def eelsdb(spectrum_type=None, title=None, author=None, element=None, formula=None,
edge=None, min_energy=None, max_energy=None, resolution=None,
min_energy_compare="gt", max_energy_compare="lt",
resolution_compare="lt", max_n=-1, monochromated=None, order=None,
order_direction="ASC", verify_certificate=True):
r"""Download spectra from the EELS Data Base.
Parameters
----------
spectrum_type: {'coreloss', 'lowloss', 'zeroloss', 'xrayabs'}, optional
title: string
Search spectra titles for a text string.
author: string, optional
Search authors for a text string.
element: string or list of strings, optional
Filter for the presence of one or more element. Each string must
correspond with a valid element symbol.
formula: string
Chemical formula of the sample.
edge: {'K', 'L1', 'L2,3', 'M2,3', 'M4,5', 'N2,3', 'N4,5' 'O2,3', 'O4,5'}, optional
Filter for spectra with a specific class of edge.
min_energy, max_energy: float, optional
Minimum and maximum energy in eV.
resolution: float, optional
Energy resolution in eV.
resolution_compare: {"lt", "eq", "gt"}, optional, default "lt"
"lt" to search for all spectra with resolution less than `resolution`.
"eq" for equal, "gt" for greater than.
min_energy_compare, max_energy_compare: {"lt", "eq", "gt"}, optional
"lt" to search for all spectra with min/max energy less than
`min_energy`\`max_energy`. "eq" for equal, "gt" for greater than.
Deafault values are "gt"/"lt" for `min_energy`\`max_energy`
respectively.
monochromated: bool or None (default)
max_n: int, default -1
Maximum number of spectra to return. -1 to return all.
order: string
Key to sort results by. Valid keys are:
* "spectrumType",
* "spectrumMin",
* "spectrumMax",
* "stepSize",
* "spectrumFormula",
* "spectrumElement",
* "spectrumUpload",
* "source_purity",
* "spectrumEdges",
* "microscope",
* "guntype",
* "beamenergy",
* "resolution",
* "monochromated",
* "acquisition_mode",
* "convergence",
* "collection",
* "probesize",
* "beamcurrent",
* "integratetime",
* "readouts",
* "detector",
* "darkcurrent",
* "gainvariation",
* "calibration",
* "zeroloss_deconv",
* "thickness",
* "deconv_fourier_log",
* "deconv_fourier_ratio",
* "deconv_stephens_deconvolution",
* "deconv_richardson_lucy",
* "deconv_maximum_entropy",
* "deconv_other",
* "assoc_spectra",
* "ref_freetext",
* "ref_doi",
* "ref_url",
* "ref_authors",
* "ref_journal",
* "ref_volume",
* "ref_issue",
* "ref_page",
* "ref_year",
* "ref_title",
* "otherURLs"
order_direction : {"ASC", "DESC"}
Sorting `order` direction.
verify_certificate: bool
If True, verify the eelsdb website certificate and raise an error
if it is invalid. If False, continue querying the database if the certificate
is invalid. (This is a potential security risk.)
Returns
-------
spectra: list
A list containing all the spectra matching the given criteria if
any.
"""
# Verify arguments
if spectrum_type is not None and spectrum_type not in {
'coreloss', 'lowloss', 'zeroloss', 'xrayabs'}:
raise ValueError("spectrum_type must be one of \'coreloss\', \'lowloss\', "
"\'zeroloss\', \'xrayabs\'.")
valid_edges = [
'K', 'L1', 'L2,3', 'M2,3', 'M4,5', 'N2,3', 'N4,5', 'O2,3', 'O4,5']
valid_order_keys = [
"spectrumType",
"spectrumMin",
"spectrumMax",
"stepSize",
"spectrumFormula",
"spectrumElement",
"spectrumUpload",
"source_purity",
"spectrumEdges",
"microscope",
"guntype",
"beamenergy",
"resolution",
"monochromated",
"acquisition_mode",
"convergence",
"collection",
"probesize",
"beamcurrent",
"integratetime",
"readouts",
"detector",
"darkcurrent",
"gainvariation",
"calibration",
"zeroloss_deconv",
"thickness",
"deconv_fourier_log",
"deconv_fourier_ratio",
"deconv_stephens_deconvolution",
"deconv_richardson_lucy",
"deconv_maximum_entropy",
"deconv_other",
"assoc_spectra",
"ref_freetext",
"ref_doi",
"ref_url",
"ref_authors",
"ref_journal",
"ref_volume",
"ref_issue",
"ref_page",
"ref_year",
"ref_title",
"otherURLs"]
if edge is not None and edge not in valid_edges:
raise ValueError("`edge` must be one of %s." % ", ".join(valid_edges))
if order is not None and order not in valid_order_keys:
raise ValueError("`order` must be one of %s." % ", ".join(
valid_order_keys))
if order_direction is not None and order_direction not in ["ASC", "DESC"]:
raise ValueError("`order_direction` must be \"ASC\" or \"DESC\".")
for kwarg, label in (
(resolution_compare, "resolution_compare"),
(min_energy_compare, "min_energy_compare"),
(max_energy_compare, "max_energy_compare")):
if kwarg not in ("lt", "gt", "eq"):
raise ValueError("`%s` must be \"lt\", \"eq\" or \"gt\"." %
label)
if monochromated is not None:
monochromated = 1 if monochromated else 0
params = {
"type": spectrum_type,
"title": title,
"author": author,
"edge": edge,
"min_energy": min_energy,
"max_energy": max_energy,
"resolution": resolution,
"resolution_compare": resolution_compare,
"monochromated": monochromated,
"formula": formula,
"min_energy_compare": min_energy_compare,
"max_energy_compare": max_energy_compare,
"per_page": max_n,
"order": order,
"order_direction": order_direction,
}
if isinstance(element, str):
params["element"] = element
else:
params["element[]"] = element
request = requests.get('http://api.eelsdb.eu/spectra', params=params, verify=verify_certificate)
spectra = []
jsons = request.json()
if "message" in jsons:
# Invalid query, EELSdb raises error.
raise IOError(
"Please report the following error to the HyperSpy developers: "
"%s" % jsons["message"])
for json_spectrum in jsons:
download_link = json_spectrum['download_link']
msa_string = requests.get(download_link, verify=verify_certificate).text
try:
s = dict2signal(parse_msa_string(msa_string)[0])
emsa = s.original_metadata
s.original_metadata = s.original_metadata.__class__(
{'json': json_spectrum})
s.original_metadata.emsa = emsa
spectra.append(s)
except:
# parse_msa_string or dict2signal may fail if the EMSA file is not
# a valid one.
_logger.exception(
"Failed to load the spectrum.\n"
"Title: %s id: %s.\n"
"Please report this error to http://eelsdb.eu/about \n" %
(json_spectrum["title"], json_spectrum["id"]))
if not spectra:
_logger.info(
"The EELS database does not contain any spectra matching your query"
". If you have some, why not submitting them "
"https://eelsdb.eu/submit-data/ ?\n")
else:
# Add some info from json to metadata
# Values with units are not yet supported by HyperSpy (v0.8) so
# we can't get map those fields.
for s in spectra:
if spectrum_type == "xrayabs":
s.set_signal_type("XAS")
json_md = s.original_metadata.json
s.metadata.General.title = json_md.title
if s.metadata.Signal.signal_type == "EELS":
if json_md.elements:
try:
s.add_elements(json_md.elements)
except ValueError:
_logger.exception(
"The following spectrum contains invalid chemical "
"element information:\n"
"Title: %s id: %s. Elements: %s.\n"
"Please report this error in "
"http://eelsdb.eu/about \n" %
(json_md.title, json_md.id, json_md.elements))
if "collection" in json_md and " mrad" in json_md.collection:
beta = float(json_md.collection.replace(" mrad", ""))
s.metadata.set_item(
"Acquisition_instrument.TEM.Detector.EELS.collection_angle",
beta)
if "convergence" in json_md and " mrad" in json_md.convergence:
alpha = float(json_md.convergence.replace(" mrad", ""))
s.metadata.set_item(
"Acquisition_instrument.TEM.convergence_angle", alpha)
if "beamenergy" in json_md and " kV" in json_md.beamenergy:
beam_energy = float(json_md.beamenergy.replace(" kV", ""))
s.metadata.set_item(
"Acquisition_instrument.TEM.beam_energy", beam_energy)
# We don't yet support units, so we cannot map the thickness
# s.metadata.set_item("Sample.thickness", json_md.thickness)
s.metadata.set_item("Sample.description", json_md.description)
s.metadata.set_item("Sample.chemical_formula", json_md.formula)
s.metadata.set_item("General.author", json_md.author.name)
s.metadata.set_item("Acquisition_instrument.TEM.microscope",
json_md.microscope)
return spectra
def eelsdb(spectrum_type=None, title=None, author=None, element=None, formula=None,
edge=None, min_energy=None, max_energy=None, resolution=None,
min_energy_compare="gt", max_energy_compare="lt",
resolution_compare="lt", max_n=-1, monochromated=None, order=None,
order_direction="ASC"):
r"""Download spectra from the EELS Data Base.
Parameters
----------
spectrum_type: {'coreloss', 'lowloss', 'zeroloss', 'xrayabs'}, optional
title: string
Search spectra titles for a text string.
author: string, optional
Search authors for a text string.
element: string or list of strings, optional
Filter for the presence of one or more element. Each string must
correspond with a valid element symbol.
formula: string
Chemical formula of the sample.
edge: {'K', 'L1', 'L2,3', 'M2,3', 'M4,5', 'N2,3', 'N4,5' 'O2,3', 'O4,5'}, optional
Filter for spectra with a specific class of edge.
min_energy, max_energy: float, optional
Minimum and maximum energy in eV.
resolution: float, optional
Energy resolution in eV.
resolution_compare: {"lt", "eq", "gt"}, optional, default "lt"
"lt" to search for all spectra with resolution less than `resolution`.
"eq" for equal, "gt" for greater than.
min_energy_compare, max_energy_compare: {"lt", "eq", "gt"}, optional
"lt" to search for all spectra with min/max energy less than
`min_energy`\`max_energy`. "eq" for equal, "gt" for greater than.
Deafault values are "gt"/"lt" for `min_energy`\`max_energy`
respectively.
monochromated: bool or None (default)
max_n: int, default -1
Maximum number of spectra to return. -1 to return all.
order: string
Key to sort results by. Valid keys are:
* "spectrumType",
* "spectrumMin",
* "spectrumMax",
* "stepSize",
* "spectrumFormula",
* "spectrumElement",
* "spectrumUpload",
* "source_purity",
* "spectrumEdges",
* "microscope",
* "guntype",
* "beamenergy",
* "resolution",
* "monochromated",
* "acquisition_mode",
* "convergence",
* "collection",
* "probesize",
* "beamcurrent",
* "integratetime",
* "readouts",
* "detector",
* "darkcurrent",
* "gainvariation",
* "calibration",
* "zeroloss_deconv",
* "thickness",
* "deconv_fourier_log",
* "deconv_fourier_ratio",
* "deconv_stephens_deconvolution",
* "deconv_richardson_lucy",
* "deconv_maximum_entropy",
* "deconv_other",
* "assoc_spectra",
* "ref_freetext",
* "ref_doi",
* "ref_url",
* "ref_authors",
* "ref_journal",
* "ref_volume",
* "ref_issue",
* "ref_page",
* "ref_year",
* "ref_title",
* "otherURLs"
order_direction : {"ASC", "DESC"}
Sorting `order` direction.
Returns
-------
spectra: list
A list containing all the spectra matching the given criteria if
any.
"""
# Verify arguments
if spectrum_type is not None and spectrum_type not in {
'coreloss', 'lowloss', 'zeroloss', 'xrayabs'}:
raise ValueError("spectrum_type must be one of \'coreloss\', \'lowloss\', "
"\'zeroloss\', \'xrayabs\'.")
valid_edges = [
'K', 'L1', 'L2,3', 'M2,3', 'M4,5', 'N2,3', 'N4,5', 'O2,3', 'O4,5']
valid_order_keys = [
"spectrumType",
"spectrumMin",
"spectrumMax",
"stepSize",
"spectrumFormula",
"spectrumElement",
"spectrumUpload",
"source_purity",
"spectrumEdges",
"microscope",
"guntype",
"beamenergy",
"resolution",
"monochromated",
"acquisition_mode",
"convergence",
"collection",
"probesize",
"beamcurrent",
"integratetime",
"readouts",
"detector",
"darkcurrent",
"gainvariation",
"calibration",
"zeroloss_deconv",
"thickness",
"deconv_fourier_log",
"deconv_fourier_ratio",
"deconv_stephens_deconvolution",
"deconv_richardson_lucy",
"deconv_maximum_entropy",
"deconv_other",
"assoc_spectra",
"ref_freetext",
"ref_doi",
"ref_url",
"ref_authors",
"ref_journal",
"ref_volume",
"ref_issue",
"ref_page",
"ref_year",
"ref_title",
"otherURLs"]
if edge is not None and edge not in valid_edges:
raise ValueError("`edge` must be one of %s." % ", ".join(valid_edges))
if order is not None and order not in valid_order_keys:
raise ValueError("`order` must be one of %s." % ", ".join(
valid_order_keys))
if order_direction is not None and order_direction not in ["ASC", "DESC"]:
raise ValueError("`order_direction` must be \"ASC\" or \"DESC\".")
for kwarg, label in (
(resolution_compare, "resolution_compare"),
(min_energy_compare, "min_energy_compare"),
(max_energy_compare, "max_energy_compare")):
if kwarg not in ("lt", "gt", "eq"):
raise ValueError("`%s` must be \"lt\", \"eq\" or \"gt\"." %
label)
if monochromated is not None:
monochromated = 1 if monochromated else 0
params = {
"type": spectrum_type,
"title": title,
"author": author,
"edge": edge,
"min_energy": min_energy,
"max_energy": max_energy,
"resolution": resolution,
"resolution_compare": resolution_compare,
"monochromated": monochromated,
"formula": formula,
"min_energy_compare": min_energy_compare,
"max_energy_compare": max_energy_compare,
"per_page": max_n,
"order": order,
"order_direction": order_direction,
}
if isinstance(element, str):
params["element"] = element
else:
params["element[]"] = element
request = requests.get('http://api.eelsdb.eu/spectra', params=params, )
spectra = []
jsons = request.json()
if "message" in jsons:
# Invalid query, EELSdb raises error.
raise IOError(
"Please report the following error to the HyperSpy developers: "
"%s" % jsons["message"])
for json_spectrum in jsons:
download_link = json_spectrum['download_link']
msa_string = requests.get(download_link).text
try:
s = dict2signal(parse_msa_string(msa_string)[0])
emsa = s.original_metadata
s.original_metadata = s.original_metadata.__class__(
{'json': json_spectrum})
s.original_metadata.emsa = emsa
spectra.append(s)
except:
# parse_msa_string or dict2signal may fail if the EMSA file is not
# a valid one.
_logger.exception(
"Failed to load the spectrum.\n"
"Title: %s id: %s.\n"
"Please report this error to http://eelsdb.eu/about \n" %
(json_spectrum["title"], json_spectrum["id"]))
if not spectra:
_logger.information(
"The EELS database does not contain any spectra matching your query"
". If you have some, why not submitting them "
"https://eelsdb.eu/submit-data/ ?\n")
else:
# Add some info from json to metadata
# Values with units are not yet supported by HyperSpy (v0.8) so
# we can't get map those fields.
for s in spectra:
if spectrum_type == "xrayabs":
s.set_signal_type("XAS")
json_md = s.original_metadata.json
s.metadata.General.title = json_md.title
if s.metadata.Signal.signal_type == "EELS":
if json_md.elements:
try:
s.add_elements(json_md.elements)
except ValueError:
_logger.exception(
"The following spectrum contains invalid chemical "
"element information:\n"
"Title: %s id: %s. Elements: %s.\n"
"Please report this error in "
"http://eelsdb.eu/about \n" %
(json_md.title, json_md.id, json_md.elements))
if "collection" in json_md and " mrad" in json_md.collection:
beta = float(json_md.collection.replace(" mrad", ""))
s.metadata.set_item(
"Acquisition_instrument.TEM.Detector.EELS.collection_angle",
beta)
if "convergence" in json_md and " mrad" in json_md.convergence:
alpha = float(json_md.convergence.replace(" mrad", ""))
s.metadata.set_item(
"Acquisition_instrument.TEM.convergence_angle", alpha)
if "beamenergy" in json_md and " kV" in json_md.beamenergy:
beam_energy = float(json_md.beamenergy.replace(" kV", ""))
s.metadata.set_item(
"Acquisition_instrument.TEM.beam_energy", beam_energy)
# We don't yet support units, so we cannot map the thickness
# s.metadata.set_item("Sample.thickness", json_md.thickness)
s.metadata.set_item("Sample.description", json_md.description)
s.metadata.set_item("Sample.chemical_formula", json_md.formula)
s.metadata.set_item("General.author", json_md.author.name)
s.metadata.set_item("Acquisition_instrument.TEM.microscope",
json_md.microscope)
return spectra