diff --git a/CMakeLists.txt b/CMakeLists.txt index 7ef422f..068430b 100644 --- a/CMakeLists.txt +++ b/CMakeLists.txt @@ -70,8 +70,8 @@ SET(CPACK_PACKAGE_DESCRIPTION_SUMMARY "A toolbox for impatient cosmologists") SET(CPACK_PACKAGE_VENDOR "Guilhem Lavaux") SET(CPACK_RESOURCE_FILE_LICENSE "${CMAKE_CURRENT_SOURCE_DIR}/LICENCE_CeCILL_V2") SET(CPACK_PACKAGE_VERSION_MAJOR "1") -SET(CPACK_PACKAGE_VERSION_MINOR "2") -SET(CPACK_PACKAGE_VERSION_PATCH "2${EXTRA_VERSION}") +SET(CPACK_PACKAGE_VERSION_MINOR "3") +SET(CPACK_PACKAGE_VERSION_PATCH "0${EXTRA_VERSION}") SET(CPACK_PACKAGE_INSTALL_DIRECTORY "CosmoToolbox-${CPACK_PACKAGE_VERSION_MAJOR}.${CPACK_PACKAGE_VERSION_MINOR}") SET(CPACK_STRIP_FILES "lib/libCosmoTool.so") SET(CPACK_SOURCE_IGNORE_FILES diff --git a/MANIFEST.in b/MANIFEST.in index 8d92fca..5c4f363 100644 --- a/MANIFEST.in +++ b/MANIFEST.in @@ -86,6 +86,7 @@ include sample/testSmooth.cpp include sample/test_cosmopower.cpp include sample/test_fft_calls.cpp include sample/test_healpix_calls.cpp +include sample/test_special.cpp include sample/testkd.cpp include sample/testkd2.cpp include sample/testkd3.cpp @@ -167,3 +168,4 @@ include src/tf_fit.hpp include src/yorick.hpp include src/yorick_nc3.cpp include src/yorick_nc4.cpp +include src/special_math.hpp diff --git a/conda/conda_build_config.yaml b/conda/conda_build_config.yaml index 288df1f..1f026b6 100644 --- a/conda/conda_build_config.yaml +++ b/conda/conda_build_config.yaml @@ -1,8 +1,10 @@ python: - - 3.7 - - 3.8 - 3.9 + - 3.8 + - 3.7 numpy: - - 1.11 - 1.19 + +gsl: + - 2.4 diff --git a/conda/meta.yaml b/conda/meta.yaml index 249bebd..3f62832 100644 --- a/conda/meta.yaml +++ b/conda/meta.yaml @@ -1,48 +1,50 @@ package: name: cosmotool - version: "1.2.2" + version: "1.3.0" source: - git_rev: 03033b6 + git_rev: a86c9a8 git_url: https://bitbucket.org/glavaux/cosmotool requirements: build: - - numpy >=1.11 + - python # [build_platform != target_platform] + - cross-python_{{ target_platform }} # [build_platform != target_platform] + - cython # [build_platform != target_platform] + - numpy # [build_platform != target_platform] - {{ compiler('c') }} - {{ compiler('cxx') }} - - python - - setuptools - - cython - - healpy - - numexpr - - cffi - - pyfftw - - gsl - - h5py + - llvm-openmp # [osx] + - libgomp # [linux] host: - python + - pip + - numpy + - pkgconfig - numexpr - cython - healpy - cffi - pyfftw - - gsl + - gsl {{ gsl }} - h5py - run: - - numpy - python + - {{ pin_compatible('numpy') }} - healpy - numexpr - cffi - pyfftw - h5py + - {{ pin_compatible('gsl') }} + - llvm-openmp test: imports: - cosmotool + requires: + - pip about: home: https://bitbucket.org/glavaux/cosmotool diff --git a/external/external_build.cmake b/external/external_build.cmake index 5459427..bbe3e77 100644 --- a/external/external_build.cmake +++ b/external/external_build.cmake @@ -8,7 +8,7 @@ SET(GENGETOPT_URL "ftp://ftp.gnu.org/gnu/gengetopt/gengetopt-2.22.5.tar.gz" CACH SET(HDF5_URL "https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-1.8/hdf5-1.8.18/src/hdf5-1.8.18.tar.bz2" CACHE STRING "URL to download HDF5 from") SET(NETCDF_URL "ftp://ftp.unidata.ucar.edu/pub/netcdf/netcdf-4.5.0.tar.gz" CACHE STRING "URL to download NetCDF from") SET(NETCDFCXX_URL "https://github.com/Unidata/netcdf-cxx4/archive/v4.3.0.tar.gz" CACHE STRING "URL to download NetCDF-C++ from") -SET(BOOST_URL "http://sourceforge.net/projects/boost/files/boost/1.61.0/boost_1_61_0.tar.gz/download" CACHE STRING "URL to download Boost from") +SET(BOOST_URL "https://boostorg.jfrog.io/artifactory/main/release/1.74.0/source/boost_1_74_0.tar.bz2" CACHE STRING "URL to download Boost from") SET(GSL_URL "ftp://ftp.gnu.org/gnu/gsl/gsl-1.15.tar.gz" CACHE STRING "URL to download GSL from ") mark_as_advanced(FFTW_URL EIGEN_URL HDF5_URL NETCDF_URL BOOST_URL GSL_URL) @@ -234,6 +234,7 @@ if (INTERNAL_BOOST) ExternalProject_Add(boost URL ${BOOST_URL} PREFIX ${BUILD_PREFIX}/boost-prefix + URL_HASH MD5=da07ca30dd1c0d1fdedbd487efee01bd CONFIGURE_COMMAND ${BOOST_SOURCE_DIR}/bootstrap.sh --prefix=${CMAKE_BINARY_DIR}/ext_build/boost BUILD_IN_SOURCE 1 diff --git a/external/patch-omptl b/external/patch-omptl index 8d5887b..9ea9d28 100644 --- a/external/patch-omptl +++ b/external/patch-omptl @@ -1,6 +1,6 @@ -diff -ur omptl.orig/omptl_algorithm omptl/omptl_algorithm ---- omptl.orig/omptl_algorithm 2017-01-16 14:58:37.996690639 +0100 -+++ omptl/omptl_algorithm 2017-01-16 15:00:26.678641720 +0100 +diff -ur omptl.old/omptl_algorithm omptl/omptl_algorithm +--- omptl.old/omptl_algorithm 2012-04-22 16:29:41.000000000 +0200 ++++ omptl/omptl_algorithm 2021-06-20 15:40:29.000000000 +0200 @@ -20,7 +20,7 @@ #define OMPTL_ALGORITHM 1 @@ -22,9 +22,9 @@ diff -ur omptl.orig/omptl_algorithm omptl/omptl_algorithm #endif #endif /* OMPTL_ALGORITHM */ -diff -ur omptl.orig/omptl_algorithm_par.h omptl/omptl_algorithm_par.h ---- omptl.orig/omptl_algorithm_par.h 2017-01-16 14:58:37.996690639 +0100 -+++ omptl/omptl_algorithm_par.h 2017-01-16 14:59:57.974126410 +0100 +diff -ur omptl.old/omptl_algorithm_par.h omptl/omptl_algorithm_par.h +--- omptl.old/omptl_algorithm_par.h 2012-04-22 16:29:41.000000000 +0200 ++++ omptl/omptl_algorithm_par.h 2021-06-20 15:40:50.000000000 +0200 @@ -21,8 +21,8 @@ #include #include @@ -36,9 +36,18 @@ diff -ur omptl.orig/omptl_algorithm_par.h omptl/omptl_algorithm_par.h #include -diff -ur omptl.orig/omptl_numeric omptl/omptl_numeric ---- omptl.orig/omptl_numeric 2017-01-16 14:58:37.996690639 +0100 -+++ omptl/omptl_numeric 2017-01-16 15:00:57.051186974 +0100 +@@ -1700,7 +1700,7 @@ + + std::vector pivot_used(pivots.size(), false); // can't be bool due to parallel write + +- const unsigned max_depth = std::floor(std::tr1::log2(P)); ++ const unsigned max_depth = unsigned(std::floor(std::log2(P))); + assert(1u << max_depth <= P); + for (unsigned i = 0; i < max_depth; ++i) + { +diff -ur omptl.old/omptl_numeric omptl/omptl_numeric +--- omptl.old/omptl_numeric 2012-04-22 16:29:41.000000000 +0200 ++++ omptl/omptl_numeric 2021-06-20 15:40:29.000000000 +0200 @@ -19,7 +19,7 @@ #define OMPTL_NUMERIC 1 @@ -63,9 +72,9 @@ diff -ur omptl.orig/omptl_numeric omptl/omptl_numeric +#include "omptl_numeric_extensions.h" #endif /* OMPTL_NUMERIC */ -diff -ur omptl.orig/omptl_numeric_extensions.h omptl/omptl_numeric_extensions.h ---- omptl.orig/omptl_numeric_extensions.h 2017-01-16 14:58:37.996690639 +0100 -+++ omptl/omptl_numeric_extensions.h 2017-01-16 14:59:21.549472508 +0100 +diff -ur omptl.old/omptl_numeric_extensions.h omptl/omptl_numeric_extensions.h +--- omptl.old/omptl_numeric_extensions.h 2012-04-22 16:29:41.000000000 +0200 ++++ omptl/omptl_numeric_extensions.h 2021-06-20 15:40:29.000000000 +0200 @@ -51,9 +51,9 @@ } // namespace @@ -78,9 +87,9 @@ diff -ur omptl.orig/omptl_numeric_extensions.h omptl/omptl_numeric_extensions.h #endif namespace omptl -diff -ur omptl.orig/omptl_numeric_par.h omptl/omptl_numeric_par.h ---- omptl.orig/omptl_numeric_par.h 2017-01-16 14:58:37.996690639 +0100 -+++ omptl/omptl_numeric_par.h 2017-01-16 14:59:36.397739066 +0100 +diff -ur omptl.old/omptl_numeric_par.h omptl/omptl_numeric_par.h +--- omptl.old/omptl_numeric_par.h 2012-04-22 16:29:41.000000000 +0200 ++++ omptl/omptl_numeric_par.h 2021-06-20 15:40:29.000000000 +0200 @@ -23,8 +23,8 @@ #include #include @@ -92,15 +101,15 @@ diff -ur omptl.orig/omptl_numeric_par.h omptl/omptl_numeric_par.h namespace omptl { -diff -ur omptl.orig/omptl_algorithm_par.h omptl/omptl_algorithm_par.h ---- omptl.orig/omptl_algorithm_par.h 2021-05-09 14:26:47.227632829 +0300 -+++ omptl/omptl_algorithm_par.h 2021-05-09 14:27:02.815744567 +0300 -@@ -1700,7 +1700,7 @@ +diff -ur omptl.old/omptl_tools.h omptl/omptl_tools.h +--- omptl.old/omptl_tools.h 2012-04-22 16:29:41.000000000 +0200 ++++ omptl/omptl_tools.h 2021-06-20 15:40:42.000000000 +0200 +@@ -25,7 +25,7 @@ + #include + #include - std::vector pivot_used(pivots.size(), false); // can't be bool due to parallel write +-#include ++#include -- const unsigned max_depth = std::floor(std::tr1::log2(P)); -+ const unsigned max_depth = unsigned(std::floor(std::tr1::log2(P))); - assert(1u << max_depth <= P); - for (unsigned i = 0; i < max_depth; ++i) - { + namespace omptl + { diff --git a/python/CMakeLists.txt b/python/CMakeLists.txt index db4bc17..7eda7ac 100644 --- a/python/CMakeLists.txt +++ b/python/CMakeLists.txt @@ -8,32 +8,32 @@ IF(CYTHON) add_custom_command( OUTPUT ${CMAKE_CURRENT_BINARY_DIR}/_cosmotool.cpp COMMAND ${CYTHON} --cplus -o ${CMAKE_CURRENT_BINARY_DIR}/_cosmotool.cpp ${CMAKE_CURRENT_SOURCE_DIR}/_cosmotool.pyx - DEPENDS ${CMAKE_CURRENT_SOURCE_DIR}/_cosmotool.pyx) + DEPENDS ${CMAKE_CURRENT_SOURCE_DIR}/_cosmotool.pyx) add_custom_command( OUTPUT ${CMAKE_CURRENT_BINARY_DIR}/_cosmo_power.cpp COMMAND ${CYTHON} --cplus -o ${CMAKE_CURRENT_BINARY_DIR}/_cosmo_power.cpp ${CMAKE_CURRENT_SOURCE_DIR}/_cosmo_power.pyx - DEPENDS ${CMAKE_CURRENT_SOURCE_DIR}/_cosmo_power.pyx) + DEPENDS ${CMAKE_CURRENT_SOURCE_DIR}/_cosmo_power.pyx) add_custom_command( OUTPUT ${CMAKE_CURRENT_BINARY_DIR}/_fast_interp.cpp COMMAND ${CYTHON} --cplus -o ${CMAKE_CURRENT_BINARY_DIR}/_fast_interp.cpp ${CMAKE_CURRENT_SOURCE_DIR}/_fast_interp.pyx - DEPENDS ${CMAKE_CURRENT_SOURCE_DIR}/_fast_interp.pyx) + DEPENDS ${CMAKE_CURRENT_SOURCE_DIR}/_fast_interp.pyx) add_custom_command( OUTPUT ${CMAKE_CURRENT_BINARY_DIR}/_cosmo_cic.cpp COMMAND ${CYTHON} --cplus -o ${CMAKE_CURRENT_BINARY_DIR}/_cosmo_cic.cpp ${CMAKE_CURRENT_SOURCE_DIR}/_cosmo_cic.pyx - DEPENDS ${CMAKE_CURRENT_SOURCE_DIR}/_cosmo_cic.pyx) + DEPENDS ${CMAKE_CURRENT_SOURCE_DIR}/_cosmo_cic.pyx) add_custom_command( OUTPUT ${CMAKE_CURRENT_BINARY_DIR}/_project.cpp COMMAND ${CYTHON} --cplus -o ${CMAKE_CURRENT_BINARY_DIR}/_project.cpp ${CMAKE_CURRENT_SOURCE_DIR}/_project.pyx - DEPENDS ${CMAKE_CURRENT_SOURCE_DIR}/_project.pyx ${CMAKE_CURRENT_SOURCE_DIR}/project_tool.hpp ) + DEPENDS ${CMAKE_CURRENT_SOURCE_DIR}/_project.pyx ${CMAKE_CURRENT_SOURCE_DIR}/project_tool.hpp ) add_custom_command( OUTPUT ${CMAKE_CURRENT_BINARY_DIR}/_cosmomath.cpp COMMAND ${CYTHON} --cplus -o ${CMAKE_CURRENT_BINARY_DIR}/_cosmomath.cpp ${CMAKE_CURRENT_SOURCE_DIR}/_cosmomath.pyx - DEPENDS ${CMAKE_CURRENT_SOURCE_DIR}/_cosmomath.pyx ) + DEPENDS ${CMAKE_CURRENT_SOURCE_DIR}/_cosmomath.pyx ) ENDIF(CYTHON) @@ -43,11 +43,11 @@ add_library(_cosmo_cic MODULE ${CMAKE_CURRENT_BINARY_DIR}/_cosmo_cic.cpp) add_library(_fast_interp MODULE ${CMAKE_CURRENT_BINARY_DIR}/_fast_interp.cpp) add_library(_project MODULE ${CMAKE_CURRENT_BINARY_DIR}/_project.cpp) add_library(_cosmomath MODULE ${CMAKE_CURRENT_BINARY_DIR}/_cosmomath.cpp) -target_include_directories(_cosmotool PRIVATE ${PYTHON_INCLUDES}) -target_include_directories(_cosmo_power PRIVATE ${PYTHON_INCLUDES}) -target_include_directories(_cosmo_cic PRIVATE ${PYTHON_INCLUDES}) -target_include_directories(_fast_interp PRIVATE ${PYTHON_INCLUDES}) -target_include_directories(_project PRIVATE ${PYTHON_INCLUDES}) +target_include_directories(_cosmotool PRIVATE ${PYTHON_INCLUDES}) +target_include_directories(_cosmo_power PRIVATE ${PYTHON_INCLUDES}) +target_include_directories(_cosmo_cic PRIVATE ${PYTHON_INCLUDES}) +target_include_directories(_fast_interp PRIVATE ${PYTHON_INCLUDES}) +target_include_directories(_project PRIVATE ${PYTHON_INCLUDES}) target_include_directories(_cosmomath PRIVATE ${PYTHON_INCLUDES}) SET(CMAKE_MODULE_LINKER_FLAGS "${CMAKE_MODULE_LINKER_FLAGS} -Bsymbolic-functions") @@ -114,10 +114,19 @@ endif (WIN32 AND NOT CYGWIN) configure_file(${CMAKE_CURRENT_SOURCE_DIR}/cosmotool/config.py.in ${CMAKE_CURRENT_BINARY_DIR}/cosmotool/config.py @ONLY) -INSTALL(TARGETS +INSTALL(TARGETS ${ct_TARGETS} + COMPONENT python LIBRARY DESTINATION ${PYTHON_SITE_PACKAGES}/cosmotool ) -INSTALL(DIRECTORY cosmotool ${CMAKE_CURRENT_BINARY_DIR}/cosmotool DESTINATION ${PYTHON_SITE_PACKAGES} +INSTALL(DIRECTORY cosmotool ${CMAKE_CURRENT_BINARY_DIR}/cosmotool + COMPONENT python DESTINATION ${PYTHON_SITE_PACKAGES} FILES_MATCHING PATTERN "*.py") + +add_custom_target( + python-install + DEPENDS ${ct_TARGETS} + COMMAND "${CMAKE_COMMAND}" -DCMAKE_INSTALL_COMPONENT=python -P + "${CMAKE_BINARY_DIR}/cmake_install.cmake") + diff --git a/python/_cosmotool.pyx b/python/_cosmotool.pyx index 3bfc88c..b2494bd 100644 --- a/python/_cosmotool.pyx +++ b/python/_cosmotool.pyx @@ -31,7 +31,7 @@ cdef extern from "loadSimu.hpp" namespace "CosmoTool": bool noAuto - cdef const int NEED_GADGET_ID + cdef const int NEED_GADGET_ID cdef const int NEED_POSITION cdef const int NEED_VELOCITY cdef const int NEED_TYPE @@ -57,36 +57,36 @@ class PySimulationBase(object): """ This is the base class to representation Simulation in CosmoTool/python. """ - + def getPositions(self): """ getPositions(self) - + Returns: - A list of three arrays holding the positions of the particles. + A list of three arrays holding the positions of the particles. The i-th element is the i-th coordinate of each particle. It may be None if the positions were not requested. """ raise NotImplementedError("getPositions is not implemented") - + def getVelocities(self): """ getVelocities(self) - + Returns: - A list of three arrays holding the velocities of the particles. + A list of three arrays holding the velocities of the particles. The i-th element is the i-th coordinate of each particle. It may be None if the velocities were not requested. """ raise NotImplementedError("getVelocities is not implemented") - + def getIdentifiers(self): """ getIdentifiers(self) - + Returns: Returns an integer array that hold the unique identifiers of - each particle. + each particle. It may be None if the identifiers were not requested. """ raise NotImplementedError("getIdentifiers is not implemented") @@ -94,10 +94,10 @@ class PySimulationBase(object): def getTypes(self): """ getTypes(self) - + Returns: Returns an integer array that hold the type of - each particle. + each particle. It may be None if the types were not requested. """ raise NotImplementedError("getTypes is not implemented") @@ -105,27 +105,27 @@ class PySimulationBase(object): def getOmega_M(self): """ getOmega_M(self) - + Returns: the mean matter density in the simulation, with respect to the critical density. - """ + """ raise NotImplementedError("getOmega_M is not implemented") - + def getOmega_Lambda(self): """ getOmega_Lambda(self) - + Returns: the mean dark energy density in the simulation, with respect to the critical density. - """ + """ raise NotImplementedError("getOmega_Lambda is not implemented") def getTime(self): """ getTime(self) - + Returns: the time the snapshot was taken in the simulation. It can have various units depending on the file format. @@ -135,7 +135,7 @@ class PySimulationBase(object): def getHubble(self): """ getHubble(self) - + Returns: the hubble constant in unit of 100 km/s/Mpc """ @@ -144,7 +144,7 @@ class PySimulationBase(object): def getBoxsize(self): """ getBoxsize(self) - + Returns: the size of the simulation box. The length unit is not fixed, though it is customary to have it in Mpc/h if the loader has @@ -155,7 +155,7 @@ class PySimulationBase(object): def getMasses(self): """ getMasses(self) - + Returns: an array with the masses of each particles, in unspecified unit that depend on the loader. @@ -165,7 +165,7 @@ class PySimulationBase(object): cdef class Simulation: """ Simulation() - + Class that directly manages internal loaded data obtained from a loader """ @@ -180,7 +180,7 @@ cdef class Simulation: property BoxSize: def __get__(Simulation self): return self.data.BoxSize - + property time: def __get__(Simulation self): return self.data.time @@ -192,15 +192,15 @@ cdef class Simulation: property Omega_M: def __get__(Simulation self): return self.data.Omega_M - + property Omega_Lambda: def __get__(Simulation self): return self.data.Omega_Lambda - + property positions: def __get__(Simulation self): return self.positions - + property velocities: def __get__(Simulation self): return self.velocities @@ -216,7 +216,7 @@ cdef class Simulation: property masses: def __get__(Simulation self): return self.masses - + property numParticles: def __get__(Simulation self): return self.data.NumPart @@ -228,7 +228,7 @@ cdef class Simulation: def __cinit__(Simulation self): self.data = 0 - + def __dealloc__(Simulation self): if self.data != 0: del self.data @@ -237,40 +237,43 @@ cdef class Simulation: class PySimulationAdaptor(PySimulationBase): """ PySimulationAdaptor(PySimulationBase_) - + This class is an adaptor for an internal type to the loader. It defines all the methods of PySimulationBase. - + Attributes: simu: a Simulation_ object """ def __init__(self,sim): self.simu = sim + def getNumParticles(self): + return self.simu.numParticles + def getBoxsize(self): return self.simu.BoxSize - + def getPositions(self): return self.simu.positions def getTypes(self): return self.simu.types - + def getVelocities(self): return self.simu.velocities - + def getIdentifiers(self): return self.simu.identifiers def getTime(self): return self.simu.time - + def getHubble(self): return self.simu.Hubble - + def getOmega_M(self): return self.simu.Omega_M - + def getOmega_Lambda(self): return self.simu.Omega_Lambda @@ -281,7 +284,7 @@ cdef class ArrayWrapper: cdef void* data_ptr cdef np.uint64_t size cdef int type_array - + cdef set_data(self, np.uint64_t size, int type_array, void* data_ptr): """ Set the data of the array This cannot be done in the constructor as it must recieve C-level @@ -294,22 +297,22 @@ cdef class ArrayWrapper: self.data_ptr = data_ptr self.size = size self.type_array = type_array - + def __array__(self): """ Here we use the __array__ method, that is called when numpy tries to get an array from the object.""" cdef np.npy_intp shape[1] - + shape[0] = self.size # Create a 1D array, of length 'size' ndarray = np.PyArray_SimpleNewFromData(1, shape, self.type_array, self.data_ptr) return ndarray - + def __dealloc__(self): """ Frees the array. This is called by Python when all the references to the object are gone. """ pass - + cdef object wrap_array(void *p, np.uint64_t s, int typ): cdef np.ndarray ndarray cdef ArrayWrapper wrapper @@ -319,7 +322,7 @@ cdef object wrap_array(void *p, np.uint64_t s, int typ): ndarray = np.array(wrapper, copy=False) ndarray.base = wrapper Py_INCREF(wrapper) - + return ndarray @@ -368,7 +371,7 @@ def loadGadget(str filename, int snapshot_id, int gadgetFormat = 1, bool loadPos """loadGadget(filename, snapshot_id, gadgetFormat = 1, loadPosition=True, loadVelocity=False, loadId=False, loadType=False) This function loads Gadget-1 snapshot format. - + If snapshot_id is negative then the snapshot is considered not to be part of a set of snapshots written by different cpu. Otherwise the filename is modified to reflect the indicated snapshot_id. @@ -376,16 +379,16 @@ def loadGadget(str filename, int snapshot_id, int gadgetFormat = 1, bool loadPos Arguments: filename (str): input filename snapshot_id (int): identifier of the gadget file if it is a multi-file snapshot - + Keyword arguments: loadPosition (bool): whether to load positions loadVelocity (bool): whether to load velocities loadId (bool): whether to load unique identifiers loadType (bool): whether to set types to particles loadMass (bool): whether to set the mass of particles - + Returns: - an PySimulationAdaptor instance. + an PySimulationAdaptor instance. """ cdef int flags @@ -419,13 +422,13 @@ def loadParallelGadget(object filename_list, int gadgetFormat = 1, bool loadPosi Arguments: filename (list): a list or tuple of filenames to load in parallel - + Keyword arguments: loadPosition (bool): indicate to load positions loadVelocity (bool): indicate to load velocities loadId (bool): indicate to load id loadType (bool): indicate to load particle types - + Returns: It loads a gadget-1 snapshot and return a cosmotool.PySimulationBase_ object. """ @@ -453,16 +456,16 @@ def loadParallelGadget(object filename_list, int gadgetFormat = 1, bool loadPosi data = alloc_simudata(num_files) for i,l in enumerate(filename_list): filenames[i] = l.encode('utf-8') - + with nogil: for i in prange(num_files): local_data = loadGadgetMulti_safe(filenames[i], flags, gadgetFormat) data[i] = local_data # data[i] = loadGadgetMulti(filenames[i].c_str(), -1, flags) - + out_arrays = [] for i in xrange(num_files): - if data[i] == 0: + if data[i] == 0: out_arrays.append(None) else: out_arrays.append(PySimulationAdaptor(wrap_simudata(data[i], flags))) @@ -473,10 +476,10 @@ def loadParallelGadget(object filename_list, int gadgetFormat = 1, bool loadPosi def writeGadget(str filename, object simulation): """writeGadget(filename, simulation) - - This function attempts to write the content of the simulation object into + + This function attempts to write the content of the simulation object into a file named `filename` using a Gadget-1 file format. - + Arguments: filename (str): output filename simulation (PySimulationBase): a simulation object @@ -486,23 +489,23 @@ def writeGadget(str filename, object simulation): cdef np.ndarray[np.int64_t, ndim=1] ids cdef np.int64_t NumPart cdef int j - + if not isinstance(simulation,PySimulationBase): raise TypeError("Second argument must be of type SimulationBase") - + NumPart = simulation.positions[0].size simdata.noAuto = True - + for j in xrange(3): pos = simulation.getPositions()[j] vel = simulation.getVelocities()[j] - + if pos.size != NumPart or vel.size != NumPart: raise ValueError("Invalid number of particles") - + simdata.Pos[j] = pos.data simdata.Vel[j] = vel.data - + ids = simulation.getIdentifiers() simdata.Id = ids.data simdata.BoxSize = simulation.getBoxsize() @@ -519,21 +522,21 @@ def writeGadget(str filename, object simulation): def loadRamses(str basepath, int snapshot_id, int cpu_id, bool doublePrecision = False, bool loadPosition = True, bool loadVelocity = False, bool loadId = False, bool loadMass = False): """ loadRamses(basepath, snapshot_id, cpu_id, doublePrecision = False, loadPosition = True, loadVelocity = False) Loads the indicated snapshot based on the cpu id, snapshot id and basepath. It is important to specify the correct precision in doublePrecision otherwise the loading will fail. There is no way of auto-detecting properly the precision of the snapshot file. - + Args: basepath (str): the base directory of the snapshot snapshot_id (int): the snapshot id cpu_id (int): the cpu id of the file to load - + Keyword args: doublePrecision (bool): By default it is False, thus singlePrecision loadPosition (bool): Whether to load positions loadVelocity (bool): Whether to load velocities loadId (bool): Whether to load identifiers - loadMass (bool): Whether to load mass value - + loadMass (bool): Whether to load mass value + Returns: - An object derived from PySimulationBase_. + An object derived from PySimulationBase_. """ cdef int flags cdef SimuData *data @@ -549,7 +552,7 @@ def loadRamses(str basepath, int snapshot_id, int cpu_id, bool doublePrecision = if loadMass: flags |= NEED_MASS - encpath = basepath.encode('utf-8') + encpath = basepath.encode('utf-8') try: data = loadRamsesSimu(encpath, snapshot_id, cpu_id, doublePrecision, flags) if data == 0: @@ -558,4 +561,4 @@ def loadRamses(str basepath, int snapshot_id, int cpu_id, bool doublePrecision = raise RuntimeError(str(e) + ' (check the float precision in snapshot)') return PySimulationAdaptor(wrap_simudata(data, flags)) - + diff --git a/python/_project.pyx b/python/_project.pyx index 6ff1d5c..bd64667 100644 --- a/python/_project.pyx +++ b/python/_project.pyx @@ -25,8 +25,8 @@ cdef extern from "openmp.hpp" namespace "CosmoTool": @cython.boundscheck(False) @cython.cdivision(True) @cython.wraparound(False) -cdef void interp3d_INTERNAL_periodic(DTYPE_t x, DTYPE_t y, - DTYPE_t z, +cdef void interp3d_INTERNAL_periodic(DTYPE_t x, DTYPE_t y, + DTYPE_t z, DTYPE_t[:,:,:] d, DTYPE_t Lbox, DTYPE_t *retval) nogil: cdef int Ngrid = d.shape[0] @@ -84,8 +84,8 @@ cdef void interp3d_INTERNAL_periodic(DTYPE_t x, DTYPE_t y, @cython.boundscheck(False) @cython.cdivision(True) @cython.wraparound(False) -cdef void ngp3d_INTERNAL_periodic(DTYPE_t x, DTYPE_t y, - DTYPE_t z, +cdef void ngp3d_INTERNAL_periodic(DTYPE_t x, DTYPE_t y, + DTYPE_t z, DTYPE_t[:,:,:] d, DTYPE_t Lbox, DTYPE_t *retval) nogil: cdef int Ngrid = d.shape[0] @@ -108,14 +108,14 @@ cdef void ngp3d_INTERNAL_periodic(DTYPE_t x, DTYPE_t y, iy = iy%Ngrid iz = iz%Ngrid - retval[0] = d[ix ,iy ,iz ] + retval[0] = d[ix ,iy ,iz ] @cython.boundscheck(False) @cython.cdivision(True) @cython.wraparound(False) -cdef void ngp3d_INTERNAL(DTYPE_t x, DTYPE_t y, - DTYPE_t z, +cdef void ngp3d_INTERNAL(DTYPE_t x, DTYPE_t y, + DTYPE_t z, DTYPE_t[:,:,:] d, DTYPE_t Lbox, DTYPE_t *retval, DTYPE_t inval) nogil: cdef int Ngrid = d.shape[0] @@ -137,16 +137,16 @@ cdef void ngp3d_INTERNAL(DTYPE_t x, DTYPE_t y, retval[0] = inval return - retval[0] = d[ix ,iy ,iz ] + retval[0] = d[ix ,iy ,iz ] @cython.boundscheck(False) @cython.cdivision(True) @cython.wraparound(False) -cdef void interp3d_INTERNAL(DTYPE_t x, DTYPE_t y, - DTYPE_t z, +cdef void interp3d_INTERNAL(DTYPE_t x, DTYPE_t y, + DTYPE_t z, DTYPE_t[:,:,:] d, DTYPE_t Lbox, DTYPE_t *retval, DTYPE_t inval) nogil: - + cdef int Ngrid = d.shape[0] cdef DTYPE_t inv_delta = Ngrid/Lbox cdef int ix, iy, iz @@ -193,13 +193,13 @@ cdef void interp3d_INTERNAL(DTYPE_t x, DTYPE_t y, d[ix+1,iy+1,iz+1] * f[1][1][1] @cython.boundscheck(False) -def interp3d(x not None, y not None, +def interp3d(x not None, y not None, z not None, npx.ndarray[DTYPE_t, ndim=3] d not None, DTYPE_t Lbox, bool periodic=False, bool centered=True, bool ngp=False, DTYPE_t inval = 0): """ interp3d(x,y,z,d,Lbox,periodic=False,centered=True,ngp=False) -> interpolated values - - Compute the tri-linear interpolation of the given field (d) at the given position (x,y,z). It assumes that they are box-centered coordinates. So (x,y,z) == (0,0,0) is equivalent to the pixel at (Nx/2,Ny/2,Nz/2) with Nx,Ny,Nz = d.shape. If periodic is set, it assumes the box is periodic + + Compute the tri-linear interpolation of the given field (d) at the given position (x,y,z). It assumes that they are box-centered coordinates. So (x,y,z) == (0,0,0) is equivalent to the pixel at (Nx/2,Ny/2,Nz/2) with Nx,Ny,Nz = d.shape. If periodic is set, it assumes the box is periodic """ cdef npx.ndarray[DTYPE_t] out cdef DTYPE_t[:] out_slice @@ -227,12 +227,12 @@ def interp3d(x not None, y not None, if type(x) == np.ndarray or type(y) == np.ndarray or type(z) == np.ndarray: if type(x) != np.ndarray or type(y) != np.ndarray or type(z) != np.ndarray: raise ValueError("All or no array. No partial arguments") - + ax = x ay = y az = z assert ax.size == ay.size and ax.size == az.size - + out = np.empty(x.shape, dtype=DTYPE) out_slice = out in_slice = d @@ -280,10 +280,10 @@ cdef DTYPE_t interp2d_INTERNAL_periodic(DTYPE_t x, DTYPE_t y, rx = (inv_delta*x + Ngrid/2) ry = (inv_delta*y + Ngrid/2) - + ix = int(floor(rx)) iy = int(floor(ry)) - + rx -= ix ry -= iy @@ -291,13 +291,13 @@ cdef DTYPE_t interp2d_INTERNAL_periodic(DTYPE_t x, DTYPE_t y, ix += Ngrid while iy < 0: iy += Ngrid - + jx = (ix+1)%Ngrid jy = (iy+1)%Ngrid - + assert ((ix >= 0) and ((jx) < Ngrid)) assert ((iy >= 0) and ((jy) < Ngrid)) - + f[0][0] = (1-rx)*(1-ry) f[1][0] = ( rx)*(1-ry) f[0][1] = (1-rx)*( ry) @@ -314,7 +314,7 @@ cdef DTYPE_t interp2d_INTERNAL_periodic(DTYPE_t x, DTYPE_t y, @cython.cdivision(True) cdef DTYPE_t interp2d_INTERNAL(DTYPE_t x, DTYPE_t y, npx.ndarray[DTYPE_t, ndim=2] d, DTYPE_t Lbox) except? 0: - + cdef int Ngrid = d.shape[0] cdef DTYPE_t inv_delta = Ngrid/Lbox cdef int ix, iy @@ -348,7 +348,7 @@ cdef DTYPE_t interp2d_INTERNAL(DTYPE_t x, DTYPE_t y, d[ix+1,iy ] * f[1][0] + \ d[ix ,iy+1] * f[0][1] + \ d[ix+1,iy+1] * f[1][1] - + def interp2d(x not None, y not None, npx.ndarray[DTYPE_t, ndim=2] d not None, DTYPE_t Lbox, bool periodic=False): @@ -362,11 +362,11 @@ def interp2d(x not None, y not None, if type(x) == np.ndarray or type(y) == np.ndarray: if type(x) != np.ndarray or type(y) != np.ndarray: raise ValueError("All or no array. No partial arguments") - + ax = x ay = y - assert ax.size == ay.size - + assert ax.size == ay.size + out = np.empty(x.shape, dtype=DTYPE) if periodic: for i in range(ax.size): @@ -381,8 +381,8 @@ def interp2d(x not None, y not None, return interp2d_INTERNAL_periodic(x, y, d, Lbox) else: return interp2d_INTERNAL(x, y, d, Lbox) - - + + @cython.boundscheck(False) @cython.cdivision(True) cdef void INTERNAL_project_cic_no_mass(DTYPE_t[:,:,:] g, @@ -450,7 +450,7 @@ cdef void INTERNAL_project_cic_no_mass_periodic(DTYPE_t[:,:,:] g, ag[b1[0],b[1],b[2]] += a[0]*c[1]*c[2] ag[b[0],b1[1],b[2]] += c[0]*a[1]*c[2] ag[b1[0],b1[1],b[2]] += a[0]*a[1]*c[2] - + ag[b[0],b[1],b1[2]] += c[0]*c[1]*a[2] ag[b1[0],b[1],b1[2]] += a[0]*c[1]*a[2] ag[b[0],b1[1],b1[2]] += c[0]*a[1]*a[2] @@ -525,20 +525,21 @@ cdef void INTERNAL_project_cic_with_mass_periodic(DTYPE_t[:,:,:] g, g[b1[0],b[1],b[2]] += a[0]*c[1]*c[2]*m0 g[b[0],b1[1],b[2]] += c[0]*a[1]*c[2]*m0 g[b1[0],b1[1],b[2]] += a[0]*a[1]*c[2]*m0 - + g[b[0],b[1],b1[2]] += c[0]*c[1]*a[2]*m0 g[b1[0],b[1],b1[2]] += a[0]*c[1]*a[2]*m0 g[b[0],b1[1],b1[2]] += c[0]*a[1]*a[2]*m0 g[b1[0],b1[1],b1[2]] += a[0]*a[1]*a[2]*m0 - -def project_cic(npx.ndarray[DTYPE_t, ndim=2] x not None, npx.ndarray[DTYPE_t, ndim=1] mass, int Ngrid, - double Lbox, bool periodic = False, centered=True): - """ - project_cic(x array (N,3), mass (may be None), Ngrid, Lbox, periodict, centered=True) - This function does a Cloud-In-Cell projection of a 3d unstructured dataset. First argument is a Nx3 array of coordinates. +def project_cic(npx.ndarray[DTYPE_t, ndim=2] x not None, npx.ndarray[DTYPE_t, ndim=1] mass, int Ngrid, + double Lbox, bool periodic = False, centered=True, output=None): + """ + project_cic(x array (N,3), mass (may be None), Ngrid, Lbox, periodict, centered=True, output=None) + + This function does a Cloud-In-Cell projection of a 3d unstructured dataset. First argument is a Nx3 array of coordinates. Second argument is an optinal mass. Ngrid is the size output grid and Lbox is the physical size of the grid. + if output is not None, it must be a numpy array with dimension NgridxNgridxNgrid. The result will be accumulated in that array. """ cdef npx.ndarray[DTYPE_t, ndim=3] g cdef double shifter @@ -558,7 +559,13 @@ def project_cic(npx.ndarray[DTYPE_t, ndim=2] x not None, npx.ndarray[DTYPE_t, nd if mass is not None and mass.shape[0] != x.shape[0]: raise ValueError("Mass array and coordinate array must have the same number of elements") - g = np.zeros((Ngrid,Ngrid,Ngrid),dtype=DTYPE) + if output is None: + g = np.zeros((Ngrid,Ngrid,Ngrid),dtype=DTYPE) + else: + if type(output) != np.ndarray: + raise ValueError("Invalid array type") + g = output + cdef DTYPE_t[:,:,:] d_g = g cdef DTYPE_t[:,:] d_x = x @@ -569,7 +576,7 @@ def project_cic(npx.ndarray[DTYPE_t, ndim=2] x not None, npx.ndarray[DTYPE_t, nd else: d_mass = mass with nogil: - INTERNAL_project_cic_with_mass(d_g, d_x, d_mass, Ngrid, Lbox, shifter) + INTERNAL_project_cic_with_mass(d_g, d_x, d_mass, Ngrid, Lbox, shifter) else: if mass is None: with nogil: @@ -577,13 +584,13 @@ def project_cic(npx.ndarray[DTYPE_t, ndim=2] x not None, npx.ndarray[DTYPE_t, nd else: d_mass = mass with nogil: - INTERNAL_project_cic_with_mass_periodic(d_g, d_x, d_mass, Ngrid, Lbox, shifter) - + INTERNAL_project_cic_with_mass_periodic(d_g, d_x, d_mass, Ngrid, Lbox, shifter) + return g def tophat_fourier_internal(npx.ndarray[DTYPE_t, ndim=1] x not None): cdef int i - cdef npx.ndarray[DTYPE_t] y + cdef npx.ndarray[DTYPE_t] y cdef DTYPE_t x0 y = np.empty(x.size, dtype=DTYPE) @@ -609,7 +616,7 @@ def tophat_fourier(x not None): return b.reshape(x.shape) - + @cython.boundscheck(False) @cython.cdivision(True) @@ -659,25 +666,25 @@ cdef DTYPE_t cube_integral_trilin(DTYPE_t u[3], DTYPE_t u0[3], int r[1], DTYPE_t if tmp_a < alpha_max: alpha_max = tmp_a j = i - + I = compute_projection(vertex_value, u, u0, alpha_max) - + for i in xrange(3): u0[i] += u[i]*alpha_max # alpha_max is the integration length # we integrate between 0 and alpha_max (curvilinear coordinates) r[0] = j - + return I @cython.boundscheck(False) cdef DTYPE_t integrator0(DTYPE_t[:,:,:] density, DTYPE_t u[3], DTYPE_t u0[3], int u_delta[3], int iu0[3], int jumper[1], DTYPE_t alpha_max) nogil: cdef DTYPE_t d - + d = density[iu0[0], iu0[1], iu0[2]] - + return cube_integral(u, u0, jumper, alpha_max)*d @cython.boundscheck(False) @@ -687,7 +694,7 @@ cdef DTYPE_t integrator1(DTYPE_t[:,:,:] density, cdef DTYPE_t d cdef int a[3][2] cdef int i - + for i in xrange(3): a[i][0] = iu0[i] a[i][1] = iu0[i]+1 @@ -705,14 +712,14 @@ cdef DTYPE_t integrator1(DTYPE_t[:,:,:] density, return cube_integral_trilin(u, u0, jumper, vertex_value, alpha_max) - + @cython.boundscheck(False) cdef DTYPE_t C_line_of_sight_projection(DTYPE_t[:,:,:] density, DTYPE_t a_u[3], DTYPE_t min_distance, DTYPE_t max_distance, DTYPE_t[:] shifter, int integrator_id) nogil except? 0: - cdef DTYPE_t u[3] + cdef DTYPE_t u[3] cdef DTYPE_t ifu0[3] cdef DTYPE_t u0[3] cdef DTYPE_t utot[3] @@ -724,7 +731,7 @@ cdef DTYPE_t C_line_of_sight_projection(DTYPE_t[:,:,:] density, cdef int completed cdef DTYPE_t I0, d, dist2, delta, s, max_distance2 cdef int jumper[1] - + cdef DTYPE_t (*integrator)(DTYPE_t[:,:,:], DTYPE_t u[3], DTYPE_t u0[3], int u_delta[3], int iu0[3], int jumper[1], DTYPE_t alpha_max) nogil @@ -747,7 +754,7 @@ cdef DTYPE_t C_line_of_sight_projection(DTYPE_t[:,:,:] density, if (not ((iu0[i]>= 0) and (iu0[i] < N))): with gil: raise RuntimeError("iu0[%d] = %d !!" % (i,iu0[i])) - + if (not (u0[i]>=0 and u0[i]<=1)): with gil: raise RuntimeError("u0[%d] = %g !" % (i,u0[i])) @@ -756,7 +763,7 @@ cdef DTYPE_t C_line_of_sight_projection(DTYPE_t[:,:,:] density, if ((iu0[0] >= N-1) or (iu0[0] <= 0) or (iu0[1] >= N-1) or (iu0[1] <= 0) or (iu0[2] >= N-1) or (iu0[2] <= 0)): - completed = 1 + completed = 1 I0 = 0 jumper[0] = 0 @@ -771,8 +778,8 @@ cdef DTYPE_t C_line_of_sight_projection(DTYPE_t[:,:,:] density, iu0[jumper[0]] += 1 u0[jumper[0]] = 0 - - if ((iu0[0] >= N-1) or (iu0[0] <= 0) or + + if ((iu0[0] >= N-1) or (iu0[0] <= 0) or (iu0[1] >= N-1) or (iu0[1] <= 0) or (iu0[2] >= N-1) or (iu0[2] <= 0)): completed = 1 @@ -787,7 +794,7 @@ cdef DTYPE_t C_line_of_sight_projection(DTYPE_t[:,:,:] density, #delta = sqrt(dist2) - max_distance #I0 -= d*delta completed = 1 - + return I0 def line_of_sight_projection(DTYPE_t[:,:,:] density not None, @@ -795,18 +802,18 @@ def line_of_sight_projection(DTYPE_t[:,:,:] density not None, DTYPE_t min_distance, DTYPE_t max_distance, DTYPE_t[:] shifter not None, int integrator_id=0): cdef DTYPE_t u[3] - + u[0] = a_u[0] u[1] = a_u[1] u[2] = a_u[2] - + return C_line_of_sight_projection(density, u, min_distance, max_distance, shifter, integrator_id) -cdef double _spherical_projloop(double theta, double phi, DTYPE_t[:,:,:] density, - double min_distance, double max_distance, +cdef double _spherical_projloop(double theta, double phi, DTYPE_t[:,:,:] density, + double min_distance, double max_distance, DTYPE_t[:] shifter, int integrator_id) nogil: cdef DTYPE_t u0[3] @@ -814,7 +821,7 @@ cdef double _spherical_projloop(double theta, double phi, DTYPE_t[:,:,:] density u0[0] = cos(phi)*stheta u0[1] = sin(phi)*stheta u0[2] = cos(theta) - + return C_line_of_sight_projection(density, u0, min_distance, max_distance, shifter, integrator_id) @@ -825,20 +832,20 @@ def spherical_projection(int Nside, DTYPE_t max_distance, int progress=1, int integrator_id=0, DTYPE_t[:] shifter = None, int booster=-1): """ spherical_projection(Nside, density, min_distance, max_distance, progress=1, integrator_id=0, shifter=None, booster=-1) - + Keyword arguments: progress (int): show progress if it is equal to 1 integrator_id (int): specify the order of integration along the line of shift shifter (DTYPE_t array): this is an array of size 3. It specifies the amount of shift to apply to the center, in unit of voxel booster (int): what is the frequency of refreshment of the progress bar. Small number decreases performance by locking the GIL. - + Arguments: Nside (int): Nside of the returned map density (NxNxN array): this is the density field, expressed as a cubic array min_distance (float): lower bound of the integration max_distance (float): upper bound of the integration - + Returns: an healpix map, as a 1-dimensional array. """ @@ -853,11 +860,11 @@ def spherical_projection(int Nside, cdef long N, N0 cdef double stheta cdef int tid - + if shifter is None: shifter = view.array(shape=(3,), format=FORMAT_DTYPE, itemsize=sizeof(DTYPE_t)) shifter[:] = 0 - + print("allocating map") outm_array = np.empty(hp.nside2npix(Nside),dtype=DTYPE) print("initializing views") @@ -870,10 +877,10 @@ def spherical_projection(int Nside, N = smp_get_max_threads() N0 = outm.size - + if booster < 0: booster = 1#000 - + job_done = view.array(shape=(N,), format="i", itemsize=sizeof(int)) job_done[:] = 0 theta,phi = hp.pix2ang(Nside, np.arange(N0)) diff --git a/requirements.txt b/requirements.txt index ef3f5d4..3a4577b 100644 --- a/requirements.txt +++ b/requirements.txt @@ -1,4 +1,4 @@ -numpy +numpy<1.19 cffi numexpr pyfftw diff --git a/setup.py b/setup.py index b8c6925..8e9dabc 100644 --- a/setup.py +++ b/setup.py @@ -168,10 +168,16 @@ class BuildCMakeExt(build_ext): # Below is just an example set of arguments for building Blender as a Python module compilers=[] - if "CC" in os.environ: - compilers.append('-DCMAKE_C_COMPILER=' + os.environ["CC"]) - if "CXX" in os.environ: - compilers.append("-DCMAKE_CXX_COMPILER=" + os.environ["CXX"]) + fill_up_settings=[ + ("CMAKE_C_COMPILER", "CC"), + ("CMAKE_CXX_COMPILER", "CXX"), + ("CMAKE_C_FLAGS", "CFLAGS"), + ("CMAKE_EXE_LINKER_FLAGS_INIT", "LDFLAGS"), + ("CMAKE_SHARED_LINKER_FLAGS_INIT", "LDFLAGS"), + ("CMAKE_MODULE_LINKER_FLAGS_INIT", "LDFLAGS")] + for cmake_flag, os_flag in fill_up_settings: + if os_flag in os.environ: + compilers.append(f"-D{cmake_flag}={os.environ[os_flag]}") self.spawn(['cmake', '-H'+SOURCE_DIR, '-B'+self.build_temp, '-DENABLE_OPENMP=ON','-DINTERNAL_BOOST=ON','-DINTERNAL_EIGEN=ON', @@ -223,7 +229,7 @@ class BuildCMakeExt(build_ext): CosmoTool_extension = CMakeExtension(name="cosmotool") setup(name='cosmotool', - version='1.2.2', + version='1.3.0', packages=["cosmotool"], package_dir={'cosmotool': 'python/cosmotool'}, install_requires=['numpy','cffi','numexpr','pyfftw','h5py'], diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt index 4f39695..c075396 100644 --- a/src/CMakeLists.txt +++ b/src/CMakeLists.txt @@ -38,6 +38,7 @@ if (HDF5_FOUND) h5_readFlash.cpp loadFlash.cpp ) + add_dependencies(CosmoHDF5 ${cosmotool_DEPS}) set_property(TARGET CosmoHDF5 PROPERTY POSITION_INDEPENDENT_CODE ${BUILD_SHARED_LIBS}) target_include_directories(CosmoHDF5 BEFORE PRIVATE ${HDF5_INCLUDE_DIR}) else(HDF5_FOUND) diff --git a/src/hdf5_array.hpp b/src/hdf5_array.hpp index 9587189..db75a33 100644 --- a/src/hdf5_array.hpp +++ b/src/hdf5_array.hpp @@ -426,7 +426,7 @@ namespace CosmoTool { #define CTOOL_HDF5_INSERT_ELEMENT(r, STRUCT, element) \ { \ ::CosmoTool::get_hdf5_data_type t; \ - position = HOFFSET(STRUCT, BOOST_PP_TUPLE_ELEM(2, 1, element)); \ + long position = HOFFSET(STRUCT, BOOST_PP_TUPLE_ELEM(2, 1, element)); \ const char *field_name = BOOST_PP_STRINGIZE(BOOST_PP_TUPLE_ELEM(2, 1, element)); \ type.insertMember(field_name, position, t.type()); \ } @@ -439,7 +439,6 @@ namespace CosmoTool { \ \ TNAME() : type(sizeof(STRUCT)) \ { \ - long position; \ BOOST_PP_SEQ_FOR_EACH(CTOOL_HDF5_INSERT_ELEMENT, STRUCT, ATTRIBUTES) \ } \ \ @@ -471,7 +470,6 @@ namespace CosmoTool { \ \ TNAME() : type(sizeof(STRUCT)) \ { \ - long position; \ BOOST_PP_SEQ_FOR_EACH(CTOOL_HDF5_INSERT_ENUM_ELEMENT, STRUCT, ATTRIBUTES) \ } \ \ diff --git a/src/yorick.hpp b/src/yorick.hpp index f38200e..dca3713 100644 --- a/src/yorick.hpp +++ b/src/yorick.hpp @@ -7,16 +7,16 @@ This software is a computer program whose purpose is to provide a toolbox for co data analysis (e.g. filters, generalized Fourier transforms, power spectra, ...) This software is governed by the CeCILL license under French law and -abiding by the rules of distribution of free software. You can use, +abiding by the rules of distribution of free software. You can use, modify and/ or redistribute the software under the terms of the CeCILL license as circulated by CEA, CNRS and INRIA at the following URL -"http://www.cecill.info". +"http://www.cecill.info". As a counterpart to the access to the source code and rights to copy, modify and redistribute granted by the license, users are provided only with a limited warranty and the software's author, the holder of the economic rights, and the successive licensors have only limited -liability. +liability. In this respect, the user's attention is drawn to the risks associated with loading, using, modifying and/or developing or reproducing the @@ -25,9 +25,9 @@ that may mean that it is complicated to manipulate, and that also therefore means that it is reserved for developers and experienced professionals having in-depth computer knowledge. Users are therefore encouraged to load and test the software's suitability as regards their -requirements in conditions enabling the security of their systems and/or -data to be ensured and, more generally, to use and operate it in the -same conditions as regards security. +requirements in conditions enabling the security of their systems and/or +data to be ensured and, more generally, to use and operate it in the +same conditions as regards security. The fact that you are presently reading this means that you have had knowledge of the CeCILL license and that you accept its terms. @@ -42,7 +42,7 @@ knowledge of the CeCILL license and that you accept its terms. #include -namespace CosmoTool +namespace CosmoTool { class ProgressiveDoubleOutputImpl @@ -75,7 +75,7 @@ namespace CosmoTool bool initialized; int *ref; ProgressiveDoubleOutputImpl *impl; - + friend ProgressiveDoubleOutput saveDoubleArrayProgressive(const char *fname, uint32_t *dimList, uint32_t rank); void decRef(); public: @@ -86,7 +86,7 @@ namespace CosmoTool virtual void addDouble(double a); - const ProgressiveDoubleOutput& operator=(const ProgressiveDoubleOutput& b); + const ProgressiveDoubleOutput& operator=(const ProgressiveDoubleOutput& b); }; template @@ -95,12 +95,12 @@ namespace CosmoTool private: int *ref; ProgressiveInputImpl *impl; - + void decRef() { if (ref == 0) return; - + (*ref)--; if (*ref == 0) { @@ -112,17 +112,17 @@ namespace CosmoTool } public: - static ProgressiveInput - loadArrayProgressive(const std::string& fname, uint32_t *&dimList, + static ProgressiveInput + loadArrayProgressive(const std::string& fname, uint32_t *&dimList, uint32_t& rank); ProgressiveInput() { - impl = 0; - ref = 0; + impl = 0; + ref = 0; } ProgressiveInput(ProgressiveInputImpl *i) { - impl = i; - ref = new int; + impl = i; + ref = new int; *ref = 1; } ProgressiveInput(const ProgressiveInput& o) { @@ -161,12 +161,12 @@ namespace CosmoTool private: int *ref; ProgressiveOutputImpl *impl; - + void decRef() { if (ref == 0) return; - + (*ref)--; if (*ref == 0) { @@ -178,17 +178,17 @@ namespace CosmoTool } public: - static ProgressiveOutput - saveArrayProgressive(const std::string& fname, uint32_t *dimList, + static ProgressiveOutput + saveArrayProgressive(const std::string& fname, uint32_t *dimList, uint32_t rank); ProgressiveOutput() { - impl = 0; - ref = 0; + impl = 0; + ref = 0; } ProgressiveOutput(ProgressiveOutputImpl *i) { - impl = i; - ref = new int; + impl = i; + ref = new int; *ref = 1; } ProgressiveOutput(const ProgressiveOutput& o) { @@ -222,10 +222,9 @@ namespace CosmoTool template void loadArray(const std::string& fname, - T*& array, uint32_t *& dimList, uint32_t& rank) - throw (NoSuchFileException); + T*& array, uint32_t *& dimList, uint32_t& rank); - ProgressiveDoubleOutput saveDoubleArrayProgressive(const char *fname, uint32_t *dimList, uint32_t rank); + ProgressiveDoubleOutput saveDoubleArrayProgressive(const char *fname, uint32_t *dimList, uint32_t rank); }; #endif diff --git a/src/yorick_nc4.cpp b/src/yorick_nc4.cpp index a0234df..e956438 100644 --- a/src/yorick_nc4.cpp +++ b/src/yorick_nc4.cpp @@ -7,16 +7,16 @@ This software is a computer program whose purpose is to provide a toolbox for co data analysis (e.g. filters, generalized Fourier transforms, power spectra, ...) This software is governed by the CeCILL license under French law and -abiding by the rules of distribution of free software. You can use, +abiding by the rules of distribution of free software. You can use, modify and/ or redistribute the software under the terms of the CeCILL license as circulated by CEA, CNRS and INRIA at the following URL -"http://www.cecill.info". +"http://www.cecill.info". As a counterpart to the access to the source code and rights to copy, modify and redistribute granted by the license, users are provided only with a limited warranty and the software's author, the holder of the economic rights, and the successive licensors have only limited -liability. +liability. In this respect, the user's attention is drawn to the risks associated with loading, using, modifying and/or developing or reproducing the @@ -25,9 +25,9 @@ that may mean that it is complicated to manipulate, and that also therefore means that it is reserved for developers and experienced professionals having in-depth computer knowledge. Users are therefore encouraged to load and test the software's suitability as regards their -requirements in conditions enabling the security of their systems and/or -data to be ensured and, more generally, to use and operate it in the -same conditions as regards security. +requirements in conditions enabling the security of their systems and/or +data to be ensured and, more generally, to use and operate it in the +same conditions as regards security. The fact that you are presently reading this means that you have had knowledge of the CeCILL license and that you accept its terms. @@ -53,7 +53,7 @@ public: vector counts; vector dimList; uint32_t rank; - + NetCDF_handle(NcFile *f, NcVar v, vector& dimList, uint32_t rank); virtual ~NetCDF_handle(); }; @@ -86,14 +86,14 @@ public: InputGenCDF(NcFile *f, NcVar v, vector& dimList, uint32_t rank) : NetCDF_handle(f,v,dimList,rank) {} - virtual ~InputGenCDF() {} + virtual ~InputGenCDF() {} virtual T read() { T a; curVar.getVar(curPos, counts, &a); - + curPos[rank-1]++; for (long i = rank-1; i >= 1; i--) { @@ -102,7 +102,7 @@ public: curPos[i-1]++; curPos[i] = 0; } - } + } return a; } @@ -120,12 +120,12 @@ public: OutputGenCDF(NcFile *f, NcVar v, vector& dimList, uint32_t rank) : NetCDF_handle(f,v,dimList,rank) {} - virtual ~OutputGenCDF() {} + virtual ~OutputGenCDF() {} virtual void put(T a) { curVar.putVar(curPos, counts, &a); - + curPos[rank-1]++; for (long i = rank-1; i >= 1; i--) { @@ -134,7 +134,7 @@ public: curPos[i-1]++; curPos[i] = 0; } - } + } } }; @@ -159,17 +159,17 @@ namespace CosmoTool { uint32_t rank) { NcFile *f = new NcFile(fname, NcFile::replace); - + vector dimArray; for (uint32_t i = 0; i < rank; i++) { char dimName[255]; - + sprintf(dimName, "dim%d", i); dimArray.push_back(f->addDim(dimName, dimList[rank-1-i])); } - - NcVar v = f->addVar("array", get_NetCDF_type(), dimArray); + + NcVar v = f->addVar("array", get_NetCDF_type(), dimArray); vector ldimList; @@ -177,7 +177,7 @@ namespace CosmoTool { ldimList.push_back(dimArray[i]); OutputGenCDF *impl = new OutputGenCDF(f, v, ldimList, rank); - return ProgressiveOutput(impl); + return ProgressiveOutput(impl); } template @@ -206,32 +206,31 @@ namespace CosmoTool { const T *array, uint32_t *dimList, uint32_t rank) { NcFile f(fname.c_str(), NcFile::replace); - + vector dimArray; for (uint32_t i = 0; i < rank; i++) { char dimName[255]; - + sprintf(dimName, "dim%d", i); dimArray.push_back(f.addDim(dimName, dimList[i])); } NcVar v = f.addVar("array", get_NetCDF_type(), dimArray); - + v.putVar(array); } template void loadArray(const std::string& fname, T*&array, uint32_t *&dimList, uint32_t& rank) - throw (NoSuchFileException) { NcFile f(fname.c_str(), NcFile::read); - + //if (!f.is_valid()) // throw NoSuchFileException(fname); - - NcVar v = f.getVar("array"); + + NcVar v = f.getVar("array"); vector dims = v.getDims(); rank = v.getDimCount(); uint32_t fullSize = 1; @@ -268,5 +267,5 @@ namespace CosmoTool { const float *array, uint32_t *dimList, uint32_t rank); template void saveArray(const std::string& fname, const double *array, uint32_t *dimList, uint32_t rank); - + }