Hands-on-ICON-data-analysis-for-beginners.md

@@ -1536,7 +1536,7 @@ We will use a script called `pyic_fig.py`, that is part of pyICON. Please refer
 
 <details><summary><b> Quick view example using command line</b></summary>
 
-```brainfuck=bash
+```bash
 pyicdir=/work/mh1421/m300466/tools/pyicon/scripts
 cd ${pyicdir}
 
@@ -1601,7 +1601,7 @@ healpy.mollview(ds_map.tas.isel(time=0), flip="geo", nest=get_nest(ds_map))
 
 <details><summary><b> Sample script using pyic_sec.py </b></summary>
     
-```brainfuck=bash
+```bash
 expid=slo1826
 datadir=/work/mh0287/m211032/Icon/Git_lev/icon.XPP.20240717/build.intel-hdext/experiments/${expid}
 examplefile=${expid}_oce_def_19900101T000000Z.nc
@@ -1626,7 +1626,7 @@ General recommendation (not a fixed rule) for remapping ICON to lon/lat:
 
 <details><summary><b> Remap r2b9 (5km) ocean to 0.25deg grid  </b></summary> 
 
-```brainfuck=bash
+```bash
 targetgrid=/work/mh0256/m300466/DPP/grid/IFS25_invertlat_gridexample.nc
 remapwgt=/work/mh0256/m300466/DPP/weights/r2b9O_IFS25invertlat_yconremapweights.nc
 srcgrid=/pool/data/ICON/grids/public/mpim/0016/icon_grid_0016_R02B09_O.nc
@@ -1656,7 +1656,7 @@ ncview ${varfile} &
 
 <details><summary><b> Remap r2b5 (80km) atmosphere to 0.25deg grid  </b></summary>   
     
-```brainfuck=bash
+```bash
 targetgrid=/work/mh0256/m300466/DPP/grid/IFS25_invertlat_gridexample.nc
 srcgrid=/pool/data/ICON/grids/public/mpim/0053/icon_grid_0053_R02B07_G.nc
 
@@ -1677,7 +1677,7 @@ ncview ${varfile} &
 
 <details><summary><b> Remap from catalogue: r2b9 (5km) ocean to 0.25deg grid </b></summary>  
 
-```brainfuck=bash
+```bash
 module use /work/k20200/k202134/hsm-tools/outtake/module
 module load hsm-tools/unstable
 module sw cdo cdo
@@ -1792,7 +1792,7 @@ ICON can only output on pressure levels if they are instantaneous outputs. For t
     
 We use C5 experiments (ICON-Sapphire) as an example. 
 
-```brainfuck=bash
+```bash
 #Find where files are located using `query_yaml`
 module use /work/k20200/k202134/hsm-tools/outtake/module
 module load hsm-tools/unstable
@@ -1801,7 +1801,7 @@ filelist_p4k7=$(query_yaml ICON C5 AMIP_P4K --search_args grid=R02B07 time=P1D -
 ```
 
 In this example, we first horizontally interpolate the relevant variables onto 1x1deg grid, and then vertically interpolate onto the pressure levels. 
-```brainfuck=bash
+```bash
 res=r2b7
 RES=R02B07
 
@@ -1854,7 +1854,7 @@ done
 
 <details><summary><b> Compute mass streamfunction and take zonal mean </b></summary>
 
-```brainfuck=bash
+```bash
 res=r2b7
 RES=R02B07
 
@@ -1888,11 +1888,11 @@ There's a driver script to produce quickplots for ICON simulations. Edits are ne
 
 <details><summary><b> Example driver script for making quick plots </b></summary>
     
-We use a DRAGON run as an example. 
-cd /work/mh1421/m300466/tools/pyicon/tools
+We use a DRAGON run as an example. \
+cd /work/mh1421/m300466/tools/pyicon/tools \
 vi run_qp_driver_dragon_r3b7-r2b9.sh
     
-```brainfuck=bash
+```bash
 #!/bin/bash
 #SBATCH --job-name=pyicon_qp
 #SBATCH --time=02:00:00
@@ -2016,7 +2016,7 @@ The observational dataset used in CVDP can be downloaded from [https://www.cesm.
 
 <details><summary><b> Download CVDP </b></summary>
     
-```brainfuck=bash
+```bash
 cd /work/mh1421/m300466/tools
 git clone https://github.com/NCAR/CVDP-ncl.git CVDP
 
@@ -2037,7 +2037,7 @@ mkdir -p icondata/ cvdpplots/ driverscripts/
 
 We use a low res DRAGON run as an example. Here is a script `go_cvdp.sh` which you can modify to run CVDP. 
 
-```brainfuck=bash
+```bash
 #!/bin/bash -x
 CDO="cdo -P 48"
 module load ncl
@@ -2169,6 +2169,34 @@ While variance/covariance gives you the combined variability on all time scales,
 
 The spectra can be simulataneously computed for each grid point on the native grid so that we can obtain 2D maps of how variability and bi-variate relations may look like on different frequency/timescales.
 
+<details><summary><b> Example script for how variance looks </b></summary>
+
+```bash
+expid=slo1774
+datadir=/work/mh0287/m211032/Icon/Git_lev/icon.XPP.20240717/build.intel-hdint/experiments/${expid}
+outdir=/work/mh1421/m300466/blah/${expid}
+varname1="t_2m"
+varname2="sp_10m"
+yyyys=1200
+yyyye=1299
+
+mkdir -p ${outdir}
+
+# Detrend 
+cdo -detrend -yearmean -select,name=${varname1},year=${yyyys}/${yyyye}/1 [ ${datadir}/slo1774_atm_2d_ml_*.nc ] ${outdir}/detrend_${varname1}_ym_${yyyys}-${yyyye}.nc
+cdo -detrend -yearmean -select,name=${varname2},year=${yyyys}/${yyyye}/1 [ ${datadir}/slo1774_atm_2d_ml_*.nc ] ${outdir}/detrend_${varname2}_ym_${yyyys}-${yyyye}.nc
+
+#Variance and regrid to 1x1deg for easy plotting
+cdo -remapycon,r360x180 -timvar ${outdir}/detrend_${varname1}_ym_${yyyys}-${yyyye}.nc ${outdir}/timvar_${expid}_${varname1}_ym_${yyyys}-${yyyye}_r360x180.nc
+cdo -remapycon,r360x180 -timvar ${outdir}/detrend_${varname2}_ym_${yyyys}-${yyyye}.nc ${outdir}/timvar_${expid}_${varname2}_ym_${yyyys}-${yyyye}_r360x180.nc
+
+#Correlation = covariance/(std(x)*std(y)), and Regrid to 1x1deg for easy plotting
+cdo -remapycon,r360x180 -div -timcovar ${outdir}/detrend_${varname1}_ym_${yyyys}-${yyyye}.nc ${outdir}/detrend_${varname2}_ym_${yyyys}-${yyyye}.nc -mul -timstd ${outdir}/detrend_${varname1}_ym_${yyyys}-${yyyye}.nc -timstd ${outdir}/detrend_${varname2}_ym_${yyyys}-${yyyye}.nc ${outdir}/timecorr_${expid}_${varname1}_${varname2}_ym_${yyyys}-${yyyye}_r360x180.nc
+
+```
+
+</details>
+
 <details><summary><b> Example script for spectral analysis </b></summary>
  
 This example uses a control CMIP7 experiment (slo1774; 160km atm resolution). The script is called `timespectra_iconxpp.sh`