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

python/_project.pyx

@@ -808,7 +808,25 @@ def spherical_projection(int Nside,
                          npx.ndarray[DTYPE_t, ndim=3] density not None,
                          DTYPE_t min_distance,
                          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.
+    """
     import healpy as hp
     import progressbar as pb
     cdef int i

python/cosmotool/borg.py

@@ -1,7 +1,7 @@
 ### 
 ### BORG code is from J. Jasche
 ###
-import StringIO
+import io
 import numpy as np
 from numpy import *
 import os.path
@@ -154,9 +154,9 @@ def get_grid_values(xx,data, ranges):
 def get_mean_density(fdir, smin, step):
     """ estimate ensemble mean
     """
-    print '-'*60
-    print 'Get 3D ensemble mean density field'
-    print '-'*60
+    print('-'*60)
+    print('Get 3D ensemble mean density field')
+    print('-'*60)
 
     fname0 = fdir + 'initial_density_'+str(0)+'.dat'
     fname1 = fdir + 'final_density_'+str(0)+'.dat'
@@ -208,9 +208,9 @@ def get_mean_density(fdir, smin, step):
 def get_mean_density_fdir(fdir,init,steps):
     """ estimate ensemble mean
     """
-    print '-'*60
-    print 'Get 3D ensemble mean density field'
-    print '-'*60
+    print('-'*60)
+    print('Get 3D ensemble mean density field')
+    print('-'*60)
 
     fname0,fname1=build_filelist(fdir)
     

python/cosmotool/cic.py

@@ -4,7 +4,7 @@ import numpy as np
 
 def cicParticles(particles, L, N):
 
-    if type(N) not in [int,long]:
+    if type(N) not in [int,int]:
       raise TypeError("N must be a numeric type")
 
     def shifted(i, t):
@@ -14,7 +14,7 @@ def cicParticles(particles, L, N):
 
     i =[]
     r = []
-    for d in xrange(3):
+    for d in range(3):
         q = ne.evaluate('(p%L)*N/L', local_dict={'p':particles[d], 'L':L, 'N':N })
         o = np.empty(q.size, dtype=np.int64)
         o[:] = np.floor(q)

python/cosmotool/cl_cic.py

@@ -163,8 +163,8 @@ class CIC_CL(object):
         # 2 dimensions
         translator['ndim'] = ndim
         translator['centered'] = '1' if centered else '0'
-        looperVariables = ','.join(['id%d' % d for d in xrange(ndim)])
-        looperFor = '\n'.join(['for (int id{dim}=0; id{dim} < 2; id{dim}++) {{'.format(dim=d) for d in xrange(ndim)])
+        looperVariables = ','.join(['id%d' % d for d in range(ndim)])
+        looperFor = '\n'.join(['for (int id{dim}=0; id{dim} < 2; id{dim}++) {{'.format(dim=d) for d in range(ndim)])
         looperForEnd = '}' * ndim
         
         kern = pragmas + CIC_PREKERNEL.format(**translator) + (CIC_KERNEL % {'looperVariables': looperVariables, 'looperFor': looperFor, 'looperForEnd':looperForEnd})

python/cosmotool/grafic.py

@@ -27,7 +27,7 @@ def readGrafic(filename):
         BoxSize = delta * Nx * h
         
         checkPoint = 4*Ny*Nz
-        for i in xrange(Nx):
+        for i in range(Nx):
             checkPoint = struct.unpack("I", f.read(4))[0]
             if checkPoint != 4*Ny*Nz:
               raise ValueError("Invalid unformatted access")
@@ -57,7 +57,7 @@ def writeGrafic(filename, field, BoxSize, scalefac, **cosmo):
                                           cosmo['omega_M_0'], cosmo['omega_lambda_0'], 100*cosmo['h'], checkPoint))
         checkPoint = 4*Ny*Nz
         field = field.reshape(field.shape, order='F')
-        for i in xrange(Nx):
+        for i in range(Nx):
             f.write(struct.pack("I", checkPoint))
             f.write(field[i].astype(np.float32).tostring())
             f.write(struct.pack("I", checkPoint))
@@ -73,7 +73,7 @@ def writeWhitePhase(filename, field):
         
         field = field.reshape(field.shape, order='F')
         checkPoint = struct.pack("I", 4*Nx*Ny)
-        for i in xrange(Nx):
+        for i in range(Nx):
             f.write(checkPoint)
             f.write(field[i].astype(np.float32).tostring())
             f.write(checkPoint)
@@ -87,7 +87,7 @@ def readWhitePhase(filename):
         
         checkPoint_ref = 4*Ny*Nz
         
-        for i in xrange(Nx):
+        for i in range(Nx):
             if struct.unpack("I", f.read(4))[0] != checkPoint_ref:
               raise ValueError("Invalid unformatted access")
               

src/CMakeLists.txt

@@ -6,7 +6,6 @@ SET(CosmoTool_SRCS
 	load_data.cpp
 	loadGadget.cpp
 	loadRamses.cpp
-	octTree.cpp
 	powerSpectrum.cpp
 	miniargs.cpp
 	growthFactor.cpp

src/octTree.hpp

@@ -55,12 +55,20 @@ namespace CosmoTool
 
   typedef octCoordType OctCoords[3];
 
+  template<class T = void>
   struct OctCell
   {
     octPtr numberLeaves;
     octPtr children[8];
+    T data;
   };
 
+  template<typename T>
+  struct OctTree_defaultUpdater {
+    void operator()(T& d) { }
+  };
+
+  template<typename T_dataUpdater = OctTree_defaultUpdater<void>, class T = void>
   class OctTree
   {
   public:
@@ -103,9 +111,10 @@ namespace CosmoTool
     
 
   protected:
+    T_dataUpdater updater;
     const FCoordinates *particles;
     octPtr numParticles;
-    OctCell *cells;
+    OctCell<T> *cells;
     float Lbox;
     octPtr lastNode;
     octPtr numCells;  
@@ -177,4 +186,6 @@ namespace CosmoTool
 };
 
 
+#include "octTree.tcc"
+
 #endif

src/octTree.tcc

@@ -39,8 +39,9 @@ knowledge of the CeCILL license and that you accept its terms.
 #include "config.hpp"
 #include "octTree.hpp"
 
+namespace CosmoTool {
+
 using namespace std;
-using namespace CosmoTool;
 
 //#define VERBOSE
 
@@ -59,7 +60,8 @@ static uint32_t mypow(uint32_t i, uint32_t p)
     return j*j*i;  
 }
 
-OctTree::OctTree(const FCoordinates *particles, octPtr numParticles, 
+template<typename Updater, typename T>
+OctTree<Updater,T>::OctTree(const FCoordinates *particles, octPtr numParticles, 
 		 uint32_t maxMeanTreeDepth, uint32_t maxAbsoluteDepth,
 		 uint32_t threshold)
 {
@@ -94,7 +96,7 @@ OctTree::OctTree(const FCoordinates *particles, octPtr numParticles,
     }
   cout << xMin[0] << " " << xMin[1] << " " << xMin[2] << " lNorm=" << lenNorm << endl; 
 
-  cells = new OctCell[numCells];
+  cells = new OctCell<T>[numCells];
   Lbox = (float)(octCoordTypeNorm+1);
 
   cells[0].numberLeaves = 0;
@@ -110,12 +112,14 @@ OctTree::OctTree(const FCoordinates *particles, octPtr numParticles,
   //#endif
 }
 
-OctTree::~OctTree()
+template<typename Updater, typename T>
+OctTree<Updater,T>::~OctTree()
 {
   delete cells;
 }
 
-void OctTree::buildTree(uint32_t maxAbsoluteDepth)
+template<typename Updater, typename T>
+void OctTree<Updater,T>::buildTree(uint32_t maxAbsoluteDepth)
 {
   for (octPtr i = 0; i < numParticles; i++)
     {
@@ -129,7 +133,8 @@ void OctTree::buildTree(uint32_t maxAbsoluteDepth)
 }
 
 
-void OctTree::insertParticle(octPtr node, 
+template<typename Updater, typename T>
+void OctTree<Updater,T>::insertParticle(octPtr node, 
 			     const OctCoords& icoord,
 			     octCoordType halfNodeLength,
 			     octPtr particleId,
@@ -208,3 +213,5 @@ void OctTree::insertParticle(octPtr node,
   cells[node].children[octPos] = newNode;
 }
 
+
+};