nrt-data 0.0.1__py3-none-any.whl

nrt/data/__init__.py

@@ -0,0 +1,308 @@
+# Copyright (C) 2024 European Union (Joint Research Centre)
+#
+# Licensed under the EUPL, Version 1.2 or - as soon they will be approved by
+# the European Commission - subsequent versions of the EUPL (the "Licence");
+# You may not use this work except in compliance with the Licence.
+# You may obtain a copy of the Licence at:
+#
+#   https://joinup.ec.europa.eu/software/page/eupl
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the Licence is distributed on an "AS IS" basis,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the Licence for the specific language governing permissions and
+# limitations under the Licence.
+
+import os
+import json
+import warnings
+
+import xarray as xr
+import rasterio
+import fiona
+import pooch
+
+# Import for backward compatibility and deprecation warnings
+from .simulate import make_ts as _make_ts
+from .simulate import make_cube_parameters as _make_cube_parameters
+from .simulate import make_cube as _make_cube
+
+
+DATA_DIR = os.path.abspath(os.path.dirname(__file__))
+
+GOODBOY = pooch.create(
+    path=pooch.os_cache("nrt-validate"),
+    base_url="https://jeodpp.jrc.ec.europa.eu/ftp/jrc-opendata/FOREST/NRT/NRT-DATA/VER1-0/",
+    registry={
+        "sentinel2_cube_subset_romania_10m.nc": None,
+        "sentinel2_cube_subset_romania_20m.nc": None,
+        "tree_cover_density_2018_romania.tif": None,
+        "germany_stratification.tif": None,
+        "germany_sample_points.fgb": None
+    }
+)
+
+
+def _load(f, return_meta=False, **kwargs):
+    """Load a file using Pooch
+
+    Args:
+        f (str): File basename
+        return_meta (bool): If True, return metadata along with the
+            array (for .tif and .fgb files). Default is False.
+        **kwargs: Keyword arguments for xarray when loading nc files
+
+    Returns:
+        Dataset, array, dictionary, or tuple depending on the file
+        type and options.
+    """
+    file_path = GOODBOY.fetch(f)
+    if f.endswith('.nc'):
+        return xr.open_dataset(file_path, **kwargs)
+    elif f.endswith('.tif'):
+        with rasterio.open(file_path) as src:
+            array = src.read(1)
+            if return_meta:
+                meta = src.meta
+                return array, meta
+            return array
+    elif f.endswith('.fgb'):
+        with fiona.open(file_path) as src:
+            data = list(src)  # Read all features into a list
+            if return_meta:
+                meta = src.meta
+                return data, meta
+            return data
+
+
+def romania_10m(**kwargs):
+    """Sentinel 2 datacube of a small forested area in Romania at 10 m resolution
+
+    Examples:
+        >>> from nrt import data
+
+        >>> s2_cube = data.romania_10m()
+        >>> # Compute NDVI
+        >>> s2_cube['ndvi'] = (s2_cube.B8 - s2_cube.B4) / (s2_cube.B8 + s2_cube.B4)
+        >>> # Filter clouds
+        >>> s2_cube = s2_cube.where(s2_cube.SCL.isin([4,5,7]))
+    """
+    return _load('sentinel2_cube_subset_romania_10m.nc', **kwargs)
+
+
+def romania_20m(**kwargs):
+    """Sentinel 2 datacube of a small forested area in Romania at 20 m resolution
+
+    Examples:
+        >>> from nrt import data
+
+        >>> s2_cube = data.romania_20m()
+        >>> # Compute NDVI
+        >>> s2_cube['ndvi'] = (s2_cube.B8A - s2_cube.B4) / (s2_cube.B8A + s2_cube.B4)
+        >>> # Filter clouds
+        >>> s2_cube = s2_cube.where(s2_cube.SCL.isin([4,5,7]))
+    """
+    return _load('sentinel2_cube_subset_romania_20m.nc', **kwargs)
+
+
+def germany_zarr(**kwargs):
+    """Sentinel 2 datacube of a forest area affected by Bark Beetle in Germany
+
+    The data covers an area of 400 km\ :sup:`2` located East of the city Cologne
+    in the North Rhine-Westphalia state of Germany. It spans a five year period
+    from 2018 to 2022 and includes the sentinel bands B02, B03, B04, B08, B11,
+    B12 and SCL. Native 10m resolution is preserved for the visible and near-infrared
+    bands while B11, B12 and SCL were resampled to 10m from their original 20m resolution.
+    The data is organized as an online zarr store on the JRC's Open Data Repository,
+    so that running the ``germany_zarr()`` function only creates a symbolic representation
+    of the dataset (dask based). Lazy chunks can be eagerly loaded by invoking the
+    ``.compute()`` method. Beware that loading the entire dataset may take a fairly
+    long time due to its size (4.8 GB).
+    Note that although data is stored as int16, the scaling factor is automatically
+    applied to convert spectral channels to unscaled surface reflectance values
+    and the corresponding data variables are casted to float64. No data pixels are
+    also automatically converted to ``np.nan``
+
+    Args:
+        **kwargs: Additional keyword arguments passed to ``xarray.open_zarr()``
+
+    Examples:
+        >>> import sys
+        >>> from nrt import data
+        >>> ds = data.germany_zarr()
+        >>> print(ds)
+        <xarray.Dataset>
+        Dimensions:      (time: 172, y: 2000, x: 2000)
+        Coordinates:
+            spatial_ref  int32 ...
+          * time         (time) datetime64[ns] 2018-02-14T10:31:31.026000 ... 2022-12...
+          * x            (x) float64 4.133e+06 4.133e+06 ... 4.153e+06 4.153e+06
+          * y            (y) float64 3.113e+06 3.113e+06 ... 3.093e+06 3.093e+06
+        Data variables:
+            B02          (time, y, x) float32 dask.array<chunksize=(10, 100, 100), meta=np.ndarray>
+            B03          (time, y, x) float32 dask.array<chunksize=(10, 100, 100), meta=np.ndarray>
+            B04          (time, y, x) float32 dask.array<chunksize=(10, 100, 100), meta=np.ndarray>
+            B08          (time, y, x) float32 dask.array<chunksize=(10, 100, 100), meta=np.ndarray>
+            B11          (time, y, x) float32 dask.array<chunksize=(10, 100, 100), meta=np.ndarray>
+            B12          (time, y, x) float32 dask.array<chunksize=(10, 100, 100), meta=np.ndarray>
+            SCL          (time, y, x) uint8 dask.array<chunksize=(10, 100, 100), meta=np.ndarray>
+        >>> # Load a subset in memory
+        >>> print(sys.getsizeof(ds.B02.data))
+        80
+        >>> ds_sub = ds.isel(x=slice(100,110), y=slice(200,210), time=slice(10,20)).compute()
+        >>> print(sys.getsizeof(ds_sub.B02.data))
+        2144
+
+    Returns:
+        xarray.Dataset: A dask based Dataset of dimension ``(time: 172, y: 2000, x: 2000)``
+        with 7 data variables.
+    """
+    ds = xr.open_zarr('https://jeodpp.jrc.ec.europa.eu/ftp/jrc-opendata/FOREST/NRT/NRT-DATA/VER1-0/germany.zarr',
+                      **kwargs)
+    return ds
+
+
+def germany_stratification(return_meta=False):
+    """Simple rule based classification of forest dynamics for germany_zarr
+
+    Raster layer in the EPSG:3035 CRS, spatially aligned with the
+    ``germany_zarr`` data cube. The classification is based on a simple
+    rule-based approach applied to a pair of manually selected cloud-free time
+    steps (2019-06-27 and 2022-06-16). NDVI and the second SWIR band are used to
+    distinguish various tree cover dynamics, based on the assumption that healthy
+    forests are generally green in summer (indicated by high NDVI values) and dark
+    in the SWIR region. "Unhealthy" forests, such as standing dead trees following
+    a bark beetle attack, may still be dark in the SWIR region but with lower
+    greenness. Non-forested land lacks these combined characteristics.
+
+    Note that this approach is relatively simple and, as a result, produces an
+    imperfect classification. Although there may be some confusion between land 
+    cover elements that are difficult to discriminate solely based on NDVI and
+    SWIR values, the layer is well-suited for purposes such as stratification in a
+    stratified sampling design.
+
+    Classes are encoded as follows::
+
+        1: Non-forested land
+        2: Stable Forest (Constantly green and dark in the SWIR region)
+        3: Forest Cover Loss (Conversion from healthy forest to non-forested land)
+        4: Forest Canopy Dieback (Loss of greenness but still dark in SWIR)
+        5: Salvage Logging (From 'unhealthy' forest to non-forested land)
+
+    Returns:
+        numpy.ndarray or (numpy.ndarray, dict): 2D array with encoded 2019-2022
+        tree cover dynamics or (data, metadata) if ``return_meta`` is True.
+    """
+    return _load('germany_stratification.tif', return_meta=return_meta)
+
+
+def germany_sample_points(return_meta=False):
+    """Feature collection of 300 sample points from the Germany test area.
+
+    These points represent pixel centers sampled using a reclassified version
+    of the ``germany_stratification`` layer. In this reclassification, all
+    disturbance strata were combined into a single stratum, resulting in
+    stratified random sampling. An equal allocation method was employed,
+    with 100 samples per stratum.
+
+    The feature collection includes a ``stratum`` property with values 1, 2,
+    or 3, representing different strata:
+
+        - 1: Non-forested stratum (2,333,767 pixels)
+        - 2: Stable forest stratum (972,184 pixels)
+        - 3: Disturbed forest stratum (694,049 pixels)
+
+    Args:
+        return_meta (bool, optional): If True, returns both the feature collection
+            and associated metadata. Defaults to False.
+
+    Examples:
+        >>> from nrt import data
+        >>> fc = data.germany_sample_points()
+        >>> set([feat['properties']['stratum'] for feat in fc])
+        {1,2,3}
+        >>> len(fc)
+        300
+
+    Returns:
+        list or tuple: If `return_meta` is False, returns a list containing the 
+        feature collection of sample points. If `return_meta` is True, returns
+        a tuple of (feature collection, metadata).
+    """
+    return _load('germany_sample_points.fgb', return_meta=return_meta)
+
+
+def romania_forest_cover_percentage(return_meta=False):
+    """Subset of Copernicus HR layer tree cover percentage - 20 m - Romania
+
+    Returns:
+        numpy.ndarray or (numpy.ndarray, dict): The data or (data, metadata)
+        if ``return_meta`` is True.
+    """
+    return _load('tree_cover_density_2018_romania.tif', return_meta=return_meta)
+
+
+def mre_crit_table():
+    """Contains a dictionary equivalent to strucchange's ``mreCritValTable``
+    The key 'sig_level' is a list of the available pre-computed significance
+    (1-alpha) values.
+
+    The other keys contain nested dictionaries, where the keys are the
+    available relative window sizes (0.25, 0.5, 1), the second keys are the
+    available periods (2, 4, 6, 8, 10) and the third keys are the functional
+    types ("max", "range").
+
+    Example:
+        >>> from nrt import data
+        >>> crit_table = data.mre_crit_table()
+        >>> win_size = 0.5
+        >>> period = 10
+        >>> functional = "max"
+        >>> alpha=0.025
+        >>> crit_values = crit_table.get(str(win_size))\
+                                    .get(str(period))\
+                                    .get(functional)
+        >>> sig_level = crit_table.get('sig_levels')
+        >>> crit_level = np.interp(1-alpha, sig_level, crit_values)
+    """
+    with open(os.path.join(DATA_DIR, "mreCritValTable.json")) as crit:
+        crit_table = json.load(crit)
+    return crit_table
+
+
+def make_ts(*args, **kwargs):
+    warnings.warn(
+        "The function 'make_ts' has been moved to 'nrt.data.simulate'. "
+        "Please update your imports to 'from nrt.data.simulate import make_ts'. "
+        "This import path will be deprecated in future versions.",
+        DeprecationWarning,
+        stacklevel=2
+    )
+    return _make_ts(*args, **kwargs)
+
+
+def make_cube_parameters(*args, **kwargs):
+    warnings.warn(
+        "The function 'make_cube_parameters' has been moved to 'nrt.data.simulate'. "
+        "Please update your imports to 'from nrt.data.simulate import make_cube_parameters'. "
+        "This import path will be deprecated in future versions.",
+        DeprecationWarning,
+        stacklevel=2
+    )
+    return _make_cube_parameters(*args, **kwargs)
+
+
+def make_cube(*args, **kwargs):
+    warnings.warn(
+        "The function 'make_cube' has been moved to 'nrt.data.simulate'. "
+        "Please update your imports to 'from nrt.data.simulate import make_cube'. "
+        "This import path will be deprecated in future versions.",
+        DeprecationWarning,
+        stacklevel=2
+    )
+    return _make_cube(*args, **kwargs)
+
+
+if __name__ == "__main__":
+    import doctest
+    doctest.testmod()

nrt/data/mreCritValTable.json

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nrt/data/simulate.py

@@ -0,0 +1,274 @@
+# Copyright (C) 2024 European Union (Joint Research Centre)
+#
+# Licensed under the EUPL, Version 1.2 or - as soon they will be approved by
+# the European Commission - subsequent versions of the EUPL (the "Licence");
+# You may not use this work except in compliance with the Licence.
+# You may obtain a copy of the Licence at:
+#
+#   https://joinup.ec.europa.eu/software/page/eupl
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the Licence is distributed on an "AS IS" basis,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the Licence for the specific language governing permissions and
+# limitations under the Licence.
+
+import numpy as np
+import xarray as xr
+
+
+def make_ts(dates, break_idx=-1, intercept=0.7, amplitude=0.15, magnitude=0.25,
+            recovery_time=1095, sigma_noise=0.02, n_outlier=3,
+            outlier_value=-0.1, n_nan=3):
+    """Simulate a harmonic time-series with optional breakpoint, noise and outliers
+
+    The time-series is generated by adding;
+    - an intercept/trend component which varies depending on the phase of the time-series
+    (stable, recovery)
+    - An annual seasonal component
+    - Random noise drawn from a normal distribution (white noise)
+    Optional outliers are then added to randomly chosen observation as well as ``np.Nan`` values.
+    Note that the seasonal cycles simulation approach used here is rather simplistic,
+    using a sinusoidal model and therefore assuming symetrical and regular behaviour
+    around the peak of the simulated variable. Actual vegetation signal is often more
+    asymetrical and irregular.
+
+    Args:
+        dates (array-like): List or array of dates (numpy.datetime64)
+        break_idx (int): Breakpoint index in the date array provided. Defaults to
+            ``-1``, corresponding to a stable time-series
+        intercept (float): Intercept of the time-series
+        amplitude (float): Amplitude of the harmonic model (note that at every point
+            of the time-series, the actual model amplitude is multiplied by the intercept
+        magnitude (float): Break magnitude (always a drop in y value)
+        recovery_time (int): Time (in days) to recover the initial intersect value
+            following a break
+        sigma_noise (float): Sigma value of the normal distribution (mean = 0) from which
+            noise values are drawn
+        n_outlier (int): Number of outliers randomly assigned to observations of the
+            time-series
+        outlier_value (float): Value to assign to outliers
+        n_nan (int): Number of ``np.nan`` (no data) assigned to observations of the
+            time-series
+
+    Example:
+        >>> from nrt.data import simulate
+        >>> import numpy as np
+        >>> import matplotlib.pyplot as plt
+
+        >>> dates = np.arange('2018-01-01', '2022-06-15', dtype='datetime64[W]')
+        >>> ts = simulate.make_ts(dates=dates, break_idx=30)
+
+        >>> plt.plot(dates, ts)
+        >>> plt.show()
+
+    Returns:
+        np.ndarray: Array of simulated values of same size as ``dates``
+    """
+    dates = dates.astype('datetime64[D]')
+    timestamps = dates.astype(int)
+    ydays = (dates - dates.astype('datetime64[Y]')).astype(int) + 1
+    y = np.empty_like(dates, dtype=np.float64)
+    # Intercept array
+    y[:] = intercept
+    # Build trend segment if break
+    if break_idx != -1:
+        # Segment bounds
+        segment_start_y = intercept - magnitude
+        segment_start_timestamp = timestamps[break_idx]
+        segment_end_timestamp = segment_start_timestamp + recovery_time
+        segment_end_idx = np.abs(segment_end_timestamp - timestamps).argmin()
+        # Compute y values
+        recovery_rate = magnitude / recovery_time
+        days_since_break = timestamps - segment_start_timestamp
+        trend_segment = (recovery_rate * days_since_break + segment_start_y)[break_idx + 1:segment_end_idx + 1]
+        # include into y
+        y[break_idx + 1:segment_end_idx + 1] = trend_segment
+    # Seasonality
+    amplitude_values = amplitude * y
+    season = amplitude * np.sin(2 * np.pi * timestamps / 365.25 - 2)
+    # noise and outliers
+    noise = np.random.normal(0, sigma_noise, dates.size)
+    # Combine the 3 (trend, season, noise) components
+    ts = y + season + noise
+    # Add optional outliers and Nans
+    outliers_idx = np.random.choice(np.arange(0, dates.size), size=n_outlier, replace=False)
+    nan_idx = np.random.choice(np.arange(0, dates.size), size=n_nan)
+    ts[outliers_idx] = outlier_value
+    ts[nan_idx] = np.nan
+    return ts
+
+
+def make_cube_parameters(shape=(100,100),
+                         break_idx_interval=(0,100),
+                         intercept_interval=(0.6, 0.8),
+                         amplitude_interval=(0.12, 0.2),
+                         magnitude_interval=(0.2, 0.3),
+                         recovery_time_interval=(800,1400),
+                         sigma_noise_interval=(0.02, 0.04),
+                         n_outliers_interval=(0,5),
+                         n_nan_interval=(0,5),
+                         unstable_proportion=0.5):
+    """Create ``xarray.Dataset`` of paramters for generation of synthetic data cube
+
+    Prepares the main input required by the the ``make_cube`` function. This
+    intermediary step eases the creation of multiple synthetic DataArrays sharing
+    similar characteristics (e.g. to simulate multispectral data)
+
+    Args:
+        shape (tuple): A size two integer tuple giving the x,y size of the Dataset to be
+            generated
+        break_idx_interval (tuple): A tuple of two integers indicating the interval
+            from which the breakpoint position in the time-series is drawn. Generate
+            array of random values passed to the ``break_idx` argument of ``make_ts``.
+            Similarly to python ranges, upper bound value is excluded from the resulting
+            array. To produce a zero filled array ``(0,1)`` can therefore be used
+            TODO: add a default to allow breakpoint at any location (conflict with Nan that indicate no break)
+        intercept_interval (tuple): A tuple of two floats providing the interval
+            from which intercept is drawn. Generate array of random values passed
+            to the ``intercept`` argument of ``make_ts``
+        amplitude_interval (tuple): A tuple of two floats indicating the interval
+            from which the seasonal amplitude parameter is drawn. Generate array
+            of random values passed to the ``amplitude`` argument of ``make_ts``
+        magnitude_interval (tuple): A tuple of two floats indicating the interval
+            from which the breakpoint magnitude parameter is drawn. Generate array
+            of random values passed to the ``magnitude`` argument of ``make_ts``
+        recovery_time_interval (tuple): A tuple of two integers indicating the interval
+            from which the recovery time parameter (in days) is drawn. Generate array
+            of random values passed to the ``recovery_time` argument of ``make_ts``
+        sigma_noise_interval (tuple): A tuple of two floats indicating the interval
+            from which the white noise level is drawn. Generate array of random
+            values passed to the ``sigma_noise` argument of ``make_ts``
+        n_outliers_interval (tuple): A tuple of two integers indicating the interval
+            from which the number of outliers is drawn. Generate array
+            of random values passed to the ``n_outliers` argument of ``make_ts``
+        n_nan_interval (tuple): A tuple of two integers indicating the interval
+            from which the number of no-data observations is drawn. Generate array
+            of random values passed to the ``n_nan` argument of ``make_ts``
+        unstable_proportion (float): Proportion of time-series containing a breakpoint.
+            The other time-series are stable.
+
+    Returns:
+        xarray.Dataset: Dataset with arrays of parameters required for the generation
+            of synthetic time-series using the spatialized version of ``make_ts``
+            (see ``make_cube``)
+
+    Examples:
+        >>> import time
+        >>> import numpy as np
+        >>> import xarray as xr
+        >>> from nrt.data import simulate
+        >>> import matplotlib.pyplot as plt
+        >>> params_nir = simulate.make_cube_parameters(shape=(20,20),
+        ...                                            n_outliers_interval=(0,1),
+        ...                                            n_nan_interval=(0,1),
+        ...                                            break_idx_interval=(50,100))
+        >>> params_red = params_nir.copy(deep=True)
+        >>> # create parameters for red, green, blue cubes by slightly adjusting intercept,
+        >>> # magnitude and amplitude parameters
+        >>> params_red['intercept'].data = np.random.uniform(0.09, 0.12, size=(20,20))
+        >>> params_red['magnitude'].data = np.random.uniform(-0.1, -0.03, size=(20,20))
+        >>> params_red['amplitude'].data = np.random.uniform(0.03, 0.07, size=(20,20))
+        >>> params_green = params_nir.copy(deep=True)
+        >>> params_green['intercept'].data = np.random.uniform(0.12, 0.20, size=(20,20))
+        >>> params_green['magnitude'].data = np.random.uniform(0.05, 0.1, size=(20,20))
+        >>> params_green['amplitude'].data = np.random.uniform(0.05, 0.08, size=(20,20))
+        >>> params_blue = params_nir.copy(deep=True)
+        >>> params_blue['intercept'].data = np.random.uniform(0.08, 0.13, size=(20,20))
+        >>> params_blue['magnitude'].data = np.random.uniform(-0.01, 0.01, size=(20,20))
+        >>> params_blue['amplitude'].data = np.random.uniform(0.02, 0.04, size=(20,20))
+        >>> dates = np.arange('2018-01-01', '2022-06-15', dtype='datetime64[W]')
+        >>> # Create cubes (DataArrays) and merge them into a sligle Dataset
+        >>> nir = data.make_cube(dates, name='nir', params_ds=params_nir)
+        >>> red = data.make_cube(dates, name='red', params_ds=params_red)
+        >>> green = data.make_cube(dates, name='green', params_ds=params_green)
+        >>> blue = data.make_cube(dates, name='blue', params_ds=params_blue)
+        >>> cube = xr.merge([blue, green, red, nir]).to_array()
+        >>> # PLot one ts
+        >>> cube.isel(x=5, y=5).plot(row='variable')
+        >>> plt.show()
+    """
+    intercept = np.random.uniform(*intercept_interval, size=shape)
+    amplitude = np.random.uniform(*amplitude_interval, size=shape)
+    magnitude = np.random.uniform(*magnitude_interval, size=shape)
+    recovery_time = np.random.randint(*recovery_time_interval, size=shape)
+    sigma_noise = np.random.uniform(*sigma_noise_interval, size=shape)
+    n_outlier = np.random.randint(*n_outliers_interval, size=shape)
+    n_nan = np.random.randint(*n_nan_interval, size=shape)
+    break_idx = np.random.randint(*break_idx_interval, size=shape)
+    # Make a proportion of these cells stable
+    size = np.multiply(*shape)
+    stable_size = size - round(unstable_proportion * size)
+    break_idx.ravel()[np.random.choice(size, stable_size, replace=False)] = -1
+    # Build Dataset of parameters
+    params = xr.Dataset(data_vars={'intercept': (['y', 'x'], intercept),
+                                   'amplitude': (['y', 'x'], amplitude),
+                                   'magnitude': (['y', 'x'], magnitude),
+                                   'recovery_time': (['y', 'x'], recovery_time),
+                                   'sigma_noise': (['y', 'x'], sigma_noise),
+                                   'n_outlier': (['y', 'x'], n_outlier),
+                                   'n_nan': (['y', 'x'], n_nan),
+                                   'break_idx': (['y', 'x'], break_idx)},
+                        coords={'y': np.arange(shape[0]),
+                                'x': np.arange(shape[1])})
+    return params
+
+
+def make_cube(dates, params_ds, outlier_value=0.1, name='ndvi'):
+    """Generate a cube of synthetic time-series
+
+    See ``make_ts`` for more details on how every single time-series is generated
+
+    Args:
+        dates (array-like): List or array of dates (numpy.datetime64)
+        params_ds (xarray.Dataset): Dataset containing arrays of time-series generation
+            parameters. See ``make_cube_parameters`` for a helper to generate such Dataset.
+            Spatial dimensions of the params_ds Dataset are used for the generated cube
+        outlier_value (float): Value to assign to outliers
+        name (str): Name of the generated variable in the DataArray
+
+    Return:
+        xarray.DataArray: Cube of synthetic time-series generated using the paramters
+            provided via ``param_ds`` Dataset.
+
+    Example:
+        >>> import time
+        >>> import numpy as np
+        >>> from nrt.data import simulate
+        >>> import matplotlib.pyplot as plt
+        >>> dates = np.arange('2018-01-01', '2022-06-15', dtype='datetime64[W]')
+        >>> params_ds = simulate.make_cube_parameters(shape=(100,100),
+        ...                                           n_outliers_interval=(0,5),
+        ...                                           n_nan_interval=(0,7),
+        ...                                           break_idx_interval=(100,dates.size - 20))
+        >>> cube = simulate.make_cube(dates=dates, params_ds=params_ds)
+        >>> # PLot one ts
+        >>> cube.isel(x=5, y=5).plot()
+        >>> plt.show()
+    """
+    nrows, ncols = params_ds.intercept.data.shape
+    # Vectorize function
+    make_ts_v = np.vectorize(make_ts, signature='(n),(),(),(),(),(),(),(),(),()->(n)')
+    # Create output array
+    out = make_ts_v(dates=dates,
+                    break_idx=params_ds.break_idx.data,
+                    intercept=params_ds.intercept.data,
+                    amplitude=params_ds.amplitude.data,
+                    magnitude=params_ds.magnitude.data,
+                    recovery_time=params_ds.recovery_time.data,
+                    sigma_noise=params_ds.sigma_noise.data,
+                    n_outlier=params_ds.n_outlier.data,
+                    outlier_value=outlier_value,
+                    n_nan=params_ds.n_nan.data)
+    # Build xarray dataset
+    xr_cube = xr.DataArray(data=np.moveaxis(out, -1, 0),
+                           coords={'time': dates,
+                                   'y': np.arange(nrows),
+                                   'x': np.arange(ncols)},
+                          name=name)
+    return xr_cube
+
+if __name__ == "__main__":
+    import doctest
+    doctest.testmod()
+

nrt_data-0.0.1.dist-info/LICENSE

@@ -0,0 +1,287 @@
+                      EUROPEAN UNION PUBLIC LICENCE v. 1.2
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+Appendix
+
+‘Compatible Licences’ according to Article 5 EUPL are:
+
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+All other changes or additions to this Appendix require the production of a new
+EUPL version.

nrt_data-0.0.1.dist-info/METADATA

@@ -0,0 +1,356 @@
+Metadata-Version: 2.1
+Name: nrt-data
+Version: 0.0.1
+Summary: nrt namespace package giving access to demo and test datasets, extracted from nrt core
+Author: Jonas Viehweger, Kenji Ose
+Author-email: Loic Dutrieux <loic.dutrieux@ec.europa.eu>
+Maintainer-email: Loic Dutrieux <loic.dutrieux@ec.europa.eu>
+License: EUROPEAN UNION PUBLIC LICENCE v. 1.2
+                              EUPL © the European Union 2007, 2016
+        
+        This European Union Public Licence (the ‘EUPL’) applies to the Work (as defined
+        below) which is provided under the terms of this Licence. Any use of the Work,
+        other than as authorised under this Licence is prohibited (to the extent such
+        use is covered by a right of the copyright holder of the Work).
+        
+        The Work is provided under the terms of this Licence when the Licensor (as
+        defined below) has placed the following notice immediately following the
+        copyright notice for the Work:
+        
+                Licensed under the EUPL
+        
+        or has expressed by any other means his willingness to license under the EUPL.
+        
+        1. Definitions
+        
+        In this Licence, the following terms have the following meaning:
+        
+        - ‘The Licence’: this Licence.
+        
+        - ‘The Original Work’: the work or software distributed or communicated by the
+          Licensor under this Licence, available as Source Code and also as Executable
+          Code as the case may be.
+        
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+          Licensee, based upon the Original Work or modifications thereof. This Licence
+          does not define the extent of modification or dependence on the Original Work
+          required in order to classify a work as a Derivative Work; this extent is
+          determined by copyright law applicable in the country mentioned in Article 15.
+        
+        - ‘The Work’: the Original Work or its Derivative Works.
+        
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+          convenient for people to study and modify.
+        
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+          available, online or offline, copies of the Work or providing access to its
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+        
+        2. Scope of the rights granted by the Licence
+        
+        The Licensor hereby grants You a worldwide, royalty-free, non-exclusive,
+        sublicensable licence to do the following, for the duration of copyright vested
+        in the Original Work:
+        
+        - use the Work in any circumstance and for all usage,
+        - reproduce the Work,
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+        the Source Code is easily and freely accessible for as long as the Licensor
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+        
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+        disclaimer of warranties. The Licensee must include a copy of such notices and a
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+        unless the Original Work is expressly distributed only under this version of the
+        Licence — for example by communicating ‘EUPL v. 1.2 only’. The Licensee
+        (becoming Licensor) cannot offer or impose any additional terms or conditions on
+        the Work or Derivative Work that alter or restrict the terms of the Licence.
+        
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+        Works or copies thereof based upon both the Work and another work licensed under
+        a Compatible Licence, this Distribution or Communication can be done under the
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+        
+        13. Miscellaneous
+        
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+        
+        - this licence shall be governed by Belgian law if the Licensor has no seat,
+          residence or registered office inside a European Union Member State.
+        
+        Appendix
+        
+        ‘Compatible Licences’ according to Article 5 EUPL are:
+        
+        - GNU General Public License (GPL) v. 2, v. 3
+        - GNU Affero General Public License (AGPL) v. 3
+        - Open Software License (OSL) v. 2.1, v. 3.0
+        - Eclipse Public License (EPL) v. 1.0
+        - CeCILL v. 2.0, v. 2.1
+        - Mozilla Public Licence (MPL) v. 2
+        - GNU Lesser General Public Licence (LGPL) v. 2.1, v. 3
+        - Creative Commons Attribution-ShareAlike v. 3.0 Unported (CC BY-SA 3.0) for
+          works other than software
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+        - Québec Free and Open-Source Licence — Reciprocity (LiLiQ-R) or Strong
+          Reciprocity (LiLiQ-R+).
+        
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+        licences without producing a new version of the EUPL, as long as they provide
+        the rights granted in Article 2 of this Licence and protect the covered Source
+        Code from exclusive appropriation.
+        
+        All other changes or additions to this Appendix require the production of a new
+        EUPL version.
+        
+Project-URL: homepage, https://code.europa.eu/jrc-forest/nrt-data
+Keywords: sentinel2,xarray,zarr,netcdf
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.9
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Requires-Python: >=3.9
+Description-Content-Type: text/x-rst
+License-File: LICENSE
+Requires-Dist: numpy
+Requires-Dist: xarray
+Requires-Dist: rasterio
+Requires-Dist: fiona
+Requires-Dist: rioxarray
+Requires-Dist: netCDF4
+Requires-Dist: zarr
+Requires-Dist: aiohttp
+Requires-Dist: fsspec
+Requires-Dist: pooch
+Provides-Extra: docs
+Requires-Dist: sphinx; extra == "docs"
+Requires-Dist: sphinx-rtd-theme; extra == "docs"
+
+********
+nrt-data
+********
+
+**nrt-data** is a companion package to `nrt <https://github.com/ec-jrc/nrt>`_, designed for near real-time monitoring of satellite image time series. It provides easy access to curated datasets for testing and demonstrating **nrt**'s capabilities.
+
+As of ``nrt==0.2.1``, the ``data`` module has been separated from the core package to simplify maintenance and keep the core **nrt** lightweight. This package is distributed as a namespace package, ensuring backward compatibility with previous versions.
+
+For more details, see the full documentation at `nrt-data.readthedocs.io <https://nrt-data.readthedocs.io/>`_.
+
+Features
+========
+
+- Access to small-sized test data in NetCDF format and associated reference data in FlatGeoBuf, managed via `Pooch <https://www.fatiando.org/pooch/latest/>`_.
+- Streaming access to larger datasets stored as cloud-optimized Zarr stores.
+- Synthetic data simulation functionalities.
+
+Installation
+============
+
+To install **nrt-data**, run:
+
+.. code-block:: bash
+
+    pip install nrt-data
+
+Please note that **nrt-data** can be installed independently of **nrt** but is incompatible with ``nrt<=0.2.1``. To check your current **nrt** version, run:
+
+.. code-block:: bash
+
+    pip freeze | grep nrt
+
+If necessary, update **nrt** by running:
+
+.. code-block:: bash
+
+    pip install -U nrt
+

nrt_data-0.0.1.dist-info/RECORD

@@ -0,0 +1,8 @@
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+nrt_data-0.0.1.dist-info/LICENSE,sha256=b8nnCcy_4Nd_v_okJ6mDKCvi64jkexzbSfIag7TR5mU,13827
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+nrt_data-0.0.1.dist-info/RECORD,,

nrt_data-0.0.1.dist-info/WHEEL

@@ -0,0 +1,5 @@
+Wheel-Version: 1.0
+Generator: setuptools (74.0.0)
+Root-Is-Purelib: true
+Tag: py3-none-any
+

nrt_data-0.0.1.dist-info/top_level.txt

@@ -0,0 +1 @@
+nrt