Import cross sections from csv

galore/cli/galore_get_cs.py

@@ -22,30 +22,64 @@
 from argparse import ArgumentParser
 import galore.cross_sections
 
+
 def main():
     parser = get_parser()
     args = parser.parse_args()
     args = vars(args)
     run(**args)
 
+
 def get_parser():
     parser = ArgumentParser()
+    # parser.add_argument('energy', type=str,
+    #                   help="""
+    #   Photon energy, expressed as source type: "he2" for He (II), "alka" for
+    #    Al k-alpha, (values from Yeh/Lindau (1985)) or as energy in keV (values
+    #    from polynomial fit to Scofield (1973)).""")
+    # parser.add_argument('elements', type=str, nargs='+', help="""
+    #    Space-separated symbols for elements in material.""")
+
     parser.add_argument('energy', type=str,
                         help="""
+        If you don't input dataset:
         Photon energy, expressed as source type: "he2" for He (II), "alka" for
         Al k-alpha, (values from Yeh/Lindau (1985)) or as energy in keV (values
-        from polynomial fit to Scofield (1973)).""")
-    parser.add_argument('elements', type=str, nargs='+', help="""
+        from polynomial fit to Scofield (1973)).
+        if you input dataset:
+        Photon energy, 1 to 1500keV for Scofield dataset, 10.2 to 8047.8 eV for Yeh dataset""")
+
+    parser.add_argument('elements',  nargs='+',
+                        help="""
         Space-separated symbols for elements in material.""")
 
+    parser.add_argument('--dataset', type=str.lower, choices=['scofield', 'yeh'],
+                        help="""Accepted values are 'Scofield' and 'Yeh """)
+
     return parser
 
-def run(energy, elements):
-    cross_sections = galore.get_cross_sections(energy, elements)
+
+def run(energy, elements, dataset=None):
+    cross_sections = galore.get_cross_sections(energy, elements, dataset)
     logging = galore.cross_sections.cross_sections_info(cross_sections)
+
+    # some input will lead to None cross sections result
+    if cross_sections is None:
+        logging.warning("The cross section is None, please check the input")
+
+    # inform user the closest energy of input
+    if dataset != None:
+        logging.warning('The closest energy of input is {energy}'.format(
+            energy=cross_sections['energy']))
+
+        # inform user if energy input is out of range
+        if dataset.lower() == 'scofield' and float(energy) > 1500:
+            logging.warning('The maximum energy of Scofield is 1500 keV')
+
     logging.info("Photoionisation cross sections per electron:")
 
     for element in elements:
+
         if 'warning' in cross_sections[element]:
             logging.warning("  {0}: {1}".format(
                 element, cross_sections[element]['warning']))

galore/cli/galore_install_data.py

@@ -0,0 +1,31 @@
+import logging
+from argparse import ArgumentParser
+import galore.cross_sections
+
+
+def main():
+    parser = get_parser()
+    args = parser.parse_args()
+    args = vars(args)
+    run(**args)
+
+
+def get_parser():
+    parser = ArgumentParser()
+    parser.add_argument('dataset', type=str.lower, choices= ['scofield','yeh'],
+                        help=""" Accepted values are 'Scofield' and 'Yeh'""")
+
+    return parser
+
+
+def run(dataset):
+    if dataset.lower() == 'scofield' or dataset.lower() == 'yeh':
+
+        url, data_file_dir, data_file_path = galore.cross_sections.get_csv_file_path(
+            dataset)
+        galore.cross_sections.galore_install_data(
+            url, data_file_dir, data_file_path)
+
+    else:
+        print("Dataset '{dataset}' was not recognised. Accepted values are 'Scofield' and 'Yeh'.".format(dataset = dataset))
+