HD-05 Spectral Data Systems for Field Spectrometry

Description: The increased use of portable spectrometers has led to a need for better data systems (databases and related spectral tools) for managing the expanding volume of field optical measurements.  This workshop will introduce emerging data systems for handing field optical measurements, with a focus on spectral measurements and optical time series (e.g. optical phenology measurements) related to ecological questions.  Emerging spectral databases and related tools for processing, analyzing, archiving and visualizing optical data will be introduced, with a focus on SPECCHIO and EcoSIS.  Examples will focus on the entire data life cycle, starting with a scientific question or hypothesis, and continuing with sampling design and protocols, data collection and processing, data upload and metadata augmentation for archiving, visualization, and information extraction (e.g. biophysical parameter estimation).

Material to be Distributed and Special Requirements: Participants are encouraged to bring their own research questions, sample data, metadata, and laptops with software installed.  It will be helpful to have any the following software installed in advance: SPECCHIO (v. 3.1.2), R Studio, and Matlab. 

SPECCHIO can be downloaded at: http://specchio.ch/app_download.php

Further SPECCHIO instructions are available at: http://specchio.ch/user_guides.php.

Internet connection will be available, as will a projector & screen for presentation (details to vary with room and number of participants). Because a good internet connection is not guaranteed, we also advise installing software and contacting us in advance with any data delivery needs.

Participants are asked to bring their spectral data in one of the following file formats:


File Format

Comments

ASD binary

Analytical Spectral Devices, old and new file formats

GER

GER instruments text files

MFR

MFR Sun Photometer text files

SVC

SVC HR-1024 files

Apogee

Apogee text files, preliminary support

ENVI SLB

ENVI spectral library files

Ocean Optics

Ocean Optics SpectraSuite text files

UniSpec

UniSpec Single Beam and Dual Beam text files

Text

Columnar, space separated spectral data as generated by ENVI/IDL

SPECPR

Spectral file format by USGS, also generated by the USGS PRISM software

Spectral Evolution

Text file format generated by Spectral Evolution instruments

XLS

Excel files with data arranged in columns, first column holds the wavelengths

Metadata is best formatted in Excel file format as this allows semi-automatic metadata augmentation within the SPECCHIO system.

 

Proposed Schedule:

Morning Session – 09:00-12:30 noon (or thereabouts) is the official session time, the afternoon session

Time

Content

Presenter

0900-0915

Introduction & Welcome

Why do we care about spectra ?
what we can learn from spectral variation in time and space
(focus on ecological applications of spectrometry)
What are Spectral Data Systems?
Brief history of efforts to develop spectral data systems
USGS, ASTER
SpecNet /EuroSpec
GeoChronos
SPECCHO
ACEAS/TERN
Successes & limitations of past efforts

John Gamon

0915-0930

SPECCHIO
Introduction to data life cycle & SPECCHIO

Andy Hueni

0930-1000

SPECCHIO Tutorial part 1

Andy Hueni

1000-1015

Break

 

1015-1030

SPECCHIO Tutorial part 2

Andy Hueni

1030-1130

Accessing SPECCHIO from Matlab and R:
Generating information by applying algorithms
Datasets will be provided where biophysical parameters are included in the metadata, allowing simple model development.

All

1130-1200

ASD R Package: R-Fieldspec

Phil Townsend

1200-1215

Wrap up of the morning session

All

1215-1315

Lunch Break

 

1315-1630

Afternoon Session
Interactive and individual work of the participants who brought their own datasets. Alternatively, work can be continued on the supplied tutorial datasets.
Tutors are on site to provide help.
Breaks are individual.

All

1630-1650

EcoSIS

The EcoSIS team and vision
Progress to date

Phil Townsend

1650-1700

Wrap up of the afternoon session
Final discussion and evaluation (audience feedback)

All