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_PolGainSolve.cpp
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/* POLGAINSOLVE - Solving cross-polarizer gains for PolConvert
Copyright (C) 2017-2022 Ivan Marti-Vidal
Nordic Node of EU ALMA Regional Center (Onsala, Sweden)
Max-Planck-Institut fuer Radioastronomie (Bonn, Germany)
University of Valencia (Spain)
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with this program. If not, see <http://www.gnu.org/licenses/>
*/
#include <Python.h>
// compiler warning that we use a deprecated NumPy API
// #define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION
//#define NO_IMPORT_ARRAY
#if PY_MAJOR_VERSION >= 3
#define NPY_NO_DEPRECATED_API 0x0
#endif
#include <numpy/npy_common.h>
#include <numpy/arrayobject.h>
#include <sys/types.h>
#include <iostream>
#include <fstream>
#include <stdlib.h>
#include <string.h>
#include <math.h>
#include <complex>
#include <dirent.h>
#include <fftw3.h>
//#include <gsl/gsl_errno.h>
//#include <gsl/gsl_linalg.h>
// cribbed from SWIG machinery
#if PY_MAJOR_VERSION >= 3
#define PyClass_Check(obj) PyObject_IsInstance(obj, (PyObject *)&PyType_Type)
#define PyInt_Check(x) PyLong_Check(x)
#define PyInt_AsLong(x) PyLong_AsLong(x)
#define PyInt_FromLong(x) PyLong_FromLong(x)
#define PyInt_FromSize_t(x) PyLong_FromSize_t(x)
#define PyString_Check(name) PyBytes_Check(name)
#define PyString_FromString(x) PyUnicode_FromString(x)
#define PyString_Format(fmt, args) PyUnicode_Format(fmt, args)
//#define PyString_AsString(str) PyBytes_AsString(str)
#define PyString_Size(str) PyBytes_Size(str)
#define PyString_InternFromString(key) PyUnicode_InternFromString(key)
#define Py_TPFLAGS_HAVE_CLASS Py_TPFLAGS_BASETYPE
#define PyString_AS_STRING(x) PyUnicode_AS_STRING(x)
#define _PyLong_FromSsize_t(x) PyLong_FromSsize_t(x)
// For PyArray_FromDimsAndData -> PyArray_SimpleNewFromData
//#define INTEGER long
//#define INTEGERCAST (const npy_intp*)
//#else
// For PyArray_FromDimsAndData -> PyArray_SimpleNewFromData
//#define INTEGER int
//#define INTEGERCAST (long int *)
#endif
// and after some hacking
#if PY_MAJOR_VERSION >= 3
#define PyString_AsString(obj) PyUnicode_AsUTF8(obj)
#endif
typedef std::complex<double> cplx64f;
typedef std::complex<float> cplx32f;
/* Docstrings */
static char module_docstring[] =
"This module provides the cross-polarization gain-solver engine.";
static char PolGainSolve_docstring[] =
"Solves for cross-polarization gains from mixed-polarization visibilities";
static char ReadData_docstring[] =
"Reads data (one IF) for PolGainSolve";
static char FreeData_docstring[] =
"Releases the data pointers of PolGainSolve";
static char GetChi2_docstring[] =
"Computes the Chi2 for a given set of cross-pol gains";
static char GetIFs_docstring[] =
"Returns the array of frequencies for a given IF";
static char DoGFF_docstring[] =
"Performs a simplified GFF (delays and rates). The reference antenna is set by not adding it to the list of fittable antennas";
static char SetFringeRates_docstring[] =
"Forces the antenna fringe-rates to the list give, before the GCPFF is performed";
static char GetNScan_docstring[] =
"Returns the number of scans for the given IF.";
static char SetFit_docstring[] =
"Allocates memory for the GCPFF.";
static char GetNchan_docstring[] =
"Returns the number of channels for the given IF.";
/* Available functions */
static PyObject *PolGainSolve(PyObject *self, PyObject *args);
static PyObject *ReadData(PyObject *self, PyObject *args);
static PyObject *GetChi2(PyObject *self, PyObject *args);
static PyObject *GetIFs(PyObject *self, PyObject *args);
static PyObject *GetNchan(PyObject *self, PyObject *args);
static PyObject *DoGFF(PyObject *self, PyObject *args);
static PyObject *SetFringeRates(PyObject *self, PyObject *args);
static PyObject *GetNScan(PyObject *self, PyObject *args);
static PyObject *FreeData(PyObject *self, PyObject *args);
static PyObject *SetFit(PyObject *self, PyObject *args);
bool solveSystem(int Neq, double *Hessian, double *Residuals, double *Solution, double *Errors);
/* Module specification */
static PyMethodDef module_methods[] = {
{"PolGainSolve", PolGainSolve, METH_VARARGS, PolGainSolve_docstring},
{"ReadData", ReadData, METH_VARARGS, ReadData_docstring},
{"GetChi2", GetChi2, METH_VARARGS, GetChi2_docstring},
{"GetIFs", GetIFs, METH_VARARGS, GetIFs_docstring},
{"DoGFF", DoGFF, METH_VARARGS, DoGFF_docstring},
{"SetFringeRates", SetFringeRates, METH_VARARGS, SetFringeRates_docstring},
{"GetNScan",GetNScan, METH_VARARGS, GetNScan_docstring},
{"GetNchan",GetNchan, METH_VARARGS, GetNchan_docstring},
{"FreeData", FreeData, METH_VARARGS, FreeData_docstring},
{"SetFit", SetFit, METH_VARARGS, SetFit_docstring},
{NULL, NULL, 0, NULL} /* terminated by list of NULLs, apparently */
};
// normally abort() is called on problems, which breaks CASA.
// here we report and save the error condition which can be
// noticed for a cleaner exit.
//int gsl_death_by = GSL_SUCCESS;
//static void gsl_death(const char * reason, const char * file,
// int line, int gsl_errno) {
// // stderr does not end up synchronized with stdout
// printf("GSL Death by '%s' in file %s at line %d: GSL Error %d\n",
// reason, file, line, gsl_errno);
// fflush(stdout); std::cout << std::flush;
// gsl_death_by = gsl_errno;
//}
static long chisqcount = 0;
//static long twincounter = 0;
/* Initialize the module */
#if PY_MAJOR_VERSION >= 3
static struct PyModuleDef pc_module_def = {
PyModuleDef_HEAD_INIT,
"_PolGainSolve", /* m_name */
module_docstring, /* m_doc */
-1, /* m_size */
module_methods, /* m_methods */
NULL,NULL,NULL,NULL /* m_reload, m_traverse, m_clear, m_free */
};
PyMODINIT_FUNC PyInit__PolGainSolve(void)
{
PyObject *m = PyModule_Create(&pc_module_def);
// import_array();
// (void)gsl_set_error_handler(gsl_death);
return(m);
}
#else
PyMODINIT_FUNC init_PolGainSolve(void)
{
PyObject *m = Py_InitModule3("_PolGainSolve", module_methods, module_docstring);import_array();
// (void)gsl_set_error_handler(gsl_death);
if (m == NULL)
return;
}
#endif
///////////////////////
char message[512];
bool doParang;
static double TWOPI = 6.283185307179586;
int MaxChan = 1;
int MAXIF = 8; // Will reallocate if needed.
int NCalAnt, Nlin, Ncirc, *Nchan, SolMode, SolAlgor;
int *IFNum;
int *Lant, *Cant, *NVis, *NLVis, *NCVis, *CalAnts, *NScan;
int *Twins[2], Ntwin;
int solveAmp, useCov, solveQU;
int *LinBasNum, NLinBas;
int NIF, NIFComp;
int NBas, NantFit, Npar=-1;
int npix = 0;
double **Frequencies, ***Rates[5], ***Delays[5];
double *Tm = nullptr;
double *BasWgt;
int *doIF, *antFit;
double *feedAngle;
double **DStokes; // = new double*[1];
double UVTAPER = 1.e9;
double Chi2Old = 0.0;
double TAvg = 1.0;
double RelWeight = 1.0;
double T0, T1, DT;
int **Ant1, **Ant2, **BasNum, **Scan;
double **Times, **ScanDur, **Weights, *CovMat, *IndVec, *SolVec;
double **UVGauss;
cplx64f **PA1, **PA2, **auxC00, **auxC01, **auxC10, **auxC11;
cplx64f **auxC00Flp, **auxC11Flp; // To better check Parangle Flip.
cplx64f ***RR, ***RL, ***LR, ***LL, **CrossSpec00, **CrossSpec11;
double *UVWeights;
double SNR_CUTOFF;
double Lambda;
bool doCov;
double Stokes[4];
// gsl_matrix_view m;
// gsl_vector_view x, v;
// gsl_permutation *perm;
bool AddCrossHand = true;
bool AddParHand = true;
bool StokesSolve;
cplx64f *G1,*G2, *G1nu, *G2nu;
double *DirDer,*MBD1,*MBD2;
int *DerIdx,*AvVis;
FILE *logFile = nullptr;
bool solveSystem(int Neq, double *HessianOrig, double *ResidualsOrig, double *Solution, double *Errors){
bool isSingular;
int i,j,k;
double *buffer = new double[Neq+1];
double f;
double *Hessian = new double[Neq*Neq];
double *Residuals = new double[Neq];
memcpy((void *)Hessian, (void *)HessianOrig, sizeof(double)*Neq*Neq);
memcpy((void *)Residuals, (void *)ResidualsOrig, sizeof(double)*Neq);
int Nmissing = 0;
int *missing = new int[Neq];
double *L = new double[Neq*Neq];
double *U = new double[Neq*Neq];
for(i=0;i<Neq;i++){Solution[i]=0.0;};
for(i=0;i<Neq*Neq;i++){L[i]=0.0;U[i]=0.0;};
for(i=0;i<Neq;i++){L[i*Neq+i]=1.0;};
// Getting null rows out of the computation:
for(i=0;i<Neq;i++){
isSingular=true;
for(j=0;j<Neq;j++){
if(HessianOrig[i*Neq+j]!=0.0){isSingular=false;break;};
};
if(isSingular){
missing[Nmissing]=i;Nmissing+=1;
// printf("Antenna %i does not seem to have valid data.\n",i);
};
};
/* performing Gaussian elimination */
for(i=0;i<Neq-1;i++){
// PIVOTING:
isSingular = false;
for(k=0;k<Nmissing;k++){
if(i==missing[k]){isSingular=true;break;};
};
if(!isSingular){
for(j=i+1;j<Neq;j++){
isSingular = false;
for(k=0;k<Nmissing;k++){
if(j==missing[k]){isSingular=true;break;};
};
if(!isSingular){
if(abs(Hessian[i*Neq + i]) < abs(Hessian[j*Neq + i])){
for(k=0;k<Neq;k++){
buffer[k] = Hessian[i*Neq + k];
Hessian[i*Neq + k] = Hessian[j*Neq + k];
Hessian[j*Neq + k] = buffer[k];
};
buffer[Neq] = Residuals[i];
Residuals[i] = Residuals[j];
Residuals[j] = buffer[Neq];
};
};
};
if(Hessian[i*Neq + i]==0.0){ //isSingular=true; return isSingular;
missing[Nmissing] = i;
Nmissing += 1;
// printf("Antenna %i does not seem to have valid data EITHER.\n",i);
} else {
for(j=i+1;j<Neq;j++){
isSingular = false;
for(k=0;k<Nmissing;k++){
if(j==missing[k]){isSingular=true;break;};
};
if(!isSingular){
f=Hessian[j*Neq + i]/Hessian[i*Neq + i];
L[j*Neq+i] = f;
for(k=0;k<Neq;k++){
Hessian[j*Neq + k]=Hessian[j*Neq + k]-f*Hessian[i*Neq + k];
};
Residuals[j] = Residuals[j]-f*Residuals[i];
} else {L[j*Neq+i]=0.0;};
};
};
};
};
// if(Hessian[Neq*Neq-1]==0.0){
// missing[Nmissing]=Neq-1;Nmissing+=1;
// printf("Antenna %i does not seem to have valid data EITHER.\n",i);
// };
for(i=0;i<Neq*Neq;i++){U[i]=Hessian[i];};
/* Backward substitution for discovering values of unknowns */
for(i=Neq-1;i>=0;i--){
isSingular=false;
for(j=0; j<Nmissing; j++){
if(missing[j]==i){isSingular=true;Solution[i]=0.0;break;};
};
if(!isSingular){
Solution[i]=Residuals[i];
for(j=i+1;j<Neq;j++){
if(i!=j){
Solution[i]=Solution[i]-Hessian[i*Neq + j]*Solution[j];
};
};
Solution[i]=Solution[i]/Hessian[i*Neq + i];
};
};
int Nfree;
Nfree = Neq - Nmissing;
double *invL = new double[Nfree*Nfree];
double *invU = new double[Nfree*Nfree];
double *Ufree = new double[Nfree*Nfree];
int ifree, jfree;
ifree=0; jfree=0;
// printf("Nfree: %i %i %i\n",Neq,Nmissing,Nfree);
for(i=0;i<Neq;i++){
isSingular=false;
for(k=0;k<Nmissing;k++){
if(i==missing[k]){isSingular=true;break;};
};
if(!isSingular){
jfree=0;
for(j=0;j<Neq;j++){
isSingular = false;
for(k=0;k<Nmissing;k++){
if(j==missing[k]){isSingular=true;break;};
};
if(!isSingular){
invL[ifree*Nfree+jfree]=L[i*Neq+j]; Ufree[ifree*Nfree+jfree]=U[i*Neq+j];
jfree+=1;
};
};
ifree += 1;
};
};
// Now, invert the smaller (nonSingular) matrices L and U:
double *ident = new double[Nfree];
for(k=0;k<Nfree;k++){
for(j=0;j<Nfree;j++){ident[j]=0.0;};
ident[k]=1.0;
for(i=Nfree-1;i>=0;i--){
invU[i*Nfree + k]=ident[i];
for(j=i+1;j<Nfree;j++){
if(i!=j){
invU[i*Nfree+k]=invU[i*Nfree+k]-Ufree[i*Nfree + j]*invU[j*Nfree+k];
};
};
invU[i*Nfree+k]=invU[i*Nfree+k]/Ufree[i*Nfree + i];
};
};
// The parameter errors are just the (sqrt of) the diagonal cov. matrix:
ifree = 0;
for(i=0;i<Neq;i++){
isSingular=false;
Errors[i]=0.0;
for(k=0;k<Nmissing;k++){
if(missing[k]==i){isSingular=true;Errors[i]=-1.0; break;};
};
if(!isSingular){
for(j=0;j<Nfree;j++){
Errors[i] += invU[ifree*Nfree+j]*invL[j*Nfree+ifree];
};
ifree += 1;
Errors[i] = std::sqrt(Errors[i]);
};
};
delete Hessian;
delete Residuals;
delete invU;
delete Ufree;
delete invL;
delete ident;
isSingular = Nmissing>0;
return isSingular;
};
static PyObject *GetNchan(PyObject *self, PyObject *args){
int cIF, k, j;
PyObject *ret;
// append after first call
if (!logFile) logFile = fopen("PolConvert.GainSolve.log","a");
fprintf(logFile,"into GetNchan...\n"); fflush(logFile);
if (!PyArg_ParseTuple(args, "i",&cIF)){
sprintf(message,"Failed GetNchan! Check inputs!\n");
fprintf(logFile,"%s",message); std::cout<<message; fflush(logFile);
ret = Py_BuildValue("i",-1);
return ret;
};
k=-1;
for (j=0; j<NIF; j++){
if(IFNum[j] == cIF){k=j;break;};
};
if(k<0){
sprintf(message,"GetNchan: IF %d not found\n", cIF);
fprintf(logFile,"%s",message); std::cout<<message; fflush(logFile);
PyObject *ret = Py_BuildValue("i",-2);
return ret;
};
fprintf(logFile,"... and got %d\n", Nchan[k]); fflush(logFile);
ret = Py_BuildValue("i",Nchan[k]);
return ret;
};
static PyObject *GetNScan(PyObject *self, PyObject *args){
int cIF, k, j;
PyObject *ret;
// append after first call
if (!logFile) logFile = fopen("PolConvert.GainSolve.log","a");
fprintf(logFile,"into GetNScan...\n"); fflush(logFile);
if (!PyArg_ParseTuple(args, "i",&cIF)){
sprintf(message,"Failed GetNScan! Check inputs!\n");
fprintf(logFile,"%s",message); std::cout<<message; fflush(logFile);
ret = Py_BuildValue("i",-1);
return ret;
};
k=-1;
for (j=0; j<NIF; j++){
if(IFNum[j] == cIF){k=j;break;};
};
if(k<0){
sprintf(message,"GetNScan: IF %d not found\n", cIF);
fprintf(logFile,"%s",message); std::cout<<message; fflush(logFile);
PyObject *ret = Py_BuildValue("i",-2);
return ret;
};
fprintf(logFile,"... and got %d\n", NScan[k]); fflush(logFile);
ret = Py_BuildValue("i",NScan[k]);
return ret;
};
static PyObject *PolGainSolve(PyObject *self, PyObject *args){
PyObject *calant, *linant, *solints, *flagBas, *logNameObj;
if (!PyArg_ParseTuple(args, "ddOOOOO",&RelWeight, &UVTAPER, &solints, &calant,
&linant,&flagBas, &logNameObj)){
sprintf(message,"Failed initialization of PolGainSolve! Check inputs!\n");
std::cout<<message;
PyObject *ret = Py_BuildValue("i",-1);
return ret;
};
UVTAPER = 2.*UVTAPER*UVTAPER;
// truncate for first call
std::string logName = PyString_AsString(logNameObj);
if (!logFile) logFile = fopen(logName.c_str(),"a");
// Assign dummy sizes to all variables:
NIF = 0;
Npar=0;
DStokes = new double*[1];
DStokes[0] = new double[4];
CovMat = new double[1];
IndVec = new double[1];
SolVec = new double[1];
G1 = new cplx64f[1];
G2 = new cplx64f[1];
G1nu = new cplx64f[1];
G2nu = new cplx64f[1];
DirDer = new double[1];
MBD1 = new double[1];
MBD2 = new double[1];
DerIdx = new int[1];
AvVis = new int[1];
Tm = new double[1];
doIF = new int[1];
antFit = new int[1];
TAvg = (double) PyInt_AsLong(PyList_GetItem(solints,1));
SolAlgor = (int) PyInt_AsLong(PyList_GetItem(solints,0));
Twins[0] = (int *)PyArray_DATA(PyList_GetItem(flagBas,0));
Twins[1] = (int *)PyArray_DATA(PyList_GetItem(flagBas,1));
Ntwin = PyArray_DIM(PyList_GetItem(flagBas,0),0);
sprintf(message,"There are %i baselines to flag\n",Ntwin);
fprintf(logFile,"%s",message); std::cout<<message; fflush(logFile);
sprintf(message,"Will pre-average the data in chunks of %.1f seconds\n",TAvg);
fprintf(logFile,"%s",message); std::cout<<message; fflush(logFile);
AddParHand = RelWeight>0.0;
AddCrossHand = true;
Lant = (int *)PyArray_DATA(linant);
Nlin = PyArray_DIM(linant,0);
CalAnts = (int *)PyArray_DATA(calant);
NCalAnt = PyArray_DIM(calant,0);
int i,j,k,l;
k=0;
int MaxAnt = 0;
for(i=0;i<NCalAnt;i++){
if(CalAnts[i]>MaxAnt){
MaxAnt=CalAnts[i];
};
};
BasNum = new int*[MaxAnt];
LinBasNum = new int[MaxAnt*(MaxAnt-1)/2];
NLinBas = 0;
bool isCal1, isCal2;
for(i=0;i<MaxAnt;i++){
BasNum[i] = new int[MaxAnt];
for(j=0;j<MaxAnt;j++){
BasNum[i][j] = -1;
};
for(j=i+1;j<MaxAnt;j++){
isCal1=false; isCal2=false;
for(l=0;l<NCalAnt;l++){
if(i==CalAnts[l]-1){isCal1=true;};
if(j==CalAnts[l]-1){isCal2=true;};
};
if (isCal1 && isCal2){
BasNum[i][j] = k;
// printf("Baseline %i-%i will have assigned number %i\n",i+1,j+1,k);
for(l=0;l<Nlin; l++){if(i==Lant[l]-1 || j==Lant[l]-1){LinBasNum[NLinBas]=k; NLinBas += 1; break; };};
k += 1;
};
};
};
printf("There are %i baselines.\n",k);
int BNum;
BasWgt = new double[k];
for(i=0;i<MaxAnt;i++){
for(j=i+1;j<MaxAnt;j++){
BNum = BasNum[i][j];
if (BNum>=0){ //printf("Weighting baselines %i\n",BNum);
BasWgt[BNum] = 1.0;} else {BasWgt[BNum]=0.0;};
for(l=0;l<Ntwin;l++){
if((Twins[0][l]==i+1 && Twins[1][l]==j+1)||(Twins[0][l]==j+1 && Twins[1][l]==i+1)){
printf("Flagging baseline %i\n",BNum); BasNum[i][j] = -1; BasWgt[BNum] = 0.0; break;
};
};
};
};
auxC00 = new cplx64f*[k];
auxC01 = new cplx64f*[k];
auxC10 = new cplx64f*[k];
auxC11 = new cplx64f*[k];
auxC00Flp = new cplx64f*[k];
auxC11Flp = new cplx64f*[k];
UVWeights = new double[k];
for(i=0;i<k;i++){
auxC00[i] = new cplx64f[3*NCalAnt+1];
auxC11[i] = new cplx64f[3*NCalAnt+1];
auxC01[i] = new cplx64f[3*NCalAnt+1];
auxC10[i] = new cplx64f[3*NCalAnt+1];
auxC00Flp[i] = new cplx64f[3*NCalAnt+1];
auxC11Flp[i] = new cplx64f[3*NCalAnt+1];
};
NBas = k;
CrossSpec00 = (cplx64f **) malloc(NBas*sizeof(cplx64f*));
CrossSpec11 = (cplx64f **) malloc(NBas*sizeof(cplx64f*));
for(i=0;i<NBas;i++){
CrossSpec00[i] = (cplx64f *) malloc(MaxChan*sizeof(cplx64f));
CrossSpec11[i] = (cplx64f *) malloc(MaxChan*sizeof(cplx64f));
};
NIF = 0;
// Set Memory:
NVis = (int *) malloc(MAXIF*sizeof(int));
IFNum = (int *) malloc(MAXIF*sizeof(int));
NCVis = (int *) malloc(MAXIF*sizeof(int));
NLVis = (int *) malloc(MAXIF*sizeof(int));
Nchan = (int *) malloc(MAXIF*sizeof(int));
Frequencies = (double **) malloc(MAXIF*sizeof(double*));
Ant1 = (int**) malloc(MAXIF*sizeof(int*));
Ant2 = (int**) malloc(MAXIF*sizeof(int*));
Scan = (int**) malloc(MAXIF*sizeof(int*));
NScan = (int*) malloc(MAXIF*sizeof(int));
Times = (double**) malloc(MAXIF*sizeof(double*));
Weights = (double**) malloc(MAXIF*sizeof(double*));
ScanDur = (double**) malloc(MAXIF*sizeof(double*));
PA1 = (cplx64f**) malloc(MAXIF*sizeof(cplx64f*));
PA2 = (cplx64f**) malloc(MAXIF*sizeof(cplx64f*));
UVGauss = (double**) malloc(MAXIF*sizeof(double*));
RR = (cplx64f***) malloc(MAXIF*sizeof(cplx64f**));
LR = (cplx64f***) malloc(MAXIF*sizeof(cplx64f**));
RL = (cplx64f***) malloc(MAXIF*sizeof(cplx64f**));
LL = (cplx64f***) malloc(MAXIF*sizeof(cplx64f**));
// Rates = (double ***) malloc(MAXIF*sizeof(double**));
for(i=0;i<5;i++){
Rates[i] = (double ***) malloc(MAXIF*sizeof(double**));
Delays[i] = (double ***) malloc(MAXIF*sizeof(double**));
};
PyObject *ret = Py_BuildValue("i",0);
return ret;
};
static PyObject *FreeData(PyObject *self, PyObject *args) {
int i,j;
if (!logFile) logFile = fopen("PolConvert.GainSolve.log","a");
sprintf(message,"Freeing Data NIF = %d\n", NIF);
fprintf(logFile,"%s",message); std::cout<<message; fflush(logFile);
for(i=0;i<NIF;i++){
for(j=0;j<NVis[i]+1;j++){
free(RR[i][j]);free(RL[i][j]);
free(LR[i][j]);free(LL[i][j]);
};
free(Ant1[i]);free(Ant2[i]);free(Scan[i]);free(Times[i]);
free(PA1[i]);free(PA2[i]);free(RR[i]);free(RL[i]);free(UVGauss[i]);
free(LR[i]);free(LL[i]);free(ScanDur[i]);free(Weights[i]);
delete Frequencies[i];
};
delete(UVWeights);
if(NIF>0){
free(NScan);free(Nchan);free(NVis);
free(NCVis);free(NLVis);free(IFNum);
free(Frequencies); free(Scan);
NIF = -1;
PyObject *ret = Py_BuildValue("i",0);
return ret;
};
// Problem with NIF. Returns error:
PyObject *ret = Py_BuildValue("i",1);
return ret;
};
// Read the data in polconvert's binary format.
// In addition, arrange the data in scans.
// MaxDT is the maximum allowed time separation between
// neighboring entries of the same scan (in seconds).
static PyObject *ReadData(PyObject *self, PyObject *args) {
int IFN;
const char *file1, *file2;
std::ifstream CPfile, MPfile;
double MaxDT;
if (!logFile) logFile = fopen("PolConvert.GainSolve.log","a");
fprintf(logFile,"ReadData entered...\n"); fflush(logFile);
if (!PyArg_ParseTuple(args, "issd", &IFN,&file1, &file2,&MaxDT)){
sprintf(message,"Failed ReadData! Check inputs! (return -1)\n");
fprintf(logFile,"%s",message); std::cout<<message; fflush(logFile);
fclose(logFile);
PyObject *ret = Py_BuildValue("i",-1);
return ret;
};
fprintf(logFile,"ReadData parsed...\n"); fflush(logFile);
int i, j, k;
double AuxT, AuxPA1, AuxPA2, AuxUV;
bool is1, is2;
CPfile.open(file1, std::ios::in | std::ios::binary);
MPfile.open(file2, std::ios::in | std::ios::binary);
NIF += 1;
//////////
// Set memory for new IF:
if (NIF > MAXIF){
fprintf(logFile,"(realloc) %d > %d\n", NIF, MAXIF); fflush(logFile);
MAXIF *= 2;
Nchan = (int*) realloc(Nchan,MAXIF*sizeof(int));
Frequencies = (double**) realloc(Frequencies,MAXIF*sizeof(double*));
NVis = (int*) realloc(NVis,MAXIF*sizeof(int));
NCVis = (int*) realloc(NCVis,MAXIF*sizeof(int));
NLVis = (int*) realloc(NLVis,MAXIF*sizeof(int));
IFNum = (int*) realloc(IFNum,MAXIF*sizeof(int));
if(!Nchan || !Frequencies || !NVis || !NCVis || !NLVis || !IFNum){
Nchan=nullptr; Frequencies=nullptr; NVis=nullptr; NCVis=nullptr; NLVis=nullptr; IFNum=nullptr;
fprintf(logFile,"(return -2)"); fflush(logFile);
PyObject *ret = Py_BuildValue("i",-2);
return ret;
};
// Set memory for the visibilities and metadata:
Ant1 = (int**) realloc(Ant1,MAXIF*sizeof(int*));
Ant2 = (int**) realloc(Ant2,MAXIF*sizeof(int*));
Scan = (int**) realloc(Scan,MAXIF*sizeof(int*));
NScan = (int*) realloc(NScan,MAXIF*sizeof(int));
Times = (double**) realloc(Times,MAXIF*sizeof(double*));
Weights = (double**) realloc(Weights,MAXIF*sizeof(double*));
ScanDur = (double**) realloc(ScanDur,MAXIF*sizeof(double*));
PA1 = (cplx64f**) realloc(PA1,MAXIF*sizeof(cplx64f*));
PA2 = (cplx64f**) realloc(PA2,MAXIF*sizeof(cplx64f*));
UVGauss = (double**) realloc(UVGauss,MAXIF*sizeof(double*));
RR = (cplx64f***) realloc(RR,MAXIF*sizeof(cplx64f**));
LR = (cplx64f***) realloc(LR,MAXIF*sizeof(cplx64f**));
RL = (cplx64f***) realloc(RL,MAXIF*sizeof(cplx64f**));
LL = (cplx64f***) realloc(LL,MAXIF*sizeof(cplx64f**));
// Rates = (double ***) realloc(Rates,MAXIF*sizeof(double**));
for(i=0;i<5;i++){
Delays[i] = (double ***) realloc(Delays[i],MAXIF*sizeof(double**));
Rates[i] = (double ***) realloc(Rates[i],MAXIF*sizeof(double**));
};
if(!Ant1 || !Ant2 || !Times || !Weights || !PA1 || !PA2 || !RR || !LR || !RL || !LL){
Ant1=nullptr; Ant2=nullptr; Times=nullptr; PA1=nullptr; PA2=nullptr; UVGauss=nullptr;
RR=nullptr; LR=nullptr; RL=nullptr; LL=nullptr; ScanDur=nullptr; Weights=nullptr;
fprintf(logFile,"(return -3)"); fflush(logFile);
PyObject *ret = Py_BuildValue("i",-3);
return ret;
};
if(!Rates[0] || !Delays[0] || !Delays[1] || !Delays[2] || !Delays[3]){
for(i=0;i<5;i++){Rates[i] = nullptr; Delays[i]=nullptr;};
fprintf(logFile,"(return -4)"); fflush(logFile);
PyObject *ret = Py_BuildValue("i",-4);
return ret;
};
};
//////////
// IF NUMBER:
IFNum[NIF-1] = IFN;
// Number of channels for this IF:
CPfile.read(reinterpret_cast<char*>(&Nchan[NIF-1]), sizeof(int));
fprintf(logFile, "IF%d has %i channels\n",IFN,Nchan[NIF-1]); fflush(logFile);
printf("IF%d (%i) has %i channels\n",IFN,NIF,Nchan[NIF-1]); fflush(stdout);
// Maximum number of channels:
if (Nchan[NIF-1] > MaxChan){
MaxChan=Nchan[NIF-1];
for (i=0; i< NBas; i++) {
CrossSpec00[i] = (cplx64f *) realloc(CrossSpec00[i],MaxChan*sizeof(cplx64f));
CrossSpec11[i] = (cplx64f *) realloc(CrossSpec11[i],MaxChan*sizeof(cplx64f));
if(!CrossSpec00[i] || !CrossSpec11[i]){
CrossSpec00[i]=nullptr; CrossSpec11[i]=nullptr;
fprintf(logFile,"(return -5)"); fflush(logFile);
PyObject *ret = Py_BuildValue("i",-5);
return ret;
};
};
};
// ignores noI
MPfile.ignore(sizeof(int));
// Have we applied parang??
MPfile.read(reinterpret_cast<char*>(&doParang), sizeof(bool));
// Get frequencies for this IF:
Frequencies[NIF-1] = new double[Nchan[NIF-1]];
CPfile.read(reinterpret_cast<char*>(Frequencies[NIF-1]), Nchan[NIF-1]*sizeof(double));
fprintf(logFile,"Freqs. %.8e %.8e\n",
Frequencies[NIF-1][0],Frequencies[NIF-1][Nchan[NIF-1]-1]);
fflush(logFile);
// Number of integration times:
int NDiffTimes = 0;
int TimeBuff = 1000;
double *DiffTimes = (double *) malloc(TimeBuff*sizeof(double));
bool isTime;
// Get Number of visibilities observed by the CalAnts (Circ Pol):
NCVis[NIF-1] = 0;
int AuxA1, AuxA2;
fprintf(logFile,"Reading CPfile...(NCalAnt=%d)\n", NCalAnt); fflush(logFile);
// eof() doesn't do what everyone thinks....
while(!CPfile.eof() && CPfile.peek() >= 0){
is1 = false; is2 = false;
// CPfile.ignore(sizeof(int));
CPfile.ignore(sizeof(double)); // daytemp
CPfile.read(reinterpret_cast<char*>(&AuxA1), sizeof(int));
CPfile.read(reinterpret_cast<char*>(&AuxA2), sizeof(int));
for (i=0; i<NCalAnt; i++) {
if (AuxA1 == CalAnts[i]){is1=true;};
if (AuxA2 == CalAnts[i]){is2=true;};
};
if(is1 && is2 && AuxA1 != AuxA2){
NCVis[NIF-1] += 1;
};
// here we are ignoring all the visibility data
CPfile.ignore(3*sizeof(double)+4*Nchan[NIF-1]*sizeof(cplx32f));
};
fprintf(logFile,"Finished CPfile...\n"); fflush(logFile);
// Get Number of visibilities observed by the CalAnts (Mix Pol):
NLVis[NIF-1] = 0;
fprintf(logFile,"Reading MPfile... (NCalAnt=%d)\n", NCalAnt); fflush(logFile);
// eof() doesn't do what everyone thinks....
while(!MPfile.eof() && MPfile.peek() >= 0){
is1 = false; is2 = false;
MPfile.ignore(sizeof(int));
MPfile.ignore(sizeof(double)); // Time
MPfile.read(reinterpret_cast<char*>(&AuxA1), sizeof(int));
MPfile.read(reinterpret_cast<char*>(&AuxA2), sizeof(int));
for (i=0; i<NCalAnt; i++) {
if (AuxA1 == CalAnts[i]){is1=true;};
if (AuxA2 == CalAnts[i]){is2=true;};
};
if(is1 && is2 && AuxA1 != AuxA2){
NLVis[NIF-1] += 1;
};
MPfile.ignore(3*sizeof(double)+12*Nchan[NIF-1]*sizeof(cplx32f));
};
fprintf(logFile,"Finished MPfile...\n"); fflush(logFile);
// Total number of visibilities:
NVis[NIF-1] = NCVis[NIF-1]+ NLVis[NIF-1];
sprintf(message,"Found %i vis in CPol and %i vis in LPol for a total of %i\n",
NCVis[NIF-1],NLVis[NIF-1],NVis[NIF-1]);
fprintf(logFile,"%s",message); fflush(logFile);
// Set memory for the visibilities:
j = NVis[NIF-1]+1;
Ant1[NIF-1] = (int*) malloc(j*sizeof(int));
Ant2[NIF-1] = (int*) malloc(j*sizeof(int));
Scan[NIF-1] = (int*) malloc(j*sizeof(int));
Times[NIF-1] = (double*) malloc(j*sizeof(double));
Weights[NIF-1] = (double*) malloc(j*sizeof(double));
PA1[NIF-1] = (cplx64f*) malloc(j*sizeof(cplx64f));
PA2[NIF-1] = (cplx64f*) malloc(j*sizeof(cplx64f));
UVGauss[NIF-1] = (double*) malloc(j*sizeof(double));
RR[NIF-1] = (cplx64f**) malloc(j*sizeof(cplx64f*));
LR[NIF-1] = (cplx64f**) malloc(j*sizeof(cplx64f*));
RL[NIF-1] = (cplx64f**) malloc(j*sizeof(cplx64f*));
LL[NIF-1] = (cplx64f**) malloc(j*sizeof(cplx64f*));
for (i=0;i<j;i++){
RR[NIF-1][i] = (cplx64f*) malloc(Nchan[NIF-1]*sizeof(cplx64f));
LR[NIF-1][i] = (cplx64f*) malloc(Nchan[NIF-1]*sizeof(cplx64f));
RL[NIF-1][i] = (cplx64f*) malloc(Nchan[NIF-1]*sizeof(cplx64f));
LL[NIF-1][i] = (cplx64f*) malloc(Nchan[NIF-1]*sizeof(cplx64f));
};
// Rewind files:
CPfile.clear();
CPfile.seekg(sizeof(int)+Nchan[NIF-1]*sizeof(double),CPfile.beg);
MPfile.clear();