additions and bug fixes in script

reduction_tools/crystfel_split.py

@@ -13,7 +13,8 @@ python crystfel_split.py -l <path-to-list-file>
                          -g <path-to-geom-file>                          
                          -c <path-to-cell-file>
                          -n <name-of-job>
-# note                   -p True/False will make a progress bar
+
+# crystfel parameter may need some editing in the function - write_crystfel_run
 
 # output
 a series of stream files from crystfel in the current working directory
@@ -48,6 +49,11 @@ def h5_split( lst, chunk_size ):
 
 def write_crystfel_run( proc_dir, name, chunk, chunk_lst_file, geom_file, cell_file ):
 
+    """
+    crystfel run file - spot-finding and indexing parameters may need some editing
+    only change from inside the quote ("")
+    """
+
     # stream file name
     stream_file = "{0}_{1}.stream".format( name, chunk )
 
@@ -62,9 +68,21 @@ def write_crystfel_run( proc_dir, name, chunk, chunk_lst_file, geom_file, cell_f
     run_sh.write( "  --output={0} \\\n".format( stream_file ) )
     run_sh.write( "  --geometry={0} \\\n".format( geom_file ) )
     run_sh.write( "  --pdb={0} \\\n".format( cell_file ) )
-    run_sh.write( "  --indexing=xgandalf-latt-cell --peaks=peakfinder8 \\\n" )
+    run_sh.write( "  --indexing=xgandalf-latt-cell \\\n" )
-    run_sh.write( "  --threshold=15 --min-snr=10 --int-radius=3,5,9 \\\n" )
+    run_sh.write( "  --peaks=peakfinder8 \\\n" )
-    run_sh.write( "  -j 32 --no-multi --no-retry --max-res=3000 --min-pix-count=2 --min-res=85\\\n" )
+    run_sh.write( "  --integration=rings-grad \\\n" )
+    run_sh.write( "  --tolerance=10.0,10.0,10.0,2,3,2 \\\n" )
+    run_sh.write( "  --threshold=10 \\\n" )
+    run_sh.write( "  --min-snr=5 \\\n" )
+    run_sh.write( "  --int-radius=3,5,9 \\\n" )
+    run_sh.write( "  -j 32 \\\n" )
+    run_sh.write( "  --no-multi \\\n" )
+    run_sh.write( "  --check-peaks \\\n" )
+    run_sh.write( "  --no-retry \\\n" )
+    run_sh.write( "  --max-res=3000 \\\n" )
+    run_sh.write( "  --min-pix-count=2 \\\n" )
+    run_sh.write( "  --local-bg-radius=4 \\\n" )
+    run_sh.write( "  --min-res=85" )
     run_sh.close()
 
     # make file executable
@@ -107,7 +125,7 @@ def wait_for_jobs( job_ids, total_jobs ):
             job_ids.difference_update(completed_jobs)
             time.sleep(30)
 
-def run_splits( cwd, name, lst, chunk_size, geom_file, cell_file, progress ):
+def run_splits( cwd, name, lst, chunk_size, geom_file, cell_file ):
 
     print( "reading SwissFEL lst file" )
     print( "creating {0} image chunks of lst".format( chunk_size ) )
@@ -158,7 +176,6 @@ def run_splits( cwd, name, lst, chunk_size, geom_file, cell_file, progress ):
     print( "DONE" )
 
     # include progress bar if required
-    if progress==True:
     wait_for_jobs(submitted_job_ids, chunk)
     print("slurm processing done")
     
@@ -195,7 +212,7 @@ if __name__ == "__main__":
         "--chunk_size",
         help="how big should each chunk be? - the bigger the chunk, the fewer jobs, the slower it will be",
         type=int,
-        default=1000
+        default=2500
     )
     parser.add_argument(
         "-g",
@@ -216,14 +233,7 @@ if __name__ == "__main__":
         type=str,
         default="split"
     )
-    parser.add_argument(
-        "-p",
-        "--progress",
-        help="gives you the option of also having a progress bar",
-        type=bool,
-        default=True
-    )
     args = parser.parse_args()
     # run geom converter
     cwd = os.getcwd()
-    run_splits( cwd, args.job_name, args.lst_file, args.chunk_size, args.geom_file, args.cell_file, args.progress )
+    run_splits( cwd, args.job_name, args.lst_file, args.chunk_size, args.geom_file, args.cell_file )