Info', 'Window thickness'],
['Detector Info', 'Window type'], ['Detector Info', 'Zero fwhm'],
['Live time'], ['Real time']]:
if _try_get_dict_val(mdict, base + m) != 'not found':
mdict['nx_meta']['warnings'].append(
['EDS'] + [m[-1] if len(m) > 1 else m[0]])
# Set the dataset type to Spectrum if any EDS tags were added
if 'EDS' in mdict['nx_meta']:
_logger.info('Detected file as Spectrum type based on presence of '
'EDS metadata')
mdict['nx_meta']['DatasetType'] = 'Spectrum'
if 'STEM' in mdict['nx_meta']['Illumination Mode']:
mdict['nx_meta']['Data Type'] = 'STEM_EDS'
else:
# no known files match this mode, so skip for coverage
mdict['nx_meta']['Data Type'] = 'TEM_EDS' # pragma: no cover
return mdict
def parse_dm3_eels_info(mdict):
"""
Parses metadata from the DigitalMicrograph tag structure that concerns any
EELS acquisition or spectrometer settings, placing it in an ``EELS``
dictionary underneath the root-level ``nx_meta`` node.
Parameters
----------
mdict : dict
A metadata dictionary as returned by :py:meth:`get_dm3_metadata`
Returns
-------
mdict : dict
The metadata dictionary with all the "EELS-specific" metadata added as
sub-node under the ``nx_meta`` root level dictionary
"""
pre_path = get_pre_path(mdict)
# EELS .dm3 tags of interest:
base = pre_path + ['EELS']
for m in [['Acquisition', 'Exposure (s)'],
['Acquisition', 'Integration time (s)'],
['Acquisition', 'Number of frames'],
["Experimental Conditions", "Collection semi-angle (mrad)"],
["Experimental Conditions", "Convergence semi-angle (mrad)"]]:
val = _try_get_dict_val(mdict, base + m)
# only add the value to this list if we found it, and it's not
# one of the "facility-wide" set values that do not have any meaning:
if val != 'not found':
# add last value of each parameter to the "EELS" sub-tree of nx_meta
_set_nest_dict_val(mdict, ['nx_meta', 'EELS'] + [m[-1]], val)
# different instruments have the spectrometer information in different
# places...
if mdict['nx_meta']['Instrument ID'] == '**REMOVED**':
base = pre_path + ['EELS', 'Acquisition', 'Spectrometer']
elif mdict['nx_meta']['Instrument ID'] == '**REMOVED**':
base = pre_path + ['EELS Spectrometer']
else:
base = None
if base is not None:
for m in [
"Aperture label", "Dispersion (eV/ch)", "Energy loss (eV)",
"Instrument name", "Drift tube enabled",
"Drift tube voltage (V)", "Slit inserted", "Slit width (eV)",
"Prism offset (V)", "Prism offset enabled "
]:
m = [m]
val = _try_get_dict_val(mdict, base + m)
if val != 'not found':
# add last value of each param to the "EELS" sub-tree of nx_meta
_set_nest_dict_val(mdict, ['nx_meta', 'EELS'] +
["Spectrometer " + m[0]], val)
# Process known tags under "processing":
# ImageTags.Processing will be a list of things done (in multiple
# TagGroups) - things like Compute thickness, etc.
val = _try_get_dict_val(mdict, pre_path + ['Processing'])
if val != 'not found' and isinstance(val, dict):
# if val is a dict, then there were processing steps applied
eels_ops = []
for k, v in val.items():
# k will be TagGroup0, TagGroup1, etc.
# v will be dictionaries specifying the process step
# AlignSIByPeak, DataPicker, SpectrumCalibrate,
# Compute Thickness, Background Removal, Signal Integration
op = v['Operation']
param = v['Parameters']
if op == 'AlignSIByPeak':
eels_ops.append('Aligned parent SI By Peak')
elif op == 'Background Removal':
val = _try_get_dict_val(param, ['Model'])
if val != 'not found':
_set_nest_dict_val(
mdict, ['nx_meta', 'EELS', 'Background Removal Model'],
val)
eels_ops.append(op)
elif op == 'SpectrumCalibrate':
eels_ops.append('Calibrated Post-acquisition')
elif op == 'Compute Thickness':
mdict = _process_thickness_metadata(mdict, pre_path + ['EELS'])
eels_ops.append(op)
elif op == 'DataPicker':
eels_ops.append('Extracted from SI')
elif op == 'Signal Integration':
eels_ops.append(op)
if eels_ops:
# remove duplicates (convert to set) and sort alphabetically:
_set_nest_dict_val(mdict, ['nx_meta', 'EELS', 'Processing Steps'],
', '.join(sorted(set(eels_ops))))
# Set the dataset type to Spectrum if any EELS tags were added
if 'EELS' in mdict['nx_meta']:
_logger.info('Detected file as Spectrum type based on presence of '
'EELS metadata')
mdict['nx_meta']['DatasetType'] = 'Spectrum'
if 'STEM' in mdict['nx_meta']['Illumination Mode']:
mdict['nx_meta']['Data Type'] = 'STEM_EELS'
else:
mdict['nx_meta']['Data Type'] = 'TEM_EELS'
return mdict
def parse_dm3_microscope_info(mdict):
"""
Parse the "important" metadata that is saved at specific places within
the DM3 tag structure into a consistent place in the metadata dictionary
returned by :py:meth:`get_dm3_metadata`. Specifically looks at the
"Microscope Info", "Session Info", and "Meta Data" nodes of the tag
structure (these are not present on every microscope)
Parameters
----------
mdict : dict
A metadata dictionary as returned by :py:meth:`get_dm3_metadata`
Returns
-------
mdict : dict
The same metadata dictionary with some values added under the
root-level ``nx_meta`` key
"""
if 'nx_meta' not in mdict: mdict['nx_meta'] = {}
pre_path = get_pre_path(mdict)
# General "microscope info" .dm3 tags (not present on all instruments):
for m in [
'Indicated Magnification', 'Actual Magnification', 'Cs(mm)',
'STEM Camera Length', 'Voltage', 'Operation Mode', 'Specimen',
'Microscope', 'Operator', 'Imaging Mode', 'Illumination Mode',
'Name', 'Field of View (\u00b5m)', 'Facility',
['Stage Position', 'Stage Alpha'], ['Stage Position', 'Stage Beta'],
['Stage Position', 'Stage X'], ['Stage Position', 'Stage Y'],
['Stage Position', 'Stage Z']
]:
base = pre_path + ['Microscope Info']
if isinstance(m, str):
m = [m]
val = _try_get_dict_val(mdict, base + m)
# only add the value to this list if we found it, and it's not one of
# the "facility-wide" set values that do not have any meaning:
if val != 'not found' and val not in ['DO NOT EDIT', 'DO NOT ENTER'] \
and val != []:
# change output of "Stage Position" to unicode characters
if 'Stage Position' in m:
m[-1] = m[-1].replace('Alpha',
'α').replace('Beta',
'β').replace('Stage ', '')
_set_nest_dict_val(mdict, ['nx_meta'] + m, val)
# General "session info" .dm3 tags (sometimes this information is stored
# here instead of under "Microscope Info":
for m in ['Detector', 'Microscope', 'Operator', 'Specimen']:
base = pre_path + ['Session Info']
if isinstance(m, str):
m = [m]
val = _try_get_dict_val(mdict, base + m)
# only add the value to this list if we found it, and it's not
# one of the "facility-wide" set values that do not have any meaning:
if val != 'not found' and val not in ['DO NOT EDIT', 'DO NOT ENTER'] \
and val != []:
_set_nest_dict_val(mdict, ['nx_meta'] + m, val)
# General "Meta Data" .dm3 tags
for m in [
'Acquisition Mode',
'Format',
'Signal',
# this one is seen sometimes in EDS signals:
['Experiment keywords', 'TagGroup1', 'Label']
]:
base = pre_path + ['Meta Data']
if isinstance(m, str):
m = [m]
val = _try_get_dict_val(mdict, base + m)
# only add the value to this list if we found it, and it's not
# one of the "facility-wide" set values that do not have any meaning:
if val != 'not found' and val not in ['DO NOT EDIT', 'DO NOT ENTER'] \
and val != []:
if 'Label' in m:
_set_nest_dict_val(mdict, ['nx_meta'] + ['Analytic Label'],
val)
else:
_set_nest_dict_val(mdict, ['nx_meta'] +
[f'Analytic {lbl}' for lbl in m], val)
# Get acquisition device name:
val = _try_get_dict_val(mdict,
pre_path + ['Acquisition', 'Device', 'Name'])
if val == 'not found':
val = _try_get_dict_val(mdict, pre_path + ['DataBar', 'Device Name'])
if val != 'not found':
_set_nest_dict_val(mdict, ['nx_meta', 'Acquisition Device'], val)
# Get exposure time:
val = _try_get_dict_val(
mdict,
pre_path + ['Acquisition', 'Parameters', 'High Level', 'Exposure (s)'])
if val == 'not found':
val = _try_get_dict_val(mdict,
pre_path + ['DataBar', 'Exposure Time (s)'])
if val != 'not found':
_set_nest_dict_val(mdict, ['nx_meta', 'Exposure Time (s)'], val)
# Get GMS version:
val = _try_get_dict_val(mdict, pre_path + ['GMS Version', 'Created'])
if val != 'not found':
_set_nest_dict_val(mdict, ['nx_meta', 'GMS Version'], val)
# Get camera binning:
val = _try_get_dict_val(
mdict,
pre_path + ['Acquisition', 'Parameters', 'High Level', 'Binning'])
if val != 'not found':
_set_nest_dict_val(mdict, ['nx_meta', 'Binning (Horizontal)'], val[0])
_set_nest_dict_val(mdict, ['nx_meta', 'Binning (Vertical)'], val[1])
# Get image processing:
# ImageTags.Acquisition.Parameters["High Level"].Processing will be
# something like "Gain normalized" - not just for EELS so move this to
# general
val = _try_get_dict_val(
mdict,
pre_path + ['Acquisition', 'Parameters', 'High Level', 'Processing'])
if val != 'not found':
_set_nest_dict_val(mdict, ['nx_meta', 'Camera/Detector Processing'],
val)
if 'Illumination Mode' in mdict['nx_meta']:
if 'STEM' in mdict['nx_meta']['Illumination Mode']:
mdict['nx_meta']['Data Type'] = 'STEM_Imaging'
return mdict
def parse_642_titan(mdict):
"""
Add/adjust metadata specific to the 642 FEI Titan
('`**REMOVED** in **REMOVED**`') to the metadata dictionary
Parameters
----------
mdict : dict
"raw" metadata dictionary as parsed by :py:func:`get_dm3_metadata`
Returns
-------
mdict : dict
The original metadata dictionary with added information specific to
files originating from this microscope with "important" values contained
under the ``nx_meta`` key at the root level
"""
# DONE: complete 642 titan metadata parsing including Tecnai tag
path_to_tecnai = _get_nest_dict_key(mdict, 'Tecnai')
if path_to_tecnai is None:
# For whatever reason, the expected Tecnai Tag is not present,
# so return to prevent errors below
return mdict
tecnai_value = _get_nest_dict_val_by_path(mdict, path_to_tecnai)
microscope_info = tecnai_value['Microscope Info']
tecnai_value['Microscope Info'] = \
process_tecnai_microscope_info(microscope_info)
_set_nest_dict_val(mdict, path_to_tecnai, tecnai_value)
# - Tecnai info:
# - ImageTags.Tecnai.Microscope_Info['Gun_Name']
# - ImageTags.Tecnai.Microscope_Info['Extractor_Voltage']
# - ImageTags.Tecnai.Microscope_Info['Gun_Lens_No']
# - ImageTags.Tecnai.Microscope_Info['Emission_Current']
# - ImageTags.Tecnai.Microscope_Info['Spot']
# - ImageTags.Tecnai.Microscope_Info['Mode']
# - C2, C3, Obj, Dif lens strength:
# - ImageTags.Tecnai.Microscope_Info['C2_Strength',
# 'C3_Strength',
# 'Obj_Strength',
# 'Dif_Strength']
# - ImageTags.Tecnai.Microscope_Info['Image_Shift_x'/'Image_Shift_y'])
# - ImageTags.Tecnai.Microscope_Info['Stage_Position_x' (y/z/theta/phi)]
# - C1/C2/Objective/SA aperture sizes:
# - ImageTags.Tecnai.Microscope_Info['(C1/C2/Obj/SA)_Aperture']
# - ImageTags.Tecnai.Microscope_Info['Filter_Settings']['Mode']
# - ImageTags.Tecnai.Microscope_Info['Filter_Settings']['Dispersion']
# - ImageTags.Tecnai.Microscope_Info['Filter_Settings']['Aperture']
# - ImageTags.Tecnai.Microscope_Info['Filter_Settings']['Prism_Shift']
# - ImageTags.Tecnai.Microscope_Info['Filter_Settings']['Drift_Tube']
# - ImageTags.Tecnai.Microscope_Info['Filter_Settings'][
# 'Total_Energy_Loss']
term_mapping = {
'Gun_Name':
'Gun Name',
'Extractor_Voltage':
'Extractor Voltage (V)',
'Camera_Length':
'Camera Length (m)',
'Gun_Lens_No':
'Gun Lens #',
'Emission_Current':
'Emission Current (μA)',
'Spot':
'Spot',
'Mode':
'Tecnai Mode',
'Defocus':
'Defocus',
'C2_Strength':
'C2 Lens Strength (%)',
'C3_Strength':
'C3 Lens Strength (%)',
'Obj_Strength':
'Objective Lens Strength (%)',
'Dif_Strength':
'Diffraction Lens Strength (%)',
'Microscope_Name':
'Tecnai Microscope Name',
'User':
'******',
'Image_Shift_x':
'Image Shift X (μm)',
'Image_Shift_y':
'Image Shift Y (μm)',
'Stage_Position_x': ['Stage Position', 'X (μm)'],
'Stage_Position_y': ['Stage Position', 'Y (μm)'],
'Stage_Position_z': ['Stage Position', 'Z (μm)'],
'Stage_Position_theta': ['Stage Position', 'θ (°)'],
'Stage_Position_phi': ['Stage Position', 'φ (°)'],
'C1_Aperture':
'C1 Aperture (μm)',
'C2_Aperture':
'C2 Aperture (μm)',
'Obj_Aperture':
'Objective Aperture (μm)',
'SA_Aperture':
'Selected Area Aperture (μm)',
('Filter_Settings', 'Mode'): ['Tecnai Filter', 'Mode'],
('Filter_Settings', 'Dispersion'):
['Tecnai Filter', 'Dispersion (eV/channel)'],
('Filter_Settings', 'Aperture'): ['Tecnai Filter', 'Aperture (mm)'],
('Filter_Settings', 'Prism_Shift'):
['Tecnai Filter', 'Prism Shift (eV)'],
('Filter_Settings', 'Drift_Tube'):
['Tecnai Filter', 'Drift Tube (eV)'],
('Filter_Settings', 'Total_Energy_Loss'):
['Tecnai Filter', 'Total Energy Loss (eV)'],
}
for in_term in term_mapping.keys():
base = list(path_to_tecnai) + ['Microscope Info']
out_term = term_mapping[in_term]
if isinstance(in_term, str):
in_term = [in_term]
elif isinstance(in_term, tuple):
in_term = list(in_term)
if isinstance(out_term, str):
out_term = [out_term]
val = _try_get_dict_val(mdict, base + in_term)
# only add the value to this list if we found it
if val != 'not found' and val not in ['DO NOT EDIT', 'DO NOT ENTER']:
_set_nest_dict_val(mdict, ['nx_meta'] + out_term, val)
path = list(path_to_tecnai) + ['Specimen Info']
val = _try_get_dict_val(mdict, path)
if val != 'not found' and \
val != 'Specimen information is not available yet':
_set_nest_dict_val(mdict, ['nx_meta', 'Specimen'], val)
# If `Tecnai Mode` is `STEM nP SA Zoom Diffraction`, it's diffraction
if 'Tecnai Mode' in mdict['nx_meta'] and \
mdict['nx_meta']['Tecnai Mode'] == 'STEM nP SA Zoom Diffraction':
_logger.info('Detected file as Diffraction type based on "Tecnai '
'Mode" == "STEM nP SA Zoom Diffraction"')
mdict['nx_meta']['DatasetType'] = 'Diffraction'
mdict['nx_meta']['Data Type'] = 'STEM_Diffraction'
# also, if `Operation Mode` is `DIFFRACTION`, it's diffraction
elif 'Operation Mode' in mdict['nx_meta'] and \
mdict['nx_meta']['Operation Mode'] == 'DIFFRACTION':
_logger.info('Detected file as Diffraction type based on "Operation '
'Mode" == "DIFFRACTION"')
mdict['nx_meta']['DatasetType'] = 'Diffraction'
mdict['nx_meta']['Data Type'] = 'TEM_Diffraction'
return mdict
def parse_beam_info(mdict, beam_name):
"""
Parameters
----------
mdict : dict
A metadata dictionary as returned by :py:meth:`get_quanta_metadata`
beam_name : str
The "beam name" read from the root-level ``Beam`` node of the
metadata dictionary
Returns
-------
mdict : dict
The same metadata dictionary with some values added under the
root-level ``nx_meta`` key
"""
# Values are in SI units, but we want easy to display, so include the
# exponential factor that will get us from input unit (such as seconds)
# to output unit (such as μs -- meaning factor = 6)
to_parse = [
([beam_name, 'EmissionCurrent'], ['Emission Current (μA)'], 6),
([beam_name, 'HFW'], ['Horizontal Field Width (μm)'], 6),
([beam_name, 'HV'], ['Voltage (kV)'], -3),
([beam_name, 'SourceTiltX'], ['Beam Tilt X'], 0),
([beam_name, 'SourceTiltY'], ['Beam Tilt Y'], 0),
([beam_name, 'StageR'], ['Stage Position', 'R'], 0),
([beam_name, 'StageTa'], ['Stage Position', 'α'], 0),
# all existing quanta images have a value of zero for beta
# ([beam_name, 'StageTb'], ['Stage Position', 'β'], 0),
([beam_name, 'StageX'], ['Stage Position', 'X'], 0),
([beam_name, 'StageY'], ['Stage Position', 'Y'], 0),
([beam_name, 'StageZ'], ['Stage Position', 'Z'], 0),
([beam_name, 'StigmatorX'], ['Stigmator X Value'], 0),
([beam_name, 'StigmatorY'], ['Stigmator Y Value'], 0),
([beam_name, 'VFW'], ['Vertical Field Width (μm)'], 6),
([beam_name, 'WD'], ['Working Distance (mm)'], 3),
]
for m_in, m_out, factor in to_parse:
val = _try_get_dict_val(mdict, m_in)
if val != 'not found' and val != '':
val = _Decimal(val) * _Decimal(str(10**factor))
_set_nest_dict_val(
mdict, ['nx_meta'] + m_out,
float(val) if isinstance(val, _Decimal) else val)
# Add beam name to metadata:
_set_nest_dict_val(mdict, ['nx_meta'] + ['Beam Name'], beam_name)
# BeamShiftX and BeamShiftY require an additional test:
bs_x_val = _try_get_dict_val(mdict, [beam_name, 'BeamShiftX'])
bs_y_val = _try_get_dict_val(mdict, [beam_name, 'BeamShiftY'])
if bs_x_val != 'not found' and _Decimal(bs_x_val) != 0:
_set_nest_dict_val(mdict, ['nx_meta'] + ['Beam Shift X'],
float(_Decimal(bs_x_val)))
if bs_y_val != 'not found' and _Decimal(bs_y_val) != 0:
_set_nest_dict_val(mdict, ['nx_meta'] + ['Beam Shift Y'],
float(_Decimal(bs_y_val)))
# only parse scan rotation if value is not zero:
# Not sure what the units of this value are... looks like radians because
# unique values range from 0 to 6.24811 - convert to degrees for display
scan_rot_val = _try_get_dict_val(mdict, [beam_name, 'ScanRotation'])
if scan_rot_val != 'not found' and _Decimal(scan_rot_val) != 0:
scan_rot_dec = _Decimal(scan_rot_val) # make scan_rot a Decimal
# get number of digits in Decimal value (so we don't artificially
# introduce extra precision)
digits = abs(scan_rot_dec.as_tuple().exponent)
# round the final float value to that number of digits
scan_rot_val = round(degrees(scan_rot_dec), digits)
_set_nest_dict_val(mdict, ['nx_meta', 'Scan Rotation (°)'],
scan_rot_val)
# TiltCorrectionAngle only if TiltCorrectionIsOn == 'yes'
tilt_corr_on = _try_get_dict_val(mdict, [beam_name, 'TiltCorrectionIsOn'])
if tilt_corr_on == 'yes':
tilt_corr_val = _try_get_dict_val(mdict,
[beam_name, 'TiltCorrectionAngle'])
if tilt_corr_val != 'not found':
tilt_corr_val = float(_Decimal(tilt_corr_val))
_set_nest_dict_val(mdict, ['nx_meta'] + ['Tilt Correction Angle'],
tilt_corr_val)
return mdict
def parse_nx_meta(mdict):
"""
Parse the "important" metadata that is saved at specific places within
the Quanta tag structure into a consistent place in the metadata dictionary
returned by :py:meth:`get_quanta_metadata`.
Parameters
----------
mdict : dict
A metadata dictionary as returned by :py:meth:`get_quanta_metadata`
Returns
-------
mdict : dict
The same metadata dictionary with some values added under the
root-level ``nx_meta`` key
"""
# The name of the beam, scan, and detector will determine which sections are
# present (have not seen more than one beam/detector -- although likely
# will be the case for dual beam FIB/SEM)
beam_name = _try_get_dict_val(mdict, ['Beam', 'Beam'])
det_name = _try_get_dict_val(mdict, ['Detectors', 'Name'])
scan_name = _try_get_dict_val(mdict, ['Beam', 'Scan'])
# some parsers are broken off into helper methods:
if beam_name != 'not found':
mdict = parse_beam_info(mdict, beam_name)
if scan_name != 'not found':
mdict = parse_scan_info(mdict, scan_name)
if det_name != 'not found':
mdict = parse_det_info(mdict, det_name)
if _try_get_dict_val(mdict, ['System']) != 'not found':
mdict = parse_system_info(mdict)
# process the rest of the metadata tags:
# process beam spot size
val = _try_get_dict_val(mdict, ['Beam', 'Spot'])
if val != 'not found':
try:
val = _Decimal(val)
except (ValueError, _invalidOp):
pass
_set_nest_dict_val(mdict, ['nx_meta'] + ['Spot Size'],
float(val) if isinstance(val, _Decimal) else val)
# process drift correction
val = _try_get_dict_val(mdict, ['Image', 'DriftCorrected'])
if val != 'not found':
# set to true if the value is 'On'
val = val == 'On'
_set_nest_dict_val(mdict, ['nx_meta'] + ['Drift Correction Applied'],
val)
# process frame integration
val = _try_get_dict_val(mdict, ['Image', 'Integrate'])
if val != 'not found':
try:
val = int(val)
if val > 1:
_set_nest_dict_val(mdict, ['nx_meta'] + ['Frames Integrated'],
val)
except ValueError:
pass
# process mag mode
val = _try_get_dict_val(mdict, ['Image', 'MagnificationMode'])
if val != 'not found':
try:
val = int(val)
except ValueError:
pass
_set_nest_dict_val(mdict, ['nx_meta'] + ['Magnification Mode'], val)
# Process "ResolutionX/Y" (data size)
x_val = _try_get_dict_val(mdict, ['Image', 'ResolutionX'])
y_val = _try_get_dict_val(mdict, ['Image', 'ResolutionY'])
try:
x_val = int(x_val)
y_val = int(y_val)
except ValueError:
pass
if x_val != 'not found' and y_val != 'not found':
_set_nest_dict_val(mdict, ['nx_meta', 'Data Dimensions'],
str((x_val, y_val)))
# test for specimen temperature value if present and non-empty
temp_val = _try_get_dict_val(mdict, ['Specimen', 'Temperature'])
if temp_val != 'not found' and temp_val != '':
try:
temp_val = _Decimal(temp_val)
except (ValueError, _invalidOp):
pass
_set_nest_dict_val(
mdict, ['nx_meta', 'Specimen Temperature (K)'],
float(temp_val) if isinstance(temp_val, _Decimal) else temp_val)
# # parse SpecTilt (think this is specimen pre-tilt, but not definite)
# # tests showed that this is always the same value as StageT, so we do not
# # need to parse this one
# val = _try_get_dict_val(mdict, ['Stage', 'SpecTilt'])
# if val != 'not found' and val != '0':
# _set_nest_dict_val(mdict, ['nx_meta', 'Stage Position',
# 'Specimen Tilt'], val)
# Get user ID (sometimes it's not correct because the person left the
# instrument logged in as the previous user, so make sure to add it to
# the warnings list
user_val = _try_get_dict_val(mdict, ['User', 'User'])
if user_val != 'not found':
_set_nest_dict_val(mdict, ['nx_meta', 'Operator'], user_val)
mdict['nx_meta']['warnings'].append(['Operator'])
# parse acquisition date and time
acq_date_val = _try_get_dict_val(mdict, ['User', 'Date'])
acq_time_val = _try_get_dict_val(mdict, ['User', 'Time'])
if acq_date_val != 'not found':
_set_nest_dict_val(mdict, ['nx_meta', 'Acquisition Date'],
acq_date_val)
if acq_time_val != 'not found':
_set_nest_dict_val(mdict, ['nx_meta', 'Acquisition Time'],
acq_time_val)
# parse vacuum mode
vac_val = _try_get_dict_val(mdict, ['Vacuum', 'UserMode'])
if user_val != 'not found':
_set_nest_dict_val(mdict, ['nx_meta', 'Vacuum Mode'], vac_val)
# parse chamber pressure
ch_pres_val = _try_get_dict_val(mdict, ['Vacuum', 'ChPressure'])
if ch_pres_val != 'not found' and ch_pres_val != '':
# keep track of original digits so we don't propagate float errors
try:
ch_pres_val = _Decimal(ch_pres_val)
except _invalidOp:
ch_pres_val = ch_pres_val
if _try_get_dict_val(mdict,
['nx_meta', 'Vacuum Mode']) == 'High vacuum':
ch_pres_str = 'Chamber Pressure (mPa)'
ch_pres_val = ch_pres_val * 10**3
else:
ch_pres_str = 'Chamber Pressure (Pa)'
ch_pres_val = ch_pres_val
_set_nest_dict_val(
mdict, ['nx_meta', ch_pres_str],
float(ch_pres_val)
if isinstance(ch_pres_val, _Decimal) else ch_pres_val)
return mdict
