/*
 *  cheetah
 *	A multi-threaded image program for analysing cspad image data from the CXI instrument at LCLS
 *
 *  Created by Anton Barty on 7/2/11.
 *  Copyright 2011 CFEL. All rights reserved.
 *	
 *	The contents of the directories 
 *		myana,
 *		cspad-gjw, and 
 *		build 
 *	can be obtained from SLAC, are copyright by the SLAC instrument development team, 
 *	and are covered by whatever license that software is distributed under. 
 * 
 *	You can modify this software 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/>.
 */




**** Guidelines for modifying the code ***

The 'main' in this program is found in cheetah.cpp
This calls functions in setup.cpp at the start and end of execution for parsing ini files, 
loading static pixel maps, allocating global variables and memory, keeping log files, and writing 
out common summed data at the end of execution.
cheetah.cpp also contains one function that is called once per cspad data frame. This function 
calculates data relating to the current frame, copies useful information including raw image data
into a worker thread structure, and passes this to worker.cpp for processing.

Global variables are all defined in the class cGlobal, which always appears in the code 
as the variable 'global'.  This holds information that is persistent between multiple images.
The class definition is found in setup.cpp
Variables containing data for one particular image are contained in threadInfo, which is passed to 
worker.cpp.  This contains all data required for processing just one data frame. 




If you modify anything:
- Be modular: Always configure new modules through the cheetah.ini file, and make modules easy to turn on and off.
- Do not statically code variables that may need to be changed or tweaked: put configurations in cheetah.ini instead
- Maintain a clean distinction between 'global' for program-level variables and 'threadInfo' for data pertaining to one frame only.
- Do not create new global variables: put it in cGlobal instead.
- Keep new modules modular: pass information using the global and threadInfo variables
- Keep it thread safe:  Use appropriate mutexes whenever writing to global variables
- Clean up your memory: worker.cpp is called once for each image, leaky memory quickly bloats out the system.

**** Library dependence ****
cheetah depends on the following libraries:
- hdf5 (http://www.hdfgroup.org/HDF5/)
- giraffe (for correlation functionality, git@github.com:feldkamp/giraffe.git, email feldkamp-at-slac.stanford.edu for questions)


//  For the correlation functionality, the cheetah needs the 'giraffe' library
//  available at git://github.com/feldkamp/giraffe.git
//
//  The giraffe library wraps the classes that, previous to Sep 2011 was in cheetah's own
//     arrayclasses.cpp,h
//     arraydataIO.cpp,h
//     crosscorrelator.cpp,h
//     fouriertransformer.cpp,h
//  
//  If the preprocessor flag CORRELATION_ENABLED is not set, cheetah does not need 
//  the giraffe library (or the supporting libraries for fftw and tiff) 
//  but, in turn, it cannot perform correlation calculations, either


**** Major contributions (in alphabetical order) ***

Anton Barty, CFEL
- Original version of this image processing code
- Multithreaded image processing
- ini file parsing
- Peakfinding and hitfinding
- Persistent background subtraction
- Dynamic suppression of hot mpixels
- Powder pattern generation
- HDF5 image data output
- Assembly and interpolation into a geometrically correct image layout
- Formats of the geometry file, and other input and output files



Matt Weaver, SLAC
- myana code, which forms the basis of the XTC processing part of this code

Thomas White, CFEL
- many fixes relating to compiling the SLAC libraries on other machines

Garth Williams, SLAC
- Routines for extracting raw cspad image data from the myana data structure

Jonas Sellberg, SLAC
- Routines for the absorption correction of the data

Jan Feldkamp, SLAC
- Routines for calculating the angular cross-correlation of a diffraction pattern