From 753f0665c32bf57018f2283b36767be91999f6a5 Mon Sep 17 00:00:00 2001
From: Beale John Henry <beale_j@ra-l-004.psi.ch>
Date: Sun, 19 Jan 2025 22:43:01 +0100
Subject: [PATCH] fixed readlines bug

---
 reduction_tools/cat_lst.py | 34 ++++++++++++++++++----------------
 1 file changed, 18 insertions(+), 16 deletions(-)

diff --git a/reduction_tools/cat_lst.py b/reduction_tools/cat_lst.py
index 42aad52..c5e3ba7 100644
--- a/reduction_tools/cat_lst.py
+++ b/reduction_tools/cat_lst.py
@@ -27,22 +27,23 @@ import os
 import numpy as np
 from sys import exit
 
-def concatenate_files( input_file_lst, output, label ):
+def concatenate_files( cwd, input_file_lst, output_name, label ):
 
-    output_file = "{0}_{1}.lst".format( output, label )
+    output_file = "{0}/{1}_{2}.lst".format( cwd, output_name, label )
 
     lines = 0
     # create output file
-    with open( output_file, "w" ) as output:
+    output = open( output_file, "w" )
 
-        # loop through input list - read and write to output file
-        for lst_file_pwd in input_file_lst.lst_pwd:
+    # loop through input list - read and write to output file
+    for lst_file_pwd in input_file_lst.lst_pwd:
+
+        lst_file = open( lst_file_pwd, "r" )
+        for line in lst_file:
+            lines = lines + 1
+            output.write( line )
             
-            # open and write to output file
-            with open( lst_file_pwd, "r" ) as lst_file:
-                lines = lines + len( lst_file.readlines() )
-                output.write( lst_file.read() )
-                lst_file.close()
+        lst_file.close()
 
     output.close()
 
@@ -127,7 +128,7 @@ def generate_lst_df( run_lst, endstation, label, pgroup, jfj ):
 
     return lst_df
 
-def main( run_lst, endstation, label, pgroup, output_file, jfj ):
+def main( cwd, run_lst, endstation, label, pgroup, output_file, jfj ):
 
     # make df of lst files
     lst_df = generate_lst_df( run_lst, endstation, label, pgroup, jfj )
@@ -138,7 +139,7 @@ def main( run_lst, endstation, label, pgroup, output_file, jfj ):
         exit()
 
     # concatinate all lst file in lst_df
-    concatenate_files( lst_df, output_file, label )
+    concatenate_files( cwd, lst_df, output_file, label )
 
 def range_of_runs(arg):
     return list(map(int, arg.split(',')))
@@ -192,6 +193,8 @@ if __name__ == "__main__":
         default=None
         )
     args = parser.parse_args()
+    # run geom converter
+    cwd = os.getcwd()
     # JFJ on/off non-JFJ light/dark logic\
     if args.label != "off" and args.label != "on" and args.label != "light" and args.label != "dark":
         print( "label flag (-l) must = either 'on' or 'off' with JFJ = True, or 'light' or 'dark' and JFJ = False." )
@@ -218,10 +221,9 @@ if __name__ == "__main__":
     print( "appending {0} lst files from runs {1}".format( args.label, run_lst ) )
     # make default name
     if not args.output:
-        output_name = "-".join( str(e) for e in run_lst )
-        output_name = "run{0}".format( output_name )
+        run_number = "-".join( str(e) for e in run_lst )
+        output_name = "run{0}".format( run_number.zfill(4) )
     else:
         output_name = args.output
     # run main
-    main( run_lst, args.endstation, args.label, args.pgroup, output_name, args.jfj )
-    print( "done" )
\ No newline at end of file
+    main( cwd, run_lst, args.endstation, args.label, args.pgroup, output_name, args.jfj )
\ No newline at end of file