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sebastic-guest pushed a commit to branch upstream-master
in repository pktools.
commit 143c64cf01bdea87fdf410ca3cd18645f1ed69a4
Author: Pieter Kempeneers <kempe...@gmail.com>
Date: Mon Feb 18 17:27:43 2013 +0100
introduced FileReaderAscii.h and updated pkstat.cc
---
src/apps/Makefile.am | 2 +-
src/apps/pkstat.cc | 103 ++++----------------
src/fileclasses/FileReaderAscii.h | 192 ++++++++++++++++++++++++++++++++++++++
src/fileclasses/Makefile.am | 2 +-
4 files changed, 211 insertions(+), 88 deletions(-)
diff --git a/src/apps/Makefile.am b/src/apps/Makefile.am
index 92d0a68..bff0785 100644
--- a/src/apps/Makefile.am
+++ b/src/apps/Makefile.am
@@ -44,7 +44,7 @@ pkdumpimg_SOURCES = pkdumpimg.cc
pkdumpogr_SOURCES = pkdumpogr.h pkdumpogr.cc
pksieve_SOURCES = pksieve.cc
pkstat_SOURCES = $(top_srcdir)/src/algorithms/Histogram.h pkstat.cc
-pkstat_LDADD = $(GSL_LIBS) $(AM_LDFLAGS)
+pkstat_LDADD = -lfileClasses $(GSL_LIBS) $(AM_LDFLAGS)
pkstatogr_SOURCES = pkstatogr.cc
pkegcs_SOURCES = pkegcs.cc
pkegcs_LDADD = -lgdal $(AM_LDFLAGS) -lgdal
diff --git a/src/apps/pkstat.cc b/src/apps/pkstat.cc
index f6940ff..1467dac 100644
--- a/src/apps/pkstat.cc
+++ b/src/apps/pkstat.cc
@@ -22,6 +22,7 @@ along with pktools. If not, see
<http://www.gnu.org/licenses/>.
#include <vector>
#include <math.h>
#include "base/Optionpk.h"
+#include "fileclasses/FileReaderAscii.h"
#include "algorithms/Histogram.h"
using namespace std;
@@ -30,8 +31,9 @@ int main(int argc, char *argv[])
{
Optionpk<string> input_opt("i","input","name of the input text file","");
Optionpk<char> fs_opt("fs","fs","field separator.",' ');
+ Optionpk<char> comment_opt("comment","comment","comment character",'#');
Optionpk<bool> output_opt("o","output","output the selected columns",false);
- Optionpk<short> col_opt("c", "column", "column nr, starting from 0", 0);
+ Optionpk<int> col_opt("c", "column", "column nr, starting from 0", 0);
Optionpk<int> range_opt("r", "range", "rows to start/end reading. Use -r 1
-r 10 to read first 10 rows where first row is header. Use 0 to read all rows
with no header.", 0);
Optionpk<bool> size_opt("size","size","sample size",false);
Optionpk<bool> mean_opt("m","mean","calculate mean value",false);
@@ -42,8 +44,8 @@ int main(int argc, char *argv[])
Optionpk<bool> stdev_opt("stdev","stdev","calculate standard
deviation",false);
Optionpk<bool> sum_opt("s","sum","calculate sum of column",false);
Optionpk<bool> minmax_opt("mm","minmax","calculate minimum and maximum
value",false);
- Optionpk<double> min_opt("min","min","calculate minimum value",0);
- Optionpk<double> max_opt("max","max","calculate maximum value",0);
+ Optionpk<double> min_opt("min","min","set minimum value",0);
+ Optionpk<double> max_opt("max","max","set maximum value",0);
Optionpk<bool> histogram_opt("hist","hist","calculate histogram",false);
Optionpk<short> nbin_opt("bin","bin","number of bins to calculate
histogram",10);
Optionpk<bool> relative_opt("rel","relative","use percentiles for histogram
to calculate histogram",false);
@@ -56,6 +58,7 @@ int main(int argc, char *argv[])
try{
doProcess=input_opt.retrieveOption(argc,argv);
fs_opt.retrieveOption(argc,argv);
+ comment_opt.retrieveOption(argc,argv);
output_opt.retrieveOption(argc,argv);
col_opt.retrieveOption(argc,argv);
range_opt.retrieveOption(argc,argv);
@@ -89,95 +92,23 @@ int main(int argc, char *argv[])
vector< vector<double> > dataVector(col_opt.size());
vector< vector<int> > histVector(col_opt.size());
- ifstream dataFile;
- if(verbose_opt[0])
- cout << "opening file " << input_opt[0] << endl;
- dataFile.open(input_opt[0].c_str());
- int nrow=0;
- bool withinRange=true;
-
- if(fs_opt[0]>' '&&fs_opt[0]<='~'){//field separator is a regular character
(minimum ASCII code is space, maximum ASCII code is tilde)
- // if(input_opt[0].find(".csv")!=string::npos){
- if(verbose_opt[0])
- cout << "reading csv file " << input_opt[0] << endl;
- string csvRecord;
- while(getline(dataFile,csvRecord)){//read a line
- withinRange=true;
- if(nrow<range_opt[0])
- withinRange=false;
- if(range_opt.size()>1)
- if(nrow>range_opt[1])
- withinRange=false;
- if(withinRange){
- istringstream csvstream(csvRecord);
- string item;
- int ncol=0;
- while(getline(csvstream,item,fs_opt[0])){//read a column
- if(verbose_opt[0])
- cout << item << " ";
- for(int icol=0;icol<col_opt.size();++icol){
- if(ncol==col_opt[icol]){
- double value=atof(item.c_str());
-
if((value>=min_opt[0]&&value<=max_opt[0])||max_opt[0]<=min_opt[0])
- dataVector[icol].push_back(value);
- }
- }
- ++ncol;
- }
- if(verbose_opt[0])
- cout << endl;
- assert(ncol>=col_opt[0]);
- }
- ++nrow;
- }
- assert(dataVector.size());
- }
- else{//space or tab delimited fields
- string spaceRecord;
- while(!getline(dataFile, spaceRecord).eof()){
- withinRange=true;
- if(nrow<range_opt[0])
- withinRange=false;
- if(range_opt.size()>1)
- if(nrow>range_opt[1])
- withinRange=false;
- if(withinRange){
- if(verbose_opt[0]>1)
- cout << spaceRecord << endl;
- istringstream lineStream(spaceRecord);
- string item;
- int ncol=0;
- while(lineStream >> item){
- if(verbose_opt[0]>1)
- cout << item << " ";
- istringstream itemStream(item);
- double value;
- itemStream >> value;
- for(int icol=0;icol<col_opt.size();++icol){
- if(ncol==col_opt[icol]){
-
if((value>=min_opt[0]&&value<=max_opt[0])||max_opt[0]<=min_opt[0])
- dataVector[icol].push_back(value);
- }
- }
- ++ncol;
- }
- if(verbose_opt[0]>1)
- cout << endl;
- if(verbose_opt[0])
- cout << "number of columns: " << ncol << endl;
- assert(ncol>=col_opt[0]);
- }
- ++nrow;
- }
- }
+ FileReaderAscii asciiReader(input_opt[0]);
+ asciiReader.setFieldSeparator(fs_opt[0]);
+ asciiReader.setComment(comment_opt[0]);
+ asciiReader.setMinRow(range_opt[0]);
+ if(range_opt.size()>1)
+ asciiReader.setMaxRow(range_opt[1]);
+ asciiReader.readData(dataVector,col_opt);
assert(dataVector.size());
- dataFile.close();
double minValue=min_opt[0];
double maxValue=max_opt[0];
Histogram hist;
for(int icol=0;icol<col_opt.size();++icol){
- assert(dataVector[icol].size());
+ if(!dataVector[icol].size()){
+ std::cerr << "Warning: dataVector[" << icol << "] is empty" << std::endl;
+ continue;
+ }
if(size_opt[0])
cout << "sample size column " << col_opt[icol] << ": " <<
dataVector[icol].size() << endl;
if(mean_opt[0])
diff --git a/src/fileclasses/FileReaderAscii.h
b/src/fileclasses/FileReaderAscii.h
new file mode 100644
index 0000000..384f558
--- /dev/null
+++ b/src/fileclasses/FileReaderAscii.h
@@ -0,0 +1,192 @@
+/**********************************************************************
+FileReaderAscii.h: class to read ASCII files using (colum based)
+Copyright (C) 2008-2013 Pieter Kempeneers
+
+This file is part of pktools
+
+pktools 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.
+
+pktools 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 pktools. If not, see <http://www.gnu.org/licenses/>.
+***********************************************************************/
+#ifndef _IMGREADERASCII_H_
+#define _IMGREADERASCII_H_
+
+#include <string>
+#include <vector>
+#include <fstream>
+
+//--------------------------------------------------------------------------
+class FileReaderAscii
+{
+public:
+ FileReaderAscii(void);
+ FileReaderAscii(const std::string& filename);
+ FileReaderAscii(const std::string& filename, const char& fieldseparator);
+ ~FileReaderAscii(void);
+ void open(const std::string& filename);
+ void close(void);
+ void setFieldSeparator(const char& fieldseparator){m_fs=fieldseparator;};
+ void setMinRow(int minRow){m_minRow=minRow;};
+ void setMaxRow(int maxRow){m_maxRow=maxRow;};
+ void setComment(char comment){m_comment=comment;};
+ template<class T> unsigned int readData(vector<vector<T> > &dataVector,
const vector<int> &cols);
+ protected:
+ std::string m_filename;
+ std::ifstream m_ifstream;
+ char m_fs;
+ char m_comment;
+ double m_min;
+ double m_max;
+ int m_minRow;
+ int m_maxRow;
+};
+
+FileReaderAscii::FileReaderAscii(void)
+ : m_min(0),m_max(0),m_minRow(0),m_maxRow(0),m_fs(' '),m_comment('#'){
+}
+
+FileReaderAscii::FileReaderAscii(const std::string& filename)
+ : m_min(0),m_max(0),m_minRow(0),m_maxRow(0),m_fs(' '),m_comment('#'){
+ open(filename);
+}
+
+FileReaderAscii::~FileReaderAscii(void)
+{
+}
+
+void FileReaderAscii::open(const std::string& filename){
+ m_filename=filename;
+ m_ifstream.open(filename.c_str(),ios_base::in);
+ if(!(m_ifstream)){
+ string errorString;
+ errorString="Error: could not open file ";
+ errorString+=filename;
+ throw(errorString);
+ }
+}
+
+void FileReaderAscii::close(){
+ m_ifstream.close();
+ // m_ifstream.clear();
+}
+
+template<class T> unsigned int FileReaderAscii::readData(vector<vector<T> >
&dataVector, const vector<int> &cols){
+ bool verbose=false;
+ dataVector.clear();
+ dataVector.resize(cols.size());
+ int nrow=0;
+ bool withinRange=true;
+ if(m_fs>' '&&m_fs<='~'){//field separator is a regular character (minimum
ASCII code is space, maximum ASCII code is tilde)
+ if(verbose)
+ cout << "reading csv file " << m_filename << endl;
+ string csvRecord;
+ while(getline(m_ifstream,csvRecord)){//read a line
+ withinRange=true;
+ if(nrow<m_minRow)
+ withinRange=false;
+ if(m_maxRow>m_minRow)
+ if(nrow>m_maxRow)
+ withinRange=false;
+ if(withinRange){
+ istringstream csvstream(csvRecord);
+ string item;
+ int ncol=0;
+ bool isComment=false;
+ while(getline(csvstream,item,m_fs)){//read a column
+ if(verbose)
+ cout << item << " ";
+ unsigned pos=item.find(m_comment);
+ if(pos!=std::string::npos){
+ if(pos>0)
+ item=item.substr(0,pos-1);
+ else
+ break;
+ if(verbose)
+ std::cout << "comment found, string is " << item << std::endl;
+ isComment=true;
+ }
+ for(int icol=0;icol<cols.size();++icol){
+ if(ncol==cols[icol]){
+ T value=string2type<T>(item);
+ if((value>=m_min&&value<=m_max)||m_max<=m_min)
+ dataVector[icol].push_back(value);
+ }
+ }
+ ++ncol;
+ if(isComment)
+ break;
+ }
+ if(verbose)
+ cout << endl;
+ if(dataVector.back().size())
+ assert(ncol>=cols[0]);
+ }
+ ++nrow;
+ }
+ assert(dataVector.size());
+ }
+ else{//space or tab delimited fields
+ if(verbose)
+ std::cout << "space or tab delimited fields" << std::endl;
+ string spaceRecord;
+ while(!getline(m_ifstream, spaceRecord).eof()){
+ withinRange=true;
+ if(nrow<m_minRow)
+ withinRange=false;
+ if(m_maxRow>m_minRow)
+ if(nrow>m_maxRow)
+ withinRange=false;
+ if(withinRange){
+ if(verbose>1)
+ cout << spaceRecord << endl;
+ istringstream lineStream(spaceRecord);
+ string item;
+ int ncol=0;
+ bool isComment=false;
+ while(lineStream >> item){
+ if(verbose)
+ cout << item << " ";
+ // istringstream itemStream(item);
+ unsigned pos=item.find(m_comment);
+ if(pos!=std::string::npos){
+ if(pos>0)
+ item=item.substr(0,pos-1);
+ else
+ break;
+ if(verbose)
+ std::cout << "comment found, string is " << item << std::endl;
+ isComment=true;
+ }
+ T value=string2type<T>(item);
+ for(int icol=0;icol<cols.size();++icol){
+ if(ncol==cols[icol]){
+ if((value>=m_min&&value<=m_max)||m_max<=m_min)
+ dataVector[icol].push_back(value);
+ }
+ }
+ ++ncol;
+ if(isComment)
+ break;
+ }
+ if(verbose>1)
+ cout << endl;
+ if(verbose)
+ cout << "number of columns: " << ncol << endl;
+ if(dataVector.back().size())
+ assert(ncol>=cols[0]);
+ }
+ ++nrow;
+ }
+ }
+ return dataVector.size();
+}
+#endif // _IMGREADERASCII_H_
diff --git a/src/fileclasses/Makefile.am b/src/fileclasses/Makefile.am
index 2c18c66..e29e5df 100644
--- a/src/fileclasses/Makefile.am
+++ b/src/fileclasses/Makefile.am
@@ -11,7 +11,7 @@ noinst_LIBRARIES = libfileClasses.a
# where to install the headers on the system
libfileClasses_adir = $(includedir)/fileclasses
# the list of header files that belong to the library (to be installed later)
-libfileClasses_a_HEADERS = FileReaderLas.h
+libfileClasses_a_HEADERS = FileReaderLas.h FileReaderAscii.h
# the sources to add to the library and to add to the source distribution
libfileClasses_a_SOURCES = $(libfileClasses_a_HEADERS) FileReaderLas.cc
endif
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