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 ====== PyWiFeS Documentation ====== ====== PyWiFeS Documentation ======
  
-==== Overview ====+This page is a starting point for running the actual reduction code.  Eventually it will also host documentation for individual function syntax. 
 + 
 +If you are interested in a high-level overview of the techniques and algorithms employed in PyWiFeS, you should head over to the [[data_reduction| main data reduction page]]. 
 + 
 +==== Data Reduction Overview ====
 Data reduction is generally run in two steps: Data reduction is generally run in two steps:
   - **Gather Metadata** - in the 'scripts/' directory of your PyWiFeS installation directory you will find the script 'generate_metadata_script.py'.  Use this to organize your metadata in the following steps:   - **Gather Metadata** - in the 'scripts/' directory of your PyWiFeS installation directory you will find the script 'generate_metadata_script.py'.  Use this to organize your metadata in the following steps:
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 Also important to note here is that an object frame only get automatically classified as a standard star if the 'OBJECT' header field is filled with a name from the standard star list defined in 'wifes_calib.py' in the 'src/' directory. Also important to note here is that an object frame only get automatically classified as a standard star if the 'OBJECT' header field is filled with a name from the standard star list defined in 'wifes_calib.py' in the 'src/' directory.
 +
 +A schematic overview of the PyWiFeS metadata heirarchy is illustrated in the Figure below.  Python dictionaries are colour green, while Python lists are coloured red.
 +
 +{{ :wiki:metadata_wifes.png?600 |}}
  
 ==== Reduction Script ==== ==== Reduction Script ====
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 The dictionary for each step has a 'suffix' key which defines how the output of that step will be stored, so for example the first step will operate on 'r0001.fits' and save its output as 'r0001.p01.fits' when the suffix is '01'.  This is so the next step know where to look for output of the previous step (e.g. step 2 looks for 'p01.fits' files and saves its output as 'p02.fits' files). The dictionary for each step has a 'suffix' key which defines how the output of that step will be stored, so for example the first step will operate on 'r0001.fits' and save its output as 'r0001.p01.fits' when the suffix is '01'.  This is so the next step know where to look for output of the previous step (e.g. step 2 looks for 'p01.fits' files and saves its output as 'p02.fits' files).
  
-The reduction steps used by default in the scripts are described in great detail on the [[default_reduction| default data reduction steps]] page.+The 'step' keyword in each step dictionary is used to determine which function to call to execute that step.  The functions by default are always 'run_step' (e.g. the 'subtract_overscan' step calls the 'run_subtract_overscan' function) which are defined in the reduction script.  These functions open the metadata and call the appropriate **pywifes** functions to operate on your data.
  
-==== Individual Function Documentation ==== +You can pass additional arguments to the main **pywifes** function being called by filling the 'args' key for a given processing step.  For example, in the 'cube_gen' step I typically pass the wavelength bounds I desire as 'args':{'wmin_set':3500, 'wmax_set':5700}, and those keyword arguments are passed to pywifes.generate_wifes_cube when it is called in the 'run_cube_gen' routine.
-Basic Preprocessing Functions +
-  * [[subtract_overscan]] +
-  * [[subtract_interslit_bias]]+
  
-Image coaddition / arithmetic +The reduction steps used by default in the scripts are described in great detail on the [[default_reduction| default data reduction steps]] page.
-  * [[imarith]] +
-  * [[imarith_mef]] +
-  * [[imcombine]] +
-  * [[imcombine_mef]] +
- +
-Cosmics Rays +
-  * [[lacos_wifes]] +
- +
-Wavelength Solution +
-  * [[derive_wifes_wave_solution]] +
-  * [[derive_wifes_skyline_solution]] +
- +
-Wire Solution +
-  * [[derive_wifes_wire_solution]] +
- +
-Flat-fielding +
-  * [[wifes_2dim_response]] +
-  * [[wifes_illumination]] +
-  * [[wifes_pixel_response]] +
- +
-WiFeS Data Formatting +
-  * [[wifes_slitlet_mef]] +
-  * [[generate_wifes_cube]] +
- +
-Flux Calibration +
-  * [[derive_wifes_calibration]] +
-  * [[calibrate_wifes_cube]] +
-  * [[derive_wifes_telluric]] +
-  * [[apply_wifes_telluric]]+
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