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SarahAlidoostSarahAlidoost
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update notebooks to use module save
1 parent 948417a commit 8e4e5b1

2 files changed

Lines changed: 51 additions & 70 deletions

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‎notebooks/run_model_in_notebook.ipynb‎

Lines changed: 45 additions & 42 deletions
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@@ -15,7 +15,8 @@
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"outputs": [],
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"source": [
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"import os\n",
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"from PyStemmusScope import StemmusScope"
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"from PyStemmusScope import StemmusScope\n",
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"from PyStemmusScope import save"
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]
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},
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{
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},
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{
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"cell_type": "code",
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"execution_count": 4,
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"execution_count": 9,
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"metadata": {},
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"outputs": [
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{
@@ -96,20 +97,20 @@
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"{'WorkDir': '/home/sarah/temp/ecoextreml/test/',\n",
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" 'SoilPropertyPath': '/home/sarah/temp/ecoextreml/data/model_parameters/soil_property/',\n",
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" 'ForcingPath': '/home/sarah/temp/ecoextreml/data/forcing/plumber2_data/',\n",
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" 'ForcingFileName': 'AU-DaS_2010-2017_OzFlux_Met.nc',\n",
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" 'ForcingFileName': 'AR-SLu_2010-2010_FLUXNET2015_Met.nc',\n",
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" 'directional': '/home/sarah/temp/ecoextreml/data/model_parameters/vegetation_property/directional/',\n",
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" 'fluspect_parameters': '/home/sarah/temp/ecoextreml/data/model_parameters/vegetation_property/fluspect_parameters/',\n",
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" 'leafangles': '/home/sarah/temp/ecoextreml/data/model_parameters/vegetation_property/leafangles/',\n",
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" 'radiationdata': '/home/sarah/temp/ecoextreml/data/model_parameters/vegetation_property/radiationdata/',\n",
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" 'soil_spectrum': '/home/sarah/temp/ecoextreml/data/model_parameters/vegetation_property/soil_spectrum/',\n",
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" 'InitialConditionPath': '/home/sarah/temp/ecoextreml/soil_initialcondition/',\n",
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" 'input_data': '/home/sarah/temp/ecoextreml/data/model_parameters/vegetation_property/input_data.xlsx',\n",
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" 'NumberOfTimeSteps': 'NA',\n",
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" 'NumberOfTimeSteps': '5',\n",
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" 'InputPath': '/will_be_created_under_WorkDir/input/AU-DaS_2022-05-11-1705/',\n",
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" 'OutputPath': '/will_be_created_under_WorkDir/output/AU-DaS_2022-05-11-1705/'}"
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" 'OutputPath': '/home/sarah/temp/ecoextreml/output/AR-SLu_2022-07-29-1451/'}"
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]
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},
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"execution_count": 4,
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"execution_count": 9,
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"metadata": {},
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"output_type": "execute_result"
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}
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},
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{
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"cell_type": "code",
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"execution_count": 6,
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"execution_count": 10,
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"metadata": {},
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"outputs": [
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{
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"name": "stdout",
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"output_type": "stream",
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"text": [
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"/home/sarah/temp/ecoextreml/test/input/ZA-Kru_2022-07-18-1630/ZA-Kru_2022-07-18-1630_config.txt\n"
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"/home/sarah/temp/ecoextreml/test/input/ZA-Kru_2022-08-03-1537/ZA-Kru_2022-08-03-1537_config.txt\n"
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]
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}
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],
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},
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{
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"cell_type": "code",
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"execution_count": 7,
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"execution_count": 11,
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"metadata": {},
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"outputs": [
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{
@@ -164,11 +165,11 @@
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" 'InitialConditionPath': '/home/sarah/temp/ecoextreml/soil_initialcondition/',\n",
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" 'input_data': '/home/sarah/temp/ecoextreml/data/model_parameters/vegetation_property/input_data.xlsx',\n",
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" 'NumberOfTimeSteps': '10',\n",
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" 'InputPath': '/home/sarah/temp/ecoextreml/test/input/ZA-Kru_2022-07-18-1630/',\n",
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" 'OutputPath': '/home/sarah/temp/ecoextreml/test/output/ZA-Kru_2022-07-18-1630/'}"
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" 'InputPath': '/home/sarah/temp/ecoextreml/test/input/ZA-Kru_2022-08-03-1537/',\n",
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" 'OutputPath': '/home/sarah/temp/ecoextreml/test/output/ZA-Kru_2022-08-03-1537/'}"
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]
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},
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"execution_count": 7,
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"execution_count": 11,
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"metadata": {},
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"output_type": "execute_result"
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}
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},
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{
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"cell_type": "code",
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"execution_count": 8,
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"execution_count": 12,
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"metadata": {},
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"outputs": [
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{
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"data": {
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"text/plain": [
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"b'Reading config from /home/sarah/temp/ecoextreml/test/input/ZA-Kru_2022-07-18-1630/ZA-Kru_2022-07-18-1630_config.txt\\n\\n The calculations start now \\r\\n The calculations end now \\r'"
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"b'Reading config from /home/sarah/temp/ecoextreml/test/input/ZA-Kru_2022-08-03-1537/ZA-Kru_2022-08-03-1537_config.txt\\n\\n The calculations start now \\r\\n The calculations end now \\r'"
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]
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},
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"execution_count": 8,
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"execution_count": 12,
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"metadata": {},
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"output_type": "execute_result"
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}
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"result"
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]
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},
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{
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"cell_type": "code",
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"execution_count": 14,
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"metadata": {},
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"outputs": [
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{
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"name": "stdout",
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"output_type": "stream",
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"text": [
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"/home/sarah/temp/ecoextreml/test/output/ZA-Kru_2022-08-03-1537/ZA-Kru_2022-08-03-1537_STEMMUS_SCOPE.nc\n"
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]
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}
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],
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"source": [
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"# save output in nercdf format\n",
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"variables_will_be_in_NetCDF_file = \"./STEMMUS_SCOPE/utils/csv_to_nc/Variables_will_be_in_NetCDF_file.csv\"\n",
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"nc_file_name = save.to_netcdf(model.config, variables_will_be_in_NetCDF_file)\n",
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"print(nc_file_name)"
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]
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},
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{
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"cell_type": "markdown",
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"metadata": {},
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},
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{
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"cell_type": "code",
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"execution_count": 9,
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"execution_count": 15,
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"metadata": {},
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"outputs": [
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{
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"name": "stdout",
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"output_type": "stream",
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"text": [
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"b'Reading config from /home/sarah/temp/ecoextreml/test/input/ZA-Kru_2022-07-18-1631/ZA-Kru_2022-07-18-1631_config.txt\\n\\n The calculations start now \\r\\n The calculations end now \\r'\n",
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"b'Reading config from /home/sarah/temp/ecoextreml/test/input/AR-SLu_2022-07-18-1631/AR-SLu_2022-07-18-1631_config.txt\\n\\n The calculations start now \\r\\n The calculations end now \\r'\n"
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"b'Reading config from /home/sarah/temp/ecoextreml/test/input/ZA-Kru_2022-08-03-1541/ZA-Kru_2022-08-03-1541_config.txt\\n\\n The calculations start now \\r\\n The calculations end now \\r'\n",
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"/home/sarah/temp/ecoextreml/test/output/ZA-Kru_2022-08-03-1541/ZA-Kru_2022-08-03-1541_STEMMUS_SCOPE.nc\n",
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"b'Reading config from /home/sarah/temp/ecoextreml/test/input/AR-SLu_2022-08-03-1541/AR-SLu_2022-08-03-1541_config.txt\\n\\n The calculations start now \\r\\n The calculations end now \\r'\n",
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"/home/sarah/temp/ecoextreml/test/output/AR-SLu_2022-08-03-1541/AR-SLu_2022-08-03-1541_STEMMUS_SCOPE.nc\n"
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]
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}
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],
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" # run the model\n",
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" result = model.run()\n",
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" print(result)\n",
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" \n",
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" # save results in a netcdf file\n",
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" nc_file_name = save.to_netcdf(model.config, variables_will_be_in_NetCDF_file)\n",
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" print(nc_file_name)\n",
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" "
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]
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},
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{
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"cell_type": "markdown",
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"metadata": {},
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"source": [
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"#### TODO: Create output directories, prepare output files"
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]
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},
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{
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"cell_type": "code",
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"execution_count": 7,
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"metadata": {},
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"outputs": [],
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"source": [
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"# convert csv files to nc files\n",
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"# path_to_generate_netcdf_script = \"path_to_generate_netcdf_script\"\n",
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"# path_to_Variables_will_be_in_NetCDF_file = \"path_to_Variables_will_be_in_NetCDF_file\"\n",
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"# for ncfile in forcing_filenames_list:\n",
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"# path_to_config = config_path_dict[ncfile]\n",
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"# result = subprocess.run([\"python\", path_to_generate_netcdf_script,\n",
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"# \"--config_file\", path_to_config, \"--variable_file\",\n",
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"# path_to_Variables_will_be_in_NetCDF_file])\n",
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"# result.check_returncode()"
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]
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}
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],
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"metadata": {

‎notebooks/run_model_in_notebook_dev.ipynb‎

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Original file line numberDiff line numberDiff line change
@@ -239,40 +239,18 @@
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"cell_type": "markdown",
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"metadata": {},
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"source": [
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"#### Create output directories, prepare output files"
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"#### save results in a netcdf file"
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]
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},
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{
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"cell_type": "code",
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"execution_count": 10,
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"execution_count": null,
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"metadata": {},
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"outputs": [
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{
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"name": "stdout",
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"output_type": "stream",
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"text": [
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"/scratch-shared/ecoextreml/stemmus_scope/output/FI-Hyy_20220621_1415/ECdata.csv\n",
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"Reading variable metadata from /home/yangl/STEMMUS_SCOPE/utils/csv_to_nc/Variables_will_be_in_NetCDF_file.csv\n",
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"Creating /scratch-shared/ecoextreml/stemmus_scope/output/FI-Hyy_20220621_1415/FI-Hyy_20220621_1415_STEMMUS_SCOPE.nc \n",
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"Reading data from file: radiation.csv\n",
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"Reading data from file: fluxes.csv\n",
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"Reading data from file: surftemp.csv\n",
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"Reading data from file: Sim_Temp.csv\n",
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"Reading data from file: Sim_Theta.csv\n",
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"Reading data from file: aerodyn.csv\n",
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"Reading data from file: ECdata.csv\n",
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"Done writing /scratch-shared/ecoextreml/stemmus_scope/output/FI-Hyy_20220621_1415/FI-Hyy_20220621_1415_STEMMUS_SCOPE.nc\n"
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]
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}
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],
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"outputs": [],
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"source": [
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"# convert csv files to nc files\n",
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"path_to_generate_netcdf_script = \"path_to_generate_netcdf_script\"\n",
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"path_to_Variables_will_be_in_NetCDF_file = \"path_to_Variables_will_be_in_NetCDF_file\"\n",
272-
"result = subprocess.run([\"python\", path_to_generate_netcdf_script,\n",
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" \"--config_file\", config_path, \"--variable_file\",\n",
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" path_to_Variables_will_be_in_NetCDF_file])\n",
275-
"result.check_returncode()"
251+
"variables_will_be_in_NetCDF_file = path_to_model / \"utils\" / \"csv_to_nc\" / \"Variables_will_be_in_NetCDF_file.csv\"\n",
252+
"nc_file_name = save.to_netcdf(model.config, variables_will_be_in_NetCDF_file)\n",
253+
"print(nc_file_name)"
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]
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},
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{

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