Merge branch 'refs/heads/dev_sim2root' into dev_io_root

grand/basis/signal.py

@@ -52,7 +52,7 @@ def find_max_with_parabola_interp_3pt(x_trace, y_trace, idx_max):
     return x_max, y_max
 
 
-def find_max_with_parabola_interp(x_trace, y_trace, idx_max, factor_hill=0.8):
+def find_max_with_parabola_interp(x_trace, y_trace, idx_max, factor_hill=0.96):
     """Parabolic interpolation of the maximum with more than 3 points
 
     trace : all values >= 0
@@ -76,6 +76,7 @@ def find_max_with_parabola_interp(x_trace, y_trace, idx_max, factor_hill=0.8):
     :param factor_hill:
     :type factor_hill:
     """
+    # y threshold mean around max (so 3 points) * factor_hill
     y_lim = (y_trace[idx_max - 1 : idx_max + 2].sum() / 3) * factor_hill
     logger.debug(f"y_lim={y_lim}")
     # 1

sim2root/CoREASRawRoot/CoreasToRawROOT.py

@@ -456,10 +456,10 @@ def CoreasToRawRoot(file, simID=None):
 
     # define time params:
     t_length = len(timestamp)
-    t_0 = timestamp[0] + t_length/2
+    t_0 = timestamp[0] + t_length/2 * TimeBinSize
     t_pre  = 800#ns
-    t_pre = t_length/2 
-    t_post = t_length/2
+    t_pre = t_length/2 * TimeBinSize
+    t_post = t_length/2 * TimeBinSize
 
     # add to ROOT tree
     # in Zhaires converter: AntennaN[ant_ID]

sim2root/CoREASRawRoot/CorsikaInfoFuncs.py

@@ -273,23 +273,7 @@ def read_long(pathLongFile):
     TODO: fix hillas_parameter - something's not working yet
     """
     with open(pathLongFile, mode="r") as file:
-        # create a temporary file to write the corrected contents
-        temp_file = io.StringIO()
-
-        for line in file:
-            # use a regex to search for a minus sign that is not part of an exponent
-            if search(r"(?<!e)(-)(?=\d)", line):
-                # if the minus sign is not part of an exponent, replace it with a space and a minus sign
-                line = line.replace("-", " -")
-            # write the corrected line to the temporary file
-            temp_file.write(line)
-
-        # set the file pointer to the beginning of the temporary file
-        temp_file.seek(0)
-
-        # read the contents of the temporary file into a list of strings
-        lines = temp_file.readlines()
-
+        lines=file.readlines()
 
 
     n_steps = int(lines[0].rstrip().split()[3])
@@ -310,7 +294,7 @@ def read_long(pathLongFile):
     hillas_parameters = []
     for line in lines:
         if bool(search("PARAMETERS", line)):
-            parts = re.split(r"\s+", line)
+            parts = line.split()
             param1, param2, xmax, param4, param5, param6 = parts[2], parts[3], parts[4], parts[5], parts[6], parts[7]
             hillas_parameters.append(xmax)
         if bool(search("CHI", line)):

sim2root/Common/IllustrateSimPipe.py

@@ -45,28 +45,32 @@ def manage_args():
         "directory",
         help="Simulation output data directory in GRANDROOT format."
     )
+    parser.add_argument(
+        "--savefig_dir",
+        type=str,
+        default=None,
+        help="Directory to save figures. Defaults to simulation output directory if not specified."
+    )
     parser.add_argument(
         "--verbose",
         choices=["debug", "info", "warning", "error", "critical"],
         default="info",
         help="logger verbosity."
     )
+    parser.add_argument( 
+        "--savefig",
+        action="store_true",
+        default=False,
+        help="save figures to files insted of displaying them."
+    )
     parser.add_argument(
-     "--savefig",
-     action="store_true",
-     default=False,
-     help="save figures to files insted of displaying them."
-     )
-    parser.add_argument(
-     "--sim",
-     default="None",
-     help="specify simulator: Coreas vs. Zhaires"
-     )
+        "--sim",
+        default="None",
+        help="specify simulator: Coreas vs. Zhaires"
+        )
     # retrieve argument
     return parser.parse_args()
 
-
-
 def plot_core_positions(directory, t_0_shift=False):
   d_input = groot.DataDirectory(directory)
 
@@ -115,7 +119,7 @@ def plot_core_positions(directory, t_0_shift=False):
   ax1.set_ylabel("Y (westing)(m)")  
   plt.tight_layout()
   if(args.savefig):
-    plt.savefig(f"{directory}/CorePositions_{myrun}.png")
+    plt.savefig(f"{plot_dir}/plots/CorePositions_{myrun}.png")
     plt.close(fig)
   else: 
     plt.show()
@@ -312,7 +316,7 @@ def plot_traces_all_levels(directory, t_0_shift=False):
 
         plt.tight_layout()
         if(args.savefig):
-          plt.savefig(f"{directory}/IllustrateSimPipe_{run_number}_{event_number}_{du_idx}_{savelabel}.png")
+          plt.savefig(f"{plot_dir}/plots/IllustrateSimPipe_{run_number}_{event_number}_{du_idx}_{savelabel}.png")
           plt.close(fig)
         else: 
           plt.show()
@@ -449,7 +453,7 @@ def plot_time_map(directory, simulator=None):
 
       plt.tight_layout()
       if(args.savefig):
-        plt.savefig(f"{directory}/TimeMap_{run_number}_{event_number}.png")
+        plt.savefig(f"{plot_dir}/plots/TimeMap_{run_number}_{event_number}.png")
         plt.close(fig)
       else: 
          plt.show()
@@ -513,7 +517,7 @@ def plot_raws(directory):
 
       plt.tight_layout()
       if(args.savefig):
-         plt.savefig(f"{directory}/rawtrace_{du}.png")
+         plt.savefig(f"{plot_dir}/plots/rawtrace_{du}.png")
          plt.close()
       else: 
          plt.show()
@@ -528,7 +532,32 @@ def plot_raws(directory):
   logger.info(mlg.string_begin_script())
   logger.info("Creating event plots in source directory "+args.directory)
 
+  # change plot directory if specified
+  if args.savefig:
+    if args.savefig_dir is None:
+      # Use simulation output directory by default
+      plot_dir = args.directory
+    else:
+      # Use specified savefig_dir
+      plot_dir = args.savefig_dir
+  else:
+    pass
+
   directory = args.directory
+  savefig = args.savefig
+  savefig_dir = args.savefig_dir
+
+  if savefig:
+    if savefig_dir is None:
+      # Use simulation output directory by default
+      plot_dir = directory
+    else:
+      # Use specified savefig_dir
+      plot_dir = savefig_dir
+  else:
+    pass
+
+
   plot_core_positions(directory)
   plot_time_map(directory, simulator=args.sim)
   plot_traces_all_levels(directory, t_0_shift=False)

sim2root/Common/sim2root.py

@@ -826,13 +826,13 @@ def form_directory_name(clargs, date, time, run_number, site):
     extra = clargs.extra.replace("_", "-")
 
     # Go through serial numbers in directory names to find a one that does not exist
-    for sn in range(1000):
+    for sn in range(5000):
         dir_name = Path(clargs.output_parent_directory, f"sim_{site}_{date}_{time}_RUN{run_number}_CD_{extra}_{sn:0>4}")
         if not dir_name.exists():
             break
-    # If directories with serial number up to 1000 already created
+    # If directories with serial number up to 5000 already created
     else:
-        print("All directories with serial number up to 1000 already exist. Please clean up some directories!")
+        print("All directories with serial number up to 5000 already exist. Please clean up some directories!")
         exit(0)
 
     return dir_name
@@ -843,7 +843,7 @@ def rename_all_files(clargs, path, start_event_number, end_event_number, run_num
     # Go through run output files
     for fn_start in ["run", "runshowersim", "runefieldsim"]:
         # Go through serial numbers in directory names to find a one that does not exist
-        for sn in range(1000):
+        for sn in range(5000):
             fn_in = Path(path, f"{fn_start}.root")
             # Proper name of the file
             fn_out = Path(path, f"{fn_start}_{run_number}_L{clargs.analysis_level}_{sn:0>4}.root")
@@ -852,7 +852,7 @@ def rename_all_files(clargs, path, start_event_number, end_event_number, run_num
                 fn_in.rename(fn_out)
                 break
         else:
-            print(f"Could not find a free filename for {fn_in} until serial number 1000. Please clean up some files!")
+            print(f"Could not find a free filename for {fn_in} until serial number 5000. Please clean up some files!")
             exit(0)
 
     # Rename the event files
@@ -863,7 +863,7 @@ def rename_event_files(clargs, path, start_event_number, end_event_number):
     # Go through event output files
     for fn_start in ["shower", "showersim", "efield"]:
         # Go through serial numbers in directory names to find a one that does not exist
-        for sn in range(1000):
+        for sn in range(5000):
             fn_in = Path(path, f"{fn_start}.root")
             # Proper name of the file
             fn_out = Path(path, f"{fn_start}_{start_event_number}-{end_event_number}_L{clargs.analysis_level}_{sn:0>4}.root")
@@ -872,7 +872,7 @@ def rename_event_files(clargs, path, start_event_number, end_event_number):
                 fn_in.rename(fn_out)
                 break
         else:
-            print(f"Could not find a free filename for {fn_in} until serial number 1000. Please clean up some files!")
+            print(f"Could not find a free filename for {fn_in} until serial number 5s000. Please clean up some files!")
             exit(0)
 
 # Simple shifting of a single x,y,z trace