added lines to log file

reduction_tools/partialator.py

@@ -92,7 +92,7 @@ def run_partialator( proc_dir, name, stream, pointgroup, model, iterations, adu
     part_sh.write( "module use MX unstable\n" )
     part_sh.write( "module load crystfel/0.10.2-rhel8\n" )
     part_sh.write( "partialator -i {0} \\\n".format( stream ) )
-    part_sh.write( "  -o merged_{0}.hkl \\\n".format( name ) )
+    part_sh.write( "  -o {0}.hkl \\\n".format( name ) )
     part_sh.write( "  -y {0} \\\n".format( pointgroup ) )
     part_sh.write( "  --model={0} \\\n".format( model ) )
     part_sh.write( "  --max-adu={0} \\\n".format( adu ) )
@@ -223,15 +223,46 @@ def get_metric( d2_series, cc_series, cut_off ):
 
     return round( cc_stat, 3 ), cc_tanh
 
+def get_overall_cc():
+
+    # open cc log file
+    cc_log_file = open( "cc.log" )
+    cc_log = cc_log_file.read()
+
+    # regex example = Overall CC = 0.5970865
+    overcc_pattern = r"Overall\sCC\s=\s(\d\.\d+)"
+    overcc = re.search( overcc_pattern, cc_log ).group(1)
+
+    return overcc
+
+def get_overall_rsplit():
+
+    # open rsplit log file
+    rsplit_log_file = open( "Rsplit.log" )
+    rsplit_log = rsplit_log_file.read()
+
+    # regex example = Overall Rsplit = 54.58 %
+    overrsplit_pattern = r"Overall\sRsplit\s=\s(\d+\.\d+)"
+    overrsplit = re.search( overrsplit_pattern, rsplit_log ).group(1)
+
+    return overrsplit
+
+def get_b():
+
+    # open rsplit log file
+    wilson_log_file = open( "wilson.log" )
+    wilson_log = wilson_log_file.read()
+
+    # regex example = B = 41.63 A^2
+    b_factor_pattern = r"B\s=\s(\d+\.\d+)\sA"
+    b_factor = re.search( b_factor_pattern, wilson_log ).group(1)
+
+    return b_factor
+
 def summary_fig( stats_df, cc_tanh, ccstar_tanh, cc_cut, ccstar_cut ):
 
     def dto1_d( x ):
         return 1/x
-        
-    def dto1_d2_rev( x ):
-        return 1/x**2
-    def dto1_d2_for( x ):
-        return 1/x**0.5
 
     # plot results
     cc_fig, axs = plt.subplots(2, 2)
@@ -247,10 +278,10 @@ def summary_fig( stats_df, cc_tanh, ccstar_tanh, cc_cut, ccstar_cut ):
     axs[0,0].plot( stats_df[ "1_d" ], stats_df.cc, color=color )
     # plot fit
     axs[0,0].plot( stats_df[ "1_d" ], cc_tanh, color="tab:grey", linestyle = "dashed" )
-    sax1 = axs[0,0].secondary_xaxis( 'top', functions=( dto1_d, dto1_d ), rotation=90 )
+    sax1 = axs[0,0].secondary_xaxis( 'top', functions=( dto1_d, dto1_d ) )
     sax1.set_xlabel('d (A)')
     axs[0,0].tick_params( axis="y", labelcolor=color )
-    axs[0,0].text( 0.1, 0.1, "CC @ 0.2 = {0}".format( cc_cut ), fontsize = 8 )
+    axs[0,0].text( 0.1, 0.1, "CC0.5 @ 0.3 = {0}".format( cc_cut ), fontsize = 8 )
 
     # cc* plot
     color = "tab:blue"
@@ -275,14 +306,11 @@ def summary_fig( stats_df, cc_tanh, ccstar_tanh, cc_cut, ccstar_cut ):
     sax3.set_xlabel( 'd (A)' )
     axs[1,0].tick_params( axis='y', labelcolor=color )
 
-
     # wilson plot
     color = "tab:purple"
     axs[1,1].set_xlabel( "1/d**2 (1/A**2)" )
     axs[1,1].set_ylabel( "lnI", color=color )
     axs[1,1].plot( stats_df[ "1_d2" ], stats_df.lnI, color=color )
-    sax4 = axs[1,1].secondary_xaxis( 'top', functions=( dto1_d2_for, dto1_d2_rev ) )
-    sax4.set_xlabel( "d (A)" )
     axs[1,1].tick_params( axis='y', labelcolor=color )
 
     # save figure
@@ -346,6 +374,15 @@ def main( cwd, name, stream, pointgroup, model, iterations, cell, shells, part_h
     logger.info( "resolution at CC0.5 at 0.3 = {0}".format( cc_cut ) )
     logger.info( "resolution at CC* at 0.7 = {0}".format( ccstar_cut ) )
 
+    # scrub other metrics
+    overcc = get_overall_cc()
+    overrsplit = get_overall_rsplit()
+    b_factor = get_b()
+
+    logger.info( "overall CC0.5 = {0}".format( overcc ) )
+    logger.info( "overall Rsplit = {0}".format( overrsplit ) )
+    logger.info( "overall B = {0}".format( b_factor ) )
+
     # show plots
     summary_fig( stats_df, cc_tanh, ccstar_tanh, cc_cut, ccstar_cut )
 
@@ -440,4 +477,4 @@ if __name__ == "__main__":
     # run main
     cwd = os.getcwd()
     print( "top working directory = {0}".format( cwd ) )
-    main( cwd, args.name, args.stream_file, args.pointgroup, args.model, args.iterations, args.cell_file, args.bins, args.resolution, args.max_adu, args.reservation )
+    main( cwd, args.name, args.stream_file, args.pointgroup, args.model, args.iterations, args.cell_file, args.bins, args.resolution, args.max_adu, args.reservation )