Merge branch 'master' of bitbucket.org:glavaux/cosmotool

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 "${CMAKE_CURRENT_SOURCE_DIR}/LICENCE_CeCILL_V2")
 SET(CPACK_PACKAGE_VERSION_MAJOR "1")
-SET(CPACK_PACKAGE_VERSION_MINOR "2")
+SET(CPACK_PACKAGE_VERSION_MINOR "3")
-SET(CPACK_PACKAGE_VERSION_PATCH "3${EXTRA_VERSION}")
+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 

conda/meta.yaml

@@ -1,6 +1,6 @@
 package:
   name: cosmotool
-  version: "1.2.3"
+  version: "1.3.0"
 
 source:
   git_rev: a86c9a8

python/CMakeLists.txt

@@ -116,8 +116,17 @@ configure_file(${CMAKE_CURRENT_SOURCE_DIR}/cosmotool/config.py.in ${CMAKE_CURREN
 
 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")
+

python/_cosmotool.pyx

@@ -247,6 +247,9 @@ class PySimulationAdaptor(PySimulationBase):
   def __init__(self,sim):
     self.simu = sim
 
+  def getNumParticles(self):
+    return self.simu.numParticles
+
   def getBoxsize(self):
     return self.simu.BoxSize
 

python/_project.pyx

@@ -533,12 +533,13 @@ cdef void INTERNAL_project_cic_with_mass_periodic(DTYPE_t[:,:,:] g,
 
 
 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):
+                double Lbox, bool periodic = False, centered=True, output=None):
     """
-    project_cic(x array (N,3), mass (may be None), Ngrid, Lbox, periodict, centered=True)
+    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")
 
+    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
 

sample/simple3DFilter.cpp

@@ -108,7 +108,7 @@ int main(int argc, char **argv)
   H5::H5File in_f(fname1, 0);
   H5::H5File out_f(outFile, H5F_ACC_TRUNC);
   array_type v1_data;
-  uint32_t N1_points, N2_points;
+  uint64_t N1_points, N2_points;
   
   array3_type bins(boost::extents[Nres][Nres][Nres]);
 
@@ -124,12 +124,12 @@ int main(int argc, char **argv)
   MyCell *allCells_1 = new MyCell[N1_points];
   
 #pragma omp parallel for schedule(static)
-  for (long i = 0; i < Nres*Nres*Nres; i++)
+  for (uint32_t i = 0; i < Nres*Nres*Nres; i++)
     bins.data()[i] = 0;
 
   cout << "Shuffling data in cells..." << endl;
 #pragma omp parallel for schedule(static)
-  for (int i = 0 ; i < N1_points; i++)
+  for (uint64_t i = 0 ; i < N1_points; i++)
     {
       for (int j = 0; j < 3; j++)
         allCells_1[i].coord[j] = v1_data[i][j];

setup.py

@@ -229,7 +229,7 @@ class BuildCMakeExt(build_ext):
 CosmoTool_extension = CMakeExtension(name="cosmotool")
 
 setup(name='cosmotool',
-      version='1.2.3',
+      version='1.3.0',
       packages=["cosmotool"],
       package_dir={'cosmotool': 'python/cosmotool'},
       install_requires=['numpy','cffi','numexpr','pyfftw','h5py'],

src/mykdtree.hpp

@@ -99,8 +99,8 @@ namespace CosmoTool {
     typename KDDef<N,CType>::CoordType r, r2;
     KDCell<N, ValType,CType> **cells;
     typename KDDef<N,CType>::CoordType *distances;
-    uint32_t currentRank;
+    uint64_t currentRank;
-    uint32_t numCells;
+    uint64_t numCells;
   };
   
 
@@ -114,7 +114,7 @@ namespace CosmoTool {
 
     RecursionMultipleInfo(const typename KDDef<N,CType>::KDCoordinates& rx,
 			  KDCell<N,ValType,CType> **cells,
-			  uint32_t numCells)
+			  uint64_t numCells)
       : queue(cells, numCells, INFINITY),traversed(0)
     {
       std::copy(rx, rx+N, x);
@@ -153,20 +153,20 @@ namespace CosmoTool {
        std::copy(replicate, replicate+N, this->replicate);
      }
 
-    uint32_t getIntersection(const coords& x, CoordType r, 
+    uint64_t getIntersection(const coords& x, CoordType r, 
 			     Cell **cells,
-			     uint32_t numCells);
+			     uint64_t numCells);
-    uint32_t getIntersection(const coords& x, CoordType r, 
+    uint64_t getIntersection(const coords& x, CoordType r, 
 			     Cell **cells,
 			     CoordType *distances,
-			     uint32_t numCells);
+			     uint64_t numCells);
-    uint32_t countCells(const coords& x, CoordType r);
+    uint64_t countCells(const coords& x, CoordType r);
 
     Cell *getNearestNeighbour(const coords& x);
 
-    void getNearestNeighbours(const coords& x, uint32_t NumCells,
+    void getNearestNeighbours(const coords& x, uint64_t NumCells,
 			      Cell **cells);
-    void getNearestNeighbours(const coords& x, uint32_t NumCells,
+    void getNearestNeighbours(const coords& x, uint64_t NumCells,
 			      Cell **cells,
 			      CoordType *distances);
 

src/mykdtree.tcc

@@ -80,9 +80,9 @@ namespace CosmoTool {
   }
 
   template<int N, typename ValType, typename CType, typename CellSplitter>
-  uint32_t KDTree<N,ValType,CType,CellSplitter>::getIntersection(const coords& x, CoordType r, 
+  uint64_t KDTree<N,ValType,CType,CellSplitter>::getIntersection(const coords& x, CoordType r, 
 						    KDTree<N,ValType,CType,CellSplitter>::Cell **cells,
-						    uint32_t numCells)
+						    uint64_t numCells)
   {
     RecursionInfoCells<N,ValType,CType> info;
 
@@ -112,10 +112,10 @@ namespace CosmoTool {
   }
 
   template<int N, typename ValType, typename CType, typename CellSplitter>
-  uint32_t KDTree<N,ValType,CType,CellSplitter>::getIntersection(const coords& x, CoordType r, 
+  uint64_t KDTree<N,ValType,CType,CellSplitter>::getIntersection(const coords& x, CoordType r, 
 						    Cell **cells,
 						    CoordType *distances,
-						    uint32_t numCells)
+						    uint64_t numCells)
   {
     RecursionInfoCells<N,ValType> info;
 
@@ -144,7 +144,7 @@ namespace CosmoTool {
   }
 
   template<int N, typename ValType, typename CType, typename CellSplitter>
-  uint32_t KDTree<N,ValType,CType,CellSplitter>::countCells(const coords& x, CoordType r)
+  uint64_t KDTree<N,ValType,CType,CellSplitter>::countCells(const coords& x, CoordType r)
   {
     RecursionInfoCells<N,ValType> info;
 
@@ -501,7 +501,7 @@ namespace CosmoTool {
   }
 
  template<int N, typename ValType, typename CType, typename CellSplitter>
- void KDTree<N,ValType,CType,CellSplitter>::getNearestNeighbours(const coords& x, uint32_t N2,
+ void KDTree<N,ValType,CType,CellSplitter>::getNearestNeighbours(const coords& x, uint64_t N2,
 						    Cell **cells)
  {
    RecursionMultipleInfo<N,ValType> info(x, cells, N2);
@@ -527,7 +527,7 @@ namespace CosmoTool {
  }
 
  template<int N, typename ValType, typename CType, typename CellSplitter>
- void KDTree<N,ValType,CType,CellSplitter>::getNearestNeighbours(const coords& x, uint32_t N2,
+ void KDTree<N,ValType,CType,CellSplitter>::getNearestNeighbours(const coords& x, uint64_t N2,
 						    Cell **cells,
 						    CoordType *distances)
  {

src/yorick.hpp

@@ -222,8 +222,7 @@ namespace CosmoTool
 
   template<typename T>
   void loadArray(const std::string& fname,
-		 T*& array, uint32_t *& dimList, uint32_t& rank)
+		 T*& array, uint32_t *& dimList, uint32_t& rank);
-    throw (NoSuchFileException);
 
   ProgressiveDoubleOutput saveDoubleArrayProgressive(const char *fname, uint32_t *dimList, uint32_t rank);
 };

src/yorick_nc4.cpp

@@ -224,7 +224,6 @@ namespace CosmoTool {
   template<typename T>
   void loadArray(const std::string& fname,
 		 T*&array, uint32_t *&dimList, uint32_t& rank)
-	throw (NoSuchFileException)
   {
     NcFile f(fname.c_str(), NcFile::read);