/* @file pmFPAHeader.h
 * @brief Functions read FITS headers for FPA components
 *
 * @author Paul Price, IfA
 * @author Eugene Magnier, IfA
 *
 * @version $Revision: 1.14 $ $Name: not supported by cvs2svn $
 * @date $Date: 2008-07-15 20:25:00 $
 * Copyright 2005-2006 Institute for Astronomy, University of Hawaii
 */

#ifndef PM_FPA_MASK_WEIGHT_H
#define PM_FPA_MASK_WEIGHT_H

/// @addtogroup Camera Camera Layout
/// @{

#if 0
/// Pixel mask values
typedef enum {
    PM_MASK_CLEAR    = 0x00,            ///< The pixel is not masked
    PM_MASK_BLANK    = 0x01,            ///< The pixel is blank or has no (valid) data
    PM_MASK_FLAT     = 0x02,            ///< The pixel is non-positive in the flat-field
    PM_MASK_DETECTOR = 0x02,            ///< The detector pixel is bad (e.g., bad column, charge trap)
    PM_MASK_SAT      = 0x04,            ///< The pixel is saturated in the image of interest
    PM_MASK_BAD      = 0x04,            ///< The pixel is low in the image of interest
    PM_MASK_RANGE    = 0x04,            ///< The pixel is out of range in the image of interest
    PM_MASK_CR       = 0x08,            ///< The pixel is probably a CR
    PM_MASK_SPARE1   = 0x10,            ///< Spare mask value
    PM_MASK_SPARE2   = 0x20,            ///< Spare mask value
    PM_MASK_SUSPECT  = 0x40,            ///< The pixel is suspected of being bad, but may not be
    PM_MASK_MARK     = 0x80,            ///< The pixel is marked as temporarily ignored
} pmMaskValue;
#define PM_MASK_MARK 0x80            ///< The pixel is marked as temporarily ignored
#define PM_MASK_SAT  0x04            ///< The pixel is saturated in the image of interest
#endif

/// Set a temporary readout mask using CELL.SATURATION and CELL.BAD
///
/// Identifies pixels that are saturated (>= CELL.SATURATION) or bad (<= CELL.BAD).  The mask that is produced
/// within the readout is temporary --- it is not added to the HDU.  This is intended for when the user is
/// iterating using pmReadoutReadNext, in which case the HDU can't be generated.
bool pmReadoutSetMask(pmReadout *readout, ///< Readout for which to set mask
                      psMaskType satMask, ///< Mask value to give saturated pixels
                      psMaskType badMask  ///< Mask value to give bad (low) pixels
    );


/// Set a temporary readout weight map using CELL.GAIN and CELL.READNOISE
///
/// Calculates weights (actually variances) for each pixel using photon statistics and the cell gain
/// (CELL.GAIN) and read noise (CELL.READNOISE).  The weight map that is produced within the readout is
/// temporary --- it is not added to the HDU.  This is intended for when the user is iterating using
/// pmReadoutReadNext, in which case the HDU can't be generated.
bool pmReadoutSetWeight(pmReadout *readout, ///< Readout for which to set weight
                        bool poisson    ///< Use poisson weights (in addition to read noise)?
                       );

/// Generate a readout mask (suitable for output) using CELL.SATURATION and CELL.BAD
///
/// Identifies pixels that are saturated (>= CELL.SATURATION) or bad (<= CELL.BAD).  The mask that is produced
/// is suitable for output (complete with HDU entry).  This is intended for most operations.
bool pmReadoutGenerateMask(pmReadout *readout, ///< Readout for which to generate mask
                           psMaskType sat, ///< Mask value to give saturated pixels
                           psMaskType bad ///< Mask value to give bad (low) pixels
    );

/// Generate a weight map (suitable for output) using CELL.GAIN and CELL.READNOISE
///
/// Calculates weights (actually variances) for each pixel using photon statistics and the cell gain
/// (CELL.GAIN) and read noise (CELL.READNOISE).  The weight map that is produced within the readout is
/// suitable for output (complete with HDU entry).  This is intended for most operations.
bool pmReadoutGenerateWeight(pmReadout *readout, ///< Readout for which to generate weight
                             bool poisson    ///< Use poisson weights (in addition to read noise)?
                            );

/// Generate mask and weight map for a readout
///
/// Calls pmReadoutGenerateMask and pmReadoutGenerateWeight for the readout
bool pmReadoutGenerateMaskWeight(pmReadout *readout, ///< Readout for which to generate mask and weights
                                 psMaskType sat, ///< Mask value to give saturated pixels
                                 psMaskType bad, ///< Mask value to give bad (low) pixels
                                 bool poisson ///< Use poisson weights (in addition to read noise)?
                                );

/// Generate mask and weight maps for all readouts within a cell
///
/// Calls pmReadoutGenerateMaskWeight for each readout within the cell.
bool pmCellGenerateMaskWeight(pmCell *cell, ///< Cell for which to generate mask and weights
                              psMaskType sat, ///< Mask value to give saturated pixels
                              psMaskType bad, ///< Mask value to give bad (low) pixels
                              bool poisson ///< Use poisson weights (in addition to read noise)?
                             );

/// Renormalise the weight map to match the actual variance
///
/// The variance in the image is measured in patches, and the variance map is adjusted so that the mean for
/// that patch corresponds.
bool pmReadoutWeightRenorm(const pmReadout *readout, // Readout to normalise
                           psMaskType maskVal, // Value to mask
                           psStatsOptions meanStat, // Statistic to measure the mean (of the variance map)
                           psStatsOptions stdevStat, // Statistic to measure the stdev (of the image)
                           int width,   // Width of patch (pixels)
                           psRandom *rng // Random number generator (for sub-sampling images)
    );

/// Explicitly mask non-finite pixels
///
/// Since unmasked non-finite pixels can occur (e.g., by out-of-range in quantisation), it is sometimes
/// necessary to mask them explicitly.  Non-finite pixels in the image or weight have their mask OR-ed with
/// the provided value.
bool pmReadoutMaskNonfinite(pmReadout *readout, ///< Readout to mask
                            psMaskType maskVal ///< Mask value to give non-finite pixels
    );

/// Apply a mask to the image and weight map
///
/// Unfortunately, image subtraction may result in a bi-modal image in masked areas, which can upset image
/// statistics (very important for quantising images so that a product can be written out!).  This function
/// sets masked areas to NAN in the image and weight.
bool pmReadoutMaskApply(pmReadout *readout, ///< Readout to mask
                        psMaskType maskVal ///< Mask value for which to apply mask
    );


/// @}
#endif
