diff --git a/README_old b/README.md similarity index 55% rename from README_old rename to README.md index 40d09e5..0953d10 100644 --- a/README_old +++ b/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 It is very +out of date.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 @@ -15,7 +62,8 @@ 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 @@ -23,7 +71,8 @@ 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. \ No newline at end of file +8. Upload the Ameriflux files to soccoro.unm.edu. diff --git a/README.txt b/README.txt deleted file mode 100644 index 7be221a..0000000 --- a/README.txt +++ /dev/null @@ -1,29 +0,0 @@ -# NMEG_FluxProc - -This is the repository for code used to process data from the New Mexico -Elevation Gradient. - - -## To use: - -This code is primarily written in and called from MATLAB and it performs -operations on data in a designated directory ("FLUXROOT"). A testing -directory with example data from an imaginary test site can be found on -the socorro ftp. - -Site specific configuration files must also be present in a designated -directory ("FLUXROOT/FluxProcConfig"). Configuration files for NMEG can be found -[here](https://github.com/gremau/NMEG_FluxProcConfig). - -An environment variables must be set for MATLAB to find the data and -configuration files on the local file structure. In the `startup.m` -file, add these lines: - - setenv('FLUXROOT', '/.../') - -where "/.../" is the path to each folder. - -FUTURE WARNING: Configuration files will soon be placed in an independent -location with a separate environmental variable. This will allow separation -of data and software configuration. -