Import cross sections from csv

galore/cli/galore_get_cs.py

@@ -22,41 +22,65 @@
 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,
+                        help=
+        """You can enter 'Scofield' or 'Yeh' """)
+
     return parser
 
-def run(energy, elements):
-    cross_sections = galore.get_cross_sections(energy, elements)
-    logging = galore.cross_sections.cross_sections_info(cross_sections)
-    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']))
-        else:
-            orbitals = cross_sections[element]
-
-            for orbital, value in orbitals.items():
-                if orbital == 'energy':
-                    pass
-                if value is None:
-                    pass
-                else:
-                    logging.info("   {0} {1}: {2:.3e}".format(element,
+
+def run(energy, elements, dataset=None):
+    cross_sections = galore.get_cross_sections(energy, elements, dataset)
+    if cross_sections is None:
+        pass
+    else: 
+        logging = galore.cross_sections.cross_sections_info(cross_sections)
+        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']))
+            else:
+                orbitals = cross_sections[element]
+
+                for orbital, value in orbitals.items():
+                    if orbital == 'energy':
+                        pass
+                    if value is None:
+                        pass
+                    else:
+                        logging.info("   {0} {1}: {2:.3e}".format(element,
                                                               orbital, value))

galore/cli/galore_install_data.py

@@ -0,0 +1,25 @@
+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('reference', type=str,
+                        help=""" 'Scofield' or 'Yeh'""")
+
+    return parser
+
+def run(reference):
+    if reference == 'Scofield' or reference == 'Yeh':
+
+        url,data_file_dir,data_file_path =galore.cross_sections.get_csv_file_path(reference)
+        galore.cross_sections.galore_install_data(url,data_file_dir,data_file_path)
+
+    else:
+        print("You can enter reference 'Scofield' or 'Yeh' ")
+