Fix/post angola

.gitignore

@@ -3,3 +3,4 @@ notebooks/.ipynb_checkpoints/
 /data/stash_select
 notebooks/data_v2/
 *.pyc
+.idea

notebooks/worksheet2.ipynb

@@ -115,15 +115,16 @@
    "source": [
     "# Provide the names of the directories where the netCDF model files are stored\n",
     "DATADIR = 'data_v2/'\n",
+    "DOMAIN = 'EAS-22'\n",
     "\n",
     "# Load and concatenate the HadGEM2-ES model cube data\n",
-    "infile = os.path.join(DATADIR, 'EAS-22/pr_EAS-22_MOHC-HadGEM2-ES_historical_r1i1p1_GERICS-REMO2015_v1_mon_*.nc')\n",
+    "infile = os.path.join(DATADIR, DOMAIN, 'pr_'+DOMAIN+'_MOHC-HadGEM2-ES_historical_r1i1p1_GERICS-REMO2015_v1_mon_*.nc')\n",
     "cubes = iris.load(infile)\n",
     "equalise_attributes(cubes)\n",
     "hadgem2 = cubes.concatenate_cube()\n",
     "\n",
     "# Load and concatenate the MPI-ESM-LR model cube data\n",
-    "infile = os.path.join(DATADIR, 'EAS-22/pr_EAS-22_MPI-M-MPI-ESM-LR_historical_r1i1p1_GERICS-REMO2015_v1_mon_*.nc')\n",
+    "infile = os.path.join(DATADIR, DOMAIN, '/pr_'+DOMAIN+'_MPI-M-MPI-ESM-LR_historical_r1i1p1_GERICS-REMO2015_v1_mon_*.nc')\n",
     "cubes = iris.load(infile)\n",
     "equalise_attributes(cubes)\n",
     "mpiesm = cubes.concatenate_cube()\n",
@@ -328,10 +329,10 @@
    "outputs": [],
    "source": [
     "# print the unit\n",
-    "print('The current unit for data is: {}'.format(hadgem2.units))\n",
+    "print('The current unit for data is: ' + hadgem2.units)\n",
     "# print the summary statistic (maximum monthly precipitation)\n",
     "maxpr = np.max(hadgem2.data)\n",
-    "print('This is an example rainfall rate (kg m-2 s-1) prior to conversion: {:f}'.format(maxpr))"
+    "print('This is an example rainfall rate (kg m-2 s-1) prior to conversion: ' + maxpr)"
    ]
   },
   {
@@ -343,10 +344,10 @@
     "# Convert units to kg m-2 day-1 (same as multiplying by 86400 seconds)\n",
     "hadgem2.convert_units('kg m-2 day-1')\n",
     "# Print cube.units to view new units for precipitation\n",
-    "print(f'The new rainfall units are: {hadgem2.units}')\n",
+    "print('The new rainfall units are: ' + hadgem2.units)\n",
     "maxpr = np.max(hadgem2.data)\n",
     "# print the summary statistic (maximum monthly precipitation) after the unit conversion\n",
-    "print(f'This is the same rainfall rate but now in (kg m-2 day-1): {maxpr:f}')"
+    "print('This is the same rainfall rate but now in (kg m-2 day-1): ' + maxpr)"
    ]
   },
   {
@@ -366,16 +367,16 @@
     "hadgem2.units = 'mm day-1'\n",
     "\n",
     "# Save the new cube as a new netCDF file\n",
-    "OUTDIR = 'data_v2/EAS-22'\n",
+    "HISTDIR = os.path.join(DATADIR, DOMAIN, 'historical')\n",
     "\n",
     "# Check to see if this directory exists, if not create it\n",
-    "if not os.path.isdir(OUTDIR):\n",
+    "if not os.path.isdir(HISTDIR):\n",
     "    # Make directory\n",
-    "    os.mkdir(OUTDIR)\n",
+    "    os.mkdir(HISTDIR)\n",
     "    # Set directory permissions \n",
-    "    os.chmod(OUTDIR, 0o776)\n",
+    "    os.chmod(HISTDIR, 0o776)\n",
     "\n",
-    "outfile = os.path.join(OUTDIR, 'hadgem2-es.mon.1986_2005.GERICS-REMO2015.pr.mmday-1.nc')\n",
+    "outfile = os.path.join(HISTDIR, 'hadgem2-es.mon.1986_2005.GERICS-REMO2015.pr.mmday-1.nc')\n",
     "iris.save(hadgem2, outfile)"
    ]
   },
@@ -402,7 +403,7 @@
     "\n",
     "\n",
     "# Save the new cube as a new netCDF file using the `outfile` filename we've provided below!\n",
-    "outfile = os.path.join(OUTDIR, 'mpi-esm-lr.mon.1986_2005.GERICS-REMO2015.pr.mmday-1.nc')\n",
+    "outfile = os.path.join(HISTDIR, 'mpi-esm-lr.mon.1986_2005.GERICS-REMO2015.pr.mmday-1.nc')\n",
     "\n"
    ]
   },
@@ -425,7 +426,7 @@
    "outputs": [],
    "source": [
     "# Set up directory for the climatology\n",
-    "CLIMDIR = 'data_v2/EAS-22/climatology'\n",
+    "CLIMDIR = os.path.join(DATADIR, DOMAIN, 'climatology')\n",
     "\n",
     "# Check to see if this directory exists, if not create it\n",
     "if not os.path.isdir(CLIMDIR):\n",
@@ -445,7 +446,7 @@
    "source": [
     "# Loop through two model runs\n",
     "for gcmid in ['hadgem2-es', 'mpi-esm-lr']:\n",
-    "    infile = os.path.join(OUTDIR, gcmid + '.mon.1986_2005.GERICS-REMO2015.pr.mmday-1.nc')\n",
+    "    infile = os.path.join(HISTDIR, gcmid + '.mon.1986_2005.GERICS-REMO2015.pr.mmday-1.nc')\n",
     "\n",
     "    # Load the data\n",
     "    data = iris.load_cube(infile)\n",
@@ -461,7 +462,7 @@
     "\n",
     "    # The cube 'data_ond' contains data from October-December for all years. \n",
     "    # The command below calculates the mean over all years.\n",
-    "    seasonal_mean = data_ond.aggregated_by(['seasons'], iris.analysis.MEAN)\n",
+    "    seasonal_mean = data_ond.collapsed('time', iris.analysis.MEAN)\n",
     "    \n",
     "    # Save the OND seasonal mean as a netCDF\n",
     "    outfile = os.path.join(CLIMDIR, gcmid + '.OND.mean.1986_2005.pr.mmday-1.nc')\n",
@@ -541,7 +542,7 @@
     "chirps_ond = chirps.extract(iris.Constraint(seasons='ond'))\n",
     "\n",
     "# Now calculate the climatological mean for this season\n",
-    "seasonal_mean = chirps_ond.aggregated_by(['seasons'], iris.analysis.MEAN)\n",
+    "seasonal_mean = chirps_ond.collapsed('time', iris.analysis.MEAN)\n",
     "\n",
     "# save the seasonal mean cube as a NetCDF file\n",
     "outfile = os.path.join(CLIMDIR, 'chirps.OND.mean.1986_2005.pr.mmday-1.nc')\n",
@@ -655,23 +656,23 @@
     "# Note this is where cube slicing is needed as you can only plot 2-coordinate\n",
     "# dimensions with qplt.contourf, so here we have selected time[0] as there is only\n",
     "# one timestep (the baseline 1986-2005 mean)\n",
-    "qplt.contourf(hadgem_cube[0], levels=levels, cmap=cm.RdBu, extend='max')\n",
+    "qplt.contourf(hadgem_cube, levels=levels, cmap=cm.RdBu, extend='max')\n",
     "                               \n",
     "\n",
     "plt.title('HadGEM2-ES model')  # plots a title for the plot\n",
     "ax = plt.gca()                 # gca function that returns the current axes\n",
     "ax.coastlines()                # adds coastlines defined by the axes of the plot\n",
     "\n",
     "plt.subplot(1, 3, 2)           # Create a new subplot for the model data; 1 row x 3 columns, 2nd plot\n",
-    "qplt.contourf(mpi_cube[0], levels=levels, cmap=cm.RdBu, extend='max')\n",
+    "qplt.contourf(mpi_cube, levels=levels, cmap=cm.RdBu, extend='max')\n",
     "\n",
     "plt.title('MPI-ESM-LR model')  # plots a title for the plot\n",
     "ax = plt.gca()                 # gca function that returns the current axes\n",
     "ax.coastlines()                # adds coastlines defined by the axes of the plot\n",
     "\n",
     "plt.subplot(1, 3, 3)           # Create a new subplot for the observed data 1 row x 3 columns, 3rd plot\n",
     "                               # This plot will be centred and below the two model plots\n",
-    "qplt.contourf(obs_cube[0], levels=levels, cmap=cm.RdBu, extend='max')\n",
+    "qplt.contourf(obs_cube, levels=levels, cmap=cm.RdBu, extend='max')\n",
     "\n",
     "plt.title('CHIRPS obs')        # plots a title for the plot\n",
     "ax = plt.gca()                 # gca function that returns the current axes\n",
@@ -746,9 +747,9 @@
  "metadata": {
   "instance_type": "ml.t3.medium",
   "kernelspec": {
-   "display_name": "pyprecis-environment",
+   "display_name": "Python 3.6.10 ('pyprecis-environment')",
    "language": "python",
-   "name": "pyprecis-environment"
+   "name": "python3"
   },
   "language_info": {
    "codemirror_mode": {
@@ -762,6 +763,11 @@
    "pygments_lexer": "ipython3",
    "version": "3.6.10"
   },
+  "vscode": {
+   "interpreter": {
+    "hash": "30fc2c9368d5cc76c4fad6f63328738b6cf0a0091c34cff8da6b063602b9d1b0"
+   }
+  },
   "widgets": {
    "state": {},
    "version": "1.1.2"

notebooks/worksheet3.ipynb

@@ -68,15 +68,16 @@
     "\n",
     "# Provide the names of the directories where the netCDF model files are stored\n",
     "DATADIR = 'data_v2/'\n",
+    "DOMAIN = 'EAS-22'\n",
     "\n",
     "# CHIRPS dir\n",
     "CHIRPSDIR = os.path.join(DATADIR, 'CHIRPS/')\n",
     "\n",
     "# Directory name where processed data is stored \n",
-    "HISTDIR = 'data_v2/EAS-22/historical'\n",
+    "HISTDIR = os.path.join(DATADIR, DOMAIN, 'historical')\n",
     "\n",
     "# Directory name where climtology data is stored \n",
-    "CLIMDIR = 'data_v2/EAS-22/climatology'"
+    "CLIMDIR = os.path.join(DATADIR, DOMAIN, 'climatology')"
    ]
   },
   {
@@ -192,8 +193,8 @@
     "\n",
     "pole_lat = hadgem2_cube.coord_system().grid_north_pole_latitude\n",
     "pole_lon = hadgem2_cube.coord_system().grid_north_pole_longitude\n",
-    "print(f'Pole Latitude: {pole_lat}')\n",
-    "print(f'Pole Longitude: {pole_lon}')"
+    "print('Pole Latitude: ' + pole_lat)\n",
+    "print('Pole Longitude: ' + pole_lon)"
    ]
   },
   {
@@ -212,8 +213,8 @@
     "lon=np.array([99.5, 100.5])\n",
     "lat=np.array([13.5, 14.5])\n",
     "rotated_lons, rotated_lats = iris.analysis.cartography.rotate_pole(lon, lat, pole_lon, pole_lat)\n",
-    "print(f'Rotated Longitudes: {rotated_lons[0]:.2f}, {rotated_lons[1]:.2f}')\n",
-    "print(f'Rotated Latitudes: {rotated_lats[0]:.2f}, {rotated_lats[1]:.2f}')"
+    "print('Rotated Longitudes: ' + round(rotated_lons[0], 2) + ' , ' + round(rotated_lons[1], 2))\n",
+    "print('Rotated Latitudes: ' + round(rotated_lats[0], 2) + ' , ' + round(rotated_lats[1], 2))"
    ]
   },
   {
@@ -247,7 +248,7 @@
     "    # save the constrained cube\n",
     "    outfile = os.path.join(CLIMDIR, gcm + '.mon.1986_2005.GERICS-REMO2015.pr.mmday-1.BK.nc')\n",
     "    iris.save(data_BK, outfile)\n",
-    "    print(f'Saved: {outfile}')"
+    "    print('Saved: ' + outfile)"
    ]
   },
   {
@@ -588,14 +589,14 @@
     "mpi_regrid = mpi_model_cube.regrid(obs_cube_sub, iris.analysis.Nearest(extrapolation_mode='mask'))\n",
     "\n",
     "# Save HadGEM2 output\n",
-    "outpath = os.path.join(CLIMDIR, 'hadgem2-es.OND.mean.1986_2005.pr.mmday-1.rg.nc')\n",
-    "iris.save(hadgem2_regrid, outpath)\n",
-    "print('Saved: {}'.format(outfile))\n",
+    "outfile = os.path.join(CLIMDIR, 'hadgem2-es.OND.mean.1986_2005.pr.mmday-1.rg.nc')\n",
+    "iris.save(hadgem2_regrid, outfile)\n",
+    "print('Saved: ' + outfile)\n",
     "\n",
     "# Save MPI-ESM output\n",
-    "outpath = os.path.join(CLIMDIR, 'mpi-esm-lr.OND.mean.1986_2005.pr.mmday-1.rg.nc')\n",
-    "iris.save(mpi_regrid, outpath)\n",
-    "print('Saved: {}'.format(outfile))"
+    "outfile = os.path.join(CLIMDIR, 'mpi-esm-lr.OND.mean.1986_2005.pr.mmday-1.rg.nc')\n",
+    "iris.save(mpi_regrid, outfile)\n",
+    "print('Saved: ' + outfile)"
    ]
   },
   {
@@ -794,10 +795,11 @@
     "'''\n",
     "# Some helpful data locations\n",
     "DATADIR = 'data_v2'\n",
+    "DOMAIN = 'EAS-22'\n",
     "CHIRPSDIR = os.path.join(DATADIR, 'CHIRPS')\n",
     "CRUDIR = os.path.join(DATADIR, 'CRU')\n",
-    "CLIMDIR = 'data_v2/EAS-22/climatology'\n",
-    "MODELDIR = os.path.join(DATADIR, 'cordex/EAS-22')\n",
+    "CLIMDIR = os.path.join(DATADIR, DOMAIN, 'climatology')\n",
+    "MODELDIR = os.path.join(DATADIR, 'cordex', DOMAIN)\n",
     "\n",
     "# Some helpful model variables\n",
     "GCMS = ['hadgem2-es', 'mpi-esm-lr']\n",
@@ -1028,9 +1030,9 @@
  "metadata": {
   "instance_type": "ml.t3.medium",
   "kernelspec": {
-   "display_name": "pyprecis-environment",
+   "display_name": "Python 3.6.10 ('pyprecis-environment')",
    "language": "python",
-   "name": "pyprecis-environment"
+   "name": "python3"
   },
   "language_info": {
    "codemirror_mode": {
@@ -1044,6 +1046,11 @@
    "pygments_lexer": "ipython3",
    "version": "3.6.10"
   },
+  "vscode": {
+   "interpreter": {
+    "hash": "30fc2c9368d5cc76c4fad6f63328738b6cf0a0091c34cff8da6b063602b9d1b0"
+   }
+  },
   "widgets": {
    "state": {},
    "version": "1.1.2"

notebooks/worksheet4.ipynb

@@ -69,10 +69,11 @@
     "import numpy.ma as ma\n",
     "\n",
     "# Some helpful data locations\n",
-    "DATADIR = 'data_v2/EAS-22/'\n",
-    "CLIMDIR = os.path.join(DATADIR, 'climatology')\n",
-    "HISTDIR = os.path.join(DATADIR, 'historical')\n",
-    "FUTRDIR = os.path.join(DATADIR, 'future')\n",
+    "DATADIR = 'data_v2'\n",
+    "DOMAIN = 'EAS-22'\n",
+    "CLIMDIR = os.path.join(DATADIR, DOMAIN, 'climatology')\n",
+    "HISTDIR = os.path.join(DATADIR, DOMAIN, 'historical')\n",
+    "FUTRDIR = os.path.join(DATADIR, DOMAIN, 'rcp85')\n",
     "GCMIDS = ['hadgem2-es', 'mpi-esm-lr']"
    ]
   },
@@ -103,12 +104,12 @@
     "    data_ond = data.extract(iris.Constraint(seasons='ond'))\n",
     "\n",
     "    # Now calculate the mean over the OND season\n",
-    "    ond_mean = data_ond.aggregated_by(['seasons'], iris.analysis.MEAN)\n",
+    "    ond_mean = data_ond.collapsed('time', iris.analysis.MEAN)\n",
     "\n",
     "    # save the OND mean as a netCDF\n",
     "    outfile = os.path.join(CLIMDIR, gcmid + '.OND.mean.2041_2060.GERICS-REMO2015.pr.mmday-1.nc')\n",
     "    iris.save(ond_mean, outfile)\n",
-    "    print('Saved: {}'.format(outfile))"
+    "    print('Saved: ' + outfile)"
    ]
   },
   {
@@ -187,7 +188,7 @@
     "    # Save the resulting cube\n",
     "    outfile = os.path.join(CLIMDIR, gcmid + '.OND.mean.diff.GERICS-REMO2015.pr.mmday-1.nc')\n",
     "    iris.save(diff, outfile)\n",
-    "    print('Saved {}'.format(outfile))\n",
+    "    print('Saved ' + outfile)\n",
     "    # Find the percentage change\n",
     "    pcent_change = iris.analysis.maths.multiply(iris.analysis.maths.divide(diff, OND_baseline), 100)\n",
     "    # remember to change the title and units to reflect the data processing\n",
@@ -196,7 +197,7 @@
     "    # And save this too\n",
     "    outfile = os.path.join(CLIMDIR, gcmid + '.OND.mean.diffperc.GERICS-REMO2015.pr.mmday-1.nc')\n",
     "    iris.save(pcent_change, outfile)\n",
-    "    print('Saved {}'.format(outfile))"
+    "    print('Saved ' + outfile)"
    ]
   },
   {
@@ -218,7 +219,7 @@
    "source": [
     "# HINT: Your filenames should have the format: \n",
     "# gcmid + '.OND.mean.' + time_periods[period] + '.GERICS-REMO2015.tm.C.nc'\n",
-    "time_periods = {'historical':'1986_2005', 'future':'2041_2060'}\n",
+    "time_periods = {'historical':'1986_2005', 'rcp85':'2041_2060'}\n",
     "\n",
     "for gcmid in GCMIDS:\n",
     "    for period in time_periods.keys():\n",
@@ -261,7 +262,7 @@
     "    # Save\n",
     "    outfile = os.path.join(CLIMDIR, gcmid + '.OND.mean.diff.GERICS-REMO2015.tm.C.nc')\n",
     "    iris.save(diff, outfile)\n",
-    "    print('Saved: {}'.format(outfile))"
+    "    print('Saved: ' + outfile)"
    ]
   },
   {
@@ -367,8 +368,8 @@
    "source": [
     "# Read in the land-sea mask. \n",
     "# The cube data array has a land fraction associated with it which we'll use to mask out ocean points.\n",
-    "land_fraction_file = 'sftlf_EAS-22_MOHC-HadGEM2-ES_historical_r0i0p0_GERICS-REMO2015_v1_fx_r0i0p0.nc'\n",
-    "land_fraction = iris.load_cube(DATADIR + land_fraction_file)\n",
+    "land_fraction_file = os.path.join(DATADIR, DOMAIN, 'sftlf_EAS-22_MOHC-HadGEM2-ES_historical_r0i0p0_GERICS-REMO2015_v1_fx_r0i0p0.nc')\n",
+    "land_fraction = iris.load_cube(land_fraction_file)\n",
     "\n",
     "# convert this to a binary (i.e. 1 or 0 mask)\n",
     "land_sea_mask = land_fraction.copy()\n",
@@ -421,7 +422,7 @@
     "    # Save the area averaged monthly future anomalies (time series)\n",
     "    outpath = os.path.join(CLIMDIR, gcmid + '.mon.2041_2060.anom.series.GERICS-REMO2015.pr.mmday-1.nc')\n",
     "    iris.save(diff, outpath)\n",
-    "    print('Saved: {}'.format(outpath))"
+    "    print('Saved: ' + outpath)"
    ]
   },
   {
@@ -476,7 +477,7 @@
     "iplt.plot(time, mpiesm, label = 'MPI-ESM-LR')\n",
     "plt.legend()\n",
     "plt.suptitle('2041-2060 Precipitation anomaly (relative to 1986-2005)')\n",
-    "plt.ylabel(f'Precipitation change ({hadgem2es.units}')\n",
+    "plt.ylabel('Precipitation change (' + hadgem2es.units +')')\n",
     "plt.xlabel('Years')\n",
     "plt.show()"
    ]
@@ -603,9 +604,9 @@
  "metadata": {
   "instance_type": "ml.t3.medium",
   "kernelspec": {
-   "display_name": "pyprecis-environment",
+   "display_name": "Python 3.6.10 ('pyprecis-environment')",
    "language": "python",
-   "name": "pyprecis-environment"
+   "name": "python3"
   },
   "language_info": {
    "codemirror_mode": {
@@ -619,6 +620,11 @@
    "pygments_lexer": "ipython3",
    "version": "3.6.10"
   },
+  "vscode": {
+   "interpreter": {
+    "hash": "30fc2c9368d5cc76c4fad6f63328738b6cf0a0091c34cff8da6b063602b9d1b0"
+   }
+  },
   "widgets": {
    "state": {},
    "version": "1.1.2"