GFitsTableBitCol.cpp
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/***************************************************************************
* GFitsTableBitCol.cpp - FITS table Bit column class *
* ----------------------------------------------------------------------- *
* copyright (C) 2008-2013 by Juergen Knoedlseder *
* ----------------------------------------------------------------------- *
* *
* 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 3 of the License, or *
* (at your option) any later version. *
* *
* This program is distributed in the hope that it will be useful, *
* but WITHOUT ANY WARRANTY; without even the implied warranty of *
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the *
* GNU General Public License for more details. *
* *
* You should have received a copy of the GNU General Public License *
* along with this program. If not, see <http://www.gnu.org/licenses/>. *
* *
***************************************************************************/
/**
* @file GFitsTableBitCol.cpp
* @brief FITS table bit column class implementation
* @author Juergen Knoedlseder
*/
/* __ Includes ___________________________________________________________ */
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif
#include <string>
#include "GException.hpp"
#include "GTools.hpp"
#include "GFitsCfitsio.hpp"
#include "GFitsTableBitCol.hpp"
/* __ Method name definitions ____________________________________________ */
#define G_INSERT "GFitsTableBitCol::insert(int&, int&)"
#define G_REMOVE "GFitsTableBitCol::remove(int&, int&)"
#define G_LOAD_COLUMN "GFitsTableBitCol::load_column()"
#define G_SAVE_COLUMN "GFitsTableBitCol::save_column()"
#define G_GET_BIT "GFitsTableBitCol::get_bit(int&,int&)"
/* __ Macros _____________________________________________________________ */
/* __ Coding definitions _________________________________________________ */
/* __ Debug definitions __________________________________________________ */
//#define G_CALL_GRAPH //!< Dump call graph in console
/*==========================================================================
= =
= Constructors/destructors =
= =
==========================================================================*/
/***********************************************************************//**
* @brief Constructor
***************************************************************************/
GFitsTableBitCol::GFitsTableBitCol(void) : GFitsTableCol()
{
// Initialise class members for clean destruction
init_members();
// Return
return;
}
/***********************************************************************//**
* @brief Constructor
*
* @param[in] name Name of column.
* @param[in] length Length of column.
* @param[in] size Vector size of column.
***************************************************************************/
GFitsTableBitCol::GFitsTableBitCol(const std::string& name,
const int& length,
const int& size) :
GFitsTableCol(name, length, size, 1)
{
// Initialise class members for clean destruction
init_members();
// Return
return;
}
/***********************************************************************//**
* @brief Copy constructor
*
* @param[in] column Table column.
***************************************************************************/
GFitsTableBitCol::GFitsTableBitCol(const GFitsTableBitCol& column) :
GFitsTableCol(column)
{
// Initialise class members for clean destruction
init_members();
// Copy members
copy_members(column);
// Return
return;
}
/***********************************************************************//**
* @brief Destructor
***************************************************************************/
GFitsTableBitCol::~GFitsTableBitCol(void)
{
// Free members
free_members();
// Return
return;
}
/*==========================================================================
= =
= Operators =
= =
==========================================================================*/
/***********************************************************************//**
* @brief Assignment operator
*
* @param[in] column Table column.
* @return Table column.
***************************************************************************/
GFitsTableBitCol& GFitsTableBitCol::operator=(const GFitsTableBitCol& column)
{
// Execute only if object is not identical
if (this != &column) {
// Copy base class members
this->GFitsTableCol::operator=(column);
// Free members
free_members();
// Initialise private members for clean destruction
init_members();
// Copy members
copy_members(column);
} // endif: object was not identical
// Return this object
return *this;
}
/***********************************************************************//**
* @brief Column data access operator
*
* @param[in] row Row of column to access.
* @param[in] inx Vector index in column row to access.
*
* Provides access to data in a column.
***************************************************************************/
bool& GFitsTableBitCol::operator()(const int& row, const int& inx)
{
// If data are not available then load them now
if (m_data == NULL) this->fetch_data();
// Set any pending Bit
set_pending();
// Get Bit
get_bit(row, inx);
// Signal that a Bit is pending. We need this here since the non-const
// operator allows changing the Bit after exiting the method, hence
// we have to signal that the actual value of 'm_bit_value' could have
// been modified and needs to be written back into the data array.
m_bit_pending = true;
// Return Bit
return m_bit_value;
}
/***********************************************************************//**
* @brief Column data access operator (const variant)
*
* @param[in] row Row of column to access.
* @param[in] inx Vector index in column row to access
*
* Provides access to data in a column.
***************************************************************************/
const bool& GFitsTableBitCol::operator()(const int& row, const int& inx) const
{
// Circumvent const correctness
GFitsTableBitCol* ptr = const_cast<GFitsTableBitCol*>(this);
// If data are not available then load them now
if (m_data == NULL) ptr->fetch_data();
// Set any pending Bit
ptr->set_pending();
// Get Bit
ptr->get_bit(row, inx);
// Return data bin
return m_bit_value;
}
/*==========================================================================
= =
= Public methods =
= =
==========================================================================*/
/***********************************************************************//**
* @brief Clear instance
*
* This method properly resets the object to an initial state.
***************************************************************************/
void GFitsTableBitCol::clear(void)
{
// Free class members (base and derived classes, derived class first)
free_members();
this->GFitsTableCol::free_members();
// Initialise members
this->GFitsTableCol::init_members();
init_members();
// Return
return;
}
/***********************************************************************//**
* @brief Clone column
***************************************************************************/
GFitsTableBitCol* GFitsTableBitCol::clone(void) const
{
return new GFitsTableBitCol(*this);
}
/***********************************************************************//**
* @brief Get string value
*
* @param[in] row Table row.
* @param[in] inx Table column vector index.
*
* Returns value of specified row and vector index as string.
***************************************************************************/
std::string GFitsTableBitCol::string(const int& row, const int& inx) const
{
// Get Bit value
bool bit = (*this)(row, inx);
// Convert bit into string
std::string result = (bit) ? "T" : "F";
// Return result
return result;
}
/***********************************************************************//**
* @brief Get double precision value
*
* @param[in] row Table row.
* @param[in] inx Table column vector index.
*
* Returns value of specified row and vector index as double precision.
***************************************************************************/
double GFitsTableBitCol::real(const int& row, const int& inx) const
{
// Get Bit value
bool bit = (*this)(row, inx);
// Convert bit into double
double result = (bit) ? 1.0 : 0.0;
// Return result
return result;
}
/***********************************************************************//**
* @brief Get integer value
*
* @param[in] row Table row.
* @param[in] inx Table column vector index.
*
* Returns value of specified row and vector index as integer.
***************************************************************************/
int GFitsTableBitCol::integer(const int& row, const int& inx) const
{
// Get Bit value
bool bit = (*this)(row, inx);
// Convert bit into double
int result = (bit) ? 1 : 0;
// Return result
return result;
}
/***********************************************************************//**
* @brief Insert rows in column
*
* @param[in] row Row after which rows should be inserted (0=first row).
* @param[in] nrows Number of rows to be inserted.
*
* @exception GException::fits_invalid_row
* Specified row is invalid.
*
* This method inserts rows into a FITS table. This implies that the column
* will be loaded into memory.
***************************************************************************/
void GFitsTableBitCol::insert(const int& row, const int& nrows)
{
// Make sure that row is valid
if (row < 0 || row > m_length) {
throw GException::fits_invalid_row(G_INSERT, row, m_length);
}
// Continue only if there are rows to be inserted
if (nrows > 0) {
// If we have no rows yet then simply set the length to the
// number of rows to be inserted
if (m_length == 0) {
m_length = nrows;
}
// ... otherwise fetch data, allocate new data and copy over
// the existing items
else {
// If data are not available then load them now
if (m_data == NULL) fetch_data();
// Set any pending Bit
set_pending();
// Compute new column length
int length = m_length + nrows;
// Compute total number of Bits in column
m_bits = m_number * length;
// Compute number of Bytes and Bits per row
m_bytes_per_row = (m_number > 0) ? ((m_number-1) / 8) + 1 : 0;
m_bits_per_row = m_bytes_per_row * 8;
// Compute length of memory array
m_size = m_bytes_per_row * length;
// Allocate new data to hold the column
unsigned char* new_data = new unsigned char[m_size];
// Compute the number of elements before the insertion point,
// the number of elements that get inserted, and the total
// number of elements after the insertion point
int n_before = m_bytes_per_row * row;
int n_insert = m_bytes_per_row * nrows;
int n_after = m_bytes_per_row * (m_length - row);
// Copy and initialise data
unsigned char* src = m_data;
unsigned char* dst = new_data;
for (int i = 0; i < n_before; ++i) {
*dst++ = *src++;
}
for (int i = 0; i < n_insert; ++i) {
*dst++ = 0;
}
for (int i = 0; i < n_after; ++i) {
*dst++ = *src++;
}
// Free old data
if (m_data != NULL) delete [] m_data;
// Set pointer to new data and store length
m_data = new_data;
m_length = length;
} // endelse: there were already data
} // endfor: there were rows to be inserted
// Return
return;
}
/***********************************************************************//**
* @brief Remove rows from column
*
* @param[in] row Row after which rows should be removed (0=first row).
* @param[in] nrows Number of rows to be removed.
*
* @exception GException::fits_invalid_row
* Specified row is invalid.
* @exception GException::fits_invalid_nrows
* Invalid number of rows specified.
*
* This method removes rows from a FITS table. This implies that the column
* will be loaded into memory.
***************************************************************************/
void GFitsTableBitCol::remove(const int& row, const int& nrows)
{
// Make sure that row is valid
if (row < 0 || row >= m_length) {
throw GException::fits_invalid_row(G_REMOVE, row, m_length-1);
}
// Make sure that we don't remove beyond the limit
if (nrows < 0 || nrows > m_length-row) {
throw GException::fits_invalid_nrows(G_REMOVE, nrows, m_length-row);
}
// Continue only if there are rows to be removed
if (nrows > 0) {
// If data are not available then load them now
if (m_data == NULL) fetch_data();
// Set any pending Bit
set_pending();
// Compute new column length
int length = m_length - nrows;
// Compute total number of Bits in column
m_bits = m_number * length;
// Compute number of Bytes and Bits per row
m_bytes_per_row = (m_number > 0) ? ((m_number-1) / 8) + 1 : 0;
m_bits_per_row = m_bytes_per_row * 8;
// Compute length of memory array
m_size = m_bytes_per_row * length;
// If we have rows remaining then allocate new data to hold
// the column
if (m_size > 0) {
// Allocate new data to hold the column
unsigned char* new_data = new unsigned char[m_size];
// Compute the number of elements before the removal point,
// the number of elements that get removed, and the total
// number of elements after the removal point
int n_before = m_bytes_per_row * row;
int n_remove = m_bytes_per_row * nrows;
int n_after = m_bytes_per_row * (length - row);
// Copy data
unsigned char* src = m_data;
unsigned char* dst = new_data;
for (int i = 0; i < n_before; ++i) {
*dst++ = *src++;
}
src += n_remove;
for (int i = 0; i < n_after; ++i) {
*dst++ = *src++;
}
// Free old data
if (m_data != NULL) delete [] m_data;
// Set pointer to new data and store length
m_data = new_data;
m_length = length;
} // endif: there are still elements after removal
// ... otherwise just remove all data
else {
// Free old data
if (m_data != NULL) delete [] m_data;
// Set pointer to new data and store length
m_data = NULL;
m_length = length;
}
} // endfor: there were rows to be removed
// Return
return;
}
/***********************************************************************//**
* @brief Set nul value
*
* @param[in] value Nul value.
*
* @todo To correctly reflect the nul value in the data, the column should
* be reloaded. However, the column may have been changed, so in principle
* saving is needed. However, we may not want to store the data, hence saving
* is also not desired. We thus have to develop a method to update the
* column information for a new nul value in place ...
***************************************************************************/
void GFitsTableBitCol::nulval(const unsigned char* value)
{
// Allocate nul value
alloc_nulval(value);
// Update column
// if (m_data != NULL) {
// save();
// load();
// }
// Return
return;
}
/*==========================================================================
= =
= Private methods =
= =
==========================================================================*/
/***********************************************************************//**
* @brief Initialise class members
***************************************************************************/
void GFitsTableBitCol::init_members(void)
{
// Optionally print call graph
#if defined(G_CALL_GRAPH)
printf("GFitsTableBitCol::init_members\n");
#endif
// Initialise members
m_type = __TBIT;
m_bits = 0;
m_bytes_per_row = 0;
m_bits_per_row = 0;
m_data = NULL;
m_nulval = NULL;
m_bit_pending = false;
m_bit_value = false;
m_bit_byte = 0;
m_bit_mask = 0;
// Optionally print call graph
#if defined(G_CALL_GRAPH)
printf("exit GFitsTableBitCol::init_members\n");
#endif
// Return
return;
}
/***********************************************************************//**
* @brief Copy class members
*
* @param[in] column Column.
*
* Sets the content of the vector column by copying from another column.
* If the code is compiled with the small memory option, and if the source
* column has not yet been loaded, then we only load the column temporarily
* for copying purposes and release it again once copying is finished.
***************************************************************************/
void GFitsTableBitCol::copy_members(const GFitsTableBitCol& column)
{
// Fetch data if necessary
bool not_loaded = (!column.is_loaded());
if (not_loaded) {
column.fetch_data();
}
// Copy attributes
m_type = column.m_type;
m_size = column.m_size;
m_varlen = column.m_varlen;
m_rowstart = column.m_rowstart;
m_bits = column.m_bits;
m_bytes_per_row = column.m_bytes_per_row;
m_bits_per_row = column.m_bits_per_row;
m_bit_pending = column.m_bit_pending;
m_bit_value = column.m_bit_value;
m_bit_byte = column.m_bit_byte;
m_bit_mask = column.m_bit_mask;
// Copy column data
if (column.m_data != NULL && m_size > 0) {
alloc_data();
for (int i = 0; i < m_size; ++i)
m_data[i] = column.m_data[i];
}
// Copy NULL value
alloc_nulval(column.m_nulval);
// Small memory option: release column if it was fetch above
#if defined(G_SMALL_MEMORY)
if (not_loaded) {
const_cast<GFitsTableBitCol*>(&column)->release_data();
}
#endif
// Return
return;
}
/***********************************************************************//**
* @brief Delete class members
***************************************************************************/
void GFitsTableBitCol::free_members(void)
{
// Optionally print call graph
#if defined(G_CALL_GRAPH)
printf("GFitsTableBitCol::free_members\n");
#endif
// Free memory
if (m_data != NULL) delete [] m_data;
if (m_nulval != NULL) delete m_nulval;
// Mark memory as freed
m_data = NULL;
m_nulval = NULL;
// Reset load flag
m_size = 0;
// Optionally print call graph
#if defined(G_CALL_GRAPH)
printf("exit GFitsTableBitCol::free_members\n");
#endif
// Return
return;
}
/***********************************************************************//**
* @brief Returns format string of ASCII table
***************************************************************************/
std::string GFitsTableBitCol::ascii_format(void) const
{
// Initialize format string
std::string format;
// Set type code
format.append("I");
// Set width
format.append(gammalib::str(m_width));
// Return format
return format;
}
/***********************************************************************//**
* @brief Allocates column data
***************************************************************************/
void GFitsTableBitCol::alloc_data(void)
{
// Optionally print call graph
#if defined(G_CALL_GRAPH)
printf("GFitsTableBitCol::alloc_data(%d)\n", m_size);
#endif
// Free any existing memory
if (m_data != NULL) delete [] m_data;
// Mark pointer as free
m_data = NULL;
// Allocate new data
if (m_size > 0) {
m_data = new unsigned char[m_size];
}
// Optionally print call graph
#if defined(G_CALL_GRAPH)
printf("exit GFitsTableBitCol::alloc_data(m_data=%x)\n", m_data);
#endif
// Return
return;
}
/***********************************************************************//**
* @brief Fetch column data
*
* This method fetches column data when needed. It is declared const, so
* that const data access methods can be implemented.
*
* If a FITS file is attached to the column the data are loaded into memory
* from the FITS file. If no FITS file is attached, memory is allocated
* to hold the column data and all cells are initialised.
*
* This method calls GFitsTableCol::load_column to do the job.
***************************************************************************/
void GFitsTableBitCol::fetch_data(void) const
{
// Load column (circumvent const correctness)
const_cast<GFitsTableBitCol*>(this)->load_column();
// Return
return;
}
/***********************************************************************//**
* @brief Resize column data
*
* @param[in] index Start index.
* @param[in] number Number of elements to add/remove.
*
* Adds or removes elements from specified index on. Adding is done if
* @p number is a positive number, removing if @p number is negative.
* Note that the method does not change the validity of the arguments.
* This needs to be done by the client.
*
* @todo Needs to be implemented
***************************************************************************/
void GFitsTableBitCol::resize_data(const int& index, const int& number)
{
//TODO
// Return
return;
}
/***********************************************************************//**
* @brief Release column data
***************************************************************************/
void GFitsTableBitCol::release_data(void)
{
// Free any existing memory
if (m_data != NULL) delete [] m_data;
// Mark pointer as free and reset loaded vector size
m_data = NULL;
m_size = 0;
// Return
return;
}
/***********************************************************************//**
* @brief Allocates null value
***************************************************************************/
void GFitsTableBitCol::alloc_nulval(const unsigned char* value)
{
// Free any existing memory
if (m_nulval != NULL) delete m_nulval;
// Mark pointer as free
m_nulval = NULL;
// If we have valid value, allocate and set nul value
if (value != NULL) {
m_nulval = new unsigned char;
*m_nulval = *value;
}
// Return
return;
}
/***********************************************************************//**
* @brief Initialise column data
***************************************************************************/
void GFitsTableBitCol::init_data(void)
{
// Initialise data if they exist
if (m_data != NULL) {
for (int i = 0; i < m_size; ++i) {
m_data[i] = 0;
}
}
// Return
return;
}
/***********************************************************************//**
* @brief Load table column from FITS file
*
* @exception GException::fits_hdu_not_found
* Specified HDU not found in FITS file.
* @exception GException::fits_error
* An error occured while loading column data from FITS file.
*
* Load Bit (vector) column into memory by reading 8 Bits at once.
***************************************************************************/
void GFitsTableBitCol::load_column(void)
{
// Compute total number of Bits in column
m_bits = m_number * m_length;
// Compute number of Bytes and Bits per row
m_bytes_per_row = (m_number > 0) ? ((m_number-1) / 8) + 1 : 0;
m_bits_per_row = m_bytes_per_row * 8;
// Compute length of memory array
m_size = m_bytes_per_row * m_length;
// Load only if the column has a positive size
if (m_size > 0) {
// Allocate and initialise fresh memory
alloc_data();
init_data();
// If a FITS file is attached then load column data from the FITS
// file
if (FPTR(m_fitsfile)->Fptr != NULL) {
// Move to the HDU
int status = 0;
status = __ffmahd(FPTR(m_fitsfile),
(FPTR(m_fitsfile)->HDUposition)+1,
NULL, &status);
if (status != 0) {
throw GException::fits_hdu_not_found(G_LOAD_COLUMN,
(FPTR(m_fitsfile)->HDUposition)+1,
status);
}
// Load data 8 Bits at once
status = __ffgcv(FPTR(m_fitsfile), __TBYTE, m_colnum, 1, 1, m_size,
m_nulval, m_data, &m_anynul, &status);
if (status != 0) {
throw GException::fits_error(G_LOAD_COLUMN, status,
"for column \""+m_name+"\".");
}
}
} // endif: column has a positive size
// Return
return;
}
/***********************************************************************//**
* @brief Save table column into FITS file
*
* @exception GException::fits_hdu_not_found
* Specified HDU not found in FITS file.
* @exception GException::fits_error
* Error occured during writing of the column data.
*
* Save Bit (vector) column into FITS file by writing 8 Bits at once.
***************************************************************************/
void GFitsTableBitCol::save_column(void)
{
// Continue only if a FITS file is connected and data have been loaded
if (FPTR(m_fitsfile)->Fptr != NULL && m_colnum > 0 && m_data != NULL) {
// Set any pending Bit
set_pending();
// Move to the HDU
int status = 0;
status = __ffmahd(FPTR(m_fitsfile),
(FPTR(m_fitsfile)->HDUposition)+1, NULL,
&status);
if (status != 0) {
throw GException::fits_hdu_not_found(G_SAVE_COLUMN,
(FPTR(m_fitsfile)->HDUposition)+1,
status);
}
// Save data 8 Bits at once
status = __ffpcn(FPTR(m_fitsfile), __TBYTE, m_colnum, 1, 1,
m_size, m_data, m_nulval, &status);
if (status != 0) {
throw GException::fits_error(G_SAVE_COLUMN, status);
}
} // endif: FITS file was connected
// Return
return;
}
/***********************************************************************//**
* @brief Get Bit for boolean access
*
* @param[in] row Row of column.
* @param[in] inx Vector index in column row.
*
* @exception GException::fits_invalid_row
* Table row out of valid range.
* @exception GException::out_of_range
* Table vector index out of valid range.
*
* Set the Bit for boolean data access. Note that this method assumes that
* the data have already been loaded.
***************************************************************************/
void GFitsTableBitCol::get_bit(const int& row, const int& inx)
{
// Check row value
#if defined(G_RANGE_CHECK)
if (row < 0 || row >= m_length) {
throw GException::fits_invalid_row(G_GET_BIT, row, m_length-1);
}
#endif
// Check inx value
#if defined(G_RANGE_CHECK)
if (inx < 0 || inx >= m_number) {
throw GException::out_of_range(G_GET_BIT, inx, 0, m_number-1);
}
#endif
// Compute Byte and Bit mask
m_bit_byte = row * m_bytes_per_row + inx / 8;
m_bit_mask = 1 << (7 - (inx % 8));
// Set Bit value
m_bit_value = (m_data[m_bit_byte] & m_bit_mask);
// Return
return;
}
/***********************************************************************//**
* @brief Set pending Bit
*
* Write the pending Bit into the data. Note that this method assumes that
* the data have already been loaded.
***************************************************************************/
void GFitsTableBitCol::set_pending(void)
{
// Continue only if we have a pending Bit
if (m_bit_pending) {
// Set or unset Bit
if (m_bit_value) {
m_data[m_bit_byte] = m_data[m_bit_byte] | m_bit_mask;
}
else {
m_data[m_bit_byte] = m_data[m_bit_byte] & ~m_bit_mask;
}
// Signal that no more Bit is pending
m_bit_pending = false;
}
// Return
return;
}