Script for netcdf not working with my file #105
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This might be and old issue. Climpact might be expecting all 3 variables, even though you only request CDD. My recommendation is to make a tx and tn variable and just put dummy data in there, then also specify the variable names in your wrapper script. Let us know if that doesn't work.
… On 19/08/2023 04:31 GMT GerardoTheMeteorologist ***@***.***> wrote:
Hi there! I've been working with climpact for my thesis and It worked perfectly when I runned the climpact.ncdf.wrapped.r script sample. I gotta say Climpact is a great project. When I tried to use it to calculate the cdd index from my total precipitation file I got this error:
Rscript scriptdeprueba.r
Loading required package: PCICt
Error in create.file.metadata(f, variable.name.map) :
At least one input file doesn't contain any of the named variables.
Calls: create.indices.from.files -> create.file.metadata
Execution halted
The script I'm running:
------------------------------------------------
This wrapper script calls the 'create.indices.from.files' function from the modified climdex.pcic.ncdf package
to calculate ETCCDI, ET-SCI and other indices, using data and parameters provided by the user.
Note even when using a threshold file, the base.range parameter must still be specified accurately.
------------------------------------------------
library(climdex.pcic.ncdf)
list of one to three input files. e.g. c("a.nc","b.nc","c.nc")
infiles="./www/sample_data/tpERA5reanalysis1980-2010.nc"
list of variable names according to above file(s)
vars=c(tp="precip")
output directory. Will be created if it does not exist.
outdir="./www/output/gridded/"
Output filename format. Must use CMIP5 filename convention. i.e. "var_timeresolution_model_scenario_run_starttime-endtime.nc"
file.template="var_daily_climpact.sample_historical_NA_1980-2010.nc"
author data
author.data=list(institution="Universidad Veracruzana", institution_id="UV")
reference period
base.range=c(1980,2010)
number of cores to use, or FALSE for single core.
cores=FALSE
list of indices to calculate, or NULL to calculate all.
indices=c("cdd") #c("hw","tnn")
input threshold file to use, or NULL for none.
thresholds.files=NULL #"./www/output/gridded/thresholds.test.1991-1997.nc"
Directory where Climpact is stored. Use full pathname. Leave as NULL if you are running this script from the Climpact directory (where this script was initially stored).
root.dir=NULL
#######################################################
Esoterics below, do not modify without a good reason.
definition used for Excess Heat Factor (EHF). "PA13" for Perkins and Alexander (2013), this is the default. "NF13" for Nairn and Fawcett (2013).
EHF_DEF = "PA13"
axis to split data on. For chunking up of grid, leave this.
axis.name="Y"
Number of data values to process at once. If you receive "Error: rows.per.slice >= 1 is not TRUE", try increasing this to 20. You might have a large grid.
maxvals=10
output compatible with FCLIMDEX. Leave this.
fclimdex.compatible=FALSE
Call the package.
create.indices.from.files(infiles,outdir,file.template,author.data,variable.name.map=vars,base.range=base.range,parallel=cores,axis.to.split.on=axis.name,climdex.vars.subset=indices,thresholds.files=thresholds.files,fclimdex.compatible=fclimdex.compatible,root.dir=root.dir,
cluster.type="SOCK",ehfdef=EHF_DEF,max.vals.millions=maxvals,wsdin_n=5,csdin_n=5,hddheatn_n=18,cddcoldn_n=18,gddgrown_n=10,rxnday_n=7,rnnmm_n=30,ntxntn_n=3,ntxbntnb_n=3,project.lat2d.coords=TRUE,
thresholds.name.map=c(tx05thresh="tx05thresh",tx10thresh="tx10thresh", tx50thresh="tx50thresh", tx90thresh="tx90thresh",tx95thresh="tx95thresh",
tn05thresh="tn05thresh",tn10thresh="tn10thresh",tn50thresh="tn50thresh",tn90thresh="tn90thresh",tn95thresh="tn95thresh",
tx90thresh_15days="tx90thresh_15days",tn90thresh_15days="tn90thresh_15days",tavg90thresh_15days="tavg90thresh_15days",
tavg05thresh="tavg05thresh",tavg95thresh="tavg95thresh",
txraw="txraw",tnraw="tnraw",precraw="precraw",
r95thresh="r95thresh", r99thresh="r99thresh"))
It would be very helpful if someone could give me a hand to figure this out.
Cheers.
Gerardo
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Hi there! I've been working with climpact for my thesis and It worked perfectly when I runned the climpact.ncdf.wrapped.r script sample. I gotta say Climpact is a great project. When I tried to use it to calculate the cdd index from my total precipitation file I got this error:
Rscript scriptdeprueba.r
Loading required package: PCICt
Error in create.file.metadata(f, variable.name.map) :
At least one input file doesn't contain any of the named variables.
Calls: create.indices.from.files -> create.file.metadata
Execution halted
The script I'm running:
------------------------------------------------
This wrapper script calls the 'create.indices.from.files' function from the modified climdex.pcic.ncdf package
to calculate ETCCDI, ET-SCI and other indices, using data and parameters provided by the user.
Note even when using a threshold file, the base.range parameter must still be specified accurately.
------------------------------------------------
library(climdex.pcic.ncdf)
list of one to three input files. e.g. c("a.nc","b.nc","c.nc")
infiles="./www/sample_data/tpERA5reanalysis1980-2010.nc"
list of variable names according to above file(s)
vars=c(tp="precip")
output directory. Will be created if it does not exist.
outdir="./www/output/gridded/"
Output filename format. Must use CMIP5 filename convention. i.e. "var_timeresolution_model_scenario_run_starttime-endtime.nc"
file.template="var_daily_climpact.sample_historical_NA_1980-2010.nc"
author data
author.data=list(institution="Universidad Veracruzana", institution_id="UV")
reference period
base.range=c(1980,2010)
number of cores to use, or FALSE for single core.
cores=FALSE
list of indices to calculate, or NULL to calculate all.
indices=c("cdd") #c("hw","tnn")
input threshold file to use, or NULL for none.
thresholds.files=NULL #"./www/output/gridded/thresholds.test.1991-1997.nc"
Directory where Climpact is stored. Use full pathname. Leave as NULL if you are running this script from the Climpact directory (where this script was initially stored).
root.dir=NULL
#######################################################
Esoterics below, do not modify without a good reason.
definition used for Excess Heat Factor (EHF). "PA13" for Perkins and Alexander (2013), this is the default. "NF13" for Nairn and Fawcett (2013).
EHF_DEF = "PA13"
axis to split data on. For chunking up of grid, leave this.
axis.name="Y"
Number of data values to process at once. If you receive "Error: rows.per.slice >= 1 is not TRUE", try increasing this to 20. You might have a large grid.
maxvals=10
output compatible with FCLIMDEX. Leave this.
fclimdex.compatible=FALSE
Call the package.
create.indices.from.files(infiles,outdir,file.template,author.data,variable.name.map=vars,base.range=base.range,parallel=cores,axis.to.split.on=axis.name,climdex.vars.subset=indices,thresholds.files=thresholds.files,fclimdex.compatible=fclimdex.compatible,root.dir=root.dir,
cluster.type="SOCK",ehfdef=EHF_DEF,max.vals.millions=maxvals,wsdin_n=5,csdin_n=5,hddheatn_n=18,cddcoldn_n=18,gddgrown_n=10,rxnday_n=7,rnnmm_n=30,ntxntn_n=3,ntxbntnb_n=3,project.lat2d.coords=TRUE,
thresholds.name.map=c(tx05thresh="tx05thresh",tx10thresh="tx10thresh", tx50thresh="tx50thresh", tx90thresh="tx90thresh",tx95thresh="tx95thresh",
tn05thresh="tn05thresh",tn10thresh="tn10thresh",tn50thresh="tn50thresh",tn90thresh="tn90thresh",tn95thresh="tn95thresh",
tx90thresh_15days="tx90thresh_15days",tn90thresh_15days="tn90thresh_15days",tavg90thresh_15days="tavg90thresh_15days",
tavg05thresh="tavg05thresh",tavg95thresh="tavg95thresh",
txraw="txraw",tnraw="tnraw",precraw="precraw",
r95thresh="r95thresh", r99thresh="r99thresh"))
It would be very helpful if someone could give me a hand to figure this out.
Cheers.
Gerardo
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