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Update the plotting R-scripts to handle output from different versions of MET. #1653

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8 of 20 tasks
JohnHalleyGotway opened this issue Feb 3, 2021 · 1 comment · Fixed by #1654
Closed
8 of 20 tasks

Update the plotting R-scripts to handle output from different versions of MET. #1653

JohnHalleyGotway opened this issue Feb 3, 2021 · 1 comment · Fixed by #1654
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@JohnHalleyGotway
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component: user support User support issue MET: Plotting Tools priority: medium Medium Priority reporting: DTC NCAR Base NCAR Base DTC Project requestor: Community General Community type: enhancement Improve something that it is currently doing
Milestone
MET 10.0.0

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@JohnHalleyGotway
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Describe the Enhancement

This issue is based on a request that came in via met-help:
https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=98517

I actually already posted updates for plot_cnt.R and plot_mpr.R prior to realizing that these scripts actually do live in the MET repository. So this task is to make the same updates in the develop branch. Also, check if the same changes are needed in any of the other R-scripts. The change is this...

  • add a -met_base command line argument
  • if not specified there, check for a MET_BASE environment variable
  • if neither are set, error out
  • read the data and extract the MET version number from the first column of the first line
  • read the corresponding header for that line type/version number from MET_BASE/table_files/met_header_columns_vX.Y.txt
  • remove the hard-coded headers from the top of these scripts

Time Estimate

4 hours.

Sub-Issues

Consider breaking the enhancement down into sub-issues.
No sub-issues required.

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None.

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?

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@JohnHalleyGotway JohnHalleyGotway added type: enhancement Improve something that it is currently doing component: utility scripts component: user support User support issue priority: medium Medium Priority requestor: Community General Community alert: NEED ACCOUNT KEY Need to assign an account key to this issue labels Feb 3, 2021
@JohnHalleyGotway JohnHalleyGotway added this to the MET 10.0.0 milestone Feb 3, 2021
@JohnHalleyGotway JohnHalleyGotway self-assigned this Feb 3, 2021
JohnHalleyGotway added a commit that referenced this issue Feb 3, 2021
@JohnHalleyGotway
Per #1653, update plot_cnt.R and plot_mpr.R to remove the version-spe…
b31b759 
…cific header columns.
@JohnHalleyGotway
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Updated plot_cnt.R and plot_mpr.R. Need to do the same for plot_ensemble.R.

JohnHalleyGotway added a commit that referenced this issue Feb 4, 2021
@JohnHalleyGotway
Per #1653, nice enhancments to these Rscripts to make them more indep…
a8ae862 
…endent of the MET version number.
JohnHalleyGotway added a commit that referenced this issue Feb 4, 2021
@JohnHalleyGotway
Per #1653, more tweaks
c930e7e
JohnHalleyGotway added a commit that referenced this issue Feb 4, 2021
@JohnHalleyGotway
Per #1653, if no input files are provided, error out with a useful me…
d2831a6 
…ssage.
@JohnHalleyGotway JohnHalleyGotway linked a pull request Feb 4, 2021 that will close this issue
Feature 1653 rscripts #1654
Merged
10 tasks
JohnHalleyGotway added a commit that referenced this issue Feb 5, 2021
@JohnHalleyGotway
Per #1653, while the scripts ran fine using R 4.0.2 on my Mac, they f…
84e0691 
…ail on eyewall using R 3.4.0. Adding as.character() to get past that error.
JohnHalleyGotway added a commit that referenced this issue Feb 5, 2021
@JohnHalleyGotway
Feature 1653 rscripts (#1654)
121964b 
* Per #1653, update plot_cnt.R and plot_mpr.R to remove the version-specific header columns.

* Per #1653, nice enhancments to these Rscripts to make them more independent of the MET version number.

* Per #1653, more tweaks

* Per #1653, if no input files are provided, error out with a useful message.

* Per #1653, while the scripts ran fine using R 4.0.2 on my Mac, they fail on eyewall using R 3.4.0. Adding as.character() to get past that error.
JohnHalleyGotway added a commit that referenced this issue Feb 5, 2021
@JohnHalleyGotway
Per #1653, update VarInfo::set_magic() to actually set MagicStr, usin…
fa6a0b1 
…g the updated logic of inserting a slash between name and level only if level does NOT begin with '('.
JohnHalleyGotway added a commit that referenced this issue Feb 5, 2021
@JohnHalleyGotway
Per #1653, for GRIB1, GRIB2, and Pinterp, I was able to remove the se…
bb7bb06 
…t_magic() function so that VarInfo::set_magic() would be called instead. That simpler anyway.
JohnHalleyGotway added a commit that referenced this issue Feb 5, 2021
@JohnHalleyGotway
Per #1653, for nc_met, nc_pinterp, and nccf, remove the line to set M…
d293b44 
…agicStr since the base class is now doing that instead.
JohnHalleyGotway added a commit that referenced this issue Feb 18, 2021
@JohnHalleyGotway @hsoh-u @jprestop
Update develop-ref after #1662 (#1669)
e9ec2c1 
* Per 1646, one line fix for cut-and-paste error. (#1647)

* Per #1644, no actual code changes here. Just formatting and spacing. For example, replace double ;; with single ;'

* Per #1644, FOUND THE BUG! It's a copy/paste error. We had var_name_map.end() that should be def_var_name_map.end(). Fixing that gets rid of the runtime hang.'

* Per #1643, redefine the contents of the existing AREA_RATIO output column from MODE. Define it as FCST/OBS object area instead of min/max. Update the User's Guide to note the change and also clarify that the MTD VOLUME_RATIO output really is FCST/OBS. (#1650)

* Feature 1644 ps_log (#1651)

* Per #1644, write rejection reason codes at verbosity 2 when there are 0 matched pairs.

* Per #1644, add a few sentences to Point-Stat, Practical Information chapter about debugging 0 matched pairs.

* The mode_conv.pl logic was slightly broken. MET PR #1650 should have broken the NB but it did not. Turns out the diffing logic is NOT properly distinguishing between single and pair object lines. It does this by looking for an underscore in the OBJECT_ID column. When we added FCST_UNITS and OBS_UNITS, that shifted OBJECT_ID up 2 spots, but the code was still checking the (0-based) 20th column instead of the 22nd. Fixing this now and will rerun NB20210202 to confirm it works again.

* The diffing logic for MODE pair lines still was not correct. We'd added the ASPECT_DIFF and CURVATURE_RATIO columns a while ago, but they were missing from the diff logic. This logic really is not good. We need to make it more robust, reading the version-specific header columns from a table file instead of hard-coding them!

* Feature 1653 rscripts (#1654)

* Per #1653, update plot_cnt.R and plot_mpr.R to remove the version-specific header columns.

* Per #1653, nice enhancments to these Rscripts to make them more independent of the MET version number.

* Per #1653, more tweaks

* Per #1653, if no input files are provided, error out with a useful message.

* Per #1653, while the scripts ran fine using R 4.0.2 on my Mac, they fail on eyewall using R 3.4.0. Adding as.character() to get past that error.

* Feature 1655 nc_log (#1656)

* #1630 Display a warning instead of error message with invalid variable if the input data is empty

* Feature 1658 grib_tables (#1659)

* Per #1658, update MXUPHL entries.

* Per #1658, updating long name for MAXREF, MAXUVV, and MAXDVV.

* Modified format of release notes

* Feature 1450 hersbach (#1662)

* Per #1450, add new ECNT columns for Hersback CRPS. Still need to actually compute the stats though.

* Per #1450, update NumArray functions to only sort if the data is not yet sorted. And check for bad data when computing the standard deviation.

* Per #1450, add code to compute the empirical CRPS value.

* Per #1450, large change to the new output for the empirical CRPS. In order to aggregate decomposed empirical CRPS reliability and potential correctly, we'd need to write (n+1)*2 additional columns. While the empirical crps can be aggregated as a weighted mean, the decomposition cannot. It just isn't feasible to do this in the ECNT line type. If this reliability and potential really are required, recommend that we add an entirely new CRPS line type instead of tacking onto ECNT. These changes simply remove reliabilit and potential from the output.

* Per #1450 and #1451, replacing single CRPS_CLIMO column with CRPSCL and CRPSCL_EMP which will be needed for #1451.

* Per #1450, delete temp files I'd accidentally committed.

* Per #1450, update the user's guide with CRPS updates.

* Fix bug replacing crpss_emp with crpss_gaus.

Co-authored-by: John Halley Gotway <[email protected]>
Co-authored-by: Howard Soh <[email protected]>
Co-authored-by: hsoh-u <[email protected]>
Co-authored-by: Julie.Prestopnik <[email protected]>
JohnHalleyGotway added a commit that referenced this issue Feb 25, 2021
@JohnHalleyGotway @hsoh-u
@jprestop @j-opatz
Update develop-ref after #1681 and #1676 (#1683)
ba0cc8e 
* Per 1646, one line fix for cut-and-paste error. (#1647)

* Per #1644, no actual code changes here. Just formatting and spacing. For example, replace double ;; with single ;'

* Per #1644, FOUND THE BUG! It's a copy/paste error. We had var_name_map.end() that should be def_var_name_map.end(). Fixing that gets rid of the runtime hang.'

* Per #1643, redefine the contents of the existing AREA_RATIO output column from MODE. Define it as FCST/OBS object area instead of min/max. Update the User's Guide to note the change and also clarify that the MTD VOLUME_RATIO output really is FCST/OBS. (#1650)

* Feature 1644 ps_log (#1651)

* Per #1644, write rejection reason codes at verbosity 2 when there are 0 matched pairs.

* Per #1644, add a few sentences to Point-Stat, Practical Information chapter about debugging 0 matched pairs.

* The mode_conv.pl logic was slightly broken. MET PR #1650 should have broken the NB but it did not. Turns out the diffing logic is NOT properly distinguishing between single and pair object lines. It does this by looking for an underscore in the OBJECT_ID column. When we added FCST_UNITS and OBS_UNITS, that shifted OBJECT_ID up 2 spots, but the code was still checking the (0-based) 20th column instead of the 22nd. Fixing this now and will rerun NB20210202 to confirm it works again.

* The diffing logic for MODE pair lines still was not correct. We'd added the ASPECT_DIFF and CURVATURE_RATIO columns a while ago, but they were missing from the diff logic. This logic really is not good. We need to make it more robust, reading the version-specific header columns from a table file instead of hard-coding them!

* Feature 1653 rscripts (#1654)

* Per #1653, update plot_cnt.R and plot_mpr.R to remove the version-specific header columns.

* Per #1653, nice enhancments to these Rscripts to make them more independent of the MET version number.

* Per #1653, more tweaks

* Per #1653, if no input files are provided, error out with a useful message.

* Per #1653, while the scripts ran fine using R 4.0.2 on my Mac, they fail on eyewall using R 3.4.0. Adding as.character() to get past that error.

* Feature 1655 nc_log (#1656)

* #1630 Display a warning instead of error message with invalid variable if the input data is empty

* Feature 1658 grib_tables (#1659)

* Per #1658, update MXUPHL entries.

* Per #1658, updating long name for MAXREF, MAXUVV, and MAXDVV.

* Modified format of release notes

* Feature 1450 hersbach (#1662)

* Per #1450, add new ECNT columns for Hersback CRPS. Still need to actually compute the stats though.

* Per #1450, update NumArray functions to only sort if the data is not yet sorted. And check for bad data when computing the standard deviation.

* Per #1450, add code to compute the empirical CRPS value.

* Per #1450, large change to the new output for the empirical CRPS. In order to aggregate decomposed empirical CRPS reliability and potential correctly, we'd need to write (n+1)*2 additional columns. While the empirical crps can be aggregated as a weighted mean, the decomposition cannot. It just isn't feasible to do this in the ECNT line type. If this reliability and potential really are required, recommend that we add an entirely new CRPS line type instead of tacking onto ECNT. These changes simply remove reliabilit and potential from the output.

* Per #1450 and #1451, replacing single CRPS_CLIMO column with CRPSCL and CRPSCL_EMP which will be needed for #1451.

* Per #1450, delete temp files I'd accidentally committed.

* Per #1450, update the user's guide with CRPS updates.

* Fix bug replacing crpss_emp with crpss_gaus.

* #1657 Added TIME_EPSILON

* #1657 Corrected 1 second offset by the precision error

* #1657 Added AccumTime

* #1657 Read the time from "bounds" attribute and set the max value from the bounds time variable

* #1657 Corrected 1 second offset by the precision error

* Per #1439, add check_mask_names() utility function which errors out if the list of masking region names is non-unique. Update Point-Stat and Grid-Stat to call it. (#1679)

* Feature 1451 crpss (#1676)

* Per #1450, add new ECNT columns for Hersback CRPS. Still need to actually compute the stats though.

* Per #1450, update NumArray functions to only sort if the data is not yet sorted. And check for bad data when computing the standard deviation.

* Per #1450, add code to compute the empirical CRPS value.

* Per #1450, large change to the new output for the empirical CRPS. In order to aggregate decomposed empirical CRPS reliability and potential correctly, we'd need to write (n+1)*2 additional columns. While the empirical crps can be aggregated as a weighted mean, the decomposition cannot. It just isn't feasible to do this in the ECNT line type. If this reliability and potential really are required, recommend that we add an entirely new CRPS line type instead of tacking onto ECNT. These changes simply remove reliabilit and potential from the output.

* Per #1450 and #1451, replacing single CRPS_CLIMO column with CRPSCL and CRPSCL_EMP which will be needed for #1451.

* Per #1450, delete temp files I'd accidentally committed.

* Per #1450, update the user's guide with CRPS updates.

* Per #1451, instead of computing the climo crps on the fly, compute and store it separately for each point.

* Per #1451, the ECNT line type will no longer be written separately for each CDF bin. Removing the bin-related arguments from the write_ecnt functions.

* Per #1451, the climo_cdf.write_bins option no longer applies. Since Ensemble-Stat will no longer compute stats separately for each climo bin, I'm removing the reference to write_bins from the Ensemble-Stat config files.

* Per #1451, compute and store the climo CRPS for each point. Also, break apart the normal climo computation into separate functions for crps, ign, and pit.

* Per #1451, update Ensemble-Stat logic to no longer subset pairs into climo CDF bins. We had done this to be consistent with the use of climo data in point and grid-stat. But this change to the handling of climo data is consitent with the NOAA/EMC approach.

* Per #1451, split out the setting of climo CDF thresholds into a separate function so that it can also be called by stat-analysis.

* Per #1451, in the Ensemble-Stat ORANK line type, rename CLIMO to CLIMO_MEAN and add a CLIMO_STDEV column.

* Per #1451, also need to update gsidens2orank to write a climo_stdev column.

* Per #1451, switch from constant pointer to ClimoCDFInfo object to a copy to make the logic of doing this in Stat-Analysis a little easier.

* Per #1451, the HiRA method in Point-Stat computes an ECNT output line type. Needed to call set_climo_cdf() there so that we know how many climo values to use when computing the empirical climo CRPS.

* Per #1451, need to store climo_cdf for both grid and point verification.

* Per #1451, update to write the CLIMO_STDEV header column for the ORANK line type.

* Per #1451, in Ensemble-Stat when doing point verification, check for empty OBS_UNIT string and write NA instead.

* Per #1451, update unit tests by enhancing the climatology call to Ensemble-Stat to also include point verification. Tweak the Ensemble-Stat cofiguration for that and also add a call to pb2nc to prepare the point observations for use.

* Per #1450, added a new section to the Ensemble-Stat chapter describing how climo mean/stdev are used in the computation of the skill scores.

* Update ensemble-stat.rst

Co-authored-by: j-opatz <[email protected]>

* #1677 Update the refence time (from time_bnds variable) (#1680)

Co-authored-by: Howard Soh <[email protected]>

* Feature 1135 stat_analysis (#1681)

* Per #1135, add fcst/obs_init/valid_inc/exc options for STAT-Analysis jobs.

* Per #1135, update all the STATAnalysis config files to include entries for the new fcst/obs_init/valid_inc/exc options.

* Per #1135, add documentation for fcst/obs_init/valid_inc/exc options to the STAT-Analysis chapter. Also, clarify the description for the existing options.

* Per #1135, adding another call to stat_analysis to check the time filtering options.

* Per #1135, just renaming stat_analysis output file.

* Apply suggestions from code review

Co-authored-by: jprestop <[email protected]>

Co-authored-by: John Halley Gotway <[email protected]>
Co-authored-by: jprestop <[email protected]>

Co-authored-by: John Halley Gotway <[email protected]>
Co-authored-by: Howard Soh <[email protected]>
Co-authored-by: hsoh-u <[email protected]>
Co-authored-by: Julie.Prestopnik <[email protected]>
Co-authored-by: j-opatz <[email protected]>
@TaraJensen TaraJensen added reporting: DTC NCAR Base NCAR Base DTC Project and removed alert: NEED ACCOUNT KEY Need to assign an account key to this issue labels Mar 31, 2021
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component: user support User support issue MET: Plotting Tools priority: medium Medium Priority reporting: DTC NCAR Base NCAR Base DTC Project requestor: Community General Community type: enhancement Improve something that it is currently doing
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Feature 1653 rscripts dtcenter/MET
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