Pruebas con Docker

.gitignore

@@ -24,3 +24,4 @@ __pycache__/
 *$py.class
 docs/build/
 docs/source/generated
+*.nc

.vscode/launch.json

@@ -4,37 +4,37 @@
     // For more information, visit: https://go.microsoft.com/fwlink/?linkid=830387
     "version": "0.2.0",
     "configurations": [
-        {
-            "name": "(gdb) Launch",
-            "type": "cppdbg",
-            "request": "launch",
-            "program": "/work/ALT/odatis/briolf/anaconda3/bin/python",
-            "args": ["/home/fbriol/Documents/workspace/lagrangian/tests/test_integration.py"],
-            "stopAtEntry": false,
-            "cwd": "${workspaceFolder}",
-            "environment": [
-                {
-                    "name": "PYTHONPATH",
-                    "value": "/home/fbriol/Documents/workspace/lagrangian/build/lib.linux-x86_64-3.7/"
-                }
-            ],
-            "externalConsole": false,
-            "MIMode": "gdb",
-            "setupCommands": [
-                {
-                    "description": "Enable pretty-printing for gdb",
-                    "text": "-enable-pretty-printing",
-                    "ignoreFailures": true
-                }
-            ]
-        },
         {
             "name": "Python: Current File",
             "type": "python",
             "request": "launch",
-            "program": "${file}",
-            "env": {"PYTHONPATH": "/home/fbriol/Documents/workspace/lagrangian/build/lib.linux-x86_64-3.7"},
-            "console": "integratedTerminal"
+            "program": "map_of_fle.py",
+            "args": [
+                "sds.ini",
+                "fsle1.nc",
+                "2023-02-08",
+                "--advection_time",
+                "20",
+                "--resolution",
+                "0.08333588",
+                "--final_separation",
+                "0.2",
+                "--x_min",
+                "-180",
+                "--x_max",
+                "180",
+                "--y_min",
+                "-60",
+                "--y_max",
+                "60",
+                "--verbose",
+                "--time_direction",
+                "forward"
+            ],
+            "console": "integratedTerminal",
+            "env": {
+                "UDUNITS2_XML_PATH": "/home/atorres/miniconda3/envs/RTD/share/udunits/udunits2.xml"
+            }
         }
     ]
 }

Dockerfile

@@ -0,0 +1,10 @@
+FROM mambaorg/micromamba:1.3.1
+
+COPY --chown=$MAMBA_USER:$MAMBA_USER env.yml /tmp/env.yml
+RUN micromamba install -y -n base -f /tmp/env.yml && \
+    micromamba clean --all --yes
+
+WORKDIR /home/mambauser
+RUN mkdir ./data
+COPY --chown=$MAMBA_USER:$MAMBA_USER docker.ini docker.ini
+COPY --chown=$MAMBA_USER:$MAMBA_USER map_of_fle.py map_of_fle.py

README.md

@@ -27,4 +27,135 @@ Documentation
 -------------
 
 For full documentation visit the [Documentation
-Page](http://lagrangian.readthedocs.io/en/latest/index.html).
+Page](http://lagrangian.readthedocs.io/en/latest/index.html).
+
+Instalar a partir de código fuente
+----------------------------------
+
+1. Crear entorno con dependencias:
+
+   ```{bash}
+   conda install -c conda-forge boost udunits2 netcdf4
+   ```
+
+2. Obtener submodulos:
+
+   ```{bash}
+   git submodule update --init --recursive
+   ```
+
+3. Instalar:
+
+   ```{bash}
+   pip install .
+   ```
+
+   ```{bash}
+   export UDUNITS2_XML_PATH=/home/atorres/miniconda3/envs/RTD/share/udunits/udunits2.xml
+   ```
+
+4. Ejecutar:
+
+   ```{bash}
+   time -v map_of_fle sds.ini 2023_07_18.nc "2023-07-18" --advection_time 10 --resolution=0.04 --final_separation 0.2 --x_min -180 --x_max 180 --y_min -60 --y_max 60 --verbose --time_direction forward
+   ```
+
+Instalar versión de Conda
+-------------------------
+
+1. Instalar entorno del proyecto y activar:
+
+   ```{bash}
+   conda env create -f env.yml
+   conda activate aviso-lagrangian
+   ```
+
+2. Ver localización paquete
+
+   ```{bash}
+   python -c "import lagrangian; print(lagrangian.__file__)"
+   ```
+
+3. Entrar en el directorio (quitar `__init__.py` del path anterior) y a continuación comentar parte de la línea 545 del fichero `console_scripts/map_of_fle.py`:
+
+   ```{python}
+   if HAVE_DASK and args.scheduler_file is not None: #or args.local_cluster:
+   ```
+
+4. Copiar los ficheros necesarios usando el script `convert_nc.py` (usar cualquier entorno de conda con `xarray` y `pandas`):
+
+   ```{bash}
+   python convert_nc.py /home/atorres/data/uv OUTPUT_DIR
+   ```
+
+5. Editar el fichero `sds.ini` y escribir una línea por cada una de las fechas necesarias
+
+6. Ejecutar:
+
+   ```{bash}
+   map_of_fle sds.ini 2023_08_07.nc "2023-08-07" --advection_time 20 --resolution=0.04 --final_separation 0.6 --initial_separation 0.2 --x_min -179.98 --x_max 179.98 --y_min -59.98 --y_max 59.98 --verbose --time_direction backward
+   ```
+
+Docker
+------
+
+1. Construir imágen
+
+   ```{bash}
+   docker build -t lagrangian .
+   ```
+
+2. Ejecutar contenedor
+
+   ```{bash}
+   docker run --user=root -it -v /home/SHARED/SATLINK/fsle:/home/mambauser/data lagrangian bash
+   ```
+
+3. Correr script del cálculo del FSLE
+
+   ```{bash}
+   python map_of_fle.py ./data/uv ./data/fsle "2023-02-28 12:00" --advection_time 20 --final_separation 0.2 --x_min -180 --nx 4320 --y_min -60 --ny 1441 --resolution 1/12 --time_direction backward
+   ```
+
+Descargar datos de FSLE
+-----------------------
+
+1. Instalar motuclient con
+
+   ```{bash}
+   pip install motuclient
+   ```
+
+2. Ejecutar cambiando la fecha (`-t` y `-T`) y el fichero de salida (`-f`):
+
+   ```{bash}
+   motuclient -u [email protected] -p 2BFeqk -m https://motu.aviso.altimetry.fr/motu-web/Motu -s AvisoFSLE -d dataset-duacs-nrt-global-allsat-madt-fsle -x -180 -X 180 -y -60 -Y 60 -t "2022-07-15" -T "2022-07-15" --outputWritten netcdf -v fsle_max -v theta_max -o "." -f "2022_07_15_fsle.nc"
+   ```
+
+3. Otro ejemplo:
+
+   ```{bash}
+   motuclient -u [email protected] -p 2BFeqk -m https://motu.aviso.altimetry.fr/motu-web/Motu -s AvisoFSLE -d dataset-duacs-nrt-global-allsat-madt-fsle -x -180 -X 180 -y -90 -Y 90 -t "2022-08-07" -T "2022-08-07" --outputWritten netcdf -v fsle_max -v theta_max -o "." -f "fsle_2022_08_07.nc"
+   ```
+
+Otra forma alternativa, desde la web:
+
+1. Entrar en [https://www.aviso.altimetry.fr/en/home.html](https://www.aviso.altimetry.fr/en/home.html)
+2. Identificarse con usuario (`[email protected]`) y contraseña (`2BFeqk`)
+3. Ir a `MY AVISO+ > My products > Lyapunov Exponents and Orientations (grids) > Extraction > DATASET-DUACS-NRT-GLOBAL-ALLSAT-MADT-FSLE`. Seleccionar `Full region` y editar la latitud a (-60, 60). Editar la fecha en el desplegable (importante destacar que la fecha que aparece es la última disponible)
+
+NOTA: Los ficheros descargados de AVISO tienen 9000 longitudes y 3000 latitudes. Para conseguir algo similar con el script, habría que usar `--resolution 0.04`. Sin embargo, no es idéntico.
+Además, los ficheros descargados tienen las siguientes longitudes:
+
+```{text}
+* lon       (lon) float64 180.0 180.0 180.1 180.1 ... 539.8 539.9 539.9 539.9
+```
+
+Esto no se corresponde con el formato habitual (-180, 180), habría que ver como transformarlo
+
+Pruebas AVISO
+-------------
+
+```{bash}
+map_of_fle duacs.ini 2023_08_07.nc "2023-08-07" --advection_time 20 --resolution=0.04 --final_separation 0.6 --initial_separation 0.2 --x_min -179.98 --x_max 179.98 --y_min -59.98 --y_max 59.98 --verbose --time_direction backward
+```

conda/environment.yml

@@ -3,5 +3,8 @@ dependencies:
   - lagrangian
   - python=3.7
   - netcdf4
+  # Evita error: ImportError: libnetcdf.so.13: cannot open shared object file: No such file or directory
+  # Referencia: https://github.com/conda-forge/vtk-feedstock/issues/85
+  - libnetcdf=4.6.2
 channels:
   - fbriol

convert_nc.py

@@ -0,0 +1,32 @@
+#!/usr/bin/env python
+
+import sys
+from pathlib import Path
+
+import pandas as pd
+import xarray as xr
+
+if len(sys.argv) != 3:
+    print(f"usage: {sys.argv[0]} INPUT_PATH OUTPUT_PATH")
+    sys.exit(1)
+
+input_path = Path(sys.argv[1])
+output_path = Path(sys.argv[2])
+
+if input_path == output_path:
+    raise ValueError("files are going to be overwritten")
+
+output_path.mkdir(parents=True, exist_ok=True)
+
+for input_nc in input_path.glob("*.nc"):
+    with xr.open_dataset(input_nc) as ds:
+        ds_subset = ds.isel(time=0)
+        ts = (
+            pd.to_datetime(ds.time.values)
+            .tz_localize("UTC")
+            .strftime("%Y-%m-%d %H:%M:%S.%f %Z")
+            .item()
+        )
+        ds_subset["ugos"].attrs["date"] = ts
+        ds_subset["vgos"].attrs["date"] = ts
+        ds_subset.to_netcdf(output_path / input_nc.name)

docker.ini

@@ -0,0 +1,47 @@
+U = /home/mambauser/data/uv/2023-02-07.nc
+U = /home/mambauser/data/uv/2023-02-08.nc
+U = /home/mambauser/data/uv/2023-02-09.nc
+U = /home/mambauser/data/uv/2023-02-10.nc
+U = /home/mambauser/data/uv/2023-02-11.nc
+U = /home/mambauser/data/uv/2023-02-12.nc
+U = /home/mambauser/data/uv/2023-02-13.nc
+U = /home/mambauser/data/uv/2023-02-14.nc
+U = /home/mambauser/data/uv/2023-02-15.nc
+U = /home/mambauser/data/uv/2023-02-16.nc
+U = /home/mambauser/data/uv/2023-02-17.nc
+U = /home/mambauser/data/uv/2023-02-18.nc
+U = /home/mambauser/data/uv/2023-02-19.nc
+U = /home/mambauser/data/uv/2023-02-20.nc
+U = /home/mambauser/data/uv/2023-02-21.nc
+U = /home/mambauser/data/uv/2023-02-22.nc
+U = /home/mambauser/data/uv/2023-02-23.nc
+U = /home/mambauser/data/uv/2023-02-24.nc
+U = /home/mambauser/data/uv/2023-02-25.nc
+U = /home/mambauser/data/uv/2023-02-26.nc
+U = /home/mambauser/data/uv/2023-02-27.nc
+U = /home/mambauser/data/uv/2023-02-28.nc
+V = /home/mambauser/data/uv/2023-02-07.nc
+V = /home/mambauser/data/uv/2023-02-08.nc
+V = /home/mambauser/data/uv/2023-02-09.nc
+V = /home/mambauser/data/uv/2023-02-10.nc
+V = /home/mambauser/data/uv/2023-02-11.nc
+V = /home/mambauser/data/uv/2023-02-12.nc
+V = /home/mambauser/data/uv/2023-02-13.nc
+V = /home/mambauser/data/uv/2023-02-14.nc
+V = /home/mambauser/data/uv/2023-02-15.nc
+V = /home/mambauser/data/uv/2023-02-16.nc
+V = /home/mambauser/data/uv/2023-02-17.nc
+V = /home/mambauser/data/uv/2023-02-18.nc
+V = /home/mambauser/data/uv/2023-02-19.nc
+V = /home/mambauser/data/uv/2023-02-20.nc
+V = /home/mambauser/data/uv/2023-02-21.nc
+V = /home/mambauser/data/uv/2023-02-22.nc
+V = /home/mambauser/data/uv/2023-02-23.nc
+V = /home/mambauser/data/uv/2023-02-24.nc
+V = /home/mambauser/data/uv/2023-02-25.nc
+V = /home/mambauser/data/uv/2023-02-26.nc
+V = /home/mambauser/data/uv/2023-02-27.nc
+V = /home/mambauser/data/uv/2023-02-28.nc
+U_NAME = uo
+V_NAME = vo
+FILL_VALUE = 0

duacs.ini

@@ -0,0 +1,47 @@
+U = /home/SHARED/SATLINK/fsle/duacs_converted/nrt_global_allsat_phy_l4_20230717_20230723.nc
+U = /home/SHARED/SATLINK/fsle/duacs_converted/nrt_global_allsat_phy_l4_20230718_20230724.nc
+U = /home/SHARED/SATLINK/fsle/duacs_converted/nrt_global_allsat_phy_l4_20230719_20230725.nc
+U = /home/SHARED/SATLINK/fsle/duacs_converted/nrt_global_allsat_phy_l4_20230720_20230726.nc
+U = /home/SHARED/SATLINK/fsle/duacs_converted/nrt_global_allsat_phy_l4_20230721_20230727.nc
+U = /home/SHARED/SATLINK/fsle/duacs_converted/nrt_global_allsat_phy_l4_20230722_20230728.nc
+U = /home/SHARED/SATLINK/fsle/duacs_converted/nrt_global_allsat_phy_l4_20230723_20230729.nc
+U = /home/SHARED/SATLINK/fsle/duacs_converted/nrt_global_allsat_phy_l4_20230724_20230730.nc
+U = /home/SHARED/SATLINK/fsle/duacs_converted/nrt_global_allsat_phy_l4_20230725_20230731.nc
+U = /home/SHARED/SATLINK/fsle/duacs_converted/nrt_global_allsat_phy_l4_20230726_20230801.nc
+U = /home/SHARED/SATLINK/fsle/duacs_converted/nrt_global_allsat_phy_l4_20230727_20230802.nc
+U = /home/SHARED/SATLINK/fsle/duacs_converted/nrt_global_allsat_phy_l4_20230728_20230803.nc
+U = /home/SHARED/SATLINK/fsle/duacs_converted/nrt_global_allsat_phy_l4_20230729_20230804.nc
+U = /home/SHARED/SATLINK/fsle/duacs_converted/nrt_global_allsat_phy_l4_20230730_20230805.nc
+U = /home/SHARED/SATLINK/fsle/duacs_converted/nrt_global_allsat_phy_l4_20230731_20230806.nc
+U = /home/SHARED/SATLINK/fsle/duacs_converted/nrt_global_allsat_phy_l4_20230801_20230807.nc
+U = /home/SHARED/SATLINK/fsle/duacs_converted/nrt_global_allsat_phy_l4_20230802_20230808.nc
+U = /home/SHARED/SATLINK/fsle/duacs_converted/nrt_global_allsat_phy_l4_20230803_20230809.nc
+U = /home/SHARED/SATLINK/fsle/duacs_converted/nrt_global_allsat_phy_l4_20230804_20230810.nc
+U = /home/SHARED/SATLINK/fsle/duacs_converted/nrt_global_allsat_phy_l4_20230805_20230811.nc
+U = /home/SHARED/SATLINK/fsle/duacs_converted/nrt_global_allsat_phy_l4_20230806_20230812.nc
+U = /home/SHARED/SATLINK/fsle/duacs_converted/nrt_global_allsat_phy_l4_20230807_20230813.nc
+V = /home/SHARED/SATLINK/fsle/duacs_converted/nrt_global_allsat_phy_l4_20230717_20230723.nc
+V = /home/SHARED/SATLINK/fsle/duacs_converted/nrt_global_allsat_phy_l4_20230718_20230724.nc
+V = /home/SHARED/SATLINK/fsle/duacs_converted/nrt_global_allsat_phy_l4_20230719_20230725.nc
+V = /home/SHARED/SATLINK/fsle/duacs_converted/nrt_global_allsat_phy_l4_20230720_20230726.nc
+V = /home/SHARED/SATLINK/fsle/duacs_converted/nrt_global_allsat_phy_l4_20230721_20230727.nc
+V = /home/SHARED/SATLINK/fsle/duacs_converted/nrt_global_allsat_phy_l4_20230722_20230728.nc
+V = /home/SHARED/SATLINK/fsle/duacs_converted/nrt_global_allsat_phy_l4_20230723_20230729.nc
+V = /home/SHARED/SATLINK/fsle/duacs_converted/nrt_global_allsat_phy_l4_20230724_20230730.nc
+V = /home/SHARED/SATLINK/fsle/duacs_converted/nrt_global_allsat_phy_l4_20230725_20230731.nc
+V = /home/SHARED/SATLINK/fsle/duacs_converted/nrt_global_allsat_phy_l4_20230726_20230801.nc
+V = /home/SHARED/SATLINK/fsle/duacs_converted/nrt_global_allsat_phy_l4_20230727_20230802.nc
+V = /home/SHARED/SATLINK/fsle/duacs_converted/nrt_global_allsat_phy_l4_20230728_20230803.nc
+V = /home/SHARED/SATLINK/fsle/duacs_converted/nrt_global_allsat_phy_l4_20230729_20230804.nc
+V = /home/SHARED/SATLINK/fsle/duacs_converted/nrt_global_allsat_phy_l4_20230730_20230805.nc
+V = /home/SHARED/SATLINK/fsle/duacs_converted/nrt_global_allsat_phy_l4_20230731_20230806.nc
+V = /home/SHARED/SATLINK/fsle/duacs_converted/nrt_global_allsat_phy_l4_20230801_20230807.nc
+V = /home/SHARED/SATLINK/fsle/duacs_converted/nrt_global_allsat_phy_l4_20230802_20230808.nc
+V = /home/SHARED/SATLINK/fsle/duacs_converted/nrt_global_allsat_phy_l4_20230803_20230809.nc
+V = /home/SHARED/SATLINK/fsle/duacs_converted/nrt_global_allsat_phy_l4_20230804_20230810.nc
+V = /home/SHARED/SATLINK/fsle/duacs_converted/nrt_global_allsat_phy_l4_20230805_20230811.nc
+V = /home/SHARED/SATLINK/fsle/duacs_converted/nrt_global_allsat_phy_l4_20230806_20230812.nc
+V = /home/SHARED/SATLINK/fsle/duacs_converted/nrt_global_allsat_phy_l4_20230807_20230813.nc
+U_NAME = ugos
+V_NAME = vgos
+FILL_VALUE = 0

env.yml

@@ -0,0 +1,16 @@
+name: aviso-lagrangian
+channels:
+  - fbriol
+  - conda-forge
+dependencies:
+  - python=3.7
+  # https://github.com/CNES/aviso-lagrangian
+  - lagrangian==3.0.0
+  - netcdf4==1.5.1.2
+  - boost==1.71.0
+  - udunits2==2.2.28
+  # Evita error: ImportError: libnetcdf.so.13: cannot open shared object file: No such file or directory
+  # Referencia: https://github.com/conda-forge/vtk-feedstock/issues/85
+  - libnetcdf==4.6.2
+  - pip:
+      - python-dateutil==2.8.2