clean up codes and add in test file

addie/processing/idl/run_sum_scans.py

@@ -3,7 +3,7 @@
 from qtpy.QtCore import Qt
 from addie.processing.idl.step2_gui_handler import Step2GuiHandler
 from addie.processing.mantid.master_table.periodic_table.material_handler \
-    import get_periodictable_formatted_element_and_number_of_atoms
+    import get_periodictable_formatted_element_and_number_of_atoms as format_ele
 import numpy as np
 import re
 
@@ -104,37 +104,48 @@ def create_output_file(self):
         print("[LOG] created file %s" % _full_output_file_name)
 
         # redpar file
+        r_max_possible = "{0:6.2F}".format(np.pi / self.q_interval_min)
+        r_range = o_gui_handler.get_r_range(r_max_possible)
+        self._runs["r_range"] = r_range
+        self._runs["q_range"] = [q_range_min, q_range_max]
         for _label in self._runs:
-            f = open(self._runs[_label]["sam_name"] + ".redpar", "w")
-            chem_form_temp = self._runs[_label]["sam_formula"]
-            list_element = chem_form_temp.split(" ")
-            formated_ele_list = []
-            for _element in list_element:
-                [formated_element, number_of_atoms, case] = get_periodictable_formatted_element_and_number_of_atoms(_element)
-                formated_ele_list.append(formated_element)
-            sample_form_str = ""
-            for item in formated_ele_list:
-                if case == 1:
-                    to_append = item + "_"
-                elif case == 2:
-                    to_append = re.findall('[A-Z][a-z]*', item)[-1]
-                    to_append += ("_" + re.findall('[0-9]+', item)[-1] + "_")
-                else:
-                    to_append = item.split("[")[1].split("]")[0] + item.split("[")[0] + "_" + item.split("]")[1] + "_"
-                sample_form_str += to_append
-            sample_form_str = sample_form_str[:-1]
-            f.write("{0:13s}{1:<s}\n".format("formula", sample_form_str))
-            f.write("{0:13s}{1:<s}\n".format("massdensity", self._runs[_label]["mass_density"]))
-            f.write("{0:13s}{1:<s}\n".format("radius", self._runs[_label]["radius"]))
-            f.write("{0:13s}{1:<s}\n".format("packfrac", self._runs[_label]["packing_fraction"]))
-            f.write("{0:13s}{1:<s}\n".format("geometry", self._runs[_label]["geometry"]))
-            [r_range_min, r_range_max] = o_gui_handler.get_r_range()
-            r_max_possible = "{0:6.2F}".format(np.pi / self.q_interval_min)
-            if r_range_min and r_range_max:
-                f.write("{0:13s}{1:<s}\n".format("rfilter", r_range_min + "," + r_range_max + "," + r_max_possible))
-            if q_range_min and q_range_max:
-                f.write("{0:13s}{1:<s}\n".format("qfilter", q_range_min + "," + q_range_max))
-            f.close()
+            if _label != "r_range" and _label != "q_range":
+                self._runs = self.collect_info_for_redpar(self._runs, _label)
+                self.write_redpar(self._runs, _label)
+
+    def collect_info_for_redpar(self, runs_info, _label):
+        chem_form_temp = runs_info[_label]["sam_formula"]
+        list_element = chem_form_temp.split(" ")
+        formated_ele_list = []
+        for _element in list_element:
+            [formated_element, number_of_atoms, case] = format_ele(_element)
+            formated_ele_list.append(formated_element)
+        sample_form_str = ""
+        for item in formated_ele_list:
+            if case == 1:
+                to_append = item + "_"
+            elif case == 2:
+                to_append = re.findall('[A-Z][a-z]*', item)[-1]
+                to_append += ("_" + re.findall('[0-9]+', item)[-1] + "_")
+            else:
+                to_append = item.split("[")[1].split("]")[0] + item.split("[")[0] + "_" + item.split("]")[1] + "_"
+            sample_form_str += to_append
+        runs_info[_label]["sam_form_used"] = sample_form_str[:-1]
+
+        return runs_info
+
+    def write_redpar(self, runs_info, _label):
+        file_name = runs_info[_label]["sam_name"] + ".redpar"
+        with open(file_name, 'w') as f:
+            f.write("{0:13s}{1:<s}\n".format("formula", runs_info[_label]["sam_form_used"]))
+            f.write("{0:13s}{1:<s}\n".format("massdensity", runs_info[_label]["mass_density"]))
+            f.write("{0:13s}{1:<s}\n".format("radius", runs_info[_label]["radius"]))
+            f.write("{0:13s}{1:<s}\n".format("packfrac", runs_info[_label]["packing_fraction"]))
+            f.write("{0:13s}{1:<s}\n".format("geometry", runs_info[_label]["geometry"]))
+            if None not in runs_info["r_range"]:
+                f.write("{0:13s}{1:<s}\n".format("rfilter", ",".join(runs_info["r_range"])))
+            if None not in runs_info["q_range"]:
+                f.write("{0:13s}{1:<s}\n".format("qfilter", ",".join(runs_info["q_range"])))
 
     def collect_runs_checked(self):
         table = self.parent.table

tests/test_files/SiO2.redpar

@@ -0,0 +1,7 @@
+formula      Si_1_O_2
+massdensity  2.5
+radius       0.15
+packfrac     0.7
+geometry     Cylinder
+rfilter      1.5,50,157.08
+qfilter      0.2,31.4