first commit

LICENSE

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+The MIT License (MIT)
+
+Copyright (c) 2020 Steven Hill
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

README.rst

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+phenocube
+=========
+
+phenocube is an python package providing a wide range of tools for working with the phenocube environment
+
+Usage
+-----
+
+Installation
+------------
+
+Requirements
+^^^^^^^^^^^^
+
+Compatibility
+-------------
+
+Licence
+-------
+
+Authors
+-------
+
+`phenocube` was written by `Steven Hill <[email protected]>`_.

phenocube/__init__.py

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+"""phenocube - phenocube is an python package providing a wide range of tools for working with the phenocube environment"""
+
+__version__ = '0.1.0'
+__author__ = 'Steven Hill <[email protected]>'
+__all__ = []

phenocube/spectralindices.py

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+def spectralindices(dataset, indices = ['NDVI'], norm = True, drop = False):
+
+    """Calculate a suite of spectral indices
+
+    Description
+    ----------
+    Takes an xarray dataset containing spectral bands, calculates one or more
+    spectral indices and adds the resulting array as a new variable in the original dataset.
+
+     Indices:
+        - EVI: Enhanced Vegetation Index (Huete 2002)
+        - LAI: Leaf Area Index (Boegh 2002)
+        - MNDWI: Modified Normalised Difference Water Index (Xu 1996)
+        - MSAVI: Modified Soil Adjusted Vegetation Index (Qi et al. 1994)
+        - NBR: Normalised Burn Ratio (Lopez Garcia 1991)
+        - NDVI: Normalised Difference Vegetation Index (Rouse 1973)
+        - NDWI: Normalised Difference Water Index (McFeeters 1996)
+        - SAVI: Soil Adjusted Vegetation Index (Huete 1988)
+
+
+    Parameters
+    ----------
+    dataset : xarray.Dataset
+        A two-dimensional or multi-dimensional array containing the spectral bands required to calculate the index.
+    indices : str or list of strs
+       A string or a list of strings giving the names of the indices to calculate
+    norm : bool, optional
+        If norm = True values are scaled to 0.0-1.0 by dividing by 10000.0
+    drop : bool, optional
+        If drop = True only the index will be returned and the other bands will be dropped
+
+    Returns
+    -------
+    dataset : xarray Dataset
+        The original xarray Dataset containing the calculated spectral indices as a DataArray.
+    """
+
+    index_dict = {
+        'NDVI': lambda dataset: (dataset.nir - dataset.red) / (dataset.nir + dataset.red),
+        'EVI': lambda dataset: ((2.5 * (dataset.nir - dataset.red)) / (dataset.nir + 6 * dataset.red - 7.5 * dataset.blue + 1)),
+        'LAI': lambda dataset: (3.618 * ((2.5 * (dataset.nir - dataset.red)) / (dataset.nir + 6 * dataset.red -7.5 * dataset.blue + 1)) - 0.118),
+        'SAVI': lambda dataset: ((1.5 * (dataset.nir - dataset.red)) / (dataset.nir + dataset.red + 0.5)),
+        'MSAVI': lambda dataset: ((2 * dataset.nir + 1 -((2 * dataset.nir + 1)**2 - 8 * (dataset.nir - dataset.red))**0.5) / 2),
+        'NBR': lambda dataset: (dataset.nir - dataset.swir2) / (dataset.nir + dataset.swir2),
+        'NDWI': lambda dataset: (dataset.green - dataset.nir) / (dataset.green + dataset.nir),
+        'MNDWI': lambda dataset: (dataset.green - dataset.swir1) / (dataset.green + dataset.swir1)
+
+    }
+
+    if drop:
+        drop_bands = list(dataset.data_vars)
+
+    for index in indices:
+        if index not in index_dict:
+            raise ValueError(f"{index} is not a valid index")
+        func = index_dict.get(str(index))
+        try:
+            if norm:
+                index_new = func(dataset / 10000.0)
+            else:
+                index_new = func(dataset / 1.0)
+        except AttributeError:
+            raise ValueError('Missing bands: The data set does not seem to contain all bands needed to calculate this index')
+
+        dataset[index] = index_new
+
+    if drop:
+        dataset = dataset.drop(drop_bands)
+
+    return(dataset)

setup.py

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+import io
+import os
+import re
+
+from setuptools import find_packages
+from setuptools import setup
+
+
+def read(filename):
+    filename = os.path.join(os.path.dirname(__file__), filename)
+    text_type = type(u"")
+    with io.open(filename, mode="r", encoding='utf-8') as fd:
+        return re.sub(text_type(r':[a-z]+:`~?(.*?)`'), text_type(r'``\1``'), fd.read())
+
+
+setup(
+    name="phenocube",
+    version="0.1.0",
+    url="https://github.com/phenocube/phenocube-py",
+    license='MIT',
+
+    author="Steven Hill",
+    author_email="[email protected]",
+
+    description="phenocube is an python package providing a wide range of tools for working with the phenocube environment",
+    long_description=read("README.rst"),
+
+    packages=find_packages(exclude=('tests',)),
+
+    install_requires=[],
+
+    classifiers=[
+        'Development Status :: 2 - Pre-Alpha',
+        'License :: OSI Approved :: MIT License',
+        'Programming Language :: Python',
+        'Programming Language :: Python :: 2',
+        'Programming Language :: Python :: 2.7',
+        'Programming Language :: Python :: 3',
+        'Programming Language :: Python :: 3.4',
+        'Programming Language :: Python :: 3.5',
+        'Programming Language :: Python :: 3.6',
+        'Programming Language :: Python :: 3.7',
+    ],
+)

tests/test_sample.py

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+# Sample Test passing with nose and pytest
+
+def test_pass():
+    assert True, "dummy sample test"

tox.ini

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+[tox]
+envlist = py27,py34,py35,py36,py37
+
+[testenv]
+commands = py.test phenocube
+deps = pytest