Merge pull request #1 from mapbox/its-a-setup

It's a setup

.gitignore

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+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+env/
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+*.egg-info/
+.installed.cfg
+*.egg
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.coverage
+.cache
+nosetests.xml
+coverage.xml
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+target/
+
+# OS X
+.DS_Store
+
+# Pyenv
+.python-version
+
+.*.swp
+
+docs/notebooks/.ipynb_checkpoints/*

.travis.yml

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+language: python
+sudo: false
+cache:
+  directories:
+    - ~/.cache/pip
+env:
+  global:
+    - PIP_WHEEL_DIR=$HOME/.cache/pip/wheels
+    - PIP_FIND_LINKS=file://$HOME/.cache/pip/wheels
+addons:
+  apt:
+    packages:
+    - libgdal1h
+    - gdal-bin
+    - libgdal-dev
+    - libatlas-dev
+    - libatlas-base-dev
+    - gfortran
+python:
+  - "2.7"
+  - "3.4"
+  - "3.5"
+before_install:
+  - "pip install -U pip"
+  - "pip install wheel"
+install:
+  - "pip wheel numpy"
+  - "pip install --use-wheel numpy"
+  - "pip wheel -r requirements.txt"
+  - "pip install --use-wheel -r requirements.txt"
+  - "pip wheel -r requirements-dev.txt"
+  - "pip install --use-wheel -r requirements-dev.txt"
+  - "pip install -e .[test]"
+script:
+  - py.test --cov rio_rgbify --cov-report term-missing
+after_success:
+  - coveralls
+

LICENSE

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+The MIT License (MIT)
+
+Copyright (c) 2016 Mapbox
+
+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.md

@@ -1,2 +1,23 @@
 # rio-rgbify
-Encoded arbitrary bit depth rasters in psuedo base-256
+Encode arbitrary bit depth rasters in psuedo base-256 as RGB
+
+[![Build Status](https://travis-ci.org/mapbox/rio-rgbify.svg)](https://travis-ci.org/mapbox/rio-rgbify)[![Coverage Status](https://coveralls.io/repos/github/mapbox/rio-rgbify/badge.svg?branch=its-a-setup)](https://coveralls.io/github/mapbox/rio-rgbify)
+
+## CLI usage
+
+```
+Usage: rio rgbify [OPTIONS] SRC_PATH DST_PATH
+
+Options:
+  -b, --base-val FLOAT   The base value of which to base the output encoding
+                         on [DEFAULT=0]
+  -i, --interval FLOAT   Describes the precision of the output,by incrementing
+                         interval [DEFAULT=1]
+  --bidx INTEGER         Band to encode [DEFAULT=1]
+  -j, --workers INTEGER  Workers to run [DEFAULT=4]
+  -v, --verbose
+  --co NAME=VALUE        Driver specific creation options.See the
+                         documentation for the selected output driver for more
+                         information.
+  --help                 Show this message and exit.
+```

requirements-dev.txt

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+affine
+cligj
+coveralls>=0.4
+delocate
+enum34
+numpy>=1.8.0
+snuggs>=1.2
+pytest
+raster-tester
+setuptools>=0.9.8
+wheel

requirements.txt

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+click
+rasterio
+rio-mucho>=0.2.1

rio_rgbify/__init__.py

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+import logging
+
+__version__ = "0.1.0"
+
+log = logging.getLogger(__name__)
+log.addHandler(logging.NullHandler())

rio_rgbify/encoders.py

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+from __future__ import division
+import numpy as np
+
+def data_to_rgb(data, baseval, interval):
+    '''
+    Given an arbitrary (rows x cols) ndarray,
+    encode the data into uint8 RGB from an arbitrary
+    base and interval
+
+    Parameters
+    -----------
+    data: ndarray
+        (rows x cols) ndarray of data to encode
+    baseval: float
+        the base value of the RGB numbering system.
+        will be treated as zero for this encoding
+    interval: float
+        the interval at which to encode
+
+    Returns
+    --------
+    ndarray: rgb data
+        a uint8 (3 x rows x cols) ndarray with the
+        data encoded
+    '''
+    data = data.astype(np.float64)
+    data -= baseval
+    data /= interval
+
+    rows, cols = data.shape
+
+    datarange = data.max() - data.min()
+
+    if _range_check(datarange):
+        raise ValueError('Data of {} larger than 256 ** 3'.format(datarange))
+
+    rgb = np.zeros((3, rows, cols), dtype=np.uint8)
+
+    rgb[2] = (((data / 256) - (data // 256)) * 256)
+    rgb[1] = ((((data // 256) / 256) - ((data // 256) // 256)) * 256)
+    rgb[0] = (((((data // 256) // 256) / 256) - (((data // 256) // 256) // 256)) * 256)
+
+    return rgb
+
+
+def _decode(data, base, interval):
+    '''
+    Utility to decode RGB encoded data
+    '''
+    data = data.astype(np.float64)
+    return base + (((data[0] * 256 * 256) + (data[1] * 256) + data[2]) * interval)
+
+
+def _range_check(datarange):
+    '''
+    Utility to check if data range is outside of precision for 3 digit base 256
+    '''
+    maxrange = 256 ** 3
+
+    return datarange > maxrange
+
+

rio_rgbify/scripts/cli.py

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+import click
+
+import rasterio as rio
+import numpy as np
+from riomucho import RioMucho
+from rasterio.rio.options import creation_options
+
+from rio_rgbify.encoders import data_to_rgb
+
+def _rgb_worker(data, window, ij, g_args):
+    return data_to_rgb(data[0][g_args['bidx'] - 1],
+        g_args['base_val'],
+        g_args['interval'])
+
+@click.command('rgbify')
+@click.argument('src_path', type=click.Path(exists=True))
+@click.argument('dst_path', type=click.Path(exists=False))
+@click.option('--base-val', '-b', type=float, default=0,
+    help='The base value of which to base the output encoding on [DEFAULT=0]')
+@click.option('--interval', '-i', type=float, default=1,
+    help='Describes the precision of the output,by incrementing interval [DEFAULT=1]')
+@click.option('--bidx', type=int, default=1,
+    help='Band to encode [DEFAULT=1]')
+@click.option('--workers', '-j', type=int, default=4,
+    help='Workers to run [DEFAULT=4]')
+@click.option('--verbose', '-v', is_flag=True, default=False)
+@click.pass_context
+@creation_options
+def rgbify(ctx, src_path, dst_path, base_val, interval, bidx, workers, verbose, creation_options):
+    with rio.open(src_path) as src:
+        meta = src.profile.copy()
+
+    meta.update(
+        count=3,
+        dtype=np.uint8
+    )
+
+    for c in creation_options:
+        meta[c] = creation_options[c]
+
+    gargs = {
+        'interval': interval,
+        'base_val': base_val,
+        'bidx': bidx
+    }
+
+    with RioMucho([src_path], dst_path, _rgb_worker,
+        options=meta,
+        global_args=gargs) as rm:
+
+        rm.run(workers)

setup.py

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+import os
+import sys
+from setuptools import setup, find_packages
+from setuptools.extension import Extension
+
+# Parse the version from the fiona module.
+with open('rio_rgbify/__init__.py') as f:
+    for line in f:
+        if line.find("__version__") >= 0:
+            version = line.split("=")[1].strip()
+            version = version.strip('"')
+            version = version.strip("'")
+            break
+
+long_description = """"""
+
+
+def read(fname):
+    return open(os.path.join(os.path.dirname(__file__), fname)).read()
+
+setup(name='rio-rgbify',
+      version=version,
+      description=u"Encode arbitrary bit depth rasters in psuedo base-256 as RGB",
+      long_description=long_description,
+      classifiers=[],
+      keywords='',
+      author=u"Damon Burgett",
+      author_email='damon@mapbox.com',
+      url='https://github.com/mapbox/rio-rgbify',
+      license='BSD',
+      packages=find_packages(exclude=['ez_setup', 'examples', 'tests']),
+      include_package_data=True,
+      zip_safe=False,
+      install_requires=["click", "rasterio", "rio-mucho"],
+      extras_require={
+          'test': ['pytest', 'pytest-cov', 'codecov']},
+      entry_points="""
+      [rasterio.rio_plugins]
+      toa=rio_rgbify.scripts.cli:rgbify
+      """
+      )

test/test_cli.py

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+from click.testing import CliRunner
+import rasterio as rio
+import numpy as np
+from rio_rgbify.scripts.cli import rgbify
+import click
+
+from tempfile import mkdtemp
+from shutil import rmtree
+import os
+
+from raster_tester.compare import affaux, upsample_array
+
+class TestingDir:
+    def __init__(self):
+        self.tmpdir = mkdtemp()
+    def __enter__(self):
+        return self
+    def __exit__(self, a, b, c):
+        rmtree(self.tmpdir)
+    def mkpath(self, filename):
+        return os.path.join(self.tmpdir, filename)
+
+def flex_compare(r1, r2, thresh=10):
+    upsample = 4
+    r1 = r1[::upsample]
+    r2 = r2[::upsample]
+    toAff, frAff = affaux(upsample)
+    r1 = upsample_array(r1, upsample, frAff, toAff)
+    r2 = upsample_array(r2, upsample, frAff, toAff)
+    tdiff = np.abs(r1.astype(np.float64) - r2.astype(np.float64))
+
+    click.echo('{0} values exceed the threshold difference with a max variance of {1}'.format(
+        np.sum(tdiff > thresh), tdiff.max()), err=True)
+
+    return not np.any(tdiff > thresh)
+
+
+def test_cli_good_elev():
+    in_elev_src = 'test/fixtures/elev.tif'
+    expected_src = 'test/expected/elev-rgb.tif'
+    with TestingDir() as tmpdir:
+        out_rgb_src = tmpdir.mkpath('rgb.tif')
+
+        runner = CliRunner()
+        result = runner.invoke(rgbify, [in_elev_src, out_rgb_src, '--interval', 0.001, '--base-val', -100])
+
+        assert result.exit_code == 0
+
+        with rio.open(out_rgb_src) as created:
+            with rio.open(expected_src) as expected:
+                carr = created.read()
+                earr = expected.read()
+                for a, b in zip(carr, earr):
+                    assert flex_compare(a, b)
+
+
+def test_cli_fail_elev():
+    in_elev_src = 'test/fixtures/elev.tif'
+    expected_src = 'test/expected/elev-rgb.tif'
+    with TestingDir() as tmpdir:
+        out_rgb_src = tmpdir.mkpath('rgb.tif')
+
+        runner = CliRunner()
+        result = runner.invoke(rgbify, [in_elev_src, out_rgb_src, '--interval', 0.00000001, '--base-val', -100])
+
+        assert result.exit_code == -1