From 84d10ce3879b5cf4f5f9d4c3de9f7c70e6e32b78 Mon Sep 17 00:00:00 2001
From: Adriaan Renting <renting@astron.nl>
Date: Thu, 18 Oct 2007 03:03:24 +0000
Subject: [PATCH] BugId: 1114 Initial check in
---
.../CS1_BinningFlagger.spec.in | 160 +++++++
Appl/CEP/CS1/CS1_BinningFlagger/Makefile.am | 15 +
Appl/CEP/CS1/CS1_BinningFlagger/configure.in | 61 +++
.../FlaggerProcessControl.h | 84 ++++
.../include/CS1_BinningFlagger/Makefile.am | 3 +
.../CS1_BinningFlagger/include/Makefile.am | 3 +
Appl/CEP/CS1/CS1_BinningFlagger/package.dox | 2 +
.../CS1_BinningFlagger/src/BinningFlagger.cc | 404 ++++++++++++++++++
.../CS1_BinningFlagger/src/BinningFlagger.h | 94 ++++
.../CEP/CS1/CS1_BinningFlagger/src/Flagger.cc | 48 +++
.../src/FlaggerProcessControl.cc | 147 +++++++
.../CEP/CS1/CS1_BinningFlagger/src/MS_File.cc | 182 ++++++++
Appl/CEP/CS1/CS1_BinningFlagger/src/MS_File.h | 68 +++
.../CS1/CS1_BinningFlagger/src/Makefile.am | 12 +
.../test/CS1_BinningFlagger.parset | 8 +
.../CS1/CS1_BinningFlagger/test/Makefile.am | 25 ++
16 files changed, 1316 insertions(+)
create mode 100644 Appl/CEP/CS1/CS1_BinningFlagger/CS1_BinningFlagger.spec.in
create mode 100644 Appl/CEP/CS1/CS1_BinningFlagger/Makefile.am
create mode 100644 Appl/CEP/CS1/CS1_BinningFlagger/configure.in
create mode 100644 Appl/CEP/CS1/CS1_BinningFlagger/include/CS1_BinningFlagger/FlaggerProcessControl.h
create mode 100644 Appl/CEP/CS1/CS1_BinningFlagger/include/CS1_BinningFlagger/Makefile.am
create mode 100644 Appl/CEP/CS1/CS1_BinningFlagger/include/Makefile.am
create mode 100644 Appl/CEP/CS1/CS1_BinningFlagger/package.dox
create mode 100644 Appl/CEP/CS1/CS1_BinningFlagger/src/BinningFlagger.cc
create mode 100644 Appl/CEP/CS1/CS1_BinningFlagger/src/BinningFlagger.h
create mode 100644 Appl/CEP/CS1/CS1_BinningFlagger/src/Flagger.cc
create mode 100644 Appl/CEP/CS1/CS1_BinningFlagger/src/FlaggerProcessControl.cc
create mode 100644 Appl/CEP/CS1/CS1_BinningFlagger/src/MS_File.cc
create mode 100644 Appl/CEP/CS1/CS1_BinningFlagger/src/MS_File.h
create mode 100644 Appl/CEP/CS1/CS1_BinningFlagger/src/Makefile.am
create mode 100644 Appl/CEP/CS1/CS1_BinningFlagger/test/CS1_BinningFlagger.parset
create mode 100644 Appl/CEP/CS1/CS1_BinningFlagger/test/Makefile.am
diff --git a/Appl/CEP/CS1/CS1_BinningFlagger/CS1_BinningFlagger.spec.in b/Appl/CEP/CS1/CS1_BinningFlagger/CS1_BinningFlagger.spec.in
new file mode 100644
index 00000000000..6fe5095bc3c
--- /dev/null
+++ b/Appl/CEP/CS1/CS1_BinningFlagger/CS1_BinningFlagger.spec.in
@@ -0,0 +1,160 @@
+# -*- Mode:rpm-spec -*-
+# CS1_Generator.spec.in
+#
+
+##############################################################################
+#
+# Preamble
+#
+##############################################################################
+
+Summary: CS1_Flagger is a small program to do flagging for the offline pipeline of CS1
+
+%define release @RPM_RELEASE@
+%define version @VERSION@
+%define pkgname @PACKAGE@
+%define pkgdir %{pkgname}-%{version}-%{release}
+%define prefix /opt/lofar
+%define configure_args @RPM_CONFIGURE_ARGS@
+##define build_kernel_version @BUILD_KERNEL_VERSION@
+
+Name: %{pkgname}
+Version: %{version}
+Release: %{release}
+Copyright: LGPL
+Group: Application/System
+Source: %{pkgname}-%{version}.tar.gz
+BuildRoot: %{_tmppath}/%{pkgdir}-root
+URL: http://www.astron.nl/~renting
+Prefix: %{prefix}
+BuildArchitectures: i386 # Target platforms, i.e., i586
+##Requires: Common = 1.2 ## define dependent packages here
+Packager: %{packager}
+Distribution: The LOFAR project
+Vendor: ASTRON
+
+AutoReqProv: no
+
+%description
+
+CS1_Flagger More detailed desciprion will follow.
+
+##############################################################################
+#
+# prep
+#
+##############################################################################
+%prep
+echo $prefix
+
+# create the build directory, untar the source
+%setup
+
+##############################################################################
+#
+# build
+#
+##############################################################################
+%build
+./configure %{configure_args} --prefix=%{prefix} && make
+
+##############################################################################
+#
+# install
+#
+##############################################################################
+%install
+# To make things work with BUILDROOT
+if [ "$RPM_BUILD_ROOT" != "%{_tmppath}/%{pkgdir}-root" ]
+then
+ echo
+ echo @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ echo @ @
+ echo @ RPM_BUILD_ROOT is not what I expected. Please clean it yourself. @
+ echo @ @
+ echo @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ echo
+else
+ echo Cleaning RPM_BUILD_ROOT: "$RPM_BUILD_ROOT"
+ rm -rf "$RPM_BUILD_ROOT"
+fi
+mkdir -p $RPM_BUILD_ROOT%{prefix}
+make DESTDIR="$RPM_BUILD_ROOT" install
+
+#uninstall
+
+##############################################################################
+#
+# verify
+#
+##############################################################################
+#verify
+
+##############################################################################
+#
+# clean
+#
+##############################################################################
+%clean
+# Call me paranoid, but I do not want to be responsible for nuking
+# someone's harddrive!
+if [ "$RPM_BUILD_ROOT" != "%{_tmppath}/%{pkgdir}-root" ]
+then
+ echo
+ echo @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ echo @ @
+ echo @ RPM_BUILD_ROOT is not what I expected. Please clean it yourself. @
+ echo @ @
+ echo @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ echo
+else
+ echo Cleaning RPM_BUILD_ROOT: "$RPM_BUILD_ROOT"
+ rm -rf "$RPM_BUILD_ROOT"
+fi
+
+##############################################################################
+#
+# files
+#
+##############################################################################
+
+# empty 'files' means all distributed files
+%files
+%defattr(-, root, root)
+%{prefix}
+
+# Your application file list goes here
+# %{prefix}/lib/lib*.so*
+
+# Documentation
+# doc COPYING ChangeLog README AUTHORS NEWS
+# doc doc/*
+
+# link the module to the correct path
+%post
+
+# before uninstall
+%preun
+
+# after uninstall
+%postun
+
+##############################################################################
+#
+# package devel
+#
+##############################################################################
+
+#package devel
+#Summary: Development files for %{pkgname}
+#Group: Applications/System
+#description devel
+#Development files for %{pkgname}.
+
+#files devel
+
+# Your development files go here
+# Programmers documentation goes here
+#doc doc
+
+# end of file
diff --git a/Appl/CEP/CS1/CS1_BinningFlagger/Makefile.am b/Appl/CEP/CS1/CS1_BinningFlagger/Makefile.am
new file mode 100644
index 00000000000..f3f5bdd622c
--- /dev/null
+++ b/Appl/CEP/CS1/CS1_BinningFlagger/Makefile.am
@@ -0,0 +1,15 @@
+SUBDIRS=src test include
+
+pkgextdir = $(prefix)/config/$(PACKAGE)
+pkgext_DATA = pkgext pkgextcppflags pkgextcxxflags pkgextldflags
+
+DISTCHECK_CONFIGURE_FLAGS= \
+ --with-common=$(prefix) \
+ --with-aips++
+
+EXTRA_DIST = \
+ Makefile.common \
+ CS1_BinningFlagger.spec \
+ autoconf_share/compiletool
+
+include $(top_srcdir)/Makefile.common
diff --git a/Appl/CEP/CS1/CS1_BinningFlagger/configure.in b/Appl/CEP/CS1/CS1_BinningFlagger/configure.in
new file mode 100644
index 00000000000..d39ea993207
--- /dev/null
+++ b/Appl/CEP/CS1/CS1_BinningFlagger/configure.in
@@ -0,0 +1,61 @@
+dnl
+dnl Process this file with autoconf to produce a configure script.
+dnl
+AC_INIT
+AM_CONFIG_HEADER(config.h)
+AM_INIT_AUTOMAKE(CS1_BinningFlagger, 1.0, no-define)
+
+dnl Initialize for LOFAR (may set compilers)
+lofar_INIT
+
+dnl Checks for programs.
+AC_LANG_CPLUSPLUS
+AC_PROG_CXX
+AC_PROG_LIBTOOL
+
+dnl Checks for libraries.
+
+dnl dnl Replace `main' with a function in -lfl:
+dnl AC_CHECK_LIB(fl, main)
+dnl dnl Replace `main' with a function in -lcosev_r:
+dnl AC_CHECK_LIB(cosev_r, main)
+dnl dnl Replace `main' with a function in -lcosnm_r:
+dnl AC_CHECK_LIB(cosnm_r, main)
+dnl dnl Replace `main' with a function in -lorb_r:
+dnl AC_CHECK_LIB(orb_r, main)
+dnl dnl Replace `main' with a function in -lpthread:
+dnl AC_CHECK_LIB(pthread, main)
+dnl dnl Replace `main' with a function in -lvport_r:
+dnl AC_CHECK_LIB(vport_r, main)
+
+dnl Checks for header files.
+AC_HEADER_STDC
+AC_CHECK_HEADERS(unistd.h)
+
+dnl Checks for typedefs, structures, and compiler characteristics.
+AC_C_CONST
+AC_TYPE_SIZE_T
+
+dnl Checks for library functions.
+AC_FUNC_VPRINTF
+
+dnl
+dnl Check for LOFAR specific things
+dnl
+lofar_GENERAL(1)
+lofar_AIPSPP(1)
+lofar_INTERNAL(LCS/ACC/PLC,PLC,,1,PLC/ProcessControl.h)
+lofar_INTERNAL(LCS/ACC/APS,APS,,1,APS/ParameterSet.h)
+lofar_EXTERNAL(boost,1,boost/logic/tribool.hpp,"")
+
+dnl
+dnl Output Makefiles
+dnl
+AC_OUTPUT(
+include/Makefile
+include/CS1_BinningFlagger/Makefile
+src/Makefile
+test/Makefile
+Makefile
+CS1_BinningFlagger.spec
+)
diff --git a/Appl/CEP/CS1/CS1_BinningFlagger/include/CS1_BinningFlagger/FlaggerProcessControl.h b/Appl/CEP/CS1/CS1_BinningFlagger/include/CS1_BinningFlagger/FlaggerProcessControl.h
new file mode 100644
index 00000000000..8d7c9765cc8
--- /dev/null
+++ b/Appl/CEP/CS1/CS1_BinningFlagger/include/CS1_BinningFlagger/FlaggerProcessControl.h
@@ -0,0 +1,84 @@
+/***************************************************************************
+ * Copyright (C) 2006 by Adriaan Renting *
+ * renting@astron.nl *
+ * *
+ * 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, write to the *
+ * Free Software Foundation, Inc., *
+ * 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA. *
+ ***************************************************************************/
+#ifndef LOFARFLAGGERPROCESSCONTROL_H
+#define LOFARFLAGGERPROCESSCONTROL_H
+
+#include <PLC/ProcessControl.h>
+#include <APS/ParameterSet.h>
+
+/**
+@author Adriaan Renting
+*/
+
+namespace LOFAR
+{
+ namespace CS1
+ {
+ class MS_File; //foreward declaration
+ class FrequencyFlagger;
+
+ class FlaggerProcessControl : public LOFAR::ACC::PLC::ProcessControl
+ {
+ private:
+ std::string itsMS;
+ bool itsExisting;
+ double itsThreshold;
+ MS_File* myMS;
+ FrequencyFlagger* itsFlagger;
+ public:
+ FlaggerProcessControl(void);
+
+ ~FlaggerProcessControl(void);
+ // \name Command to control the processes.
+ // There are a dozen commands that can be sent to a application process
+ // to control its flow. The return values for these command are:<br>
+ // - True - Command executed succesfully.
+ // - False - Command could not be executed.
+ //
+ // @{
+
+ // During the \c define state the process check the contents of the
+ // ParameterSet it received during start-up. When everthing seems ok the
+ // process constructs the communication channels for exchanging data
+ // with the other processes. The connection are NOT made in the stage.
+ tribool define (void);
+
+ // When a process receives an \c init command it allocates the buffers it
+ // needs an makes the connections with the other processes. When the
+ // process succeeds in this it is ready for dataprocessing (or whatever
+ // task the process has).
+ tribool init (void);
+
+ // During the \c run phase the process does the work it is designed for.
+ // The run phase stays active until another command is send.
+ tribool run (void);
+
+ tribool pause(const std::string&);
+ tribool quit(void);
+ tribool recover(const std::string&);
+ tribool reinit(const std::string&);
+ tribool snapshot(const std::string&);
+ std::string askInfo(const std::string&);
+
+ }; //class FlaggerProcessControl
+ } //namespace CS1_Flagger
+}; //namespace LOFAR
+
+#endif
diff --git a/Appl/CEP/CS1/CS1_BinningFlagger/include/CS1_BinningFlagger/Makefile.am b/Appl/CEP/CS1/CS1_BinningFlagger/include/CS1_BinningFlagger/Makefile.am
new file mode 100644
index 00000000000..c471295b641
--- /dev/null
+++ b/Appl/CEP/CS1/CS1_BinningFlagger/include/CS1_BinningFlagger/Makefile.am
@@ -0,0 +1,3 @@
+pkginclude_HEADERS = FlaggerProcessControl.h
+
+include $(top_srcdir)/Makefile.common
diff --git a/Appl/CEP/CS1/CS1_BinningFlagger/include/Makefile.am b/Appl/CEP/CS1/CS1_BinningFlagger/include/Makefile.am
new file mode 100644
index 00000000000..dbb8180464d
--- /dev/null
+++ b/Appl/CEP/CS1/CS1_BinningFlagger/include/Makefile.am
@@ -0,0 +1,3 @@
+SUBDIRS = CS1_FrequencyFlagger
+
+include $(top_srcdir)/Makefile.common
diff --git a/Appl/CEP/CS1/CS1_BinningFlagger/package.dox b/Appl/CEP/CS1/CS1_BinningFlagger/package.dox
new file mode 100644
index 00000000000..15e4659f8a0
--- /dev/null
+++ b/Appl/CEP/CS1/CS1_BinningFlagger/package.dox
@@ -0,0 +1,2 @@
+// \ingroup CS1
+// \defgroup CS1_BinningFlagger CS1_BinningFlagger Description
diff --git a/Appl/CEP/CS1/CS1_BinningFlagger/src/BinningFlagger.cc b/Appl/CEP/CS1/CS1_BinningFlagger/src/BinningFlagger.cc
new file mode 100644
index 00000000000..908b70f329d
--- /dev/null
+++ b/Appl/CEP/CS1/CS1_BinningFlagger/src/BinningFlagger.cc
@@ -0,0 +1,404 @@
+/***************************************************************************
+ * Copyright (C) 2006 by ASTRON, Adriaan Renting *
+ * renting@astron.nl *
+ * *
+ * 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, write to the *
+ * Free Software Foundation, Inc., *
+ * 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA. *
+ ***************************************************************************/
+#include <tables/Tables.h>
+#include <tables/Tables/TableIter.h>
+#include "FrequencyFlagger.h"
+#include <casa/Quanta/MVEpoch.h>
+
+using namespace casa;
+
+enum CorrelationTypes {None=0,I=1,Q=2,U=3,V=4,RR=5,RL=6,LR=7,LL=8,XX=9,XY=10,YX=11,YY=12}; //found somewhere in AIPS++, don't remember where
+
+//===============>>> itoa <<<===============
+//ANSI C++ doesn't seem to have a decent function for this, or I'm not aware of it. Need to rename it to IntToStr(), to avoid confusion
+std::string itoa(int value, int base=10)
+{ // found on http://www.jb.man.ac.uk/~slowe/cpp/itoa.html
+ //maybe copyright Robert Jan Schaper, Ray-Yuan Sheu, Rodrigo de Salvo Braz, Wes Garland and John Maloney
+ enum { kMaxDigits = 35 };
+ std::string buf;
+ buf.reserve( kMaxDigits ); // Pre-allocate enough space.
+ // check that the base if valid
+ if (base < 2 || base > 16) return buf;
+ int quotient = value;
+ // Translating number to string with base:
+ do {
+ buf += "0123456789abcdef"[ std::abs( quotient % base ) ];
+ quotient /= base;
+ } while ( quotient );
+ // Append the negative sign for base 10
+ if ( value < 0 && base == 10) buf += '-';
+ std::reverse( buf.begin(), buf.end() );
+ return buf;
+}
+namespace LOFAR
+{
+ namespace CS1
+ {
+ //===============>>> FrequencyFlagger::FrequencyFlagger <<<===============
+ /* initialize some meta data and get the datastorage the right size. */
+ FrequencyFlagger::FrequencyFlagger(MS_File* InputMSfile,
+ double InputThreshold)
+ {
+ MSfile = InputMSfile;
+ Threshold = InputThreshold;
+ NumAntennae = (*MSfile).itsNumAntennae;
+ NumPairs = (*MSfile).itsNumPairs;
+ NumBands = (*MSfile).itsNumBands;
+ NumChannels = (*MSfile).itsNumChannels;
+ NumPolarizations = (*MSfile).itsNumPolarizations;
+ NoiseLevel = (*MSfile).itsNoiseLevel;
+ NumTimeslots = (*MSfile).itsNumTimeslots;
+ AntennaNames = (*MSfile).itsAntennaNames;
+
+ PairsIndex.resize(NumPairs);
+ Statistics = Cube<int>(NumBands, NumAntennae, NumAntennae, 0);
+
+ TimeslotData.resize(NumPolarizations, NumChannels, NumPairs*NumBands);
+ Flags.resize(NumPolarizations, NumChannels, NumPairs*NumBands);
+
+ int index = 0;
+ for (int i = 0; i < NumAntennae; i++)
+ { for(int j = i; j < NumAntennae; j++)
+ { PairsIndex[index] = pairii(i, j);
+ BaselineIndex[pairii(i, j)] = index++;
+ }
+ }
+ ComputeBaselineLengths();
+ }
+
+ //===============>>> FrequencyFlagger::~FrequencyFlagger <<<===============
+
+ FrequencyFlagger::~FrequencyFlagger()
+ {
+ }
+
+ //===============>>> FrequencyFlagger::ComputeBaselineLengths <<<===============
+ /* compute baseline lengths, and determine the longest one.*/
+ void FrequencyFlagger::ComputeBaselineLengths()
+ {
+ MaxBaselineLength = 0.0;
+ BaselineLengths.resize(NumPairs);
+ //Antenna positions
+ MSAntenna antenna = (*MSfile).antenna();
+ ROArrayColumn<Double> position(antenna, "POSITION");
+ for (int i = 0; i < NumAntennae; i++ )
+ {
+ for (int j = i; j < NumAntennae; j++)
+ {
+ Vector<Double> p(position(i) - position(j));
+ double temp = sqrt(p(0)*p(0) + p(1)*p(1) + p(2)*p(2));
+ BaselineLengths[BaselineIndex[pairii(i, j)]] = temp;
+ if (temp > MaxBaselineLength && temp < 3000000) //radius of the Earth in meters? WSRT sometimes has fake telescopes at 3854243
+ { MaxBaselineLength = temp; // non-existent antenna's can have position (0,0,0)
+ }
+ }
+ }
+ }
+
+ //===============>>> FrequencyFlagger::FlagDataOrBaselines <<<===============
+ /*This function outputs the gathered statistics.*/
+ void FrequencyFlagger::ProcessStatistics()
+ {
+ vector<int> bands(NumBands);
+ vector<int> antennae(NumAntennae);
+ unsigned int namelength = 6;
+ for(int i = 0; i < NumAntennae; i++)
+ {
+ if (namelength < AntennaNames[i].size())
+ { namelength = AntennaNames[i].size();
+ }
+ }
+ for (int i = 0; i < NumBands; i++)
+ {
+ cout << "Band: " << i+1 << endl;
+ cout << string(namelength+1,' ');
+ for(int j = 0; j < NumAntennae; j++)
+ {
+ string out = AntennaNames[j];
+ out.resize(namelength+1,' ');
+ cout << out;
+ }
+ cout << endl;
+ for(int j = 0; j < NumAntennae; j++)
+ {
+ string out = AntennaNames[j];
+ out.resize(namelength+1,' ');
+ cout << out;
+ for(int k = 0; k < NumAntennae; k++)
+ {
+ if (k < j) //We print a complete array, but we have inspected only those where k >= j
+ {
+ int val = 100 * Statistics(i,k,j) / (NumChannels * NumTimeslots * NumPolarizations);
+ bands[i] += val;
+ antennae[j] += val;
+ antennae[k] += val;
+ string out = itoa(val) + "%";
+ out.resize(namelength+1,' ');
+ cout << out;
+ }
+ else
+ {
+ int val = 100 * Statistics(i,j,k) / (NumChannels * NumTimeslots * NumPolarizations);
+ bands[i] += val;
+ antennae[j] += val;
+ antennae[k] += val;
+ string out = itoa(val) + "%";
+ out.resize(namelength+1,' ');
+ cout << out;
+ }
+ /*{ cout << rms << "Faulty baseline detected: Antenna " << j+1
+ << ":" << k+1 << " SpectralWindow: "<< i+1 << endl;
+ }
+ }*/
+ }
+ cout << endl;
+ }
+ }
+ cout << "Bands (flagged %): ";
+ for (int i = 0; i < NumBands; i++)
+ {
+ string out = string("Band") + itoa(i);
+ out.resize(namelength+1,' ');
+ cout << out;
+ }
+ cout << endl << " ";
+ for (int i = 0; i < NumBands; i++)
+ {
+ string out = itoa(bands[i] / (NumAntennae*NumAntennae)) + "%";
+ out.resize(namelength+1,' ');
+ cout << out;
+ }
+ cout << endl << "Antennae (flagged %): " ;
+ for(int j = 0; j < NumAntennae; j++)
+ {
+ string out = AntennaNames[j];
+ out.resize(namelength+1,' ');
+ cout << out;
+ }
+ cout << endl << " ";
+ for (int i = 0; i < NumAntennae; i++)
+ {
+ string out = itoa(antennae[i] / (NumBands*NumAntennae*2)) + "%";
+ out.resize(namelength+1,' ');
+ cout << out;
+ }
+ cout << endl;
+ }
+ //===============>>> FrequencyFlagger::FlagTimeslot <<<===============
+ /* This function inspects each visibility in a cetain baseline-band
+ and flags on complexe distance, then determines to flag the entire baseline-band
+ based on the RMS of the points it didn't flag.*/
+ bool FrequencyFlagger::FlagBaselineBand(Matrix<Bool> Flags,
+ Matrix<Complex> Timeslots,
+ int* flagCounter,
+ double FlagThreshold)
+ {
+ vector<double> MS(NumPolarizations, 0.0);
+ vector<double> RMS(NumPolarizations);
+ vector<int> RMSCounter(NumPolarizations, 0);
+ bool FlagCompleteRow = true;
+ int flagcount = 0;
+ for (int j = NumPolarizations-1; j >= 0; j--)
+ {
+ for (int i = NumChannels-1; i >= 0; i--) //calculata RMS of unflagged datapoints
+ {
+ if (!ExistingFlags || !Flags(j, i))
+ { double temp = pow(abs(Timeslots(j, i)), 2);
+ if (!isNaN(temp))
+ {
+ MS[j] += temp;
+ RMSCounter[j] += 1;
+ }
+ }
+ }
+ if (RMSCounter[j])
+ { RMS[j] = sqrt(MS[j] /RMSCounter[j]);
+ for (int i = NumChannels-1; i >= 0; i--)
+ {
+ if (!ExistingFlags || !Flags(j, i))
+ { double temp = abs(Timeslots(j, i));
+ bool flag = isNaN(temp) || RMS[j] * FlagThreshold < temp;
+ //cout << RMS[j] << " " << (RMS[j] * FlagThreshold) << " " << temp << " " << (flag) << endl;
+ if (flag)
+ { flagcount++;
+ }
+ else
+ { FlagCompleteRow = false;
+ }
+ Flags(j, i) = flag || (ExistingFlags && Flags(j, i));
+ }
+ }
+ }
+ else
+ {
+ flagcount += NumChannels;
+ Flags.row(j) = true;
+ }
+ }
+ //these need to be separated out into a different function for clarity
+ if (flagcount > 0.9 * NumChannels * NumPolarizations) //more as 90% bad
+ {
+ FlagCompleteRow = true;
+ Flags = true;
+ flagcount = NumChannels * NumPolarizations;
+ }
+ (*flagCounter) += flagcount;
+ return FlagCompleteRow;
+ }
+ //===============>>> FrequencyFlagger::FlagBaseline <<<===============
+ /* This function iterates over baseline and band and uses FlagBaselineBand() to determine
+ for each one if it needs to be flagged. It treats the autocorrelations separately,
+ to detect entire malfunctioning telescopes. Finally it writes the flags.
+ */
+ void FrequencyFlagger::FlagTimeslot(TableIterator* flag_iter,
+ bool ExistingFlags)
+ {
+ vector<bool> FlagCompleteRow(NumPairs*NumBands);
+ vector<int> stats(NumPairs*NumBands);
+ for (int i = 0; i < NumBands; i++)
+ {
+ for(int j = 0; j < NumAntennae; j++)
+ {
+ for(int k = j; k < NumAntennae; k++)
+ {
+ int index = i*NumPairs + BaselineIndex[pairii(j, k)];
+ if ((BaselineLengths[BaselineIndex[pairii(j, k)]] < 3000000))//radius of the Earth in meters? WSRT sometimes has fake telescopes at 3854243 m
+ { //we skip the non-existent telescopes
+ FlagCompleteRow[index] = FlagBaselineBand(Flags.xyPlane(index),
+ TimeslotData.xyPlane(index),
+ &(stats[index]),
+ Threshold);
+ }
+ }
+ }
+ //this code could be separated in to different functions
+ for(int j = 0; j < NumAntennae; j++) //write the data
+ {
+ for(int k = j; k < NumAntennae; k++)
+ {
+ int index = i*NumPairs + BaselineIndex[pairii(j, k)];
+ Matrix<Bool> flags = Flags.xyPlane(index);
+ if (FlagCompleteRow[index])
+ {
+ Matrix<Bool> flags = Flags.xyPlane(index);
+ flags = true;
+ Statistics(i,j,k) += NumChannels * NumPolarizations;
+ }
+ else
+ { Statistics(i,j,k) += stats[index];
+ }
+ (*MSfile).WriteDataPointFlags(flag_iter, &flags, FlagCompleteRow[index], ExistingFlags);
+ (*flag_iter)++;
+ }
+ }
+ }
+ }
+
+ //===============>>> FrequencyFlagger::UpdateTimeslotData <<<===============
+ /* This function reads the visibility data for one timeslot and checks if
+ a mosaicing mode is active*/
+ /* The datastructure Timeslotdata is rather complex because it flattens
+ half-filled antenna x antenna x bands matrix into a vector of NumPairs X bands length. */
+ bool FrequencyFlagger::UpdateTimeslotData(vector<int>* OldFields,
+ vector<int>* OldBands,
+ int* TimeCounter,
+ Table* TimeslotTable,
+ double* Time)
+ {
+ int rowcount = (*TimeslotTable).nrow();
+ ROTableVector<Int> antenna1((*TimeslotTable), "ANTENNA1");
+ ROTableVector<Int> antenna2((*TimeslotTable), "ANTENNA2");
+ ROTableVector<Int> bandnr ((*TimeslotTable), "DATA_DESC_ID");
+ ROTableVector<Int> fieldid ((*TimeslotTable), "FIELD_ID");
+ ROTableVector<Double> time ((*TimeslotTable), "TIME_CENTROID");//for testing purposes
+ ROArrayColumn<Complex> data ((*TimeslotTable), "DATA");
+ ROArrayColumn<Bool> flags ((*TimeslotTable), "FLAG");
+ Cube<Complex> Data(NumPolarizations, NumChannels, rowcount);
+ Cube<Bool> Flags(NumPolarizations, NumChannels, rowcount);
+
+ data.getColumn(Data); //We're not checking Data.nrow() Data.ncolumn(), assuming all data is the same size.
+ flags.getColumn(Flags); //We're not checking Data.nrow() Data.ncolumn(), assuming all data is the same size.
+ (*Time) = time(0);//for testing purposes, might be useful in the future
+
+ bool NewField_or_Frequency = false;
+
+ for (int i = 0; i < rowcount; i++)
+ {
+ int bi = BaselineIndex[pairii(antenna1(i), antenna2(i))];
+ int field = fieldid(i);
+ int band = bandnr(i);
+ int index = (band % NumBands) * NumPairs + bi;
+ if ((*TimeCounter))
+ {
+ if (field != (*OldFields)[bi]) //pointing mosaicing
+ { NewField_or_Frequency = true;
+ }
+ if (band != (*OldBands)[index]) //frequency mosaicing
+ { NewField_or_Frequency = true;
+ }
+ }
+ (*OldFields)[bi] = field;
+ (*OldBands)[index] = band;
+
+ TimeslotData.xyPlane(index) = Data.xyPlane(i);
+ Flags.xyPlane(index) = Flags.xyPlane(i); //TimeslotData is only WindowSize size!
+ }
+ return NewField_or_Frequency; //assuming everybody is changing field or frequency at the same time!
+ }
+
+ //===============>>> FrequencyFlagger::FlagDataOrBaselines <<<===============
+ /* This function iterates over the data per timeslot and uses Flagtimeslot()
+ to actually flag datapoints (if flagDatapoints), and entire baselines (if flagRMS)*/
+ void FrequencyFlagger::FlagDataOrBaselines(bool existing)
+ {
+ TableIterator timeslot_iter = (*MSfile).TimeslotIterator();
+ TableIterator flag_iter = (*MSfile).TimeAntennaIterator();
+ double Time = 0.0;//for testing purposes
+ vector<int> OldFields(NumPairs); //to check on multipointing and mosaicing
+ vector<int> OldBands(NumPairs*NumBands); //to check on multifrequency and freq mosaicing
+ ExistingFlags = existing;
+ int step = NumTimeslots / 10 + 1; //not exact but it'll do
+ int row = 0;
+
+ while (!timeslot_iter.pastEnd())
+ {
+ Table TimeslotTable = timeslot_iter.table();
+ bool NewFieldorFreq = UpdateTimeslotData(&OldFields,
+ &OldBands,
+ &row,
+ &TimeslotTable,
+ &Time);
+ //cout << "Processing: " << MVTime(Time/(24*3600)).string(MVTime::YMD) << endl; //for testing purposes
+
+ FlagTimeslot(&flag_iter, ExistingFlags);
+ timeslot_iter++;
+ if (row++ % step == 0) // to tell the user how much % we have processed,
+ { cout << 10*(row/step) << "%" << endl; //not very accurate for low numbers of timeslots, but it'll do for now
+ }
+ if (NewFieldorFreq)
+ { // at the moment we can't realy handle this?
+ cout << "Error new field or frequency detected" << endl;
+ }
+ }
+ ProcessStatistics(); //is there a baseline that should be flagged?
+ }
+ //===============>>> FrequencyFlagger <<<===============
+ }; // namespace CS1
+}; // namespace LOFAR
diff --git a/Appl/CEP/CS1/CS1_BinningFlagger/src/BinningFlagger.h b/Appl/CEP/CS1/CS1_BinningFlagger/src/BinningFlagger.h
new file mode 100644
index 00000000000..b4a924d9d77
--- /dev/null
+++ b/Appl/CEP/CS1/CS1_BinningFlagger/src/BinningFlagger.h
@@ -0,0 +1,94 @@
+/***************************************************************************
+ * Copyright (C) 2006 by ASTRON, Adriaan Renting *
+ * renting@astron.nl *
+ * *
+ * 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, write to the *
+ * Free Software Foundation, Inc., *
+ * 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA. *
+ ***************************************************************************/
+#ifndef __FLAGGER_COMPLEXMEDIANFLAGGER_H__
+#define __FLAGGER_COMPLEXMEDIANFLAGGER_H__
+
+#include <casa/Arrays.h>
+#include <utility>
+#include <vector>
+#include <list>
+#include <map>
+#include "MS_File.h"
+
+namespace LOFAR
+{
+ namespace CS1
+ {
+ using casa::Cube;
+ using casa::Matrix;
+ using casa::Complex;
+ using casa::Int;
+ using casa::Double;
+ using casa::Bool;
+ using casa::Table;
+ using std::list;
+ using std::vector;
+
+ typedef pair<int, int> pairii;
+
+ class FrequencyFlagger
+ {
+ public:
+ FrequencyFlagger(MS_File* MSfile,
+ double Threshold);
+ ~FrequencyFlagger();
+
+ void FlagDataOrBaselines(bool ExistingFlags);
+
+ protected:
+ int NumAntennae;
+ int NumPairs;
+ int NumBands;
+ int NumChannels;
+ int NumPolarizations;
+ int NumTimeslots;
+ double Threshold;
+ double MaxBaselineLength;
+ double NoiseLevel;
+ bool ExistingFlags;
+ vector<double> BaselineLengths;
+ vector<pairii> PairsIndex;
+ map<pairii, int> BaselineIndex;
+ Cube<Complex> TimeslotData;
+ Cube<Bool> Flags;
+ vector<casa::String> AntennaNames;
+ Cube< int > Statistics;
+ MS_File* MSfile;
+
+ void DeterminePolarizationsToCheck(Bool UseOnlyXpolarizations);
+ void ComputeBaselineLengths();
+ void ProcessStatistics();
+ bool FlagBaselineBand(Matrix<Bool> Flags,
+ Matrix<Complex> Timeslots,
+ int* flagCounter,
+ double FlagThreshold);
+ void FlagTimeslot(casa::TableIterator* flag_iter,
+ bool ExistingFlags);
+ bool UpdateTimeslotData(vector<int>* OldFields,
+ vector<int>* OldBands,
+ int* TimeCounter,
+ Table* TimeslotTable,
+ double* Time);
+ private:
+ }; // FrequencyFlagger
+ }; // namespace CS1
+}; // namespace LOFAR
+
+#endif // __FLAGGER_COMPLEXMEDIANFLAGGER_H__
diff --git a/Appl/CEP/CS1/CS1_BinningFlagger/src/Flagger.cc b/Appl/CEP/CS1/CS1_BinningFlagger/src/Flagger.cc
new file mode 100644
index 00000000000..de83a958788
--- /dev/null
+++ b/Appl/CEP/CS1/CS1_BinningFlagger/src/Flagger.cc
@@ -0,0 +1,48 @@
+/***************************************************************************
+ * Copyright (C) 2006 by ASTRON, Adriaan Renting *
+ * renting@astron.nl *
+ * *
+ * 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, write to the *
+ * Free Software Foundation, Inc., *
+ * 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA. *
+ ***************************************************************************/
+
+
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+#include <libgen.h>
+#include <PLC/ACCmain.h>
+#include <casa/Exceptions.h>
+#include <CS1_Flagger/FlaggerProcessControl.h>
+
+int main(int argc, char *argv[])
+{
+ try
+ {
+ INIT_LOGGER(basename(argv[0]));
+ LOFAR::CS1::FlaggerProcessControl myProcess;
+ return LOFAR::ACC::PLC::ACCmain(argc, argv, &myProcess);
+ } //try
+ catch(casa::AipsError& err)
+ {
+ std::cerr << "Aips++ error detected: " << err.getMesg() << std::endl;
+ return -2;
+ }
+ catch(...)
+ {
+ std::cerr << "** PROBLEM **: Unhandled exception caught." << std::endl;
+ return -3;
+ }
+}
diff --git a/Appl/CEP/CS1/CS1_BinningFlagger/src/FlaggerProcessControl.cc b/Appl/CEP/CS1/CS1_BinningFlagger/src/FlaggerProcessControl.cc
new file mode 100644
index 00000000000..233d87ef381
--- /dev/null
+++ b/Appl/CEP/CS1/CS1_BinningFlagger/src/FlaggerProcessControl.cc
@@ -0,0 +1,147 @@
+/***************************************************************************
+ * Copyright (C) 2006 by ASTRON, Adriaan Renting *
+ * renting@astron.nl *
+ * *
+ * 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, write to the *
+ * Free Software Foundation, Inc., *
+ * 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA. *
+ ***************************************************************************/
+
+#include <iostream>
+#include <cstdlib>
+#include <iostream>
+#include <casa/Inputs/Input.h>
+#include <ms/MeasurementSets.h>
+
+#include <CS1_FrequencyFlagger/FlaggerProcessControl.h>
+#include "MS_File.h"
+#include "FrequencyFlagger.h"
+
+#define FLAGGER_VERSION "0.20"
+// 0.10 initial version
+// 0.20 added more algorithms
+
+namespace LOFAR
+{
+ namespace CS1
+ {
+ //===============>>> FlaggerProcessControl::FlaggerProcessControl <<<===============
+ FlaggerProcessControl::FlaggerProcessControl()
+ : ProcessControl()
+ {
+ myMS = NULL;
+ itsFlagger = NULL;
+ }
+
+ //===============>>> FlaggerProcessControl::~FlaggerProcessControl <<<==============
+ FlaggerProcessControl::~FlaggerProcessControl()
+ {
+ if (myMS)
+ { delete myMS;
+ }
+ if (itsFlagger)
+ { delete itsFlagger;
+ }
+ }
+
+ //===============>>> FlaggerProcessControl::define <<<==============================
+ tribool FlaggerProcessControl::define()
+ {
+ LOFAR::ACC::APS::ParameterSet* ParamSet = LOFAR::ACC::APS::globalParameterSet();
+ itsMS = ParamSet->getString("ms");
+ itsExisting = ParamSet->getBool("existing");
+ itsThreshold = ParamSet->getDouble("threshold");
+ return true;
+ }
+
+ //===============>>> FlaggerProcessControl::run <<<=================================
+ tribool FlaggerProcessControl::run()
+ {
+ try{
+ std::cout << "Runnning flagger please wait..." << std::endl;
+ itsFlagger->FlagDataOrBaselines(itsExisting);
+ }
+ catch(casa::AipsError& err)
+ {
+ std::cerr << "Aips++ error detected: " << err.getMesg() << std::endl;
+ return false;
+ }
+ return true;
+ }
+
+ //===============>>> FlaggerProcessControl::init <<<================================
+ tribool FlaggerProcessControl::init()
+ {
+ try {
+ using std::cout;
+ using std::cerr;
+ using std::endl;
+
+ cout << string(FLAGGER_VERSION) + string(" autoflagging by Adriaan Renting for LOFAR CS1 data\n") +
+ string("This is experimental software, please report errors or requests to renting@astron.nl\n") +
+ string("Documentation can be found at: www.lofar.org/operations/doku.php?id=engineering:software:postprocessing_software\n");
+ cout << itsMS << endl;
+ myMS = new MS_File(itsMS);
+ itsFlagger = new FrequencyFlagger (myMS, itsThreshold);
+ }
+ catch(casa::AipsError& err)
+ {
+ std::cerr << "Aips++ error detected: " << err.getMesg() << std::endl;
+ return false;
+ }
+ return true;
+ }
+
+ //===============>>> FlaggerProcessControl::pause <<<===============================
+ tribool FlaggerProcessControl::pause(const std::string&)
+ { return false;
+ }
+
+ //===============>>> FlaggerProcessControl::quit <<<================================
+ tribool FlaggerProcessControl::quit()
+ {
+ if (myMS)
+ {
+ delete myMS;
+ myMS = NULL;
+ }
+ if (itsFlagger)
+ {
+ delete itsFlagger;
+ itsFlagger = NULL;
+ }
+ return true;
+ }
+
+ //===============>>> FlaggerProcessControl::recover <<<=============================
+ tribool FlaggerProcessControl::recover(const std::string&)
+ { return false;
+ }
+
+ //===============>>> FlaggerProcessControl::reinit <<<==============================
+ tribool FlaggerProcessControl::reinit(const std::string&)
+ { return false;
+ }
+
+ //===============>>> FlaggerProcessControl::askInfo <<<=============================
+ std::string FlaggerProcessControl::askInfo(const std::string&)
+ { return std::string("");
+ }
+
+ //===============>>> FlaggerProcessControl::snapshot <<<============================
+ tribool FlaggerProcessControl::snapshot(const std::string&)
+ { return false;
+ }
+ } //namespace CS1
+}; //namespace LOFAR
diff --git a/Appl/CEP/CS1/CS1_BinningFlagger/src/MS_File.cc b/Appl/CEP/CS1/CS1_BinningFlagger/src/MS_File.cc
new file mode 100644
index 00000000000..92968f9ed91
--- /dev/null
+++ b/Appl/CEP/CS1/CS1_BinningFlagger/src/MS_File.cc
@@ -0,0 +1,182 @@
+/***************************************************************************
+ * Copyright (C) 2006 by ASTRON, Adriaan Renting *
+ * renting@astron.nl *
+ * *
+ * 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, write to the *
+ * Free Software Foundation, Inc., *
+ * 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA. *
+ ***************************************************************************/
+#include <casa/BasicMath/Math.h>
+#include <casa/Arrays.h>
+//#include <casa/Quanta/MVTime.h>
+
+#include <iostream>
+
+#include "MS_File.h"
+
+using namespace casa;
+
+namespace LOFAR
+{
+ namespace CS1
+ {
+ //===============>>> MS_File::MS_File <<<===============
+
+ MS_File::MS_File(const std::string& msname)
+ {
+ MSName = msname;
+ MS = new MeasurementSet(MSName, Table::Update);
+ init();
+ }
+
+ //===============>>> MS_File::~MS_File <<<===============
+
+ MS_File::~MS_File()
+ {
+ delete MS;
+ }
+
+ //===============>>> MS_File::init <<<===============
+
+ void MS_File::init()
+ {
+ //Number of samples
+ itsNumSamples = (*MS).nrow();
+ std::cout << "NumSamples" << itsNumSamples << std::endl;
+ //Number of Fields
+ MSField fields = (*MS).field();
+ itsNumFields = fields.nrow();
+ std::cout << "NumFields" << itsNumFields << std::endl;
+
+ //Number of Antennae
+ MSAntenna antennae = (*MS).antenna();
+ itsNumAntennae = antennae.nrow();
+ std::cout << "NumAntennae" << itsNumAntennae << std::endl;
+
+ //Antenna Names
+ ROScalarColumn<String> ANT_NAME_col(antennae, "NAME");
+ Vector<String> ant_names = ANT_NAME_col.getColumn();
+ ant_names.tovector(itsAntennaNames);
+
+ //Number of channels in the Band
+ MSSpectralWindow spectral_window = (*MS).spectralWindow();
+ ROScalarColumn<Int> NUM_CHAN_col(spectral_window, "NUM_CHAN");
+ itsNumChannels = NUM_CHAN_col(0);
+ std::cout << "NumChannels" << itsNumChannels << std::endl;
+
+ //Number of polarizations
+ MSPolarization polarization = (*MS).polarization();
+ ROScalarColumn<Int> NUM_CORR_col(polarization, "NUM_CORR");
+ itsNumPolarizations = NUM_CORR_col(0);
+ ROArrayColumn<Int> CORR_TYPE_col(polarization, "CORR_TYPE");
+ itsPolarizations.resize(itsNumPolarizations);
+ CORR_TYPE_col.get(0, itsPolarizations);
+ std::cout << "NumPolarizations" << itsNumPolarizations << std::endl;
+
+ //calculate theoretical noise level
+ ROScalarColumn<Double> EXPOSURE_col((*MS), "EXPOSURE");
+ Double exposure = EXPOSURE_col(0);
+
+ ROScalarColumn<Double> TOTAL_BANDWIDTH_col(spectral_window, "TOTAL_BANDWIDTH");
+ Double bandwidth = TOTAL_BANDWIDTH_col(0) / itsNumChannels;
+
+ itsNoiseLevel = 1.0 / sqrt(bandwidth * exposure);
+ std::cout << "Noiselevel" << itsNoiseLevel << std::endl;
+
+ //calculate number of timeslots
+ ROScalarColumn<Double> INTERVAL_col((*MS), "INTERVAL");
+ Double interval = INTERVAL_col(0);
+
+ //Number of timeslots
+ ROScalarColumn<Double> TIME_CENTROID_col((*MS), "TIME_CENTROID");
+ Double firstdate = TIME_CENTROID_col(0);
+ Double lastdate = TIME_CENTROID_col(itsNumSamples-1);
+ std::cout << "interval" << interval << std::endl;
+
+ itsNumTimeslots = (int)((lastdate-firstdate)/interval) + 1;
+ std::cout << "Numtimeslots" << itsNumTimeslots << std::endl;
+
+ //calculate number of baselines.
+ itsNumPairs = (itsNumAntennae) * (itsNumAntennae + 1) / 2; //Triangular numbers formula
+ std::cout << "NumPairs" << itsNumPairs << std::endl;
+
+ //calculate number of Bands
+ itsNumBands = itsNumSamples / (itsNumPairs * itsNumTimeslots);
+ std::cout << "NumBands" << itsNumBands << std::endl;
+
+ }
+
+ //===============>>> MS_File::BaselineIterator <<<===============
+
+ MSAntenna MS_File::antenna()
+ {
+ return (*MS).antenna();
+ }
+
+ //===============>>> MS_File::BaselineIterator <<<===============
+
+ TableIterator MS_File::TimeslotIterator()
+ {
+ Block<String> ms_iteration_variables(1);
+ ms_iteration_variables[0] = "TIME_CENTROID";
+
+ return TableIterator((*MS), ms_iteration_variables);
+ }
+
+ //===============>>> MS_File::BaselineIterator <<<===============
+
+ TableIterator MS_File::TimeAntennaIterator()
+ {
+ Block<String> ms_iteration_variables(4);
+ ms_iteration_variables[0] = "TIME_CENTROID";
+ ms_iteration_variables[1] = "DATA_DESC_ID";
+ ms_iteration_variables[2] = "ANTENNA1";
+ ms_iteration_variables[3] = "ANTENNA2";
+
+ return TableIterator((*MS), ms_iteration_variables);
+ }
+
+ //===============>>> MS_File::WriteDataPointFlags <<<===============
+
+ void MS_File::WriteDataPointFlags(TableIterator* flag_iter,
+ Matrix<Bool>* Flags,
+ Bool FlagCompleteRow,
+ bool ExistingFlags)
+ {
+ Table FlagTable = (*flag_iter).table();
+ // ROTableVector<Int> antenna1(FlagTable, "ANTENNA1");
+ // ROTableVector<Int> antenna2(FlagTable, "ANTENNA2");
+ // ROTableVector<Int> bandnr (FlagTable, "DATA_DESC_ID");
+ // ROTableVector<Double> time (FlagTable, "TIME_CENTROID");
+ ArrayColumn <Bool> flags (FlagTable, "FLAG");
+ ScalarColumn <Bool> flag_row(FlagTable, "FLAG_ROW");
+ // ArrayColumn<String> flag_desc((*TimeslotTable), "FLAG_CATEGORY");
+ if (ExistingFlags)
+ {
+ Matrix<Bool> OldFlags;
+ Bool OldFlagCompleteRow;
+ flags.get(0, OldFlags);
+ flag_row.get(0, OldFlagCompleteRow);
+ flags.put(0, OldFlags || (*Flags));
+ }
+ else
+ {
+ flags.put(0, (*Flags));
+ }
+ flag_row.put(0, FlagCompleteRow);
+ }
+ //===============>>> MS_File <<<===============
+ }; // namespace CS1
+}; // namespace LOFAR
+
diff --git a/Appl/CEP/CS1/CS1_BinningFlagger/src/MS_File.h b/Appl/CEP/CS1/CS1_BinningFlagger/src/MS_File.h
new file mode 100644
index 00000000000..fce2744b04e
--- /dev/null
+++ b/Appl/CEP/CS1/CS1_BinningFlagger/src/MS_File.h
@@ -0,0 +1,68 @@
+/***************************************************************************
+ * Copyright (C) 2006 by ASTRON, Adriaan Renting *
+ * renting@astron.nl *
+ * *
+ * 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, write to the *
+ * Free Software Foundation, Inc., *
+ * 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA. *
+ ***************************************************************************/
+#ifndef __FLAGGER_MS_FILE_H__
+#define __FLAGGER_MS_FILE_H__
+
+#include <ms/MeasurementSets.h>
+#include <vector>
+#include <string>
+#include <tables/Tables.h>
+#include <tables/Tables/TableIter.h>
+
+namespace LOFAR
+{
+ namespace CS1
+ {
+ class MS_File
+ {
+ public:
+ MS_File(const std::string& msname);
+ ~MS_File();
+
+ int itsNumSamples;
+ int itsNumAntennae;
+ int itsNumFields;
+ int itsNumBands;
+ int itsNumChannels;
+ int itsNumPolarizations;
+ int itsNumPairs;
+ int itsNumTimeslots;
+ double itsNoiseLevel;
+ std::vector<casa::String> itsAntennaNames;
+ casa::Vector<casa::Int> itsPolarizations;
+
+ casa::TableIterator TimeslotIterator();
+ casa::TableIterator TimeAntennaIterator();
+ casa::MSAntenna antenna();
+ void WriteDataPointFlags(casa::TableIterator* flag_iter,
+ casa::Matrix<casa::Bool>* Flags,
+ bool FlagcompleteRow,
+ bool ExistingFlags);
+
+ protected:
+ string MSName;
+ casa::MeasurementSet* MS;
+ void init();
+ private:
+ }; // MS_File
+ }; // namespace CS1
+}; // namespace LOFAR
+
+#endif // __FLAGGER_MS_FILE_H__
diff --git a/Appl/CEP/CS1/CS1_BinningFlagger/src/Makefile.am b/Appl/CEP/CS1/CS1_BinningFlagger/src/Makefile.am
new file mode 100644
index 00000000000..12c73792218
--- /dev/null
+++ b/Appl/CEP/CS1/CS1_BinningFlagger/src/Makefile.am
@@ -0,0 +1,12 @@
+bin_PROGRAMS = CS1_FrequencyFlagger
+
+CS1_FrequencyFlagger_SOURCES = Flagger.cc \
+ FrequencyFlagger.cc \
+ FrequencyFlagger.h \
+ MS_File.cc \
+ MS_File.h \
+ FlaggerProcessControl.cc
+CS1_FrequencyFlagger_LDADD =
+CS1_FrequencyFlagger_DEPENDENCIES = $(LOFAR_DEPEND)
+
+include $(top_srcdir)/Makefile.common
diff --git a/Appl/CEP/CS1/CS1_BinningFlagger/test/CS1_BinningFlagger.parset b/Appl/CEP/CS1/CS1_BinningFlagger/test/CS1_BinningFlagger.parset
new file mode 100644
index 00000000000..5635bb6c229
--- /dev/null
+++ b/Appl/CEP/CS1/CS1_BinningFlagger/test/CS1_BinningFlagger.parset
@@ -0,0 +1,8 @@
+ms=/mnt/flaggerdata/test.MS
+window=13
+crosspol=false
+min=15
+max=15
+flagrms=true
+flagdata=true
+existing=false
diff --git a/Appl/CEP/CS1/CS1_BinningFlagger/test/Makefile.am b/Appl/CEP/CS1/CS1_BinningFlagger/test/Makefile.am
new file mode 100644
index 00000000000..7d336cc2beb
--- /dev/null
+++ b/Appl/CEP/CS1/CS1_BinningFlagger/test/Makefile.am
@@ -0,0 +1,25 @@
+check_PROGRAMS =
+
+# programs to run through supplied checktools
+CHECKTOOLPROGS =
+#ENDCHECKTOOLPROGS
+
+# scripts used to run tests
+TESTSCRIPTS =
+
+# scripts and possible programs to run tests
+TESTS = $(TESTSCRIPTS)
+
+XFAIL_TESTS =
+
+# all files (.run, .stdout, .in, .log_prop, etc.) needed to run tests
+EXTRA_DIST = $(TESTSCRIPTS) CS1_BinningFlagger.parset
+
+# Lines to build a test program testprg
+#testprg_SOURCES = testprg.cc
+#testprg_LDADD = ../src/libcs1_inputsection.la
+#testprg_DEPENDENCIES = ../src/libcs1_inputsection.la $(LOFAR_DEPEND)
+
+
+
+include $(top_srcdir)/Makefile.common
--
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