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JulienDoernerJulienDoerner
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Merge pull request #527 from JulienDoerner/numpy2
Numpy2 implementation and updates on testing
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‎.github/workflows/testing_OSX.yml‎

Lines changed: 18 additions & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -13,14 +13,18 @@ jobs:
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cc: "clang"
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fc: "gfortran-14"
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swig_builtin: "On" #uses swig 4.0.2
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py: "/usr/bin/python3"
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py: "/usr/bin/python3" # python 3.14
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steps:
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- name: Checkout repository
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uses: actions/checkout@v4
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- name: Preinstall
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run: |
22-
brew install hdf5 fftw cfitsio muparser libomp swig python3
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pip install numpy==1.26.4 cmake
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brew install hdf5 fftw cfitsio muparser libomp swig
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python3 -m venv venv
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source venv/bin/activate
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python -m pip install --upgrade pip
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pip install numpy cmake
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pip show numpy # cross-check numpy version for Python_NumPy_INCLUDE_DIR
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- name: Set up the build
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env:
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CXX: ${{ matrix.config.cxx }}
@@ -30,7 +34,17 @@ jobs:
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run: |
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mkdir build
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cd build
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cmake .. -DENABLE_PYTHON=True -DENABLE_TESTING=On -DENABLE_SWIG_BUILTIN=${{ matrix.config.swig_builtin }} -DSIMD_EXTENSIONS="none"
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cmake .. \
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-DCMAKE_INSTALL_PREFIX=$GITHUB_WORKSPACE/venv \
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-DENABLE_PYTHON=True \
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-DPython_EXECUTABLE=$GITHUB_WORKSPACE/venv/bin/python \
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-DCMAKE_CXX_STANDARD=17 \
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-DCMAKE_CXX_FLAGS="-std=c++17 -stdlib=libc++" \
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-DENABLE_TESTING=On \
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-DENABLE_SWIG_BUILTIN=${{ matrix.config.swig_builtin }} \
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-DPython_INSTALL_PACKAGE_DIR=$GITHUB_WORKSPACE/venv/lib/python3.14/site-packages
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- name: Build CRPropa
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run: |
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cd build

‎.github/workflows/testing_ubuntu20.yml‎

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This file was deleted.

‎.github/workflows/testing_ubuntu22.yml‎

Lines changed: 4 additions & 1 deletion
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@@ -21,7 +21,10 @@ jobs:
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- name: Preinstall
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run: |
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sudo apt-get update
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sudo apt-get install libmuparser-dev python3 python3-numpy python3-setuptools libhdf5-serial-dev libomp5 libomp-dev libfftw3-dev libcfitsio-dev lcov
24+
sudo apt-get install libmuparser-dev python3 python3-setuptools libhdf5-serial-dev libomp5 libomp-dev libfftw3-dev libcfitsio-dev lcov
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pip install --upgrade pip
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pip install numpy
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pip show numpy
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- name: Set up the build
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env:
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CXX: ${{ matrix.config.cxx }}

‎.github/workflows/testing_ubuntu24.yml‎

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Original file line numberDiff line numberDiff line change
@@ -0,0 +1,93 @@
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name: crpropa-testing_ubuntu24
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on: [push, pull_request]
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jobs:
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x64:
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runs-on: ${{ matrix.config.os }}
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strategy:
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fail-fast: false
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matrix:
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config:
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- name: "ubuntu-24"
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os: ubuntu-24.04
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cxx: "g++-14"
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cc: "gcc-14"
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fc: "gfortran-14"
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swig_builtin: "On"
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py: "/usr/bin/python3"
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steps:
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- name: Checkout repository
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uses: actions/checkout@v4
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- name: Preinstall
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run: |
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sudo apt-get update
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sudo apt-get install libmuparser-dev python-dev-is-python3 libhdf5-serial-dev libomp5 libomp-dev libfftw3-dev libcfitsio-dev lcov
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pip install numpy
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- name: Set up the build
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env:
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CXX: ${{ matrix.config.cxx }}
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CC: ${{ matrix.config.cc }}
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FC: ${{ matrix.config.fc }}
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run: |
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mkdir build
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cd build
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cmake .. -DENABLE_PYTHON=True -DENABLE_TESTING=On -DENABLE_SWIG_BUILTIN=${{ matrix.config.swig_builtin }} -DSIMD_EXTENSIONS="none"
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- name: Build CRPropa
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run: |
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cd build
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make
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- name: Run tests
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run: |
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cd build
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make test
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- name: Archive test results
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if: always()
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uses: actions/upload-artifact@v4
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with:
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name: "test-report_${{matrix.config.os}}"
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path: build/Testing/Temporary/LastTest.log
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arm:
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runs-on: ${{ matrix.config.os }}
51+
strategy:
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fail-fast: false
53+
matrix:
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config:
55+
- name: "ubuntu-24"
56+
os: ubuntu-24.04-arm
57+
cxx: "g++-14"
58+
cc: "gcc-14"
59+
fc: "gfortran-14"
60+
swig_builtin: "On"
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py: "/usr/bin/python3"
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steps:
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- name: Checkout repository
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uses: actions/checkout@v4
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- name: Preinstall
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run: |
67+
sudo apt-get update
68+
sudo apt-get install libmuparser-dev python-dev-is-python3 libhdf5-serial-dev libomp5 libomp-dev libfftw3-dev libcfitsio-dev lcov
69+
pip install numpy
70+
pip show numpy
71+
- name: Set up the build
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env:
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CXX: ${{ matrix.config.cxx }}
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CC: ${{ matrix.config.cc }}
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FC: ${{ matrix.config.fc }}
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run: |
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mkdir build
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cd build
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cmake .. -DENABLE_PYTHON=True -DENABLE_TESTING=On -DENABLE_SWIG_BUILTIN=${{ matrix.config.swig_builtin }} -DSIMD_EXTENSIONS="none"
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- name: Build CRPropa
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run: |
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cd build
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make
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- name: Run tests
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run: |
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cd build
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make test
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- name: Archive test results
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if: always()
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uses: actions/upload-artifact@v4
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with:
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name: "test-report_${{matrix.config.os}}"
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path: build/Testing/Temporary/LastTest.log

‎CMakeLists.txt‎

Lines changed: 19 additions & 11 deletions
Original file line numberDiff line numberDiff line change
@@ -157,7 +157,7 @@ list(APPEND CRPROPA_EXTRA_LIBRARIES sophia gfortran)
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list(APPEND CRPROPA_EXTRA_INCLUDES libs/sophia)
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159159
# Galactic magnetic lenses
160-
option(ENABLE_GALACTICMAGNETICLENS "Galactic Magnetic Lens" ON)
160+
option(ENABLE_GALACTICMAGNETICLENS "Galactic Magnetic Lens" OFF)
161161
option(INSTALL_EIGEN "Install provided EIGEN headers" OFF)
162162
SET(EIGEN_PATH "" CACHE STRING "Use EIGEN from this path instead of the version shipped with CRPropa")
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SET(WITH_GALACTIC_LENSES FALSE)
@@ -453,6 +453,8 @@ find_package(Python 3.0 REQUIRED COMPONENTS Interpreter Development NumPy)
453453
if(ENABLE_PYTHON AND Python_FOUND)
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find_package(SWIG 3.0 REQUIRED)
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include_directories(${Python_INCLUDE_DIRS})
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add_definitions(-DCRPROPA_HAVE_PYTHON)
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list(APPEND CRPROPA_SWIG_DEFINES -DCRPROPA_HAVE_PYTHON)
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457459
# print Python info in detail
458460
message(STATUS "Python: Found!")
@@ -467,23 +469,29 @@ if(ENABLE_PYTHON AND Python_FOUND)
467469
message(STATUS " development libraries: NOT found!")
468470
endif(Python_Development_FOUND)
469471

470-
472+
471473
# use Python_INSTALL_PACKAGE_DIR if provided; otherwise, install in Python_SITELIB
472474
set(Python_INSTALL_PACKAGE_DIR "${Python_SITELIB}" CACHE PATH "folder in which the python package is installed")
473475
message(STATUS " package install directory: ${Python_INSTALL_PACKAGE_DIR}")
474-
475-
476+
476477
# look for NumPy
477478
if(Python_NumPy_FOUND)
478-
set(CMAKE_SWIG_FLAGS -DWITHNUMPY ${CRP})
479-
list(APPEND CRPROPA_SWIG_DEFINES -DWITHNUMPY)
480-
include_directories(${Python_NumPy_INCLUDE_DIRS})
481-
message(STATUS "NumPy: Found!")
482-
message(STATUS " headers: ${Python_NumPy_INCLUDE_DIRS} (version ${Python_NumPy_VERSION})")
479+
set(CMAKE_SWIG_FLAGS -DWITHNUMPY ${CRP})
480+
list(APPEND CRPROPA_SWIG_DEFINES -DWITHNUMPY)
481+
include_directories(${Python_NumPy_INCLUDE_DIRS})
482+
message(STATUS "NumPy: Found!")
483+
message(STATUS " headers: ${Python_NumPy_INCLUDE_DIRS} (version ${Python_NumPy_VERSION})")
483484
elseif(Python_NumPy_FOUND)
484-
message(STATUS "NumPy: NOT found!")
485-
message(STATUS " CRPropa might work just fine with Python, but features like Galactic lenses will not be available.")
485+
message(STATUS "NumPy: NOT found!")
486+
message(STATUS " CRPropa might work just fine with Python, but features like Galactic lenses will not be available.")
486487
endif(Python_NumPy_FOUND)
488+
489+
# deactivate lenses if NumPy version is >= 2.0
490+
if(Python_NumPy_VERSION VERSION_GREATER_EQUAL 2.0 AND WITH_GALACTIC_LENSES)
491+
set(WITH_GALACTIC_LENSES FALSE CACHE BOOL "" FORCE)
492+
set(ENABLE_GALACTICMAGNETICLENS OFF CACHE BOOL "" FORCE)
493+
message(WARNING "NumPy version >= 2.0 detected, disabling Galactic lenses support")
494+
endif()
487495

488496
if(SWIG_VERSION VERSION_GREATER 4.0)
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# Use swig 4 builtin doxygen instead of external program

‎doc/pages/example_notebooks/targeting/Targeting.ipynb‎

Lines changed: 31 additions & 28 deletions
Original file line numberDiff line numberDiff line change
@@ -91,43 +91,46 @@
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},
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{
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"cell_type": "code",
94-
"execution_count": 3,
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"execution_count": null,
9595
"metadata": {},
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"outputs": [],
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"source": [
9898
"import healpy as hp\n",
9999
"import matplotlib.pylab as plt\n",
100+
"import crpropa as crp\n",
100101
"\n",
101-
"crdata = np.genfromtxt('TargetedEmission.txt')\n",
102-
"Id = crdata[:,3]\n",
103-
"E = crdata[:,4] * EeV\n",
104-
"px = crdata[:,8]\n",
105-
"py = crdata[:,9]\n",
106-
"pz = crdata[:,10]\n",
107-
"w = crdata[:,29]\n",
108-
"lons = np.arctan2(-1. * py, -1. *px)\n",
109-
"lats = np.pi / 2 - np.arccos( -pz / np.sqrt(px*px + py*py+ pz*pz) )\n",
102+
"# If CRPropa was compiled without the GalacticMagneticLens the ParticleMapsContainer does not exist\n",
103+
"if hasattr(crp, 'ParticleMapsContainer'):\n",
104+
" crdata = np.genfromtxt('TargetedEmission.txt')\n",
105+
" Id = crdata[:,3]\n",
106+
" E = crdata[:,4] * EeV\n",
107+
" px = crdata[:,8]\n",
108+
" py = crdata[:,9]\n",
109+
" pz = crdata[:,10]\n",
110+
" w = crdata[:,29]\n",
111+
" lons = np.arctan2(-1. * py, -1. *px)\n",
112+
" lats = np.pi / 2 - np.arccos( -pz / np.sqrt(px*px + py*py+ pz*pz) )\n",
110113
"\n",
111-
"M = ParticleMapsContainer()\n",
112-
"for i in range(len(E)):\n",
113-
" M.addParticle(int(Id[i]), E[i], lons[i], lats[i], w[i])\n",
114+
" M = ParticleMapsContainer()\n",
115+
" for i in range(len(E)):\n",
116+
" M.addParticle(int(Id[i]), E[i], lons[i], lats[i], w[i])\n",
114117
"\n",
115-
"###################################################################\n",
116-
"# WARNING\n",
117-
"# The calls M.getEnergies()/getParticleIds()/getMap() all segfault.\n",
118-
"################################################################### \n",
118+
" ###################################################################\n",
119+
" # WARNING\n",
120+
" # The calls M.getEnergies()/getParticleIds()/getMap() all segfault.\n",
121+
" ################################################################### \n",
119122
"\n",
120-
"#stack all maps\n",
121-
"#crMap = np.zeros(49152)\n",
122-
"#for pid in M.getParticleIds():\n",
123-
" #energies = M.getEnergies(int(pid))\n",
124-
" #for i, energy in enumerate(energies):\n",
125-
" #continue\n",
126-
" #crMap += M.getMap(int(pid), energy * eV )\n",
127-
"#\n",
128-
"##plot maps using healpy\n",
129-
"#hp.mollview(map=crMap, title='Targeted emission')\n",
130-
"#plt.show()"
123+
" #stack all maps\n",
124+
" #crMap = np.zeros(49152)\n",
125+
" #for pid in M.getParticleIds():\n",
126+
" #energies = M.getEnergies(int(pid))\n",
127+
" #for i, energy in enumerate(energies):\n",
128+
" #continue\n",
129+
" #crMap += M.getMap(int(pid), energy * eV )\n",
130+
" #\n",
131+
" ##plot maps using healpy\n",
132+
" #hp.mollview(map=crMap, title='Targeted emission')\n",
133+
" #plt.show()"
131134
]
132135
},
133136
{

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