Updated and merged README files

gremau · Jul 8, 2016 · 60adcaa · 60adcaa
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diff --git a/README_old → README.md b/README_old → README.md
@@ -1,11 +1,58 @@
-UNM New Mexico Elevation Gradient data processing manual
+# NMEG_FluxProc
 
-Timothy W. Hilton (hilton@unm.edu)
-July 2012
+[This](https://github.com/gremau/NMEG_FluxProc) is the repository for
+FluxProc code used to process data from the New Mexico Elevation Gradient.
+It is primarily written in and called from MATLAB.
+
+
+## Local setup
+
+### Data and configuration directories
+
+The FluxProc code performs operations on data in a designated directory
+("FLUXROOT"). An example FLUXROOT directory with data from an imaginary
+site can be downloaded from the socorro ftp and used to test the FluxProc
+code.
+
+Site specific configuration files must also be present in the FLUXROOT
+path, and FluxProc is currently set to look for them in
+"FLUXROOT/FluxProcConfig". Configuration files for NMEG sites, including
+the test site mentioned above can be found [here]
+(https://github.com/gremau/NMEG_FluxProcConfig).
+
+### Paths and environment variables.
+
+An environment variables must be set for FluxProc to find the FLUXROOT
+directory on the local file structure. In the `startup.m` file, add
+these lines:
+
+    setenv('FLUXROOT', '/.../')
+
+where "/.../" is the path to the FLUXROOT directory.
+
+Once this is done, start MATLAB, add the NMEG_FluxProc to your path:
+
+    addpath('path/to/FluxProc')
+
+Enter the directory:
+
+    cd 'path/to/FluxProc'
+
+The rest of the paths needed for FluxProc can be set using
+
+    fluxproc_setpaths
+
+Now FluxProc code should be initialized and ready to use the data and
+configuration files in the FLUXROOT directory.
+
+## Further documentation
+
+Below is the old UNM New Mexico Elevation Gradient data processing manual,
+by Timothy W. Hilton (hilton@unm.edu) from around July 2012. It is very
+out of date. We will begin updating the documentation in the near future.
+
+### OVERVIEW
 
-========
-OVERVIEW
-========
 
 This README presents Matlab functions we have developed to process and
 view data collected from the New Mexico Elevation Gradient (NMEG) eddy
@@ -15,15 +62,17 @@ In general, user-level main functions (things that are intended to be
 called from a Matlab command line) are named UNM_*.m, and helper
 functions do not have the "UNM_" prefix.
 
--- Documentation --
+** Documentation **
+
 I have tried to consistently include in each m-file descriptive
 documentation immediately following the function definition so that
 calling 'help' or 'doc' on the function from the Matlab prompt will
 display self-contained documentation.  Thus, this readme document will
 not discuss function usage and interfaces in detail -- use the Matlab
 help!
 
--- Source control management --
+** Source control management **
+
 The code is version-controlled in a Mercurial
 (http://mercurial.selenic.com/) repository.  It is not necessary to
 use the version control; you may simply ignore the .hg subdirectory,
@@ -33,40 +82,41 @@ Mercurial (or source control management tools in general) and wish to
 learn how to use it.  The revision history steps sequentially back to
 15 August 2011.
 
-===========================
-USER-LEVEL FUNCTION SUMMARY
-===========================
+
+### USER-LEVEL FUNCTION SUMMARY
 
 There are four main user-level data processing matlab functions:
-UNM_retrieve_card_data_GUI.m
-UNM_RemoveBadData.m
-UNM_fill_met_gaps_from_nearby_site.m
-UNM_Ameriflux_file_maker_TWH.m
+
+* UNM_retrieve_card_data_GUI.m
+* UNM_RemoveBadData.m
+* UNM_fill_met_gaps_from_nearby_site.m
+* UNM_Ameriflux_file_maker_TWH.m
 
 There are several functions to parse data files from various stages of
 the data processing pipeline into Matlab:
-UNM_parse_QC_txt_file.m
-UNM_parse_QC_xls_file.m
-UNM_parse_fluxall_txt_file.m
-UNM_parse_fluxall_xls_file.m
-UNM_parse_gapfilled_partitioned_output.m
-UNM_parse_sev_met_data.m
-UNM_parse_valles_met_data.m
-parse_forgapfilling_file.m
-parse_ameriflux_file.m
+
+* UNM_parse_QC_txt_file.m
+* UNM_parse_QC_xls_file.m
+* UNM_parse_fluxall_txt_file.m
+* UNM_parse_fluxall_xls_file.m
+* UNM_parse_gapfilled_partitioned_output.m
+* UNM_parse_sev_met_data.m
+* UNM_parse_valles_met_data.m
+* parse_forgapfilling_file.m
+* parse_ameriflux_file.m
 
 There are also a number of functions to visualize flux data.  Some are
 called from within the processing functions listed above; some of
 these are sometimes independently useful.
-plot_fingerprint.m
-UNM_site_plot_doy_time_offsets.m
-UNM_site_plot_fullyear_time_offsets.m
-plot_siteyear_fingerprint_2x3array.m
-plot_siteyear_fingerprint_single.m
 
-================================
-DATA PROCESSING PIPELINE SUMMARY
-================================
+* plot_fingerprint.m
+* UNM_site_plot_doy_time_offsets.m
+* UNM_site_plot_fullyear_time_offsets.m
+* plot_siteyear_fingerprint_2x3array.m
+* plot_siteyear_fingerprint_single.m
+
+
+### DATA PROCESSING PIPELINE SUMMARY
 
 The steps for processing incoming data from the field sites.  I have
 attempted to make the processing routines somewhat robust to data
@@ -95,4 +145,4 @@ debug.
 6. From bash, call download_partitioned_data to download the gapfilled
    partitioned data.
 7. Call UNM_Ameriflux_file_maker_TWH.m
-8. Upload the Ameriflux files to soccoro.unm.edu.
+8. Upload the Ameriflux files to soccoro.unm.edu.
diff --git a/README.txt b/README.txt