From 1484cce0a3b7620879065269625d2db206ee3316 Mon Sep 17 00:00:00 2001
From: AS <aaron.spring@mpimet.mpg.de>
Date: Mon, 10 May 2021 15:19:47 +0200
Subject: [PATCH] git lfs track submissions/*.nc and ML_forecast template
---
notebooks/ML_forecast.ipynb | 1003 +++++++++++++++++++++++++++++++++++
submissions/.gitattributes | 1 +
2 files changed, 1004 insertions(+)
create mode 100644 notebooks/ML_forecast.ipynb
create mode 100644 submissions/.gitattributes
diff --git a/notebooks/ML_forecast.ipynb b/notebooks/ML_forecast.ipynb
new file mode 100644
index 0000000..575ffe5
--- /dev/null
+++ b/notebooks/ML_forecast.ipynb
@@ -0,0 +1,1003 @@
+{
+ "cells": [
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "# Train ML model to correct predictions of week 3-4 & 5-6\n",
+ "\n",
+ "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",
+ "metadata": {},
+ "source": [
+ "# Synopsis"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "## Data used\n",
+ "\n",
+ "Training-input for Machine Learning model:\n",
+ "- hindcasts of models: ECMWF\n",
+ "\n",
+ "Forecast-input for Machine Learning model:\n",
+ "- real-time 2020 forecasts of the same models\n",
+ "\n",
+ "Compare Machine Learning model forecast against:\n",
+ "- `CPC` observations 2020"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "## Method: (`name`) mean bias reduction\n",
+ "\n",
+ "- calculate bias from 2000-2019\n",
+ "- remove bias from 2020 forecast"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "## Resources used\n",
+ "for training\n",
+ "\n",
+ "- platform: renku\n",
+ "- memory: 8 GB\n",
+ "- processors: 2 CPU\n",
+ "- storage required: 10 GB"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "## Safeguards\n",
+ "\n",
+ "All points have to be [x] checked. If not, your submission is invalid.\n",
+ "\n",
+ "Changes to the code after submissions are not possible, as the `commit` before the `tag` will be reviewed.\n",
+ "(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",
+ "metadata": {},
+ "source": [
+ "### Safeguards to prevent [overfitting](https://en.wikipedia.org/wiki/Overfitting?wprov=sfti1) \n",
+ "\n",
+ "If the organizers suspect overfitting, your contribution can be disqualified.\n",
+ "\n",
+ " - [ ] We didnt use 2020 observations in training (explicit overfitting and cheating)\n",
+ " - [ ] We didnt repeatedly verify my model on 2020 observations and incrementally improved my RPSS (implicit overfitting)\n",
+ " - [ ] We tried our best to prevent [data leakage](https://en.wikipedia.org/wiki/Leakage_(machine_learning)?wprov=sfti1).\n",
+ " - [ ] We separate 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.\n",
+ " - [ ] We did use `test` explicitly in training or implicitly in incrementally adjusting parameters.\n",
+ " - [ ] We considered [cross-validation](https://en.wikipedia.org/wiki/Cross-validation_(statistics))."
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "### Safeguards for Reproducibility\n",
+ "Notebook/code must be independently reproducible from scratch by the organizers (after the competition), if not possible: no prize\n",
+ " - [ ] All training data is publicly available (no pre-trained private neural networks, as they are not reproducible for us)\n",
+ " - [ ] Code is well documented, readable and reproducible.\n",
+ " - [ ] Code to reproduce runs within a day."
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "# Todos to improve template\n",
+ "\n",
+ "This is just a demo.\n",
+ "\n",
+ "- [ ] for both variables\n",
+ "- [ ] for both `lead_time`s\n",
+ "- [ ] ensure probabilistic prediction outcome with `category` dim"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "# Imports"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 1,
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "from tensorflow.keras.layers import Input, Dense, Flatten\n",
+ "from tensorflow.keras.models import Sequential\n",
+ "\n",
+ "import matplotlib.pyplot as plt\n",
+ "\n",
+ "import xarray as xr\n",
+ "xr.set_options(display_style='text')\n",
+ "\n",
+ "from dask.utils import format_bytes\n",
+ "import xskillscore as xs"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "# Get training data\n",
+ "\n",
+ "preprocessing of input data may be done in separate notebook/script"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "## Hindcast\n",
+ "\n",
+ "get weekly initialized hindcasts"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 2,
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "v='tp'"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 3,
+ "metadata": {},
+ "outputs": [
+ {
+ "name": "stdout",
+ "output_type": "stream",
+ "text": [
+ "\u001b[33m\u001b[1mWarning: \u001b[0mRun CLI commands only from project's root directory.\n",
+ "\u001b[0m\n"
+ ]
+ }
+ ],
+ "source": [
+ "# preprocessed as renku dataset\n",
+ "!renku storage pull ../data/ECMWF_hc_tp_weekly_2000_2019.zarr/"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 4,
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "hc_weekly = xr.open_zarr('../data/ECMWF_hc_tp_weekly_2000_2019.zarr')"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 5,
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "def add_time_from_forecast_reference_time_and_step(benchmark, init_dim='time'):\n",
+ " \"\"\"Creates time(forecast_reference_time, step).\n",
+ " \n",
+ " step: pd.Timedelta\n",
+ " forecast_reference_time: datetime\n",
+ " \"\"\"\n",
+ " times = xr.concat(\n",
+ " [\n",
+ " xr.DataArray(\n",
+ " benchmark[init_dim] + step,\n",
+ " dims=init_dim,\n",
+ " coords={init_dim: benchmark[init_dim]},\n",
+ " )\n",
+ " for step in benchmark.step\n",
+ " ],\n",
+ " dim=\"step\",\n",
+ " join=\"inner\",\n",
+ " compat=\"broadcast_equals\",\n",
+ " )\n",
+ " benchmark = benchmark.assign_coords(valid_time=times)\n",
+ " return benchmark"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 6,
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "hc_weekly = add_time_from_forecast_reference_time_and_step(hc_weekly)"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "## Observations\n",
+ "corresponding to hindcasts"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 7,
+ "metadata": {},
+ "outputs": [
+ {
+ "name": "stdout",
+ "output_type": "stream",
+ "text": [
+ "\u001b[33m\u001b[1mWarning: \u001b[0mRun CLI commands only from project's root directory.\n",
+ "\u001b[0m\n"
+ ]
+ }
+ ],
+ "source": [
+ "# as prepared renku datasets FIXME\n",
+ "!renku storage pull ../data/cpc-rain-1998-2020-weekly-averaged-1.5-deg/rain_verification_1998_2020.nc"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 8,
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "obs = xr.open_dataset(f'../data/cpc-rain-1998-2020-weekly-averaged-1.5-deg/rain_verification_1998_2020.nc', chunks={}).rename({'rain':v,'time':'valid_time'})"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "# ML model"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "based on [Weatherbench](https://github.com/pangeo-data/WeatherBench/blob/master/quickstart.ipynb)"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 9,
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "import sys\n",
+ "sys.path.insert(1, '/work/s2s-ai-competition-bootstrap/WeatherBench')\n",
+ "from src.train_nn import DataGenerator, PeriodicConv2D, create_predictions\n",
+ "import tensorflow.keras as keras"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 10,
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "bs=32\n",
+ "\n",
+ "import numpy as np\n",
+ "class DataGenerator(keras.utils.Sequence):\n",
+ " def __init__(self, ds, verif, step, batch_size=bs, shuffle=True, load=True, mean=None, std=None):\n",
+ " \"\"\"\n",
+ " Data generator for WeatherBench data.\n",
+ " Template from https://stanford.edu/~shervine/blog/keras-how-to-generate-data-on-the-fly\n",
+ " Args:\n",
+ " ds: model\n",
+ " verif: obs\n",
+ " step: Lead_time/step as in model\n",
+ " batch_size: Batch size\n",
+ " shuffle: bool. If True, data is shuffled.\n",
+ " load: bool. If True, datadet is loaded into RAM.\n",
+ " mean: If None, compute mean from data.\n",
+ " std: If None, compute standard deviation from data.\n",
+ " \n",
+ " Todo:\n",
+ " - use number\n",
+ " - dont use .sel(step=step) to train over all steps at once\n",
+ " \"\"\"\n",
+ "\n",
+ " self.ds = ds\n",
+ " self.batch_size = batch_size\n",
+ " self.shuffle = shuffle\n",
+ " self.lead_time = step\n",
+ "\n",
+ "\n",
+ " self.data = ds.transpose('time', ...).sel(step=step)\n",
+ " self.mean = self.data.mean('time').compute() if mean is None else mean\n",
+ " self.std = self.data.std('time').compute() if std is None else std\n",
+ " \n",
+ " self.verif_data = verif.transpose('time', ...).sel(step=step)\n",
+ " self.verif_mean = self.verif_data.mean('time').compute() if mean is None else mean\n",
+ " self.verif_std = self.verif_data.std('time').compute() if std is None else std\n",
+ "\n",
+ " # Normalize\n",
+ " self.data = (self.data - self.mean) / self.std\n",
+ " self.verif_data = (self.verif_data - self.verif_mean) / self.verif_std\n",
+ " \n",
+ " self.n_samples = self.data.time.size\n",
+ " self.time = ds.time\n",
+ "\n",
+ " self.on_epoch_end()\n",
+ "\n",
+ " # For some weird reason calling .load() earlier messes up the mean and std computations\n",
+ " if load: print('Loading data into RAM'); self.data.load()\n",
+ "\n",
+ " def __len__(self):\n",
+ " 'Denotes the number of batches per epoch'\n",
+ " return int(np.ceil(self.n_samples / self.batch_size))\n",
+ "\n",
+ " def __getitem__(self, i):\n",
+ " 'Generate one batch of data'\n",
+ " idxs = self.idxs[i * self.batch_size:(i + 1) * self.batch_size]\n",
+ " # got all nan if nans not masked\n",
+ " X = self.data.isel(time=idxs).fillna(0.).values\n",
+ " y = self.verif_data.isel(time=idxs).fillna(0.).values\n",
+ " return X, y\n",
+ "\n",
+ " def on_epoch_end(self):\n",
+ " 'Updates indexes after each epoch'\n",
+ " self.idxs = np.arange(self.n_samples)\n",
+ " if self.shuffle == True:\n",
+ " np.random.shuffle(self.idxs)"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "# just train model for week 5: FIXME: finally it should be 2 bi-weekly `lead_time`\n",
+ "step = hc_weekly.isel(step=2).step\n",
+ "\n",
+ "step"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 12,
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "# mask\n",
+ "hc_weekly = hc_weekly.where(obs.isel(valid_time=0,drop=True).notnull())"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "## data prep: train, valid, test"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 2,
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "# time is the forecast_reference_time\n",
+ "time_train_start,time_train_end='2000','2017'\n",
+ "time_valid_start,time_valid_end='2018','2019'\n",
+ "time_test = '2020'"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 14,
+ "metadata": {},
+ "outputs": [
+ {
+ "name": "stderr",
+ "output_type": "stream",
+ "text": [
+ "/opt/conda/lib/python3.7/site-packages/dask/array/numpy_compat.py:40: RuntimeWarning: invalid value encountered in true_divide\n",
+ " x = np.divide(x1, x2, out)\n",
+ "/opt/conda/lib/python3.7/site-packages/dask/array/numpy_compat.py:40: RuntimeWarning: invalid value encountered in true_divide\n",
+ " x = np.divide(x1, x2, out)\n",
+ "/opt/conda/lib/python3.7/site-packages/dask/array/numpy_compat.py:40: RuntimeWarning: invalid value encountered in true_divide\n",
+ " x = np.divide(x1, x2, out)\n",
+ "/opt/conda/lib/python3.7/site-packages/dask/array/numpy_compat.py:40: RuntimeWarning: invalid value encountered in true_divide\n",
+ " x = np.divide(x1, x2, out)\n"
+ ]
+ },
+ {
+ "name": "stdout",
+ "output_type": "stream",
+ "text": [
+ "Loading data into RAM\n"
+ ]
+ }
+ ],
+ "source": [
+ "dg_train = DataGenerator(\n",
+ " hc_weekly.isel(number=0).sel(time=slice(time_train_start,time_train_end))[v],\n",
+ " obs.sel(valid_time=hc_weekly.valid_time, method='nearest')[v].sel(time=slice(time_train_start,time_train_end)),\n",
+ " step=step, batch_size=bs, load=True)"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 15,
+ "metadata": {},
+ "outputs": [
+ {
+ "name": "stdout",
+ "output_type": "stream",
+ "text": [
+ "Loading data into RAM\n"
+ ]
+ }
+ ],
+ "source": [
+ "dg_valid = DataGenerator(\n",
+ " hc_weekly.isel(number=0).sel(time=slice(time_valid_start,time_valid_end))[v],\n",
+ " obs.sel(valid_time=hc_weekly.valid_time, method='nearest')[v].sel(time=slice(time_valid_start,time_valid_end)),\n",
+ " step=step, batch_size=bs, mean=dg_train.mean, std=dg_train.std, shuffle=False)"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 16,
+ "metadata": {},
+ "outputs": [
+ {
+ "name": "stdout",
+ "output_type": "stream",
+ "text": [
+ "Loading data into RAM\n"
+ ]
+ }
+ ],
+ "source": [
+ "dg_test = DataGenerator(hc_weekly.isel(number=0).sel(time=time_test)[v],\n",
+ " obs.sel(valid_time=hc_weekly.valid_time, method='nearest')[v].sel(time=time_test),\n",
+ " step, batch_size=bs, mean=dg_train.mean, std=dg_train.std, shuffle=False)"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 17,
+ "metadata": {},
+ "outputs": [
+ {
+ "data": {
+ "text/plain": [
+ "((32, 121, 240), (32, 121, 240))"
+ ]
+ },
+ "execution_count": 17,
+ "metadata": {},
+ "output_type": "execute_result"
+ }
+ ],
+ "source": [
+ "X, y = dg_valid[0]\n",
+ "X.shape, y.shape"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "# short look into training data: large biases\n",
+ "# any problem from normalizing?\n",
+ "i=4\n",
+ "xr.DataArray(np.vstack([X[i],y[i]])).plot(yincrease=False, robust=True)"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "## `fit`"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 19,
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "cnn = keras.models.Sequential([\n",
+ " PeriodicConv2D(filters=32, kernel_size=5, conv_kwargs={'activation':'relu'}, input_shape=(32, 64, 1)),\n",
+ " PeriodicConv2D(filters=1, kernel_size=5)\n",
+ "])"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 21,
+ "metadata": {},
+ "outputs": [
+ {
+ "name": "stdout",
+ "output_type": "stream",
+ "text": [
+ "Model: \"sequential\"\n",
+ "_________________________________________________________________\n",
+ "Layer (type) Output Shape Param # \n",
+ "=================================================================\n",
+ "periodic_conv2d (PeriodicCon (None, 32, 64, 32) 832 \n",
+ "_________________________________________________________________\n",
+ "periodic_conv2d_1 (PeriodicC (None, 32, 64, 1) 801 \n",
+ "=================================================================\n",
+ "Total params: 1,633\n",
+ "Trainable params: 1,633\n",
+ "Non-trainable params: 0\n",
+ "_________________________________________________________________\n"
+ ]
+ }
+ ],
+ "source": [
+ "cnn.summary()"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 22,
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "cnn.compile(keras.optimizers.Adam(1e-4), 'mse')"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 23,
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "import warnings\n",
+ "warnings.simplefilter(\"ignore\")"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 24,
+ "metadata": {},
+ "outputs": [
+ {
+ "name": "stdout",
+ "output_type": "stream",
+ "text": [
+ "30/30 [==============================] - 70s 2s/step - loss: 0.3419 - val_loss: 0.6589\n"
+ ]
+ },
+ {
+ "data": {
+ "text/plain": [
+ "<tensorflow.python.keras.callbacks.History at 0x7f094c44efd0>"
+ ]
+ },
+ "execution_count": 24,
+ "metadata": {},
+ "output_type": "execute_result"
+ }
+ ],
+ "source": [
+ "cnn.fit(dg_train, epochs=1, validation_data=dg_valid)"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "## `predict`"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "def create_predictions(model, dg, step):\n",
+ " \"\"\"Create non-iterative predictions\"\"\"\n",
+ " preds = model.predict(dg).squeeze()\n",
+ " # Unnormalize\n",
+ " preds = preds * dg.std.values + dg.mean.values\n",
+ " da = xr.DataArray(\n",
+ " preds,\n",
+ " dims=['time', 'latitude', 'longitude'],\n",
+ " coords={'time': dg.ds.time, 'latitude': dg.ds.latitude, 'longitude': dg.ds.longitude},\n",
+ " )\n",
+ " da=da.assign_coords(step=step)\n",
+ " return da"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 25,
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "preds = create_predictions(cnn, dg_test, step)"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 26,
+ "metadata": {},
+ "outputs": [
+ {
+ "data": {
+ "text/plain": [
+ "Coordinates:\n",
+ " * time (time) datetime64[ns] 2000-01-02 2000-01-09 ... 2000-12-31\n",
+ " * latitude (latitude) float64 90.0 88.5 87.0 85.5 ... -87.0 -88.5 -90.0\n",
+ " * longitude (longitude) float64 0.0 1.5 3.0 4.5 ... 354.0 355.5 357.0 358.5\n",
+ " surface int64 ...\n",
+ " step timedelta64[ns] 35 days"
+ ]
+ },
+ "execution_count": 26,
+ "metadata": {},
+ "output_type": "execute_result"
+ }
+ ],
+ "source": [
+ "preds.coords"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "### Validate predictions"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 27,
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "obs_test = obs.sel(valid_time=hc_weekly.valid_time, method='nearest')[v].sel(time=time_test)"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "rmse_ML = xs.rmse(preds, obs_test.sel(step=step), dim='time')\n",
+ "rmse_ML.plot(robust=True)\n",
+ "plt.title('RMSE ML predictions 2020')"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "#### predict over all steps"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 31,
+ "metadata": {},
+ "outputs": [
+ {
+ "name": "stdout",
+ "output_type": "stream",
+ "text": [
+ "Loading data into RAM\n",
+ "Loading data into RAM\n",
+ "Loading data into RAM\n",
+ "Loading data into RAM\n"
+ ]
+ }
+ ],
+ "source": [
+ "# this is not useful but results have expected dimensions\n",
+ "# actually train for each step and use all members for training and validation\n",
+ "\n",
+ "preds=[]\n",
+ "for step in hc_weekly.step:\n",
+ " dg_test = DataGenerator(hc_weekly.isel(number=0).sel(time=slice(time_test))[v], obs_test,\n",
+ " step=step, batch_size=bs, mean=dg_train.mean, std=dg_train.std, shuffle=False)\n",
+ " preds.append(create_predictions(cnn, dg_test, step))\n",
+ "preds = xr.concat(preds, 'step')\n",
+ "preds['step']=hc_weekly.step\n",
+ "preds=preds.to_dataset(name=v)"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 32,
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "preds = preds.expand_dims('number').rename({'time':'forecast_reference_time'})"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 33,
+ "metadata": {},
+ "outputs": [
+ {
+ "data": {
+ "text/plain": [
+ "Coordinates:\n",
+ " * forecast_reference_time (forecast_reference_time) datetime64[ns] 2000-01...\n",
+ " * latitude (latitude) float64 90.0 88.5 87.0 ... -88.5 -90.0\n",
+ " * longitude (longitude) float64 0.0 1.5 3.0 ... 357.0 358.5\n",
+ " surface int64 ...\n",
+ " * step (step) timedelta64[ns] 21 days 28 days ... 42 days"
+ ]
+ },
+ "execution_count": 33,
+ "metadata": {},
+ "output_type": "execute_result"
+ }
+ ],
+ "source": [
+ "preds.coords"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "# todo: convert preds to preds_as_terciles"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "metadata": {},
+ "outputs": [],
+ "source": []
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "# Submission"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "preds.sizes # expect: category(3), longitude, latitude, step(2), forecast_time (53)"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "format_bytes(preds.nbytes)"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 36,
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "preds.to_netcdf('submissions/ML_prediction_2020.nc')"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "!git commit -m 'method name'"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "!git tag \"predefined-tag-0.0.1\" # if this is to be checked by scorer\n",
+ "git push --tags"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "metadata": {},
+ "outputs": [],
+ "source": []
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "metadata": {},
+ "outputs": [],
+ "source": []
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "metadata": {},
+ "outputs": [],
+ "source": []
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "metadata": {},
+ "outputs": [],
+ "source": []
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "# Misc"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "## reforecasts for `ML_model`\n",
+ "- required for terciles\n",
+ "- dependent of `lead_time/step`"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 37,
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "# running a reforecast based on training data\n",
+ "# todo: require cnn todo bi-weekly predictions, otherwise average step/lead_time bi-weekly\n",
+ "preds = create_predictions(cnn, dg_train, step)"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 38,
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "quantile_kwargs={'q':[.33,.66], 'skipna':False}"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 39,
+ "metadata": {},
+ "outputs": [
+ {
+ "data": {
+ "text/plain": [
+ "Coordinates:\n",
+ " * latitude (latitude) float64 90.0 88.5 87.0 ... -88.5 -90.0\n",
+ " * longitude (longitude) float64 0.0 1.5 3.0 ... 357.0 358.5\n",
+ " * category_edge (category_edge) float64 0.33 0.66\n",
+ " * forecast_reference_time (forecast_reference_time) int64 1 2 3 ... 51 52 53"
+ ]
+ },
+ "execution_count": 39,
+ "metadata": {},
+ "output_type": "execute_result"
+ }
+ ],
+ "source": [
+ "ML_terciles = preds.groupby('time.weekofyear').quantile(dim=['time'], **quantile_kwargs).rename({'quantile':'category_edge','weekofyear':'forecast_reference_time'}).compute()\n",
+ "ML_terciles.coords"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 40,
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "#ML_terciles.isel(forecast_reference_time=[0,24]).plot(col='category_edge',row='forecast_reference_time')"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 41,
+ "metadata": {},
+ "outputs": [
+ {
+ "data": {
+ "text/plain": [
+ "'24.63 MB'"
+ ]
+ },
+ "execution_count": 41,
+ "metadata": {},
+ "output_type": "execute_result"
+ }
+ ],
+ "source": [
+ "format_bytes(ML_terciles.nbytes) # *2 for variable; *2 for steps"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 42,
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "ML_terciles.to_netcdf('ML_terciles.nc')"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "metadata": {},
+ "outputs": [],
+ "source": []
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "metadata": {},
+ "outputs": [],
+ "source": []
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "metadata": {},
+ "outputs": [],
+ "source": []
+ }
+ ],
+ "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": "3.7.6"
+ },
+ "toc-autonumbering": true
+ },
+ "nbformat": 4,
+ "nbformat_minor": 4
+}
diff --git a/submissions/.gitattributes b/submissions/.gitattributes
new file mode 100644
index 0000000..d77cc4d
--- /dev/null
+++ b/submissions/.gitattributes
@@ -0,0 +1 @@
+“*.nc†filter=lfs diff=lfs merge=lfs -text
--
GitLab