Merge branch 'fix_scripts' into 'master'

Update scripts.py, clip(-10, 1) and penalize

See merge request aaron.spring/s2s-ai-challenge-template!9

CHANGELOG.md

@@ -2,6 +2,15 @@
 
 ### unreleased
 
+- Order of processing gridded `RPSS` to final score: (#7, !9, [s2s-ai-competition-scoring-image!2](https://renkulab.io/gitlab/tasko.olevski/s2s-ai-competition-scoring-image/-/merge_requests/2), [Aaron Spring](https://renkulab.io/gitlab/aaron.spring))
+    1. `RPSS`
+    2. penalize #7 
+    3. `clip(-10,1)`
+    4. mean over `forecast_time`
+    5. spatially weighted mean [90N-60S]
+    6. mean over `lead_time` and `data_vars`
+- Dont forget to `git add current_notebook.ipynb` also to ensure that consistent training pipeline and submission file are tagged, added to notebooks. (!9, [Aaron Spring](https://renkulab.io/gitlab/aaron.spring))
+- Rerun [`ML_train_and_predict.ipynb`](https://renkulab.io/gitlab/aaron.spring/s2s-ai-challenge-template/-/blob/master/notebooks/ML_train_and_predict.ipynb) (!9, [Aaron Spring](https://renkulab.io/gitlab/aaron.spring))
 - Fix typo in safeguards in [ML_forecast_template.ipynb](https://renkulab.io/gitlab/aaron.spring/s2s-ai-challenge-template/-/blob/master/notebooks/ML_forecast_template.ipynb): "We did NOT use `test` explicitly in training or implicitly in incrementally adjusting parameters."" (!8, [Aaron Spring](https://renkulab.io/gitlab/aaron.spring))
 - Add notebooks showcasing accessing output of different models from different sources: (!2, [Aaron Spring](https://renkulab.io/gitlab/aaron.spring))
     - S2S-Project models:

notebooks/ML_forecast_template.ipynb

 %% Cell type:markdown id: tags:
 
 # Train ML model for predictions of week 3-4 & 5-6
 
 This notebook create a Machine Learning `ML_model` to predict weeks 3-4 & 5-6 based on `S2S` weeks 3-4 & 5-6 forecasts and is compared to `CPC` observations for the [`s2s-ai-challenge`](https://s2s-ai-challenge.github.io/).
 
 %% Cell type:markdown id: tags:
 
 # Synopsis
 
 %% Cell type:markdown id: tags:
 
 ## Method: `name`
 
 - decription
 - a few details
 
 %% Cell type:markdown id: tags:
 
 ## Data used
 
 Training-input for Machine Learning model:
 - renku datasets, climetlab, IRIDL
 
 Forecast-input for Machine Learning model:
 - renku datasets, climetlab, IRIDL
 
 Compare Machine Learning model forecast against ground truth:
 - renku datasets, climetlab, IRIDL
 
 %% Cell type:markdown id: tags:
 
 ## Resources used
 for training, details in reproducibility
 
 - platform: renku
 - memory: 8 GB
 - processors: 2 CPU
 - storage required: 10 GB
 
 %% Cell type:markdown id: tags:
 
 ## Safeguards
 
 All points have to be [x] checked. If not, your submission is invalid.
 
 Changes to the code after submissions are not possible, as the `commit` before the `tag` will be reviewed.
 (Only in exceptions and if previous effort in reproducibility can be found, it may be allowed to improve readability and reproducibility after November 1st 2021.)
 
 %% Cell type:markdown id: tags:
 
 ### Safeguards to prevent [overfitting](https://en.wikipedia.org/wiki/Overfitting?wprov=sfti1)
 
 If the organizers suspect overfitting, your contribution can be disqualified.
 
   - [ ] We did not use 2020 observations in training (explicit overfitting and cheating)
   - [ ] We did not repeatedly verify my model on 2020 observations and incrementally improved my RPSS (implicit overfitting)
   - [ ] We provide RPSS scores for the training period with script `skill_by_year`, see in section 6.3 `predict`.
   - [ ] We tried our best to prevent [data leakage](https://en.wikipedia.org/wiki/Leakage_(machine_learning)?wprov=sfti1).
   - [ ] We honor the `train-validate-test` [split principle](https://en.wikipedia.org/wiki/Training,_validation,_and_test_sets). This means that the hindcast data is split into `train` and `validate`, whereas `test` is withheld.
   - [ ] We did not use `test` explicitly in training or implicitly in incrementally adjusting parameters.
   - [ ] We considered [cross-validation](https://en.wikipedia.org/wiki/Cross-validation_(statistics)).
 
 %% Cell type:markdown id: tags:
 
 ### Safeguards for Reproducibility
 Notebook/code must be independently reproducible from scratch by the organizers (after the competition), if not possible: no prize
   - [ ] All training data is publicly available (no pre-trained private neural networks, as they are not reproducible for us)
   - [ ] Code is well documented, readable and reproducible.
   - [ ] Code to reproduce training and predictions is preferred to run within a day on the described architecture. If the training takes longer than a day, please justify why this is needed. Please do not submit training piplelines, which take weeks to train.
 
 %% Cell type:markdown id: tags:
 
 # Todos to improve template
 
 This is just a demo.
 
 - [ ] for both variables
 - [ ] for both `lead_time`s
 - [ ] ensure probabilistic prediction outcome with `category` dim
 
 %% Cell type:markdown id: tags:
 
 # Imports
 
 %% Cell type:code id: tags:
 
 ``` python
 from tensorflow.keras.layers import Input, Dense, Flatten
 from tensorflow.keras.models import Sequential
 
 import matplotlib.pyplot as plt
 
 import xarray as xr
 xr.set_options(display_style='text')
 
 from dask.utils import format_bytes
 import xskillscore as xs
 ```
 
 %% Cell type:markdown id: tags:
 
 # Get training data
 
 preprocessing of input data may be done in separate notebook/script
 
 %% Cell type:markdown id: tags:
 
 ## Hindcast
 
 get weekly initialized hindcasts
 
 %% Cell type:code id: tags:
 
 ``` python
 # consider renku datasets
 #! renku storage pull path
 ```
 
 %% Cell type:code id: tags:
 
 ``` python
 ```
 
 %% Cell type:markdown id: tags:
 
 ## Observations
 corresponding to hindcasts
 
 %% Cell type:code id: tags:
 
 ``` python
 # consider renku datasets
 #! renku storage pull path
 ```
 
 %% Cell type:code id: tags:
 
 ``` python
 ```
 
 %% Cell type:markdown id: tags:
 
 # ML model
 
 %% Cell type:code id: tags:
 
 ``` python
 bs=32
 
 import numpy as np
 class DataGenerator(keras.utils.Sequence):
     def __init__(self):
         """
         Data generator
 
         Template from https://stanford.edu/~shervine/blog/keras-how-to-generate-data-on-the-fly
 
         Args:
 
         """
 
         self.on_epoch_end()
 
         # For some weird reason calling .load() earlier messes up the mean and std computations
         if load: print('Loading data into RAM'); self.data.load()
 
     def __len__(self):
         'Denotes the number of batches per epoch'
         return int(np.ceil(self.n_samples / self.batch_size))
 
     def __getitem__(self, i):
         'Generate one batch of data'
         idxs = self.idxs[i * self.batch_size:(i + 1) * self.batch_size]
         # got all nan if nans not masked
         X = self.data.isel(time=idxs).fillna(0.).values
         y = self.verif_data.isel(time=idxs).fillna(0.).values
         return X, y
 
     def on_epoch_end(self):
         'Updates indexes after each epoch'
         self.idxs = np.arange(self.n_samples)
         if self.shuffle == True:
             np.random.shuffle(self.idxs)
 ```
 
 %% Cell type:markdown id: tags:
 
 ## data prep: train, valid, test
 
 %% Cell type:code id: tags:
 
 ``` python
 # time is the forecast_reference_time
 time_train_start,time_train_end='2000','2017'
 time_valid_start,time_valid_end='2018','2019'
 time_test = '2020'
 ```
 
 %% Cell type:code id: tags:
 
 ``` python
 dg_train = DataGenerator()
 ```
 
 %% Cell type:code id: tags:
 
 ``` python
 dg_valid = DataGenerator()
 ```
 
 %% Cell type:code id: tags:
 
 ``` python
 dg_test = DataGenerator()
 ```
 
 %% Cell type:markdown id: tags:
 
 ## `fit`
 
 %% Cell type:code id: tags:
 
 ``` python
 cnn = keras.models.Sequential([])
 ```
 
 %% Cell type:code id: tags:
 
 ``` python
 cnn.summary()
 ```
 
 %% Cell type:code id: tags:
 
 ``` python
 cnn.compile(keras.optimizers.Adam(1e-4), 'mse')
 ```
 
 %% Cell type:code id: tags:
 
 ``` python
 import warnings
 warnings.simplefilter("ignore")
 ```
 
 %% Cell type:code id: tags:
 
 ``` python
 cnn.fit(dg_train, epochs=1, validation_data=dg_valid)
 ```
 
 %% Cell type:markdown id: tags:
 
 ## `predict`
 
-Create predictions and print `mean(variable, lead_time, longitude, weighted latitude)` RPSS for all years as calculated by `skill_by_year`. For now RPS, todo: change to RPSS.
+Create predictions and print `mean(variable, lead_time, longitude, weighted latitude)` RPSS for all years as calculated by `skill_by_year`.
 
 %% Cell type:code id: tags:
 
 ``` python
 from scripts import skill_by_year
 ```
 
 %% Cell type:code id: tags:
 
 ``` python
 def create_predictions(model, dg):
     """Create non-iterative predictions"""
     preds = model.predict(dg).squeeze()
     # transform
 
     return preds
 ```
 
 %% Cell type:markdown id: tags:
 
 ### `predict` training period in-sample
 
 %% Cell type:code id: tags:
 
 ``` python
 preds_is = create_predictions(cnn, dg_train)
 ```
 
 %% Cell type:code id: tags:
 
 ``` python
 skill_by_year(preds_is)
 ```
 
 %% Cell type:markdown id: tags:
 
 ### `predict` valid out-of-sample
 
 %% Cell type:code id: tags:
 
 ``` python
 preds_os = create_predictions(cnn, dg_valid)
 ```
 
 %% Cell type:code id: tags:
 
 ``` python
 skill_by_year(preds_os)
 ```
 
 %% Cell type:markdown id: tags:
 
 ### `predict` test
 
 %% Cell type:code id: tags:
 
 ``` python
 preds_test = create_predictions(cnn, dg_test)
 ```
 
 %% Cell type:code id: tags:
 
 ``` python
 skill_by_year(preds_test)
 ```
 
 %% Cell type:markdown id: tags:
 
 # Submission
 
 %% Cell type:code id: tags:
 
 ``` python
 preds_test.sizes # expect: category(3), longitude, latitude, lead_time(2), forecast_time (53)
 ```
 
 %% Cell type:code id: tags:
 
 ``` python
 from scripts import assert_predictions_2020
 assert_predictions_2020(preds_test)
 ```
 
 %% Cell type:code id: tags:
 
 ``` python
 preds_test.to_netcdf('../submissions/ML_prediction_2020.nc')
 ```
 
 %% Cell type:code id: tags:
 
 ``` python
 #!git add ../submissions/ML_prediction_2020.nc
+#!git add ML_forecast_template.ipynb
 ```
 
 %% Cell type:code id: tags:
 
 ``` python
 #!git commit -m "commit submission for my_method_name" # whatever message you want
 ```
 
 %% Cell type:code id: tags:
 
 ``` python
 #!git tag "submission-my_method_name-0.0.1" # if this is to be checked by scorer, only the last submitted==tagged version will be considered
 ```
 
 %% Cell type:code id: tags:
 
 ``` python
 #!git push --tags
 ```
 
 %% Cell type:code id: tags:
 
 ``` python
 ```
 
 %% Cell type:markdown id: tags:
 
 # Reproducibility
 
 %% Cell type:markdown id: tags:
 
 ## memory
 
 %% Cell type:code id: tags:
 
 ``` python
 # https://phoenixnap.com/kb/linux-commands-check-memory-usage
 !free -g
 ```
 
 %% Cell type:markdown id: tags:
 
 ## CPU
 
 %% Cell type:code id: tags:
 
 ``` python
 !lscpu
 ```
 
 %% Cell type:markdown id: tags:
 
 ## software
 
 %% Cell type:code id: tags:
 
 ``` python
 !conda list
 ```
 
 %% Cell type:code id: tags:
 
 ``` python
 ```

notebooks/mean_bias_reduction.ipynb

 %% Cell type:markdown id: tags:
 
 # Train ML model to correct predictions of week 3-4 & 5-6
 
 This notebook create a Machine Learning `ML_model` to predict weeks 3-4 & 5-6 based on `S2S` weeks 3-4 & 5-6 forecasts and is compared to `CPC` observations for the [`s2s-ai-challenge`](https://s2s-ai-challenge.github.io/).
 
 %% Cell type:markdown id: tags:
 
 # Synopsis
 
 %% Cell type:markdown id: tags:
 
 ## Method: `mean bias reduction`
 
 - calculate the mean bias from 2000-2019 deterministic ensemble mean forecast
 - remove that mean bias from 2020 forecast deterministic ensemble mean forecast
 - no Machine Learning used here
 
 %% Cell type:markdown id: tags:
 
 ## Data used
 
 type: renku datasets
 
 Training-input for Machine Learning model:
 - hindcasts of models:
     - ECMWF: `ecmwf_hindcast-input_2000-2019_biweekly_deterministic.zarr`
 
 Forecast-input for Machine Learning model:
 - real-time 2020 forecasts of models:
     - ECMWF: `ecmwf_forecast-input_2020_biweekly_deterministic.zarr`
 
 Compare Machine Learning model forecast against against ground truth:
 - `CPC` observations:
     - `hindcast-like-observations_biweekly_deterministic.zarr`
     - `forecast-like-observations_2020_biweekly_deterministic.zarr`
 
 %% Cell type:markdown id: tags:
 
 ## Resources used
 for training, details in reproducibility
 
 - platform: MPI-M supercompute 1 Node
 - memory: 64 GB
 - processors: 36 CPU
 - storage required: 10 GB
 
 %% Cell type:markdown id: tags:
 
 ## Safeguards
 
 All points have to be [x] checked. If not, your submission is invalid.
 
 Changes to the code after submissions are not possible, as the `commit` before the `tag` will be reviewed.
 (Only in exceptions and if previous effort in reproducibility can be found, it may be allowed to improve readability and reproducibility after November 1st 2021.)
 
 %% Cell type:markdown id: tags:
 
 ### Safeguards to prevent [overfitting](https://en.wikipedia.org/wiki/Overfitting?wprov=sfti1)
 
 If the organizers suspect overfitting, your contribution can be disqualified.
 
   - [x] We didnt use 2020 observations in training (explicit overfitting and cheating)
   - [x] We didnt repeatedly verify my model on 2020 observations and incrementally improved my RPSS (implicit overfitting)
   - [x] We provide RPSS scores for the training period with script `skill_by_year`, see in section 6.3 `predict`.
   - [x] We tried our best to prevent [data leakage](https://en.wikipedia.org/wiki/Leakage_(machine_learning)?wprov=sfti1).
   - [x] We honor the `train-validate-test` [split principle](https://en.wikipedia.org/wiki/Training,_validation,_and_test_sets). This means that the hindcast data is split into `train` and `validate`, whereas `test` is withheld.
   - [x] We did use `test` explicitly in training or implicitly in incrementally adjusting parameters.
   - [x] We considered [cross-validation](https://en.wikipedia.org/wiki/Cross-validation_(statistics)).
 
 %% Cell type:markdown id: tags:
 
 ### Safeguards for Reproducibility
 Notebook/code must be independently reproducible from scratch by the organizers (after the competition), if not possible: no prize
   - [x] All training data is publicly available (no pre-trained private neural networks, as they are not reproducible for us)
   - [x] Code is well documented, readable and reproducible.
   - [x] Code to reproduce training and predictions is preferred to run within a day on the described architecture. If the training takes longer than a day, please justify why this is needed. Please do not submit training piplelines, which take weeks to train.
 
 %% Cell type:markdown id: tags:
 
 # Imports
 
 %% Cell type:code id: tags:
 
 ``` python
 import xarray as xr
 xr.set_options(display_style='text')
 import numpy as np
 
 from dask.utils import format_bytes
 import xskillscore as xs
 ```
 
 %% Cell type:markdown id: tags:
 
 # Get training data
 
 preprocessing of input data may be done in separate notebook/script
 
 %% Cell type:markdown id: tags:
 
 ## Hindcast
 
 get weekly initialized hindcasts
 
 %% Cell type:code id: tags:
 
 ``` python
 # preprocessed as renku dataset
 !renku storage pull ../data/ecmwf_hindcast-input_2000-2019_biweekly_deterministic.zarr
 ```
 
 %% Cell type:code id: tags:
 
 ``` python
 hind_2000_2019 = xr.open_zarr("../data/ecmwf_hindcast-input_2000-2019_biweekly_deterministic.zarr", consolidated=True)
 ```
 
 %% Cell type:code id: tags:
 
 ``` python
 # preprocessed as renku dataset
 !renku storage pull ../data/ecmwf_forecast-input_2020_biweekly_deterministic.zarr
 ```
 
 %% Cell type:code id: tags:
 
 ``` python
 fct_2020 = xr.open_zarr("../data/ecmwf_forecast-input_2020_biweekly_deterministic.zarr", consolidated=True)
 ```
 
 %% Cell type:markdown id: tags:
 
 ## Observations
 corresponding to hindcasts
 
 %% Cell type:code id: tags:
 
 ``` python
 # preprocessed as renku dataset
 !renku storage pull ../data/hindcast-like-observations_2000-2019_biweekly_deterministic.zarr
 ```
 
 %% Cell type:code id: tags:
 
 ``` python
 obs_2000_2019 = xr.open_zarr("../data/hindcast-like-observations_2000-2019_biweekly_deterministic.zarr", consolidated=True)
 ```
 
 %% Cell type:code id: tags:
 
 ``` python
 # preprocessed as renku dataset
 !renku storage pull ../data/forecast-like-observations_2020_biweekly_deterministic.zarr
 ```
 
 %% Cell type:code id: tags:
 
 ``` python
 obs_2020 = xr.open_zarr("../data/forecast-like-observations_2020_biweekly_deterministic.zarr", consolidated=True)
 ```
 
 %% Cell type:markdown id: tags:
 
 # no ML model
 
 %% Cell type:markdown id: tags:
 
 Here, we just remove the mean bias from the ensemble mean forecast.
 
 %% Cell type:code id: tags:
 
 ``` python
 bias_2000_2019 = (hind_2000_2019.mean('realization') - obs_2000_2019).groupby('forecast_time.weekofyear').mean().compute()
 ```
 
 %%%% Output: stream
 
     /work/mh0727/m300524/conda-envs/s2s-ai/lib/python3.7/site-packages/xarray/core/accessor_dt.py:381: FutureWarning: dt.weekofyear and dt.week have been deprecated. Please use dt.isocalendar().week instead.
       FutureWarning,
     /work/mh0727/m300524/conda-envs/s2s-ai/lib/python3.7/site-packages/dask/array/numpy_compat.py:40: RuntimeWarning: invalid value encountered in true_divide
       x = np.divide(x1, x2, out)
 
 %% Cell type:markdown id: tags:
 
 ## `predict`
 
-Create predictions and print `mean(variable, lead_time, longitude, weighted latitude)` RPSS for all years as calculated by `skill_by_year`. For now RPS, todo: change to RPSS.
+Create predictions and print `mean(variable, lead_time, longitude, weighted latitude)` RPSS for all years as calculated by `skill_by_year`.
 
 %% Cell type:code id: tags:
 
 ``` python
 from scripts import make_probabilistic
 ```
 
 %% Cell type:code id: tags:
 
 ``` python
 !renku storage pull ../data/hindcast-like-observations_2000-2019_biweekly_tercile-edges.nc
 ```
 
 %% Cell type:code id: tags: