Generation of Time

Series
René R. Colditz
 Quality of time series

Quality analysis and

Stack of NDVI (2001) interpolation of NDVI
(2001)
 Quality of Time Series
Time series without quality analysis Time series with quality analysis

8-day composite time series of 2001, color composite (RGB) of MODIS band 7 (SWIR), 2 (NIR), 1 (Red)
 Quality of time series

10-day composite of PAL Result of Interpolation

 Content

• Sensors and products for time series

• Robust semi-automated time series generation
– Use of data quality information
– Reduction of data noise, e.g. atmospheric influences
• Considerations
• Harmonic analysis
• Automated processing

• Examples of time series analysis

– Regions with high temporal variability in Africa
– Phenology analysis and rain response in South Africa
– Differences in data collections for Germany
– Time series in land cover mapping and change detection of Germany
 Time Series and remote sensing

• Time Series: temporally ordered sequence of observations,

usually measured in equal and discrete distances
• Temporally high resolution data enable the observation of
processes
– Not feasible with mono or bitemporal data
– Phenology of vegetation units, seasonality
• Independent information
• continuous coverage of
– An area
– For a longer period

Minimization of artefacts
 Motivation

• Land cover
– Classification
– Monitoring

Time
• Modeling
– Plant growth c e
p a
– Budgeting Space S
• Analysis of phenology
• Variation/Change in

Intensity
seasonality
• Change versus Modification

Time
 Sensors for Time Series Generation

Meteosat, NOAA SeaWiFS SPOT MODIS MERIS- AWIFS- Rapid Sentinel

(MSG) AVHRR VEGETA ENVISAT IRS-P6 Eye (5 2 (2 sat.)
TION sat.)

Spatial 2.5-5 km, 1,100 1,100 1,000 250, 500, 300 60 6.5 10, 20, 60
[m] (1-3 km) 1,000

Spectral 3, (12) 5 8 4 36 15 4 5 13
bands

Temporal 30, (15) Daily Daily Daily 1-2 days 3 24 days, Daily Daily
minutes overlap at
high lat.

Swath Hemi- 3,000 2,800 2,200 2,300 1,150 740 77, 285,
[km] sphere pointable pointable

period Since Since Since Since Since Since Since Planned Planned
1977, 1981 1997 1998 2000 2002 2003 2008 2012
(2004)
 MODIS - Sensor

• MODerate resoultion Imaging

Spectroradiometer
• Onboard Terra (EOS-AM, Dec 1999)
and Aqua (EOS-PM, May 2002)
• Swath: 2,300km, global
• Resolution
– Spatial: 250 to 1,000m spatial resolution
Terra platform
– Radiometric: 12 bit radiometric resolution (http://terra.nasa.gov/About/index.php)

– Temporal: 1-2 days

– Spectral: 36 bands from visible to thermal infrared
• Standardized preprocessing: radiometric, geometric, atmospheric
correction
• Standardized processing of value-added products
• Extensive data quality indicators
 MODIS – Levels, Gridding
Level Example
0 (raw) Data from antenna
1 (radiance) Radiometrically (L1A) and geometrically (L1B)
corrected
2 (reflectance) Atmospherically corrected (L2), Gridding (L2G)
3 (value-added) Vegetation Index, Land surface temperature…
4 (modeled) Leaf area index, Net primary productivity

http://nsidc.org/data/
modis/landgrid.html
 MODIS Land Products
Product Level Spatial (m) Temporal
(days)
Surface reflectance L2G, L3 250, 500 1, 8
Land surface temperature / L2, L3 1,000, 5,000, Swath, 1,
Emissivity 0.05° 8, 31
Land cover / Land cover change L3 1,000, 0.05° 96, 365
Vegetation indices L3 250, 500, 1,000 16, 31
Thermal anomalies / Fire L2, L3 1,000 Swath, 1, 8
Leaf area index / Fraction of L4 1,000 8
photosynthetically active radiation
Net primary vegetation production L4 1,000 8
Bidirection reflectance distribution L3 1,000, 16
function / Albedo 0.05/0.25°
Vegetation conversion / Vegetation L3 250, 500 96, 365
continuous fields
Suitable for time series generation
TIME SERIES GENERATOR
 TiSeG: Workflow

• utilizes free IDL virtual machine

• employed in research and
several national and international
organizations
 Time Series Generation
Original data Quality analysis Improved data
spatial

33 97 33 97

good bad

temporal
100 100
Number of invalid pixels [%]

80 80

Maximum gap length,

cumulative [%]
60 60

40 40

161 225 20 20
161 225
Number of invalid pixels
Maximum gap length
0 0
1 25 49 73 97 121 145 169 193 217 241 265 289 313 337 361
Days

interpolation
11

0.8
0.8

0.6
0.6
NDVI
NDVI

0.4
0.4

0.2
0.2

289 353 Original Interpolated

Interpolated 289 353
00
11 25
25 49
49 73
73 97
97 121
121 145
145 169
169 193
193 217
217 241
241 265
265 289
289 313
313 337
337 361
361
Days
Days
-0.2 NDVI 1 -0.2 NDVI 1
Data Availability Indices
 Data Availability Indices, Temporal

Number of invalid data Maximum gap length

100 100

Proportion of data, cumulative [%]

80 80
Number of invalid data [%]

60 60

40 40

20 20

0 0
1 33 65 97 129 161 193 225 257 289 321 353 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20
Day of year Maximum gap length [composites]

Stricter settings yield less valid data

8 day composites for Germany in 2001

 Data Availability Indices, Spatial

lenient moderate strict very strict

Number of invalid data

high

low
Maximum gap length

high

low
 Interpolation: Regional Analysis

Arable – Magdeburger Boerde Pasture - Alpine Foreland

0.9 0.9

0.8 0.8

0.7 0.7

0.6 0.6

0.5 0.5
NDVI

NDVI
0.4 0.4

0.3 0.3

0.2 0.2

0.1 0.1

0 0
1 33 65 97 129 161 193 225 257 289 321 353 1 33 65 97 129 161 193 225 257 289 321 353
Days of year Days of year

original lenient moderate strict very strict

1 0000

0
 Interpolation: Regional Analysis

Broadleaf Forest – Harz Coniferous Forest – Harz

0.9 0.9

0.8 0.8

0.7 0.7

0.6 0.6

0.5 0.5
NDVI

NDVI
0.4 0.4

0.3 0.3

0.2 0.2

0.1 0.1

0 0
1 33 65 97 129 161 193 225 257 289 321 353 1 33 65 97 129 161 193 225 257 289 321 353
Days of year Days of year

original lenient moderate strict very strict

1 0000

0
 NDVI Time Series
Original NDVI time series Improved NDVI time series, setting strict

-0.2 NDVI 1

8-day composite NDVI time series of 2001

CONSIDERATIONS
Methods: Temporal Interpolation
Methods: Temporal Interpolation - Algorithms
Methods: Temporal Interpolation - Algorithms

Absolute mean of difference to the reference graph

 Time Series Assessment

Bar plot of mean standard deviation of selected

natural regions and land cover classes

∑ σ ( R , LC )
i
σ ( R , LC ) = i =1

R ...region
LC ...land cover type
N ...length of time series
 Time Series Assessment
Average absolute difference between locally smoothed and reference time series

i+F / 2

∑ original k
smoothi = k =i − F / 2

F
N

∑ smooth i − original i
difference = i=0

F ... filter size

N ...length of time series
 Time Series Assessment
Spatial display of maximum significant lag Cumulative plot of the proportion of
pixels becoming insignificant with
increasing lag

N −k
r...autocorrelation coeffcient
∑ (x i − x )( xi + k − x )
k...lag
rk = i =0
N
N...length of time series
∑ (x i − x)2
i =0 z...confidence
s...standard error
k −1
1 + 2 ⋅ ∑ (r j ) 2 rk
j =1 zk =
sk = sk
N
HARMONIC ANALYSIS
 Harmonic Analysis

• Harmonic analysis
– Decomposes a complex function in a sum of simple sine/cosine
functions
Maximum
Explained
number
variance
of Harmonics

Analysis: how
Fourier Inverse Fourier
many Harmonics
transformation transformation
are required
 Harmonic Analysis

• Requires:
– Time series to be analyzed / smoothed N layers
– Maximum number of harmonics Value
– Cumulative explained variance Value

• Returns:
– Smoothed time series N layers
– Cumulative explained variance 1 layer
– Number of harmonics 1 layer
– Phase N/2 layer
– Amplitude N/2 layer
– Explained variance of each harmonic N/2 layer
 Harmonic analysis

Evergreen broadleaf Savanna

 Harmonic analysis

good acceptable

intermediate average
AUTOMATED PROCESSING
 Automated Processing

• The use of a ranked quality index for time series

generation
– Select useable quality and gap length to be interpolated
– Stepwise approach for each quality level
• Determine data of quality (which have not been interpolated before)
• Interpolate gaps if possible
– Fill or interpolate remaining data gaps

• Output
– Improved time series
– Gap length
– Quality
– Summary table
Automated Processing
Automated Processing
TIME SERIES PROCESSING OF
AVHRR
 AVHRR Pathfinder data

global continental tiles

Spatial res. 1 degree 8 km 8 km 8 km
Temporal 10 day and 10 day and 10 day and daily
res. monthly monthly monthly
Availability 07/1981 – 07/1981 – 07/1981 – 07/1981 –
12/2001 12/2001 12/2003 12/1999
Products NDVI and NDVI and NDVI and NDVI, refl.
refl. bands refl. bands refl. bands Bands,
angles, cloud
index, quality

Sensors: NOAA 7, 9, 11, 14, derived from 4km GAC data

Overpass: approximately 2pm
Ancillary: Latitude, Longitude, Elevation, Land sea mask
 Time series processing

PAL Data set

Iterative interpolation
approach using
meta data

Outlier analysis

Moving average
smoothing

Maximum value
compositing
 Time series comparison

Bare Ground

Open Shrubland

Closed Shrubland

Wooded Grassland

Woodland

Deciduous Broadleaf
Forest

http://glcf.umiacs.umd.edu/data/landcover
(modified)
ANALYSIS OF SEASONALITY
AND TEMPORAL VARIABILITY
IN AFRICA
 Time Series Analysis Techniques

Classifying the seasonality

• Harmonic analysis (Fourier transformation)
– Calculation of explained variance for each harmonic
– Selection of harmonic with highest (weighted) explained variance

non-modal uni-modal bi-modal

 Regions with High Temporal Variability
8-km Pathfinder AVHRR Land data for Africa from 1982 - 2000
 Regions with High Temporal Variability
Dominating modality in 19 years Land cover classification of AVHRR PAL
data from 1992-1993 (Hansen et al., 2000).
 Regions with High Temporal Variability

Correspondence of land cover classes with types of seasonality [%]

Non-modal Uni-modal Bi-modal

Evergreen broadleaf forest 0 13 87

Decidious broadleaf forest 0 46 54

Woodland 0 79 21

Wooded grassland 1 85 14

Closed shrubland 28 38 34

Open shrubland 78 7 14

Grassland 4 58 37

Cropland 1 65 34

Bare ground 99 0 1
 Changes in modality

Changes in modality Unsupervised Classification

of change in modality image
and recode using change in
modality
ANALYSIS OF TEMPORAL
VARIABILITY IN SOUTH
AFRICA
2000/2001 2001/2002

-0.2 EVI 1
Characterization of seasonality
Regions with High Temporal Variability
 Time Series Analysis Techniques

Computing the temporal shift

• Temporal cross-correlation
– Pixels belonging to the same type of seasonality in both years
– Pixels belonging to uni- or bi-modal seasonality in both years
 Temporal cross-correlation

Maximum cross correlation coefficient

2000 - 2002 2001 - 2003

-0.2 1
 Temporal cross-correlation
Temporal shifts of EVI between consecutive years
RAIN RESPONSE OF
VEGETATION IN SOUTH
AFRICA
Average 10-day EVI 10-day precipitation averag

-0.2 EVI 1 0 Rain 150

2000-2001 mean [mm]
Temporal correlation between precipitation and EVI

? Best maximum ?
Steady EVI
Intensity

Unsteady precipitation
Time
 Temporal correlation between precipitation and EVI
2000-2001 2001-2002

Temporal
cross-correlation
between
precipitation
and EVI
2003-2004 2005-2006
-80 0 80
DIFFERENCES IN MODIS DATA
COLLECTIONS
 Differences in C4 and C5 Data

• MOD13 Product changes in QA-SDS

– Full Land/Sea mask
– No BRDF-compositing, this technique never became operational
– Additional Reliability dataset
Differences in C4 and C5 Data
Differences in C4 and C5 Data
TIME SERIES IN LAND COVER
MAPPING
 Land Cover Update and Change Detection

2001 2003 2005

Legende

CORINE level 1
Urban
Agricultural land
Forest and natural land
Wetland
Water
 Land Cover Update and Change Detection

100

95

90

85
Agreement [%]

80

75

70

65

60

55

50
0 10 20 30 40 50 60 70 80 90 100 -5 -3 -1 1 3 5
Certainty [%] Mean of relative difference [%]
Land Cover Update and Change Detection

Mean absolute
difference 2001 - 2002
 Summary

• Quality is rarely used but critical to understand, assess,

and analyse the data
• TiSeG
– Efficient tool for high-quality time series generation
– Trade-off between high data quality and sufficient quantity
– Data availability indices crucial for semi-automatic processing
– Applicable world-wide and concept extendable to other sensors

• Newest features
– Automated processing
– Harmonic analysis included
 Summary

• Mapping phenology, seasonality, and variability

important for understanding ecosystems
– Impossible without time series
– High quality data needed

• Coupling vegetation signal and driving climate data,

e.g. temperature and precipitation

• Mapping land cover with time series

 Literature
• Brown, M.E., Pinzon, J.E., Didan, K., Morisette, J.T. and Tucker, C.J., 2006. Evaluation of the
consistency of long-term NDVI time series derived from AVHRR, SPOT-Vegetation, SeaWiFS,
MODIS, and Landsat ETM+ sensors. IEEE Transactions on Geoscience and Remote Sensing, 44(7),
pp. 1787-1793.
• de Beurs, K.M. and Henebry, G.M., 2005b. A statistical framework for the analysis of long image time
series. International Journal of Remote Sensing, 26(8), pp. 1551-1573.
• Fensholt, R., Theis Nielsen, T. and Stisen, W., 2006. Evaluation of AVHRR PAL and GIMMS 10-day
composite NDVI time series products using SPOT-4 vegetation data for the African continent.
International Journal of Remote Sensing, 27(13), pp. 2719-2733.
• JÖNSSON, P. and EKLUNDH, L., 2004, TIMESAT - a program for analysing time-series of satellite
sensor data, Computers and Geosciences, 30, 833-845.
• JÖNSSON, P., and EKLUNDH, L., 2002, Seasonality extraction by function fitting to time-series of
satellite sensor data. IEEE Transactions on Geoscience and Remote Sensing, 40 (8), 1824-1832.
• Lunetta, R.S., Knight, J.F., Ediriwickrema, J., Lyon, J. and Worthy, L.D., 2006. Land-cover change
detection using multi-temporal MODIS NDVI data. Remote Sensing of Environment, 105, pp. 142-
154.
• Roerink, G.J., Menenti, M. and Verhoef, W., 2000. Reconstructing cloudfree NDVI composites using
Fourier analysis of time series. International Journal of Remote Sensing, 21(9), pp. 1911-1917.
• Tucker, C.J., Pinzon, J.E., Brown, M.E., Slayback, D.A., Pak, E.W., Mahoney, R., Vermote, E.F. and
el Saleous, N.Z., 2005. An extended AVHRR 8-km NDVI dataset compatible with MODIS and SPOT
vegetation NDVI data. International Journal of Remote Sensing, 26(20), pp. 4485–4498.
• Udelhoven, T. (2006): TimeStats: a software tool for analyzing spatial-temporal raster data archives:
In: 1st Conference on Remote Sensing and Geoinformation Processing in the Assessment and
Monitoring of Land Degradation and Desertification, 7th-9th September 2005, Trier, 8p.
 Literature
• Colditz, R.R., Conrad, C., Wehrmann, T., Schmidt, M., Dech, S., 2006a Generation and assessment
of MODIS time series using quality information. In: IEEE International Geoscience and Remote
Sensing Symposium, IGARSS 2006, July 31st - August 4th 2006, Denver, CO, 6 pages.
• Colditz, R.R., Conrad, C., Rücker, G.R., Schweitzer, C., Fistric, S., Schmidt, M. and Dech, S.W.,
2005. Ableitung von phänologischen Verlaufsmustern aus MODIS-Zeitserien und Möglichkeiten der
Anwendung. In: J. Strobl, T. Blaschke and G. Griesebner (Editors), AGIT. Beiträge zum 17. AGIT-
Symposium Salzburg, Salzburg, pp. 94-99.
• Colditz, R.R., Conrad, C., Schmidt, M., Schramm, M., Schmidt, M. and Dech, S.W., 2006b. Mapping
regions of high temporal variability in Africa, ISPRS mid-term symposium 2006 - remote sensing:
from pixels to processes, Enschede, the Netherlands, pp. 6 pages.
• Colditz, R.R., Conrad, C., Wehrmann, T., Schmidt, M., Dech, S., 2008, TiSeG – A flexible software
tool for time series generation of MODIS data utilizing the quality assessment science data set. IEEE
Transactions on Geoscience and Remote Sensing, 46 (10): 3296-3308.
• Colditz, R.R., Conrad, C., Wehrmann, T., Schmidt, M., Dech, S., 2008, Analysis of the quality of
collection 4 and 5 vegetation index time series from MODIS. In: Stein, A., Shi, W., Bijker, W., Quality
aspects in spatial data mining. CRC Press, 161-173. Also published in ISPRS Spatial Data Quality
Symposium, June 13th – 15th 2007, Enschede, The Netherlands.
• Colditz, R.R., Gessner, U., Conrad, C., van Zyl, D., Malherbe, J., Newby, T., Landmann, T., Schmidt,
M. and Dech, S.W., 2007c. Dynamics of MODIS time series for ecological applications in southern
Africa, Fourth International Workshop on the Analysis of Multitemporal Remote Sensing Images
(Multitemp 2007), Leuven, Belgium, pp. CD-ROM.
 Software

• TimeSat (Dr. Per Jönsson and Dr. Lars Eklundh)

– http://www.nateko.lu.se/personal/Lars.Eklundh/TIMESAT/timesat.html
– Time series filtering
– Seasonality extraction
– Runs on Matlab with GUI and Fortran source code
• TimeStats (Dr. Thomas Udelhoven)
– udelhove@lippmann.lu
– Software for time series analysis
– Many time series functionalities of standard statistical packages (SAS, SPSS, S+)
are combined
– Runs in ENVI environment
• HANTS: http://www.ittvis.com/codebank/search.asp?FID=532
• Beam: http://141.4.215.13/
• GIOVANNI: http://daac.gsfc.nasa.gov/techlab/giovanni/
• LDOPE: http://lpdaac.usgs.gov/landdaac/tools/ldope/
• MRT: http://lpdaac.usgs.gov/landdaac/tools/modis/index.asp
 TiSeG availability

• TiSeG is a stand-alone software package

• Requirements
– Windows XP or higher
– Sufficiently fast computer, DUAL Processor recommended
– A lot of disk space (generally necessary for MODIS data)
– IDL VM (freely available from RSI Inc. (http://www.rsinc.com/)
• Easy installation: Copy files to directory and setting of one
Environment variable

 Available for free

 User support with updates, improvements and bug-fixes
 TiSeG Team and Literature

René R. Colditz Christopher Conrad Thilo Wehrmann

CONABIO University of Wuerzburg German Aerospace Center

TiSeG framework TiSeG framework TiSeG framework

Module integration Harmonic analysis
Quality assessment
 Time Series of Mexico
16-day 1km NDVI time series of 2005

-0.2 NDVI 1