grdwindinversion 0.2.4__tar.gz → 0.2.6__tar.gz

grdwindinversion-0.2.6/.github/workflows/build.yml

@@ -0,0 +1,40 @@
+name: Build and Upload Conda Package
+
+on:
+  release:
+    types:
+      - created
+
+jobs:
+  build-and-upload-conda-package:
+    if: true 
+    runs-on: ubuntu-latest
+    #${{ github.event.workflow_run.conclusion == 'success' }}
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v3
+        with:
+          fetch-depth: 0
+
+      - name: Set up Miniconda
+        uses: conda-incubator/setup-miniconda@v2
+        with:
+          auto-update-conda: true
+          python-version: 3.9
+
+      - name: Install conda-build
+        run: |
+          conda init
+          source ~/.bashrc
+          conda activate base
+          conda install -y -c conda-forge conda-build anaconda-client
+
+      - name: Build and Upload Conda package
+        env:
+          ANACONDA_TOKEN: ${{ secrets.ANACONDA_TOKEN }}
+        run: |
+          cd recipe
+          conda init
+          source ~/.bashrc 
+          conda activate base
+          conda-build . --token $ANACONDA_TOKEN --user tcevaer -c tcevaer -c conda-forge

grdwindinversion-0.2.6/.github/workflows/ci.yml

@@ -0,0 +1,101 @@
+name: CI Workflow for grdwindinversion
+
+on:
+    push:
+        branches:
+            - main
+    pull_request:
+        branches:
+            - main
+
+jobs:
+    test:
+        runs-on: ubuntu-latest
+        timeout-minutes: 360 # 6 hours limit for the job
+
+        steps:
+            # Checkout the code
+          - name: Checkout code
+            uses: actions/checkout@v4
+
+          - uses: mamba-org/setup-micromamba@v1
+            with:
+                micromamba-version: "1.5.9-1" # any version from https://github.com/mamba-org/micromamba-releases
+                channels: tcevaer, conda-forge
+                init-shell: bash
+                post-cleanup: "all"
+
+          - name: Configure Conda channel priority to disabled
+            run: |
+                conda config --set channel_priority disabled
+
+          - name: Create environment and install tools
+            run: micromamba create -n grdwind_env pytest conda-build boa python=3.10 -y
+
+          - name: Build package
+            run: |
+                cd recipe
+                eval "$(micromamba shell hook --shell bash)"
+                micromamba activate grdwind_env
+                conda mambabuild .
+
+          # Install the built package into the environment
+          - name: Install the built package
+            run: |
+                eval "$(micromamba shell hook --shell bash)"
+                micromamba activate grdwind_env
+                conda install --use-local grdwindinversion -y
+
+            # Cache the test data if previously downloaded (up to 10 GB limit for the cache)
+            # WARNING : modify the key if the data is modified !!
+          - name: Cache test data
+            uses: actions/cache@v4
+            id: cache
+            with:
+                path: ./test_data
+                key: test-data-v3
+                restore-keys: test-data-v3
+
+            # Download test data if not already cached
+          - name: Download test data
+            if: steps.cache.outputs.cache-hit != 'true' # Only download if cache miss
+            run: |
+                  mkdir -p ./test_data/
+                  wget https://cloud.ifremer.fr/index.php/s/ExLQ2TnYAqozPWE/download -O /tmp/ecmwf.zip
+                  unzip /tmp/ecmwf.zip -d ./test_data/
+                  wget https://cloud.ifremer.fr/index.php/s/kRgdOOPsjoZieZR/download -O /tmp/l1.zip
+                  unzip /tmp/l1.zip -d ./test_data/
+            timeout-minutes: 200 # Adjust depending on the size of your data
+
+            # Set up xsar configuration
+          - name: Setup xsar configuration
+            run: |
+                  mkdir -p ~/.xsar
+                  echo "data_dir: /tmp" > ~/.xsar/config.yaml
+                  echo "auxiliary_dir: ./test_data/auxiliary" >> ~/.xsar/config.yaml
+                  echo "path_dataframe_aux: ./test_data/auxiliary/active_aux.csv" >> ~/.xsar/config.yaml
+
+            # Set up grdwindinversion configuration
+          - name: Setup grdwindinversion configuration
+            run: |
+                  mkdir -p ~/.grdwindinversion
+                  echo "'ecmwf_0100_1h': ./test_data/ECMWF/forecast/hourly/0100deg/netcdf_light/%Y/%j/ECMWF_FORECAST_0100_%Y%m%d%H%M_10U_10V.nc" > ~/.grdwindinversion/data_config.yaml
+                  echo "'ecmwf_0125_1h': ./test_data/ECMWF/0.125deg/1h/forecasts/%Y/%j/ecmwf_%Y%m%d%H%M.nc" >> ~/.grdwindinversion/data_config.yaml
+                  #echo "'nc_luts_path': ./test_data/GMFS/nc_luts" >> ~/.grdwindinversion/data_config.yaml
+                  #echo "'lut_cmod7_path': './test_data/GMFS/v1.6/GMF_cmod7_official/cmod7_and_python_script'" >> ~/.grdwindinversion/data_config.yaml
+                  #echo "'lut_ms1ahw_path': './test_data/GMFS/v1.6/GMF_cmodms1ahw'" >> ~/.grdwindinversion/data_config.yaml
+
+            # Run the tests
+          - name: Run tests
+            run: |
+                  eval "$(micromamba shell hook --shell bash)"
+                  micromamba activate grdwind_env
+                  pytest
+
+                  # Optionally, upload test artifacts (NetCDF files or logs) if needed
+                  #- name: Upload test artifacts
+                  #  if: failure()  # Only upload on failure
+                  #  uses: actions/upload-artifact@v2
+                  #  with:
+                  #    name: test-output
+                  #    path: ./test_output/

{grdwindinversion-0.2.4 → grdwindinversion-0.2.6}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: grdwindinversion
-Version: 0.2.4
+Version: 0.2.6
 Summary: Package to perform Wind inversion from GRD Level-1 SAR images
 License: MIT
 Classifier: Development Status :: 2 - Pre-Alpha
@@ -27,6 +27,9 @@ Requires-Dist: numpy
 Requires-Dist: scipy
 Requires-Dist: fsspec
 Requires-Dist: aiohttp
+Requires-Dist: xarray-safe-s1
+Requires-Dist: xradarsat2
+Requires-Dist: xarray-safe-rcm
 
 
 # grdwindinversion

{grdwindinversion-0.2.4 → grdwindinversion-0.2.6}/grdwindinversion/inversion.py

@@ -98,7 +98,7 @@ def getOutputName2(input_file, outdir, sensor, meta, subdir=True):
         regex = re.compile(
             "([A-Z0-9]+)_OK([0-9]+)_PK([0-9]+)_(.*?)_(.*?)_(.*?)_(.*?)_(.*?)_(.*?)_(.*?)")
         template = string.Template(
-            "${MISSIONID}_OK${DATA1}_PK${DATA2}_${DATA3}_${BEAM_MODE}_${DATE}_${TIME}_${POLARIZATION1}_${POLARIZATION2}_${PRODUCT}")
+            "${MISSIONID}_OK${DATA1}_PK${DATA2}_${DATA3}_${BEAM}_${DATE}_${TIME}_${POLARIZATION1}_${POLARIZATION2}_${PRODUCT}")
         match = regex.match(basename_match)
         MISSIONID, DATA1, DATA2, DATA3, BEAM_MODE, DATE, TIME, POLARIZATION1, POLARIZATION2, LAST = match.groups()
         new_format = f"{MISSIONID.lower()}-{BEAM_MODE.lower()}-owi-xx-{meta_start_date.lower()}-{meta_stop_date.lower()}-_____-_____.nc"
@@ -243,7 +243,7 @@ def inverse(dual_pol, inc, sigma0, sigma0_dual, ancillary_wind, dsig_cr, model_c
     See Also
     --------
     xsarsea documentation
-    https://cyclobs.ifremer.fr/static/sarwing_datarmor/xsarsea/examples/windspeed_inversion.html
+    https://cerweb.ifremer.fr/datarmor/doc_sphinx/xsarsea/
     """
     logging.debug("inversion")
 
@@ -282,7 +282,7 @@ def inverse(dual_pol, inc, sigma0, sigma0_dual, ancillary_wind, dsig_cr, model_c
     return wind_co, None, None
 
 
-def makeL2asOwi(xr_dataset, dual_pol, copol, crosspol, add_streaks):
+def makeL2asOwi(xr_dataset, dual_pol, copol, crosspol, add_streaks, apply_flattening):
     """
     Rename xr_dataset variables and attributes to match naming convention.
 
@@ -392,13 +392,18 @@ def makeL2asOwi(xr_dataset, dual_pol, copol, crosspol, add_streaks):
 
         xr_dataset = xr_dataset.rename({
             'dsig_cross': 'owiDsig_cross',
-            'nesz_cross_final': 'owiNesz_cross_final',
             'winddir_cross': 'owiWindDirection_cross',
             'winddir_dual': 'owiWindDirection',
             'windspeed_cross': 'owiWindSpeed_cross',
             'windspeed_dual': 'owiWindSpeed',
             'sigma0_detrend_cross': 'owiNrcs_detrend_cross'
         })
+
+        if apply_flattening:
+            xr_dataset = xr_dataset.rename({
+                'nesz_cross_flattened': 'owiNesz_cross_flattened',
+            })
+
         # nrcs cross
         xr_dataset['owiNrcs_cross'] = xr_dataset['sigma0_ocean'].sel(
             pol=crosspol)
@@ -635,15 +640,7 @@ def preprocess(filename, outdir, config_path, overwrite=False, add_streaks=False
     config["l2_params"]["model_cross"] = model_cross
     config["sensor_longname"] = sensor_longname
 
-    # need to load gmfs before inversion
-    gmfs_impl = [x for x in [model_co, model_cross] if "gmf_" in x]
-    windspeed.gmfs.GmfModel.activate_gmfs_impl(gmfs_impl)
-    sarwings_luts = [x for x in [model_co, model_cross]
-                     if x.startswith("sarwing_lut_")]
-
-    if len(sarwings_luts) > 0:
-        windspeed.register_sarwing_luts(getConf()["sarwing_luts_path"])
-
+    # need to load LUTs before inversion
     nc_luts = [x for x in [model_co, model_cross] if x.startswith("nc_lut")]
 
     if len(nc_luts) > 0:
@@ -767,22 +764,17 @@ def preprocess(filename, outdir, config_path, overwrite=False, add_streaks=False
         xr_dataset['sigma0_detrend_cross'] = xsarsea.sigma0_detrend(
             xr_dataset.sigma0.sel(pol=crosspol), xr_dataset.incidence, model=model_cross)
         if config["apply_flattening"]:
-            xr_dataset = xr_dataset.assign(nesz_cross_final=(
+            xr_dataset = xr_dataset.assign(nesz_cross_flattened=(
                 ['line', 'sample'], windspeed.nesz_flattening(xr_dataset.nesz.sel(pol=crosspol), xr_dataset.incidence)))
-            xr_dataset['nesz_cross_final'].attrs[
+            xr_dataset['nesz_cross_flattened'].attrs[
                 "comment"] = 'nesz has been flattened using windspeed.nesz_flattening'
-
+            # dsig
+            xr_dataset["dsig_cross"] = windspeed.get_dsig(config["dsig_"+crosspol_gmf+"_NAME"], xr_dataset.incidence,
+                                                          xr_dataset['sigma0_ocean'].sel(pol=crosspol), xr_dataset.nesz_cross_flattened)
         else:
-            xr_dataset = xr_dataset.assign(
-                nesz_cross_final=(['line', 'sample'], xr_dataset.nesz.sel(pol=crosspol).values))
-            xr_dataset['nesz_cross_final'].attrs["comment"] = 'nesz has not been flattened'
-
-        xr_dataset.nesz_cross_final.attrs['units'] = 'm^2 / m^2'
-        xr_dataset.nesz_cross_final.attrs['long_name'] = 'Noise Equivalent SigmaNaught'
-
-        # dsig
-        xr_dataset["dsig_cross"] = windspeed.get_dsig(config["dsig_"+crosspol_gmf+"_NAME"], xr_dataset.incidence,
-                                                      xr_dataset['sigma0_ocean'].sel(pol=crosspol), xr_dataset.nesz_cross_final)
+            # dsig
+            xr_dataset["dsig_cross"] = windspeed.get_dsig(config["dsig_"+crosspol_gmf+"_NAME"], xr_dataset.incidence,
+                                                          xr_dataset['sigma0_ocean'].sel(pol=crosspol), xr_dataset['sigma0_ocean'].sel(pol=crosspol))
 
         xr_dataset.dsig_cross.attrs['comment'] = 'variable used to ponderate copol and crosspol'
         xr_dataset.dsig_cross.attrs['formula_used'] = config["dsig_" +
@@ -936,8 +928,7 @@ def makeL2(filename, outdir, config_path, overwrite=False, generateCSV=True, add
 
         xr_dataset['winddir_dual'] = transform_winddir(
             wind_dual, xr_dataset.ground_heading, winddir_convention=config["winddir_convention"])
-        xr_dataset['winddir_dual'].attrs["model"] = "%s (%s) & %s (%s)" % (
-            model_co, copol, model_cross, crosspol)
+        xr_dataset["winddir_dual"].attrs["model"] = "winddir_dual is a copy of copol wind direction"
 
         xr_dataset = xr_dataset.assign(
             windspeed_cross=(['line', 'sample'], windspeed_cr))
@@ -949,7 +940,7 @@ def makeL2(filename, outdir, config_path, overwrite=False, generateCSV=True, add
 
         xr_dataset['winddir_cross'] = xr_dataset['winddir_dual'].copy()
         xr_dataset['winddir_cross'].attrs = xr_dataset['winddir_dual'].attrs
-        xr_dataset["winddir_cross"].attrs["model"] = "No model used ; content is a copy of dualpol wind direction"
+        xr_dataset["winddir_cross"].attrs["model"] = "winddir_cross is a copy of copol wind direction"
 
     if config["winddir_convention"] == "oceanographic":
         attrs = xr_dataset['ancillary_wind_direction'].attrs
@@ -960,7 +951,7 @@ def makeL2(filename, outdir, config_path, overwrite=False, generateCSV=True, add
             "long_name"] = f"{ancillary_name} wind direction in oceanographic convention (clockwise, to), ex: 0°=to north, 90°=to east"
 
     xr_dataset, encoding = makeL2asOwi(
-        xr_dataset, dual_pol, copol, crosspol, add_streaks=add_streaks)
+        xr_dataset, dual_pol, copol, crosspol, add_streaks=add_streaks, apply_flattening=config["apply_flattening"])
 
     #  add attributes
     firstMeasurementTime = None

{grdwindinversion-0.2.4 → grdwindinversion-0.2.6}/grdwindinversion.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: grdwindinversion
-Version: 0.2.4
+Version: 0.2.6
 Summary: Package to perform Wind inversion from GRD Level-1 SAR images
 License: MIT
 Classifier: Development Status :: 2 - Pre-Alpha
@@ -27,6 +27,9 @@ Requires-Dist: numpy
 Requires-Dist: scipy
 Requires-Dist: fsspec
 Requires-Dist: aiohttp
+Requires-Dist: xarray-safe-s1
+Requires-Dist: xradarsat2
+Requires-Dist: xarray-safe-rcm
 
 
 # grdwindinversion

{grdwindinversion-0.2.4 → grdwindinversion-0.2.6}/grdwindinversion.egg-info/SOURCES.txt

@@ -13,6 +13,7 @@ requirements_dev.txt
 requirements_doc.txt
 tox.ini
 .github/dependabot.yml
+.github/workflows/build.yml
 .github/workflows/ci.yml
 .github/workflows/publish.yml
 ci/requirements/docs.yaml
@@ -32,7 +33,6 @@ docs/usage.rst
 docs/_static/css/grdwindinversion.css
 docs/examples/wind-inversion-from-grd.ipynb
 grdwindinversion/.gitignore
-grdwindinversion/.travis.yml
 grdwindinversion/__init__.py
 grdwindinversion/config_prod.yaml
 grdwindinversion/config_prod_recal.yaml

{grdwindinversion-0.2.4 → grdwindinversion-0.2.6}/grdwindinversion.egg-info/requires.txt

@@ -7,3 +7,6 @@ numpy
 scipy
 fsspec
 aiohttp
+xarray-safe-s1
+xradarsat2
+xarray-safe-rcm

{grdwindinversion-0.2.4 → grdwindinversion-0.2.6}/pyproject.toml

@@ -14,6 +14,9 @@ dependencies = [
     "scipy",
     "fsspec",
     "aiohttp",
+    "xarray-safe-s1",
+    "xradarsat2",
+    "xarray-safe-rcm"
 ]
 
 dynamic = ["version"]

grdwindinversion-0.2.4/.github/workflows/ci.yml

@@ -1,98 +0,0 @@
-name: CI Workflow for grdwindinversion
-
-on:
-    push:
-        branches:
-            - main
-    pull_request:
-        branches:
-            - main
-
-jobs:
-    test:
-        runs-on: ubuntu-latest
-        timeout-minutes: 360 # 6 hours limit for the job
-  
-        steps:
-          # Checkout the code
-          - name: Checkout code
-            uses: actions/checkout@v4
-
-          - uses: mamba-org/setup-micromamba@v1
-            with:
-                micromamba-version: "1.5.9-1" # any version from https://github.com/mamba-org/micromamba-releases
-                channels: tcevaer, conda-forge, defaults
-                init-shell: bash
-                post-cleanup: "all"
-
-          - name: Create environment and install tools
-            run: micromamba create -n grdwind_env pytest conda-build boa python=3.10 -y -c tcevaer -c conda-forge
-
-          - name: Build package
-            run: |
-                cd recipe
-                eval "$(micromamba shell hook --shell bash)"
-                micromamba activate grdwind_env
-                conda mambabuild . -c tcevaer -c conda-forge
-
-          # Install the built package into the environment
-          - name: Install the built package
-            run: |
-                eval "$(micromamba shell hook --shell bash)"
-                micromamba activate grdwind_env
-                conda install --use-local grdwindinversion -y -c tcevaer -c conda-forge
-
-          # Cache the test data if previously downloaded (up to 10 GB limit for the cache)
-          # WARNING : modify the key if the data is modified !!
-          - name: Cache test data
-            uses: actions/cache@v4
-            id: cache
-            with:
-              path: ./test_data
-              key: test-data-v3
-              restore-keys: test-data-v3
-
-          # Download test data if not already cached
-          - name: Download test data
-            if: steps.cache.outputs.cache-hit != 'true' # Only download if cache miss
-            run: |
-                mkdir -p ./test_data/
-                wget https://cloud.ifremer.fr/index.php/s/ExLQ2TnYAqozPWE/download -O /tmp/ecmwf.zip
-                unzip /tmp/ecmwf.zip -d ./test_data/
-                wget https://cloud.ifremer.fr/index.php/s/kRgdOOPsjoZieZR/download -O /tmp/l1.zip
-                unzip /tmp/l1.zip -d ./test_data/
-            timeout-minutes: 200 # Adjust depending on the size of your data
-
-          # Set up xsar configuration
-          - name: Setup xsar configuration
-            run: |
-                mkdir -p ~/.xsar
-                echo "data_dir: /tmp" > ~/.xsar/config.yaml
-                echo "auxiliary_dir: ./test_data/auxiliary" >> ~/.xsar/config.yaml
-                echo "path_dataframe_aux: ./test_data/auxiliary/active_aux.csv" >> ~/.xsar/config.yaml
-
-          # Set up grdwindinversion configuration
-          - name: Setup grdwindinversion configuration
-            run: |
-                mkdir -p ~/.grdwindinversion
-                echo "'ecmwf_0100_1h': ./test_data/ECMWF/forecast/hourly/0100deg/netcdf_light/%Y/%j/ECMWF_FORECAST_0100_%Y%m%d%H%M_10U_10V.nc" > ~/.grdwindinversion/data_config.yaml
-                echo "'ecmwf_0125_1h': ./test_data/ECMWF/0.125deg/1h/forecasts/%Y/%j/ecmwf_%Y%m%d%H%M.nc" >> ~/.grdwindinversion/data_config.yaml
-                #echo "'sarwing_luts_path': './test_data/GMFS/v1.6/'" >> ~/.grdwindinversion/data_config.yaml
-                #echo "'nc_luts_path': ./test_data/GMFS/nc_luts" >> ~/.grdwindinversion/data_config.yaml
-                #echo "'lut_cmod7_path': './test_data/GMFS/v1.6/GMF_cmod7_official/cmod7_and_python_script'" >> ~/.grdwindinversion/data_config.yaml
-                #echo "'lut_ms1ahw_path': './test_data/GMFS/v1.6/GMF_cmodms1ahw'" >> ~/.grdwindinversion/data_config.yaml
-
-          # Run the tests
-          - name: Run tests
-            run: |
-                eval "$(micromamba shell hook --shell bash)"
-                micromamba activate grdwind_env
-                pytest
-
-                # Optionally, upload test artifacts (NetCDF files or logs) if needed
-                #- name: Upload test artifacts
-                #  if: failure()  # Only upload on failure
-                #  uses: actions/upload-artifact@v2
-                #  with:
-                #    name: test-output
-                #    path: ./test_output/

grdwindinversion-0.2.4/grdwindinversion/.travis.yml

@@ -1,28 +0,0 @@
-# Config file for automatic testing at travis-ci.com
-
-language: python
-python:
-  - 3.8
-  - 3.7
-  - 3.6
-
-# Command to install dependencies, e.g. pip install -r requirements.txt --use-mirrors
-install: pip install -U tox-travis
-
-# Command to run tests, e.g. python setup.py test
-script: tox
-
-# Assuming you have installed the travis-ci CLI tool, after you
-# create the Github repo and add it to Travis, run the
-# following command to finish PyPI deployment setup:
-# $ travis encrypt --add deploy.password
-deploy:
-  provider: pypi
-  distributions: sdist bdist_wheel
-  user: agrouaze
-  password:
-    secure: PLEASE_REPLACE_ME
-  on:
-    tags: true
-    repo: agrouaze/grdwindinversion
-    python: 3.8