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_PolConvert.cpp
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/*
# Copyright (c) Ivan Marti-Vidal 2015-2023.
# EU ALMA Regional Center. Nordic node (Sweden).
# 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 2 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/>,
# or write to the Free Software Foundation, Inc.,
# 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
#
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are
# met:
#
# a. Redistributions of source code must retain the above copyright
# notice, this list of conditions and the following disclaimer.
# b. Redistributions in binary form must reproduce the above copyright
# notice, this list of conditions and the following disclaimer in the
# documentation and/or other materials provided with the
# distribution.
# c. Neither the name of the author nor the names of contributors may
# be used to endorse or promote products derived from this software
# without specific prior written permission.
#
#
#THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
#"AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
#LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
#A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
#OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
#SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
#LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
#DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
#THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
#(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
#OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
#
#
#
*/
//z old code 1, new code 0
//#define IVAN_OLD 1
//z straight up merge
//#define IVAN_MERGE 0
#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 <stdio.h>
#include <sys/types.h>
#include <new>
#include <ctime>
#include <sys/stat.h>
#include <string.h>
#include <dirent.h>
#include <iostream>
#include <fstream>
#include <complex.h>
#include "./DataIO.h"
#include "./DataIOFITS.h"
#include "./DataIOSWIN.h"
#include "./CalTable.h"
#include "./Weighter.h"
#include <sstream>
// 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)
#endif
// and after some hacking
#if PY_MAJOR_VERSION >= 3
#define PyString_AsString(obj) PyUnicode_AsUTF8(obj)
#endif
/* Docstrings */
static char module_docstring[] =
"This module provides an interface for PolConvert.";
static char PolConvert_docstring[] =
"Converts mixed-polarization visibilities into pure circular-polarization basis";
static char setPCMode_docstring[] =
"Sets the running mode to either ALMA (true; the default) or non-ALMA (false).";
/* Available functions */
static PyObject *PolConvert(PyObject *self, PyObject *args);
static PyObject *setPCMode(PyObject *self, PyObject *args);
/* Module specification */
static PyMethodDef module_methods[] = {
{"PolConvert", PolConvert, METH_VARARGS, PolConvert_docstring},
{"setPCMode", setPCMode, METH_VARARGS, setPCMode_docstring},
{NULL, NULL, 0, NULL} /* terminated by list of NULLs, apparently */
};
bool PCMode;
/* Initialize the module */
#if PY_MAJOR_VERSION >= 3
static struct PyModuleDef pc_module_def = {
PyModuleDef_HEAD_INIT,
"_PolConvert", /* 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__PolConvert(void)
{
PCMode = true; /* ALMA mode by default */
PyObject *m = PyModule_Create(&pc_module_def);
return(m);
}
#else
PyMODINIT_FUNC init_PolConvert(void)
{
PCMode = true; /* ALMA mode by default */
PyObject *m = Py_InitModule3("_PolConvert", module_methods, module_docstring);
if (m == NULL)
return;
}
#endif
// Set the mode to non-ALMA, if the argument is 0 (false).
static PyObject *setPCMode(PyObject *self, PyObject *args){
PyObject *ret;
int whichMode;
if (!PyArg_ParseTuple(args, "i",&whichMode)){
printf("FAILED PolConvert! Unable to parse arguments!\n");
fflush(stdout);
ret = Py_BuildValue("i",-1);
return ret;
};
if(whichMode==0){
PCMode=false;
printf("PolConvert interface will change to non-ALMA.\n");
fflush(stdout);
} else {
/* PCMode=true */
printf("PolConvert interface remains in ALMA mode.\n");
fflush(stdout);
};
ret = Py_BuildValue("i",0);
return ret;
};
//////////////////////////////////
// MAIN FUNCTION:
static PyObject *PolConvert(PyObject *self, PyObject *args)
{
static const std::complex<float> oneOverSqrt2 = 0.7071067811;
static const cplx32f Im = cplx32f(0.,1.);
long i,j,k,auxI;
int ii, ij, ik, il, im;
int IFoffset;
// initialization warnings:
PyObject *ngain = nullptr, *nsum = nullptr, *gains = nullptr;
PyObject *ikind = nullptr, *dterms = nullptr, *plotRange;
PyObject *IDI, *antnum, *tempPy, *ret;
PyObject *allphants = nullptr, *nphtimes = nullptr;
PyObject *phanttimes, *Range, *SWAP;
PyObject *doIF, *metadata, *refAnts = nullptr, *ACorrPy, *logNameObj;
PyObject *asdmTimes, *plIF, *isLinearObj, *XYaddObj, *ALMAstuff;
PyObject *antcoordObj, *soucoordObj, *antmountObj, *timeranges;
int nALMA, plAnt, nPhase = 0, doTest, doConj, doNorm;
int calField, verbose, doParI;
int currFile;
double doSolve;
bool isSWIN, doParang;
int AutoCorrMedianWindow;
printf("Parsing arguments\n");
if (!PyArg_ParseTuple(args, "iOiOiiOOOOOidiiOOOOOOiOiiOO",
&nALMA, &plIF, &plAnt, &doIF, &IFoffset, &AutoCorrMedianWindow, // 0-5
&SWAP, &IDI, &antnum, &plotRange, // 6-9
&Range, &doTest, &doSolve, &doConj, // 10-13
&doNorm, &XYaddObj, &metadata, &soucoordObj, // 14-17
&antcoordObj, &antmountObj, &isLinearObj, &calField, //18-21
&ACorrPy, &doParI, &verbose, &logNameObj, &ALMAstuff)) { //22-26
printf("FAILED PolConvert! Unable to parse arguments!\n");
fflush(stdout);
ret = Py_BuildValue("i",-1);
return ret;
};
// Load ALMA-specific stuff
if(PCMode){
nPhase = PyList_Size(PyList_GetItem(ALMAstuff,5));
ngain = PyList_GetItem(ALMAstuff,0);
nsum = PyList_GetItem(ALMAstuff,1);
ikind = PyList_GetItem(ALMAstuff,2);
gains = PyList_GetItem(ALMAstuff,3);
dterms = PyList_GetItem(ALMAstuff,4);
allphants = PyList_GetItem(ALMAstuff,5);
nphtimes = PyList_GetItem(ALMAstuff,6);
phanttimes = PyList_GetItem(ALMAstuff,7);
refAnts = PyList_GetItem(ALMAstuff,8);
asdmTimes = PyList_GetItem(ALMAstuff,9);
timeranges = PyList_GetItem(ALMAstuff,10);
isLinearObj = PyList_GetItem(ALMAstuff,11);
};
// cleanup: isLinearObj from arguments is overridden by ALMAstuff..
// XYaddObj is PrioriGains
doParang = (doParI!=0);
printf("Parsed arguments\n");
// default return value set now in case there is an error:
ret = Py_BuildValue("i",1);
if (verbose){
std::cout<<"\n\n VERBOSE MODE ON\n\n";
fflush(stdout);
};
// OPEN LOG FILE:
char message[2048];
std::string logName = PyString_AsString(logNameObj);
FILE *logFile = fopen(logName.c_str(),"a");
// Echo some calibration information:
if(calField>=0){
sprintf(message,"\nWill use field %i as calibrator/plot\n",calField);
fprintf(logFile,"%s",message); std::cout<<message; fflush(logFile);
} else {
sprintf(message,"\nWill use all fields in the timerange\n");
fprintf(logFile,"%s",message); std::cout<<message; fflush(logFile);
};
// Sort out if SWIN files or FITS-IDI files are gonig to be converted:
// (if the length of the metadata list is zero, this is a FITS-IDI file)
int SWINnIF = (int) PyList_Size(metadata)-1 ;
isSWIN = SWINnIF > 0;
sprintf(message,"\nisSwin is %s\n", isSWIN ? "True" : "False");
fprintf(logFile,"%s",message); std::cout<<message; fflush(logFile);
int nSWINFiles = 1; // compiler warning
std::string* SWINFiles, outputfits;
if (isSWIN) {
nSWINFiles = (int) PyList_Size(IDI) ;
SWINFiles = new std::string[nSWINFiles];
for (ii=0; ii<nSWINFiles; ii++){
SWINFiles[ii] = PyString_AsString(PyList_GetItem(IDI,ii));
sprintf(message,"file[%i] %s\n\n",ii,SWINFiles[ii].c_str());
fprintf(logFile,"%s",message); std::cout<<message; fflush(logFile);
};
sprintf(message,"\nCONVERTING %i SWIN (DiFX) FILES\n\n",nSWINFiles);
fprintf(logFile,"%s",message); std::cout<<message; fflush(logFile);
} else {
SWINFiles = new std::string[nSWINFiles]; // compiler warning
outputfits = PyString_AsString(IDI);
sprintf(message,"\nOUTPUT FITS-IDI FILE: %s \n\n",outputfits.c_str());
fprintf(logFile,"%s",message); std::cout<<message; fflush(logFile);
};
// Specific for ALMA:
double *BadTimes = nullptr;
int NBadTimes = 0;
if(PCMode){
// Time ranges with unphased signal:
BadTimes = (double *)PyArray_DATA(timeranges);
NBadTimes = (int) PyArray_DIM(timeranges,0);
};
// If SWIN, read the frequency channels from the metadata:
int *SWINnchan = nullptr;
double **SWINFreqs = nullptr;
double jd0 = 0.0;
if (isSWIN) {
SWINFreqs = new double*[SWINnIF];
SWINnchan = new int[SWINnIF];
for (ii=0; ii<SWINnIF; ii++) {
SWINFreqs[ii] = (double *)PyArray_DATA(PyList_GetItem(metadata,ii));
SWINnchan[ii] = ((int *) PyArray_DIMS(PyList_GetItem(metadata,ii)))[0] ;
};
jd0 = PyFloat_AsDouble(PyList_GetItem(metadata,SWINnIF));
};
int *ACorrs = (int *)PyArray_DATA(ACorrPy);
// Do we just test?
if (doTest) {
sprintf(message,"\nWill compute, but not update the output file(s)\n");
fprintf(logFile,"%s",message); std::cout<<message; fflush(logFile);
};
// return value if there is an error:
ret = Py_BuildValue("i",1);
// Times to analyse:
double *plRange = (double *)PyArray_DATA(plotRange);
double *doRange = (double *)PyArray_DATA(Range);
// READ PRIORI GAINS:
int NPGain, NPIF;
NPGain = PyList_Size(PyList_GetItem(XYaddObj,0));
NPIF = PyList_Size(PyList_GetItem(PyList_GetItem(XYaddObj,0),0));
sprintf(message,"Array sizes: NPGain = %i NPIF = %i\n", NPGain, NPIF);
fprintf(logFile,"%s",message); std::cout<<message; fflush(logFile);
cplx32f ****PrioriGains = new cplx32f***[nSWINFiles];
for(k=0;k<nSWINFiles;k++){
PrioriGains[k] = new cplx32f **[NPGain];
for (i=0;i<NPGain;i++){
PrioriGains[k][i] = new cplx32f*[NPIF];
for (j=0; j<NPIF; j++){
PrioriGains[k][i][j] = (cplx32f *) PyArray_DATA(PyList_GetItem(PyList_GetItem(PyList_GetItem(XYaddObj,k),i),j));
};
};
};
// Array and Observation Geometry:
ArrayGeometry *Geometry = new ArrayGeometry;
double *AntCoordArr = (double *)PyArray_DATA(antcoordObj);
int *AntMountArr = (int *)PyArray_DATA(antmountObj);
double *SouCoordArr = (double *)PyArray_DATA(PyList_GetItem(soucoordObj,1));
double *SouCoordRA = (double *)PyArray_DATA(PyList_GetItem(soucoordObj,0));
Geometry->NtotSou = (int) PyArray_DIM(PyList_GetItem(soucoordObj,1),0);
Geometry->NtotAnt = (int) PyArray_DIM(antcoordObj,0);
int Nbas = Geometry->NtotAnt*(Geometry->NtotAnt-1)/2;
sprintf(message,"Array sizes: Nbas = %i NtotAnt = %i NtotSou = %i\n",
Nbas, Geometry->NtotAnt, Geometry->NtotSou);
fprintf(logFile,"%s",message); std::cout<<message; fflush(logFile);
Geometry->BaseLine[0] = new double[Nbas+Geometry->NtotAnt+1];
Geometry->BaseLine[1] = new double[Nbas+Geometry->NtotAnt+1];
Geometry->BaseLine[2] = new double[Nbas+Geometry->NtotAnt+1];
Geometry->SinDec = new double[Geometry->NtotSou];
Geometry->CosDec = new double[Geometry->NtotSou];
Geometry->RA = new double[Geometry->NtotSou];
Geometry->AntLon = new double[Geometry->NtotAnt];
Geometry->Mount = new int[Geometry->NtotAnt];
Geometry->Lat = new double[Geometry->NtotAnt];
Geometry->BasNum = new int*[Geometry->NtotAnt];
for (i=0; i<Geometry->NtotAnt;i++){
Geometry->BasNum[i] = new int[Geometry->NtotAnt];
};
int Inum = 1, I3, J3;
double RR;
for (i=0; i<Geometry->NtotAnt;i++){
I3 = 3*i;
Geometry->AntLon[i] = atan2(AntCoordArr[I3+1],AntCoordArr[I3]);
RR = sqrt(AntCoordArr[I3]*AntCoordArr[I3] + AntCoordArr[I3+1]*AntCoordArr[I3+1]) ;
Geometry->Lat[i] = atan2(AntCoordArr[I3+2],RR);
Geometry->Mount[i] = AntMountArr[i];
for (j=i; j<Geometry->NtotAnt;j++){
J3 = 3*j;
Geometry->BasNum[i][j] = Inum;
Geometry->BasNum[j][i] = -Inum;
Geometry->BaseLine[0][Inum] = (AntCoordArr[I3] - AntCoordArr[J3]);
Geometry->BaseLine[1][Inum] = (AntCoordArr[I3+1] - AntCoordArr[J3+1]);
Geometry->BaseLine[2][Inum] = (AntCoordArr[I3+2] - AntCoordArr[J3+2]);
Inum += 1;
};
};
for (i=0; i<Geometry->NtotSou;i++){
Geometry->SinDec[i] = sin(SouCoordArr[i]);
Geometry->CosDec[i] = cos(SouCoordArr[i]);
Geometry->RA[i] = SouCoordRA[i];
};
// Read info for linear-polarization antennas:
double *time0, *time1;
long nASDMEntries;
int *ASDMant, *ALMARef;
double **ASDMtimes;
long *nASDMtimes;
Weighter *ALMAWeight;
////////////////////////////////////////////////
/////////////////////////////////
/// SPECIFIC FOR ALMA:
if(PCMode){
time0 = (double *)PyArray_DATA(PyList_GetItem(asdmTimes,0));
time1 = (double *)PyArray_DATA(PyList_GetItem(asdmTimes,1));
nASDMEntries = ((long *) PyArray_DIMS(PyList_GetItem(asdmTimes,0)))[0];
///////////
// Useful to determine which ALMA antennas are phased up at each time:
sprintf(message,"Array sizes: nPhase = %i nALMA = %i\n", nPhase, nALMA);
fprintf(logFile,"%s",message); std::cout<<message; fflush(logFile);
ASDMant = new int[nPhase];
ASDMtimes = new double*[nPhase];
nASDMtimes = new long[nPhase];
// refAnts may be used uninitialized
ALMARef = (int *)PyArray_DATA(refAnts);
for (ii=0; ii<nPhase; ii++){
nASDMtimes[ii] = (long)PyInt_AsLong(PyList_GetItem(nphtimes,ii));
ASDMant[ii] = (int)PyInt_AsLong(PyList_GetItem(allphants,ii));
ASDMtimes[ii] = (double *)PyArray_DATA(PyList_GetItem(phanttimes,ii));
};
// BadTimes not initialized
ALMAWeight = new Weighter(nPhase,nASDMtimes,nASDMEntries,ASDMant,ASDMtimes,ALMARef,time0,time1,BadTimes, NBadTimes, logFile);
} else { // If ALMA is not used, set weights to dummy:
ALMAWeight = new Weighter(logFile);
};
///////////
//////////////////////////////////////////////
// ALLOCATE MEMORY
int **kind = new int*[nALMA];
bool **isLinear = new bool*[nALMA];
int *ngainTabs = new int[nALMA];
int *almanums = new int[nALMA];
int *nsumArr = new int[nALMA];
long ***ntimeArr = new long**[nALMA];
long **nchanArr = new long*[nALMA];
double ***freqsArr = new double**[nALMA];
double ****timesArr = new double***[nALMA];
double ****gainsArrR1 = new double***[nALMA];
double ****gainsArrI1 = new double***[nALMA];
double ****gainsArrR2 = new double***[nALMA];
double ****gainsArrI2 = new double***[nALMA];
bool ****gainflag = new bool***[nALMA];
long *nchanDt = new long[nALMA];
long **ndttimeArr = new long*[nALMA];
double **dtfreqsArr = new double*[nALMA];
double ***dttimesArr = new double**[nALMA];
double ***dtermsArrR1 = new double**[nALMA];
double ***dtermsArrI1 = new double**[nALMA];
double ***dtermsArrR2 = new double**[nALMA];
double ***dtermsArrI2 = new double**[nALMA];
bool ***dtflag = new bool**[nALMA];
bool *XYSWAP = new bool[nALMA];
for (i=0;i<nALMA;i++){
isLinear[i] = (bool *)PyArray_DATA(PyList_GetItem(isLinearObj,i));
almanums[i] = (int)PyInt_AsLong(PyList_GetItem(antnum,i));
XYSWAP[i] = (bool)PyInt_AsLong(PyList_GetItem(SWAP,i));
if(XYSWAP[i]){
sprintf(message,"\nWill swap X/Y channels for antenna #%i.\n",
almanums[i]);
fprintf(logFile,"%s",message); std::cout<<message; fflush(logFile);
};
// Arrays with gain information. If ALMA is not used, we set them to
// summy values:
if(PCMode){
ngainTabs[i] = (int)PyInt_AsLong(PyList_GetItem(ngain,i));
kind[i] = new int[ngainTabs[i]];
nsumArr[i] = (int)PyInt_AsLong(PyList_GetItem(nsum,i));
ntimeArr[i] = new long*[ngainTabs[i]];
nchanArr[i] = new long[ngainTabs[i]];
timesArr[i] = new double**[ngainTabs[i]];
gainsArrR1[i] = new double**[ngainTabs[i]];
gainsArrI1[i] = new double**[ngainTabs[i]];
gainsArrR2[i] = new double**[ngainTabs[i]];
gainsArrI2[i] = new double**[ngainTabs[i]];
gainflag[i] = new bool**[ngainTabs[i]];
freqsArr[i] = new double*[ngainTabs[i]];
} else {
ngainTabs[i] = 1;
nsumArr[i] = 1;
};
};
//////////////////////////////////////////////
//////////////////////////////////////////////
// READ CALIBRATION TABLES (ALMA CASE):
if(PCMode){
for (i=0;i<nALMA;i++){
nchanDt[i] = PyArray_DIM(PyList_GetItem(PyList_GetItem(dterms,i),0),0);
dtfreqsArr[i] = (double *)PyArray_DATA(PyList_GetItem(PyList_GetItem(dterms,i),0));
dttimesArr[i] = new double*[nsumArr[i]];
ndttimeArr[i] = new long[nsumArr[i]];
dtflag[i] = new bool*[nsumArr[i]];
dtermsArrR1[i] = new double*[nsumArr[i]];
dtermsArrI1[i] = new double*[nsumArr[i]];
dtermsArrR2[i] = new double*[nsumArr[i]];
dtermsArrI2[i] = new double*[nsumArr[i]];
for (j=0;j<nsumArr[i];j++){
dttimesArr[i][j] = new double[1];
dttimesArr[i][j][0] = 0.0;
ndttimeArr[i][j] = 1;
dtermsArrR1[i][j] = (double *)PyArray_DATA(
PyList_GetItem(PyList_GetItem(PyList_GetItem(dterms,i),j+1),0));
dtermsArrI1[i][j] = (double *)PyArray_DATA(
PyList_GetItem(PyList_GetItem(PyList_GetItem(dterms,i),j+1),1));
dtermsArrR2[i][j] = (double *)PyArray_DATA(
PyList_GetItem(PyList_GetItem(PyList_GetItem(dterms,i),j+1),2));
dtermsArrI2[i][j] = (double *)PyArray_DATA(
PyList_GetItem(PyList_GetItem(PyList_GetItem(dterms,i),j+1),3));
dtflag[i][j] = (bool *)PyArray_DATA(
PyList_GetItem(PyList_GetItem(PyList_GetItem(dterms,i),j+1),4));
};
for (j=0; j<ngainTabs[i]; j++){
tempPy = PyList_GetItem(PyList_GetItem(gains,i),j);
kind[i][j] = (int)PyInt_AsLong(PyList_GetItem(PyList_GetItem(ikind,i),j));
nchanArr[i][j] = PyArray_DIM(PyList_GetItem(tempPy,0),0);
freqsArr[i][j] = (double *)PyArray_DATA(PyList_GetItem(tempPy,0));
ntimeArr[i][j] = new long[nsumArr[i]];
timesArr[i][j] = new double*[nsumArr[i]];
gainsArrR1[i][j] = new double*[nsumArr[i]];
gainsArrI1[i][j] = new double*[nsumArr[i]];
gainsArrR2[i][j] = new double*[nsumArr[i]];
gainsArrI2[i][j] = new double*[nsumArr[i]];
gainflag[i][j] = new bool*[nsumArr[i]];
for (k=0; k<nsumArr[i]; k++){
ntimeArr[i][j][k] = PyArray_DIM(PyList_GetItem(PyList_GetItem(tempPy,k+1),0),0);
timesArr[i][j][k] = (double *)PyArray_DATA(
PyList_GetItem(PyList_GetItem(tempPy,k+1),0));
gainsArrR1[i][j][k] = (double *)PyArray_DATA(
PyList_GetItem(PyList_GetItem(tempPy,k+1),1));
gainsArrI1[i][j][k] = (double *)PyArray_DATA(
PyList_GetItem(PyList_GetItem(tempPy,k+1),2));
gainsArrR2[i][j][k] = (double *)PyArray_DATA(
PyList_GetItem(PyList_GetItem(tempPy,k+1),3));
gainsArrI2[i][j][k] = (double *)PyArray_DATA(
PyList_GetItem(PyList_GetItem(tempPy,k+1),4));
gainflag[i][j][k] = (bool *)PyArray_DATA(
PyList_GetItem(PyList_GetItem(tempPy,k+1),5));
};
};
};
};
// ALLOCATE MEMORY FOR CALIBRATION INSTANCES:
CalTable ***allgains = new CalTable**[nALMA];
CalTable **alldterms = new CalTable*[nALMA];
// CREATE CALIBRATION INSTANCES:
for (i=0; i<nALMA; i++){
allgains[i] = new CalTable*[ngainTabs[i]];
// ALMA CASE: ACTUAL CALIBRATION INFORMATION OF THE PHASED ARRAY:
if(PCMode){
alldterms[i] = new CalTable(2,dtermsArrR1[i],dtermsArrI1[i],
dtermsArrR2[i],dtermsArrI2[i],dtfreqsArr[i],dttimesArr[i],
nsumArr[i],ndttimeArr[i], nchanDt[i],dtflag[i],true,logFile,
false); // verbose);
for (j=0; j<ngainTabs[i];j++){
/*
printf("CALLING GAIN %i WITH %i\n",j,kind[i][j]);fflush(stdout);
printf("GAINS R1: %.3e\n",gainsArrR1[i][j][0][0]);
printf("GAINS I1: %.3e\n",gainsArrI1[i][j][0][0]);
printf("GAINS R2: %.3e\n",gainsArrR2[i][j][0][0]);
printf("GAINS I2: %.3e\n",gainsArrI2[i][j][0][0]);
printf("FREQS: %.3e\n",freqsArr[i][j][0]);
printf("TIMES: %.3e\n",timesArr[i][j][0][0]);
printf("NA: %i\n",nsumArr[i]);
printf("NTI: %i\n",ntimeArr[i][j][0]);
printf("FG: %i\n",gainflag[i][j][0][0]);
printf("IL: %i\n",isLinear[i][j]);
*/
allgains[i][j] = new CalTable(kind[i][j],gainsArrR1[i][j],
gainsArrI1[i][j],gainsArrR2[i][j],gainsArrI2[i][j],freqsArr[i][j],
timesArr[i][j],nsumArr[i],ntimeArr[i][j], nchanArr[i][j],
gainflag[i][j],isLinear[i][j],logFile,
false); // verbose);
};
// NON-ALMA CASE: DUMMY GAINS.
} else {
alldterms[i] = new CalTable(2,logFile);
allgains[i][0] = new CalTable(0,logFile);
};
};
fflush(logFile);
/////////////////////////////////
// READ VLBI DATA:
// How many IFs do we convert?
int nIFconv = (int) PyList_Size(doIF) ;
bool doAll = false;
// How many IFs do we plot?
int nIFplot = (int) PyList_Size(plIF) ;
int IFs2Plot[nIFplot];
for (ii=0; ii<nIFplot; ii++) {
IFs2Plot[ii] = (int)PyInt_AsLong(PyList_GetItem(plIF,ii)) - 1;
};
// If no IF list was given, convert all of them:
// if (nIFconv==0){nIFconv = DifXData->getNfreqs(); doAll=true;};
// Which IFs do we convert?
int IFs2Conv[nIFconv];
for (ii=0; ii<nIFconv; ii++) {
if (doAll){IFs2Conv[ii]=ii;} else {
IFs2Conv[ii] = (int)PyInt_AsLong(PyList_GetItem(doIF,ii)) - 1;
};
};
DataIO *DifXData ; // Polymorphism to SWIN or FITS-IDI.
bool OverWrite= true; // Always force overwrite (for now)
bool iDoSolve = doSolve >= 0.0;
if (isSWIN) {
sprintf(message,"\n\n Opening and preparing SWIN files.\n");
fprintf(logFile,"%s",message); std::cout<<message; fflush(logFile);
DifXData = new DataIOSWIN(nSWINFiles, SWINFiles, nALMA,
almanums, doRange, SWINnIF, SWINnchan, nIFconv, IFs2Conv, IFoffset, AutoCorrMedianWindow, ACorrs, SWINFreqs,
OverWrite, doTest, iDoSolve, calField, jd0, Geometry, doParang, logFile);
} else {
sprintf(message,"\n\n Opening FITS-IDI file and reading header.\n");
fprintf(logFile,"%s",message); std::cout<<message; fflush(logFile);
DifXData = new DataIOFITS(outputfits, nALMA, almanums,
doRange, nIFconv, IFs2Conv, OverWrite, doConj, iDoSolve, calField, Geometry, doParang, logFile);
};
if(!DifXData->succeed()){
sprintf(message,"\nERROR WITH DATA FILE(S)!\n");
fprintf(logFile,"%s",message); std::cout<<message; fflush(logFile);
ret = Py_BuildValue("i",-1);
return ret;
};
sprintf(message,"\n\nFirst observing Julian day: %11.2f\n",DifXData->getDay0());
fprintf(logFile,"%s",message); std::cout<<message; fflush(logFile);
int nnu = DifXData->getNfreqs();
int ALMARefAnt = -1; // If no calAPP is used, do not look for any extra X-Y phase offset.
int nchans[nnu];
int maxnchan=0;
for (ii=0; ii<nnu; ii++) {
nchans[ii] = DifXData->getNchan(ii);
if (nchans[ii]>maxnchan) {maxnchan=nchans[ii];};
};
sprintf(message,"\n The VLBI IFs have a maximum of %i channels\n",maxnchan);
fprintf(logFile,"%s",message); std::cout<<message; fflush(logFile);
/////////////////////////////////
/////////////////////////////////
// ALLOCATE MEMORY FOR CALIBRATION MATRICES:
double DifXFreqs[maxnchan];
// Gains:
std::complex<float> ***AnG[nALMA], ***AnDt[nALMA];
bool *Weight[nALMA];
// K matrix (beware: 3rd dimension of the matrix elements is now real/imag; not X/Y!):
std::complex<float> **K[nALMA][2][2];
// part of K matrix that is unlikely to change much with time (i.e., BP, D-terms, X/Y delay):
std::complex<float> **Kfrozen[nALMA][2][2];
// Ktotal will be the calibration+conversion matrix (i.e., just multiply V by it, to get final V):
std::complex<float> *Ktotal[nALMA][2][2];
for (ij=0; ij<nALMA; ij++) {
auxI = nsumArr[ij];
AnG[ij] = new std::complex<float> **[auxI];
AnDt[ij] = new std::complex<float> **[auxI];
Weight[ij] = new bool [auxI];
for (ii=0; ii<auxI; ii++) {
AnG[ij][ii] = new std::complex<float> *[2];
AnG[ij][ii][0] = new std::complex<float>[maxnchan];
AnG[ij][ii][1] = new std::complex<float>[maxnchan];
AnDt[ij][ii] = new std::complex<float> *[2];
AnDt[ij][ii][0] = new std::complex<float>[maxnchan];
AnDt[ij][ii][1] = new std::complex<float>[maxnchan];
};
// K matrix:
for (ii=0; ii<2; ii++) {
for (ik=0; ik<2; ik++) {
K[ij][ii][ik] = new std::complex<float> *[auxI];
Kfrozen[ij][ii][ik] = new std::complex<float> *[auxI];
Ktotal[ij][ii][ik] = new std::complex<float>[maxnchan];
for (il=0; il<auxI; il++) {
K[ij][ii][ik][il] = new std::complex<float>[maxnchan];
Kfrozen[ij][ii][ik][il] = new std::complex<float>[maxnchan];
};
};
};
};
// Some extra auxiliary variables:
double currT, lastTFailed;
int currAnt, currAntIdx, currNant, otherAnt,currF;
bool notinlist, gchanged=true, dtchanged=true, toconj;
lastTFailed = 0.0;
long countNvis;
std::complex<float> AD, BC, auxD;
auxD = 0.0;
float NormFac[2];
float AntTab;
std::complex<float> DetInv;
std::complex<float> Kinv[2][2];
std::complex<float> H[2][2];
std::complex<float> HSw[2][2];
H[0][0] = 1.; H[0][1] = Im;
H[1][0] = 1.; H[1][1] = -Im;
HSw[0][0] = Im; HSw[0][1] = 1.;
HSw[1][0] = -Im; HSw[1][1] = 1.;
std::complex<float> gainXY[2];
std::complex<float> gainRatio[maxnchan];
std::complex<float> absGainRatio;
bool allflagged, auxB1, auxB2, Phased ;
sprintf(message,"\n Will modify %li visibilities (lin-lin counted twice).\n\n",
DifXData->getMixedNvis());
fprintf(logFile,"%s",message); std::cout<<message; fflush(logFile);
// TIME RANGE FOR PLOTTING:
plRange[0] = ((plRange[0]+DifXData->getDay0())-2400000.5)*86400.;
plRange[1] = ((plRange[1]+DifXData->getDay0())-2400000.5)*86400.;
// TIME RANGE FOR CORRECTING:
doRange[0] = ((doRange[0]+DifXData->getDay0())-2400000.5)*86400.;
doRange[1] = ((doRange[1]+DifXData->getDay0())-2400000.5)*86400.;
/////////////////////////////////
FILE **plotFile = new FILE*[nIFplot+nIFconv]();
FILE *gainsFile = (FILE*)0;
// Prepare plotting or solving files:
// In the ALMA case, IFs2Plot holds the subset of IFs to plot;
// in the non-ALMA case, we need to create all of them for solving.
int noI = -1;
// Only generate these files if the plotting time range is within the
// conversion time range:
if (plRange[0]!= plRange[1] && plRange[0]<=doRange[1] && plRange[1]>=doRange[0]) {
// We have added a new boolean to the header (which states whether the
// parallactic angle correction has been applied).
if (PCMode) {
for (ii=0; ii<nIFplot; ii++) { // ALMA plot case
sprintf(message,"POLCONVERT.FRINGE/POLCONVERT.FRINGE_IF%i",IFs2Plot[ii]+1);
fprintf(logFile,"%s",message); std::cout<<message; fflush(logFile);
printf("Writing %s\n", message);
plotFile[ii] = fopen(message,"wb");
if (!plotFile[ii]) {
sprintf(message,"Could not create PCMode plot file "
"POLCONVERT.FRINGE/POLCONVERT.FRINGE_IF%i, errno %d\n", IFs2Plot[ii]+1, errno);
fprintf(logFile,"%s",message); std::cout<<message; fflush(logFile);
};
if (IFs2Plot[ii]>=0 && IFs2Plot[ii]<nnu){
fwrite(&nchans[IFs2Plot[ii]],sizeof(int),1,plotFile[ii]);
} else {
fwrite(&noI,sizeof(int),1,plotFile[ii]);
};
fwrite(&doParang,sizeof(bool),1,plotFile[ii]);
};
} else {
for (ii=0; ii<nIFconv; ii++) { // non-ALMA solve case
sprintf(message,"POLCONVERT.FRINGE/POLCONVERT.FRINGE_IF%i",IFs2Conv[ii]+1);
printf("Writing %s\n", message);
plotFile[ii] = fopen(message,"wb");
if (!plotFile[ii]) {
sprintf(message,"Could not create plot non-PCMode file "
"POLCONVERT.FRINGE/POLCONVERT.FRINGE_IF%i, errno %d\n", IFs2Conv[ii]+1, errno);
fprintf(logFile,"%s\n",message); std::cout<<message; fflush(logFile);
};
if (IFs2Conv[ii]>=0 && IFs2Conv[ii]<nnu){
fwrite(&nchans[IFs2Conv[ii]],sizeof(int),1,plotFile[ii]);
} else {
fwrite(&noI,sizeof(int),1,plotFile[ii]);
};
fwrite(&doParang,sizeof(bool),1,plotFile[ii]);
};
};
} else {;
// let the human know why nothing was plotted
sprintf(message,"not plotted: %lg != %lg && %lg <= %lg && %lg >= %lg violated",
plRange[0], plRange[1], plRange[0], doRange[1], plRange[1], doRange[0]);
fprintf(logFile,"%s",message); std::cout<<message; fflush(logFile);
}
if(doNorm){
printf("CREATING GAIN FILE.\n");
sprintf(message,"POLCONVERT.GAINS opened for writing");
fprintf(logFile,"%s",message); std::cout<<message; fflush(logFile);
gainsFile = fopen("POLCONVERT.GAINS","wb");
};
sprintf(message,"\n POLCONVERTING THE DATA.\n\n");
fprintf(logFile,"%s",message); std::cout<<message; fflush(logFile);
/////////////////////////////////////
// APPLY AUTO-CORRELATIONS CORRECTION:
for (currAntIdx=0; currAntIdx<nALMA; currAntIdx++) {
for (k=0;k<nSWINFiles;k++){
for (im=0; im<nIFconv; im++) {
ii = IFs2Conv[im];
for (ij=0; ij<nchans[ii]; ij++){
PrioriGains[k][currAntIdx][im][ij] *=
DifXData->getAmpRatio(currAntIdx, ii, ij);
// DifXData->getAmpRatio(currAntIdx, im, ij);
};
};
};
};
//////////////////////////////////////////////////////////
///////////////////////////////////
// MAIN LOOP FOR CORRECTION (LOOP OVER IFs):
////////////////////////////////////
// Start of iteration over IFs
////////////////////////////////////
for (im=0; im<nIFconv; im++) {
ii = IFs2Conv[im];
int IFplot = -1; // flags the no-plot case of ALMA mode
char pltmsg[20];
for (ij=0; ij<nIFplot; ij++){
if (IFs2Plot[ij]==ii){IFplot=ij; break;};
};
if (PCMode && IFplot < 0) { sprintf(pltmsg, "not plotted"); }
else if (PCMode) { sprintf(pltmsg, "fringe plot"); }