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data_file_manager.cpp
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data_file_manager.cpp
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// viewpoints - interactive linked scatterplots and more.
// copyright 2005 Creon Levit and Paul Gazis, all rights reserved.
//***************************************************************************
// File name: data_file_manager.cpp
//
// Class definitions:
// Data_File_Manager -- Data file manager
//
// Classes referenced:
// Various BLITZ templates
//
// Required packages
// GSL 1.6 -- Gnu Scientific Library package for Windows
// Blitz++ 0.9 -- Various math routines
//
// Compiler directives:
// May require D__WIN32__ for the C++ compiler
//
// Purpose: Source code for <data_file_manager.h>
//
// Author: Creon Levit 2005-2006
// Modified: P. R. Gazis 23-SEP-2008
//***************************************************************************
// Include the necessary include libraries
#include "include_libraries_vp.h"
// Include globals
#include "global_definitions_vp.h"
// Include associated headers and source code
#include "data_file_manager.h"
#include "column_info.h"
#include "plot_window.h"
// These includes should not be necessary and have been commented out
// #include "Vp_File_Chooser.H" // PRG's new file chooser
// #include "Vp_File_Chooser.cpp" // PRG's new file chooser
// Be sure to define the static data member to hold column info
std::vector<Column_Info> Data_File_Manager::column_info;
// Set static data members for class Data_File_Manager::
string Data_File_Manager::SELECTION_LABEL = "SELECTION_BY_VP";
string Data_File_Manager::BINARY_FILE_WITH_ASCII_VALUES_LABEL =
"BINARY_FILE_WITH_ASCII_VP";
Fl_Window* Data_File_Manager::edit_labels_window = NULL;
Fl_Check_Browser* Data_File_Manager::edit_labels_widget = NULL;
int Data_File_Manager::needs_restore_panels_ = 0;
// Define and set maximums length of header lines and number of lines in the
// header block
const int Data_File_Manager::MAX_HEADER_LENGTH = MAXVARS*100;
const int Data_File_Manager::MAX_HEADER_LINES = 2000;
const bool include_line_number = false; // MCL XXX This should be an option
//***************************************************************************
// Data_File_Manager::Data_File_Manager() -- Default constructor, calls the
// initializer.
Data_File_Manager::Data_File_Manager() : delimiter_char_( ' '),
bad_value_proxy_( 0.0), maxpoints_( MAXPOINTS), maxvars_( MAXVARS),
inputFileType_( 0), outputFileType_( 0),
readSelectionInfo_( 0), doAppend( 0), doMerge( 0),
writeAllData_( 1), writeSelectionInfo_( 0), doCommentedLabels_( 0),
isColumnMajor( 0), isSavedFile_( 0), nDataRows_( 0), nDataColumns_( 0)
{
sDirectory_ = "."; // Default pathname
initialize();
}
//***************************************************************************
// Data_File_Manager::initialize() -- Reset control parameters.
void Data_File_Manager::initialize()
{
// Set default format information for file reads.
delimiter_char_ = ' ';
bad_value_proxy_ = 0.0;
maxpoints_ = MAXPOINTS;
maxvars_ = MAXVARS;
// Set default local values for file reads.
inputFileType_ = 0;
outputFileType_ = 1;
isAsciiData = 1-inputFileType_; // Conversion needed for legacy reasons
doAppend = 0;
doMerge = 0;
readSelectionInfo_ = 1;
writeAllData_ = 1;
writeSelectionInfo_ = 0;
isSavedFile_ = 0;
nDataRows_ = 0;
nDataColumns_ = 0;
needs_restore_panels_ = 0;
isColumnMajor = 1;
nSkipHeaderLines = 0; // Number of header lines to skip
// sDirectory_ = "."; // Default pathname -- NOT NEEDED!
inFileSpec = ""; // Default input filespec
outFileSpec = "";
dataFileSpec = "";
// Initialize the number of points and variables specified by the command
// line arguments. NOTE: 0 means read to EOF or end of line.
npoints_cmd_line = 0;
nvars_cmd_line = 0;
// Initialize number of points and variables
// npoints = MAXPOINTS;
// nvars = MAXVARS;
npoints = maxpoints_;
nvars = maxvars_;
}
//***************************************************************************
// Data_File_Manager::copy_state( *dfm) -- Copy control parameters from
// another object.
void Data_File_Manager::copy_state( Data_File_Manager* dfm)
{
// Copy format information for file reads.
delimiter_char_ = dfm->delimiter_char_;
bad_value_proxy_ = dfm->bad_value_proxy_;
maxpoints_ = dfm->maxpoints_;
maxvars_ = dfm->maxvars_;
// Copy local values for file reads.
inputFileType_ = dfm->inputFileType_;
outputFileType_ = dfm->outputFileType_;
isAsciiData = 1-inputFileType_; // Conversion needed for legacy reasons
doAppend = dfm->doAppend;
doMerge = dfm->doMerge;
readSelectionInfo_ = dfm->readSelectionInfo_;
writeAllData_ = dfm->writeAllData_;
writeSelectionInfo_ = dfm->writeSelectionInfo_;
isSavedFile_ = dfm->isSavedFile_;
nDataRows_ = dfm->nDataRows_;
nDataColumns_ = dfm->nDataColumns_;
needs_restore_panels_ = dfm->needs_restore_panels_;
isColumnMajor = dfm->isColumnMajor;
nSkipHeaderLines = dfm->nSkipHeaderLines; // Number of lines to skip
sDirectory_ = dfm->sDirectory_;
inFileSpec = dfm->inFileSpec; // ""; // Default input filespec
outFileSpec = dfm->outFileSpec;
dataFileSpec =dfm->dataFileSpec;
// Initialize the number of points and variables specified by the command
// line arguments. NOTE: 0 means read to EOF or end of line.
npoints_cmd_line = dfm->npoints_cmd_line;
nvars_cmd_line = dfm->nvars_cmd_line;
// Regenerate global number of points and variables. Note that the last
// Column_Info object is the dummy variable '-nothing-'
nvars = n_vars();
npoints = n_points();
}
//***************************************************************************
// Data_File_Manager::findInputFile() -- Query user to find the input file.
// Class Vp_File_Chooser is used in preference to a Vp_File_Chooser method
// to obtain access to member functions such as directory() and to allow the
// possibility of a derived class with additional controls in the window.
// Returns 0 if successful.
int Data_File_Manager::findInputFile()
{
// Print empty line to console for reasons of aesthetics
cout << endl;
// Generate text, file extensions, etc, for this file type. XXX PRG: Most
// of this should be moved to Vp_File_Chooser
string title;
string pattern;
if( inputFileType_ == 0) {
title = "Open data file";
pattern = "*.{txt,lis,asc}\tAll Files (*)";
}
else if( inputFileType_ == 1) {
title = "Open data file";
pattern = "*.bin\tAll Files (*)";
}
else if( inputFileType_ == 2) {
title = "Open data file";
pattern = "*.{fit,fits}\tAll Files (*)";
}
else {
title = "Open data file";
pattern = "*.bin\tAll Files (*)";
}
// Initialize read status and filespec. NOTE: cInFileSpec is defined as
// const char* for use with Vp_File_Chooser, which means it could be
// destroyed by the relevant destructors!
const char *cInFileSpec = sDirectory_.c_str();
// Instantiate and show an Vp_File_Chooser widget. NOTE: The pathname must
// be passed as a variable or the window will begin in some root directory.
Vp_File_Chooser* file_chooser =
new Vp_File_Chooser(
cInFileSpec, pattern.c_str(), Vp_File_Chooser::SINGLE, title.c_str());
file_chooser->fileType( inputFileType_);
// Comment this out to use the value file_chooser provides
// file_chooser->doCommentedLabels( doCommentedLabels_);
// Loop: Select fileSpecs until a non-directory is obtained. NOTE: If all
// goes well, this should be handled by the file_chooser object
while( 1) {
if( cInFileSpec != NULL) file_chooser->directory( cInFileSpec);
// Loop: wait until the file selection is done
file_chooser->show();
while( file_chooser->shown()) Fl::wait();
cInFileSpec = file_chooser->value();
// If no file was specified then quit
if( cInFileSpec == NULL) {
cerr << "Data_File_Manager::findInputFile: "
<< "No input file was specified" << endl;
break;
}
// In FLTK 1.1.7 under Windows, the fl_filename_isdir method doesn't work,
// so try to open this file to see if it is a directory. If it is, set
// the pathname and continue. Otherwise merely update the pathname.
FILE* pFile = fopen( cInFileSpec, "r");
if( pFile == NULL) {
file_chooser->directory( cInFileSpec);
directory( (string) cInFileSpec);
continue;
}
else {
directory( (string) file_chooser->directory());
}
fclose( pFile);
break;
}
// If no file was specified then report, deallocate the Vp_File_Chooser
// object, and quit.
if( cInFileSpec == NULL) {
cerr << "Data_File_Manager::findInputFile: "
<< "No input file was specified" << endl;
delete file_chooser; // WARNING! Destroys cInFileSpec!
return -1;
}
// Query Vp_File_Chooser object to get the file type, delimiter character,
// and usage of a comment character with the column label information
inputFileType_ = file_chooser->fileType();
delimiter_char_ = file_chooser->delimiter_char();
if( file_chooser->doCommentedLabels() != 0) doCommentedLabels_ = 1;
else doCommentedLabels_ = 0;
// Load the inFileSpec string
inFileSpec.assign( (string) cInFileSpec);
if( inputFileType_ == 0)
cout << "Data_File_Manager::inputFile: Reading ASCII data from <";
else if( inputFileType_ == 1)
cout << "Data_File_Manager::findInputFile: Reading binary data from <";
else if( inputFileType_ == 2)
cout << "Data_File_Manager::findInputFile: Reading FITS extension from <";
else
cout << "Data_File_Manager::findInputFile: Reading binary data from <";
cout << inFileSpec.c_str() << ">" << endl;
// Deallocate the file_chooser object
delete file_chooser; // WARNING! This destroys cInFileSpec!
// Perform partial initialization and return success
// nSkipHeaderLines = 1;
nSkipHeaderLines = 0;
npoints_cmd_line = 0;
nvars_cmd_line = 0;
// npoints = MAXPOINTS;
// nvars = MAXVARS;
npoints = maxpoints_;
nvars = maxvars_;
return 0;
}
//***************************************************************************
// Data_File_Manager::load_data_file( inFileSpec) -- Copy the input filespec,
// then invoke load_data_file to load this file.
int Data_File_Manager::load_data_file( string inFileSpec)
{
input_filespec( inFileSpec);
return load_data_file();
}
//***************************************************************************
// Data_File_Manager::load_data_file() -- Read an ASCII or binary data file,
// resize arrays to allocate meomory. Returns 0 if successful.
int Data_File_Manager::load_data_file()
{
// PRG XXX: Would it be possible or desirable to examine the file directly
// here to determine or verify its format?
if( inFileSpec.length() <= 0) {
cout << "Data_File_Manager::load_data_file: "
<< "No input file was specified" << endl;
return -1;
}
// If this is an append or merge operation, save the existing data and
// column labels in temporary buffers
unsigned uHaveOldData = 0;
int old_npoints=0, old_nvars=0;
std::vector<Column_Info> old_column_info;
blitz::Array<int,1> old_selected;
if( preserve_old_data_mode || doAppend > 0 || doMerge > 0) {
uHaveOldData = 1;
old_column_info = column_info;
old_nvars = n_vars();
old_npoints = n_points();
old_selected.resize(old_npoints);
old_selected = selected;
}
// Initialize READ_SELECTED here
// read_selected.resize( npoints);
// read_selected.resize( MAXPOINTS);
read_selected.resize( maxpoints_);
read_selected = 0;
// Read data file.If there was a problem, create default data to prevent
// a crash, then quit before something terrible happens! NOTE: The read
// methods load selection information, but don't resize read_selected;
cout << "Data_File_Manager::load_data_file: Reading input data from <"
<< inFileSpec.c_str() << ">" << endl;
int iReadStatus = 0;
if( inputFileType_ == 0) iReadStatus = read_ascii_file_with_headers();
else if( inputFileType_ == 2) iReadStatus = read_table_from_fits_file();
else iReadStatus = read_binary_file_with_headers();
if( iReadStatus != 0) {
cout << "Data_File_Manager::load_data_file: "
<< "Problems reading file <" << inFileSpec.c_str() << ">" << endl;
if( !uHaveOldData) create_default_data( 4);
else {
nvars = old_nvars;
npoints = old_npoints;
resize_global_arrays();
column_info = old_column_info;
selected = old_selected;
uHaveOldData = 0;
}
return -1;
}
else
cout << "Data_File_Manager::load_data_file: Finished reading file <"
<< inFileSpec.c_str() << ">" << endl;
// Resize the READ_SELECTED array here
if( npoints>0) read_selected.resizeAndPreserve( npoints);
// Remove trivial columns
if( npoints>0 && trivial_columns_mode) remove_trivial_columns();
// If only one or fewer records are available, generate default data to
// prevent a crash, then quit before something terrible happens!
if( npoints <= 0 ||
(( doAppend == 0 && doMerge == 0) && ( nvars <= 1 || npoints <= 1))) {
cerr << " -WARNING: Insufficient data, " << nvars << "x" << npoints
<< " samples.\nCheck delimiter character." << endl;
string sWarning = "";
sWarning.append( "WARNING: Insufficient number of attributes or samples\n.");
sWarning.append( "Check delimiter value and 'commented labels' setting.\n");
if( !uHaveOldData) {
sWarning.append( "Generating default data.");
create_default_data( 4);
}
else {
sWarning.append( "Restoring existing data.");
nvars = old_nvars;
npoints = old_npoints;
resize_global_arrays();
column_info = old_column_info;
selected = old_selected;
uHaveOldData = 0;
}
make_confirmation_window( sWarning.c_str(), 1, 3);
return -1;
}
else {
cout << "Data_File_Manager::load_data_file: Loaded " << npoints
<< " samples with " << nvars << " fields" << endl;
}
// MCL XXX Now that we're done reading, we can update nvars to count possible
// additional program-generated variables (presently only the line number).
if( include_line_number) nvars = nvars+1;
// Compare array sizes and finish the append or merge operation
if( doAppend > 0 | doMerge > 0) {
// If array sizes aren't consistent, restore the old data and column
// labels. Otherwise, reverse old and new arrays along the relevant
// dimensions, copy the old data to the new array, reverse the new array
// again, and copy new column labels if this was a merge operation.
if( ( doAppend > 0 && nvars != old_nvars) ||
( doMerge > 0 && npoints != old_npoints)) {
cout << "Old (" << old_nvars << "x" << old_npoints
<< ") array doesn't match new (" << nvars << "x" << npoints
<< ") array" << endl;
char cBuf[ 80];
sprintf(
cBuf, "Array sizes old(%ix%i) vs new(%ix%i) don't match.\n",
old_npoints, old_nvars, npoints, nvars);
string sWarning = "";
sWarning.append( cBuf);
sWarning.append( "Restoring old data.");
make_confirmation_window( sWarning.c_str(), 1);
nvars = old_nvars;
npoints = old_npoints;
resize_global_arrays();
column_info = old_column_info;
selected = old_selected;
return -1;
}
else if( doAppend > 0) {
// Current (e.g., new) column info and lookup table indices in the
// current (new) common data array must be revised first, before the
// current and old data arrays are appended.
for( int j=0; j<nvars; j++) {
column_info[j].add_info_and_update_data( old_column_info[j]);
}
// Enlarge buffer that contains old data to make space for current data
// and make sure current data buffer is the right size
int all_npoints = npoints + old_npoints;
for( int j=0; j<nvars; j++) {
(old_column_info[j].points).resizeAndPreserve(all_npoints);
(column_info[j].points).resizeAndPreserve(npoints);
}
// Append current data to old data and resize the current data buffer
for( int j=0; j<nvars; j++) {
(old_column_info[j].points(blitz::Range(old_npoints,all_npoints-1))) =
column_info[j].points;
(column_info[j].points).resize( all_npoints-1);
}
// Move combined data set back to the current data buffer
column_info = old_column_info;
npoints = all_npoints;
// Loop: Examine the vector of Column_Info objects to alphabetize
// ASCII values and renumber the data.
int nReordered = 0;
for( int j=0; j<nvars; j++) {
if( column_info[j].update_ascii_values_and_data() >=0) nReordered++;
}
}
else {
int all_nvars = nvars + old_nvars;
// This old code is retained for archival purposes to document how
// BLITZ arrays had to be reversed, appended, and re-reversed
// points.reverseSelf( blitz::firstDim);
// old_npoints.reverseSelf( blitz::firstDim);
// points.resizeAndPreserve( all_nvars, npoints);
// points(
// blitz::Range( nvars, all_nvars-1),
// blitz::Range( 0, npoints-1)) = old_npoints;
// points.reverseSelf( blitz::firstDim);
// Update the number of variables
nvars = all_nvars;
// Add new columns of data to the old data buffer
old_column_info.pop_back();
for( unsigned int i=0; i<column_info.size(); i++) {
old_column_info.push_back( column_info[ i]);
}
// Copy old data buffer to the current data buffer
column_info = old_column_info;
}
// Free memory in case this isn't handled by the compiler.
old_column_info.erase( old_column_info.begin(), old_column_info.end());
}
// If we read a different number of points then we anticipated, we must resize
// and preserve the current data buffer. Note this can take lot of time and
// memory temporarily. XXX it would be better to handle the growth/shrinkage
// of this buffer while reading.
if( npoints != npoints_cmd_line)
for( int j=0; j<nvars; j++)
(column_info[j].points).resizeAndPreserve( npoints);
// Now that we know the number of variables and points we've read, we can
// allocate and/or reallocateResize the other global arrays. NOTE: This
// will invoke reset_selection_arrays()
resize_global_arrays();
// Straighten out selection information. WARNING: This will die horribly
// if array sizes are not consistent
if( doMerge) selected = old_selected;
else if( doAppend) {
int new_npoints = read_selected.rows();
old_npoints = old_selected.rows();
// Make sure arrays sizes are consistent
if( npoints != new_npoints + old_npoints) {
cerr << "Data_File_Manager::load_data_file: ERROR, "
<< "selection arrays aren't consistent!" << endl
<< " old(" << old_npoints << ") + new(" << new_npoints
<< ") != total(" << npoints << ")" << endl;
}
selected( blitz::Range( 0, new_npoints-1)) = read_selected;
selected( blitz::Range( new_npoints, npoints-1)) = old_selected;
// selected( blitz::Range( 0, new_npoints-1)) =
// read_selected( blitz::Range( 0, new_npoints-1));
// selected( blitz::Range( new_npoints, npoints-1)) =
// old_selected( blitz::Range( 0, old_npoints-1));
}
else selected = read_selected;
read_selected.free();
old_selected.free();
// Refresh edit window, if it exists.
refresh_edit_column_info();
// Update dataFileSpec, set saved file flag, and report success
dataFileSpec = inFileSpec;
isAsciiData = 1-inputFileType_; // COnversion needed for legacy reasons
if( doAppend > 0 | doMerge > 0) isSavedFile_ = 0;
else isSavedFile_ = 1;
return 0;
}
//***************************************************************************
// Data_File_Manager::extract_column_labels( sLine, doDefault) -- Generate
// or extract column labels and selection flag and store them in the static
// member vector of Column_Info objects
int Data_File_Manager::extract_column_labels( string sLine, int doDefault)
{
// Initialize the static member vector of Column_Info objects
int nLabels = 0;
nvars = 0;
column_info.erase( column_info.begin(), column_info.end());
// If requested, examine the line, count the number of values, and use this
// information to generate a set of default column labels.
if( doDefault != 0) {
// If the delimiter character is not a tab, replace all tabs in the
// LINE string with spaces
if( delimiter_char_ != '\t') replace( sLine.begin(), sLine.end(), '\t', ' ');
// Loop: Insert the LINE string into a stream, define a buffer, read and
// count successive tokens, generate default column labels and load the
// vector of Column_Info objects, and report results. NOTE: whitespace-
// and character-delimited files must be handled differently
std::stringstream ss( sLine);
std::string buf;
Column_Info column_info_buf;
if( delimiter_char_ == ' ') {
while( ss >> buf) {
nvars++;
char cbuf[ 80];
(void) sprintf( cbuf, "%d", nvars);
buf = "Column_";
buf.append( cbuf);
column_info_buf.label = string( buf);
column_info.push_back( column_info_buf);
}
}
else {
while( getline( ss, buf, delimiter_char_)) {
nvars++;
char cbuf[ 80];
(void) sprintf( cbuf, "%d", nvars);
buf = "Column_";
buf.append( cbuf);
column_info_buf.label = string( buf);
column_info.push_back( column_info_buf);
}
}
nvars = column_info.size();
cout << " -Generated " << nvars
<< " default column labels." << endl;
}
// ...otherwise, examine the input line to extract column labels.
else {
// Discard the leading comment character, if any, of the SLINE string.
// The rest of the line is assumed to contain column labels
if( sLine.find_first_of( "!#%") == 0) sLine.erase( 0, 1);
// Loop: Insert the SLINE string into a stream, define a buffer, read
// successive labels into the buffer, then load them into the vector of
// Column_Info objects, and report results. NOTE: whitespace- and
// character-delimited labels must be handled differently. Also, it is
// necessary to trim whitespace and verify character-delimited labels.
std::stringstream ss( sLine);
std::string buf;
Column_Info column_info_buf;
if( delimiter_char_ == ' ')
while( ss >> buf) {
column_info_buf.label = string( buf);
column_info.push_back( column_info_buf);
}
else {
while( getline( ss, buf, delimiter_char_)) {
string::size_type notwhite = buf.find_first_not_of( " ");
buf.erase( 0, notwhite);
notwhite = buf.find_last_not_of( " \n");
buf.erase( notwhite+1);
if( buf.size() <= 0) buf = "Dummy";
column_info_buf.label = string( buf);
column_info.push_back( column_info_buf);
}
}
nvars = column_info.size();
cout << " -Extracted " << nvars << " column labels." << endl;
}
// If there were more than NVARS_CMD_LINE variables in the file, truncate
// the vector of Column_Info objects, reset NVARS, and warn the user.
if( nvars_cmd_line > 0 && nvars > nvars_cmd_line) {
column_info.erase( column_info.begin()+nvars_cmd_line, column_info.end());
nvars = column_info.size();
cerr << " -WARNING: Too many variables, truncated list to " << nvars
<< " column labels." << endl;
}
// Examine the number of Column_Info objects that remain. If it is too
// low or high, report error, close input file, and quit. Otherwise
// report success.
// if( nvars <= 1) {
if( doMerge == 0 && nvars <= 1) {
cerr << " -WARNING, insufficient number of columns (" << nvars
<< "), check for correct delimiter character"
<< endl;
string sWarning = "";
sWarning.append( "WARNING: Couldn't identify enough columns of data\n.");
sWarning.append( "Check delimiter value and 'commented labels' setting.");
make_confirmation_window( sWarning.c_str(), 1);
return -1;
}
// if( nvars > MAXVARS) {
if( nvars > maxvars_) {
cerr << " -WARNING, too many data columns, "
<< "increase MAXVARS and recompile"
<< endl;
make_confirmation_window( "WARNING: Too many data columns.", 1);
return -1;
}
cout << " -Examined header of <" << inFileSpec.c_str() << ">," << endl
<< " There should be " << nvars
<< " fields (columns) per record (row)" << endl;
// If requested, add a column to contain line numbers but don't increment
// NVARS. Note: this is old code thatmay no longer wirk
Column_Info column_info_buf;
if( include_line_number) {
column_info_buf.label = string( "-line number-");
column_info.push_back( column_info_buf);
}
// Add a final dummy column label that says '-nothing-' but don't
// increment NVARS.
column_info_buf.label = string( "-nothing-");
column_info.push_back( column_info_buf);
// Update NLABELS to include the final dummy column label and report
// label information
nLabels = column_info.size();
cout << " -Read " << nLabels << "/" << nLabels;
if( delimiter_char_ == ' ') cout << " whitespace-delimited ";
else if( delimiter_char_ == ',') cout << " comma-delimited ";
else cout << " custom-delimited ";
cout << "column_labels:" << endl;
// Clever output formatting to keep line lengths under control. NOTE:
// This will misbehave if some label is more than 80 characters long.
cout << " ";
int nLineLength = 4;
for( unsigned int i=0; i < column_info.size(); i++ ) {
nLineLength += 2+(column_info[ i].label).length();
if( nLineLength > 80) {
cout << endl << " ";
nLineLength = 4 + (column_info[ i].label).length();
}
cout << " (" << column_info[ i].label << ")";
}
cout << endl;
// Check the last column of data to see if it is the selection label,
// SELECTION_LABEL. Note that since NVARS was not incremented, this
// will be the column BEFORE the new final column labelled '-nothing-'.
readSelectionInfo_ = 0;
if( (column_info[nvars-1].label).compare( 0, SELECTION_LABEL.size(), SELECTION_LABEL) == 0) {
readSelectionInfo_ = 1;
cout << " -Read selection info-" << endl;
}
// Return the number of labels. Note that this will include any
// additional non-data columns added after the NVARS data columns.
return nLabels;
}
//***************************************************************************
// Data_File_Manager::extract_column_types( sLine) -- Examine a line of data
// to determine which columns contain ASCII values. NOTE: This should be
// consolidated with some other method to avoid duplicate code.
void Data_File_Manager::extract_column_types( string sLine)
{
// If the delimiter character is not a tab, replace tabs with spaces
if( delimiter_char_ != '\t')
replace( sLine.begin(), sLine.end(), '\t', ' ');
// Loop: Insert the string into a stream and read it
std::stringstream ss( sLine);
unsigned isBadData = 0;
string sToken;
// double xValue;
for( int j=0; j<nvars; j++) {
// Get the next word. NOTE: whitespace-delimited and character-
// delimited files must be handled differently. PROBLEM: This may not
// handle missing values correctly, if at all.
if( delimiter_char_ == ' ') ss >> sToken;
else {
std::string buf;
getline( ss, buf, delimiter_char_);
// Check for missing data
string::size_type notwhite = buf.find_first_not_of( " ");
buf.erase( 0, notwhite);
notwhite = buf.find_last_not_of( " ");
buf.erase( notwhite+1);
if( buf.size() <= 0) sToken = string( "BAD_VALUE_PROXY");
else {
stringstream bufstream;
bufstream << buf;
bufstream >> sToken;
}
}
// Issue warning and quit if this line doesn't contain enough data
if( ss.eof() && j<nvars-1) {
cerr << " -WARNING, extract_column_types reports "
<< "not enough data on first line!" << endl
<< " skipping entire line." << endl;
isBadData = 1;
break;
}
// Issue warning and quit if this line contains unreadable data. NOTE:
// This should never happen, because error flags were cleared above.
if( !ss.good() && j<nvars-1) {
cerr << " -WARNING, extract_column_types reports unreadable data "
<< "(binary or ASCII?) on first line at column " << j+1
<< "," << endl
<< " skipping entire line." << endl;
isBadData = 1;
break;
}
// Attempt to use strod and examine values and pointers to determine if
// token can be parsed as a double. This code doesn't work
// int hasASCII = 0;
// char **cEnd;
// char cToken[80];
// double xTest = std::strtod( sToken.c_str(), cEnd);
// if( xValue == 0 && cEnd != &(sToken.c_str())) hasASCII = 1;
// else hasASCII = 0;
// Convert token to a stringstream and try to read it to determine if it
// can be parsed as a double. If the stringstream >> operator returns 0,
// the read failed and the token couldn't be parsed. WARNING: It remains
// to be determined if this works on all compilers!
int hasASCII = 0;
std::istringstream inpStream( sToken);
double inpValue = 0.0;
if( inpStream >> inpValue) hasASCII = 0;
else hasASCII = 1;
// Treat the string 'NaN' as numerical. Yes, it might be better to
// convert sToken to uppercase, but I'm lazy
if( sToken.compare( "NAN") == 0 ||
sToken.compare( "NaN") == 0 ||
sToken.compare( "nan") == 0) hasASCII = 0;
// Load information into the vector of Column_Info objects
column_info[ j].hasASCII = hasASCII;
}
}
//***************************************************************************
// Data_File_Manager::remove_column_of_selection_info() -- If selection
// information was found, remove the second-to-last column element in the
// vector of Column_Info objects, which is assumed to contain the selection
// label, SELECTION_LABEL, then update and return the number of data columns.
int Data_File_Manager::remove_column_of_selection_info()
{
int nColumns = column_info.size();
if( readSelectionInfo_) {
int iTarget = nColumns-1;
vector<Column_Info>::iterator pTarget = column_info.end();
iTarget--;
iTarget--;
pTarget--;
pTarget--;
// if( include_line_number) {
// iTarget--;
// pTarget--;
// }
column_info.erase( pTarget);
nColumns = column_info.size();
cout << " -Removed column[" << iTarget << "/" << nColumns
<< "] with selection information" << endl;
}
return nColumns;
}
//***************************************************************************
// Data_File_Manager::read_ascii_file_with_headers() -- Reads and ASCII file.
// Step 1: Open an ASCII file for input. Step 2: Read and discard the header
// block. Step 3: Generate column labels. Step 4: Read the data block.
// Step 5: Close the file. Returns 0 if successful.
int Data_File_Manager::read_ascii_file_with_headers()
{
istream* inStream;
ifstream inFile;
// STEP 1: Either read from stdin, bypassing openning of input file, or
// attempt to open input file and make sure it exists.
if( read_from_stdin) {
inStream = &cin;
}
else {
inFile.open( inFileSpec.c_str(), ios::in);
if( inFile.bad() || !inFile.is_open()) {
cerr << "read_ascii_file_with_headers:" << endl
<< " -ERROR, couldn't open <" << inFileSpec.c_str()
<< ">" << endl;
return 1;
}
else {
cout << "read_ascii_file_with_headers:" << endl
<< " -Opened <" << inFileSpec.c_str() << ">" << endl;
}
inStream = &inFile;
}
// STEP 2: Read and discard the header block, but save the last line of
// the header in the LASTHEADERLINE buffer
// Loop: Read successive lines to find and store the last line of the
// header block. NOTE: Since tellg() and seekg() don't seem to work
// properly with getline() with all compilers, this must be accomplished
// by reading and counting each line explicitly.
std::string line = "";
std::string lastHeaderLine = "";
int nRead = 0, nHeaderLines = 0;
for( int iLine = 0; iLine < MAX_HEADER_LINES; iLine++) {
if( inStream->eof() != 0) break;
(void) getline( *inStream, line, '\n');
nRead++;
// Skip empty lines without updating the LASTHEADERLINE buffer
if( line.length() == 0) {
nHeaderLines++;
continue;
}
// If this line is supposed to be skipped or if it begins with a comment
// character, skip it and update the LASTHEADERLINE buffer
if( iLine < nSkipHeaderLines ||
line.length() == 0 || line.find_first_of( "!#%") == 0) {
lastHeaderLine = line;
nHeaderLines++;
continue;
}
break;
}
cout << " -Header block contains " << nHeaderLines
<< " header lines." << endl;
// STEP 3: Get column labels from either the last line of the header
// block or the first line of the data block. Under certain conditions,
// generate default column labels.
// If the DOCOMMENTEDLABELS_ flag is set, unset the UREADNEXTLINE flag to
// preserve LINE as the first record in the data block, then examine the
// last line of the header block. If this doesn't exist or is empty,
// generate default column labels, if it contains information, parse this
// to extract column labels. Otherwise, parse the first line of the data
// block to extract column labels, and if these all seem to be numeric,
// replace them with default column labels and unset the UREADNEXTLINE
// flag as described above.
int nLabels = 0;
unsigned uReadNextLine = 1;
if( doCommentedLabels_) {
uReadNextLine = 0;
if( nHeaderLines == 0 || lastHeaderLine.length() == 0)
nLabels = extract_column_labels( line, 1);
else nLabels = extract_column_labels( lastHeaderLine, 0);
}
else {
nLabels = extract_column_labels( line, 0);
extract_column_types( line);
if( n_ascii_columns() <= 0 && nLabels > 0) {
uReadNextLine = 0;
extract_column_labels( line, 1);
}
}
// If there were problems, close file and quit
if( nLabels < 0 && !read_from_stdin) {
cout << "Data_File_Manager::read_ascii_file_with_headers: "
<< "Couldn't identify any column labels." << endl;
inFile.close();
return 1;
}
// STEP 4: Read the data block
// Now we know the number of variables, NVARS, so if we also know the
// number of points (e.g. from the command line) we can size the main
// points array once and for all, and not waste memory.
if( npoints_cmd_line > 0) npoints = npoints_cmd_line;
// else npoints = MAXPOINTS;
else npoints = maxpoints_;
nDataColumns_ = nvars;
if( include_line_number) nDataColumns_++; // Add column for line number
if( readSelectionInfo_) nDataColumns_--; // Don't store selection info
for( int j=0; j<nDataColumns_; j++)
(column_info[j].points).resize( npoints);
// Loop: Read successive lines from the file
int nSkip = 0;
nDataRows_ = 0;
int nTestCycle = 0, nUnreadableData = 0;
while( !inStream->eof() && nDataRows_<npoints) {
// Get the next line, check for EOF, and increment accounting information
if( uReadNextLine) {
(void) getline( *inStream, line, '\n');
if( inStream->eof()) break; // Break here to make accounting work right
nRead++;
}
// Skip blank lines and comment lines
if( line.length() == 0 || line.find_first_of( "!#%") == 0) {
nSkip++;
uReadNextLine = 1;
continue;
}
uReadNextLine = 1;
nTestCycle++;
// Invoke member function to examine the first line of data to identify
// columns that contain ASCII values and load this information into the
// vector of column_info objects
if( nDataRows_ == 0) extract_column_types( line);
// If the delimiter character is not a tab, replace tabs with spaces
if( delimiter_char_ != '\t')
replace( line.begin(), line.end(), '\t', ' ');
// Loop: Insert the string into a stream and read it
std::stringstream ss( line);
unsigned isBadData = 0;
double xValue;
string sToken;
for( int j=0; j<nvars; j++) {
// Read the next word as double or a string, depending on whether or
// not this column contains ASCII values. NOTE: whitespace-delimited
// and character-delimited files must be handled differently.
// PROBLEM: This isn't handling missing values correctly
if( delimiter_char_ == ' ') {
// if( column_info[j].hasASCII == 0) ss >> xValue;
// else ss >> sToken;
ss >> sToken;
if( column_info[j].hasASCII == 0) {
stringstream bufstream;
bufstream << sToken;
bufstream >> xValue;
if( sToken.compare( 0, 3, "NaN") == 0) xValue = bad_value_proxy_;
}
}
else {
std::string buf;
getline( ss, buf, delimiter_char_);
// Check for missing data