added % indexed + and sort index column

reduction_tools/auto_process.py

@@ -212,7 +212,8 @@ def scrub_index( index_dir_name ):
     gamma, gamma_err = get_index_cell( index_log, "gamma" )
 
     # put results into df
-    data = [ { "images" : int( images ), "indexed" : int( indexed ),
+    per_index = round( int( indexed )/int( images )*100, 2 )
+    data = [ { "images" : int( images ), "indexed" : int( indexed ), "indexed%" : per_index,
                "index_res" : float( ind_res ), "index_res_err" : float( ind_res_err ),
                "obs" : float( obs ), "obs_err" : float( obs_err ),
                "a" : float( a ), "a_err" : float( a_err ),
@@ -350,12 +351,27 @@ def main( script_dir, cwd, runs,
 
             # re-run check hkl
             print( "running cc check/compare" )
+            # move to partialator directory
             os.chdir( part_run_name )
             check_run_file = part.run_compare_check( "{0}/{1}".format( proc_dir, part_run_name ), part_run_name, cell_file, bins, cc )
             submit_cmd = [ "{0}".format( check_run_file ) ]
             subprocess.call( submit_cmd )
             print( "done" )
 
+            # get partialator metrics
+            try:
+                overcc = part.get_overall_cc()
+            except:
+                overcc = np.nan
+            try:
+                overrsplit = part.get_overall_rsplit()
+            except:
+                overrsplit = np.nan
+            try:
+                b_factor = part.get_b()
+            except AttributeError as e:
+                b_factor = np.nan
+
             # make mtz
             print( "making final mtz" )
             cell = read_cell( cell_file )
@@ -371,21 +387,15 @@ def main( script_dir, cwd, runs,
                 shutil.move( F_file, proc_dir )
             except shutil.Error as e:
                 pass
+
+            # move back to top directory
+            os.chdir( proc_dir )
         
         else:
             print( "partialator not run. {0} > indexed".format( partialator_limit ) )
-            os.chdir( part_run_name )
-            try:
-                cc = scrub_cc( part_run_name )
-            except AttributeError as e:
-                cc = np.nan
-
-        # get partialator metrics
-        overcc = part.get_overall_cc()
-        overrsplit = part.get_overall_rsplit()
-        try:
-            b_factor = part.get_b()
-        except AttributeError as e:
+            cc = np.nan
+            overcc = np.nan
+            overrsplit = np.nan
             b_factor = np.nan
 
         # collate meta data
@@ -409,9 +419,10 @@ def main( script_dir, cwd, runs,
 
     # output stats table
     print( df )
+    df = df.reset_index( drop=True )
     df.to_csv( "auto_process_summary.csv", sep="," )
 
-    print( "finished all!" )
+    print( "finished all" )