Minor changes.

docs/conf.py

@@ -16,9 +16,9 @@ import os
 import sys
 from datetime import date
 from pkg_resources import get_distribution
-sys.path.insert(0, os.path.abspath('../..'))
-sys.path.insert(0, os.path.abspath('.'))
+
 import orcasong
+#sys.path.insert(0, os.path.abspath('.'))
 
 
 # -- Project information -----------------------------------------------------

orcasong/make_nn_images.py

@@ -314,7 +314,7 @@ def get_file_particle_type(fname):
         String that specifies the type of particles that are contained in the file: ['undefined', 'muon', 'neutrino'].
 
     """
-    event_pump = kp.io.hdf5.HDF5Pump(filename=fname) # TODO suppress print of hdf5pump and close pump afterwards
+    event_pump = kp.io.hdf5.HDF5Pump(filename=fname, verbose=False) # TODO suppress print of hdf5pump
 
     if 'McTracks' not in event_pump[0]:
         file_particle_type = 'undefined'
@@ -427,8 +427,8 @@ def make_nn_images(fname, detx_filepath, config):
     filename_output = filename.replace('.','_')
 
     # set random km3pipe (=numpy) seed
+    print('Setting a Global Random State with the seed < 42 >.')
     km.GlobalRandomState(seed=42)
-    print('Set a Global Random State with the seed < 42 >.')
 
     geo, x_bin_edges, y_bin_edges, z_bin_edges = calculate_bin_edges(n_bins, det_geo, detx_filepath, do4d)
     pdf_2d_plots = PdfPages(output_dirpath + '/orcasong_output/4dTo2d/' + filename_output + '_plots.pdf') if do2d_plots[0] is True else None
@@ -439,9 +439,9 @@ def make_nn_images(fname, detx_filepath, config):
 
     # Initialize OrcaSong Event Pipeline
 
-    pipe = kp.Pipeline(timeit=True)
-    pipe.attach(km.common.StatusBar, every=50)
-    pipe.attach(km.common.MemoryObserver, every=50)
+    pipe = kp.Pipeline() # add timeit=True argument for profiling
+    pipe.attach(km.common.StatusBar, every=200)
+    pipe.attach(km.common.MemoryObserver, every=400)
     pipe.attach(kp.io.hdf5.HDF5Pump, filename=fname)
     pipe.attach(km.common.Keep, keys=['EventInfo', 'Header', 'RawHeader', 'McTracks', 'Hits', 'McHits'])
     pipe.attach(EventDataExtractor,

user/job_submission_scripts/submit_data_to_images.sh

 #!/bin/bash
 #
-#PBS -l nodes=1:ppn=4:sl,walltime=20:00:00
+#PBS -l nodes=1:ppn=4:sl,walltime=5:00:00
 #PBS -o /home/woody/capn/mppi033h/logs/orcasong/submit_data_to_images_${PBS_JOBID}_${PBS_ARRAYID}.out -e /home/woody/capn/mppi033h/logs/orcasong/submit_data_to_images_${PBS_JOBID}_${PBS_ARRAYID}.err
 # first non-empty non-comment line ends PBS options
 
 # Submit with 'qsub -t 1-x submit_data_to_images.sh'
-# This script uses the data_to_images.py file in order to convert all .h5 raw MC files to .h5 event "images" (CNN input).
+# This script uses the make_nn_images.py file in order to convert all .h5 raw MC files to .h5 event "images" (CNN input).
 # Currently available ORCA 115l sim files:
 # neutrinos: 600 files each for 1-5 GeV prod (muon-CC, elec-CC/NC) number of jobs needed = 5 with files_per_job=120,
 #            else (3-100 GeV prod)
@@ -13,8 +13,8 @@
 #            elec-CC = 1200 files, number of jobs needed = 10 with files_per_job=120
 #            elec-NC = 1200 files, number of jobs needed = 10 with files_per_job=120
 #            tau-CC = 1800 files (half the n_evts of other interaction channels), number of jobs needed = 15 with files_per_job=120 and half walltime
-# mupage: 20000 files, with files_per_job=250, 80 jobs needed with 20h walltime.
-# random_noise: 500 files, with files_per_job=20 , 25 jobs needed with 20h walltime.
+# mupage: 20000 files, with files_per_job=200, 100 jobs needed with 5h walltime.
+# random_noise: 500 files, with files_per_job=100 , 5 jobs needed with 5h walltime.
 
 
 #--- USER INPUT ---#
@@ -24,10 +24,10 @@ python_env_folder=/home/hpc/capn/mppi033h/.virtualenv/python_3_env/
 job_logs_folder=/home/woody/capn/mppi033h/logs/orcasong/cout
 
 detx_filepath=/home/woody/capn/mppi033h/Code/OrcaSong/user/detx_files/orca_115strings_av23min20mhorizontal_18OMs_alt9mvertical_v1.detx
-config_file=/home/woody/capn/mppi033h/Code/OrcaSong/user/config/orca_115l_mupage_rn_neutr_classifier/conf_ORCA_115l_random_noise_xyz-c.toml
+config_file=/home/woody/capn/mppi033h/Code/OrcaSong/user/config/orca_115l_mupage_rn_neutr_classifier/conf_ORCA_115l_mupage_xyz-t.toml
 
-particle_type=random_noise
-mc_prod=random_noise
+particle_type=mupage
+mc_prod=mupage
 
 # total number of files per job
 # For neutrinos 3-100GeV:
@@ -35,8 +35,8 @@ mc_prod=random_noise
 # For neutrinos 1-5GeV:
 # muon-CC/elec-CC/elec-NC n=120 with PBS -l nodes=1:ppn=4:sl,walltime=5:00:00
 # For mupage: n=250 with PBS -l nodes=1:ppn=4:sl,walltime=5:00:00
-# For random_noise: n=20 with PBS -l nodes=1:ppn=4:sl,walltime=5:00:00
-files_per_job=20 # must be dividible by 4!
+# For random_noise: n=100 with PBS -l nodes=1:ppn=4:sl,walltime=5:00:00
+files_per_job=250 # must be dividible by 4!
 
 #--- USER INPUT ---#
 
@@ -87,9 +87,9 @@ do
     thread3=$((${file_no_loop_start} + 2))
     thread4=$((${file_no_loop_start} + 3))
 
-    (time taskset -c 0  make_nn_images -c ${config_file} ${folder}/${filename}.${thread1}.h5 ${detx_filepath} > ${job_logs_folder}/${filename}.${thread1}.txt) &
-    (time taskset -c 1  make_nn_images -c ${config_file} ${folder}/${filename}.${thread2}.h5 ${detx_filepath} > ${job_logs_folder}/${filename}.${thread2}.txt) &
-    (time taskset -c 2  make_nn_images -c ${config_file} ${folder}/${filename}.${thread3}.h5 ${detx_filepath} > ${job_logs_folder}/${filename}.${thread3}.txt) &
-    (time taskset -c 3  make_nn_images -c ${config_file} ${folder}/${filename}.${thread4}.h5 ${detx_filepath} > ${job_logs_folder}/${filename}.${thread4}.txt) &
+    (time taskset -c 0  make_nn_images ${folder}/${filename}.${thread1}.h5 ${detx_filepath} ${config_file} > ${job_logs_folder}/${filename}.${thread1}.txt) &
+    (time taskset -c 1  make_nn_images ${folder}/${filename}.${thread2}.h5 ${detx_filepath} ${config_file} > ${job_logs_folder}/${filename}.${thread2}.txt) &
+    (time taskset -c 2  make_nn_images ${folder}/${filename}.${thread3}.h5 ${detx_filepath} ${config_file} > ${job_logs_folder}/${filename}.${thread3}.txt) &
+    (time taskset -c 3  make_nn_images ${folder}/${filename}.${thread4}.h5 ${detx_filepath} ${config_file} > ${job_logs_folder}/${filename}.${thread4}.txt) &
     wait
 done
\ No newline at end of file