From 770dce2ad41ba1ef2d5e4637b1a70a973914cbba Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Andr=C3=A9=20Offringa?= <offringa@astron.nl>
Date: Mon, 31 Jan 2011 14:18:18 +0000
Subject: [PATCH] Bug 1491: adding some script creaters
---
.gitattributes | 5 +-
.../include/AOFlagger/ref/concatenatescript.h | 61 +++++++++++++++++++
.../include/AOFlagger/ref/copyallscript.h | 12 +++-
.../AOFlagger/include/AOFlagger/ref/reffile.h | 14 ++++-
.../include/AOFlagger/ref/reffileentry.h | 6 ++
.../include/AOFlagger/ref/refmovescript.h | 56 +++++++++++++++++
CEP/DP3/AOFlagger/package.dox | 12 ++++
CEP/DP3/AOFlagger/src/CMakeLists.txt | 2 +-
.../{aocopyallscript.cpp => aorefscript.cpp} | 17 +++++-
9 files changed, 176 insertions(+), 9 deletions(-)
create mode 100644 CEP/DP3/AOFlagger/include/AOFlagger/ref/concatenatescript.h
create mode 100644 CEP/DP3/AOFlagger/include/AOFlagger/ref/refmovescript.h
create mode 100644 CEP/DP3/AOFlagger/package.dox
rename CEP/DP3/AOFlagger/src/{aocopyallscript.cpp => aorefscript.cpp} (73%)
diff --git a/.gitattributes b/.gitattributes
index 2cbdedc39fd..415afbbf2e0 100644
--- a/.gitattributes
+++ b/.gitattributes
@@ -227,10 +227,12 @@ CEP/DP3/AOFlagger/include/AOFlagger/msio/timefrequencydata.h -text
CEP/DP3/AOFlagger/include/AOFlagger/msio/timefrequencyimager.h -text
CEP/DP3/AOFlagger/include/AOFlagger/msio/timefrequencymetadata.h -text
CEP/DP3/AOFlagger/include/AOFlagger/msio/types.h -text
+CEP/DP3/AOFlagger/include/AOFlagger/ref/concatenatescript.h -text
CEP/DP3/AOFlagger/include/AOFlagger/ref/copyallscript.h -text
CEP/DP3/AOFlagger/include/AOFlagger/ref/reffile.h -text
CEP/DP3/AOFlagger/include/AOFlagger/ref/reffileentry.h -text
CEP/DP3/AOFlagger/include/AOFlagger/ref/reffileexception.h -text
+CEP/DP3/AOFlagger/include/AOFlagger/ref/refmovescript.h -text
CEP/DP3/AOFlagger/include/AOFlagger/rfi/antennaflagcountplot.h -text
CEP/DP3/AOFlagger/include/AOFlagger/rfi/eigenvalue.h -text
CEP/DP3/AOFlagger/include/AOFlagger/rfi/frequencyflagcountplot.h -text
@@ -323,6 +325,7 @@ CEP/DP3/AOFlagger/include/AOFlagger/util/stopwatch.h -text
CEP/DP3/AOFlagger/include/AOFlagger/util/types.h -text
CEP/DP3/AOFlagger/include/AOFlagger/util/xmlwriter.h -text
CEP/DP3/AOFlagger/include/AOFlagger/vectortypes.h -text
+CEP/DP3/AOFlagger/package.dox -text
CEP/DP3/AOFlagger/scripts/CMakeLists-AOFlagger-without-lofarstman.txt -text
CEP/DP3/AOFlagger/scripts/CMakeLists-CEP.txt -text
CEP/DP3/AOFlagger/scripts/CMakeLists-Common-src-without-lofarstman.txt -text
@@ -351,8 +354,8 @@ CEP/DP3/AOFlagger/scripts/distributed/statistics.rfis -text
CEP/DP3/AOFlagger/scripts/package-without-lofarstman.sh -text
CEP/DP3/AOFlagger/scripts/package.sh -text
CEP/DP3/AOFlagger/src/CMakeLists.txt -text
-CEP/DP3/AOFlagger/src/aocopyallscript.cpp -text
CEP/DP3/AOFlagger/src/aofrequencyfilter.cpp -text
+CEP/DP3/AOFlagger/src/aorefscript.cpp -text
CEP/DP3/AOFlagger/src/cleaner.cpp -text
CEP/DP3/AOFlagger/src/colormapper.cpp -text
CEP/DP3/AOFlagger/src/createuv.cpp -text
diff --git a/CEP/DP3/AOFlagger/include/AOFlagger/ref/concatenatescript.h b/CEP/DP3/AOFlagger/include/AOFlagger/ref/concatenatescript.h
new file mode 100644
index 00000000000..441ad196a28
--- /dev/null
+++ b/CEP/DP3/AOFlagger/include/AOFlagger/ref/concatenatescript.h
@@ -0,0 +1,61 @@
+/***************************************************************************
+ * Copyright (C) 2011 by A.R. Offringa *
+ * offringa@astro.rug.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 AO_CONCATENATESCRIPT_H
+#define AO_CONCATENATESCRIPT_H
+
+#include <iostream>
+#include <string>
+
+#include <AOFlagger/ref/reffile.h>
+
+namespace AOTools
+{
+ class ConcatenateScript
+ {
+ public:
+ static void Make(std::ostream &stream, const std::string &refFilePath, const std::string &destination)
+ {
+ RefFile file(refFilePath);
+
+ stream <<
+ "#!/usr/bin/env python\n\n"
+ "import pyrap.tables as pt\n\n"
+ "pt.concatms([";
+
+ RefFile::const_iterator i=file.begin();
+ if(i!=file.end())
+ {
+ stream << '\"' << i->Path() << '\"';
+ ++i;
+ }
+
+ while(i!=file.end())
+ {
+ stream << ", \"/net/" << i->Node() << i->Path() << '\"';
+ ++i;
+ }
+
+ stream << "], \"" << destination << "\")\n";
+ }
+ };
+}
+
+#endif // AO_CONCATENATESCRIPT_H
diff --git a/CEP/DP3/AOFlagger/include/AOFlagger/ref/copyallscript.h b/CEP/DP3/AOFlagger/include/AOFlagger/ref/copyallscript.h
index 64361a1efb4..5df56def3bb 100644
--- a/CEP/DP3/AOFlagger/include/AOFlagger/ref/copyallscript.h
+++ b/CEP/DP3/AOFlagger/include/AOFlagger/ref/copyallscript.h
@@ -39,6 +39,12 @@ namespace AOTools
typedef std::map<std::string, PathList> PathsPerNodeType;
typedef std::pair<std::string, PathList> NodeAndPaths;
+ std::string correctedDest;
+ if(*destination.rbegin() == '/')
+ correctedDest = destination;
+ else
+ correctedDest = destination + "/";
+
RefFile file(refFilePath);
PathsPerNodeType pathsPerNode;
@@ -58,7 +64,7 @@ namespace AOTools
stream <<
"#! /bin/bash\n"
"# Created by aocopyallscript to move sets in \n# " << refFilePath << "\n"
- "# to local path\n# " << destination << "\n"
+ "# to local path\n# " << correctedDest << "\n"
"# Set contains " << file.Count() << " MS directories\n"
"# Number of nodes: " << pathsPerNode.size() << "\n";
for(PathsPerNodeType::const_iterator i=pathsPerNode.begin(); i!=pathsPerNode.end(); ++i)
@@ -68,13 +74,13 @@ namespace AOTools
stream
<< "function copy_" << node << " {\n"
- << " mkdir -p " << destination << "\n";
+ << " ssh " << node << " -C \"mkdir -p " << correctedDest << "\"\n";
for(PathList::const_iterator p=paths.begin();p!=paths.end();++p)
{
const std::string &path = *p;
stream
<< " echo " << path << " \\(" << node << "\\)\n"
- << " ssh " << node << " -C \"cp -r " << path << " " << destination << "\"\n";
+ << " ssh " << node << " -C \"cp -r " << path << " " << correctedDest << "\"\n";
}
stream
<< "}\n\n";
diff --git a/CEP/DP3/AOFlagger/include/AOFlagger/ref/reffile.h b/CEP/DP3/AOFlagger/include/AOFlagger/ref/reffile.h
index 075678d6942..f2aa1f45efc 100644
--- a/CEP/DP3/AOFlagger/include/AOFlagger/ref/reffile.h
+++ b/CEP/DP3/AOFlagger/include/AOFlagger/ref/reffile.h
@@ -23,6 +23,7 @@
#include <fstream>
#include <string>
+#include <vector>
#include <AOFlagger/ref/reffileentry.h>
#include <AOFlagger/ref/reffileexception.h>
@@ -55,6 +56,12 @@ namespace AOTools
}
}
+ void Write(std::ostream &destination) const
+ {
+ for(const_iterator i=begin();i!=end();++i)
+ i->write(destination);
+ }
+
size_t Count() const
{
return _entries.size();
@@ -65,6 +72,11 @@ namespace AOTools
return _entries[index];
}
+ void Add(const RefFileEntry &entry)
+ {
+ _entries.push_back(entry);
+ }
+
const_iterator begin() const
{
return _entries.begin();
@@ -74,7 +86,7 @@ namespace AOTools
{
return _entries.end();
}
-
+
private:
RefFile(const RefFile &) // don't allow copy
{
diff --git a/CEP/DP3/AOFlagger/include/AOFlagger/ref/reffileentry.h b/CEP/DP3/AOFlagger/include/AOFlagger/ref/reffileentry.h
index 082b42b3497..4525d9f658c 100644
--- a/CEP/DP3/AOFlagger/include/AOFlagger/ref/reffileentry.h
+++ b/CEP/DP3/AOFlagger/include/AOFlagger/ref/reffileentry.h
@@ -58,6 +58,7 @@ namespace AOTools
unsigned Size() const { return _size; }
const std::string &Node() const { return _node; }
+ void SetPath(const std::string &path) { _path = path; }
private:
std::string _path;
std::string _frequency;
@@ -78,6 +79,11 @@ namespace AOTools
return true;
}
+ void write(std::ostream &stream) const
+ {
+ stream << _path << ' ' << _frequency << ' ' << _size << ' ' << _node << "\n";
+ }
+
void assignFromString(const std::string &line)
{
std::string::const_iterator i=line.begin();
diff --git a/CEP/DP3/AOFlagger/include/AOFlagger/ref/refmovescript.h b/CEP/DP3/AOFlagger/include/AOFlagger/ref/refmovescript.h
new file mode 100644
index 00000000000..4ed38ea510a
--- /dev/null
+++ b/CEP/DP3/AOFlagger/include/AOFlagger/ref/refmovescript.h
@@ -0,0 +1,56 @@
+/***************************************************************************
+ * Copyright (C) 2011 by A.R. Offringa *
+ * offringa@astro.rug.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 AO_REFMOVESCRIPT_H
+#define AO_REFMOVESCRIPT_H
+
+#include <iostream>
+#include <string>
+
+#include <boost/filesystem.hpp>
+
+#include <AOFlagger/ref/reffile.h>
+
+namespace AOTools
+{
+ class RefMoveScript
+ {
+ public:
+ static void Make(std::ostream &stream, const std::string &refFilePath, const std::string &destination)
+ {
+ RefFile file(refFilePath);
+ RefFile destFile;
+
+ const boost::filesystem::path destPath(destination);
+
+ for(RefFile::const_iterator i=file.begin();i!=file.end();++i)
+ {
+ RefFileEntry entry = *i;
+ boost::filesystem::path entryPath(entry.Path());
+ entry.SetPath((destPath / entryPath.filename()).directory_string());
+ destFile.Add(entry);
+ }
+
+ destFile.Write(stream);
+ }
+ };
+}
+
+#endif // AO_REFMOVESCRIPT_H
diff --git a/CEP/DP3/AOFlagger/package.dox b/CEP/DP3/AOFlagger/package.dox
new file mode 100644
index 00000000000..609d8c743cf
--- /dev/null
+++ b/CEP/DP3/AOFlagger/package.dox
@@ -0,0 +1,12 @@
+// \ingroup DP3
+//
+// \defgroup AOFlagger AOFlagger (flagger framework based on the
+// SumThreshold method)
+//
+// This package contains several programs related to flagging,
+// most important the programs "rficonsole" and "rfigui". See
+// the LOFAR cookbook for general info.
+//
+// @{
+// \defgroup AOFlagger AOFlagger
+// @}
diff --git a/CEP/DP3/AOFlagger/src/CMakeLists.txt b/CEP/DP3/AOFlagger/src/CMakeLists.txt
index 60ecf1d07b1..73104a9edd4 100644
--- a/CEP/DP3/AOFlagger/src/CMakeLists.txt
+++ b/CEP/DP3/AOFlagger/src/CMakeLists.txt
@@ -6,7 +6,7 @@ lofar_add_bin_program(rfihistory rfihistory.cpp)
lofar_add_bin_program(aofrequencyfilter aofrequencyfilter.cpp rfi/thresholdtools.cpp util/rng.cpp msio/image2d.cpp msio/fitsfile.cpp util/aologger.cpp)
-lofar_add_bin_program(aocopyallscript aocopyallscript.cpp)
+lofar_add_bin_program(aorefscript aorefscript.cpp)
set(GUI_PLOT_FILES
gui/plot/horizontalplotscale.cpp
diff --git a/CEP/DP3/AOFlagger/src/aocopyallscript.cpp b/CEP/DP3/AOFlagger/src/aorefscript.cpp
similarity index 73%
rename from CEP/DP3/AOFlagger/src/aocopyallscript.cpp
rename to CEP/DP3/AOFlagger/src/aorefscript.cpp
index 216d84ec879..938a86e36ad 100644
--- a/CEP/DP3/AOFlagger/src/aocopyallscript.cpp
+++ b/CEP/DP3/AOFlagger/src/aorefscript.cpp
@@ -20,18 +20,29 @@
#include <iostream>
+#include <AOFlagger/ref/concatenatescript.h>
#include <AOFlagger/ref/copyallscript.h>
+#include <AOFlagger/ref/refmovescript.h>
using namespace std;
int main(int argc, char *argv[])
{
- if(argc != 3)
+ if(argc != 4)
{
- cerr << "Syntax: " << argv[0] << " <reffile> <local-destination>\n";
+ cerr << "Syntax: " << argv[0] << " <scripttype> <reffile> <local-destination>\n"
+ "script types: concatenate, copyall, refmove\n";
return -1;
} else {
- AOTools::CopyAllScript::Make(cout, argv[1], argv[2]);
+ string type(argv[1]);
+ if(type == "concatenate")
+ AOTools::ConcatenateScript::Make(cout, argv[2], argv[3]);
+ else if(type =="copyall")
+ AOTools::CopyAllScript::Make(cout, argv[2], argv[3]);
+ else if(type =="refmove")
+ AOTools::RefMoveScript::Make(cout, argv[2], argv[3]);
+ else
+ cerr << "Incorrect script type given." << "\n";
return 0;
}
}
--
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