/modape

MODIS Assimilation and Processing Engine

Primary LanguagePythonMIT LicenseMIT

MODAPE

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The MODIS Assimilation and Processing Engine combines a state-of-the art Whittaker smoother, implemented as fast C-extension through Cython and including a V-curve optimization of the smoothing parameter, with a HDF5 based processing chain optimized for MODIS data.

The sub-module modape.whittaker includes the following variations of the Whittaker smoother with 2nd order differences:

  • ws2d: Whittaker with fixed smoothing parameter (s)
  • ws2dp: Whittaker with fixed smoothing parameter (s) and expectile smoothing using asymmetric weights
  • ws2doptv: Whittaker with V-curve optimization of the smoothing parameter
  • ws2doptvp: Whittaker with V-curve optimization of the smoothing parameter and expectile smoothing using asymmetric weights

The MODIS processing chain consists of the following executables, which can be called through commandline:

  • modis_download: Query and download raw MODIS products (requires Earthdata credentials)
  • modis_collect: Collect raw MODIS data into daily datacubes stored in an HDF5 file
  • modis_smooth: Smooth, gapfill and interpolate raw MODIS data using the implemented Whittaker smoother
  • modis_window: Extract mosaic(s) of multiple MODIS tiles, or subset(s) of a global/tiled MODIS product and export it as GeoTIFF raster in WGS1984 coordinate system

Additional executables:

  • csv_smooth: Smooth timeseries stored within a CSV file
  • modis_info: Retrieve metadata from created HDF5 files

For a more information please check out the documentation!

Installation

Dependencies:

modape depends on these packages:

  • click
  • gdal
  • h5py
  • numpy
  • pandas
  • python-cmr
  • requests

Some of these packages (eg. GDAL) can be difficult to build, especially on windows machines. In the latter case it's advisable to download an unofficial binary wheel from Christoph Gohlke's Unofficial Windows Binaries for Python Extension Packages and install it locally with pip install before installing modape.

Installation from github:

$ git clone https://github.com/WFP-VAM/modape
$ cd modape
$ pip3 install .

Installation from PyPi:

$ pip3 install modape

Bugs, typos & feature requests

If you find a bug, see a typo, have some kind of troubles running the module or just simply want to have a feature added, please submit an issue!

References:

P. H. C. Eilers, V. Pesendorfer and R. Bonifacio, "Automatic smoothing of remote sensing data," 2017 9th International Workshop on the Analysis of Multitemporal Remote Sensing Images (MultiTemp), Brugge, 2017, pp. 1-3. doi: 10.1109/Multi-Temp.2017.8076705 URL: http://ieeexplore.ieee.org/stamp/stamp.jsp?tp=&arnumber=8076705&isnumber=8035194

Core Whittaker function adapted from whit2 function from R package ptw:

Bloemberg, T. G. et al. (2010) "Improved Parametric Time Warping for Proteomics", Chemometrics and Intelligent Laboratory Systems, 104 (1), 65-74

Wehrens, R. et al. (2015) "Fast parametric warping of peak lists", Bioinformatics, in press.