Using Data INterpolating Empirical

Orthogonal Functions (DINEOF)

Algorithm for filling missing data of
AVHHR satellite images

Case study of reconstruction of Chlorophyll-a missing data over the

Mediterranean using MyOcean satellite data products

November 2014

Andreas Nikolaidis, Stavros Stylianou, Georgios Georgiou, Diofantos Hadjimitsis,

Evangelos Akylas
 Using DINEOF Algorithm for filling missing data of AVHHR satellite images

The problem

Filling the gaps, generated by the existence of clouds, rain, or simply due to
incomplete track coverage of upper atmospheric layers, is one of the most
common problems, faced during the processing of AVHHR satellite data.

Many methods have been tested out over the years for solving this problem,
with different results, regarding the field of application and the expertise of the
scientists involved.

The most common approach is using a spatial function which gives the form of
the wave at a given moment and a temporal function which characterizes the
variation of the wave over time.

Determining of these functions then allows one to bypass severe data

accumulation.
Using DINEOF Algorithm for filling missing data of AVHHR satellite images

Introduction

Scope:
Examination of daily Chlorophyll-a mass concentration,
over the Mediterranean Sea, during the period
Dec. 21-2013 - Jan. 5-2014 (16 days).

Source:
Moderate Resolution Imaging Spectroradiometer (MODIS
Aqua) satellites, Level 3, 1 km grid data, collected by OC-
CNR-ROMA-IT*, available by MyOcean**
(*) R.Santoleri,G. Volpe, S. Marullo and B. Buongiorno Nardelli (2008), Open Waters Optical Remote Sensing of the Mediterranean Sea, in
Remote Sensing of the European Seas, edited by V. Barale and M. Gade, pp. 103-116, Springer.
(**) http://www.myocean.eu/
Using DINEOF Algorithm for filling missing data of AVHHR satellite images

Input Data
Using DINEOF Algorithm for filling missing data of AVHHR satellite images

The Method

DINEOF Algorithm:
Data INterpolating Empirical Orthogonal Function (DINEOF) is a method to fill in missing data from
geophysical fields, such as chlorophyll-a, or sea surface temperatures and salinities.

The EOF decomposition is computed by the singular value decomposition (SVD) method, which gives
the spatial EOFs(U), the singular values matrix (S) and the temporal EOFs(V). Missing data are
reconstructed by the truncated EOFs via the formula:

where
Xi,j are the missing data;
i,j are the spatial and temporal indices of the missing data;
p is the number of EOFs mode used for the reconstruction;
c represents the c-th column, hence Uc and Vc are the c-th column of spatial and temporal EOFs and Sc is the c-th
singular value.
Successive repetitions (iterations) of the formula performed, until the predefined convergence criterion
reached.

Ref.: Alvera-Azcárate A., Barth A.,Sirjacobs D., Lenartz F., Beckers J.-M.. Data Interpolating Empirical Orthogonal Functions (DINEOF): a tool for geophysical data analyses.
Medit. Mar. Sci., 5-11, (2011), Rixen M., Beckers J. M.,, EOF Calculations and Data Filling from Incomplete Oceanographic Datasets. Journal of Atmospheric and Oceanic
Technology, Vol. 20(12), pp. 1839-1856, (2003), Nikolaidis A., Georgiou G., Hadjimitsis D. and E. Akylas, Applying a DINEOF algorithm on cloudy sea-surface temperature
satellite data over the eastern Mediterranean Sea, Central European Journal of Geosciences 6(1), pp. 1-16, (2014), DINEOF home page
http://modb.oce.ulg.ac.be/mediawiki/index.php/DINEOF
Using DINEOF Algorithm for filling missing data of AVHHR satellite images

The Toolbox

Requirements:
- Windows 8
- ArcGIS
10.2
Using DINEOF Algorithm for filling missing data of AVHHR satellite images

Installation

Toolbox size ~20 Mb

Using DINEOF Algorithm for filling missing data of AVHHR satellite images

Initialization

1. Toolbox selection/activation

2. Viewing the toolbox

Using DINEOF Algorithm for filling missing data of AVHHR satellite images

Usage

Input and mask file selection

Using DINEOF Algorithm for filling missing data of AVHHR satellite images

First impression

All input data appeared in one raster.

Using DINEOF Algorithm for filling missing data of AVHHR satellite images

Preprocessing

DINEOF algorithm can be tuned for specific

experiments, (ie by increasing the number of EOF
modes, or the iterations)

All settings can reset to default values and are

directly visible:
Using DINEOF Algorithm for filling missing data of AVHHR satellite images

Execution
Special features of current version:

- memory limitations anticipated by “cutting” the original

data to smaller with respect to the data size

- results produced in separated raster files, available

for further processing

Execution time depends on the data

size.

In this example,about 1.5 hours are

required to cover all Mediterranean
for 16 time steps.
Using DINEOF Algorithm for filling missing data of AVHHR satellite images

Flowchart
- Netcdf formatted files

- Algorithm configuration
changes (if any) and
preparation of code execution:

- Application is based on the following

utilities:

❖  ArcObjects
❖  Climatic Data Operators (CDO)
❖  NCO utilities
❖  Generic Mapping Tools (GMT)
❖  python
❖  VB.Net
Filling the missing data of AVHHR satellite images using the DINEOF Algorithm

Results

- Detailed execution
information included in
Log file

- New raster files (.tiff)

produced for
every time-step
Using DINEOF Algorithm for filling missing data of AVHHR satellite images

Output Data
Using DINEOF Algorithm for filling missing data of AVHHR satellite images

Epilogue

❖  Generated raster data, can be further processed by

various methods, providing the source of previously
non-existent information.

❖  In this case study a Boundary Clean Spatial Analysis

algorithm was applied, for smoothing existing ‘rough’
edges.

❖  This tool applies a new platform in a well known GIS

environment, for future similar experiments.
Using DINEOF Algorithm for filling missing data of AVHHR satellite images

The End

Thank you for your attention!