Index: /branches/eam_branch_20080706/ppImage/doc/masks.txt
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+
+Masks and ppImage:
+
+In most operations, ppImage uses masks to identify the good and bad
+pixels in the science image being processed.  In some cases, the
+ppImage analysis may operate explicitly on a mask.  For example, we
+may want to generate a jpeg image of the masked pixels.  
+
+There are three ways in which ppImage may set the masked pixels:
+
+1) ppImage may directly load in the mask associated with a science
+   image.  
+
+2) ppImage may load a default ('standard') mask from the command line
+   or the detrend database.  
+
+3) ppImage may set masks for pixels based on their data values.
+
+ppImage and psphot also use one special mask bit to identify pixels
+currently being used or skipped for an analysis.  
+
+Mask values used by ppImage:
+
+** intrinsic mask values **
+DARK     : the pixel has poor dark behavior : dark current is excessive or non-linear
+FLAT     : the pixel has poor flat behavior : non-linear or excessive correction
+BLANK    : pixel has no valid data (eg, outside of active detector region)
+DETECTOR : unspecified bad detector response 
+
+** extrinsic mask values **
+LOW      : pixel is below minimum allowed value
+SAT      : pixel is saturated, above max value
+RANGE    : pixel is out-of-range in an unspecified way
+
+CR       : pixel is part of a cosmic ray
+GHOST    : pixel is part of a ghost
+
+    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