[Met_help] A problem

[John Halley Gotway]

Yes, that script makes use of some functions defined in the "fields"
package.  And I think the fields package must rely on the "gdata" package.
 Those R packages will need to be available on your machine to run these
tools.

Please refer to instructions about how to download additional R packages. 
For example, this site might help:
http://wiki.r-project.org/rwiki/doku.php?id=getting-started:installation:packages

Thanks,
John

> Hello, I have run the sample scripts mode_quilt_plot.R. But there is a
> problem, that is :
> Error in library(fields) : there is no package called 'fields'
> Execution halted
> But in the R-2.9.0/library , there is no "fields" and "gdata" library. If
> I need to download the additional library?
> Thank you very much!
>
>
>
> ÔÚ2009-07-07£¬"John Halley Gotway" <johnhg at rap.ucar.edu> дµÀ£º
>>Take a look in the MODE output file you sent me
>> (mode_APCP_06_SFC_vs_APCP_06_SFC_060000L_20070707_060000V_060000A_obj.txt).
>>  And look in the column labeled "OBJECT_ID".  You'll see that there are
>> only
>>3 entries: O001, O002, and O003.  The 'O' in front means that these are
>> observation objects, as opposed to 'F' for forecast objects.
>>
>>When you run your first job, you're passing the "-fcst" flag which says
>> to only keep lines for forecast objects.  And since the 3 lines in that
>> file are all for observation objects, that's why there
>>are 0 lines kept.  The file "job_summary_APCP_06_simple_fcst.txt" isn't
>> created since there are no lines to dump.
>>
>>Make sense?
>>
>>Also, MODE-Analysis is most useful to run to summarize many MODE output
>> files.  For example, if you've run MODE on a month's worth of data and
>> want to summarize the object attributes/differences,
>>MODE-Analysis can be very helpful.  But if you're just looking at a
>> single case, it may be easier to just open up that single output file and
>> read the MODE output.
>>
>>Thanks,
>>John
>>
>>zhxubinchaoshan wrote:
>>> OK,I send you the two files, thanks for your help!
>>>
>>>
>>>
>>>
>>> ÔÚ2009-07-07£¬"John Halley Gotway" <johnhg at rap.ucar.edu> дµÀ£º
>>>> Hello,
>>>>
>>>> The MODE-Analysis tool (and Stat-Analysis) may be run with or without
>>>> a config file.  Most of the time it's easiest to just run them from
>>>> the command line without using a config file.  I find that
>>>> it's only helpful to use the config file when I'm doing some
>>>> complicated filtering on the data.
>>>>
>>>> So could you please send me two things:
>>>> (1) The command line (or script) you use to call MODE-Analysis.
>>>> (2) The MODE output file(s) that you're trying to analyze.
>>>>
>>>> I'll try running MODE-Analysis and tell you what's going on.
>>>>
>>>> Thanks,
>>>> John
>>>>
>>>> zhxubinchaoshan wrote:
>>>>> Thanks for your reply!
>>>>> When I run the MODE-Analysis, I got the hint is that :
>>>>> *** Running MODE-Analysis to compute column summaries for simple
>>>>> forecast objects ***
>>>>>
>>>>>
>>>>>
>>>>> Total mode lines read =  3
>>>>> Total mode lines kept =  0
>>>>>
>>>>>
>>>>> *** Running MODE-Analysis to compute column summaries for simple
>>>>> observation objects ***
>>>>>
>>>>>
>>>>>
>>>>> Total mode lines read =  3
>>>>> Total mode lines kept =  3
>>>>>
>>>>> And then I failed to get the file
>>>>> job_summary_APCP_06_simple_fcst.txt, and all the variables in the
>>>>> file job_summary_APCP_06_simple_fcst.out are zero.
>>>>>
>>>>> I have sent you the file MODEAnalysisConfig,can you tell me what the
>>>>> problem is?
>>>>>
>>>>> And I want to know that if the MODE-Analysis is not necessary,
>>>>> because I found I can get the verification of WRF output after
>>>>> running the MODE tools.
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> Total mode lines read =  3
>>>>> Total mode lines kept =  3
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> ÔÚ2009-07-07£¬"John Halley Gotway" <johnhg at rap.ucar.edu> дµÀ£º
>>>>>> Great, I'm glad to hear that you got the lat/lon's figured out, and
>>>>>> are able to run MODE!
>>>>>>
>>>>>> As for your questions on thresholding, let me explain a little...
>>>>>>
>>>>>> The TS or ETS is computed by the Grid-Stat and Point-Stat tools.
>>>>>> The user selects a threshold value of interest, and that threshold
>>>>>> is applied to forecast/observation matched pairs to determine hits,
>>>>>> misses, false alarms, and correct negatives.  The ETS (and several
>>>>>> other contingency table statistics) are derived from those values.
>>>>>>
>>>>>> In MODE, we use a two-step method to define objects.  First, we
>>>>>> apply a convolution filter to the raw fields.  The user decides how
>>>>>> much smoothing is to be done by setting the "fcst_conv_radius" and
>>>>>> "obs_conv_radius" parameters.  Second, we threshold the convolved
>>>>>> field using the "fcst_conv_thresh" and "obs_conv_thresh" parameters.
>>>>>>  And from that thresholded field, we define the objects.
>>>>>>
>>>>>> To answer your question directly, I believe the general answer is
>>>>>> NO, those thresholds aren't doing exactly the same thing.  Grid-Stat
>>>>>> and Point-Stat are thresholding the RAW fcst/obs values.  Whereas
>>>>>> MODE is thresholding the convolved, smoothed fields.  So in general
>>>>>> they won't result in exactly the same grid points being turned on.
>>>>>>
>>>>>> HOWEVER, if you set the convolution radii in MODE equal to 0, no
>>>>>> convolution will be done, and you will be thresholding the raw
>>>>>> field.  But that generally isn't recommended because you'll likely
>>>>>> end
>>>>>> up with a large number of very small objects that'll be difficult to
>>>>>> work with.
>>>>>>
>>>>>> Hope that helps.
>>>>>>
>>>>>> John
>>>>>>
>>>>>> zhxubinchaoshan wrote:
>>>>>>> Thanks for your suggestions! And I have figure out the problem by
>>>>>>> your suggestion. The problem is that my lat's and lon's switched.
>>>>>>> In the calculating of TS or ETS, there is a parameter 'threshold'.
>>>>>>> And in the MODE tool, there is a parameter 'obs_conv_thresh'. Are
>>>>>>> they the same?
>>>>>>> As we know, in the forecast system, we generally make contrast
>>>>>>> between different threshold TS or ETS. So if I can make contrast
>>>>>>> between MODE results with different threshold, just by changing the
>>>>>>> parameter 'obs_conv_thresh'?
>>>>>>> Thank you very much!
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> ÔÚ2009-07-02£¬"John Halley Gotway" <johnhg at rap.ucar.edu> дµÀ£º
>>>>>>>> I took a look at the data file files you sent.  The problem is
>>>>>>>> clearly in the generation of the observation file.  The forecast
>>>>>>>> file is fine... the only reason the image looks funny in the
>>>>>>>> PostScript
>>>>>>>> file you sent is that you're masking the bad data values from the
>>>>>>>> observation field onto the forecast.  Try setting
>>>>>>>> "mask_missing_flag = 0" in the MODE config file, rerun the data,
>>>>>>>> and you'll see that
>>>>>>>> the forecast field is fine.
>>>>>>>>
>>>>>>>> So there's some problem in how you're generating the observation
>>>>>>>> file.  I see this type of problem all the time in when I'm
>>>>>>>> converting data.  You just have some indexing out of order when
>>>>>>>> you're
>>>>>>>> creating the observation NetCDF file.  I'd suggest playing around
>>>>>>>> with the tool you're using to create the NetCDF file and look at
>>>>>>>> how you're ordering the data.  Perhaps you have your lat's and
>>>>>>>> lon's
>>>>>>>> switched... or you have x where you should have nx - x.... or
>>>>>>>> something like that.
>>>>>>>>
>>>>>>>> You can check how the observation NetCDF file looks by viewing it
>>>>>>>> using "ncview".  Once it looks good in "ncview" it should work
>>>>>>>> fine for MODE.
>>>>>>>>
>>>>>>>> Good luck.  I'm guessing it's a minor issue in how you're ordering
>>>>>>>> the data, and once you figure it out, it'll all work fine.
>>>>>>>>
>>>>>>>> Thanks,
>>>>>>>> John
>>>>>>>>
>>>>>>>> zhxubinchaoshan wrote:
>>>>>>>>> Thanks for your reply!
>>>>>>>>> When I run MODE, I am comparing a forecast netCDF file to an
>>>>>>>>> observed netCDF file. The observed netCDF file is produced
>>>>>>>>> according to the pcp_combine output format.
>>>>>>>>> I send the MODE output to you, can you help me check how the
>>>>>>>>> problem come out?
>>>>>>>>> Thank you very much!
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> ÔÚ2009-07-01£¬"John Halley Gotway" <johnhg at rap.ucar.edu> дµÀ£º
>>>>>>>>>> When you run MODE are you comparing a forecast GRIB file to an
>>>>>>>>>> observed GRIB file?  If that is the case, you can run the
>>>>>>>>>> "copygb" utility to interpolate GRIB files from one grid to
>>>>>>>>>> another.
>>>>>>>>>>
>>>>>>>>>> The "copygb" utility is included as part of the
>>>>>>>>>> WRF-PostProcessor or may be downloaded/compiled separately.
>>>>>>>>>>
>>>>>>>>>> Here's some info about copygb:
>>>>>>>>>> http://www.cpc.noaa.gov/products/wesley/copygb.html
>>>>>>>>>> Slides 24-29 of the PDF file:
>>>>>>>>>> http://www.mmm.ucar.edu/wrf/users/tutorial/200901/wpp.pdf
>>>>>>>>>>
>>>>>>>>>> And I've also attached the copygb documentation file that's
>>>>>>>>>> included with the code.
>>>>>>>>>>
>>>>>>>>>> You can use it to regrid one dataset to another so that they're
>>>>>>>>>> on the same grid when running MODE.  Hope that helps.
>>>>>>>>>>
>>>>>>>>>> John
>>>>>>>>>>
>>>>>>>>>> zhxubinchaoshan wrote:
>>>>>>>>>>> Hello, I have interpolate my precipitation data from station
>>>>>>>>>>> observations to grid using the Cressman method. But the
>>>>>>>>>>> Cressman method I used is form GRADS. So the grid interpolated
>>>>>>>>>>> is not consistent with the one in WRF model. So when I run the
>>>>>>>>>>> MODE, I found the raw observation graphic is wrong.
>>>>>>>>>>> So my question is : Do I need to interpolate my precipitation
>>>>>>>>>>> data in consistent with the WRF model grid?
>>>>>>>>>>> And if I need to do that, is there any good method you can
>>>>>>>>>>> provide for me to do it?
>>>>>>>>>>> Thanks very much!
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> ÔÚ2009-06-30£¬"John Halley Gotway" <johnhg at rap.ucar.edu> дµÀ£º
>>>>>>>>>>>> Hello,
>>>>>>>>>>>>
>>>>>>>>>>>> You are correct.  The 2 most important parameters in the MODE
>>>>>>>>>>>> configuration file are the convolution radius and the
>>>>>>>>>>>> convolution threshold.  They determine how the objects are
>>>>>>>>>>>> defined from the raw field.
>>>>>>>>>>>>
>>>>>>>>>>>> And actually, there are 4 entries in the config file for these
>>>>>>>>>>>> - 2 for the forecast field and 2 for the observation field:
>>>>>>>>>>>> fcst_conv_radius
>>>>>>>>>>>> obs_conv_radius
>>>>>>>>>>>> fcst_conv_thresh
>>>>>>>>>>>> obs_conv_thresh
>>>>>>>>>>>>
>>>>>>>>>>>> But if you're comparing the same field between the fcst and
>>>>>>>>>>>> obs, just set the obs settings to the same values as the fcst.
>>>>>>>>>>>>
>>>>>>>>>>>> To address your question... unfortunately, there is no one
>>>>>>>>>>>> answer based on the model resolution.  Instead, it's up to the
>>>>>>>>>>>> user to decide what scale of objects to analyze.
>>>>>>>>>>>>
>>>>>>>>>>>> But here are some guidelines:
>>>>>>>>>>>> - Setting the convolution radius lower will make the objects
>>>>>>>>>>>> less smooth and more detailed.
>>>>>>>>>>>> - Setting the convolution radius higher will make the objects
>>>>>>>>>>>> smoother.
>>>>>>>>>>>> - Setting the threshold lower will make the objects bigger.
>>>>>>>>>>>> - Setting the threshold higher will make the objects smaller.
>>>>>>>>>>>>
>>>>>>>>>>>> It's up to you to decide how you'd like to define the objects
>>>>>>>>>>>> based on what type of features you'd like to extract from the
>>>>>>>>>>>> field.  For example, when running MODE on precip, you may
>>>>>>>>>>>> define objects
>>>>>>>>>>>> that are pretty large and smooth to represent large systems or
>>>>>>>>>>>> MCS's.  Or you may define them to be pretty small and detailed
>>>>>>>>>>>> to capture convection.  You need to ask yourself the question,
>>>>>>>>>>>> what
>>>>>>>>>>>> features am I trying to analyze in my output?
>>>>>>>>>>>>
>>>>>>>>>>>> You'll just need to play around with running MODE to get a
>>>>>>>>>>>> sense of how the settings work.  Choose a setting for the
>>>>>>>>>>>> convolution radius (5, 10, 15, 20 grid squares?).  Just pick
>>>>>>>>>>>> one and set it.  Then
>>>>>>>>>>>> set the convolution threshold to some value - for precip, just
>>>>>>>>>>>> try "gt0.0".  Then run MODE.  And bring up the output
>>>>>>>>>>>> PostScript file in a window.  Next, adjust the convolution
>>>>>>>>>>>> threshold, rerun MODE,
>>>>>>>>>>>> and observe how the objects change.  Once you get a sense for
>>>>>>>>>>>> how the convolution threshold works, try fixing that one and
>>>>>>>>>>>> playing with the convolution radius, moving it up and down,
>>>>>>>>>>>> and observing the
>>>>>>>>>>>> changes in the PostScript output.  At first, I'd suggest
>>>>>>>>>>>> keeping radius or threshold fixed, while you adjust the other
>>>>>>>>>>>> one.
>>>>>>>>>>>>
>>>>>>>>>>>> Sorry I can't provide more help.  You'll need to play around
>>>>>>>>>>>> with it to get a sense of what it's doing.  If you try to run
>>>>>>>>>>>> MODE to define a lot of objects (more than about 15 in each
>>>>>>>>>>>> field), it'll
>>>>>>>>>>>> take a lot longer to run since there's more calculations to
>>>>>>>>>>>> perform for each object.
>>>>>>>>>>>>
>>>>>>>>>>>> Once you do find some settings you like, feel free to send
>>>>>>>>>>>> some sample data to us for advice on interpreting the output.
>>>>>>>>>>>> If you do send some output, be sure to send the MODE
>>>>>>>>>>>> configuration file you
>>>>>>>>>>>> used and the PostScript plots.
>>>>>>>>>>>>
>>>>>>>>>>>> Thanks,
>>>>>>>>>>>> John Halley Gotway
>>>>>>>>>>>> johnhg at ucar.edu
>>>>>>>>>>>>
>>>>>>>>>>>> zhxubinchaoshan wrote:
>>>>>>>>>>>>> Hello,I am using the MODE tool in MET for verification.
>>>>>>>>>>>>> And I have some problems about the parameters in it. In the
>>>>>>>>>>>>> WrfModeConfig, there are two important parameters.They are
>>>>>>>>>>>>> obs_conv_radius and obs_conv_thresh.I have read some
>>>>>>>>>>>>> referances, and I found that how to specify these two
>>>>>>>>>>>>> parameters is dependent on my model resolution. If my model
>>>>>>>>>>>>> resolution is 12km, how can I specify these two parameters?
>>>>>>>>>>>>> Thank you very much!
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>> ÔÚ2009-05-13£¬"John Halley Gotway" <johnhg at rap.ucar.edu>
>>>>>>>>>>>>> дµÀ£º
>>>>>>>>>>>>>> Great.  Glad that did the trick for you.
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> John
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> zhxubinchaoshan wrote:
>>>>>>>>>>>>>>> Thanks for your reply!It can work now!
>>>>>>>>>>>>>>> The problem is the "fcst_var". By your suggestion, I change
>>>>>>>>>>>>>>> "APCP_6" to "APCP_06", and then it can work successfully!
>>>>>>>>>>>>>>> Thank you!
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> ÔÚ2009-05-11£¬"John Halley Gotway" <johnhg at rap.ucar.edu>
>>>>>>>>>>>>>>> дµÀ£º
>>>>>>>>>>>>>>>> Hello,
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> What this warning message is telling you is that the
>>>>>>>>>>>>>>>> Stat-Analysis tool is
>>>>>>>>>>>>>>>> looking in the directory "out/rain" for *.stat files, but
>>>>>>>>>>>>>>>> it is not
>>>>>>>>>>>>>>>> finding any lines in those files that EXACTLY match the
>>>>>>>>>>>>>>>> job you've
>>>>>>>>>>>>>>>> specified.
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> When I experience a problem like this, my usual approach
>>>>>>>>>>>>>>>> is to take a step
>>>>>>>>>>>>>>>> back and under-specify the job just to make sure I'm
>>>>>>>>>>>>>>>> matching some lines.
>>>>>>>>>>>>>>>> Then I take a look at the STAT lines that went into the
>>>>>>>>>>>>>>>> job and adjust
>>>>>>>>>>>>>>> >from there.  For example, you may try the following:
>>>>>>>>>>>>>>>> (1) Run this Stat-Analysis job on the command line:
>>>>>>>>>>>>>>>> ../bin/stat_analysis -lookin ./out/rain \
>>>>>>>>>>>>>>>> -job aggregate_stat -line_type FHO -out_line_type CTS \
>>>>>>>>>>>>>>>> -dump_row tmp.stat
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> (2) Did this job run successfully? Did it find any input
>>>>>>>>>>>>>>>> FHO lines to use?
>>>>>>>>>>>>>>>> If not, then maybe there aren't any FHO lines in your STAT
>>>>>>>>>>>>>>>> files.  If it
>>>>>>>>>>>>>>>> did find FHO lines, and the job ran fine, proceed to the
>>>>>>>>>>>>>>>> next step.
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> (3) Take a look in the file "tmp.stat".  How would you
>>>>>>>>>>>>>>>> like to filter this
>>>>>>>>>>>>>>>> data down more?  Do you see "APCP_6" in the column for
>>>>>>>>>>>>>>>> "fcst_var"?  Or
>>>>>>>>>>>>>>>> maybe it's actually "APCP_06"?  Try adding that to the
>>>>>>>>>>>>>>>> job:
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> ../bin/stat_analysis -lookin ./out/rain \
>>>>>>>>>>>>>>>> -job aggregate_stat -line_type FHO -fcst_var APCP_6
>>>>>>>>>>>>>>>> -out_line_type CTS \
>>>>>>>>>>>>>>>> -dump_row tmp.stat
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> (4) Did this job run successfully, or was there a problem
>>>>>>>>>>>>>>>> with how you
>>>>>>>>>>>>>>>> specified the "fcst_var".  Now check the "tmp.stat" file
>>>>>>>>>>>>>>>> again, and adjust
>>>>>>>>>>>>>>>> your job as necessary.  One hint though, when running
>>>>>>>>>>>>>>>> Stat-Analysis jobs
>>>>>>>>>>>>>>>> like this on the command line, you'll usually need to put
>>>>>>>>>>>>>>>> a backslash
>>>>>>>>>>>>>>>> before special characters like this: -fcst_thresh
>>>>>>>>>>>>>>>> "\>0.000"
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> So I'd suggest approaching the problem like that.  If you
>>>>>>>>>>>>>>>> can't figure it
>>>>>>>>>>>>>>>> out, feel free to send along all of the STAT files in your
>>>>>>>>>>>>>>>> "out/rain"
>>>>>>>>>>>>>>>> directory, the Stat-Analysis config file you're using, and
>>>>>>>>>>>>>>>> the command
>>>>>>>>>>>>>>>> line you're using... and I'll try to figure out what's
>>>>>>>>>>>>>>>> going on.
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> Good luck.
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> John Halley Gotway
>>>>>>>>>>>>>>>> johnhg at ucar.edu
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> When I run the Stat_analysis Tool, I get the error below:
>>>>>>>>>>>>>>>>> WARNING: do_job_aggr_stat() -> no matching STAT lines
>>>>>>>>>>>>>>>>> found for job: -job
>>>>>>>>>>>>>>>>> aggregate_stat -fcst_var APCP_6 -fcst_thresh >0.000
>>>>>>>>>>>>>>>>> -line_type FHO
>>>>>>>>>>>>>>>>> -dump_row
>>>>>>>>>>>>>>>>> ./out/stat_analysis/job_aggregate_stat_FHO_CTS.stat
>>>>>>>>>>>>>>>>> -out_line_type CTS -out_alpha 0.050000
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> And my command is :
>>>>>>>>>>>>>>>>>  ../bin/stat_analysis -config ./STATAnalysisConfig_07
>>>>>>>>>>>>>>>>> -lookin ./out/rain
>>>>>>>>>>>>>>>>> -out ./out/stat_analysis/stat_analysis.out
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> Can you tell me how to figure out the problem above?
>>>>>>>>>>>>>>>>> Thank you very much!
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>>>>>>> Met_help mailing list
>>>>>>>>>>>>>>>>> Met_help at mailman.ucar.edu
>>>>>>>>>>>>>>>>> http://mailman.ucar.edu/mailman/listinfo/met_help
>>>>>>>>>>>>>>>>>
>>>
>