Update source files for photon emitter, custom ptracer, and relevant examples

.gitignore

@@ -7,7 +7,7 @@
 /.vs
 
 # Jupyter
-/.ipynb_checkpoints
+*.ipynb_checkpoints
 
 # Python
 __pycache__
@@ -28,3 +28,8 @@ __pycache__
 /docs/src/quickstart
 /docs/src/generated
 /docs/resources
+
+# new png output / csv input
+/MPhys/Single_Emitter/png/* 
+*1000000*csv
+/MPhys/Single_Emitter/cluster*

MPhys/Direct import/photons_detected_spectral.csv

@@ -11,3 +11,4 @@
 9,3.31874,-0.104399,106.604,1066.64,0.00247168,0.0478558,0.998851,270.5980936414827
 10,3.31874,-0.136313,113.606,1136.73,0.0439212,0.0743342,0.996266,383.72751894873835
 11,3.31874,-0.122911,110.665,1107.29,-0.0439221,0.125615,0.991106,402.6323520971465
+

MPhys/Direct import/python input.ipynb

@@ -2,7 +2,11 @@
  "cells": [
   {
    "cell_type": "code",
+<<<<<<< HEAD
+   "execution_count": 1,
+=======
    "execution_count": 3,
+>>>>>>> dev
    "id": "a07ccfc1",
    "metadata": {},
    "outputs": [],

MPhys/Rich_Geometry/One emitter for One photon .ipynb

@@ -47,7 +47,7 @@
     "\n",
     "#load data from original G4 output (csv format)\n",
     "column_names = [\"time (ps)\", \"x\", \"y\", \"z\", \"px\", \"py\", \"pz\", \"E (MeV)\"]\n",
-    "photon_data_full = pd.read_csv('/hepgpu6-data1/kevans/Photons_1000000_filtered.csv', names = column_names, nrows=100000)\n",
+    "photon_data_full = pd.read_csv('./test_data/Photons_1000000_filtered.csv', names = column_names, nrows=100000)\n",
     "initial_number_of_photons = photon_data_full.count()[0]\n",
     "\n",
     "def ev_to_nm (energy):\n",
@@ -81,7 +81,7 @@
     "photon_detected.reset_index(drop=True, inplace= True)\n",
     "\n",
     "#Can be removed later. Outputs characteristics of saved photons.\n",
-    "photon_detected.to_csv('./photons_detected_spectral.csv' )\n",
+    "photon_detected.to_csv('./test_photons_detected_spectral.csv' )\n",
     "final_number_of_photons = photon_detected.count()[0]\n",
     "fraction_detected = final_number_of_photons/initial_number_of_photons\n",
     "print (\"{0:.4} of emitted photon in G4 are actually detected.\".format(fraction_detected))"
@@ -118,7 +118,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "tree = ET.parse('base_geometry.xml')\n",
+    "tree = ET.parse('test_data/base_geometry.xml')\n",
     "root = tree.getroot()\n",
     "for emitter in root.iter('emitter'):\n",
     "    print(emitter.attrib)"
@@ -141,7 +141,7 @@
    ],
    "source": [
     "# parse the xml file to get information from the 1st mirror\n",
-    "tree = ET.parse('base_geometry.xml')\n",
+    "tree = ET.parse('test_data/base_geometry.xml')\n",
     "root = tree.getroot()\n",
     "for shape in root.iter('shape'):\n",
     "    if shape.get('id') == 'mirror_spherical':\n",
@@ -241,7 +241,7 @@
     "def add_spot_emitter(x, z, y, x_target, z_target, y_target, cutoff_angle):\n",
     "    \n",
     "    # parsing the xml file of the scene\n",
-    "    tree = ET.parse('base_geometry.xml')\n",
+    "    tree = ET.parse('test_data/base_geometry.xml')\n",
     "    root = tree.getroot()\n",
     "    # add a spot emitter to the scene\n",
     "    ### here, the y and z axis are switched (because the scene is rotated by 90 degrees?) ###\n",
@@ -316,7 +316,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.10.9"
+   "version": "3.10.12"
   }
  },
  "nbformat": 4,

MPhys/Single_Emitter/Write_binary_file.ipynb

@@ -45,7 +45,7 @@
     "\n",
     "#load data from original G4 output (csv format)\n",
     "column_names = [\"time (ps)\", \"x\", \"y\", \"z\", \"px\", \"py\", \"pz\", \"E (MeV)\"]\n",
-    "photon_data_full = pd.read_csv('/hepgpu6-data1/kevans/Photons_1000000_filtered.csv', names = column_names)\n",
+    "photon_data_full = pd.read_csv('./Photons_1000000_filtered.csv', names = column_names)\n",
     "initial_number_of_photons = photon_data_full.count()[0]\n",
     "\n",
     "def ev_to_nm (energy):\n",
@@ -118,7 +118,7 @@
    "source": [
     "import struct\n",
     "\n",
-    "with open(\"photon_geometry.bin\", \"wb\") as f:\n",
+    "with open(\"test_photon_geometry.bin\", \"wb\") as f:\n",
     "    f.write(struct.pack(\"<Q\", len(x_position)))  # Use 'Q' format for 64-bit unsigned integer (size_t)\n",
     "    for x1, y1, z1, x2, y2, z2 in zip(x_position, y_position, z_position, x_target, y_target, z_target):\n",
     "        f.write(struct.pack(\"<f\", x1))\n",

MPhys/Single_Emitter/cluster_instructions_history.txt

@@ -0,0 +1,48 @@
+ History of instructions run on noether HEP cluster to setup and run the Single_Emitter example script.
+
+ 1000  exit
+ 1001  cd
+ 1002  cd PhotonPropagation/mitsuba3-manchester/build_view_LCG105/
+ 1003  source /cvmfs/sft.cern.ch/lcg/views/LCG_105/x86_64-el9-clang16-opt/setup.sh
+ 1004  env
+ 1005  env | grep LD_LIBRARY_PATH
+ 1006  env | grep LD_LIBRARY_PATH | grep unknown
+ 1007  export LD_LIBRARY_PATH=/cvmfs/sft.cern.ch/lcg/releases/clang/16.0.3-9dda8/x86_64-el9/lib/x86_64-unknown-linux-gnu/:${LD_LIBRARY_PATH)
+ 1008  export LD_LIBRARY_PATH=/cvmfs/sft.cern.ch/lcg/releases/clang/16.0.3-9dda8/x86_64-el9/lib/x86_64-unknown-linux-gnu:${LD_LIBRARY_PATH)
+ 1009  export LD_LIBRARY_PATH=/cvmfs/sft.cern.ch/lcg/releases/clang/16.0.3-9dda8/x86_64-el9/lib/x86_64-unknown-linux-gnu:${LD_LIBRARY_PATH}
+ 1010  env
+ 1011  env | grep LD_LIBRARY_PATH
+ 1012  ls
+ 1013  cmake -GNinja ..
+ 1014  vi mitsuba.conf
+ 1015  cmake -GNinja ..
+ 1016  ninja
+ 1017  ls
+ 1018  source setpath.sh
+ 1019  cd ..
+ 1020  ls
+ 1021  cd MPhys/
+ 1022  ls
+ 1023  cd Rich_Geometry/
+ 1024  ls
+ 1025  cd ../Direct\ import/
+ 1026  ls
+ 1027  cd ../Single_Emitter/
+ 1028  ls
+ 1029  python
+ 1030  pip
+ 1031  pip list
+ 1032  python
+ 1033  ls
+ 1034  python single_emitter_test_new.py
+ 1035  ls
+ 1036  mkdir cluster_new_and_diff
+ 1037  mv diff\ image* new\* cluster_new_and_diff/
+ 1038  ls
+ 1039  ls cluster_new_and_diff/
+ 1040  mv new\ intensity\ \=\ * cluster_new_and_diff/
+ 1041  ls
+ 1042  mv new\ emit\ to\ the\ right\ wall.png cluster_new_and_diff/
+ 1043  ls
+ 1044  ls -ltr
+ 1045  history

MPhys/Single_Emitter/concatenate_pandas_photon_dataframes.py

@@ -0,0 +1,9 @@
+import pandas as pd
+
+photon_detected = pd.read_csv('test_new_photons_detected_spectral.csv')
+
+# There were just under 10^6 elements in this dataset, so to get to 10^8, concatenate 110 of these together...
+
+photon_detected_large = pd.concat([photon_detected for _ in range(110)])
+
+photon_detected_large.to_csv('test_new_photons_detected_spectral_100000000.csv')

MPhys/Single_Emitter/csv/llvm_mono_timing_for_n_photons.csv

@@ -0,0 +1,10 @@
+1.000000000000000000e+00,1.978044509887695243e-02,5.607190132141113420e-02,8.485283851623535156e-01
+1.000000000000000000e+01,1.936111450195312361e-02,5.309574604034424106e-02,1.049047136306762606e+00
+1.000000000000000000e+02,2.888579368591308663e-02,7.119491100311278742e-02,1.225476455688476518e+00
+1.000000000000000000e+03,1.932477951049804688e-02,4.470925331115722934e-02,8.123323678970336692e-01
+1.000000000000000000e+04,2.192444801330566476e-02,5.377616882324218889e-02,9.610966920852661577e-01
+1.000000000000000000e+05,3.175868988037109514e-02,7.066752910614013117e-02,1.037675070762634322e+00
+1.000000000000000000e+06,1.672561883926391713e-01,2.040284633636474665e-01,1.135952997207641646e+00
+1.000000000000000000e+07,7.786815166473388672e-01,8.227706670761107954e-01,1.780820298194885298e+00
+1.869004000000000000e+07,2.066783022880554377e+00,2.117531561851501376e+00,3.189863014221191229e+00
+1.869004000000000000e+07,2.178409934043884277e+00,2.264196181297302157e+00,3.304263281822204412e+00