pyTEMlib 0.2025.4.1__py3-none-any.whl → 0.2025.9.1__py3-none-any.whl

pyTEMlib/eels_tools/eels_database.py

@@ -0,0 +1,134 @@
+"""
+eels_tools
+Model based quantification of electron energy-loss data
+Copyright by Gerd Duscher
+
+"""
+import numpy as np
+import requests
+
+
+
+##########################
+# EELS Database
+##########################
+
+
+def read_msa(msa_string):
+    """read msa formated file"""
+    parameters = {}
+    y = []
+    x = []
+    # Read the keywords
+    data_section = False
+    msa_lines = msa_string.split('\n')
+
+    for line in msa_lines:
+        if data_section is False:
+            if len(line) > 0:
+                if line[0] == "#":
+                    try:
+                        key, value = line.split(': ')
+                        value = value.strip()
+                    except ValueError:
+                        key = line
+                        value = None
+                    key = key.strip('#').strip()
+
+                    if key != 'SPECTRUM':
+                        parameters[key] = value
+                    else:
+                        data_section = True
+        else:
+            # Read the data
+
+            if len(line) > 0 and line[0] != "#" and line.strip():
+                if parameters['DATATYPE'] == 'XY':
+                    xy = line.replace(',', ' ').strip().split()
+                    y.append(float(xy[1]))
+                    x.append(float(xy[0]))
+                elif parameters['DATATYPE'] == 'Y':
+                    print('y')
+                    data = [
+                        float(i) for i in line.replace(',', ' ').strip().split()]
+                    y.extend(data)
+    parameters['data'] = np.array(y)
+    if 'XPERCHAN' in parameters:
+        parameters['XPERCHAN'] = str(parameters['XPERCHAN']).split(' ', maxsplit=1)[0]
+        parameters['OFFSET'] = str(parameters['OFFSET']).split(' ', maxsplit=1)[0]
+        dispersion = float(parameters['XPERCHAN'])  # eV per channel
+        offset = float(parameters['OFFSET'])  # eV offset
+        parameters['energy_scale'] = np.arange(len(y)) * dispersion + offset
+    return parameters
+
+
+def get_spectrum_eels_db(formula=None, edge=None, title=None, element=None):
+    """
+    get spectra from EELS database
+    chemical formula and edge is accepted.
+    Could expose more of the search parameters
+    """
+    valid_edges = ['K', 'L1', 'L2,3', 'M2,3', 'M4,5', 'N2,3', 'N4,5', 'O2,3', 'O4,5']
+    if edge is not None and edge not in valid_edges:
+        print('edge should be a in ', valid_edges)
+
+    spectrum_type = None
+    author = 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
+    # 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']
+
+    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,
+        'element': element,
+        "min_energy_compare": min_energy_compare,
+        "max_energy_compare": max_energy_compare,
+        "per_page": max_n,
+        "order": order,
+        "order_direction": order_direction,
+    }
+
+    request = requests.get('http://api.eelsdb.eu/spectra', params=params, verify=True, timeout=10)
+    # spectra = []
+    jsons = request.json()
+    if "message" in jsons:
+        # Invalid query, EELSdb raises error.
+        raise IOError(
+            f"Please report the following error to the HyperSpy developers: ",
+            f"{jsons['message']}")
+    reference_spectra = {}
+    for json_spectrum in jsons:
+        download_link = json_spectrum['download_link']
+        # print(download_link)
+        msa_string = requests.get(download_link, verify=verify_certificate, timeout=10).text
+        # print(msa_string[:100])
+        parameters = read_msa(msa_string)
+        if 'XPERCHAN' in parameters:
+            reference_spectra[parameters['TITLE']] = parameters
+            print(parameters['TITLE'])
+    print(f'found {len(reference_spectra.keys())} spectra in EELS database)')
+
+    return reference_spectra