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Merged in python3 (pull request #5)

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Port to python3, large code cleanup

* Fixed command line for cosmotool

* Fix path

* Dump command line is log file

* Fix important typo

* Modify paths for example

* Fix path again

* Use an explicit constructor

* Change file to open (python 2->3)

* python3 fix for xrange in periodic_kdtree.py

* Fixed index for Np, numPart, numZones, numZonesTot, partID, zoneID in catalogUtil.py
This commit is contained in:
Guilhem Lavaux 2020-12-29 08:56:33 +00:00
parent 8249256508
commit affb56ff48
392 changed files with 4092 additions and 260938 deletions
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45
c_tools/mock/generateFromCatalog.cpp
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@ -28,7 +28,7 @@
#include <string>
#include "generateFromCatalog_conf.h"
#include "contour_pixels.hpp"
#include <netcdfcpp.h>
#include <netcdf>
#include <CosmoTool/fortran.hpp>
#include <gsl/gsl_interp.h>
#include <gsl/gsl_integration.h>
@ -38,6 +38,7 @@
using namespace std;
using boost::format;
using namespace CosmoTool;
using namespace netCDF;
struct NYU_Data
{
@ -457,13 +458,11 @@ void generateSurfaceMask(generateFromCatalog_info& args ,
void saveData(ParticleData& pdata)
{
NcFile f("particles.nc", NcFile::Replace);
assert(f.is_valid());
NcFile f("particles.nc", NcFile::replace);
NcDim *d = f.add_dim("space", 3);
NcDim *p = f.add_dim("Np", pdata.pos.size());
NcVar *v = f.add_var("particles", ncDouble, d, p);
NcDim d = f.addDim("space", 3);
NcDim p = f.addDim("Np", pdata.pos.size());
NcVar v = f.addVar("particles", ncDouble, {d, p});
double *x = new double[pdata.pos.size()];
for (int j = 0; j < 3; j++)
@ -472,11 +471,11 @@ void saveData(ParticleData& pdata)
for (int i = 0; i < pdata.pos.size(); i++)
x[i] = pdata.pos[i].xyz[j];
v->put_rec(d, x, j);
v.putVar({size_t(j), 0}, {1, pdata.pos.size()}, x);
}
v = f.add_var("id_gal", ncInt, p);
v->put(&pdata.id_gal[0], pdata.id_gal.size());
v = f.addVar("id_gal", ncInt, std::vector<NcDim>({p}));
v.putVar(&pdata.id_gal[0]);
delete[] x;
@ -533,30 +532,30 @@ void saveForZobov(ParticleData& pdata, const string& fname, const string& paramn
}
f.endCheckpoint();
NcFile fp(paramname.c_str(), NcFile::Replace);
NcFile fp(paramname.c_str(), NcFile::replace);
fp.add_att("range_x_min", -Lmax/100.);
fp.add_att("range_x_max", Lmax/100.);
fp.add_att("range_y_min", -Lmax/100.);
fp.add_att("range_y_max", Lmax/100.);
fp.add_att("range_z_min", -Lmax/100.);
fp.add_att("range_z_max", Lmax/100.);
fp.add_att("mask_index", pdata.mask_index); // PMS
fp.add_att("is_observation", 1); // PMS
fp.putAtt("range_x_min", ncDouble, -Lmax/100.);
fp.putAtt("range_x_max", ncDouble, Lmax/100.);
fp.putAtt("range_y_min", ncDouble, -Lmax/100.);
fp.putAtt("range_y_max", ncDouble, Lmax/100.);
fp.putAtt("range_z_min", ncDouble, -Lmax/100.);
fp.putAtt("range_z_max", ncDouble, Lmax/100.);
fp.putAtt("mask_index", ncInt, pdata.mask_index); // PMS
fp.putAtt("is_observation", ncInt, 1); // PMS
int nOutputPart = pdata.mask_index;
//int nOutputPart = pdata.pos.size();
NcDim *NumPart_dim = fp.add_dim("numpart_dim", nOutputPart);
NcVar *v = fp.add_var("particle_ids", ncInt, NumPart_dim);
//NcVar *v2 = fp.add_var("expansion", ncDouble, NumPart_dim);
NcDim NumPart_dim = fp.addDim("numpart_dim", nOutputPart);
NcVar v = fp.addVar("particle_ids", ncInt, NumPart_dim);
//NcVar v2 = fp.addVar("expansion", ncDouble, NumPart_dim);
//double *expansion_fac = new double[pdata.pos.size()];
//for (int i = 0; i < pdata.pos.size(); i++)
// expansion_fac[i] = 1.0;
v->put(&pdata.id_gal[0], nOutputPart);
v.putVar({0}, {size_t(nOutputPart)}, &pdata.id_gal[0]);
//v2->put(expansion_fac, pdata.pos.size());
//delete[] expansion_fac;