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Changeset 3002 for branches – NEMO

Changeset 3002 for branches


Ignore:
Timestamp:
2011-10-26T19:26:37+02:00 (13 years ago)
Author:
djlea
Message:

Update documentation for obstools and dataplot. Removal of dataplot code not needed. Addition of headers to some dataplot code. Addition of .exe to command example in obstools.

Location:
branches/dev_2802_OBStools
Files:
2 added
16 deleted
19 edited

Legend:

Unmodified
Added
Removed

  • branches/dev_2802_OBStools/DOC/TexFiles/Chapters/Chap_OBS.tex

    r2483 r3002  
    784784interpolating polynomial in the spline are set to zero. 
    785785At the bottom boundary, this is done using the land-ocean mask. 
     786 
     787 
     788\section{Observation Utilities} 
     789 
     790Some tools for viewing and processing of observation and feedback files are provided in the NEMO 
     791repository for convenience. These are OBSTOOLS which is a series of Fortran programs which are helpful to 
     792deal with feedback files. They do such tasks as observation file conversion, printing of file contents, 
     793some basic statistical analysis of feedback files. The other tool is an IDL program called dataplot which 
     794uses a graphical interface to visualise observations and feedback files. OBSTOOLS and dataplot are 
     795described in more detail below.   
     796 
     797\subsection{OBSTOOLS} 
     798 
     799A series of Fortran utilities is provided with NEMO called OBSTOOLS. This are helpful in handling 
     800observation files and the feedback file output from the NEMO observation operator. The utilities are as 
     801follows 
     802 
     803\subsubsection{corio2fb} 
     804 
     805The program corio2fb converts profile observation files from the Coriolis format to the standard feedback 
     806format. The program is called in the following way: 
     807 
     808\begin{alltt} 
     809\footnotesize 
     810\begin{verbatim} 
     811corio2fb.exe outputfile inputfile1 inputfile2 ... 
     812\end{verbatim} 
     813\end{alltt} 
     814 
     815\subsubsection{enact2fb} 
     816 
     817The program enact2fb converts profile observation files from the ENACT format to the standard feedback 
     818format. The program is called in the following way: 
     819 
     820\begin{alltt} 
     821\footnotesize 
     822\begin{verbatim} 
     823enact2fb.exe outputfile inputfile1 inputfile2 ... 
     824\end{verbatim} 
     825\end{alltt} 
     826 
     827\subsubsection{fbcomb} 
     828 
     829The program fbcomb combines multiple feedback files produced by individual processors in an MPI run of 
     830NEMO into a single feedback file. The program is called in the following way: 
     831 
     832\begin{alltt} 
     833\footnotesize 
     834\begin{verbatim} 
     835fbcomb.exe outputfile inputfile1 inputfile2 ... 
     836\end{verbatim} 
     837\end{alltt} 
     838 
     839\subsubsection{fbmatchup} 
     840 
     841The program fbmatchup will match observations from two feedback files. The program is called in the 
     842following way: 
     843 
     844\begin{alltt} 
     845\footnotesize 
     846\begin{verbatim} 
     847fbmatchup.exe outputfile inputfile1 varname1 inputfile2 varname2 ... 
     848\end{verbatim} 
     849\end{alltt} 
     850 
     851 
     852\subsubsection{fbprint} 
     853 
     854The program fbprint will print the contents of a feedback file or files to standard output. Selected 
     855information can be output using optional arguments. The program is called in the following way: 
     856 
     857\begin{alltt} 
     858\footnotesize 
     859\begin{verbatim} 
     860fbprint.exe [options] inputfile 
     861 
     862options: 
     863     -b            shorter output 
     864     -q            Select observations based on QC flags 
     865     -Q            Select observations based on QC flags 
     866     -B            Select observations based on QC flags 
     867     -u            unsorted 
     868     -s ID         select station ID   
     869     -t TYPE       select observation type 
     870     -v NUM1-NUM2  select variable range to print by number (default all) 
     871     -a NUM1-NUM2  select additional variable range to print by number (default all) 
     872     -e NUM1-NUM2  select extra variable range to print by number (default all) 
     873     -d            output date range 
     874     -D            print depths 
     875     -z            use zipped files 
     876\end{verbatim} 
     877\end{alltt} 
     878 
     879\subsubsection{fbsel} 
     880 
     881The program fbsel will select or subsample observations. The program is called in the following way: 
     882 
     883\begin{alltt} 
     884\footnotesize 
     885\begin{verbatim} 
     886fbsel.exe <input filename> <output filename> 
     887\end{verbatim} 
     888\end{alltt} 
     889 
     890\subsubsection{fbstat} 
     891 
     892The program fbstat will output summary statistics in different global areas into a number of files. The 
     893program is called in the following way: 
     894 
     895\begin{alltt} 
     896\footnotesize 
     897\begin{verbatim} 
     898fbstat.exe [-nmlev] <filenames> 
     899\end{verbatim} 
     900\end{alltt} 
     901 
     902\subsubsection{fbthin} 
     903 
     904The program fbthin will thin the data to 1 degree resolution. The code could easily be modified to thin to 
     905a different resolution. The program is called in the following way: 
     906 
     907\begin{alltt} 
     908\footnotesize 
     909\begin{verbatim} 
     910fbthin.exe inputfile outputfile 
     911\end{verbatim} 
     912\end{alltt} 
     913 
     914\subsubsection{sla2fb} 
     915 
     916The program sla2fb will convert an AVISO SLA format file to feedback format. The program is called in the 
     917following way: 
     918 
     919\begin{alltt} 
     920\footnotesize 
     921\begin{verbatim} 
     922sla2fb.exe [-s type] outputfile inputfile1 inputfile2 ... 
     923 
     924Option: 
     925     -s            Select altimeter data_source 
     926\end{verbatim} 
     927\end{alltt} 
     928 
     929\subsubsection{vel2fb} 
     930 
     931The program vel2fb will convert TAO/PIRATA/RAMA currents files to feedback format. The program is called in the 
     932following way: 
     933 
     934\begin{alltt} 
     935\footnotesize 
     936\begin{verbatim} 
     937vel2fb.exe outputfile inputfile1 inputfile2 ... 
     938\end{verbatim} 
     939\end{alltt} 
     940 
     941\subsection{dataplot} 
     942 
     943An IDL program called dataplot is included which uses a graphical interface to visualise observations and 
     944feedback files. It is possible to zoom in, plot individual profiles and calculate some basic statistics. To 
     945plot some data 
     946 
     947\begin{alltt} 
     948\footnotesize 
     949\begin{verbatim} 
     950IDL> dataplot, "filename" 
     951\end{verbatim} 
     952\end{alltt} 
     953 
     954To read multiple files into dataplot, for example multiple feedback files from different 
     955processors or from different days, the easiest method is to use the spawn command to generate a list of 
     956files which can then be passed to dataplot. 
     957 
     958\begin{alltt} 
     959\footnotesize 
     960\begin{verbatim} 
     961IDL> spawn, 'ls profb*', files 
     962IDL> dataplot, files 
     963\end{verbatim} 
     964\end{alltt} 
     965 
     966Fig~\ref{fig:obsdataplotmain} shows the main window which is launched when dataplot starts. This is split 
     967into three parts. At the top there is a menu bar which contains a variety of drop down menus. Areas - zooms 
     968into prespecified regions; plot - plots the data as a timeseries or a T-S diagram if appropriate; Find - 
     969allows data to be searches; Config - sets various configuration options. 
     970 
     971The middle part is a plot of the geographical location of the observations. This will plot the observation 
     972value, the model background value or observation minus background value depending on the option selected in 
     973the radio button at the bottom of the window. The plotting range can be changed by clicking on the colour 
     974bar. The title of the plot gives some basic information about the date range and depth range shown, the 
     975extreme values, and the mean and rms values. It is possible to zoom in using a drag-box. You may also zoom 
     976in or out using the mouse wheel. 
     977 
     978The bottom part of the window controls what is visible in the plot above. There are two bars which select 
     979the level range plotted (for profile data). The other bars below select the date range shown. The bottom of 
     980the figure allows the choice to plot the mean, root mean square, standard deviation, mean square values. As 
     981mentioned above here you can choose to plot the observation value, the model background value or 
     982observation minus background value. The next group of radio buttons selects the map projection. This can 
     983either be regular latitude longitude grid, or north or south polar stereographic. The next group of 
     984radio buttons will plot bad observations, switch to salinity and plot density for profile observations. The 
     985rightmost group of buttons will print the plot window as a postscript, save it as png, or exit from 
     986dataplot. 
     987 
     988%>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
     989\begin{figure}     \begin{center} 
     990\includegraphics[width=10cm,height=12cm,angle=-90.]{./TexFiles/Figures/Fig_OBS_dataplot_main} 
     991\caption{      \label{fig:obsdataplotmain} 
     992Main window of dataplot.} 
     993\end{center}     \end{figure} 
     994%>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
     995 
     996If a profile point is clicked with the mouse button a plot of the observation and background values 
     997as a function of depth (Fig~\ref{fig:obsdataplotprofile}). 
     998 
     999%>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
     1000\begin{figure}     \begin{center} 
     1001\includegraphics[width=10cm,height=12cm,angle=-90.]{./TexFiles/Figures/Fig_OBS_dataplot_prof} 
     1002\caption{      \label{fig:obsdataplotprofile} 
     1003Profile plot from dataplot.} 
     1004\end{center}     \end{figure} 
     1005%>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
     1006 
     1007 
     1008 
     1009 

  • branches/dev_2802_OBStools/NEMOGCM/TOOLS/OBSTOOLS/dataplot/colorbar_idl.pro

    r2945 r3002  
    22PRO colorbar_idl, datain, colors, lablevels, datalevels, data=data, $ 
    33   textcolor=textcolor, mincolor=mincolor, position=position 
    4  
     4;-------------------------------------------------------------------- 
    55; datain - gives the range of values which are represented by colors 
    66; colors - color values 
    77; lablevels - label levels 
    8 ; D. J. Lea Nov 2008 
    9 ;- 
    10  
    11 ; remember graphics keywords 
     8; 
     9; Author:  D. J. Lea    Nov 2008 
     10;-------------------------------------------------------------------- 
     11 
     12; keep current graphics keywords 
    1213 
    1314psave=!p 

  • branches/dev_2802_OBStools/NEMOGCM/TOOLS/OBSTOOLS/dataplot/dataplot.pro

    r2945 r3002  
    33; IDL widget based plotting routine for plotting observation and background values 
    44; 
    5 ; D. J. Lea     -  Feb 2008 
     5; Author: D. J. Lea     -  Feb 2008 
    66; 
    77;+---------------------------------------------------------------------------------------- 

  • branches/dev_2802_OBStools/NEMOGCM/TOOLS/OBSTOOLS/dataplot/dataplot_txttimeseries.pro

    r2945 r3002  
    1 ; plot mean and rms 
    2  
    31pro plotts1, arrsv, title, typestr, minperc=minperc, $ 
    42   juldatemin=juldatemin, juldatemax=juldatemax, $ 
    53        emax=emax, emin=emin 
    6  
    7  
     4;+-------------------------------------------------------- 
     5; plot mean and rms timeseries 
     6; 
     7; Author:  D. J. Lea      Feb 2008 
     8;+-------------------------------------------------------- 
    89 
    910;date_label = LABEL_DATE(DATE_FORMAT = $  

  • branches/dev_2802_OBStools/NEMOGCM/TOOLS/OBSTOOLS/dataplot/nice_contourlevels.pro

    r2945 r3002  
    11function nice_contourlevels, data, nlevels=nlevels 
     2;+---------------------------------------------------------------------------------------- 
     3; nice_contourlevels.pro 
     4; 
     5; Select nice contour levels based on the data input and the number of levels 
     6; 
     7; Author:  D. J. Lea     -  Feb 2008 
     8; 
     9;+---------------------------------------------------------------------------------------- 
    210 
    311if (n_elements(nlevels) eq 0) then nlevels=15 

  • branches/dev_2802_OBStools/NEMOGCM/TOOLS/OBSTOOLS/dataplot/pr2.pro

    r2945 r3002  
    2424         file=file,$ 
    2525         destination=destination 
    26 ;+ 
     26;+---------------------------------------------------------- 
    2727; NAME:pr2 
    2828; like pr, but uses nice fonts 
     29; 
     30; Author:  D. J. Lea        Feb 2008 
     31;+---------------------------------------------------------- 
    2932 
    3033COMMON pr2, view_landscape 

  • branches/dev_2802_OBStools/NEMOGCM/TOOLS/OBSTOOLS/dataplot/prend2.pro

    r2945 r3002  
    1   PRO PREND2,in_printer,keep=keep,noprint=noprint,double=double,$ 
     1PRO PREND2,in_printer,keep=keep,noprint=noprint,double=double,$ 
    22    view=view,spin_landscape_ps=spin_landscape_ps,$ 
    33    eps_preview=eps_preview,colour_preview=colour_preview,$ 
    … …  
    55;+ 
    66; NAME:prend 
     7;  
     8; Author:  D. J. Lea       Feb 2008 
    79 
    810COMMON pr2, view_landscape 
    911 
    10   if keyword_set(view) then begin 
    11    
     12device,/close           
     13set_plot,'x' 
     14 
     15if keyword_set(view) then begin 
     16 
    1217; get filename of postscript device   
    13    
    14       r = fstat(!D.UNIT) 
    15            filename = r.name 
    16    
    17           if (view_landscape) then begin 
    18         spawn,'gv -landscape -swap '+filename 
    19      endif else begin 
    20              spawn,'gv '+filename  
    21      endelse 
    2218 
    23   endif 
     19   r = fstat(!D.UNIT) 
     20   filename = r.name 
    2421 
    25   set_plot,'x' 
     22   if (view_landscape) then begin 
     23      spawn,'gv -landscape -swap '+filename 
     24   endif else begin 
     25      spawn,'gv '+filename  
     26   endelse 
    2627 
     28endif 
    2729 
    2830!p.font=-1 

  • branches/dev_2802_OBStools/NEMOGCM/TOOLS/OBSTOOLS/dataplot/read_cdfobs.pro

    r2945 r3002  
    1010               ProfileNum=ProfileNum, error=error, $ 
    1111               notfussy=notfussy,VarName=VarName   
    12 ;- 
     12;+-------------------------------------------------------------------------- 
     13; Read in observation and feedback files 
     14; detects filetype and calls the appropriate reading routine 
     15; 
     16; Author:  D. J. Lea       Feb 2008 
     17;+-------------------------------------------------------------------------- 
     18 
    1319; Declare error label.  
    1420ON_IOERROR, IOERROR  

  • branches/dev_2802_OBStools/NEMOGCM/TOOLS/OBSTOOLS/dataplot/read_seaice.pro

    r2945 r3002  
    55               nodates=nodates, quiet=quiet 
    66;------------------------------------------------------------ 
    7 ;PVWave program to read in netcdf files of altimeter data. 
     7;IDL program to read in netcdf files of sea ice data. 
     8; 
     9;Author:   D. J. Lea       Feb 2008 
    810; 
    911;------------------------------------------------------------ 

  • branches/dev_2802_OBStools/NEMOGCM/TOOLS/OBSTOOLS/dataplot/read_sla.pro

    r2945 r3002  
    77;+----------------------------------------------------------- 
    88;IDL program to read in netcdf files of altimeter data. 
     9; 
     10;Author:  D. J. Lea       - Feb 2008 
    911; 
    1012;------------------------------------------------------------ 

  • branches/dev_2802_OBStools/NEMOGCM/TOOLS/OBSTOOLS/dataplot/read_sst.pro

    r2945 r3002  
    55               quiet=quiet 
    66;------------------------------------------------------------ 
    7 ;PVWave program to read in netcdf files of altimeter data. 
     7;IDL program to read in netcdf files of altimeter data. 
     8; 
     9;Author:  D. J. Lea        - Feb 2008 
    810; 
    911;------------------------------------------------------------ 

  • branches/dev_2802_OBStools/NEMOGCM/TOOLS/OBSTOOLS/dataplot/sec_to_dt.pro

    r2945 r3002  
    7777;    print, 'n_elements(days) ', n_elements(days) 
    7878 
    79     ; get the julian and hen add the days, then back to julian 
     79    ; get the julian and then add the days, then back to julian 
    8080 
    8181;    FOR i=0L, N_ELEMENTS(days)-1 DO BEGIN 

  • branches/dev_2802_OBStools/NEMOGCM/TOOLS/OBSTOOLS/src/fbmatchup.F90

    r3000 r3002  
    1111   !!  
    1212   !!   Usage: 
    13    !!     fbmatchup outputfile inputfile1 varname1 inputfile2 varname2 ... 
     13   !!     fbmatchup.exe outputfile inputfile1 varname1 inputfile2 varname2 ... 
    1414   !! 
    1515   !!   Optional:  

  • branches/dev_2802_OBStools/NEMOGCM/TOOLS/OBSTOOLS/src/fbprint.F90

    r3000 r3002  
    1111   !! 
    1212   !!   Usage : 
    13    !!     fbprint [options] inputfile 
     13   !!     fbprint.exe [options] inputfile 
    1414   !!   Options : 
    1515   !!     -b            shorter output 

  • branches/dev_2802_OBStools/NEMOGCM/TOOLS/OBSTOOLS/src/fbsel.F90

    r3000 r3002  
    1111   !! 
    1212   !!   Usage: 
    13    !!     fbsel <input filename> <output filename> 
     13   !!     fbsel.exe <input filename> <output filename> 
    1414   !! 
    1515   !!   History : 

  • branches/dev_2802_OBStools/NEMOGCM/TOOLS/OBSTOOLS/src/fbstat.F90

    r3000 r3002  
    1212   !! 
    1313   !!   Usage: 
    14    !!     fbstat [-nmlev] <filenames> 
     14   !!     fbstat.exe [-nmlev] <filenames> 
    1515   !!   Optional: 
    1616   !!     namelist = namfbstat.in 

  • branches/dev_2802_OBStools/NEMOGCM/TOOLS/OBSTOOLS/src/fbthin.F90

    r3000 r3002  
    1111   !! 
    1212   !!   Usage: 
    13    !!     fbthin inputfile outputfile 
     13   !!     fbthin.exe inputfile outputfile 
    1414   !! 
    1515   !!   Required: 

  • branches/dev_2802_OBStools/NEMOGCM/TOOLS/OBSTOOLS/src/sla2fb.F90

    r3000 r3002  
    1111   !! 
    1212   !!   Usage: 
    13    !!     sla2fb [-s type] outputfile inputfile1 inputfile2 ... 
     13   !!     sla2fb.exe [-s type] outputfile inputfile1 inputfile2 ... 
    1414   !!   Option: 
    1515   !!     -s            Select altimeter data_source 

  • branches/dev_2802_OBStools/NEMOGCM/TOOLS/OBSTOOLS/src/vel2fb.F90

    r3000 r3002  
    1111   !! 
    1212   !!   Usage: 
    13    !!     vel2fb outputfile inputfile1 inputfile2 ... 
     13   !!     vel2fb.exe outputfile inputfile1 inputfile2 ... 
    1414   !!  
    1515   !!   History : 
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