diff --git a/.codacy.yml b/.codacy.yml new file mode 100755 index 0000000000000000000000000000000000000000..0bc0d39b0f2175fbc21f61847dace53b65460c48 --- /dev/null +++ b/.codacy.yml @@ -0,0 +1,21 @@ +# codacy configuration file + +--- + +engines: + coverage: + enabled: true + metrics: + enabled: true + duplication: + enabled: true + prospector: + enabled: true + pylint: + enabled: true + python_version: 3 + +exclude_paths: [ + 'doc/**', + 'data/**', +] diff --git a/.gitignore b/.gitignore new file mode 100644 index 0000000000000000000000000000000000000000..e5d46f5e2567228ab637f935c9d2dcdc3087f550 --- /dev/null +++ b/.gitignore @@ -0,0 +1,9 @@ +.idea +logs +tests/basic_nes_tests_alba.py +tests/test_bash_nord3v2-alba.cmd +notebooks/.ipynb_checkpoints +.ipynb_checkpoints +nes/__pycache__ +nes/nc_projections/__pycache__ +jupyter_notebooks \ No newline at end of file diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml new file mode 100755 index 0000000000000000000000000000000000000000..fa94e79884bd390fd4dbbeedaa7305a15bf35438 --- /dev/null +++ b/.gitlab-ci.yml @@ -0,0 +1,34 @@ +before_script: + - export GIT_SSL_NO_VERIFY=1 + - export PATH="$HOME/miniconda2/bin:$PATH" + +stages: + - prepare + - test + - report + - clean + +cache: + paths: + - test/report + +prepare: + stage: prepare + script: + - conda update conda + +test_python3: + stage: test + script: + - git submodule sync --recursive + - git submodule update --init --recursive + - conda env update -f environment.yml -n nes python=3.7 + - source activate nes + - python run_test.py + +clean: + stage: clean + script: + - conda clean --all --yes + + diff --git a/.prospector.yml b/.prospector.yml new file mode 100755 index 0000000000000000000000000000000000000000..b9c6fa952133de951c9005edb1b2f01d9bcb851b --- /dev/null +++ b/.prospector.yml @@ -0,0 +1,36 @@ +# prospector configuration file + +--- + +output-format: grouped + +strictness: veryhigh +doc-warnings: true +test-warnings: true +member-warnings: false + +pyroma: + run: true + +pydocroma: + run: true + +pep8: + disable: [ + E501, # Line-length, already controlled by pylint + ] + +pep257: + run: true + # see http://pep257.readthedocs.io/en/latest/error_codes.html + disable: [ + # For short descriptions it makes sense not to end with a period: + D400, # First line should end with a period + # Disable because not part of PEP257 official convention: + D203, # 1 blank line required before class docstring + D212, # Multi-line docstring summary should start at the first line + D213, # Multi-line docstring summary should start at the second line + D404, # First word of the docstring should not be This + D107, # We are using numpy style and constructor should be documented in class docstring + D105, # Docstring in magic methods should not be required: we all now what they are for + ] diff --git a/CHANGELOG.md b/CHANGELOG.md new file mode 100644 index 0000000000000000000000000000000000000000..16777801e873500ffb73768bfadaac2700d660ff --- /dev/null +++ b/CHANGELOG.md @@ -0,0 +1,42 @@ +# NES CHANGELOG + +### 0.9.0 +* Release date: 2022/08/12 +* Changes and new features: + * First beta release + * Open: + * NetCDF: + * Regular Latitude-Longitude + * Rotated Lat-Lon + * Lambert Conformal Conic + * Mercator + * Points + * Points + * Points in GHOST format + * Parallelization: + * Balanced / Unbalanced + * By time axis + * By Y axis + * By X axis + * Create: + * NetCDF: + * Regular Latitude-Longitude + * Rotated Lat-Lon + * Lambert Conformal Conic + * Mercator + * Points + * Write: + * NetCDF + * Grib2 + * Interpolation: + * Vertical interpolation + * Horizontal interpolation + * Nearest Neighbours + * Statistics: + * Daily_mean + * Daily_max + * Daily_min + * Last time step + * Methods: + * Concatenate (variables of the same period in different files) + \ No newline at end of file diff --git a/Jupyter_notebooks/1-introduction.ipynb b/Jupyter_notebooks/1-introduction.ipynb new file mode 100644 index 0000000000000000000000000000000000000000..615860d3bed82415dcc5a0269940034654a10415 --- /dev/null +++ b/Jupyter_notebooks/1-introduction.ipynb @@ -0,0 +1,501 @@ +{ + "cells": [ + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "# Introduction to NES - NetCDF for Earth Science" + ] + }, + { + "cell_type": "code", + "execution_count": 1, + "metadata": {}, + "outputs": [], + "source": [ + "from nes import *" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "## Open NetCDF" + ] + }, + { + "cell_type": "code", + "execution_count": 2, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "CPU times: user 175 ms, sys: 159 ms, total: 335 ms\n", + "Wall time: 15.7 s\n" + ] + } + ], + "source": [ + "cams_file = \"/gpfs/scratch/bsc32/bsc32538/a4mg/nmmb-monarch/ARCHIVE/000/2022050312/MONARCH_d01_2022050312.nc\"\n", + "%time nessy = open_netcdf(path=cams_file, info=True)" + ] + }, + { + "cell_type": "code", + "execution_count": 3, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "" + ] + }, + "execution_count": 3, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "nessy" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "### Time\n", + "NES.time : list of time steps (datetime)" + ] + }, + { + "cell_type": "code", + "execution_count": 4, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "[datetime.datetime(2022, 5, 3, 12, 0),\n", + " datetime.datetime(2022, 5, 3, 13, 0),\n", + " datetime.datetime(2022, 5, 3, 14, 0),\n", + " datetime.datetime(2022, 5, 3, 15, 0),\n", + " datetime.datetime(2022, 5, 3, 16, 0),\n", + " datetime.datetime(2022, 5, 3, 17, 0),\n", + " datetime.datetime(2022, 5, 3, 18, 0),\n", + " datetime.datetime(2022, 5, 3, 19, 0),\n", + " datetime.datetime(2022, 5, 3, 20, 0),\n", + " datetime.datetime(2022, 5, 3, 21, 0),\n", + " datetime.datetime(2022, 5, 3, 22, 0),\n", + " datetime.datetime(2022, 5, 3, 23, 0),\n", + " datetime.datetime(2022, 5, 4, 0, 0),\n", + " datetime.datetime(2022, 5, 4, 1, 0),\n", + " datetime.datetime(2022, 5, 4, 2, 0),\n", + " datetime.datetime(2022, 5, 4, 3, 0),\n", + " datetime.datetime(2022, 5, 4, 4, 0),\n", + " datetime.datetime(2022, 5, 4, 5, 0),\n", + " datetime.datetime(2022, 5, 4, 6, 0),\n", + " datetime.datetime(2022, 5, 4, 7, 0),\n", + " datetime.datetime(2022, 5, 4, 8, 0),\n", + " datetime.datetime(2022, 5, 4, 9, 0),\n", + " datetime.datetime(2022, 5, 4, 10, 0),\n", + " datetime.datetime(2022, 5, 4, 11, 0),\n", + " datetime.datetime(2022, 5, 4, 12, 0),\n", + " datetime.datetime(2022, 5, 4, 13, 0),\n", + " datetime.datetime(2022, 5, 4, 14, 0),\n", + " datetime.datetime(2022, 5, 4, 15, 0),\n", + " datetime.datetime(2022, 5, 4, 16, 0),\n", + " datetime.datetime(2022, 5, 4, 17, 0),\n", + " datetime.datetime(2022, 5, 4, 18, 0),\n", + " datetime.datetime(2022, 5, 4, 19, 0),\n", + " datetime.datetime(2022, 5, 4, 20, 0),\n", + " datetime.datetime(2022, 5, 4, 21, 0),\n", + " datetime.datetime(2022, 5, 4, 22, 0),\n", + " datetime.datetime(2022, 5, 4, 23, 0),\n", + " datetime.datetime(2022, 5, 5, 0, 0),\n", + " datetime.datetime(2022, 5, 5, 1, 0),\n", + " datetime.datetime(2022, 5, 5, 2, 0),\n", + " datetime.datetime(2022, 5, 5, 3, 0),\n", + " datetime.datetime(2022, 5, 5, 4, 0),\n", + " datetime.datetime(2022, 5, 5, 5, 0),\n", + " datetime.datetime(2022, 5, 5, 6, 0),\n", + " datetime.datetime(2022, 5, 5, 7, 0),\n", + " datetime.datetime(2022, 5, 5, 8, 0),\n", + " datetime.datetime(2022, 5, 5, 9, 0),\n", + " datetime.datetime(2022, 5, 5, 10, 0),\n", + " datetime.datetime(2022, 5, 5, 11, 0),\n", + " datetime.datetime(2022, 5, 5, 12, 0),\n", + " datetime.datetime(2022, 5, 5, 13, 0),\n", + " datetime.datetime(2022, 5, 5, 14, 0),\n", + " datetime.datetime(2022, 5, 5, 15, 0),\n", + " datetime.datetime(2022, 5, 5, 16, 0),\n", + " datetime.datetime(2022, 5, 5, 17, 0),\n", + " datetime.datetime(2022, 5, 5, 18, 0),\n", + " datetime.datetime(2022, 5, 5, 19, 0),\n", + " datetime.datetime(2022, 5, 5, 20, 0),\n", + " datetime.datetime(2022, 5, 5, 21, 0),\n", + " datetime.datetime(2022, 5, 5, 22, 0),\n", + " datetime.datetime(2022, 5, 5, 23, 0),\n", + " datetime.datetime(2022, 5, 6, 0, 0),\n", + " datetime.datetime(2022, 5, 6, 1, 0),\n", + " datetime.datetime(2022, 5, 6, 2, 0),\n", + " datetime.datetime(2022, 5, 6, 3, 0),\n", + " datetime.datetime(2022, 5, 6, 4, 0),\n", + " datetime.datetime(2022, 5, 6, 5, 0),\n", + " datetime.datetime(2022, 5, 6, 6, 0),\n", + " datetime.datetime(2022, 5, 6, 7, 0),\n", + " datetime.datetime(2022, 5, 6, 8, 0),\n", + " datetime.datetime(2022, 5, 6, 9, 0),\n", + " datetime.datetime(2022, 5, 6, 10, 0),\n", + " datetime.datetime(2022, 5, 6, 11, 0),\n", + " datetime.datetime(2022, 5, 6, 12, 0),\n", + " datetime.datetime(2022, 5, 6, 13, 0),\n", + " datetime.datetime(2022, 5, 6, 14, 0),\n", + " datetime.datetime(2022, 5, 6, 15, 0),\n", + " datetime.datetime(2022, 5, 6, 16, 0),\n", + " datetime.datetime(2022, 5, 6, 17, 0),\n", + " datetime.datetime(2022, 5, 6, 18, 0),\n", + " datetime.datetime(2022, 5, 6, 19, 0),\n", + " datetime.datetime(2022, 5, 6, 20, 0),\n", + " datetime.datetime(2022, 5, 6, 21, 0),\n", + " datetime.datetime(2022, 5, 6, 22, 0),\n", + " datetime.datetime(2022, 5, 6, 23, 0),\n", + " datetime.datetime(2022, 5, 7, 0, 0),\n", + " datetime.datetime(2022, 5, 7, 1, 0),\n", + " datetime.datetime(2022, 5, 7, 2, 0),\n", + " datetime.datetime(2022, 5, 7, 3, 0),\n", + " datetime.datetime(2022, 5, 7, 4, 0),\n", + " datetime.datetime(2022, 5, 7, 5, 0),\n", + " datetime.datetime(2022, 5, 7, 6, 0),\n", + " datetime.datetime(2022, 5, 7, 7, 0),\n", + " datetime.datetime(2022, 5, 7, 8, 0),\n", + " datetime.datetime(2022, 5, 7, 9, 0),\n", + " datetime.datetime(2022, 5, 7, 10, 0),\n", + " datetime.datetime(2022, 5, 7, 11, 0),\n", + " datetime.datetime(2022, 5, 7, 12, 0),\n", + " datetime.datetime(2022, 5, 7, 13, 0),\n", + " datetime.datetime(2022, 5, 7, 14, 0),\n", + " datetime.datetime(2022, 5, 7, 15, 0),\n", + " datetime.datetime(2022, 5, 7, 16, 0),\n", + " datetime.datetime(2022, 5, 7, 17, 0),\n", + " datetime.datetime(2022, 5, 7, 18, 0),\n", + " datetime.datetime(2022, 5, 7, 19, 0),\n", + " datetime.datetime(2022, 5, 7, 20, 0),\n", + " datetime.datetime(2022, 5, 7, 21, 0),\n", + " datetime.datetime(2022, 5, 7, 22, 0),\n", + " datetime.datetime(2022, 5, 7, 23, 0),\n", + " datetime.datetime(2022, 5, 8, 0, 0)]" + ] + }, + "execution_count": 4, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "nessy.time" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "### Level, Latitude, Longitude" + ] + }, + { + "cell_type": "code", + "execution_count": 5, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "{'data': masked_array(data=[ 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13,\n", + " 14, 15, 16, 17, 18, 19, 20, 21, 22, 23],\n", + " mask=False,\n", + " fill_value=999999,\n", + " dtype=int32),\n", + " 'dimensions': ('lm',),\n", + " 'units': '',\n", + " 'long_name': 'layer id'}" + ] + }, + "execution_count": 5, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "nessy.lev" + ] + }, + { + "cell_type": "code", + "execution_count": 6, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "{'data': masked_array(\n", + " data=[[16.371021, 16.43293 , 16.494629, ..., 16.494629, 16.43293 ,\n", + " 16.371021],\n", + " [16.503883, 16.565914, 16.627739, ..., 16.627739, 16.565918,\n", + " 16.503883],\n", + " [16.636723, 16.69888 , 16.760828, ..., 16.760828, 16.698881,\n", + " 16.636723],\n", + " ...,\n", + " [58.41168 , 58.525536, 58.63936 , ..., 58.63936 , 58.525547,\n", + " 58.41168 ],\n", + " [58.49049 , 58.604454, 58.718372, ..., 58.718372, 58.604454,\n", + " 58.49049 ],\n", + " [58.56883 , 58.6829 , 58.796925, ..., 58.796925, 58.682903,\n", + " 58.56883 ]],\n", + " mask=False,\n", + " fill_value=1e+20,\n", + " dtype=float32),\n", + " 'dimensions': ('rlat', 'rlon'),\n", + " 'long_name': 'latitude',\n", + " 'units': 'degrees_north',\n", + " 'standard_name': 'latitude',\n", + " 'coordinates': 'lon lat'}" + ] + }, + "execution_count": 6, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "nessy.lat" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "### Variables\n", + "\n", + "- List of variables in lazy mode: No data" + ] + }, + { + "cell_type": "code", + "execution_count": 7, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "dict_keys(['lmp', 'IM', 'JM', 'LM', 'IHRST', 'I_PAR_STA', 'J_PAR_STA', 'NPHS', 'NCLOD', 'NHEAT', 'NPREC', 'NRDLW', 'NRDSW', 'NSRFC', 'AVGMAXLEN', 'MDRMINout', 'MDRMAXout', 'MDIMINout', 'MDIMAXout', 'IDAT', 'DXH', 'SG1', 'SG2', 'DSG1', 'DSG2', 'SGML1', 'SGML2', 'SLDPTH', 'ISLTYP', 'IVGTYP', 'NCFRCV', 'NCFRST', 'FIS', 'GLAT', 'GLON', 'PD', 'VLAT', 'VLON', 'ACPREC', 'CUPREC', 'MIXHT', 'PBLH', 'RLWTOA', 'RSWIN', 'U10', 'USTAR', 'V10', 'RMOL', 'T2', 'relative_humidity_2m', 'T', 'U', 'V', 'SH2O', 'SMC', 'STC', 'AERO_ACPREC', 'AERO_CUPREC', 'AERO_DEPDRY', 'AERO_OPT_R', 'DRE_SW_TOA', 'DRE_SW_SFC', 'DRE_LW_TOA', 'DRE_LW_SFC', 'ENG_SW_SFC', 'ADRYDEP', 'WETDEP', 'PH_NO2', 'HSUM', 'POLR', 'aerosol_optical_depth_dim', 'aerosol_optical_depth', 'satellite_AOD_dim', 'satellite_AOD', 'aerosol_loading_dim', 'aerosol_loading', 'clear_sky_AOD_dim', 'clear_sky_AOD', 'layer_thickness', 'mid_layer_pressure', 'interface_pressure', 'relative_humidity', 'mid_layer_height', 'mid_layer_height_agl', 'air_density', 'dry_pm10_mass', 'dry_pm2p5_mass', 'QC', 'QR', 'QS', 'QG', 'aero_dust_001', 'aero_dust_002', 'aero_dust_003', 'aero_dust_004', 'aero_dust_005', 'aero_dust_006', 'aero_dust_007', 'aero_dust_008', 'aero_ssa_001', 'aero_ssa_002', 'aero_ssa_003', 'aero_ssa_004', 'aero_ssa_005', 'aero_ssa_006', 'aero_ssa_007', 'aero_ssa_008', 'aero_om_001', 'aero_om_002', 'aero_om_003', 'aero_om_004', 'aero_om_005', 'aero_om_006', 'aero_bc_001', 'aero_bc_002', 'aero_so4_001', 'aero_no3_001', 'aero_no3_002', 'aero_no3_003', 'aero_nh4_001', 'aero_unsp_001', 'aero_unsp_002', 'aero_unsp_003', 'aero_unsp_004', 'aero_unsp_005', 'aero_pol_001', 'aero_pol_002', 'aero_pol_003', 'aero_pol_004', 'aero_pol_005', 'aero_pol_006', 'aero_pol_007', 'aero_pol_008', 'aero_pol_009', 'aero_pol_010', 'NO2', 'NO', 'O3', 'NO3', 'N2O5', 'HNO3', 'HONO', 'PNA', 'H2O2', 'NTR', 'ROOH', 'FORM', 'ALD2', 'ALDX', 'PAR', 'CO', 'MEPX', 'MEOH', 'FACD', 'PAN', 'PACD', 'AACD', 'PANX', 'OLE', 'ETH', 'IOLE', 'TOL', 'CRES', 'OPEN', 'MGLY', 'XYL', 'ISOP', 'ISPD', 'TERP', 'SO2', 'SULF', 'ETOH', 'ETHA', 'CL2', 'HOCL', 'FMCL', 'HCL', 'BENZENE', 'SESQ', 'NH3', 'DMS', 'SOAP_I', 'SOAP_T', 'SOAP_F', 'SOAP_A', 'O', 'O1D', 'OH', 'HO2', 'XO2', 'XO2N', 'MEO2', 'HCO3', 'C2O3', 'CXO3', 'ROR', 'TO2', 'TOLRO2', 'CRO', 'XYLRO2', 'ISOPRXN', 'TRPRXN', 'SULRXN', 'CL', 'CLO', 'TOLNRXN', 'TOLHRXN', 'XYLNRXN', 'XYLHRXN', 'BENZRO2', 'BNZNRXN', 'BNZHRXN', 'SESQRXN', 'aerosol_extinction_dim', 'aerosol_extinction_DUST_1', 'aerosol_extinction_DUST_2', 'aerosol_extinction_DUST_3', 'aerosol_extinction_DUST_4', 'aerosol_extinction_DUST_5', 'aerosol_extinction_DUST_6', 'aerosol_extinction_DUST_7', 'aerosol_extinction_DUST_8', 'aerosol_extinction_SALT_total', 'aerosol_extinction_OM_total', 'aerosol_extinction_BC_total', 'aerosol_extinction_SO4_total', 'aerosol_extinction_NO3_total', 'aerosol_extinction_NH4_total', 'aerosol_extinction_UNSPC_1', 'aerosol_extinction_UNSPC_2', 'aerosol_extinction_UNSPC_3', 'aerosol_extinction_UNSPC_4', 'aerosol_extinction_UNSPC_5', 'aerosol_extinction_POLLEN_total'])" + ] + }, + "execution_count": 7, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "nessy.variables.keys()" + ] + }, + { + "cell_type": "code", + "execution_count": 8, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "{'O3': {'data': None,\n", + " 'dimensions': ('time', 'lm', 'rlat', 'rlon'),\n", + " 'long_name': 'TRACERS_054',\n", + " 'units': 'unknown',\n", + " 'standard_name': 'TRACERS_054',\n", + " 'coordinates': 'lon lat',\n", + " 'grid_mapping': 'rotated_pole'}}" + ] + }, + "execution_count": 8, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "# Selecting only one variable and descarting the rest.\n", + "nessy.keep_vars('O3')\n", + "nessy.variables" + ] + }, + { + "cell_type": "code", + "execution_count": 9, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Rank 000: Loading O3 var (1/1)\n", + "Rank 000: Loaded O3 var ((109, 24, 361, 467))\n", + "CPU times: user 1.21 s, sys: 7.1 s, total: 8.32 s\n", + "Wall time: 42 s\n" + ] + } + ], + "source": [ + "# Loading variable data from NetCDF file\n", + "%time nessy.load()" + ] + }, + { + "cell_type": "code", + "execution_count": 10, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "(109, 24, 361, 467)\n", + "('time', 'lm', 'rlat', 'rlon')\n" + ] + } + ], + "source": [ + "print(nessy.variables['O3']['data'].shape)\n", + "print(nessy.variables['O3']['dimensions'])" + ] + }, + { + "cell_type": "code", + "execution_count": 11, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "CPU times: user 723 ms, sys: 719 ms, total: 1.44 s\n", + "Wall time: 14.3 s\n" + ] + } + ], + "source": [ + "# Writing NetCDF\n", + "%time nessy.to_netcdf('o3_test.nc')" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "## Statistics" + ] + }, + { + "cell_type": "code", + "execution_count": 12, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "CPU times: user 403 ms, sys: 206 ms, total: 609 ms\n", + "Wall time: 611 ms\n" + ] + } + ], + "source": [ + "%time nessy.daily_statistic(op=\"mean\")" + ] + }, + { + "cell_type": "code", + "execution_count": 13, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "(5, 24, 361, 467)\n", + "('time', 'lm', 'rlat', 'rlon')\n" + ] + } + ], + "source": [ + "print(nessy.variables['O3']['data'].shape)\n", + "print(nessy.variables['O3']['dimensions'])" + ] + }, + { + "cell_type": "code", + "execution_count": 14, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "CPU times: user 49.2 ms, sys: 30.3 ms, total: 79.4 ms\n", + "Wall time: 837 ms\n" + ] + } + ], + "source": [ + "%time nessy.to_netcdf('o3_daily_mean_test.nc')" + ] + }, + { + "cell_type": "code", + "execution_count": 15, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Metadata 'cell_methods': time: mean (interval: 1hr)\n", + "Time: [datetime.datetime(2022, 5, 3, 0, 0), datetime.datetime(2022, 5, 4, 0, 0), datetime.datetime(2022, 5, 5, 0, 0), datetime.datetime(2022, 5, 6, 0, 0), datetime.datetime(2022, 5, 7, 0, 0)]\n", + "Time bounds: 5\n", + "[datetime.datetime(2022, 5, 3, 12, 0), datetime.datetime(2022, 5, 3, 23, 0)]\n" + ] + } + ], + "source": [ + "print(\"Metadata 'cell_methods':\", nessy.variables['O3']['cell_methods'])\n", + "\n", + "print(\"Time:\", nessy.time)\n", + "print(\"Time bounds:\", len(nessy.time_bnds))\n", + "\n", + "print(nessy.time_bnds[0])" + ] + } + ], + "metadata": { + "kernelspec": { + "display_name": "Python 3", + "language": "python", + "name": "python3" + }, + "language_info": { + "codemirror_mode": { + "name": "ipython", + "version": 3 + }, + "file_extension": ".py", + "mimetype": "text/x-python", + "name": "python", + "nbconvert_exporter": "python", + "pygments_lexer": "ipython3", + "version": "3.7.4" + } + }, + "nbformat": 4, + "nbformat_minor": 4 +} diff --git a/Jupyter_notebooks/1.1-regular_grids.ipynb b/Jupyter_notebooks/1.1-regular_grids.ipynb new file mode 100644 index 0000000000000000000000000000000000000000..c6733d6d81818c4b45234704f8b4fd7b1a539eb5 --- /dev/null +++ b/Jupyter_notebooks/1.1-regular_grids.ipynb @@ -0,0 +1,2358 @@ +{ + "cells": [ + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "# How to read and write regular grids" + ] + }, + { + "cell_type": "code", + "execution_count": 1, + "metadata": {}, + "outputs": [], + "source": [ + "import xarray as xr\n", + "from netCDF4 import Dataset\n", + "from nes import *" + ] + }, + { + "cell_type": "code", + "execution_count": 2, + "metadata": {}, + "outputs": [], + "source": [ + "nc_path_1 = '/gpfs/scratch/bsc32/bsc32538/mr_multiplyby/original_file/MONARCH_d01_2008123100.nc'" + ] + }, + { + "cell_type": "code", + "execution_count": 3, + "metadata": {}, + "outputs": [], + "source": [ + "# ERROR when files have lat_bnds, lon_bnds \n", + "#nc_path_1 = '/esarchive/exp/ecearth/a2vx/original_files/cmorfiles-fixed/CMIP/EC-Earth-Consortium/EC-Earth3-AerChem/historical/r4i1p1f1/Amon/ch4/gn/v20200609/ch4_Amon_EC-Earth3-AerChem_historical_r4i1p1f1_gn_185001-185012.nc'" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "## 1. Read dataset" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "### Open with xarray" + ] + }, + { + "cell_type": "code", + "execution_count": 4, + "metadata": {}, + "outputs": [ + { + "name": "stderr", + "output_type": "stream", + "text": [ + "/gpfs/projects/bsc32/software/suselinux/11/software/xarray/0.19.0-foss-2019b-Python-3.7.4/lib/python3.7/site-packages/xarray/conventions.py:520: SerializationWarning: variable 'IM' has multiple fill values {-999999, -32767}, decoding all values to NaN.\n", + " decode_timedelta=decode_timedelta,\n", + "/gpfs/projects/bsc32/software/suselinux/11/software/xarray/0.19.0-foss-2019b-Python-3.7.4/lib/python3.7/site-packages/xarray/conventions.py:520: SerializationWarning: variable 'JM' has multiple fill values {-999999, -32767}, decoding all values to NaN.\n", + " decode_timedelta=decode_timedelta,\n", + "/gpfs/projects/bsc32/software/suselinux/11/software/xarray/0.19.0-foss-2019b-Python-3.7.4/lib/python3.7/site-packages/xarray/conventions.py:520: SerializationWarning: variable 'LM' has multiple fill values {-999999, -32767}, decoding all values to NaN.\n", + " decode_timedelta=decode_timedelta,\n", + "/gpfs/projects/bsc32/software/suselinux/11/software/xarray/0.19.0-foss-2019b-Python-3.7.4/lib/python3.7/site-packages/xarray/conventions.py:520: SerializationWarning: variable 'IHRST' has multiple fill values {-999999, -32767}, decoding all values to NaN.\n", + " decode_timedelta=decode_timedelta,\n", + "/gpfs/projects/bsc32/software/suselinux/11/software/xarray/0.19.0-foss-2019b-Python-3.7.4/lib/python3.7/site-packages/xarray/conventions.py:520: SerializationWarning: variable 'I_PAR_STA' has multiple fill values {-999999, -32767}, decoding all values to NaN.\n", + " decode_timedelta=decode_timedelta,\n", + "/gpfs/projects/bsc32/software/suselinux/11/software/xarray/0.19.0-foss-2019b-Python-3.7.4/lib/python3.7/site-packages/xarray/conventions.py:520: SerializationWarning: variable 'J_PAR_STA' has multiple fill values {-999999, -32767}, decoding all values to NaN.\n", + " decode_timedelta=decode_timedelta,\n", + "/gpfs/projects/bsc32/software/suselinux/11/software/xarray/0.19.0-foss-2019b-Python-3.7.4/lib/python3.7/site-packages/xarray/conventions.py:520: SerializationWarning: variable 'NPHS' has multiple fill values {-999999, -32767}, decoding all values to NaN.\n", + " decode_timedelta=decode_timedelta,\n", + "/gpfs/projects/bsc32/software/suselinux/11/software/xarray/0.19.0-foss-2019b-Python-3.7.4/lib/python3.7/site-packages/xarray/conventions.py:520: SerializationWarning: variable 'NCLOD' has multiple fill values {-999999, -32767}, decoding all values to NaN.\n", + " decode_timedelta=decode_timedelta,\n", + "/gpfs/projects/bsc32/software/suselinux/11/software/xarray/0.19.0-foss-2019b-Python-3.7.4/lib/python3.7/site-packages/xarray/conventions.py:520: SerializationWarning: variable 'NHEAT' has multiple fill values {-999999, -32767}, decoding all values to NaN.\n", + " decode_timedelta=decode_timedelta,\n", + "/gpfs/projects/bsc32/software/suselinux/11/software/xarray/0.19.0-foss-2019b-Python-3.7.4/lib/python3.7/site-packages/xarray/conventions.py:520: SerializationWarning: variable 'NPREC' has multiple fill values {-999999, -32767}, decoding all values to NaN.\n", + " decode_timedelta=decode_timedelta,\n", + "/gpfs/projects/bsc32/software/suselinux/11/software/xarray/0.19.0-foss-2019b-Python-3.7.4/lib/python3.7/site-packages/xarray/conventions.py:520: SerializationWarning: variable 'NRDLW' has multiple fill values {-999999, -32767}, decoding all values to NaN.\n", + " decode_timedelta=decode_timedelta,\n", + "/gpfs/projects/bsc32/software/suselinux/11/software/xarray/0.19.0-foss-2019b-Python-3.7.4/lib/python3.7/site-packages/xarray/conventions.py:520: SerializationWarning: variable 'NRDSW' has multiple fill values {-999999, -32767}, decoding all values to NaN.\n", + " decode_timedelta=decode_timedelta,\n", + "/gpfs/projects/bsc32/software/suselinux/11/software/xarray/0.19.0-foss-2019b-Python-3.7.4/lib/python3.7/site-packages/xarray/conventions.py:520: SerializationWarning: variable 'NSRFC' has multiple fill values {-999999, -32767}, decoding all values to NaN.\n", + " decode_timedelta=decode_timedelta,\n", + "/gpfs/projects/bsc32/software/suselinux/11/software/xarray/0.19.0-foss-2019b-Python-3.7.4/lib/python3.7/site-packages/xarray/conventions.py:520: SerializationWarning: variable 'AVGMAXLEN' has multiple fill values {-999999, -32767}, decoding all values to NaN.\n", + " decode_timedelta=decode_timedelta,\n", + "/gpfs/projects/bsc32/software/suselinux/11/software/xarray/0.19.0-foss-2019b-Python-3.7.4/lib/python3.7/site-packages/xarray/conventions.py:520: SerializationWarning: variable 'MDRMINout' has multiple fill values {-999999, -32767}, decoding all values to NaN.\n", + " decode_timedelta=decode_timedelta,\n", + "/gpfs/projects/bsc32/software/suselinux/11/software/xarray/0.19.0-foss-2019b-Python-3.7.4/lib/python3.7/site-packages/xarray/conventions.py:520: SerializationWarning: variable 'MDRMAXout' has multiple fill values {-999999, -32767}, decoding all values to NaN.\n", + " decode_timedelta=decode_timedelta,\n", + "/gpfs/projects/bsc32/software/suselinux/11/software/xarray/0.19.0-foss-2019b-Python-3.7.4/lib/python3.7/site-packages/xarray/conventions.py:520: SerializationWarning: variable 'MDIMINout' has multiple fill values {-999999, -32767}, decoding all values to NaN.\n", + " decode_timedelta=decode_timedelta,\n", + "/gpfs/projects/bsc32/software/suselinux/11/software/xarray/0.19.0-foss-2019b-Python-3.7.4/lib/python3.7/site-packages/xarray/conventions.py:520: SerializationWarning: variable 'MDIMAXout' has multiple fill values {-999999, -32767}, decoding all values to NaN.\n", + " decode_timedelta=decode_timedelta,\n", + "/gpfs/projects/bsc32/software/suselinux/11/software/xarray/0.19.0-foss-2019b-Python-3.7.4/lib/python3.7/site-packages/xarray/conventions.py:520: SerializationWarning: variable 'DXH' has multiple fill values {-999999.0, -32767.0}, decoding all values to NaN.\n", + " decode_timedelta=decode_timedelta,\n", + "/gpfs/projects/bsc32/software/suselinux/11/software/xarray/0.19.0-foss-2019b-Python-3.7.4/lib/python3.7/site-packages/xarray/conventions.py:520: SerializationWarning: variable 'SG1' has multiple fill values {-999999.0, -32767.0}, decoding all values to NaN.\n", + " decode_timedelta=decode_timedelta,\n", + "/gpfs/projects/bsc32/software/suselinux/11/software/xarray/0.19.0-foss-2019b-Python-3.7.4/lib/python3.7/site-packages/xarray/conventions.py:520: SerializationWarning: variable 'SG2' has multiple fill values {-999999.0, -32767.0}, decoding all values to NaN.\n", + " decode_timedelta=decode_timedelta,\n", + "/gpfs/projects/bsc32/software/suselinux/11/software/xarray/0.19.0-foss-2019b-Python-3.7.4/lib/python3.7/site-packages/xarray/conventions.py:520: SerializationWarning: variable 'DSG1' has multiple fill values {-999999.0, -32767.0}, decoding all values to NaN.\n", + " decode_timedelta=decode_timedelta,\n", + "/gpfs/projects/bsc32/software/suselinux/11/software/xarray/0.19.0-foss-2019b-Python-3.7.4/lib/python3.7/site-packages/xarray/conventions.py:520: SerializationWarning: variable 'DSG2' has multiple fill values {-999999.0, -32767.0}, decoding all values to NaN.\n", + " decode_timedelta=decode_timedelta,\n", + "/gpfs/projects/bsc32/software/suselinux/11/software/xarray/0.19.0-foss-2019b-Python-3.7.4/lib/python3.7/site-packages/xarray/conventions.py:520: SerializationWarning: variable 'SGML1' has multiple fill values {-999999.0, -32767.0}, decoding all values to NaN.\n", + " decode_timedelta=decode_timedelta,\n", + "/gpfs/projects/bsc32/software/suselinux/11/software/xarray/0.19.0-foss-2019b-Python-3.7.4/lib/python3.7/site-packages/xarray/conventions.py:520: SerializationWarning: variable 'SGML2' has multiple fill values {-999999.0, -32767.0}, decoding all values to NaN.\n", + " decode_timedelta=decode_timedelta,\n", + "/gpfs/projects/bsc32/software/suselinux/11/software/xarray/0.19.0-foss-2019b-Python-3.7.4/lib/python3.7/site-packages/xarray/conventions.py:520: SerializationWarning: variable 'SLDPTH' has multiple fill values {-999999.0, -32767.0}, decoding all values to NaN.\n", + " decode_timedelta=decode_timedelta,\n", + 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"/gpfs/projects/bsc32/software/suselinux/11/software/xarray/0.19.0-foss-2019b-Python-3.7.4/lib/python3.7/site-packages/xarray/conventions.py:520: SerializationWarning: variable 'NCFRST' has multiple fill values {-999999, -32767}, decoding all values to NaN.\n", + " decode_timedelta=decode_timedelta,\n", + "/gpfs/projects/bsc32/software/suselinux/11/software/xarray/0.19.0-foss-2019b-Python-3.7.4/lib/python3.7/site-packages/xarray/conventions.py:520: SerializationWarning: variable 'FIS' has multiple fill values {-999999.0, -32767.0}, decoding all values to NaN.\n", + " decode_timedelta=decode_timedelta,\n", + "/gpfs/projects/bsc32/software/suselinux/11/software/xarray/0.19.0-foss-2019b-Python-3.7.4/lib/python3.7/site-packages/xarray/conventions.py:520: SerializationWarning: variable 'GLAT' has multiple fill values {-999999.0, -32767.0}, decoding all values to NaN.\n", + " decode_timedelta=decode_timedelta,\n", + 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"/gpfs/projects/bsc32/software/suselinux/11/software/xarray/0.19.0-foss-2019b-Python-3.7.4/lib/python3.7/site-packages/xarray/conventions.py:520: SerializationWarning: variable 'PH_NO2' has multiple fill values {-999999.0, -32767.0}, decoding all values to NaN.\n", + " decode_timedelta=decode_timedelta,\n", + "/gpfs/projects/bsc32/software/suselinux/11/software/xarray/0.19.0-foss-2019b-Python-3.7.4/lib/python3.7/site-packages/xarray/conventions.py:520: SerializationWarning: variable 'AEROSSA' has multiple fill values {-999999.0, -32767.0}, decoding all values to NaN.\n", + " decode_timedelta=decode_timedelta,\n", + "/gpfs/projects/bsc32/software/suselinux/11/software/xarray/0.19.0-foss-2019b-Python-3.7.4/lib/python3.7/site-packages/xarray/conventions.py:520: SerializationWarning: variable 'aerosol_optical_depth' has multiple fill values {-999999.0, -32767.0}, decoding all values to NaN.\n", + " decode_timedelta=decode_timedelta,\n", + "/gpfs/projects/bsc32/software/suselinux/11/software/xarray/0.19.0-foss-2019b-Python-3.7.4/lib/python3.7/site-packages/xarray/conventions.py:520: SerializationWarning: variable 'satellite_AOD' has multiple fill values {-999999.0, -32767.0}, decoding all values to NaN.\n", + " decode_timedelta=decode_timedelta,\n", + "/gpfs/projects/bsc32/software/suselinux/11/software/xarray/0.19.0-foss-2019b-Python-3.7.4/lib/python3.7/site-packages/xarray/conventions.py:520: SerializationWarning: variable 'aerosol_loading' has multiple fill values {-999999.0, -32767.0}, decoding all values to NaN.\n", + " decode_timedelta=decode_timedelta,\n", + "/gpfs/projects/bsc32/software/suselinux/11/software/xarray/0.19.0-foss-2019b-Python-3.7.4/lib/python3.7/site-packages/xarray/conventions.py:520: SerializationWarning: variable 'clear_sky_AOD' has multiple fill values {-999999.0, -32767.0}, decoding all values to NaN.\n", + " decode_timedelta=decode_timedelta,\n", + "/gpfs/projects/bsc32/software/suselinux/11/software/xarray/0.19.0-foss-2019b-Python-3.7.4/lib/python3.7/site-packages/xarray/conventions.py:520: SerializationWarning: variable 'layer_thickness' has multiple fill values {-999999.0, -32767.0}, decoding all values to NaN.\n", + " decode_timedelta=decode_timedelta,\n", + "/gpfs/projects/bsc32/software/suselinux/11/software/xarray/0.19.0-foss-2019b-Python-3.7.4/lib/python3.7/site-packages/xarray/conventions.py:520: SerializationWarning: variable 'mid_layer_pressure' has multiple fill values {-999999.0, -32767.0}, decoding all values to NaN.\n", + " decode_timedelta=decode_timedelta,\n", + "/gpfs/projects/bsc32/software/suselinux/11/software/xarray/0.19.0-foss-2019b-Python-3.7.4/lib/python3.7/site-packages/xarray/conventions.py:520: SerializationWarning: variable 'interface_pressure' has multiple fill values {-999999.0, -32767.0}, decoding all values to NaN.\n", + " decode_timedelta=decode_timedelta,\n", + "/gpfs/projects/bsc32/software/suselinux/11/software/xarray/0.19.0-foss-2019b-Python-3.7.4/lib/python3.7/site-packages/xarray/conventions.py:520: SerializationWarning: variable 'relative_humidity' has multiple fill values {-999999.0, -32767.0}, decoding all values to NaN.\n", + " decode_timedelta=decode_timedelta,\n", + "/gpfs/projects/bsc32/software/suselinux/11/software/xarray/0.19.0-foss-2019b-Python-3.7.4/lib/python3.7/site-packages/xarray/conventions.py:520: SerializationWarning: variable 'mid_layer_height' has multiple fill values {-999999.0, -32767.0}, decoding all values to NaN.\n", + " decode_timedelta=decode_timedelta,\n", + "/gpfs/projects/bsc32/software/suselinux/11/software/xarray/0.19.0-foss-2019b-Python-3.7.4/lib/python3.7/site-packages/xarray/conventions.py:520: SerializationWarning: variable 'mid_layer_height_agl' has multiple fill values {-999999.0, -32767.0}, decoding all values to NaN.\n", + " decode_timedelta=decode_timedelta,\n", + "/gpfs/projects/bsc32/software/suselinux/11/software/xarray/0.19.0-foss-2019b-Python-3.7.4/lib/python3.7/site-packages/xarray/conventions.py:520: SerializationWarning: variable 'air_density' has multiple fill values {-999999.0, -32767.0}, decoding all values to NaN.\n", + " decode_timedelta=decode_timedelta,\n", + "/gpfs/projects/bsc32/software/suselinux/11/software/xarray/0.19.0-foss-2019b-Python-3.7.4/lib/python3.7/site-packages/xarray/conventions.py:520: SerializationWarning: variable 'dry_pm10_mass' has multiple fill values {-999999.0, -32767.0}, decoding all values to NaN.\n", + " decode_timedelta=decode_timedelta,\n", + "/gpfs/projects/bsc32/software/suselinux/11/software/xarray/0.19.0-foss-2019b-Python-3.7.4/lib/python3.7/site-packages/xarray/conventions.py:520: SerializationWarning: variable 'dry_pm2p5_mass' has multiple fill values {-999999.0, -32767.0}, decoding all values to NaN.\n", + " decode_timedelta=decode_timedelta,\n", + "/gpfs/projects/bsc32/software/suselinux/11/software/xarray/0.19.0-foss-2019b-Python-3.7.4/lib/python3.7/site-packages/xarray/conventions.py:520: SerializationWarning: variable 'QC' has multiple fill values {-999999.0, -32767.0}, decoding all values to NaN.\n", + " decode_timedelta=decode_timedelta,\n", + "/gpfs/projects/bsc32/software/suselinux/11/software/xarray/0.19.0-foss-2019b-Python-3.7.4/lib/python3.7/site-packages/xarray/conventions.py:520: SerializationWarning: variable 'QR' has multiple fill values {-999999.0, -32767.0}, decoding all values to NaN.\n", + " decode_timedelta=decode_timedelta,\n", + "/gpfs/projects/bsc32/software/suselinux/11/software/xarray/0.19.0-foss-2019b-Python-3.7.4/lib/python3.7/site-packages/xarray/conventions.py:520: SerializationWarning: variable 'QS' has multiple fill values {-999999.0, -32767.0}, decoding all values to NaN.\n", + " decode_timedelta=decode_timedelta,\n", + "/gpfs/projects/bsc32/software/suselinux/11/software/xarray/0.19.0-foss-2019b-Python-3.7.4/lib/python3.7/site-packages/xarray/conventions.py:520: SerializationWarning: variable 'QG' has multiple fill values {-999999.0, -32767.0}, decoding all values to NaN.\n", + " decode_timedelta=decode_timedelta,\n", + "/gpfs/projects/bsc32/software/suselinux/11/software/xarray/0.19.0-foss-2019b-Python-3.7.4/lib/python3.7/site-packages/xarray/conventions.py:520: SerializationWarning: variable 'aero_dust_001' has multiple fill values {-999999.0, -32767.0}, decoding all values to NaN.\n", + " decode_timedelta=decode_timedelta,\n", + "/gpfs/projects/bsc32/software/suselinux/11/software/xarray/0.19.0-foss-2019b-Python-3.7.4/lib/python3.7/site-packages/xarray/conventions.py:520: SerializationWarning: variable 'aero_dust_002' has multiple fill values {-999999.0, -32767.0}, decoding all values to NaN.\n", + " decode_timedelta=decode_timedelta,\n", + "/gpfs/projects/bsc32/software/suselinux/11/software/xarray/0.19.0-foss-2019b-Python-3.7.4/lib/python3.7/site-packages/xarray/conventions.py:520: SerializationWarning: variable 'aero_dust_003' has multiple fill values {-999999.0, -32767.0}, decoding all values to NaN.\n", + " decode_timedelta=decode_timedelta,\n", + "/gpfs/projects/bsc32/software/suselinux/11/software/xarray/0.19.0-foss-2019b-Python-3.7.4/lib/python3.7/site-packages/xarray/conventions.py:520: SerializationWarning: variable 'aero_dust_004' has multiple fill values {-999999.0, -32767.0}, decoding all values to NaN.\n", + " decode_timedelta=decode_timedelta,\n", + "/gpfs/projects/bsc32/software/suselinux/11/software/xarray/0.19.0-foss-2019b-Python-3.7.4/lib/python3.7/site-packages/xarray/conventions.py:520: SerializationWarning: variable 'aero_dust_005' has multiple fill values {-999999.0, -32767.0}, decoding all values to NaN.\n", + " decode_timedelta=decode_timedelta,\n", + "/gpfs/projects/bsc32/software/suselinux/11/software/xarray/0.19.0-foss-2019b-Python-3.7.4/lib/python3.7/site-packages/xarray/conventions.py:520: SerializationWarning: variable 'aero_dust_006' has multiple fill values {-999999.0, -32767.0}, decoding all values to NaN.\n", + " decode_timedelta=decode_timedelta,\n", + "/gpfs/projects/bsc32/software/suselinux/11/software/xarray/0.19.0-foss-2019b-Python-3.7.4/lib/python3.7/site-packages/xarray/conventions.py:520: SerializationWarning: variable 'aero_dust_007' has multiple fill values {-999999.0, -32767.0}, decoding all values to NaN.\n", + " decode_timedelta=decode_timedelta,\n", + "/gpfs/projects/bsc32/software/suselinux/11/software/xarray/0.19.0-foss-2019b-Python-3.7.4/lib/python3.7/site-packages/xarray/conventions.py:520: SerializationWarning: variable 'aero_dust_008' has multiple fill values {-999999.0, -32767.0}, decoding all values to NaN.\n", + " decode_timedelta=decode_timedelta,\n", + "/gpfs/projects/bsc32/software/suselinux/11/software/xarray/0.19.0-foss-2019b-Python-3.7.4/lib/python3.7/site-packages/xarray/conventions.py:520: SerializationWarning: variable 'aero_flex_001' has multiple fill values {-999999.0, -32767.0}, decoding all values to NaN.\n", + " decode_timedelta=decode_timedelta,\n", + "/gpfs/projects/bsc32/software/suselinux/11/software/xarray/0.19.0-foss-2019b-Python-3.7.4/lib/python3.7/site-packages/xarray/conventions.py:520: SerializationWarning: variable 'aero_flex_002' has multiple fill values {-999999.0, -32767.0}, decoding all values to NaN.\n", + " decode_timedelta=decode_timedelta,\n", + "/gpfs/projects/bsc32/software/suselinux/11/software/xarray/0.19.0-foss-2019b-Python-3.7.4/lib/python3.7/site-packages/xarray/conventions.py:520: SerializationWarning: variable 'aero_flex_003' has multiple fill values {-999999.0, -32767.0}, decoding all values to NaN.\n", + " decode_timedelta=decode_timedelta,\n", + "/gpfs/projects/bsc32/software/suselinux/11/software/xarray/0.19.0-foss-2019b-Python-3.7.4/lib/python3.7/site-packages/xarray/conventions.py:520: SerializationWarning: variable 'aero_flex_004' has multiple fill values {-999999.0, -32767.0}, decoding all values to NaN.\n", + " decode_timedelta=decode_timedelta,\n", + "/gpfs/projects/bsc32/software/suselinux/11/software/xarray/0.19.0-foss-2019b-Python-3.7.4/lib/python3.7/site-packages/xarray/conventions.py:520: SerializationWarning: variable 'aero_flex_005' has multiple fill values {-999999.0, -32767.0}, decoding all values to NaN.\n", + " decode_timedelta=decode_timedelta,\n", + "/gpfs/projects/bsc32/software/suselinux/11/software/xarray/0.19.0-foss-2019b-Python-3.7.4/lib/python3.7/site-packages/xarray/conventions.py:520: SerializationWarning: variable 'aero_flex_006' has multiple fill values {-999999.0, -32767.0}, decoding all values to NaN.\n", + " decode_timedelta=decode_timedelta,\n", + "/gpfs/projects/bsc32/software/suselinux/11/software/xarray/0.19.0-foss-2019b-Python-3.7.4/lib/python3.7/site-packages/xarray/conventions.py:520: SerializationWarning: variable 'aero_flex_007' has multiple fill values {-999999.0, -32767.0}, decoding all values to NaN.\n", + " decode_timedelta=decode_timedelta,\n", + "/gpfs/projects/bsc32/software/suselinux/11/software/xarray/0.19.0-foss-2019b-Python-3.7.4/lib/python3.7/site-packages/xarray/conventions.py:520: SerializationWarning: variable 'aero_flex_008' has multiple fill values {-999999.0, -32767.0}, decoding all values to NaN.\n", + " decode_timedelta=decode_timedelta,\n", + "/gpfs/projects/bsc32/software/suselinux/11/software/xarray/0.19.0-foss-2019b-Python-3.7.4/lib/python3.7/site-packages/xarray/conventions.py:520: SerializationWarning: variable 'aero_flex_009' has multiple fill values {-999999.0, -32767.0}, decoding all values to NaN.\n", + " decode_timedelta=decode_timedelta,\n", + "/gpfs/projects/bsc32/software/suselinux/11/software/xarray/0.19.0-foss-2019b-Python-3.7.4/lib/python3.7/site-packages/xarray/conventions.py:520: SerializationWarning: variable 'aero_flex_010' has multiple fill values {-999999.0, -32767.0}, decoding all values to NaN.\n", + " decode_timedelta=decode_timedelta,\n", + "/gpfs/projects/bsc32/software/suselinux/11/software/xarray/0.19.0-foss-2019b-Python-3.7.4/lib/python3.7/site-packages/xarray/conventions.py:520: SerializationWarning: variable 'aero_flex_011' has multiple fill values {-999999.0, -32767.0}, decoding all values to NaN.\n", + " decode_timedelta=decode_timedelta,\n", + "/gpfs/projects/bsc32/software/suselinux/11/software/xarray/0.19.0-foss-2019b-Python-3.7.4/lib/python3.7/site-packages/xarray/conventions.py:520: SerializationWarning: variable 'aero_flex_012' has multiple fill values {-999999.0, -32767.0}, decoding all values to NaN.\n", + " decode_timedelta=decode_timedelta,\n", + "/gpfs/projects/bsc32/software/suselinux/11/software/xarray/0.19.0-foss-2019b-Python-3.7.4/lib/python3.7/site-packages/xarray/conventions.py:520: SerializationWarning: variable 'aero_flex_013' has multiple fill values {-999999.0, -32767.0}, decoding all values to NaN.\n", + " decode_timedelta=decode_timedelta,\n", + "/gpfs/projects/bsc32/software/suselinux/11/software/xarray/0.19.0-foss-2019b-Python-3.7.4/lib/python3.7/site-packages/xarray/conventions.py:520: SerializationWarning: variable 'aero_flex_014' has multiple fill values {-999999.0, -32767.0}, decoding all values to NaN.\n", + " decode_timedelta=decode_timedelta,\n", + "/gpfs/projects/bsc32/software/suselinux/11/software/xarray/0.19.0-foss-2019b-Python-3.7.4/lib/python3.7/site-packages/xarray/conventions.py:520: SerializationWarning: variable 'aero_flex_015' has multiple fill values {-999999.0, -32767.0}, decoding all values to NaN.\n", + " decode_timedelta=decode_timedelta,\n", + "/gpfs/projects/bsc32/software/suselinux/11/software/xarray/0.19.0-foss-2019b-Python-3.7.4/lib/python3.7/site-packages/xarray/conventions.py:520: SerializationWarning: variable 'aero_flex_016' has multiple fill values {-999999.0, -32767.0}, decoding all values to NaN.\n", + " decode_timedelta=decode_timedelta,\n", + "/gpfs/projects/bsc32/software/suselinux/11/software/xarray/0.19.0-foss-2019b-Python-3.7.4/lib/python3.7/site-packages/xarray/conventions.py:520: SerializationWarning: variable 'aero_flex_017' has multiple fill values {-999999.0, -32767.0}, decoding all values to NaN.\n", + " decode_timedelta=decode_timedelta,\n", + "/gpfs/projects/bsc32/software/suselinux/11/software/xarray/0.19.0-foss-2019b-Python-3.7.4/lib/python3.7/site-packages/xarray/conventions.py:520: SerializationWarning: variable 'aero_flex_018' has multiple fill values {-999999.0, -32767.0}, decoding all values to NaN.\n", + " decode_timedelta=decode_timedelta,\n", + "/gpfs/projects/bsc32/software/suselinux/11/software/xarray/0.19.0-foss-2019b-Python-3.7.4/lib/python3.7/site-packages/xarray/conventions.py:520: SerializationWarning: variable 'aero_flex_019' has multiple fill values {-999999.0, -32767.0}, decoding all values to NaN.\n", + " decode_timedelta=decode_timedelta,\n", + "/gpfs/projects/bsc32/software/suselinux/11/software/xarray/0.19.0-foss-2019b-Python-3.7.4/lib/python3.7/site-packages/xarray/conventions.py:520: SerializationWarning: variable 'aero_flex_020' has multiple fill values {-999999.0, -32767.0}, decoding all values to NaN.\n", + " decode_timedelta=decode_timedelta,\n", + "/gpfs/projects/bsc32/software/suselinux/11/software/xarray/0.19.0-foss-2019b-Python-3.7.4/lib/python3.7/site-packages/xarray/conventions.py:520: SerializationWarning: variable 'aero_flex_021' has multiple fill values {-999999.0, -32767.0}, decoding all values to NaN.\n", + " decode_timedelta=decode_timedelta,\n", + "/gpfs/projects/bsc32/software/suselinux/11/software/xarray/0.19.0-foss-2019b-Python-3.7.4/lib/python3.7/site-packages/xarray/conventions.py:520: SerializationWarning: variable 'aero_flex_022' has multiple fill values {-999999.0, -32767.0}, decoding all values to NaN.\n", + " decode_timedelta=decode_timedelta,\n", + "/gpfs/projects/bsc32/software/suselinux/11/software/xarray/0.19.0-foss-2019b-Python-3.7.4/lib/python3.7/site-packages/xarray/conventions.py:520: SerializationWarning: variable 'aero_flex_023' has multiple fill values {-999999.0, -32767.0}, decoding all values to NaN.\n", + " decode_timedelta=decode_timedelta,\n", + "/gpfs/projects/bsc32/software/suselinux/11/software/xarray/0.19.0-foss-2019b-Python-3.7.4/lib/python3.7/site-packages/xarray/conventions.py:520: SerializationWarning: variable 'aero_flex_024' has multiple fill values {-999999.0, -32767.0}, decoding all values to NaN.\n", + " decode_timedelta=decode_timedelta,\n", + 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<xarray.Dataset>\n",
+       "Dimensions:                    (time: 9, lm: 48, lmp: 49, lon: 257, lat: 181, idat: 3, soil_lm: 4, num_aero: 88, num_aero_r: 3, num_aero_1: 89, num_engy: 7, num_gas_total: 1, aerosol_optical_depth_dim: 8, satellite_AOD_dim: 2, aerosol_loading_dim: 8, clear_sky_AOD_dim: 8, aerosol_extinction_dim: 8)\n",
+       "Coordinates:\n",
+       "  * time                       (time) datetime64[ns] 2008-12-31 ... 2009-01-01\n",
+       "  * lm                         (lm) int32 0 1 2 3 4 5 6 ... 41 42 43 44 45 46 47\n",
+       "  * lmp                        (lmp) int32 0 1 2 3 4 5 6 ... 43 44 45 46 47 48\n",
+       "  * lon                        (lon) float32 -180.0 -178.6 ... 178.6 180.0\n",
+       "  * lat                        (lat) float32 -90.0 -89.0 -88.0 ... 89.0 90.0\n",
+       "  * aerosol_optical_depth_dim  (aerosol_optical_depth_dim) |S100 b'DUST_1    ...\n",
+       "  * satellite_AOD_dim          (satellite_AOD_dim) |S100 b'MODIS TERRA 550 nm...\n",
+       "  * aerosol_loading_dim        (aerosol_loading_dim) |S100 b'DUST_1          ...\n",
+       "  * clear_sky_AOD_dim          (clear_sky_AOD_dim) |S100 b'DUST_1            ...\n",
+       "  * aerosol_extinction_dim     (aerosol_extinction_dim) |S100 b'DUST_1       ...\n",
+       "Dimensions without coordinates: idat, soil_lm, num_aero, num_aero_r, num_aero_1, num_engy, num_gas_total\n",
+       "Data variables: (12/302)\n",
+       "    IM                         float64 257.0\n",
+       "    JM                         float64 181.0\n",
+       "    LM                         float64 48.0\n",
+       "    IHRST                      float64 0.0\n",
+       "    I_PAR_STA                  float64 1.0\n",
+       "    J_PAR_STA                  float64 1.0\n",
+       "    ...                         ...\n",
+       "    aerosol_extinction_DUST_3  (time, lm, lat, lon) float32 ...\n",
+       "    aerosol_extinction_DUST_4  (time, lm, lat, lon) float32 ...\n",
+       "    aerosol_extinction_DUST_5  (time, lm, lat, lon) float32 ...\n",
+       "    aerosol_extinction_DUST_6  (time, lm, lat, lon) float32 ...\n",
+       "    aerosol_extinction_DUST_7  (time, lm, lat, lon) float32 ...\n",
+       "    aerosol_extinction_DUST_8  (time, lm, lat, lon) float32 ...\n",
+       "Attributes:\n",
+       "    Domain:       Global\n",
+       "    Conventions:  None\n",
+       "    history:      MONARCHv1.0 netcdf file.\n",
+       "    comment:      Generated on marenostrum4
" + ], + "text/plain": [ + "\n", + "Dimensions: (time: 9, lm: 48, lmp: 49, lon: 257, lat: 181, idat: 3, soil_lm: 4, num_aero: 88, num_aero_r: 3, num_aero_1: 89, num_engy: 7, num_gas_total: 1, aerosol_optical_depth_dim: 8, satellite_AOD_dim: 2, aerosol_loading_dim: 8, clear_sky_AOD_dim: 8, aerosol_extinction_dim: 8)\n", + "Coordinates:\n", + " * time (time) datetime64[ns] 2008-12-31 ... 2009-01-01\n", + " * lm (lm) int32 0 1 2 3 4 5 6 ... 41 42 43 44 45 46 47\n", + " * lmp (lmp) int32 0 1 2 3 4 5 6 ... 43 44 45 46 47 48\n", + " * lon (lon) float32 -180.0 -178.6 ... 178.6 180.0\n", + " * lat (lat) float32 -90.0 -89.0 -88.0 ... 89.0 90.0\n", + " * aerosol_optical_depth_dim (aerosol_optical_depth_dim) |S100 b'DUST_1 ...\n", + " * satellite_AOD_dim (satellite_AOD_dim) |S100 b'MODIS TERRA 550 nm...\n", + " * aerosol_loading_dim (aerosol_loading_dim) |S100 b'DUST_1 ...\n", + " * clear_sky_AOD_dim (clear_sky_AOD_dim) |S100 b'DUST_1 ...\n", + " * aerosol_extinction_dim (aerosol_extinction_dim) 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"xr.open_dataset(nc_path_1)" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "### Open with NES" + ] + }, + { + "cell_type": "code", + "execution_count": 5, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "" + ] + }, + "execution_count": 5, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "nessy_1 = open_netcdf(path=nc_path_1, info=True)\n", + "nessy_1" + ] + }, + { + "cell_type": "code", + "execution_count": 6, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "[datetime.datetime(2008, 12, 31, 0, 0),\n", + " datetime.datetime(2008, 12, 31, 3, 0),\n", + " datetime.datetime(2008, 12, 31, 6, 0),\n", + " datetime.datetime(2008, 12, 31, 9, 0),\n", + " datetime.datetime(2008, 12, 31, 12, 0),\n", + " datetime.datetime(2008, 12, 31, 15, 0),\n", + " datetime.datetime(2008, 12, 31, 18, 0),\n", + " datetime.datetime(2008, 12, 31, 21, 0),\n", + " datetime.datetime(2009, 1, 1, 0, 0)]" + ] + }, + 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0.],\n", + " ...,\n", + " [0., 0., 0., ..., 0., 0., 0.],\n", + " [0., 0., 0., ..., 0., 0., 0.],\n", + " [0., 0., 0., ..., 0., 0., 0.]],\n", + " \n", + " [[0., 0., 0., ..., 0., 0., 0.],\n", + " [0., 0., 0., ..., 0., 0., 0.],\n", + " [0., 0., 0., ..., 0., 0., 0.],\n", + " ...,\n", + " [0., 0., 0., ..., 0., 0., 0.],\n", + " [0., 0., 0., ..., 0., 0., 0.],\n", + " [0., 0., 0., ..., 0., 0., 0.]],\n", + " \n", + " ...,\n", + " \n", + " [[0., 0., 0., ..., 0., 0., 0.],\n", + " [0., 0., 0., ..., 0., 0., 0.],\n", + " [0., 0., 0., ..., 0., 0., 0.],\n", + " ...,\n", + " [0., 0., 0., ..., 0., 0., 0.],\n", + " [0., 0., 0., ..., 0., 0., 0.],\n", + " [0., 0., 0., ..., 0., 0., 0.]],\n", + " \n", + " [[0., 0., 0., ..., 0., 0., 0.],\n", + " [0., 0., 0., ..., 0., 0., 0.],\n", + " [0., 0., 0., ..., 0., 0., 0.],\n", + " ...,\n", + " [0., 0., 0., ..., 0., 0., 0.],\n", + " [0., 0., 0., ..., 0., 0., 0.],\n", + " [0., 0., 0., ..., 0., 0., 0.]],\n", + " \n", + " [[0., 0., 0., ..., 0., 0., 0.],\n", + " [0., 0., 0., ..., 0., 0., 0.],\n", + " [0., 0., 0., ..., 0., 0., 0.],\n", + " ...,\n", + " [0., 0., 0., ..., 0., 0., 0.],\n", + " [0., 0., 0., ..., 0., 0., 0.],\n", + " [0., 0., 0., ..., 0., 0., 0.]]]],\n", + " mask=False,\n", + " fill_value=1e+20,\n", + " dtype=float32),\n", + " 'dimensions': ('time', 'lm', 'lat', 'lon'),\n", + " 'long_name': 'O3',\n", + " 'units': 'unknown',\n", + " 'standard_name': 'O3'}}" + ] + }, + "execution_count": 12, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "nessy_1.variables" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "## 2. Write dataset" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "### Write with NES" + ] + }, + { + "cell_type": "code", + "execution_count": 13, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Rank 000: Creating regular_file_1.nc\n", + "Rank 000: NetCDF ready to write\n", + "Rank 000: Dimensions done\n", + "Rank 000: Writing O3 var (1/1)\n", + "Rank 000: Var O3 created (1/1)\n", + "Rank 000: Filling O3)\n", + "Rank 000: Var O3 data (1/1)\n", + "Rank 000: Var O3 completed (1/1)\n" + ] + } + ], + "source": [ + "nessy_1.to_netcdf('regular_file_1.nc', info=True)" + ] + }, + { + "cell_type": "markdown", + "metadata": { + "toc-hr-collapsed": true + }, + "source": [ + "### Reopen with NES" + ] + }, + { + "cell_type": "code", + "execution_count": 14, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "" + ] + }, + "execution_count": 14, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "nessy_2 = open_netcdf('regular_file_1.nc', info=True)\n", + "nessy_2" + ] + }, + { + "cell_type": "code", + "execution_count": 15, + "metadata": {}, + "outputs": [ + { + "data": { + "text/html": [ + "
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+       "Dimensions:  (time: 9, lev: 48, lat: 181, lon: 257)\n",
+       "Coordinates:\n",
+       "  * time     (time) datetime64[ns] 2008-12-31 2008-12-31T03:00:00 ... 2009-01-01\n",
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+       "Data variables:\n",
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+       "    crs      |S1 b''\n",
+       "Attributes:\n",
+       "    Domain:       Global\n",
+       "    Conventions:  CF-1.7\n",
+       "    history:      MONARCHv1.0 netcdf file.\n",
+       "    comment:      Generated on marenostrum4
" + ], + "text/plain": [ + "\n", + "Dimensions: (time: 9, lev: 48, lat: 181, lon: 257)\n", + "Coordinates:\n", + " * time (time) datetime64[ns] 2008-12-31 2008-12-31T03:00:00 ... 2009-01-01\n", + " * lev (lev) float64 0.0 1.0 2.0 3.0 4.0 5.0 ... 43.0 44.0 45.0 46.0 47.0\n", + " * lat (lat) float64 -90.0 -89.0 -88.0 -87.0 -86.0 ... 87.0 88.0 89.0 90.0\n", + " * lon (lon) float64 -180.0 -178.6 -177.2 -175.8 ... 177.2 178.6 180.0\n", + "Data variables:\n", + " O3 (time, lev, lat, lon) float32 ...\n", + " crs |S1 ...\n", + "Attributes:\n", + " Domain: Global\n", + " Conventions: CF-1.7\n", + " history: MONARCHv1.0 netcdf file.\n", + " comment: Generated on marenostrum4" + ] + }, + "execution_count": 15, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "xr.open_dataset('regular_file_1.nc')" + ] + } + ], + "metadata": { + "kernelspec": { + "display_name": "Python 3", + "language": "python", + "name": "python3" + }, + "language_info": { + "codemirror_mode": { + "name": "ipython", + "version": 3 + }, + "file_extension": ".py", + "mimetype": "text/x-python", + "name": "python", + "nbconvert_exporter": "python", + "pygments_lexer": "ipython3", + "version": "3.7.4" + } + }, + "nbformat": 4, + "nbformat_minor": 4 +} diff --git a/Jupyter_notebooks/1.2-rotated_grids.ipynb b/Jupyter_notebooks/1.2-rotated_grids.ipynb new file mode 100644 index 0000000000000000000000000000000000000000..4cff1df6df2c0bf97ae9c90b55077140afc990b6 --- /dev/null +++ b/Jupyter_notebooks/1.2-rotated_grids.ipynb @@ -0,0 +1,1276 @@ +{ + "cells": [ + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "# How to read and write rotated grids" + ] + }, + { + "cell_type": "code", + "execution_count": 1, + "metadata": {}, + "outputs": [], + "source": [ + "import xarray as xr\n", + "from nes import *" + ] + }, + { + "cell_type": "code", + "execution_count": 2, + "metadata": {}, + "outputs": [], + "source": [ + "nc_path_1 = '/gpfs/scratch/bsc32/bsc32538/mr_multiplyby/OUT/stats_bnds/monarch/a45g/regional/daily_max/O3_all/O3_all-000_2021080300.nc'" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "## 1. Read dataset" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "### Open with xarray" + ] + }, + { + "cell_type": "code", + "execution_count": 3, + "metadata": {}, + "outputs": [ + { + "data": { + "text/html": [ + "
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<xarray.Dataset>\n",
+       "Dimensions:       (time: 1, nv: 2, lev: 24, rlat: 271, rlon: 351)\n",
+       "Coordinates:\n",
+       "  * time          (time) datetime64[ns] 2021-08-03\n",
+       "  * lev           (lev) float64 0.0 1.0 2.0 3.0 4.0 ... 19.0 20.0 21.0 22.0 23.0\n",
+       "    lat           (rlat, rlon) float64 16.35 16.43 16.52 ... 58.83 58.68 58.53\n",
+       "    lon           (rlat, rlon) float64 -22.18 -22.02 -21.85 ... 88.05 88.23\n",
+       "  * rlat          (rlat) float64 -27.0 -26.8 -26.6 -26.4 ... 26.4 26.6 26.8 27.0\n",
+       "  * rlon          (rlon) float64 -35.0 -34.8 -34.6 -34.4 ... 34.4 34.6 34.8 35.0\n",
+       "Dimensions without coordinates: nv\n",
+       "Data variables:\n",
+       "    time_bnds     (time, nv) datetime64[ns] 2021-08-03 2021-08-07\n",
+       "    O3_all        (time, lev, rlat, rlon) float32 ...\n",
+       "    rotated_pole  |S1 b''\n",
+       "Attributes:\n",
+       "    Conventions:  CF-1.7\n",
+       "    comment:      Generated on marenostrum4
" + ], + "text/plain": [ + "\n", + "Dimensions: (time: 1, nv: 2, lev: 24, rlat: 271, rlon: 351)\n", + "Coordinates:\n", + " * time (time) datetime64[ns] 2021-08-03\n", + " * lev (lev) float64 0.0 1.0 2.0 3.0 4.0 ... 19.0 20.0 21.0 22.0 23.0\n", + " lat (rlat, rlon) float64 ...\n", + " lon (rlat, rlon) float64 ...\n", + " * rlat (rlat) float64 -27.0 -26.8 -26.6 -26.4 ... 26.4 26.6 26.8 27.0\n", + " * rlon (rlon) float64 -35.0 -34.8 -34.6 -34.4 ... 34.4 34.6 34.8 35.0\n", + "Dimensions without coordinates: nv\n", + "Data variables:\n", + " time_bnds (time, nv) datetime64[ns] ...\n", + " O3_all (time, lev, rlat, rlon) float32 ...\n", + " rotated_pole |S1 ...\n", + "Attributes:\n", + " Conventions: CF-1.7\n", + " comment: Generated on marenostrum4" + ] + }, + "execution_count": 3, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "xr.open_dataset(nc_path_1)" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "### Open with NES" + ] + }, + { + "cell_type": "code", + "execution_count": 4, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "" + ] + }, + "execution_count": 4, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "nessy_1 = open_netcdf(path=nc_path_1, info=True)\n", + "nessy_1" + ] + }, + { + "cell_type": "code", + "execution_count": 5, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "[datetime.datetime(2021, 8, 3, 0, 0)]" + ] + }, + "execution_count": 5, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "nessy_1.time" + ] + }, + { + "cell_type": "code", + "execution_count": 6, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "{'data': masked_array(data=[ 0., 1., 2., 3., 4., 5., 6., 7., 8., 9., 10.,\n", + " 11., 12., 13., 14., 15., 16., 17., 18., 19., 20., 21.,\n", + " 22., 23.],\n", + " mask=False,\n", + " fill_value=1e+20),\n", + " 'dimensions': ('lev',),\n", + " 'units': '',\n", + " 'positive': 'up'}" + ] + }, + "execution_count": 6, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "nessy_1.lev" + ] + }, + { + "cell_type": "code", + "execution_count": 7, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "{'data': masked_array(\n", + " data=[[16.35033798, 16.43292999, 16.51514626, ..., 16.51514626,\n", + " 16.43292999, 16.35033798],\n", + " [16.52742577, 16.61023903, 16.69267654, ..., 16.69267654,\n", + " 16.61024284, 16.52742577],\n", + " [16.70447159, 16.78750801, 16.87016678, ..., 16.87016678,\n", + " 16.78750992, 16.70447159],\n", + " ...,\n", + " [58.32094955, 58.47268295, 58.62430954, ..., 58.62430954,\n", + " 58.47268295, 58.32094955],\n", + " [58.42628479, 58.57820129, 58.73002625, ..., 58.73002625,\n", + " 58.57820129, 58.42628479],\n", + " [58.53079224, 58.68289948, 58.83491898, ..., 58.83491898,\n", + " 58.68290329, 58.53079224]],\n", + " mask=False,\n", + " fill_value=1e+20),\n", + " 'dimensions': ('rlat', 'rlon'),\n", + " 'units': 'degrees_north',\n", + " 'axis': 'Y',\n", + " 'long_name': 'latitude coordinate',\n", + " 'standard_name': 'latitude'}" + ] + }, + "execution_count": 7, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "nessy_1.lat" + ] + }, + { + "cell_type": "code", + "execution_count": 8, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "{'data': masked_array(\n", + " data=[[-22.18126488, -22.01667213, -21.85179901, ..., 41.8517952 ,\n", + " 42.01666641, 42.18125916],\n", + " [-22.27817917, -22.11318588, -21.94790459, ..., 41.94789886,\n", + " 42.11317444, 42.27817154],\n", + " [-22.37526703, -22.2098732 , -22.04418945, ..., 42.04418564,\n", + " 42.2098732 , 42.37526321],\n", + " ...,\n", + " [-67.57766724, -67.39706421, -67.21534729, ..., 87.21533966,\n", + " 87.39705658, 87.57765961],\n", + " [-67.90187836, -67.72247314, -67.54193878, ..., 87.54193878,\n", + " 87.72245789, 87.90187073],\n", + " [-68.22803497, -68.04981995, -67.87051392, ..., 87.87050629,\n", + " 88.04981995, 88.22803497]],\n", + " mask=False,\n", + " fill_value=1e+20),\n", + " 'dimensions': ('rlat', 'rlon'),\n", + " 'units': 'degrees_east',\n", + " 'axis': 'X',\n", + " 'long_name': 'longitude coordinate',\n", + " 'standard_name': 'longitude'}" + ] + }, + "execution_count": 8, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "nessy_1.lon" + ] + }, + { + "cell_type": "code", + "execution_count": 9, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Rank 000: Loading O3_all var (1/1)\n", + "Rank 000: Loaded O3_all var ((1, 24, 271, 351))\n" + ] + } + ], + "source": [ + "nessy_1.load()" + ] + }, + { + "cell_type": "code", + "execution_count": 10, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "{'O3_all': {'data': masked_array(\n", + " data=[[[[2.82636070e-09, 2.83436141e-09, 2.82522827e-09, ...,\n", + " 2.96334601e-09, 2.94810221e-09, 2.91839553e-09],\n", + " [2.80930834e-09, 2.57182142e-09, 2.55521360e-09, ...,\n", + " 2.56395216e-09, 2.55890820e-09, 2.89073032e-09],\n", + " [2.79031842e-09, 2.53415999e-09, 2.50317100e-09, ...,\n", + " 2.56737764e-09, 2.58685584e-09, 2.85498758e-09],\n", + " ...,\n", + " [4.54469973e-09, 2.31674457e-09, 2.22753971e-09, ...,\n", + " 3.90127353e-09, 3.89643118e-09, 3.95452204e-09],\n", + " [4.54129534e-09, 3.39469808e-09, 2.30205255e-09, ...,\n", + " 3.88824706e-09, 3.88372090e-09, 3.95252631e-09],\n", + " [4.55012028e-09, 4.54941684e-09, 4.55885596e-09, ...,\n", + " 3.93945099e-09, 3.94256938e-09, 3.94736510e-09]],\n", + " \n", + " [[1.61966751e-09, 1.62850033e-09, 1.62801062e-09, ...,\n", + " 1.74583636e-09, 1.74684045e-09, 1.74125825e-09],\n", + " [1.60704539e-09, 1.41438683e-09, 1.39824063e-09, ...,\n", + " 1.43241041e-09, 1.45136980e-09, 1.73744363e-09],\n", + " [1.59303792e-09, 1.41264567e-09, 1.43958856e-09, ...,\n", + " 1.43522705e-09, 1.45869528e-09, 1.72746673e-09],\n", + " ...,\n", + " [3.39471939e-09, 2.65527422e-09, 2.22850582e-09, ...,\n", + " 3.00350167e-09, 3.02176750e-09, 3.04009262e-09],\n", + " [3.42592332e-09, 2.81851942e-09, 2.28753505e-09, ...,\n", + " 2.99818836e-09, 2.99247205e-09, 3.04403525e-09],\n", + " [3.43113582e-09, 3.43824125e-09, 3.44929552e-09, ...,\n", + " 3.05421777e-09, 3.04752024e-09, 3.04445491e-09]],\n", + " \n", + " [[6.52169652e-10, 6.62677024e-10, 6.71934786e-10, ...,\n", + " 6.84429291e-10, 6.85826118e-10, 6.81504464e-10],\n", + " [6.54959087e-10, 6.65219158e-10, 6.72430500e-10, ...,\n", + " 7.02121916e-10, 6.88325397e-10, 6.78990253e-10],\n", + " [6.57915333e-10, 6.72102929e-10, 6.82566170e-10, ...,\n", + " 7.10820458e-10, 7.07094217e-10, 6.77522760e-10],\n", + " ...,\n", + " [2.26027863e-09, 2.27629537e-09, 2.22616392e-09, ...,\n", + " 1.80253423e-09, 1.80225357e-09, 1.75757697e-09],\n", + " [2.25028196e-09, 2.24872521e-09, 2.25445618e-09, ...,\n", + " 1.78916737e-09, 1.75583581e-09, 1.73717007e-09],\n", + " [2.25827335e-09, 2.26974151e-09, 2.28325270e-09, ...,\n", + " 1.80090465e-09, 1.77703174e-09, 1.75434933e-09]],\n", + " \n", + " ...,\n", + " \n", + " [[6.20177729e-11, 6.26959387e-11, 6.28658792e-11, ...,\n", + " 7.74274672e-11, 7.81546980e-11, 7.60479180e-11],\n", + " [6.20486787e-11, 4.91600684e-11, 4.88878833e-11, ...,\n", + " 8.30884250e-11, 8.02152303e-11, 7.64004970e-11],\n", + " [6.20976950e-11, 4.84989236e-11, 4.85273696e-11, ...,\n", + " 8.46209977e-11, 8.60716498e-11, 9.29777644e-11],\n", + " ...,\n", + " [6.15721710e-11, 5.85051035e-11, 5.68927752e-11, ...,\n", + " 7.66955388e-11, 7.87262894e-11, 8.41871295e-11],\n", + " [6.17081941e-11, 5.77536560e-11, 5.71826440e-11, ...,\n", + " 8.49015233e-11, 8.82505458e-11, 9.20043208e-11],\n", + " [6.09760506e-11, 6.03529102e-11, 6.24047411e-11, ...,\n", + " 9.69636524e-11, 9.73700426e-11, 9.67554162e-11]],\n", + " \n", + " [[6.17567178e-11, 6.23894963e-11, 6.25706292e-11, ...,\n", + " 9.04916420e-11, 8.90077803e-11, 8.43536768e-11],\n", + " [6.17901147e-11, 4.59270816e-11, 4.57923699e-11, ...,\n", + " 1.06383589e-10, 1.05693093e-10, 9.44862175e-11],\n", + " [6.18271337e-11, 4.17853495e-11, 3.94594427e-11, ...,\n", + " 1.34135009e-10, 1.37096737e-10, 1.13853482e-10],\n", + " ...,\n", + " [5.87425456e-11, 5.60845814e-11, 5.33429169e-11, ...,\n", + " 6.52061183e-11, 6.64711411e-11, 7.06842501e-11],\n", + " [5.92315016e-11, 5.72428251e-11, 5.51245403e-11, ...,\n", + " 7.10893150e-11, 7.38196310e-11, 7.53354532e-11],\n", + " [5.72967125e-11, 5.87497967e-11, 6.08200851e-11, ...,\n", + " 7.97847274e-11, 8.28124236e-11, 7.89215707e-11]],\n", + " \n", + " [[6.15217946e-11, 6.21571961e-11, 6.23377391e-11, ...,\n", + " 1.08401239e-10, 1.07494236e-10, 1.08711720e-10],\n", + " [6.15563989e-11, 4.56989759e-11, 4.46428450e-11, ...,\n", + " 1.30999808e-10, 1.26581134e-10, 1.39005307e-10],\n", + " [6.15933693e-11, 3.98656906e-11, 3.75483949e-11, ...,\n", + " 1.37105632e-10, 1.48587462e-10, 1.83946344e-10],\n", + " ...,\n", + " [4.68582569e-11, 4.44464673e-11, 4.43960736e-11, ...,\n", + " 5.86025117e-11, 5.84869791e-11, 6.32652056e-11],\n", + " [4.99817097e-11, 4.49490271e-11, 4.43218864e-11, ...,\n", + " 6.19639479e-11, 6.07859180e-11, 6.55651922e-11],\n", + " [4.98553143e-11, 4.61104453e-11, 4.96835975e-11, ...,\n", + " 6.42673414e-11, 6.38328765e-11, 6.38894007e-11]]]],\n", + " mask=False,\n", + " fill_value=1e+20,\n", + " dtype=float32),\n", + " 'dimensions': ('time', 'lev', 'rlat', 'rlon'),\n", + " 'units': 'kg/m3',\n", + " 'long_name': 'TRACERS_044',\n", + " 'coordinates': 'lat lon',\n", + " 'cell_methods': 'time: maximum (interval: 1hr)',\n", + " 'grid_mapping': 'rotated_pole'}}" + ] + }, + "execution_count": 10, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "nessy_1.variables" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "## 2. Write dataset" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "### Write with NES" + ] + }, + { + "cell_type": "code", + "execution_count": 11, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Rank 000: Creating rotated_file_1.nc\n", + "Rank 000: NetCDF ready to write\n", + "Rank 000: Dimensions done\n", + "Rank 000: Writing O3_all var (1/1)\n", + "Rank 000: Var O3_all created (1/1)\n", + "Rank 000: Filling O3_all)\n", + "Rank 000: Var O3_all data (1/1)\n", + "Rank 000: Var O3_all completed (1/1)\n" + ] + } + ], + "source": [ + "nessy_1.to_netcdf('rotated_file_1.nc', info=True)" + ] + }, + { + "cell_type": "markdown", + "metadata": { + "toc-hr-collapsed": true + }, + "source": [ + "### Reopen with NES" + ] + }, + { + "cell_type": "code", + "execution_count": 12, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "" + ] + }, + "execution_count": 12, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "nessy_2 = open_netcdf('rotated_file_1.nc', info=True)\n", + "nessy_2" + ] + }, + { + "cell_type": "code", + "execution_count": 13, + "metadata": {}, + "outputs": [ + { + "data": { + "text/html": [ + "
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<xarray.Dataset>\n",
+       "Dimensions:       (time: 1, time_nv: 2, lev: 24, rlat: 271, rlon: 351)\n",
+       "Coordinates:\n",
+       "  * time          (time) datetime64[ns] 2021-08-03\n",
+       "  * lev           (lev) float64 0.0 1.0 2.0 3.0 4.0 ... 19.0 20.0 21.0 22.0 23.0\n",
+       "    lat           (rlat, rlon) float64 16.35 16.43 16.52 ... 58.83 58.68 58.53\n",
+       "    lon           (rlat, rlon) float64 -22.18 -22.02 -21.85 ... 88.05 88.23\n",
+       "  * rlat          (rlat) float64 -27.0 -26.8 -26.6 -26.4 ... 26.4 26.6 26.8 27.0\n",
+       "  * rlon          (rlon) float64 -35.0 -34.8 -34.6 -34.4 ... 34.4 34.6 34.8 35.0\n",
+       "Dimensions without coordinates: time_nv\n",
+       "Data variables:\n",
+       "    time_bnds     (time, time_nv) datetime64[ns] 2021-08-03 2021-08-07\n",
+       "    O3_all        (time, lev, rlat, rlon) float32 ...\n",
+       "    rotated_pole  |S1 b''\n",
+       "Attributes:\n",
+       "    Conventions:  CF-1.7\n",
+       "    comment:      Generated on marenostrum4
" + ], + "text/plain": [ + "\n", + "Dimensions: (time: 1, time_nv: 2, lev: 24, rlat: 271, rlon: 351)\n", + "Coordinates:\n", + " * time (time) datetime64[ns] 2021-08-03\n", + " * lev (lev) float64 0.0 1.0 2.0 3.0 4.0 ... 19.0 20.0 21.0 22.0 23.0\n", + " lat (rlat, rlon) float64 ...\n", + " lon (rlat, rlon) float64 ...\n", + " * rlat (rlat) float64 -27.0 -26.8 -26.6 -26.4 ... 26.4 26.6 26.8 27.0\n", + " * rlon (rlon) float64 -35.0 -34.8 -34.6 -34.4 ... 34.4 34.6 34.8 35.0\n", + "Dimensions without coordinates: time_nv\n", + "Data variables:\n", + " time_bnds (time, time_nv) datetime64[ns] ...\n", + " O3_all (time, lev, rlat, rlon) float32 ...\n", + " rotated_pole |S1 ...\n", + "Attributes:\n", + " Conventions: CF-1.7\n", + " comment: Generated on marenostrum4" + ] + }, + "execution_count": 13, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "xr.open_dataset('rotated_file_1.nc')" + ] + } + ], + "metadata": { + "kernelspec": { + "display_name": "Python 3", + "language": "python", + "name": "python3" + }, + "language_info": { + "codemirror_mode": { + "name": "ipython", + "version": 3 + }, + "file_extension": ".py", + "mimetype": "text/x-python", + "name": "python", + "nbconvert_exporter": "python", + "pygments_lexer": "ipython3", + "version": "3.7.4" + } + }, + "nbformat": 4, + "nbformat_minor": 4 +} diff --git a/Jupyter_notebooks/1.3-points_grids.ipynb b/Jupyter_notebooks/1.3-points_grids.ipynb new file mode 100644 index 0000000000000000000000000000000000000000..966ab17efc2bc372b374a42703695727d852c786 --- /dev/null +++ b/Jupyter_notebooks/1.3-points_grids.ipynb @@ -0,0 +1,4624 @@ +{ + "cells": [ + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "# How to read and write observational datasets" + ] + }, + { + "cell_type": "code", + "execution_count": 1, + "metadata": {}, + "outputs": [], + "source": [ + "from nes import *\n", + "import xarray as xr" + ] + }, + { + "cell_type": "code", + "execution_count": 2, + "metadata": {}, + "outputs": [], + "source": [ + "# nc_path_1 = '/esarchive/obs/eea/eionet/hourly/pm10/pm10_202107.nc' # EIONET\n", + "nc_path_1 = '/esarchive/obs/nilu/ebas/daily/pm10/pm10_201507.nc' # EBAS" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "## 1. Read and write - Non-GHOST type" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "### Open with xarray" + ] + }, + { + "cell_type": "code", + "execution_count": 3, + "metadata": {}, + "outputs": [ + { + "data": { + "text/html": [ + "
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<xarray.Dataset>\n",
+       "Dimensions:                       (station: 84, time: 31)\n",
+       "Coordinates:\n",
+       "  * time                          (time) datetime64[ns] 2015-07-01 ... 2015-0...\n",
+       "Dimensions without coordinates: station\n",
+       "Data variables: (12/19)\n",
+       "    station_start_date            (station) |S75 b'1980-01-01' ... b'nan'\n",
+       "    station_zone                  (station) |S75 b'nan' b'nan' ... b'nan' b'nan'\n",
+       "    street_type                   (station) |S75 b'nan' b'nan' ... b'nan' b'nan'\n",
+       "    country_code                  (station) |S75 b'CH' b'CH' ... b'NL' b'IT'\n",
+       "    ccaa                          (station) |S75 b'nan' b'nan' ... b'nan' b'nan'\n",
+       "    station_name                  (station) |S75 b'payerne' ... b'lamezia terme'\n",
+       "    ...                            ...\n",
+       "    station_code                  (station) |S75 b'CH0002R' ... b'IT0016R'\n",
+       "    longitude                     (station) float32 6.944 8.905 ... 6.277 16.23\n",
+       "    station_end_date              (station) |S75 b'nan' b'nan' ... b'nan' b'nan'\n",
+       "    station_rural_back            (station) |S75 b'nan' b'nan' ... b'nan' b'nan'\n",
+       "    latitude                      (station) float32 46.81 47.48 ... 53.33 38.88\n",
+       "    station_ozone_classification  (station) |S75 b'rural' b'rural' ... b'nan'
" + ], + "text/plain": [ + "\n", + "Dimensions: (station: 84, time: 31)\n", + "Coordinates:\n", + " * time (time) datetime64[ns] 2015-07-01 ... 2015-0...\n", + "Dimensions without coordinates: station\n", + "Data variables: (12/19)\n", + " station_start_date (station) |S75 ...\n", + " station_zone (station) |S75 ...\n", + " street_type (station) |S75 ...\n", + " country_code (station) |S75 ...\n", + " ccaa (station) |S75 ...\n", + " station_name (station) |S75 ...\n", + " ... ...\n", + " station_code (station) |S75 ...\n", + " longitude (station) float32 ...\n", + " station_end_date (station) |S75 ...\n", + " station_rural_back (station) |S75 ...\n", + " latitude (station) float32 ...\n", + " station_ozone_classification (station) |S75 ..." + ] + }, + "execution_count": 3, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "xr.open_dataset(nc_path_1)" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "### Open with NES" + ] + }, + { + "cell_type": "code", + "execution_count": 4, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "" + ] + }, + "execution_count": 4, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "nessy_1 = open_netcdf(path=nc_path_1, info=True, parallel_method='X')\n", + "nessy_1" + ] + }, + { + "cell_type": "code", + "execution_count": 5, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "[datetime.datetime(2015, 7, 1, 0, 0),\n", + " datetime.datetime(2015, 7, 1, 1, 0),\n", + " datetime.datetime(2015, 7, 1, 2, 0),\n", + " datetime.datetime(2015, 7, 1, 3, 0),\n", + " datetime.datetime(2015, 7, 1, 4, 0),\n", + " datetime.datetime(2015, 7, 1, 5, 0),\n", + " datetime.datetime(2015, 7, 1, 6, 0),\n", + " datetime.datetime(2015, 7, 1, 7, 0),\n", + " datetime.datetime(2015, 7, 1, 8, 0),\n", + " datetime.datetime(2015, 7, 1, 9, 0),\n", + " datetime.datetime(2015, 7, 1, 10, 0),\n", + " datetime.datetime(2015, 7, 1, 11, 0),\n", + " datetime.datetime(2015, 7, 1, 12, 0),\n", + " datetime.datetime(2015, 7, 1, 13, 0),\n", + " datetime.datetime(2015, 7, 1, 14, 0),\n", + " datetime.datetime(2015, 7, 1, 15, 0),\n", + " datetime.datetime(2015, 7, 1, 16, 0),\n", + " datetime.datetime(2015, 7, 1, 17, 0),\n", + " datetime.datetime(2015, 7, 1, 18, 0),\n", + " datetime.datetime(2015, 7, 1, 19, 0),\n", + " datetime.datetime(2015, 7, 1, 20, 0),\n", + " datetime.datetime(2015, 7, 1, 21, 0),\n", + " datetime.datetime(2015, 7, 1, 22, 0),\n", + " datetime.datetime(2015, 7, 1, 23, 0),\n", + " datetime.datetime(2015, 7, 2, 0, 0),\n", + " datetime.datetime(2015, 7, 2, 1, 0),\n", + " datetime.datetime(2015, 7, 2, 2, 0),\n", + " datetime.datetime(2015, 7, 2, 3, 0),\n", + " datetime.datetime(2015, 7, 2, 4, 0),\n", + " datetime.datetime(2015, 7, 2, 5, 0),\n", + " datetime.datetime(2015, 7, 2, 6, 0)]" + ] + }, + "execution_count": 5, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "nessy_1.time" + ] + }, + { + "cell_type": "code", + "execution_count": 6, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "{'data': array([0]), 'units': ''}" + ] + }, + "execution_count": 6, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "nessy_1.lev" + ] + }, + { + "cell_type": "code", + "execution_count": 7, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "{'data': array([ 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16,\n", + " 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33,\n", + " 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50,\n", + " 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67,\n", + " 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83]),\n", + " 'units': ''}" + ] + }, + "execution_count": 7, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "nessy_1.station" + ] + }, + { + "cell_type": "code", + "execution_count": 8, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "{'data': masked_array(data=[46.813057, 47.479767, 47.04947 , 47.06741 , 35.039165,\n", + " 56.354443, 56.711666, 55.694107, 59.494446, 58.37611 ,\n", + " 39.546944, 42.720554, 39.87528 , 37.23722 , 43.439167,\n", + " 41.274166, 42.319168, 38.47278 , 39.08278 , 41.238888,\n", + " 41.39389 , 42.634724, 37.051945, 51.57108 , 55.79216 ,\n", + " 46.966667, 51.933334, 64.1 , 45.814445, 58.433 ,\n", + " 65.833336, 62.783333, 60.366665, 51.814445, 50.73639 ,\n", + " 54.754166, 54.125275, 43.404 , 63.84889 , 56.028057,\n", + " 58.80111 , 57.393612, 45.56139 , 48.942223, 49.04222 ,\n", + " 78.90667 , 52.802223, 52.083332, 53.662117, 27.28999 ,\n", + " 51.54111 , 47.83861 , 40.384445, 47.766666, 51.974445,\n", + " 49.573395, 54.433334, 56.161945, 59.779167, 40.3358 ,\n", + " 49.733334, 54.9 , 52.11667 , 43.15 , 35.316666,\n", + " 55.37611 , 47.914722, 53.166668, 42.1 , 60.53002 ,\n", + " 51.53014 , 52.86861 , 55.375 , 54.925556, 50.65 ,\n", + " 49.066666, 31.34274 , 68. , 46.5475 , 52.3 ,\n", + " 46.677776, 52.178074, 53.33389 , 38.8763 ],\n", + " mask=False,\n", + " fill_value=1e+20,\n", + " dtype=float32),\n", + " 'dimensions': ('station',),\n", + " 'units': 'degrees_north',\n", + " 'long_name': 'latitude',\n", + " 'standard_name': 'latitude',\n", + " 'axis': 'Y'}" + ] + }, + "execution_count": 8, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "nessy_1.lat" + ] + }, + { + "cell_type": "code", + "execution_count": 9, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "{'data': masked_array(data=[ 6.944469, 8.904696, 6.979203, 8.463339,\n", + " 33.05806 , 9.603059, 11.533614, 12.088669,\n", + " 25.930569, 21.845013, -4.350556, -8.923611,\n", + " 4.316389, -3.534167, -4.85 , -3.1425 ,\n", + " 3.315833, -6.923611, -1.101111, -5.8975 ,\n", + " 0.734722, -7.704722, -6.555278, -1.325286,\n", + " -3.2429 , 19.55 , -10.233334, -21.016945,\n", + " 8.637225, 8.269 , 13.916667, 8.883333,\n", + " 11.066667, 21.97139 , 15.739722, 17.534445,\n", + " 22.038055, 21.947 , 15.335577, 13.149458,\n", + " 17.381958, 11.91418 , 14.862789, 19.592232,\n", + " 22.259731, 11.888333, 10.759444, 6.566667,\n", + " 17.934017, 33.749886, 5.853611, 14.441389,\n", + " 44.260582, 16.766666, 4.923611, 15.080278,\n", + " 12.733333, 21.173056, 21.377222, 18.1245 ,\n", + " 16.05 , 37.8 , 5.2 , 19.133333,\n", + " 25.666668, 21.030556, 7.908611, 13.033333,\n", + " 12.633333, 27.66754 , 12.93386 , -6.924722,\n", + " -7.342778, 8.309722, 10.766667, 13.6 ,\n", + " 27.217775, 24.237223, 7.985 , 4.5 ,\n", + " 12.972222, -6.364524, 6.277222, 16.2322 ],\n", + " mask=False,\n", + " fill_value=1e+20,\n", + " dtype=float32),\n", + " 'dimensions': ('station',),\n", + " 'units': 'degrees_east',\n", + " 'long_name': 'longitude',\n", + " 'standard_name': 'longitude',\n", + " 'axis': 'X'}" + ] + }, + "execution_count": 9, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "nessy_1.lon" + ] + }, + { + "cell_type": "code", + "execution_count": 10, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Rank 000: Loading station_start_date var (1/17)\n", + "Rank 000: Loaded station_start_date var ((84,))\n", + "Rank 000: Loading station_zone var (2/17)\n", + "Rank 000: Loaded station_zone var ((84,))\n", + "Rank 000: Loading street_type var (3/17)\n", + "Rank 000: Loaded street_type var ((84,))\n", + "Rank 000: Loading country_code var (4/17)\n", + "Rank 000: Loaded country_code var ((84,))\n", + "Rank 000: Loading ccaa var (5/17)\n", + "Rank 000: Loaded ccaa var ((84,))\n", + "Rank 000: Loading station_name var (6/17)\n", + "Rank 000: Loaded station_name var ((84,))\n", + "Rank 000: Loading station_area var (7/17)\n", + "Rank 000: Loaded station_area var ((84,))\n", + "Rank 000: Loading city var (8/17)\n", + "Rank 000: Loaded city var ((84,))\n", + "Rank 000: Loading pm10 var (9/17)\n", + "Rank 000: Loaded pm10 var ((31, 84))\n", + "Rank 000: Loading station_emep var (10/17)\n", + "Rank 000: Loaded station_emep var ((84,))\n", + "Rank 000: Loading station_type var (11/17)\n", + "Rank 000: Loaded station_type var ((84,))\n", + "Rank 000: Loading country var (12/17)\n", + "Rank 000: Loaded country var ((84,))\n", + "Rank 000: Loading altitude var (13/17)\n", + "Rank 000: Loaded altitude var ((84,))\n", + "Rank 000: Loading station_code var (14/17)\n", + "Rank 000: Loaded station_code var ((84,))\n", + "Rank 000: Loading station_end_date var (15/17)\n", + "Rank 000: Loaded station_end_date var ((84,))\n", + "Rank 000: Loading station_rural_back var (16/17)\n", + "Rank 000: Loaded station_rural_back var ((84,))\n", + "Rank 000: Loading station_ozone_classification var (17/17)\n", + "Rank 000: Loaded station_ozone_classification var ((84,))\n" + ] + } + ], + "source": [ + "nessy_1.load()" + ] + }, + { + "cell_type": "code", + "execution_count": 11, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "{'station_start_date': {'data': array(['1980-01-01', '1980-01-01', '1991-05-01', '1991-05-01',\n", + " '1996-10-01', '1978-10-01', '1987-01-01', '2010-07-01',\n", + " '1985-01-06', '1994-05-01', '1987-11-01', '1992-01-01',\n", + " '1992-06-01', '1995-11-01', '1998-09-01', '1998-01-01',\n", + " '1997-07-01', '1999-03-03', '1997-06-11', '2000-08-01',\n", + " '2000-11-01', '2001-01-31', '2007-10-03', '1976-06-22',\n", + " '2006-01-01', '1980-01-01', '2001-01-01', '1900-01-01',\n", + " '1985-11-01', '2009-01-01', '1971-12-01', '1978-02-01',\n", + " '1997-01-01', '1967-09-15', '1981-01-01', '1995-01-01',\n", + " '1984-12-01', '2011-01-01', '1979-01-09', '1984-01-09',\n", + " '1990-01-01', '2002-01-01', '1996-05-01', '1997-01-01',\n", + " '1997-01-01', 'nan', 'nan', 'nan', 'nan', 'nan', 'nan', 'nan',\n", + " 'nan', 'nan', 'nan', 'nan', 'nan', 'nan', 'nan', 'nan', 'nan',\n", + " 'nan', 'nan', 'nan', 'nan', 'nan', 'nan', 'nan', 'nan', 'nan',\n", + " 'nan', 'nan', 'nan', 'nan', 'nan', 'nan', 'nan', 'nan', 'nan',\n", + " 'nan', 'nan', 'nan', 'nan', 'nan'], dtype='" + ] + }, + "execution_count": 14, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "nessy_2 = open_netcdf('points_file_1.nc', info=True, parallel_method='X')\n", + "nessy_2" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "### Reopen with xarray" + ] + }, + { + "cell_type": "code", + "execution_count": 15, + "metadata": {}, + "outputs": [ + { + "data": { + "text/html": [ + "
\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "
<xarray.Dataset>\n",
+       "Dimensions:                       (time: 31, station: 84)\n",
+       "Coordinates:\n",
+       "  * time                          (time) datetime64[ns] 2015-07-01 ... 2015-0...\n",
+       "  * station                       (station) float64 0.0 1.0 2.0 ... 82.0 83.0\n",
+       "Data variables: (12/19)\n",
+       "    station_start_date            (station) |S75 b'1980-01-01' ... b'nan'\n",
+       "    station_zone                  (station) |S75 b'nan' b'nan' ... b'nan' b'nan'\n",
+       "    street_type                   (station) |S75 b'nan' b'nan' ... b'nan' b'nan'\n",
+       "    country_code                  (station) |S75 b'CH' b'CH' ... b'NL' b'IT'\n",
+       "    ccaa                          (station) |S75 b'nan' b'nan' ... b'nan' b'nan'\n",
+       "    station_name                  (station) |S75 b'payerne' ... b'lamezia terme'\n",
+       "    ...                            ...\n",
+       "    station_code                  (station) |S75 b'CH0002R' ... b'IT0016R'\n",
+       "    station_end_date              (station) |S75 b'nan' b'nan' ... b'nan' b'nan'\n",
+       "    station_rural_back            (station) |S75 b'nan' b'nan' ... b'nan' b'nan'\n",
+       "    station_ozone_classification  (station) |S75 b'rural' b'rural' ... b'nan'\n",
+       "    lat                           (station) float64 46.81 47.48 ... 53.33 38.88\n",
+       "    lon                           (station) float64 6.944 8.905 ... 6.277 16.23\n",
+       "Attributes:\n",
+       "    Conventions:  CF-1.7
" + ], + "text/plain": [ + "\n", + "Dimensions: (time: 31, station: 84)\n", + "Coordinates:\n", + " * time (time) datetime64[ns] 2015-07-01 ... 2015-0...\n", + " * station (station) float64 0.0 1.0 2.0 ... 82.0 83.0\n", + "Data variables: (12/19)\n", + " station_start_date (station) |S75 ...\n", + " station_zone (station) |S75 ...\n", + " street_type (station) |S75 ...\n", + " country_code (station) |S75 ...\n", + " ccaa (station) |S75 ...\n", + " station_name (station) |S75 ...\n", + " ... ...\n", + " station_code (station) |S75 ...\n", + " station_end_date (station) |S75 ...\n", + " station_rural_back (station) |S75 ...\n", + " station_ozone_classification (station) |S75 ...\n", + " lat (station) float64 ...\n", + " lon (station) float64 ...\n", + "Attributes:\n", + " Conventions: CF-1.7" + ] + }, + "execution_count": 15, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "xr.open_dataset('points_file_1.nc')" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "## 2. Read and write - GHOST type" + ] + }, + { + "cell_type": "code", + "execution_count": 16, + "metadata": {}, + "outputs": [], + "source": [ + "# nc_path_2 = '/gpfs/projects/bsc32/AC_cache/obs/ghost/EBAS/1.4/hourly/sconcno2/sconcno2_202004.nc' #EBAS\n", + "# nc_path_2 = '/gpfs/projects/bsc32/AC_cache/obs/ghost/AERONET_v3/1.3.3/hourly/od1020aero/od1020aero_201907.nc' # AERONET\n", + "# nc_path_2 = '/gpfs/projects/bsc32/AC_cache/obs/ghost/CANADA_NAPS/1.4/daily/sconcno2/sconcno2_202011.nc' # CANADA NAPS\n", + "# nc_path_2 = '/gpfs/projects/bsc32/AC_cache/obs/ghost/CHILE_SINCA/1.4/monthly/pm10/pm10_201905.nc' # CHILE SINCA\n", + "nc_path_2 = '/gpfs/projects/bsc32/AC_cache/obs/ghost/EANET/1.4/daily/sconcso4/sconcso4_201911.nc' # EANET" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "### Open with xarray" + ] + }, + { + "cell_type": "code", + "execution_count": 17, + "metadata": {}, + "outputs": [ + { + "data": { + "text/html": [ + "
\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "
<xarray.Dataset>\n",
+       "Dimensions:                                                           (station: 3, time: 30, N_flag_codes: 190, N_qa_codes: 77)\n",
+       "Coordinates:\n",
+       "  * time                                                              (time) datetime64[ns] ...\n",
+       "Dimensions without coordinates: station, N_flag_codes, N_qa_codes\n",
+       "Data variables: (12/177)\n",
+       "    ASTER_v3_altitude                                                 (station) float32 ...\n",
+       "    EDGAR_v4.3.2_annual_average_BC_emissions                          (station) float32 ...\n",
+       "    EDGAR_v4.3.2_annual_average_CO_emissions                          (station) float32 ...\n",
+       "    EDGAR_v4.3.2_annual_average_NH3_emissions                         (station) float32 ...\n",
+       "    EDGAR_v4.3.2_annual_average_NMVOC_emissions                       (station) float32 ...\n",
+       "    EDGAR_v4.3.2_annual_average_NOx_emissions                         (station) float32 ...\n",
+       "    ...                                                                ...\n",
+       "    street_type                                                       (station) object ...\n",
+       "    street_width                                                      (station) float32 ...\n",
+       "    terrain                                                           (station) object ...\n",
+       "    vertical_datum                                                    (station) object ...\n",
+       "    weekday_weekend_code                                              (station, time) uint8 ...\n",
+       "    sconcso4_prefiltered_defaultqa                                    (station, time) float32 ...\n",
+       "Attributes:\n",
+       "    title:          Surface sulphate data in the EANET network in 2019-11.\n",
+       "    institution:    Barcelona Supercomputing Center\n",
+       "    source:         Surface observations\n",
+       "    creator_name:   Dene R. Bowdalo\n",
+       "    creator_email:  dene.bowdalo@bsc.es\n",
+       "    version:        1.4