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1. Landcover SPECCHIO_UserGuide_V2 1 1 docx Version 2 1 1 02 11 2010 SPECCHIO Page 48 User Guide of 103 Description d Numerical field with buffer This consists of a main numerical field and a buffer that when filled generates expressions of the type field name gt main value buffer AND field name lt main value buffer When applied to e g spatial metadata like latitude the effect is similar to buffering functions found in GIS systems Latitude 40 Buffer size 5 e Multiple selection list 0 N elements can be selected deselected from the list by using ctrl and the mouse button Note that the expressions built from the selected elements are logically related by OR and not by AND l e the resulting expression has the SQL syntax field name in lt id gt lt id gt Figure 53 and Figure 54 show the query condition tab with some of the fields filled The SQL query resulting from these entries is as follows SELECT count FROM spectrum campaign specchio user position sampling geometry WHERE specchio user first name like spe OR specchio user last name like spe AND spectrum landcover id 49 AND position latitude gt 50 0 AND po sition latitude lt 30 0 AND position altitude gt 30 0 AND position altitude lt 70 0 AND sampling geometry illumination zenith gt 40 0 AND sam pling geometry illumination zenith lt 50 0 AND spectrum measurement u
2. 0 0 0 0 Capture date 2005 9 12 10 9 50 Loading date 2007 8 24 14 48 53 Is reference spectrum Yes 9 No Required quality level B M Attained quality level B Spectral plot e e Spectral Il W Bc M y 0 4 ue a ce NJ o 1000 2000 3000 Position Latitude 40 3849133333333 Longitude 175 621526666667 Altitude m 52 Location Landcover Data i CORINE Landcover gt L3 Artificial Surfaces I b 3 Anriciiltiiral Areas Figure 36 An example of mandatory field colouring SPECCHIO_UserGuide_V2 1 1 docx Version 2 1 1 02 11 2010 SPECCHIO Page 39 User Guide of 103 5 2 6 2 8 Showing the Quality Compliance in the Metadata Browser Tree The metadata browser can display information about the quality compliance of the spectrum and the campaign To switch on this option select the Show quality compliance in tree checkbox in the control panel cf Figure 37 Tree nodes that do not yet comply with the required quality level are indicated by an asterisk Quality compliance is propagated upwards in the tree If a spectrum does not comply then all par ent hierarchies and the campaign itself will show an asterisk cf Figure 38 for an example Note that enabling this option reduces the responsiveness of the GUI as compliance checks have to be carried out on every metadata field Show quality compliance in tree Figure 37 Show quality compliance in
3. ID list Space 1 Space SELECT SPECTRUM ID FROM Factory all involved tables WHERE all constraints AND re quired PK FK combinations Group by sensor instrument calibration measurement unit Space 2 Figure 5 Building spaces based on user defined subspace projections The Space Factory returns a list of the created spaces Each space can now in turn be used as an input argument of a plotting class instance Utilizing the Space Factory ensures that all spectra contained by a space have a common wavelength per band and the same measurement unit i e the following processing modules do not need to carry out uniformity checks but can apply their algorithms directly e g plotting of spectral vectors against the common wavelengths of the space Interactive flexible and configurable data processing is based on the concept of the Space Net work Such networks consist of processing modules and data sinks sources connected by directed edges aa ee ego eee eee fF 3w Qunenaenam Dammnmdbemmmendb mm 0 Goo ou ou ou uU UD UD ee UD UM Un UU es Space transformation D b p i b i Processing I x _ p b Module x _ pb i P by i P by k MM IIL RE ZI lt lt X Figure 6 Transformation into a new space by a processing module Processing modules are effecting a transformation on a space i e the spectral data vectors of the input
4. Sh ve i P po ed e Figure 49 UTC Time Correction dialog 5 2 Querying Data SPECCHIO features an intuitive way to query data by the means of the Query Builder see Figure 52 To start the Query Builder select Data Processing amp Output Build query from the main menu see Figure 50 SPECCHIO_UserGuide_V2 1 1 docx Version 2 1 1 02 11 2010 SPECCHIO Page 46 User Guide of 103 Two principal ways of data selection are supported a by specifying the needed data using a spectral data browser in the Browser tab and b by entering restricting conditions in the Query conditions tab Actions on both of these tabs will result in the automatic building of an SQL query The query is updated in real time on each user input The number of resulting rows should the query be executed is displayed and updated along with the SQL query The query can be copied from the text area for e g direct execution in an SQL prompt The selected spectra can be fed into four different further modules by pressing the respective but tons Show report File export Process and Spectral Plot Reports are described in 5 2 8 File exports are detailed in 5 2 9 Interactive processing is elaborated in 5 2 10 Data Processing amp Output Build query 00 SEMPER Figure 50 Build query menu entry The data displayed in the Spectral Data browser can be restricted to the data
5. 00 Network Processor a 0 0 Type Sensor instrument Space D 647 Vectors 10 a v crrPPPEEPEPEPEIS lt gt J Figure 150 Space Network Processor window with space containing the target spectra Add Radiance to Reflectance Transformation as a new processing module to the processing plane by clicking the menu button over the processing plane and selecting the module 8 0 0 Module Selection Modules OK B O Radiance to Reflectance Transformation Ref Panel Corr Factors Correct for Ref Panel Delta Waveband Filter Broadband Filter b Narrowband Filter Visualisation Module File Export Module Proof of Concept Figure 151 Selection of the Radiance to Reflectance Transformation module Connect the new module with the input space space 0 by clicking the menu button over the module and selecting Set Input Spaces in the module menu Figure 152 and choosing space number 0 as input space Figure 153 Proc module Radiance to Reflectance Settings Autamatic colartinn fram NR Configure L Set Input Spaces Status Figure 152 Module menu Proc module Radis Settings Auto 6 0 0 Status Input Space Cancel Figure 153 Input space selection for the Radiance to Reflectance Transformation module SPECCHIO_UserGuide_V2 1 1 docx Version 2 1 1 02 11 2010 SPECCHIO Page 97 User Guide of 103 A new space is added to the processing plane au
6. Cancel HET Figure 8 Specifying a pathname under UNIX using the dot as entry in the filename box SPECCHIO_UserGuide_V2 1 1 docx Version 2 1 1 02 11 2010 SPECCHIO Page 20 User Guide of 103 Depending on the UNIX windowing system some of the dialogs are not properly displayed unless they are maximized 5 2 2 Main Window The main window offers the main menu of the application and a progress report panel where the progress of certain processes e g file loading is reported cf Figure 9 The database connection status is shown in the progress report panel as well The panel on the right side is currently not used but might be employed to display e g a log of operations or general user information All SPECCHIO functionality is started by entries in the main menu Database Connection Info Progress report panel Main menu 600 sPECCHIOV2 0 Database Data Processing amp Output Data Maintenance Help Database connection status RN JESiszeCHIO Spectral Database System Connected as specchio to specchio localhost o Figure 9 Main window 5 2 3 Connecting to a Database SPECCHIO can be configured to automatically log into a database at the startup In that case the connection parameters are read from the db_config txt file The database connection information panel see also 5 2 2 always reflects the current connection status Connect to a different database instance or change the database
7. SPECCHIO addresses this by the means of metadata quality levels cf 4 3 In the Metadata Editor activate the checkboxes Highlight mandatory fields and Show quality com pliance in tree Select the bfern 001 spectrum in the Spectral Data Browser and set the required quality level of this spectrum to B cf Figure 137 ih Ts Figure 137 Required quality level set to B All required field should now be highlighted Update the spectrum on the database If the quality compliance is not shown in the tree have it displayed properly by selecting your campaign explic itly again in the Campaign Selection of the Metadata Editor cf Figure 22 All non complying spectra plus the containing hierarchies are marked with an asterisk cf Figure 138 Andy veg example Campaigi Vegetation example Blackfern amp 7 sitet um bfern 002 a heeaer OM Figure 138 Non quality compliance indicated by asterisks Fill in the missing metadata for the bfern 001 spectrum Cloud cover 1 okta or less but not zero Measurement type Single Sampling Environment Field Target Homogeneity homogenous Sensor zenith 0 Sensor azimuth 180 this is equivalent to the principal plane opposite the sun Sensor distance 1 Illumination zenith 40 Illumination azimuth O In the Southern hemisphere the sun stands in the North at midday Target type Add a new target type by clicking the Add
8. button then specify the target type as Tree and set it s abundance 100 L LJ E EJ EJ EJ EJ DJ EL LJ SPECCHIO_UserGuide_V2 1 1 docx Version 2 1 1 02 11 2010 SPECCHIO Page 91 User Guide of 103 Target type di Sel Target type Tree v Abundance 100 After updating the spectrum in the database the non compliance indicators in the spectral data browser should be removed 6 3 Part 2 GER Files Data set GER_example Relevant sections 5 2 4 5 2 5 5 2 5 1 5 2 7 5 2 9 The GER files are contained in the GER example folder Explore the folder You will notice that there are 10 files as created by the GER instrument Create a new campaign to hold GER files cf Figure 139 Create new campaign Campaign name ahueni ger example Main directory PISPECCHIO datalGER example Figure 139 Creation of a GER example campaign After creating the campaign load the spectral data into the database by selecting Data Input gt Load campaign data and selecting the campaign you just created cf Figure 140 Load Spectral Data Campaign name Jahueni ger example R4 Spectral data of the selected campaign will be loaded into the database Figure 140 Loading spectral data into the GER campaign Open the Query Builder Open the tree of the GER campaign and study the contents The files have been automatically split into target and reference spectra cf F
9. Preliminary support for SpectraSuite Data Files Increased number of decimals in CSV file output SPECCHIO_UserGuide_V2 1 1 docx Version 2 1 1 02 11 2010 SPECCHIO Page 5 User Guide of 103 Table of Contents 1 MPEFOOU GU OI se siccee erence ties catee aitere Getta m 8 2 Installation and Configuration cccscceeseeeeeeceeeeeeseneeceneeeeeseneseneeseeesenenees 9 NN BataDaS ed RE EN 9 ZEB VIRI Ce Pee 9 2 1 2 WNOeDNOIK ACCOSSuua da vule unes E au tatto tola is n tpe E Mp PCI asian tence races 9 22 SPECGCHIO ADDIICAUOD Su oni rim p dimos deett mi p ie a NARI LI P MM MR MIDI D UE 9 ZEE Java Ice pem EURAN 9 2 2 2 JApplicauonm BUNGIS 2 rp eae aae I M Iia IE E MELLE 9 22 2 SPECCHIO Application EHesus a ntes bien E aetema m De cU ede 9 222 2 JavauLabtary EXIenstOlSco ies cono tto eno pb ee eet e e LEE 10 2 2 3 MICKOSON VVIRCOWS socer i radpribunto civ Np rion breton teen Wr ncs Mes M M M PT UD UE LII 10 228 AN puc E 10 ZO NEP Ser Mile nito o NETT m NET erm 10 3 Design of Sampling Experiments and Data Structuring 11 S NE O vs RONN 11 2 2 lerarchical SUC e coi v tta d td eaa dites ned Uu Ea v acne mala E bela cdm VOY M Sti ae 11 3 3 Directory Structure and Spectral Files c ccccccccsscccseeceeecceeeceeeceeeeceeecueesueeeeeesseeeeseeseeeeanes 12 3 3 1 Structure to store Reflectance Spectra of several Species and Sampling Sit
10. SPECCHIO provides input and output interfaces to the file system Input file formats are ASD binary file as produced by the ASD FieldSpecPro FS3 spectroradiometers O ENVI Spectral library files SLB and SLI O GER signature files as produced by the GER 3700 Files produced by other GER in struments remain subject to testing O TXT space formatted text files O MFR Photometer OUT files O Apogee files restricted to one tested file format only O SVC HR 1024 files using PDA acquisition Proprietary sensor definition file Sensor definition files are an efficient way of defining new sensors in the database O XML type file format for campaign imports for data transfer between SPECCHIO data bases Output can be written in three data formats O CSV Comma Separated Values for subsequent import into various 3 party applica tions like spreadsheets or statistic packages O ENVI Spectral Library SLB O XML type file format for campaign exports for data transfer between SPECCHIO data bases SPECCHIO_UserGuide_V2 1 1 docx Version 2 1 1 02 11 2010 SPECCHIO Page 19 User Guide of 103 5 1 3 SPECCHIO Operation SPECCHIO is campaign based i e spectral data is grouped by campaigns Advisably a new cam paign is created to hold data for every new sampling experiment The spectral data files of a cam paign must be held by a folder structure similar to the hierarchical structure introduced in 3 2 This structuring allows the aut
11. Vegetation Example I spectrum_name Add trees Common Highlight mandatory fields Mi Highlight shared fields f Show quality compliance in tree f Override conflict detection target type Add Campaign Data Update Hierarchy Data Update l Sensor and Instrument Data Sensor ASD FS FR 3 Hn Foreoptic NIL Spectrum Data Update Name INR ASD e Show Instrument Info o Reference Data E Vegetation Example Campaign v f Vegetation example Reference name NIL Show Reference Info v f Blackfern gt sitel gt L3 Cabbage tree v f Lemonwood v sitel 1 lemonwoo 000 lemonwoo 001 lemonwoo 002 lemonwoo 003 E lemonwoo 005 lemonwoo 006 lemonwoo 007 Blackfern Figure 34 Example of shared field colouring 5 2 6 2 7 Mandatory Field Colouring When a required quality level has been selected for a spectrum the mandatory fields can be high lighted cf 4 3 for more information on metadata quality cf Figure 36 for an example of mandatory field colouring To use mandatory field colouring tick the Highlight mandatory fields checkbox in the control panel cf Figure 35 SPECCHIO_UserGuide_V2 1 1 docx Version 2 1 1 02 11 2010 SPECCHIO Page 38 User Guide of 103 vi Highlight mandatory fields Figure 35 Highlight mandatory fields checkbox Spectrum Data Filename bfern 001 File comment
12. 103 T Type Spectral Space D 6 0 Proc module Broadband filtering Type Sensor Instrument Space 1 Settings Filtering 1 bands i Status Waiting for data Vectors 554 Vectors 554 Vis module Time Line Explorer Settings Status Waiting for data Figure 89 Processing chain for the exploration of the narrowband MFR channels in the Time Line Explorer 5 2 10 6 File Export Module File export modules can be attached to any space and do not generate an output space but write the data to a file A file export module must be configured using its configuration dialog Figure 90 The dialog is identical to the one described in 5 2 9 eoo File output File format csv lt OoOO M Target directory Brwse X Base name ff Options f Split header and body Time format e yyyy MM dd HH mm ss O Milliseconds since 1st Jan 1970 00 00 00 Figure 90 File export configuration The spectral data written to the file reflects the data content of the space The metadata is however mainly read from the database and may show some contradictions to the state of the space 5 2 11 Data Administration Apart from the Data Remover the Campaign Export and the Instrumentation Administration tools all functions described hereafter are available to the SPECCHIO database administrator only Some data administration GUIs are provided however some of the data definition must be done using M
13. 17 11 26 59 2005 08 17 11 27 59 2005 08 17 11 28 59 2005 08 17 11 30 00 an as d SE SE SE SE m Tn Tn an ds ds SE SE JE SE Figure 19 Automatically created total and diffuse hierarchies for MFR data 5 2 5 4 SVC HR 1024 Files This version of SPECCHIO supports SVC HR 1024 files provided that they were captured using a PDA files acquired with a laptop are different in file format and are not recognised by the current file loading routine The HR 1024 stores radiances of reflectance panel target and the computed target reflectance During the data loading SPECCHIO automatically generates a hierarchical structure to store these files see Figure 20 setting up data links that connect the reflectance to the target radiance Radi ance data link and connecting the target radiance to the reference radiance Spectralon data link If the instrument was set to acquire radiances only i e no white reference taken then no special structure will be created SPECCHIO_UserGuide_V2 1 1 docx Version 2 1 1 02 11 2010 SPECCHIO User Guide Page 25 of 103 Note it is highly recommended to enter the instrument into the database and load a wavelengths calibration the wavelengths between instruments differ quite a lot and the blueprint sensor defini tion in SPECCHIO is only a poor representation of the real wavelengths CJ HR Instrument Test Campaign HR Instrument Cj radiances 9 targets HR 071710 0017 sig H
14. Figure 143 Specifying target and reference directories Datalink Datalinks triticaa 000 Spectralon data Figure 144 Example of an automatic created datalink The illumination geometry i e the sun zenith angle and azimuth can be calculated automatically if the spatial position latitude and longitude and the capture time in UTC are known For the given dataset we assume that the time is local time and not UTC This can be corrected by the special function Correct local time to UTC cf 5 2 6 2 10 5 In the time correction dialog select the Gonio_example folder because the time shift should be applied to both target and reference spectra The time difference to GMT is 2 hrs East as the sampling took place during summer in Switzerland i e daylight saving applies cf Figure 145 SPECCHIO_UserGuide_V2 1 1 docx Version 2 1 1 02 11 2010 SPECCHIO Page 94 User Guide of 103 UTC Time Correction jspecchio test Andy_veg_example Campaign H Andy_GER_example Campaign Andy Gonio example Campaign PE EDIT Selected hierarchy Gonio example No of spectra 70 Hours East of GMT 2 Figure 145 Applying a time shift to goniometer data As a next step the coordinates of the sampling area must be defined A position of N47 22 400 E08 32 438 is assumed Positions must be entered as floating point degrees GARMIN hddd ddddd format This yields N47 37333 E08 54
15. KNOW YOUR DAU eis ccs rocco sorceress ursa Sek asa actos ovuRc usu mee uU vata unlrsuEus duit Lec 83 02 4 iE XDOMING Data tO CoV NH HMEe 84 6 2 5 Exporting Data to ENVI Spectral Libraries ccc cccccccc ccc eeeeeeeceeeeeeeeeeeeeeseeeeeeeeeneeneees 86 6026 EditiigMetbadald i ederent ene a eq mese tuae ees E eed hicieron iit DUE 87 2c Pan GER E cR mws 91 64 Parto Direciondl 8e ene mn iC bots ebbe CC LE EC dir 92 6 5 Part 4 Data Querying Processing and Exploration eeeeeeeeeeeeeeeeeeeeeenee 95 6 5 1 Converting Radiances to Reflectances esses nennen nennen nnn nnns 95 0 5 2 Data GQUOFPBS xus er nette ec deceat pep CMM etia eL M ID D DLL D UE CDI ELI ACE 98 7 Change History Mee 100 Lal SPECCHIO App iiGaOn Taenia E A En abe 100 JP NEM 2G 9 510 Ml cat or 0 po honoree ety ce oer PAO ae RE Ec nT Pe 100 TI FKEA BUGS sco scr a a nutu cos UM noice AE we EL E MI Es 100 LEES NEM KNOW BUGS oerein e a wamaecu al mareten lead angele aaedenh ie Ghats a 102 Ae SPECGHIO ata aS E ee ee dese rc En ete aed det ios va Wie eee ene 102 152 Added FH edltles oo etc help a iind ested NE EIE 102 8 References ee 102 SPECCHIO_UserGuide_V2 1 1 docx Version 2 1 1 02 11 2010 SPECCHIO Page 8 User Guide of 103 1 Introduction SPECCHIO is a spectral database combined with user friendly interface software designed to store spectral data acquire
16. LUGER test Campaign gt Jaz Campaign Show report File export X Process Spectral Plot MSD gt JDoe Test Campaign gt 3 bugger Dude test Camp4ign Split spaces by sensor dnd unit only gt another bugger test Gampaign gt HR no GPS Campaign gt LU dc time Campaig gt 3 Hyper I Net Ipfercomparison Campaign eee ID li Fil Spectra Dara Show report button apace P i TePo Process button Spectral Plot button Browser option tick button Figure 52 Query Builder dialog 17 The query conditions tab is grouped similarly to the Metadata Editor The basic query GUI components are a Simple combobox One out of several options can be selected The default All incl none imposes no restriction on the rows to be returned INR 45D wv All incl none INR ASD Instrument b Combobox with wildcard box One of several options in the combobox can be se lected Alternatively a wildcard string can be entered in the wildcard box Standard SQL wildcards can be used These are for any string expression and _ for one character Note that when selecting a combobox entry the wildcard string is auto matically blanked Similarly if a specific combobox entry is selected and wildcards are entered the combobox reverts to the default All incl none AI Andy Hueni Juerg Schopfer c Wildcard text field This takes any SQL wildcard string Investigator Description
17. Processing using the Space Network Starting with version 2 0 SPECCHIO offers interactive configurable data processing The concept is based on the feature spaces Landgrebe 1997 and complex process flows can be realised by building networks consisting of spaces and processing modules For detailed information please refer to Hueni Kneubuehler et al 2009 Spaces are used throughout the system for processing visualisation and file output In all these cases vector data must be related to spectral dimensions and this information is held by the space Moreover a space can hold only spectra that are of the same dimension The Space Factory is a conceptual central component of the SPECCHIO system It creates new spaces based on given inputs and contains the logic to form non mixed spaces Assume the use case of displaying spectral plots of a number of spectra In a first step the user will select the spectra to be plotted by effecting a subspace projection H ni Nieke et al 2007 Internally this will yield a number of record id s that are matching the user s selection These ids are now handed to the Space Factory Internally spaces are created for all existing combinations of the respective sensors instruments calibrations and measurement units associated with the spectra see Figure 5 SPECCHIO_UserGuide_V2 1 1 docx Version 2 1 1 02 11 2010 SPECCHIO Page 17 User Guide of 103 Space list User defined subspace projection
18. SPECCHIO_UserGuide_V2 1 1 docx Version 2 1 1 02 11 2010 SPECCHIO Page 88 User Guide of 103 ahueni_veg_example Campaigi Vegetation example 3 BlackFern S sitel bfern 001 1 bfern 002 1 bfern 003 1 bfern 004 hearer ONC Figure 130 Selecting Blackfern in the Spectral Data Browser of the Metadata Editor By selecting multiple spectra e g by selecting a folder or several single spectra you automatically enter the so called group update modus All data that you enter will apply to all the selected spec tra Note that some fields are not editable but greyed and inactive These fields contain already individual spectrum metadata and are therefore disabled As all the spectra under the Blackfern hierarchy are of the same plant species and entering the plant names can be done for all spectra with a single operation To enter a new name click Add in the Names section First type the common name Blackfern then specify the type as Common from the list cf Figure 131 In a similar manner enter the Latin name Cyathea medullaris Spectrum name d PIE Mame Blackfern Te TTE Figure 131 Entering a common name The names now appear as shown in Figure 132 Note that the Update button of the Spectrum Data section has been activated Perform now the update on the database by clicking the Update button Spectrum names BlackFern Co
19. Sensor name ASD FSFR Mo of channels 2151 Instrument name INR ASD Instrument owner INR Massey University Reflectance Instrument number 6421 1 i FOY degrees 1 000 1 500 2 000 2 500 Wavelength nm Pictures Show pictures bfern 002 Campaign name Vegetation Example Campaign desc Reflectance Filename bfern 002 Capture date 2005 09 11 23 09 54 1 000 1 500 2 000 2 500 Wavelength nm Required quality level B Blackfern 5 2 9 File Output File output is invoked by selecting the Show report button in the Query Builder see 5 2 7 A File output dialog will appear see Figure 57 Two file formats are currently supported O CSV data is written to a text file as comma separated values This file type can be e g read into Excel O ENVI SLB ENVI spectral library file consisting of a header file name hdr and a body file name slb Spectral data are written as floating point values either 32bit or 64bit depending on the architecture of the machine the datatype field in header file is set accordingly datatype 4 or 5 respectively SPECCHIO_UserGuide_V2 1 1 docx Version 2 1 1 02 11 2010 SPECCHIO Page 52 User Guide of 103 A target directory must be specified by clicking on the Browse button All files that are created during file output will be written to this direct
20. be defined by the administrator Use the Add Edit and Remove buttons next to the list to change to contents of the list Associated Measurements 1 Add any number of measurements geo physical parameters associated with the cur rent spectral measurement Ask your administrator if physical units are missing Sensor and Instrument Data cf also 4 5 4 Sensor sensor name Name name of an instrument this is the name given to the instrument by its owner Foreoptic degrees Button to bring up a new window showing information about the instrument see Figure 28 L L1 L1 E Instrument Settings O Instrument settings depending on the sensor Automatically generated from the spec tral input file Reference Data O Name of the used reference panel Button to bring up a new window showing information about the reference panel see Figure 29 SPECCHIO_UserGuide_V2 1 1 docx Version 2 1 1 02 11 2010 SPECCHIO Page 33 User Guide of 103 Pictures Alist of pictures plus captions To add a new picture click on the Add button to the right of the list To remove a picture bring up the context sensitive menu on Windows click the right mouse button and choose Remove To change the caption simply edit the text in the text box below the picture Currently only the JPEG format is supported Note pictures should be reduced in size before loading to the database for speed rea sons Appropriate sizes are around 400 500
21. data source name MediaCatalogMergedDB OLE DB Provider Spectral DB Befresh MediaCatalogw ebDB OLE DB Provider Microsoft Jet 4 0 OLE DB Provider C Use connection string Microsoft OLE DB Provider For Data Mining Services Microsoft OLE DB Provider for Intemet Publishing nc Microsoft OLE DB Provider for OLAP Services 8 0 2 Enter information ta log on to the server Microsoft OLE DB Provider for Oracle i Microsoft OLE DB Provider for Qutlook Search User name SpectraProc Microsoft OLE DB Provider for SQL Server Microsoft OLE DB Simple Provider Password MSDataShape DLE DB Provider for Microsoft Directory Services Blank password Allow saving password 3 Enter the initial catalog to use OK Cancel Help OK Cancel Help Figure 110 Data Link Properties Provider tab left and Connection tab right In the Connection tab select the data source from the dropdown list and enter again the username and password Figure 110 Click OK The database is now listed in ArcCatalog and the tables are displayed when selecting the database Figure 110 1 ArcCatalog ArcInfo Database Connections SpectralDB odc File Edit View Go Tools Window Help g HB CX DE Hse A Qi d D Location Database Connections SpectraIDB ode i e Stylesheet FGDCESA v x Contents Preview Metadata Name Type EE band range MySQL Table Database Connections E derivative MySQL Table Add OLE
22. etu 35 520 24 Group Updates eode oe E eleme cel obo Un eee et iusso estu ee lint n neus 35 5 2 6 2 5 Oyerridime the Contlict Detection oe oot n eee iue e E eee 36 35 3 6 2 0 Shared Field COLOUEIIUD eco teo n bet obe Un re euis Som iue T 36 25 2 0 2 7 Mandatory Field Colouring iu vetro bre ei oe Eee a eee 37 5 2 6 2 8 Showing the Quality Compliance in the Metadata Browser Tree eeeese 39 254 0 2 0 J9ermiionot Data LKS 25 ooo OU dor aoi a Hoo Oo EON De LEES dd 39 35 2 0 2 10 Special FUNC ONS i arrepto Ee tav ta iv tau aatem a a te Los Eo Eod Oen eun nU 40 527 VIN R te Te 45 520 IRGBOIt GefleratllOEl usando tassa textus ze IR DEG E oa ee ERR Quel desta hie ceo ecu segue nae Pup a sene ae 50 5279 IIO e HET RES 51 329 CSV Pile Foma o odisea tu ius ctea opi DUM UE MILAN ORUM UP E eee 53 5 2 10 Interactive Processing using Space Networks eeeeesseeeeeeeeeenenen 54 5 2 10 1 Graphical Representations of Spaces and Modules cccccccccccccececceeceeeeeeeeeeeeeeeeeeeeeaeeaaaaas 55 5 2 10 2 Adding Modules and linking with Spaces sse nnns 56 5 2 10 5 ConftguratiomofMOGWU eS eerta ae tats deus ct ea SINUS ee A NUN OS Fem rossa adu a uten 27 5 2 10 4 Processing Module Descriptions oe oe dua tea pe UN S PADRES ea ba noes unen 57 5 2 10 4 1 Radiance to Reflectance Transformation esses eene eene eene nennen nnns 5d 52 50 42 Reference Panel Correction
23. is updated The critical ones are position environmental data and sampling geometry For these only existing entries will be updated i e if a group of spectra is updated and one of these spectra has no previ ous position record then no new record will be inserted This effect is due to the database model and additional software logic would be required to handle these special cases If you use the conflict overriding option check carefully the results of your updates FREE EERE EERE EEE E EERE EEE EEE EERE EEE EEE EERE EERE EEE EERE REED Perri rl Figure 32 Override conflict detection checkbox 5 2 6 2 6 Shared Field Colouring SPECCHIO_UserGuide_V2 1 1 docx Version 2 1 1 02 11 2010 SPECCHIO Page 37 User Guide of 103 Tick this checkbox see Figure 33 to show which fields of the current spectra selection are shared with other spectra It may help to understand what data is shared and what the effect of an update might be update of shared records M Highlight shared fields Figure 33 Highlight shared fields checkbox See Figure 34 for an example of shared field colouring The spectrum lemonwoo 004 shares spectrum name and pictures with all other spectra under the site1 folder of the Lemonwood folder The instrument information is not shared as each spectrum has a direct link to the appropriate instrument Special Functions Campaign Data Hierarchy Data _ Spectrum Data Current Campaign
24. new dialog enter your name veg example as campaign name e g ahueni veg example Set the Main directory to the Vegetation example folder cf Figure 117 Create new campaign Campaign name ahueni veg example Main directory CHIO dataWegetation example Figure 117 Creation of a new campaign for the vegetation example Press the create button and a message box should pop up informing about the successful creation of the campaign cf Figure 11882 Message 1 New campaign ahueni veg example successfully created Figure 118 Message box informing on successful campaign creation Once the campaign has been created load the spectral data of your campaign by selecting Data Input gt Load campaign data and selecting the campaign you just created cf Figure 119 SPECCHIO_UserGuide_V2 1 1 docx Version 2 1 1 02 11 2010 SPECCHIO Page 83 User Guide of 103 Load Spectral Data Campaign name ahueni_veg_example iy Spectral data of the selected campaign will be loaded into the database Figure 119 Loading spectral data into a campaign A message box pops up when the campaign has been loaded cf Figure 120 A total of 64 spec tral files should now have been loaded into the database Message 1 64 files successfully processed Figure 120 Message box showing the number of processed files during campaign loading 6 2 3 Get to Know Your Data Relevant secti
25. number of target types becomes a handling problem for the user 4 5 4 Sensors and Instruments SPECCHIO defines sensors and instruments While these terms are sometimes interchanged in everyday scientific language it is important to understand that sensors and instruments are mod elled as two different entities in the database Sensors define the physical setup of sensors i e number of channels average wavelength and FWHM per channel sensor type number usually a code given by the manufacturer e g 4 for ASD FSFR sensor Sensors are defined only once in the database Instruments on the other hand are existing instances of a certain sensor type There can be several different instruments that are all of one sensor type Instruments also have a defined owner and a history of calibrations Consider the example of a GER 3700 instrument this instrument is an instance of a GER 3700 sensor The sensor defines the average wavelength per channel As long as no calibration for the instrument has been entered into the database the channels defined in the sensor will be used for plotting and exporting spectral data When calibrations are entered for instruments they override the sensor specifications For further information please refer to H ni et al 2007 Instruments that change the number of stored spectral bands based on user configurations such as is possible with the new SVC HR 1024 are not yet supported 4 6 Spaces Space Factory and Data
26. of charge to interested parties Please direct expressions of interest to admin specchio ch 2 1 2 Network Access Note this mainly applies if a locally administred instance of the SPECCHIO database must be con figured for network access The SPECCHIO application can access the database over the network if the following configura tions are performed The IP addresses of all machines from which the users can connect are added to the user privileges Alternatively a range of IP addresses can be configured using a net mask see MySQL online documentation for details or a value of 9e will allow access from any possible machine The port of the MySQL server 3306 by default must not be blocked by firewall 2 2 SPECCHIO Application 2 2 1 Java Version SPECCHIO requires Java runtime environment JRE version 1 5 and higher To check the java version on your system open a system prompt i e command window under Windows terminal for Macintosh and UNIX systems and type java version The output will be similar to java version 1 5 0 06 Java TM 2 Runtime Environment Standard Edition build 1 5 0 06 b05 Java HotSpot TM Client VM build 1 5 0 06 b05 mixed mode 2 2 2 Application Bundle The SPECCHIO application plus the needed libraries are supplied as application bundle in ZIP file format As a first step you must un zip the ZIP archive The files contained in the bundle are described hereafter 2 2 2 1 SPECCHIO Ap
27. of the current user by clicking the tickbox Show only my data see Figure 51 use M Show only my data HP specchio gt L3 ADS40 Gnd Truth Rheinau Campaign Figure 51 Restricting the data displayed in the spectral data browser to the current user For the options Spectral Plot and Process the building of spaces can be controlled by switching on off the Space split option if selected spaces will only be created per sensor type and meas urement unit if deselected spaces will be created per sensor type measurement unit instrument and instrument calibration SPECCHIO_UserGuide_V2 1 1 docx Version 2 1 1 02 11 2010 SPECCHIO Page 47 User Guide of 103 Restri N f resulti in data E Browser tab Query conditions tab Auto built SQL query UHIDROFEESHIHOE current user tick box rows eoo Query Builder Query conditions Show only my data E specchio gt 0 AgRes Root Density and Water Content Campaign Y EB Vegetation Example Campaign SQL Query autobuilt v Vegetation example posure j SELECT count FROM spectrum WHERE spectrum id in 5259 5260 521 5265 5266 5267 5268 5269 5270 5271f 5272 5273 5274 5275 gt m gt Lu Cabbage tree gt 3 Lemonwood Y HR Instrument Test Campaign Y EJ HR Instrument gt Lu radiances Y E reflectances HR 071710 0017 sig fi Po oo MUM HR 071710 0018 sig Number of resulting rows HR 080910 0010 sig gt ASD test Campaign gt
28. the documentation 1 1c 31 01 2008 A Hueni Added spectral plot to metadata editor Added campaign export functionality Time format option in the export dialog Bugfix Position Location field in Metadata editor now accepts alphanumeric input SPECCHIO_UserGuide_V2 1 1 docx Version 2 1 1 02 11 2010 SPECCHIO Page 3 User Guide of 103 1 2 29 05 2008 A Hueni Major rework of the Metadata Editor Super fast group updates Shared data highlighting Shared data update reimplementation Shared data awareness for gonio and sun angle calculations Direct selection of gonio and sun angle calcula tions from the sampling geometry field 15 06 2008 Added campaign import function Some bugfixes 1 3a 25 07 2008 A Hueni SPECCHIO would stall during data export due to the jgraph extension not being found The application has been recompiled to include the jgraph extension in the needed extension list and jgraph is now bundled with the SPECCHIO application 1 3c 26 09 2008 A Hueni a A switch in the Query Browser that lets you restrict the data to your own data only b The Data Browser in the Metadata Editor is now con tained in a scroll pane and thus also displays correctly on small screens 12 03 2009 A Hueni Major update Database schema update to include reference panel handling including correction factors and un certainty Processing extension Instrument and reference panel handling tools Updated export import fu
29. tree checkbox me Vegetation Example Campaign A vegetation_example 3 Blackfern sitel 1 bfern O01 bfern 002 bfern 003 bfern O004 bfern O005 bfern O006 Figure 38 Quality non compliance indicated by asterisks in the metadata browser 5 2 6 2 9 Definition of Data Links Data links can be defined on spectrum and hierarchy level i e spectra link to spectra and hierarch ies to hierarchies The definition of links is explained for spectrum datalinks hereafter The defini tion of hierarchy datalinks is identical in terms of user interactions Clicking on New right to the datalink list cf Figure 39 will open a new dialog cf Figure 40 Datalink Figure 39 Datalink list and New and Delete buttons In this dialog use the spectral data browser to select the spectrum that shall be linked The selected spectrum will be displayed in the right side in a read only field Select the link type from the list box Click OK to create this link Note that the function Link targets to references provides a quicker and easier option to create reference panel links see 5 2 6 2 10 2 SPECCHIO_UserGuide_V2 1 1 docx Version 2 1 1 02 11 2010 SPECCHIO Page 40 User Guide of 103 Datalink details Sele Photometer Campaign small_MFR_set Campaign MFR2 Campaign 2006 6 24 Em EN datetest Campaign 30 08 2005 MFR Campaign O Y
30. 0 5 2 Spectral Scatter Plot Use this plot to display values per spectral band as singular points This is useful to plot e g data of sensors with just one band e g MFR broadband as single values cannot be visualized as line plots Scatter plots are also useful to show the variation of the values per band Figure 80 shows an example of the variation per channel for several MFR sunphotometer readings Note the generation of scatter plots of several spectra with high dimensionality tends to be quite slow SPECCHIO_UserGuide_V2 1 1 docx Version 2 1 1 02 11 2010 SPECCHIO Page 64 User Guide of 103 Radiance 400 600 800 1000 Wavelength nm Figure 80 Scatterplot showing the variation per channel for several MFR sunphotometer readings 5 2 10 5 3 Gonio Sampling Points Plot Use this plot to visualise the sampling positions of directional measurements acquired by a goni ometer system The plot is not expecting any specific number of points or particular geometry The sampling points are projected from their angular definition zenith azimuth onto a 2d Cartesian coordinate system Figure 81 Goniometer Sampling points Figure 81 Goniometer sampling point positions 5 2 10 5 4 Gonio Hemisphere Explorer The Hemisphere Explorer allows the interactive exploration of a spectrodirectional dataset typically acquired by a goniometer system Figure 82 shows an explorer window displaying a LAGOS La boratory goniometer system data
31. 063 In the Metadata Editor select the Gonio example hierarchy in the Spectral Data Browser As the position applies to all spectra of the campaign a group update should be carried out Now enter the latitude 47 37333 and longitude 8 54063 Longitudes East of Greenwich are negative Having entered position and time do not forget to press the Update button the calculation of the illumination geometry can be carried out by clicking the Calc Sun Angles button cf Figure 146 E gonio Campaign Sensor azimuth illumi v Bl Gees cue gt i reference Sensor distance illumi v target triticaa 001 Calc Gonio Angles Calc Sun Angles triticaa 002 T 600 Sun Angle Calculation triticaa 003 triticaa 004 No of spectra 70 triticaa 005 triticaa 007 e Ceemei d 5 triticaa 008 In f Figure 146 Sun angle calculation for goniometer data Use the Spectral Browser of the Metadata Editor to check the sun angles that have been calcu lated Every spectrum has been assigned slightly differing sun angles according to the individual capturing time The angles of the goniometer can be calculated for each spectrum using the Calc Gonio Angles function cf 5 2 6 2 10 1 Select the target hierarchy and click the Calc Gonio Angles button On the left side of the dialog the number of spectra in the selected hierarchy is displayed 63 spectra There are three spectra missing fro
32. 1 02 11 2010
33. 10 52 36 AM longitude 01116 9879 E 01116 9933 E latitude 4806 4988 N 4806 5075 N gpstime 084748 000 085034 000 comm 8224 8224 8224 8224 8224 8224 SPECCHIO_UserGuide_V2 1 1 docx Version 2 1 1 02 11 2010 SPECCHIO User Guide Page 26 of 103 memory slot 0 O factors data 350 6 127369 73 4658 17 3 66 352 1 130962 30 4815 39 3 68 353 7 132239 65 4916 35 3 72 355 3 128726 40 4836 48 3 76 356 8 124030 10 4677 99 3 77 358 4 123421 08 4677 13 3 79 359 9 130810 10 4966 42 3 80 5 2 5 5 Apogee Files Apogee files are supported but not extensively tested as yet The file format currently recognised is shown below File cachimbalito2Np5 2 TRM TRANS Wave 733 53nm Pix 1050 val 25 767 Time 23ms Avg 7 Sm 0 Sg 0 Tc on Xt 1 Ch 1 400 00 1 102E 000 400 50 1 131E 000 401 00 1 205E 000 401 50 1 257E 000 402 00 1 260E 000 402 50 1 336E 000 403 00 1 341E 000 403 50 1 418E 000 404 00 1 451E 000 404 50 1 444E 000 1 488E4000 405 00 5 2 5 6 ENVI Spectral Library Files These files can contain more than one spectrum Upon loading each spectrum is saved separately Note that the sensor definition i e central wavelengths is not read from the ENVI header file Spectra loaded from ENVI SLB or ENVI SLI files are automatically assigned a sensor based on the number of channels if existing this approach my produce wrong sensor assignments Use the Metadata Editor to set a sensor if needed Spectra n
34. 1076 Spectra Averaged 10 HR4C1076 Boxcar Smoothing O CHR4C1076 Correct for Electrical Dark No HR4C1076 Strobe Lamp Enabled No HRA4C1076 Correct for Detector Non linearity No HR4C1076 Correct for Stray Light No HR4C1076 Number of Pixels in Processed Spectrum 3648 gt gt gt gt gt Begin Processed Spectral Data lt lt lt lt lt Wavelength nm radiance w m 2 sr 1 nm 1 717 00000 0 17904775 717 02000 0 17878146 717 04000 0 17849983 717 06000 0 17820124 The expected file extension is currently set to csv although the files are not comma separated as such The instrument number is taken to be the last four numbers of the spectrometer name e g 1076 in the above example The time format is expected to be as in the above example i e it is probably depending on the settings of the controlling post processing computer 0 2 6 Editing Metadata The SPECCHIO Metadata Editor is a powerful tool that allows you to enter metadata in a stream lined way thus minimising the required user input To open the metadata editor select Data Input gt Edit metadata Figure 21 eepe Data Output Create new campaign Load campaign data Figure 21 Selection of current study 5 2 6 1 Description of the Metadata GUI elements The campaign editor consists of a control panel on the left side and a data area on the right side with three tabs for campaign hierarchy and spectrum data cf Figure 22 The control pan
35. 19 22 2 Main VVINGOW c b ae 20 5 2 9 Connecting toa Database o eo e etic ei ee eee e tm ee 20 5 24 Crea ng a new Campalgh si e petet toto medics texit m tex det te uem eo eiu 21 5 29 Loading Campaldn Data e tonto Io Pi at It hoes eee be t um ee au 22 5 2 Du ASD PIES usi RT i orici ee ID M D EE 23 MLN GER SENE Fil oSer on orici tian dedo hu oe ufu asiste 23 SPECCHIO_UserGuide_V2 1 1 docx Version 2 1 1 02 11 2010 SPECCHIO Page 6 User Guide of 103 D222 AVE R OLD FICS dato atte ot eden QUUD Hte uu co Mat MR cso rc aen e uou eau bua 24 242454 VE HARTO ATF eSa utes aust etn ubt buda Cann iowa erit Osee dos Rut alendis 24 as ME us alm r m M 26 212 540 JEN TE Spectral Ebra BIeS oo ee enter ia in re bc en Doe et b etum eu uiebur 26 22r XDspaee FOrmmatted Text DH eS i uiii oe aUe dete aei dine pado oU Eat ad ca Uri E 26 5 2 5 8 Ocean Optics Spectrasuite Data Files sot o e eto DOM ta th pix pieta e eee 27 526 Eding Metadata i i D te bre ee tei dia vedeu cis det xri ancien utei de dades edds 2 5 2 6 1 Description of the Metadata GUI elements 00 0 0 sse nnns 27 5 2 6 2 Operation Principles of the Metadata Editor sse nnns 35 5 3 6 2 1 Display MeLadaltao sena eie el rain sg toe Bea is o un a Eu Sl taal 35 520 222 DARELUCORBIIGIS eri i cte etic tle nee Ar ect Eu te ane DEAD teintes 35 35 0 2 3 Updates dnd Beselstssieseie iim tine ec ans is to um T
36. 7 Spectra listed in the Spectral Library Viewer SPECCHIO_UserGuide_V2 1 1 docx Version 2 1 1 02 11 2010 SPECCHIO Page 87 User Guide of 103 r Spectral Library Plots on terra File Edit Options Plot_Function Help Spectral Library Plots 0 8 0 6 0 4 Ui 0 0 500 1000 1500 2000 25C Wavelength Figure 128 Blackfern spectra as Spectral Library Plots 6 2 6 Editing Metadata Relevant section 5 2 6 Open the metadata editor by selecting Data Input gt Edit metadata from the main menu and select your campaign Note that in the Campaign Data tab your name is automatically listed as Investiga tor Enter some description into the description text field e g Just a test Note that as soon as you change some data in the metadata editor the relevant Update button in this case the button in the campaign data section gets activated cf Figure 129 Perform the update by clicking on the update button This stores your changes in the database The update is done when the Update button reverts to being grey and inactive Campaign Data Hierarchy Data Campaign name ahueni veg example Spectrum Data Just a test Description ahueni veg example Campaign Path oriDesktopiSPECCHIO dataivegetation example Figure 129 Editing the description of a campaign Switch to the Spectrum Data tab and select the Blackfern folder in the Spectral Data Browser cf Figure 130
37. A message box will appear once the export is finished Use your file system browser to have a look at the output file that has been written into the output directory you specified cf Figure 124 The file name is partly auto generated and includes the following parts O blackfern the base name you specified O INR ASD name of the instrument used to sample the data O ASD FS FR 3 the sensor type Blackfern INR ASD ASD FS FR 3 csv Figure 124 Exported CSV file CSV files can be conveniently loaded into spreadsheet and statistics applications Alternatively you can view them in a text editor CSV files can be split into header and body where the header contains all metadata and the body consists of the channel and spectral information Figure 125 shows a spectral plot of the first six Blackfern spectra in Microsoft Excel The first col umn contains the central wavelength of the bands in nanometres 0 025169 0 026092 0 026704 0 026678 0 025368 0 025327 0 025193 0 024652 0 025456 0 025762 0 025551 0 024526 0 025853 0 026994 0 025604 0 0261 0 026092 0 02507 0 02431 0 024443 0 021602 0 021689 0 020632 0 025169 0 027224 0 022059 0 021206 0 021851 0 026092 0 02736 0 023043 0 022523 0 022516 0 026704 0 028278 i Series3 Series4 Series5 Series6 500 1000 1500 2000 2500 3000 Figure 125 Example of a spectral XY plot in Microsoft Excel SPECCHIO_UserGuide_V2 1 1 do
38. AND spectrum campaign id cam paign campaign id As a matter of fact the spectra selected by this query all belong to the goniometer campaign that you created in this tutorial The same result set is returned when the goniometer campaign is selec ted implicitly The result set can be further restricted by e g sampling geometry conditions Narrow the search for spectra with zenith angles between 0 and 30 by entering a sensor zenith angle of 15 and a buffer size of 15 and sensor azimuth of 90 with buffer size 90 cf Figure 157 Sampling geometry Sensor zenith 15 Buffer size 15 Sensor azimuth 90 Buffer size 90 Figure 157 Specifying a sensor zenith azimuth angles and buffer values The resulting SQL statement should look like SELECT count FROM spectrum campaign sampling_geometry WHERE cam paign name V2 0 Gonio Test AND campaign user id 1 AND sam pling geometry sensor zenith gt 0 0 AND sampling geometry sensor zenith lt 30 0 AND sampling geometry sensor azimuth gt 0 0 AND sam pling geometry sensor azimuth lt 180 0 AND spectrum measurement type id 2 AND spectrum campaign id campaign campaign id AND spec trum sampling geometry id sampling geometry sampling geometry id The number of resulting rows should be 17 Press the Process button in the Query Builder to load the selected data into the Space Network Processor Add a new Visualisation Module configure it as Gonio He
39. DB Connection E derivative_calc_method MySQL Table Add Spatial Database Conr Ez feature space MySQL Table 3 feature space type MySQL Table a Address Locators a Jibrary MySQL Table j GIS Servers E mixture MySQL Table amp Search Results E pca_data MySQL Table E sensor MySQL Table 3 sensor element MySQL Table Gg sensor response type MySQL Table E3 site MySQL Table E smoothing Filter MySQL Table E smoothing Filter type MySQL Table E species MySQL Table IERI spectrum MySQL Table E statistic MySQL Table E3 study MySQL Table E waveband_filter MySQL Table E waveband filter range MySQL Table Bile OLE DB Connection selected Figure 111 SPECCHIO and tables in ArcCatalog 5 2 12 3 Adding Table Data to a Map To add table data to a map select Add Data in ArcMap and choose the SPECCHIO under Data base Connections Figure 112 Then select the spectrum table as the data source Figure 113 The spectra positions can then be displayed on the map by selecting Display XY Data and using the longitude and latitude fields of the site table as X and Y coordinates SPECCHIO_UserGuide_V2 1 1 docx Version 2 1 1 02 11 2010 SPECCHIO User Guide Lookin Database Connections v al gla Add OLE DB Connection Add Spatial Database Connection fz SpectralDB odc Name SpectralDB odc Show of type Datasets and Layers lpr v Cancel Figure 112 Selecting the specchio datab
40. DY csv Bib mixed instr INR ASD_cal1_HDR csv Bal mixed instr RSL ASD 1 BODY csv Bah mixed instr_RSL ASD 1_HDR csv Bal mixed instr RSL GER 3700_BODY csv Bal mixed instr_RSL GER 3700_HDR csv The option Split header and body is only available for CSV files ENVI SLBs are automatically split into header and body Two time formats are possible Select the Milliseconds if you easily want to plot a timeline 600 File output File format CSV HH Target directory Users andyhueni Data Studies RSL SPECCHIO Project SPECCHIO Output Browse Base name Blackfern Options Split header and body Time format 9 yyyy MM dd HH mm ss C Milliseconds since 1st Jan 1970 00 00 00 OK Cancel Figure 57 File output dialog SPECCHIO_UserGuide_V2 1 1 docx Version 2 1 1 02 11 2010 SPECCHIO User Guide 5 2 9 1 CSV File Format The CSV file format contains a header and a body If the file is not split then header and body are written into the same file Metadata are essentially adding dimensions a dataset i e the total dimension is given by number of spectral bands number of metadata fields The dimension of an output file is therefore Number of rows lines total spectrum dimension Number of columns number of spectra 1 dimension name column The line format is specified by lt dimension name gt lt value gt lt value gt A file example showing part of a header and body foll
41. HIO Page 84 User Guide of 103 Query Builder Browser Query conditions specchio_test a Andy veg example Campaign Vegetation example Blackfern a sitet Cabbage_tree sitel cabbage 000 cabbage 001 cabbage 002 cabbage 003 cabbage 004 cabbage 005 cabbage 006 cabbage 007 cabbage 008 cabbage 009 a site2 E Lemonwood eeee08080080 86 Figure 121 Vegetation example campaign shown in the Spectral Data Browser of the Query Builder Spectral plot i Campaign name v2 0 Veg Example 0 Campaign desc Y J c a U EY ES co Filename bfern 001 Comment 3000 Figure 122 Part of the report on Blackfern spectra 6 2 4 Exporting Data to CSV Relevant sections 5 2 7 5 2 9 Select File Export in the Query Builder first select some data as described in 6 2 3 Specify CSV as file format an output directory use the Browse button to select a directory and a base filename and then press OK cf Figure 123 see also 5 2 9 SPECCHIO_UserGuide_V2 1 1 docx Version 2 1 1 02 11 2010 SPECCHIO Page 85 User Guide of 103 eoo ile output File format CSV H Users andyhueni Data Studies RSL SPECCHIO Project SPECCHIO Output Blackfern Browse Target directory Base name Options Split header and body Time format 9 yyyy MM dd HH mm ss Milliseconds since 1st Jan 1970 00 00 00 OK Cancel 5 Figure 123 File export dialog
42. L Brand name Spectralon Reference type White reference panel Manufacturer Labsphere Inc Field spectralon panel Figure 29 Reference panel information window 5 2 6 2 Operation Principles of the Metadata Editor 5 2 6 2 1 Displaying Metadata The campaign tab automatically shows the campaign metadata of the selected campaign To display hierarchy metadata select a hierarchy level in the spectral data browser To display spectrum metadata use the spectral data browser to select a a single spectrum b multiple spectra use shift and ctrl keys c a single hierarchy or d multiple hierarchies use shift and ctrl keys Note on Mac systems the ctrl key is mapped to the key 5 2 6 2 2 Data Conflicts Selecting several spectra at once can lead to data conflicts E g the filename of spectra is usually unique per hierarchy Therefore a filename cannot be displayed in the Filename field when more than one spectrum is selected A conflict check is automatically carried out when a multiple selec tion happens All conflicting fields are cleared and set to read only and thus cannot be changed by the user 5 2 6 2 3 Updates and Resets The Update button of the concerned metadata tab is activated as soon as a metadata field is edited by the user cf Figure 30 for an example Clicking Update will commit all the changes that have been entered in the metadata fields of the relevant tab to the database Clicking Reset wil
43. O Page 45 User Guide of 103 ee ee eee MFR2 Campaign CIMFR 2 a total diffuse a direct a datetest Campaign Figure 48 Direct irradiance hierarchy 5 2 6 2 10 5 UTC Time Correction This tool is provided to handle cases where the capturing time is not in UTC Technically it applies a time shift based on the number of hours entered by the user in the UTC Time Correction dialog see Figure 49 Select the hierarchy containing the spectra that need to be time shifted The selected hierarchy and the number of spectra are shown on the left in read only fields The hours are specified as East of GMT The time shift is implemented as Date time in milliseconds Date time in milliseconds hours east of gmt millies per hour This means that if a time shift happens across midnight the calendar date of the capture time will also be shifted back or forth depending on the value of hours east of gmt E g for a local capture time around 10am in Oceania a time shift of around 12 hours East of GMT is needed The UTC time will then be 10pm the previous day UTC Time Correction specchio calib id test seems to work Campaigi units Campaign Blackfern Campaign 5 83 bFern O01 bfern 002 bFern 003 bfern 004 No of spectra 17 bfern 005 j bfern 006 Hours East of GMT 12 bFern O07 bfern 008 bfern 009 bFern O10 bFern 011 bFern 012 bFern 013 bFern 014 Selected hierarchy sitel
44. Pelosi pete tiit dio ot ace le io osa det pet E 57 5 2 10 4 5 Correct for Reference Panel Non Idealigess aei ti dade dott ace eei eo tas net erui ue 58 Oe DE Mia tes EE C TE 59 5 2400 As Wave band FINO cites ee octies epa sleicat must E pter 60 5 2 10 4 6 Broadband and Narrowband Filters essen 61 SLIOS WasaelisauomiVlodules eode Diei iat oia ite gue faq a ut Hades qus tas togata fedet 62 SOS TOSS Spectral Line POE occidi ioi ostia ot tabe ot bates ast deett iecit E idees 63 5 2410 5 2 ospeak ocan r DIOE enden iati eati ost a tadiosu lacia E et dee 63 5 2 50 55 Gono Sampling Points Piot uu eii otto etate sec tt deu tdt let iidem TE 64 5 2 10 5 2 Gomo Hemisphere EXploEPeE eei ote ot bata itne tot deu odiosa ides det eei T 64 5 2 0 5 5 Dime Dime DIO aucune etie enestin E et adus 66 5 2 10 5 6 Linie Eine Epor ease on esegue obO dde out tasted aed dut uae deep a opui DU boo tart 67 5 20268 Bale Export WOU Ne uci hito dou Danes a ideae dte itat ecb 68 9 24 ataoxominieialOE scaussdertaniudce bti rte vd Fert eda e aur orci desto FS eo aet autc fep 68 Scl Remove dadld uses den rdteii ideo aati ancients a Une adalat i o Sanaa dLe ii Du U ua dt iEE 69 5 2 122 Campen B SDOEE edsicass ee a ne ene ed Rn ee ua iuses uide ne ene eee eee ne dr Dp ee 69 IAES Catia at oii LIMP ONE sese taeg ince tattenscete sna sae lunes eso uates ee Doi uides e but tt 69 5 2 11 4 AOSTInIHOD OT new Senso apnea nia deest eso ua
45. R 071710 0018 siq references HR 071710 0017 sig HR 071710 0018 sig reflectances HR 071710 0017 siq HR 071710 0018 sig Figure 20 Automatically generated hierarchy for HR 1024 files Examples of two valid files is given below Spectra Vista HR 1024 name My Documents HR1024_Data HR 071710 0017 sig instrument HR 0761008 integration 2 22 20 12 50 30 scan time 1 1 optic LENS14 LENS14 temp 31 29 0 41 5 71 31 53 0 41 5 77 battery 7 7 7 7 error 0 O units Radiance Radiance time 7 18 10 9 47 09 AM 7 18 10 9 47 31 AM longitude 11121 2335 w 11121 2324 W latitude 5330 5955 N 5330 5964 N gpstime 154336 000 154356 000 comm memory slot 0 O factors data 344 2 56023 55 4381 86 7 82 345 8 54418 00 4186 00 7 69 347 3 56037 65 4365 57 7 79 348 9 59474 63 4568 75 7 68 Spectra Vista SIG Data name My Documents HR1024_Data HR 080910 0010 sig instrument HR 0971030 integration 20 19 2 30 200 60 30 scan time 3 scan settings AD AI external data seti 8524 8224 8224 8224 8224 8224 8224 8224 8224 8224 8224 8224 8224 external data set2 8224 8224 8224 8224 8224 8224 8224 8224 8224 8224 8224 8224 8224 external data dark 0 0 0 0 0 0 0 0 external data mask O optic LENS 4 LENS 4 temp 36 21 9 08 5 30 36 45 9 08 5 37 battery 7 5 7 4 error 0 O units Radiance Radiance time 8 9 10 10 49 47 AM 8 9 10
46. R sunphotometer which features one panchromatic band and 6 narrower bands The value ranges of the broad and narrow bands are very different and even a simple plot cannot be created satisfactorily see Figure 75 The broadband channel has been placed at the likely centre wavelength of 673nm As the bands of the MFR are defined in the order of the broad band followed by the narrowbands in the database the plot shows two spectral lines Mixing broad and narrowbands should not be done from a physical point of view 500 400 600 800 1000 Wavelength nm Figure 75 Spectral plot of broad and narrowband MFR channels Figure 76 shows a space processing network that illustrates the function of broad and narrowband filters SPECCHIO_UserGuide_V2 1 1 docx Version 2 1 1 02 11 2010 SPECCHIO Page 62 User Guide of 103 j Proc module Broadband filtering 1 Type Sensor instrument Space Settings Filtering 1 bands Type Spectral Space D 7 Status Waiting for data D 6 Vectors 1 Vectors 1 Proc module Narrowband filtering Settings Filtering 6 bands Vis module Spectral Line Plot Settings Status Waiting for data Status Waiting for data Vis module Spectral Line Plot 2 Vis module Spectral Scatter Plot Settings Type Spectral Space Settings Status Waiting for data Status Waiting for data Vectors 1 Figure 76 A space processing network demonstrating the function of broad and narrowband
47. SPECCHIO Page 1 User Guide of 103 PCHIO User Guide Version 2 1 1 Date 02 11 2010 Status Valid Author A Hueni Remote Sensing Laboratories University of Zurich File SPECCHIO_UserGuide_V2 1 1 docx Pages 103 Classification Distribution SPECCHIO Users measurements products policy SPECCHIO_UserGuide_V2 1 1 docx Version 2 1 1 02 11 2010 SPECCHIO Page 2 User Guide of 103 History Version Date Author jRemak Cs 15 12 2006 First valid version 0 2 13 02 2007 A Hueni Instructions for entering pathnames under UNIX Updated installation description Bug fix update Tutorial 1 0c 14 02 2007 A Hueni Bug fixes and added features Version number of this document is now synchronized with the software version number Some changes due to input from the first tutorial session 1 0f 29 05 2007 A Hueni Added features txt file reader CORINE landcover class displayed as tree in Metadata editor 1 1 18 10 2007 A Hueni Updates due to adding multi user capabilities to the data model and ap plication pre configuration of database connection details via the db config txt file Admin functions not visible for normal users Bug fixes 1 1a 03 11 2007 A Hueni Software updates and bug fixes mmm Description of plot control other minor changes Change of the application bundle to flat file structure in order to prevent installation problems Reflection of that change in
48. a number given to a sensor e g the ASD FSFR sensor has type number 4 The type number is usually part of spectral data files and the data loader can use it to automatically assign the correct sensor to a spectrum The FWHM is currently not read into the database SPECCHIO_UserGuide_V2 1 1 docx Version 2 1 1 02 11 2010 SPECCHIO Page 71 User Guide of 103 Company Type no no of channels 2 ASD FSFR ASD Fieldspec FR ASD 4 2151 3 Band Average Wavelength nm Full Width at Half the Maximum FWHM nm 350 351 352 353 354 355 356 357 358 359 CO c0 0 c B0 NA MO NO NO hO NO NO NO IND ND IO Figure 95 Part of a sensor definition file being edited in Excel 5 2 11 5 Instrumentation Administration The instrumentation administration comprises metadata editing for instruments and reference pan els Any user can open the dialogs but only administrators will be able to commit any changes to the database Editing data is identical with the function of the Metadata editor for spectral data Every change of a field activates the Update button The dialog consists of two tabs a Instrument Data and b Reference Data 5 2 11 5 1 Instrument Administration The instrument data tab allows adding editing and removing instruments and editing their meta data Figure 96 eno Instrumentation Metadata Editor Pictures Current Instrument Pictures Instrument Data Instrument name ImagingCent
49. adiances are ob served in the principal plane The illumination source is at azimuth position 180 in the shown plot SPECCHIO_UserGuide_V2 1 1 docx Version 2 1 1 02 11 2010 SPECCHIO Page 100 User Guide of 103 7 Change History 7 1 SPECCHIO Application 7 1 1 Added Features SPECCHIO Version V1 0c Spectra names are read from ENVI slb header files and stored as 14 02 2007 part of the filenames in the database Spectra names from slb headers are also inserted into the spectra name table with a name type of ENVI Hdr Database connection status is shown in main window 14 02 2007 Added ENVI SLI files to recognized file types 21 02 2007 Automatic connect to localhost when louie geo unizh ch is not 21 02 2007 available Better error messages when connections to database fail Landcover type selection in Metadata Editor now based on tree 10 04 2007 display Support for loading TXT files 29 05 2007 Multiuser support 18 10 2007 Database connections configurable via db config txt file Lazy loading algorithm for spectral databrowser allows efficient 03 11 2007 working with large datasets Super fast group updates Shared data highlighting Shared data 03 06 2008 update reimplementation Shared data awareness for gonio and sun angle calculations Direct selection of gonio and sun angle calculations from the sampling geometry field Several progress reports added report Added help menu item and specchio info dialog
50. ads lagos artificial turf 2008 06 13 11 39 58 xml Import Cancel Figure 93 Campaign Import Dialog The import function resolves all primary key foreign key relations making the imported campaign fitting seamless into the existing data environment i e no possible conflicts between the imported and already existing campaigns Note the involved databases must have matching database version This is currently not checked Further issues of system table duplication may arise if e g institute or user information are not identical in both databases 5 2 11 4 Definition of new Sensors New sensor can be defined by loading a sensor definition file Select Data Maintenance Load sensor definition from the main menu In the Read Sensor Definition File dialog specify the sensor definition file and click OK to read the file and insert a new sensor into the database cf Figure 94 Read Sensor Defintion File Sensor definition File fies RSL SPECCHIO ProjectiSensor DefinitionsNASDSensorData txt Figure 94 Read Sensor Definition File dialog Sensor definition files are tab separated text files that can be edited in e g Excel cf Figure 95 The file format is as follows Name Description Company Type no no of channels sensor name gt sensor descr company name type number no of channels Band Average Wavelength nm FWHM nm band number wavelength lt fwhm gt The type number is
51. aly sis on the Example of New Zealand Native Plants Institute of Natural Resources Palmerston North Massey University Hueni A M Kneubuehler et al 2009 PROCESSING EXTENSION FOR THE SPECTRAL DATABASE SPECCHIO EARSeL SIG IS Tel Aviv Israel SPECCHIO_UserGuide_V2 1 1 docx Version 2 1 1 02 11 2010 SPECCHIO Page 103 User Guide of 103 Huni A J Nieke et al 2007 Metadata of Spectral Data Collections 5th EARSeL Workshop on Imaging Spectroscopy Bruges Belgium ISO IEC 1996 Information technology Syntactic metalanguage Extended BNF 14977 Ge neva Switzerland ISO IEC Copyright Office Landgrebe D 1997 On Information Extraction Principles for Hyperspectral Data West Lafayette IN Purdue University schopfer J 2008 SPECTRODIREC TIONAL GROUND BASED REMOTE SENSING USING DUAL VIEW GONIOMETRY Zurich Remote Sensing Laboratories Schopfer J S Dangel et al 2007 Dual Field of View Goniometer System FIGOS ISPMSRS 12 14 March 2007 Davos Switzerland U S Naval Observatory 2003 What is Universal Time from http aa usno navy mil fag docs UT html University of Washington undated Total Cloud Amounts from http www atmos washington edu gcg MG tepps SPOON photoen cover html Wirth N 1977 What can we do about the unnecessary diversity of notation for syntactic defini tions Communications of the ACM 20 11 822 823 SPECCHIO_UserGuide_V2 1 1 docx Version 2 1
52. ames are read from the header file if available and stored in the database as spectral name entry with a spectral name type ENVI Hdr Note the import routine expects the spectral library files to have extensions of either slb or sli a valid example is given hereafter my spectra slb my spectra hdr 5 2 5 7 TXT Space Formatted Text Files These files are formatted as follows specified using EBNF Wirth 1977 ISO IEC 1996 txt file header data header wsp wl wsp spectrum name data d line d line wsp wavelength wsp value wsp space An example follows wvl mean 090499 mean 020599 350 000 00246756 O22 SM So L000 0 024691 7 0 0228430 3923000 0 0247316 0 0229652 309 000 0 0248502 0 0231014 354 000 0 0250081 D 222472 355x000 0 0250736 0 0232273 226 2000 0 0249993 050233909 Sod 00 0 00249174 0 0233902 SPECCHIO_UserGuide_V2 1 1 docx Version 2 1 1 02 11 2010 SPECCHIO Page 27 User Guide of 103 358 000 0 0250481 0 0234734 359 000 0 0252141 0 0235376 360 000 0 0253346 0 0236057 361 000 0 0253806 0 0236832 5 2 5 8 Ocean Optics SpectraSuite Data Files The format of these files is as follows SpectraSuite Data File E Hebe oH HE eH HS FEE Hee EHE HE HER E HER Date wed Sep 15 19 14 15 CEST 2010 User telerilevamento Dark Spectrum Present NO Reference Spectrum Present NO Number of Sampled Component Spectra 1 Spectrometers HR4C1076 Integration Time usec 1000000 HR4C
53. antime 5 2 5 2 GER Signature Files These files hold two spectral measurements at once the target and the white reference spectrum When loading GER files two additional hierarchies are automatically created named targets and references The target and the reference keep the same filename cf Figure 18 A data link of the type Spectralon is automatically inserted linking the target to the reference spectrum SPECCHIO_UserGuide_V2 1 1 docx Version 2 1 1 02 11 2010 SPECCHIO Page 24 User Guide of 103 targets GRO0S3005 078 references GRO0S3005 078 Figure 18 Automatically created hierarchies for GER files 5 2 5 3 MFR OUT Files These files contain the capture time the sun zenith angle and the spectral data for total diffuse and direct irradiance The sun angle and the direct irradiance data are discarded and only the total and diffuse spectra are stored Upon insert into the database two new sub hierarchies named total and diffuse are automatically created cf Figure 19 The filenames assigned to the spectra are auto generated using the capturing date and time small_MFR_set Campaign E Small MFR Set E total 2005 08 17 11 21 59 2005 08 17 11 22 59 2005 08 17 11 23 59 2005 08 17 11 24 59 2005 08 17 11 25 59 2005 08 17 11 26 59 2005 08 17 11 27 59 2005 08 17 11 28 59 2005 08 17 11 30 00 use 2005 08 17 11 21 59 2005 08 17 11 22 59 2005 08 17 11 23 59 2005 08 17 11 24 59 2005 08 17 11 25 59 2005 08
54. ase as data source Look in 9 SpectralDB odc el gla Es ii 22 band range 22 derivative sensor element E3 sensor response type ZE derivative calc method Es site 22 feature space 22 feature space type 22 mixture sz pca data E smoothing Filter E smoothing filter type 22 species E3 spectrum E statistic 5 study waveband Filter waveband Filter range Name site Show of type Datasets and Layers lyr Y Cancel Figure 113 Selecting the spectrum table as data source SPECCHIO_UserGuide_V2 1 1 docx Page 79 of 103 Version 2 1 1 02 11 2010 SPECCHIO Page 80 User Guide of 103 6 Tutorial 6 1 Overview The tutorial is comprised of four parts illustrating the functionality of SPECCHIO 1 Loading Editing and Retrieving Data The folder and directory structure of a sampling campaign the creation of a new cam paign loading of data editing of metadata and data retrieval is shown on a vegetation example The data set contains ASD spectra of New Zealand native plants 2 Handling of GER Files The automatic splitting of GER files into target and reference radiances upon loading is demonstrated using a RSL GER3700 dataset 3 Directional Data The handling of directional data including sun angle and sensor geometry calculation and automated linking of target to reference spectra is demonstrated using RSL FIGOS goniometer data 4 Data Querying Processing a
55. atabase user are contained in a combobox in the Load Spectral Data dialog Select the campaign that you want to load and click the Load but ton The loading progress is shown in the main window A message box will appear once all data has been loaded to the system If a campaign is ongoing over a longer period of time new data can be added by first loading the new files and hierarchies into the existing file structure on the hard disc and then running the load ing process again Each spectral data loading process will check if hierarchies and spectra already exist in the database Only new hierarchies and spectra will be inserted Load Spectral Data Campaign name Jahueni veg example iy Spectral data of the selected campaign will be loaded into the database Figure 17 Load Spectral Data dialog If a directory contains unknown file types an according warning message is shown OOO Messager Unknown file types in directory Users andyhueni Data Studies RSL SPECCHIO Project Campaigns Vordemwald 04 _ Data will not be loaded Please check the file types and refer to the user guide for a list of supported files Co Make sure that the files in the indicated directory are supported by SPECCHIO 5 2 5 1 ASD Files SPECCHIO has been tested with ASD FS3 ASD FS PRO and ASD FSVNIR binary files The new file format introduced by ASD is currently NOT supported please use the old file format in the me
56. atial positions can be set using the metadata editor The database tables can be accessed by a GIS system if ODBC connections are supported The connection is shown here on the example of ArcGIS on Microsoft Windows 5 2 12 1 Setting up the SPECCHIO DB as a Data Source Note that before the SPECCHIO DB can be configured as a data source the MySQL ODBC driver available from the MySQL website must be installed on the system Start Data Sources ODBC from the Windows administrative tools In the New Data Source dia log Figure 107 select the MySQL ODBC Driver and click on Finish Create New Data Source Microsoft ODBC for Oracle Microsoft Paradox Driver db Microsoft Paradox T reiber db Microsoft Text Driver txt csv Microsoft Text Treiber t t csv Microsoft Visual FoxPro Driver Microsoft Visual FoxPro T reiber SQL Server n3 C0 eee EM caros Figure 107 New Data Source dialog SPECCHIO_UserGuide_V2 1 1 docx Version 2 1 1 02 11 2010 SPECCHIO User Guide Page 77 of 103 This brings up the ODBC configuration dialog Figure 108 Type in a name for the Data Source Name Set the Server to the address of the database server Enter the User name and Password Select the database schema containing the spectral data from the Database dropdown list B Connector ODBC 3 51 12 Configure Data Source Name TN Connector ODBC Connect Options Advanced MySQL Connector ODBC Conf
57. ave indeed been saved and are now correctly displayed E g for the spectrum triticaa 040 you should find a sensor zenith of 30 and azimuth 270 cf Figure 148 triticaa Us6 Sampling geometry Data Lriticaa 037 triticaa 038 Sensor zenith Illumination zenith 48 439388 T Sensor azimuth Illumination azimuth 100 58999 e triticaa 041 Sensor distance Illumination distance Lriticaa 043 Figure 148 Calculated sensor zenith and azimuth angles 6 5 Part 4 Data Querying Processing and Exploration 6 5 1 Converting Radiances to Reflectances Data set GER example The GER example data set contains reference and target measurements that have been linked automatically during data load Our goal is the conversion of target radiances to reflectances using the respective function of the Space Network Processor Open the Query Builder browse to your GER example select the targets hierarchy Figure 149 and press the Process button Y BS GER example gt ia gt i references Figure 149 Selection of the target hierarchy of the GER example data set SPECCHIO_UserGuide_V2 1 1 docx Version 2 1 1 02 11 2010 SPECCHIO Page 96 User Guide of 103 A Space Network Processor window will open containing a space holding the ten target spectra Figure 150 The dimensionality of the space is 647 which is equal to the number of bands of the GER instrument
58. box tration and Space Network Processor for wavelength calibration Instrument settings support 7 1 2 Fixed Bugs SPECCHIO Problem Version V1 0a ENVI SLB does not load into Modification of HDR file 19 01 2007 ENVI Group update using the over Individual update is now enforced 24 01 2007 V1 2 vn 1 il 3 2 0 1 i ride conflict detection option in this case on positions is not updating all positions if each spectrum has its own position ASD files zero coordinates Check for zero coordinates is car 24 01 2007 i e no GPS unit connected ried out during reading of ASD SPECCHIO_UserGuide_V2 1 1 docx Version 2 1 1 02 11 2010 SPECCHIO User Guide V1 0b 2 X aX fo em 3 0 a 2 0 2 0c 2 i during sampling trigger the files Positions are only inserted if creation of a positional record lat long and altitude are all differ in the database with zero lat ent from zero long and altitude entries Some hidden dot files e g DStore prevent the correct loading of campaigns crashes loading process The ENVI slb date bug fix Explicitly create date array in asd crashes the loader process file reader constructor when determining the spectral file loader class Sensor definition loader Add default narrowband element crashes because of new ele type id in insert procedure ment type id Previously inserted pictures Clear added picture list in picture are adde
59. cember 4 2008 10 52 AM RSL 002 SRT 99 020 jpg Thursday December 4 2008 10 50 AM RSL 003 SRT 99 100 jpg Thursday December 4 2008 10 49 AM SRT 99 020 report 44110 2 1 txt Wednesday January 12 2005 12 30 PM l SRT 99 100 report 44110 1 1 with sigma txt Wednesday December 24 2008 9 34 AM SRT 99 100 report 44110 1 1 txt Wednesday January 12 2005 12 28 PM File Format All Files Ez Figure 106 Calibration file selection dialog A calibration file holds the calibration factors and uncertainty estimations for a reference panel in a tab separated value file wv rho sigma 250 0 98 0 02 251 0 98 0 02 252 0 981 0 02 253 0 98 0 02 254 0 98 0 02 255 0 981 0 02 256 0 98 0 02 257 0 98 0 02 258 0 98 0 02 259 0 981 0 02 260 0 98 0 02 261 0 98 0 02 262 0 978 0 02 263 0 979 0 02 The wvl column holds the wavelength in nanometers rho is the calibration factor linking the meas ured reference panel to the laboratory or national reference l e in the above example the panel is 98 reflective compared with an ideal panel Sigma is the uncertainty estimate of rho expressed as one standard deviation Note that before loading the calibration file a sensor definition fitting the wavelengths of the calibra tion must be loaded to the database E g in the case of Spectralon reference panels the sensor definition is the Perkin Elmer Lambda 19 sensor The calibration factors are used during the reference panel corr
60. ction from where the wind originates in 45 degree steps N NE E SE S SW W NW E d a eg Landcover Data i CORINE Landcover gt L3 Artificial Surfaces gt L3 Agricultural Areas v B3 Forest and Semi Natural Areas Y B3 Forests E Coniferous forest 1 Mixed forest t Environmental Data Cloud cover octas 1 okta or less but not zero HH Rel humidity Ambient temperature Wind speed l calm TA Air pressure Wind direction NIL HH General Data Measurement unit Reflectance HH Sampling Environment Field HB Measurement type Single HH Target homogeneity homogenous H4 Illumination source Sun HH Goniometer None HH Sampling geometry Data Sensor zenith Illumination zenith 134 695 Sensor azimuth Illumination azimuth 226 031 Sensor distance 1 Illumination distance Calc Gonio Angles Calc Sun Angles Figure 25 Spectrum data tab part 2 SPECCHIO_UserGuide_V2 1 1 docx Version 2 1 1 02 11 2010 SPECCHIO Page 32 User Guide of 103 General Data Measurement unit Name of the spectral measurement unit reflectance absorbance transmittance DN radiance Measurement type single directional or temporal cf also 4 5 2 1 Illumination source currently only the sun and a QTH lamp are defined as possible en ergy source However other sources can be entered by the administrator if needed O Sampling environment Defines the general type of e
61. culation is needed first remove the direct hierarchy from the database using the Data Re mover dialog Select the hierarchy containing the total and diffuse hierarchies Note that they must be named total and diffuse This will be autogenerated in the case of MFR file input The selected hierarchy and the number of total diffuse spectra pairs will be shown Click OK to calculate the direct irradiance A new hierarchy will be created called direct see Figure 48 containing all direct irradiance spectra Details on the algorithm For each channel i direct irr i tot_irr i diff_irr i cos sun_zenith Direct Irradiance Calculation SLB Campaign L gonio Campaign mixed instr Campaign Gosh its a monster Campaign 1 gonio slb Campaign 7 SLB out Campaign sun angles Campaign Photometer Campaign j CA Selected hierarchy MFR Photometer total diffuse No of spectra pairs total diffuse 198 l small MFR set Campaign 41 MFR2 Campaign 1 datetest Campaign 79 30 08 2005 MFR Campaign intial shared insert Campaign Vegetation Example Campaign 3 gonio with gaps Campaign targets and references Campaign Select hierarchy containing photometer data b bed be n bee n be n be n e n e Figure 47 Direct Irradiance Calculation dialog SPECCHIO_UserGuide_V2 1 1 docx Version 2 1 1 02 11 2010 SPECCHI
62. current processing status text and progress bar During processing the progress is shown by the progress bar 0 Type Sensor Instrument Space D 2151 N Vectors 17 Status Waiting for data Proc module Radiance to Reflectance Settings Automatic selection from DB Figure 61 Examples of the graphical representation of a space left and a processing module right SPECCHIO_UserGuide_V2 1 1 docx Version 2 1 1 02 11 2010 SPECCHIO Page 56 User Guide of 103 Spaces and modules can be rearranged by dragging with the mouse The edges are updated automatically A group of elements can be moved as single block Selecting the elements by dragging a box around them using the mouse then drag the selection Figure 62 0 Proc module Get Panel Correction Factors 1 Ref panel cor factors Type Sensor instrument Space Settings Type Spectral Space D 2151 aj EAS ALZ D 2251 Status Waiting for data Vectors TEE Vectors zem Proc module Correct for Panel 3 Settings Automatic selection from DB ke Type Spectral Space D 2151 Vectors 1 Proc module Waveband filtering Settings Status Waiting for data Status Waiting for data 4 Ref Panel cor Reflectance Type Spectral Space D 2151 Vectors 1 Figure 62 Multiple selection of elements after dragging a box around them 5 2 10 2 Adding Modules and linking with Spaces To add a module click the mouse menu button over some emp
63. cx Version 2 1 1 02 11 2010 SPECCHIO Page 86 User Guide of 103 6 2 5 Exporting Data to ENVI Spectral Libraries Relevant sections 5 2 7 5 2 9 Note this exercise assumes that you have access to ENVI If this is not the case you may skip it As a first step repeat the process of file exporting as described for CSV Files in 6 2 4 but change the file format to ENVI SLB To open SLB files in ENVI start ENVI and select Spectral gt Spectral Libraries gt Spectral Library Viewer Specify an input file by selecting the slb file cf Figure 126 Please Select a File on terra y Directoru hone rslLi ahueni Filter Files Vea2 INR ASD_cali hdr Vea2 INR ASD_cali slb Directories Vegies INR ASD_cali hdr Vegies INR ASD_cali slb bfern_INR ASD_cal1 hdr dt black INR ASD_cal1 hdr l s gconf black INR RSI cali slb gconfd blackfern RSL ASD 1 cali csv Selection fern INPRS ASD_cali slb OK Filter Cancel Figure 126 Selecting an sib file to load as spectral library The spectra names can then be displayed in the Spectral Library viewer cf Figure 127 and plot ted as Spectral Library Plots Note that the maximum range of the Y axis must be set to 1 manually as otherwise only noise will be visible cf Figure 128 mm Spectral Library Viewer c 2 ER File Options Library bfern INR ASD_cali slb 2151 ba Wavelength 350 to 2500 Nanometers Fern 006 Figure 12
64. d along with new pic metadata object tures Pictures not updated on Revalidate the metadata editor screen in metadata editor Some dialogs e g Query Builder are not opening cor rectly after changing the data base connection this only applies if the dialogs were opened already with the former connection not working table thousands of spectra Shared data update delete not Major redesign of the metadata editor update and shared data functions Datalink group update some Clear internal lists after updates how inserting too many rows Various architecture dependant data type for ENVI SLBs thread safety for SQL statement builder Foreoptic is now treated as FOV and bare fibre FOVs are correctly inserted for ASD readings Update default statement and con nection in the SQL Statement builder instance upon reconnect ENVI SLB loading problems Data type awareness on input Warning message if un known file types exist in di rectory Copy Paste not working in Update allowed key list numeric fields in the Metadata Editor Memory leaks spectra loading Fix of memory leaks and spaces Config file routine more ro Application crashing when bust Page 101 of 103 26 01 2007 14 02 2007 14 02 2007 14 02 2007 18 10 2007 18 10 2007 18 10 2007 03 11 2007 03 11 2007 29 05 2008 15 06 2008 05 03 2009 26 03 2009 07 07 2009 02 09 2010 SPECCHIO_Us
65. d by spectroradiometers and associated metadata SPECCHIO was devel oped to support long term usability and data sharing between researchers For further information please refer to the SPECCHIO website www specchio ch and to the fol lowing articles Hueni A Kneubuehler M and Schaepman M 2010 DATA EXCHANGE BETWEEN SPECTRAL DATABASES IGARSS Hawaii USA Hueni A Malthus T Kneubuehler M and Schaepman M submitted Data Exchange between distributed Spectral Databases Computers amp Geosciences Hueni A and Kneubuehler M 2009 SPECCHIO A Free Spectral Data Management and Pro cessing System SPIE Optics and Photonics San Diego CA Hueni A Rey S Schlapfer D Schopfer J and Kneubuehler M 2009 VISUALISATION PROCESSING AND STORAGE OF SPECTRODIRECTIONAL DATA BASED ON THE SPECTRAL DATABASE SPECCHIO IGARSS 09 Cape Town South Africa Hueni A Kneubuehler M Nieke J Itten K 2009 PROCESSING EXTENSION FOR THE SPECTRAL DATABASE SPECCHIO In Proceedings EARSeL SIG IS Tel Aviv Israel Hueni A Nieke J Schopfer J Kneub hler M and Itten K 2009 The spectral database SPECCHIO for improved long term usability and data sharing Computers amp Geosciences 35 3 557 565 Hueni A Schopfer J Schlapfer D Kneubuehler M Nieke J 2008 PRE PROCESSING OF DUAL VIEW FIGOS DATA TOWARDS OPERATIONAL BRDF RETRIEVAL In Proceedings ISPRS Beijing H ni A and Kneub hle
66. de Northern hemisphere coordinates are positive southern negative O Longitude West of Greenwich positive East of Greenwich negative Altitude metres above sea level Location free text Campaign Data Hierarchy Data Spectrum Data Filename bfern 007 File comment 0 00 0 0 P Capture date 2005 9 12 10 10 28 Loading date 2007 8 24 14 48 55 Is reference spectrum Q Yes No Required quality level None Attained quality level Spectral plot Spectral Reflectance 1000 2000 3000 Datalink f y b Datalinks M9 New Delete Position Latitude 40 3848883333333 Longitude 175 621613333333 Altitude m 41 8 Location Massey Uni Campus Palmerston North NZ SPECCHIO_UserGuide_V2 1 1 docx Version 2 1 1 02 11 2010 SPECCHIO Page 31 User Guide of 103 Figure 24 Spectrum data tab part 1 L andcover Data These landcover classes are based on the CORINE landcover scheme They are ordered into three levels and visualized in the Metadata Editor using a tree structure Only level 3 is stored for spectra Levels 1 and 2 are merely displayed to help the selection of level 3 Environmental Data Cloud cover in octas cf also 4 5 1 Ambient temperature in degrees Celsius Air pressure hPa Relative humidity as percentage Wind speed calm breezy windy stormy Wind direction dire
67. dete of Override conflicts gt Campaign Data Reset N LI and Update Hierarchy Data Reset and Update Spectrum Data Reset thane ie d y cm I x Pd and Update Spectral Data Browser andcover Data Figure 22 Metadata editor showing the campaign tab A description of the information displayed by the tabs follows Read only fields will be mentioned explicitly all other fields are editable by default The campaign tab shows the following information Campaign name Description of the campaign some free text 1 Investigator the person in charge of this campaign i e the user defining and loading the campaign This field is filled automatically SPECCHIO_UserGuide_V2 1 1 docx Version 2 1 1 02 11 2010 SPECCHIO Page 29 User Guide of 103 Path the file system path pointing to the main directory This can be changed by click ing on the Browse button next to it Use this to change the campaign file path if the campaign folder was shifted on the hard disc after the creation of the campaign The hierarchy data tab displays information about the currently selected data hierarchy cf Figure 23 O Name hierarchy name taken from the corresponding folder name read only O Description free text 1 Datalinks links to other hierarchies cf also 4 4 Campaign Data Hierarchy Data Spectrum Data Mame sitel Description Figure 23 Hierarchy data tab The spectrum data tab displays in
68. e selected to change their position again This conflict is detected upon carrying out an update and an according option window is display cf Figure 31 The number of affected records is shown as well as the involved data group and the field name Selecting Apply to shared record will update the shared record i e all members of the original spectra group will refer to these new settings Selecting Create new record for selected spectra will create a new entry in the database i e the original shared data is not changed Selecting Cancel update action will not perform any update of the concerned field BOL Shared data update You are about to update a shared data record shared by 17 spectra Sf sampling geometry sensor_zenith T n P Create new record for selected spectra V Apply to shared record PV Cancel update action D Figure 31 Shared data update warning for the sensor zenith field of the sampling geometry data group 5 2 6 2 5 Overriding the Conflict Detection The conflict detection that disables updates of non shared data in spectra groups can be switched off by selecting the Override conflict detection checkbox on the control panel cf Figure 32 Be sure that you know what you are doing all previously individual metadata of the selected spec tra might be replaced with the new data Overriding conflicts may lead to some unwanted effects depending on what metadata parameter it
69. ection procedure as described in 5 2 10 4 2 and 5 2 10 4 3 5 2 11 6 Database Upgrade Attention before upgrading your database make a backup Selecting the database upgrade functionality automatically determines the current version of the database and carry out incremental updates till it reaches the latest version of the database If the database is up to date the following message will appear SPECCHIO_UserGuide_V2 1 1 docx Version 2 1 1 02 11 2010 SPECCHIO Page 76 User Guide of 103 eoo DB Upgrade Database is up to date current version 2 1 ae Mit E If the database has a lower version than the latest available version a message like to following appears l eio DB Upgrade Upgrade from Version 2 0 to Version 2 1 m uL Click OK to carry out the upgrade Once finished the following message will appear Number of errors should be zero if not revert to your backup start the SPECCHIO application from the com mand line then carry out the DB upgrade again all statements are printed on the screen including the error messages If in doubt contact admin specchio ch EJ H n BNN nnm Database upgrade completed Number of errors Cox 5 2 12 Linking to a GIS System If a GPS unit is used to record the spatial position of the sampling sites during the sampling pro cess every site in the database contains the latitude longitude and altitude in WGS84 format Al ternatively sp
70. el contains the following elements from top to bottom SPECCHIO_UserGuide_V2 1 1 docx Version 2 1 1 02 11 2010 SPECCHIO Page 28 User Guide of 103 O Campaign selection only one campaign can be edited at the same time in one editor Note that several metadata editors can be open simultaneously each editing a differ ent campaign Note also that only campaigns belonging to the current user can be edited Checkbox to highlight mandatory fields mandatory fields only exist if a required quality level has been selected Checkbox to highlight the shared data fields Checkbox to show the quality compliance in the tree of the spectral browser Checkbox to override the conflict detection when updating spectral groups Reset and Update buttons for campaign hierarchy and spectrum data Spectral data browser that visualises the structure of the campaign as a tree The data displayed in the hierarchy and spectrum data tabs depends on the selection in the spectral data browser cf also 4 1 Multiple selections are possible by using shift or control keys while selecting items with the mouse LJ E deg Eg TE us Special Functions Menu Campaign Tab Hierarchy Tab Spectrum Tab Campaign Selection Highlighting of mandatory fields Me ta Editor Highlighting of i One shared fields Cumet Campaigr Spectrum vegetation E le 44 Show quality Plight mandatory field _ compliance in tree rr light shared Feld Live de t
71. erGuide_V2 1 1 docx Version 2 1 1 02 11 2010 SPECCHIO Page 102 User Guide of 103 unexpected CR LF in db_ config file Fix memory leaks 15 09 2010 7 1 3 Known Bugs SPECCHIO Problem Workaround Version V2 0 Target type abundance Number Always enter a target abundance when exception when no abundance defining target types specified Duplicate key error on update only No user workaround Write email to certain tables and not always occur SPECCHIO admin ring either Attained quality level is wrongly set even if not all fields comply Conflict detection is not working for If in doubt check the links of the involved data links spectra to ensure they are set correctly The datalinks will be replaced by new link ing functions in the near future 7 2 SPECCHIO Database 7 2 1 Added Features Database Version 1 0a Changed the column type of latitude longitude and illumination 24 01 2007 angles from Float to Double to increase precision 1 1 Multiuser capability added 15 10 2007 0 Various new features reference panel links for spectra reference 05 03 2009 panels calibrations and according uncertainties DB version Instrument settings table 07 07 2009 1 1 Changes for compatibility with the campaign export function 29 05 2008 2 HR 1024 support Associated measurements support 02 09 2010 8 References Hueni A 2006 Field Spectroradiometer Data Acquisition Organisation Processing and An
72. erarchical directory structure Figure 1 Spectrum 1 Spectrum 1 Spectrum 1 Spectrum 2 Spectrum 2 Spectrum 2 Spectrum n Spectrum n Spectrum n Figure 1 Hierarchical directory structure Although the term species is used it essentially represents the different classes found in a study These classes can either be assigned due to already existing classification systems for e g plants or minerals In other cases a hypothesis might exist that a number of objects can be separated into classes If so the setup of the experiment should mirror this hypothesis If no such assumption ex ists all objects can be put into the same class i e species and the identification of classes could then be carried out by e g cluster analysis SPECCHIO builds up on the above concept of hierarchies However there is no restriction on the number of levels used Thus any level number 0 N can be used SPECCHIO_UserGuide_V2 1 1 docx Version 2 1 1 02 11 2010 SPECCHIO Page 12 User Guide of 103 3 3 Directory Structure and Spectral Files This section lists examples of data structures employed to hold the files generated by spectroradi ometers Note that SPECCHIO enforces no particular structure The provided examples are mere suggestions based on experience and you may decide to choose a different approach 3 3 1 Structure to store Reflectance Spectra of several Species and Sampling Sites A hierarchical structure as introduced in 3 2 is used to build t
73. es 12 3 3 2 Structure to store Reference and Target Spectra ccccceccceccceececeeeceeeseeeeeeeeseeeeseeeseeees 12 4 SPECCHIO Concepts iain divae Ere Va ixa cusa I OE ouis Mud SAT e EE Rr SEEN ED IEEE 13 4 1 Modelling of Hierarchies in the SPECCHIO Database and GUI eeeeeessees 13 wA HME DIa RR ER ULT hoe emia eet oleate 13 4 3 Metadata Quality Levels sess eene nennen nnn nna nnne sanas nsa n a sanas nnus 14 BAe IBN CR U M 15 ASG Metadala TT cess 15 sto MEE UU EO Mm 15 4 5 2 Measurement Typo Seisean a s tou a eoe uto sentina d coqui es io ttim ld fisse Mu pedis 15 z XO MJETE S e EE 16 4 5 4 Sensors and IDs UBdelte seirene But suo eph NU Rite aot Onde b do ub Aes ub ton i eb DRE 16 4 6 Spaces Space Factory and Data Processing using the Space Network 16 9 XOBeraliOlloua iones cd scasgbli ctas pie MM un LA e MM E DE M E EUIEES MUR 18 S QOOVOIVIOW et Ui M ir rini du UM EM ee A 18 SM MEO Hcc a a 18 SA 2 Testes dte des oisteeunsatustes auta asbcul vods M eeu oum ditat naque edad SA 18 Sko SPEOCHIO ODSFatOllesssucitsaditxtbutuedenb ipe spud tUi etae cU RU ud tus aulem Dass tu uU oA SN EE CETT 19 52 SHEOGGHIO JADDIESUOD scitis ns qud vedo m Sera V ded coe Abou bur Nae Mac Mei cU 19 OZ LOOK ANG Feel me
74. es No intial_shared_insert Campaign C Vegetation Example Campaign spectrum datalink gonio with gaps Campaign Ov targets and references Campaign 3 Targets and References Link type reflrad_240606_Hema_Triti targi S E reflrad_240606_Hema_Triti_refe EIU CENE v Mee vi new J Dette v Delete triticaa Q006 n New Delete triticaa 018 Ltriticaa 030 triticaa 042 Ltriticaa 054 Ltriticaa 066 ll Location targets and references Campaign A B C Targets and References Landcover Data c reflrad 240606 Hema Triti tar 0 t mt riticaa 001 LandcoverlevelI Mone triticaa 002 am heibhie NN Bee de ee las al TT Alama Figure 40 Definition of a datalink on spectrum level ull 5 2 6 2 10 Special Functions The metadata editor provides some special data processing functions They are either accessed via the metadata editor menu cf Figure 41 or via actions buttons in the spectrum tab Sal Special Functions Link targets to references Calculate direct irradiance Correct local time to UTC Figure 41 Metadata editor Special Functions menu Note The special functions offered by the menu do not depend on the currently selected campaign in the metadata editor but offer access to all campaigns SPECCHIO_UserGuide_V2 1 1 docx Version 2 1 1 02 11 2010 SPECCHIO Page 41 User Guide of 103 5 2 6 2 10 1 Calculation
75. example in Figure 2 Note the added top node Vegetation Example Campaign Vegetation Example Campaign Vegetation example Blackfern site1 Cabbage tree sitel cabbage 000 cabbage 001 cabbage 002 cabbage 003 cabbage 004 cabbage 005 cabbage 006 cabbage 007 cabbage 008 cabbage 009 9 site2 E Lemonwood site1 E site2 bA e eeee 888 6 Figure 4 Example of a Spectral Data Browser component showing the directory structure holding spectral files 4 2 Time Data SPECCHIO expects time data in UTC Coordinated Universal Time For practical purposes UTC is considered equivalent to GMT however the term UTC is recommended for technical contexts U S Naval Observatory 2003 The above implies that all computers capturing data for use in SPECCHIO should have their timezone set to GMT and their system time adjusted to UTC The capturing date time can be modi fied in the database using a special function in the Metadata Editor if a time different to UTC was used SPECCHIO_UserGuide_V2 1 1 docx Version 2 1 1 02 11 2010 SPECCHIO Page 14 User Guide of 103 4 3 Metadata Quality Levels The concept of metadata quality levels has been introduced to add a quality measure to spectral data It is clear that by describing more metadata the spectral data quality is not improved as such However the metadata can serve to increase the user confidence in the data as it defines the cir cumstances of
76. ference spectra This function is applicable for campaigns where target and reference spectra are collected in sepa rate spectral files This is e g the case for campaigns utilising the ASD spectroradiometer in radi ance mode In order to tie the target to its corresponding white reference spectrum a datalink on spectrum level must be inserted This could be achieved manually for each spectrum using the metadata editor Target and reference spectra must be stored in separate hierarchies The example shown in Figure 44 is taken from a goniometer campaign In the left spectral data browser select the hierarchy con taining the targets In the right browser select the hierarchy containing the references The selected hierarchies are displayed in the read only fields on the right side of the dialog Click link to create datalinks between targets and references Details on the algorithm The linking utilises the capture time stamps of the spectra Consider two timelines one for the tar gets and one for the references A target must link to the most recent reference with the constraint that the reference capture time is smaller than the target capture time see Figure 45 SPECCHIO_UserGuide_V2 1 1 docx Version 2 1 1 02 11 2010 SPECCHIO Page 43 User Guide of 103 Link Target to Reference Targets References SLB Campaign C SLB Campaign gonio Campaign gonio Campaign mixed instr Campaign mixed instr Campaign Gosh its a monster Campai
77. filters The plot shown in Figure 75 was generated by the Spectral Line Plot of space number O Figure 77 shows the plots of space 2 Broadband value as a scatter plot and space 3 Narrowband channels as a spectral curve 800 400 Wavelength nm Wavelength nm Figure 77 Plots of the narrowband channels left and of the broadband channel right 5 2 10 5 Visualisation Modules Visualisation modules can be attached to any space and do not generate an output space but dis play a new window containing the respective plot or data explorer A visualisation module can be configured to produce a number of plots explorers as listed in the following sections Data explorers are graphical components that allow interactive data exploration The titles of the plot windows do contain information about the plot type and the space the data was read from Figure 78 O Gonio Sampling Points Plot Space no 0 Goniometer Sampling points Figure 78 Information displayed in the window title SPECCHIO_UserGuide_V2 1 1 docx Version 2 1 1 02 11 2010 SPECCHIO Page 63 User Guide of 103 5 2 10 5 1 Spectral Line Plot Use this plot to display one or more spectra as continuous curves Spectra are plotted with an automatic colour shift from red to blue for easier interpretation 1 0 Reflectance 0 5 0 0 0 1000 2000 3000 Wavelength nm Figure 79 Spectral line plot of snow avalanche reflectance spectra 5 2 1
78. formation about the selected spectrum or spectra The data ele ments have been put into groups cf Figure 24 Figure 26 These are described hereafter in de tail Spectrum Data O Filename usually the filename of the spectral file in some cases filenames are auto matically produces read only O File comment Automatically contains user comments entered when capturing the spectrum e g possible with ASD s R3 capturing software Capture date in 24h format UTC read only Loading date in 24h format system time Is reference an option that can define this spectrum as being a reference spectrum Only specchio admin can set this field O Required quality level a user definable level of metadata quality that this spectrum should reach cf also 4 3 Attained quality level this field stays empty as long as not all required metadata ac cording to the required quality level have been captured Once all required data are en tered the attained quality level will be equal to the required quality level read only Spectral plot a plot of the spectrum read only BED Datalink 1 Datalinks lists all data links that this spectrum has to other spectra cf also 4 4 and 5 2 6 2 9 SPECCHIO_UserGuide_V2 1 1 docx Version 2 1 1 02 11 2010 SPECCHIO Page 30 User Guide of 103 Position Spatial and descriptive information about the capturing location Coordinates are entered as de grees and fractions of degrees O Latitu
79. gn Gosh its a monster Campaign gonio slb Campaign gonio slb Campaign SLB out Campaign SLB out Campaign sun angles Campaign sun angles Campaign Target hierarchy Photometer Campaign Photometer Campaign errad 240606 Heme Tri targets small MFR set Campaign small MFR set Campaign MFR2 Campaign MFR2 Campaign Reference hierarchy datetest Campaign onrad 2 0606 eme Tri references 30 08 2005 MFR Campaign C datetest Campaign 30 08 2005 MFR Campaign intial shared insert Campaign C Vegetation Example Campaign Vegetation Example Campaign gonio with gaps Campaign gonio with gaps Campaign targets and references Campaign targets and references Campaign m Targets and References E Targets and References cC preflrad 240606_Hema_Triti ta fMi s jreflrad 240606 Hema Trititar reflrad 240606 Hema Triti re e re preflrad 240606 Hema Triti rd gt ee ee ee ee ee ee n be ee Et ee ee Ee H H be ee Ee DLR EP RP EE TEM ee H H H H Figure 44 Link Target to Reference dialog Reference panel spectra timeline Entity timelines Target spectra timeline TS Targetspectrum gt Referencing in the database via datalink RS Reference panel spectrum Figure 45 Referencing of reference panel spectra by target spectra based on timeline information 5 2 6 2 10 3 Calculation of Sun Angles The sun angles are stored as part of the sampling geometry namely as illumination zenith and azimuth Sun a
80. h text field The sampling points plot shows the sampling point positions projected onto a 2d Cartesian coordi nate system Figure 85 One of these points is always selected indicated by the little square around it Information about the selected point is shown in the text fields on the right of the plot filename of the respective spectrum azimuth and zenith angles of the observation geometry Changing the selected sampling point by clicking the mouse on another point changes the spec trum displayed in the spectrum plot automatically The azimuth angle is measured relative to the solar principal plane i e 0 principal plane oppos ite of the illumination source Goniometer Sampling points Sampling Point Information Filename hem_a 001 Azimuth 0 Zenith 75 Figure 85 Sampling point position plot and information about the selected sampling point The spectral plot component displays the spectrum of the selected sampling point Figure 86 A red vertical line indicates the current wavelength as selected by the band selection slider The text fields on the right of the plot display spectral statistics of the current spectrum Spectral plot Spectrum Statistics Mean 0 00409 Min O0 Max 0 00844 Stddev 0 064 1000 2000 3000 Figure 86 Spectral plot component with wavelength indicator and spectrum statistic information 5 2 10 5 5 Time Line Plot Use a time line plot to plot a spectral band versus time Figure 87
81. hat the input spaces must have identical number of vectors and dimensionalities The delta module takes two input spaces Figure 70 Input Space Selection Spectra A Spectra B 0 0 0008 Demn 13 3 Cancel A A 4 4 LE E i Figure 70 Input space selection for the Delta module A possible use is the calculation of the difference between recorded reflectance and reference panel corrected reflectance Figure 71 shows a processing network for this purpose and Figure 72 shows the according spectral plots generated by the network SPECCHIO_UserGuide_V2 1 1 docx Version 2 1 1 02 11 2010 SPECCHIO Page 60 User Guide of 103 o Proc module Get Panel Correction Factors 1 Ref panel cor factors Type Sensor instrument Space Settings Type Spectral Space D 2151 2 I Nai i D 2251 Vectors 1 Vectors 1 ce 3 Vis module Spectral Line Plot Type Spectral Space Settings D 2151 Status Waiting for data i Vectors 1 Status Waiting for data Proc module Waveband filtering Settings Proc module Delta Proc module Correct for Panel Settings Delta A B Settings Automatic selection from DB Status Waiting for data Status Waiting for data 5 Delta Sl eal coer Vis module Spectral Line Plot Type Spectral Space Type Spectral Space Settings D 2151 D 2151 a Status Waiting for data Vectors 1 Vectors 1 Vis module Spectral Line Plot Settings Status Waiti
82. he directory structure that holds the spectral files Ideally this directory structure is setup when designing the experiment Figure 2 shows an example of a directory structure containing ASD spectral files The main direc tory Vegetation example holds all species directories of the study This main directory is the folder that needs to be specified when creating a campaign in the database cf 5 2 4 The species direc tories contain the site directories The site directories contain all spectral files collected at these sites The spectral files are auto numbered by the ASD capturing software Folders x Name Size Type Vegetation example cabbage 000 9KB 000 File 5 Blackfern E cabbage 001 9KB 001 File sitet E cabbage 002 9KB 002 File 3 Cabbage _tree f cabbage 003 9KB 003 File sitel E cabbage 004 9KB 004 File site2 E cabbage 005 9KB O05 File Lemonwood E cabbage 006 9KB 006 File site1 E cabbage 007 9KB 007File site2 E cabbage 008 9KB 008 File sites E cabbage 009 9KB 009 File Figure 2 Example of a directory structures holding spectral files Campaigns can contain spectra measured with different instruments and sensors i e instruments of different sensor types and instruments with different calibration dates The only restriction that is imposed is that a hierarchy i e a folder can contain only one file type 3 3 2 Structure to store Reference and Target Spectra If a s
83. ig txt and the libraries to some new directory on your user account To start the software locally either double click the SPECCHIO App V x xx jar file may not work on all UNIX systems or alternatively open a shell terminal navigate to the directory containing the applications and type java jar SPECCHIO App V x xx jar For remote execution when having installed the application in your home drive which is mapped on to the servers type ssh X server name java jar lt path gt SPECCHIO App V x xx jar E g to use terra as server with version 1 0c of the SPECCHIO application ssh X terra java jar home rsl1 ahueni SPECCHIO SPECCHIO App V1 0Oc jar 2 2 5 Apple Macintosh O Double click the ZIP file This will automatically unzip the file and create a new folder containing all SPECCHIO files O Copy the unzipped folder into the Applications or some other directory of your choice O Double click the SPECCHIO App V x xx jar file to run SPECCHIO SPECCHIO_UserGuide_V2 1 1 docx Version 2 1 1 02 11 2010 SPECCHIO Page 11 User Guide of 103 3 Design of Sampling Experiments and Data Structuring This section contains a description of a setup of a possible spectral sampling campaign Users designing their own sampling campaigns and planning to load them into SPECCHIO can find some basic ideas on campaign planning and data structuring hereafter 3 1 Overview The data collected during sampling campaigns must be o
84. iguration Data Source Name Spectral DB Description Server User Password Database This dialog is used to edit a Data Source Name DSN it022005 massey ac nz SpectraProc spectral db Figure 108 MySQL ODBC Configuration dialog 5 2 12 2 Establishing a Database Connection in ArcCatalog Start ArcCatalog and select Add OLE DB Connection Figure 109 A ArcCatalog ArcInfo Database Connections File Edit View Go Tools Window Help t G3 8p P5 KG X EE EE Ba a M e CON Location D atabase Connections Stylesheet s A HZ y E Catalog ue Database Connections Add OLE DB Connection Add Spatial Database Conr QB Address Locators fa GIS Servers BA Search Results X Contents Preview Metadata Name Add OLE DB Connection Add Spatial Database Connection Figure 109 Adding an OLE DB Connection in ArcCatalog In the Data Link Properties select Microsoft OLE DB Provider for ODBC Drivers Figure 110 and click Next gt gt SPECCHIO_UserGuide_V2 1 1 docx Version 2 1 1 02 11 2010 SPECCHIO Page 78 User Guide of 103 Data Link Properties Data Link Properties Provider Connection Advanced All Provider Connection Advanced Al Select the data you want to connect to Specify the following to connect to ODBC data OLE DB Provider s 1 Specify the source of data MediaCatalogDB OLE DB Provider f Use
85. igure 141 Remember that GER instruments write the sampled radiances of target and white reference into the same file The names of the corresponding targets and references are identical e g target GR083005 080 is as sociated with reference GR083005 080 SPECCHIO_UserGuide_V2 1 1 docx Version 2 1 1 02 11 2010 SPECCHIO User Guide specchio_test Andy veg example Campaign m Andy GER example Campaign GER example targets GRO83005 081 GROS3005 082 GROS3005 083 GROS3005 084 GROS83005 085 GRO83005 086 GRO83005 087 GRO83005 088 GRO83005 089 references GRO83005 081 GRO83005 082 GROS3005 083 GRO83005 084 GRO83005 085 GRO83005 086 GROS3005 087 GRO83005 088 GRO83005 089 e eeee dE SE SE SE eeee SE SE JE SE Radiance Radiance 125 000 100 000 4 75 000 50 000 25 000 1 j VA GR083005 080 1 000 1 500 2 000 2 500 Wavelength nm GR083005 080 MN 500 1 000 1 500 2 000 2 500 Wavelength nm Page 92 of 103 Campaign name Campaign desc Filename Capture date Required quality level mn i den Andy GER example GR OS3005 080 2005 09 30 11 32 57 Campaign name Campaign desc Filename Capture date Required quality level Andy GER example GROS3005 080 2005 09 30 11 32 57 Figure 141 GER files split into target and reference spectra left and report sh
86. ilder in the background Figure 60 shows the common elements of the Space Network Processor processing plane spaces edges context sensitive menu of the processing plane and the Run button SPECCHIO_UserGuide_V2 1 1 docx Version 2 1 1 02 11 2010 SPECCHIO Page 55 User Guide of 103 Context sensitive menu of the Space Edge Processing plane Processing plane ANDO Sr ace Network Processor 0 Type Sensor instrument Space D 2151 Vectors 66 Proc module Radiance to Reflectance j A ic selection fi Settings utomatic selection from DB Add Module Status Waiting for data 1 Type Spectral Space D 2151 Vector 66 A A INOLTRE c re a ee ea ee el X ee eee ee ceo ceo 0o 0o eee Figure 60 Elements of the Space Network Processor 5 2 10 1 Graphical Representations of Spaces and Modules Spaces and modules are depicted as rectangular boxes Figure 61 The space displays the following information O A unique number zero in the example below A space type which can be Sensor Instrument Space if loaded from the database or Spectral Space if generated by a processing module Adimension D which is equal to the number of spectral bands of the spectra held by this space O A number of vectors which is equal to the number of spectra held by this space The module displays the following A module name O Information about the configuration if applicable The
87. ing the data Folders x Name Size Type cha A Vegetation_example File Folder C3 Vegetation example Hidblackfern jpg 143KB ACDSee Pro JPEG Bild Blackfern TPG lemonwood jpg 125KB ACDSee Pro JPEG Bild Cabbage_tree C3 Lemonwood Figure 135 Location of the species pictures To apply the Blackfern picture to all Blackfern spectra select the Blackfern hierarchy in the Spectral Data Browser Click Add in the Pictures section browse to the Tutorial folder and select black fern jpg To enter a caption simply type it into the editable field below the picture cf Figure 136 Then update the database Pictures Blackfern near Atawhai Rd Palmerston Nth Figure 136 Example of a picture with a caption SPECCHIO_UserGuide_V2 1 1 docx Version 2 1 1 02 11 2010 SPECCHIO Page 90 User Guide of 103 In a similar manner insert the supplied lemonwood jpg picture for all Lemonwood spectra Note that performing group updates not only speeds up the input process but also minimizes the amount of data stored in the database All spectra in the selected group are referencing a single entry in the database thus avoiding data redundancy A general problem of spectral data collections is the quality and trustability of the data This is es pecially true if the data were collected by third parties and the sampling conditions are unknown One way to improve the usability and shareability of spectral data is to include more metadata
88. iolated To insert a new instrument click Insert new instrument A new record is created in the database and the instrument name is set to dummy Figure 99 Instrument Data 4 dummy Instrument name dummy Instrument Data Reset J Instrument owner NIL Serial number H Insert new Instrument Sensor ASD FS FR 3 M M Delete instrument Figure 99 New dummy instrument The instrument can now be renamed and it s metadata filled accordingly To add a new calibration to an instrument click the menu button over the Calibrations section of the Instrumentation Metadata Editor and choose Add calibration or Add calibration from file Figure 100 Selecting Add calibration from file will bring up a file choosing dialog Two file types can be cur rently used to load calibration factors from a HR 1024 spectral files for loading the wavelengths calibration and b TXT files as further detailed in the section on reference panels below there is currently no real use in loading TXT files for instrument calibrations as only wavelengths are ac tively used in the system and these can currently only be loaded from HR 1024 spectral files SPECCHIO_UserGuide_V2 1 1 docx Version 2 1 1 02 11 2010 SPECCHIO User Guide Calibration Data Calibrations Add calibration from file Add calibration Remove calibration Figure 100 Addi
89. l discard any changes and redisplay the values as currently stored in the database Spectrum Data Reset Update Figure 30 Activated Update button for the spectrum data tab The updates have been carried out when the Update button reverts to being grey and disabled 5 2 6 2 4 Group Updates SPECCHIO_UserGuide_V2 1 1 docx Version 2 1 1 02 11 2010 SPECCHIO Page 36 User Guide of 103 Group updates are an efficient way to define metadata that is identical for a group of spectra E g consider the case of a shrub being sampled ten times in the field with no GPS unit connected to the system All ten spectra will have roughly the same spatial position and thus can be updated as a group To carry out a group update select all spectra being part of the group Note that only non conflicting fields can be updated via group updates see 5 2 6 2 5 how to perform updates on conflicting data Enter the data that is shared by the spectra group for the above example latitude longitude and altitude Click Update All spectra in the group will be updated to have a spatial position with the entered lat long and altitude Note that all spectra of the spectra group are now referencing the same position record in the database i e there is no data redundancy This shared record principle leads to conflicts when updating or deleting one or several spectra that belong to the same group In the above example three out of ten spectra would b
90. m name Name All incl none Figure 54 Query conditions tab part 2 5 2 8 Report Generation Reports are generated by selecting the Show report button in the Query Builder see 5 2 7 The report consists of a Java frame displaying a list of spectrum report panels Thus for each spectrum being the result of a query built in the Query Builder one spectrum report panel is added to the report frame A spectrum report consists of two main elements a a spectral plot on the left side and b a scrol lable list containing metadata values see Figure 55 Pictures saved for a spectrum can be dis played by clicking on the button Show pictures at the bottom of the metadata list This will bring up a new frame containing all pictures of this spectrum see Figure 56 The spectral plot y axis is automatically scaled in order to correctly display spectra even when ex hibiting strong atmospheric noise in the usual regions of 1350 1440nm 1790 1980nm and 2360 2500nm The algorithm consists of calculating the mean and standard deviation in the wavelength region 300 1200nm The maximum of the y axis is then given by mean 3 standard deviation Spectra having no sensor definition cannot be plotted For sensors comprising broad and narrow band elements e g MFR only the narrow bands will be plotted SPECCHIO_UserGuide_V2 1 1 docx Version 2 1 1 02 11 2010 SPECCHIO Page 51 User Guide of 103 Spectrum Report bfe rn 001
91. m the normal total of 66 If you study the names of the target spectra it seems that the missing spectra numbers are 55 56 and 57 Specify the gaps as 55 56 57 and press Insert gaps The total number of positions is shown in the field Spectra dummies i e 66 in this case Press Calculate The list above the Calculate button now contains the positions starting at zero the calculated angles and the spectrum filenames Scroll down till you find the inserted dummies called gap dummy cf Figure 147 SPECCHIO_UserGuide_V2 1 1 docx Version 2 1 1 02 11 2010 SPECCHIO Page 95 User Guide of 103 IO Goniometer Angle Calculation Selected hierarchy target 53 300 60 triticaa 062 No of spectra 63 54 300 75 gap dummy i 55 330 75 gap dummy 1 Gaps 55 56 57 56 330 60 gap dummy Spectra dummies 66 Insert gaps L Calculate OK Jj Cancel Figure 147 Inserted gaps and resulting angles At this point you would have to refer to your field protocol in order to confirm that the gaps you specified did occur at the calculated angles Let us assume that number 57 actually exists but number 60 is missing Change the gap specification to 55 56 60 Press Insert gaps and Calcu late and check the list again Once you are satisfied with the calculated angles press Ok to store the angles in the database Use the Metadata Editor to check that the angles h
92. misphere Explorer and con nect it with the input space Figure 158 SPECCHIO_UserGuide_V2 1 1 docx Version 2 1 1 02 11 2010 SPECCHIO Page 99 User Guide of 103 ADO Space Network Processor Alpha Release 0 Type Sensor instrument Space D 2151 Vectors 17 Run Vis module Gonio Hemisphere Explorer Settings Status Waiting for data E Figure 158 Gonio Hemisphere Explorer connected to the input space Press the Run button of the Space Network Processor A Gonio Hemisphere Explorer window will open Figure 159 eo o Gonio Hemisphere Explorer Space no 0 lA Hemispherical Radiance Plot Spectral plot liu Spectrum Statistics 0 10 Mean 0 01442 3 Min O0 0 05 Max 0 10237 Stddev 0 1227 Sampling Point Information Filename triticaa 004 Azimuth O Zenith 30 e a Band 1 431 861 1291 1721 2151 Wvl nm 557 0 Figure 159 Gonio Hemisphere Explorer showing the data points selected in the Query Browser Note that according to the selection in the Query Browser only a limited number of points are dis played The Gonio Hemisphere Explorer can handle any number of spectrodirectional data points and could thus be used on data stemming from different goniometer systems as well The data comprises spectrodirectional measurements of a wheat field triticale The hemispherical plot nicely illustrates the backward scattering of vegetation canopies highest r
93. mmon Cyathea Medularis Latin Figure 132 Spectrum names All three species Blackfern Cabbage Tree and Lemonwood are typical for New Zealand forests They all share a common landcover type To set the landcover for all spectra first select the top folder called Vegetation example ahueni veg example Campaigi ommum i Blackfern c sitel bfern 001 bfern 002 hearer OM SPECCHIO_UserGuide_V2 1 1 docx Version 2 1 1 02 11 2010 SPECCHIO Page 89 User Guide of 103 Figure 133 Selecting the top folder Vegetation_example Now select the landcover type Deciduous Forest in the CORINE landcover tree cf Figure 134 Press Update to apply the selected landcover type to all spectra of this campaign You can now check the fact that indeed all spectra have this landcover type set by selecting single spectra in the Spectral Data Browser Landcover Data CORINE Landcover Artificial Surfaces Agricultural Areas Forest and Semi Natural Areas BC Forests zu a eciduous Forest 4 amp Coniferous Forest 4 Mixed Forest a Scrub and or herbaceous associations Figure 134 Specification of the landcover Pictures taken at the sampling sites can be entered into the spectral database Pictures for Black fern and Lemonwood are provided in the vegetation example zip file You will find the pictures alongside with the Vegetation example folder in the directory where you un zipp
94. mon Cyathea medullaris Latin Tree 100 0 021688519 0 021206077 0 022523083 0 023339724 0 021277064 0 022375558 Version 2 1 1 02 11 2010 SPECCHIO Page 54 User Guide of 103 5 2 10 Interactive Processing using Space Networks For an introduction to the concept of the Space Processing Network please refer to 4 6 Pressing the Process button in the Query Builder interface starts the processing tool A number of spaces are placed on the processing plane of the Space Network Processor depending on the query built in Query Builder Figure 59 shows a space containing 66 spectra created based on a selection in the Query Builder gt pace Network Proce OT Browser Queryc 3 Show only my data Type Sensor Instrument Space gt L3 mona test Campaign D 2151 gt test byte arr Campaign Succ 66 gt 33 Soil and Water Experiment Camp v lagos_artificial_turf Campaign v lagos_artificial_turf Y E hem a 20 gt C TTTTE gt i reference gt hem b 30 gt i hem c 40 gt 3 FEK4B Andys Spectra Campaign gt 3 mfr Campaign gt L3sdb admin test Campaign Number of resulting rows gt 33 Avalanche Study Campaign gt ithe new test Campaign 66 gt 33 Overcast sky Campaign gt DIY slbs Campaign E m todays test campaign Campaign gt rsl instruments Campaign A gt test after load fiddling Campaign M Figure 59 Space Network Processor interface with the Query Bu
95. n To display the configuration dialog of a module click menu over the module and select Configure The possible configuration settings of each module are detailed in the respective module descrip tion 5 2 10 4 Processing Module Descriptions 5 2 10 4 1 Radiance to Reflectance Transformation The module Radiance to Reflectance is building ratios of target and reference panel ra diances p vs Ley As a prerequisite datalinks of the type Spectralon must exist between the target spectra and the corresponding reference spectra For an explanation of how such links are created please refer to 5 2 6 2 10 2 5 2 10 4 2 Reference Panel Correction Factors This module retrieves the correction factors for all reference panels that were used during data acquisition of the spectra contained by the input space As prerequisites a reference panel must be set for the input spectra using the Metadata Editor Figure 65 and calibration data for the panel must have been loaded to the database Calibration data loading is a task of the system administrator For details on the reference panel administration see 5 2 11 5 Reference Data Reference name RSL Field Spectralon 10 RSL 003 SRT 99 100 HH Show Reference Info Figure 65 Reference panel setting in the Metadata Editor If no calibration data can be found a warning is displayed and the module creates no output space Figure 66 shows a processing chain that select
96. n in Figure 69 a waveband filtering is applied to the correction factors as these were measured with a larger wavelength range 0 Proc module Get Panel Correction Factors 1 Ref panel cor factors Type Sensor instrument Space Settings Type Spectral Space D 2151 i Sr LLLA li D 2251 Status Waiting for data Vectors 1 Vectors 1 2 Proc module Waveband filtering Type Spectral Space Settings D 2151 Vectors 1 Status Waiting for data Proc module Correct for Panel 3 Ref Panel corr Refi Settings Automatic selection from DB Type Spectral Space Status Waiting for data D 2151 Vectors 1 Figure 69 Space Processing Network for reference panel correction The panel correction can be applied to radiance or reflectance values However correcting radian ces for the panel will only make sense if followed by a radiance to reflectance conversion such that SPECCHIO_UserGuide_V2 1 1 docx Version 2 1 1 02 11 2010 SPECCHIO Page 59 User Guide of 103 p L far p ref L ref The correction procedure can handle multiple reference panels and multiple calibration coefficients and will apply the correct coefficients to the appropriate spectra 5 2 10 4 4 Delta This module calculates a delta value i e the difference between two inputs A and B Delta A B where A B MXN matrix of M spectra of dimensionality N Thus a delta vector is calculated by where m 1 M This implies t
97. nctionality 26 03 2009 ENVI spectral library loading problem has been addressed 2 0c 07 07 2009 A Hueni Numeric fields in the Metadata Editor now accept copy amp paste operations Support for new DB fields for in strument settings SPECCHIO_UserGuide_V2 1 1 docx Version 2 1 1 02 11 2010 SPECCHIO Page 4 User Guide of 103 02 09 2010 A Hueni Added instrument settings support Added associated measurements support Names and Target Type dialogues have combobox values now updated when editing existing data Copy amp paste operations now also work under Windows Config file reading routine more robust multiple CR LF possible and not causing a crash Time selection for file output now works from the space network processor as well Solved memory problem when loading 3000 spectra plus further memory leaks Bug fix for picture loading in instrumentation admin Added support for the SVC HR1024 instrument Added calibration definition for instruments Added preliminary support for Apogee instrument A Hueni Added button for direct spectral plot from Query Browser Selection of space splitting approach in Query Browser Added filename wildcard field in Query Browser Progress info and multithreading for Data Remover Added handling for SVC HR 1024 instruments measuring in radiance mode A Hueni Bugfix for space splitting in Query Browser Bugfix for campaign restriction in Query Browser
98. nd Exploration Each part contains several exercises that are listed in a logical order In order to support the learn ing process every exercise lists the relevant sections in the User Guide All tutorial data are available for downloading on www specchio ch The test data sets used for the specific tutorial parts are explicitly specified at the start of the re spective section 6 1 1 SPECCHIO Online Test Database Relevant section 5 2 3 An online test database is provided on db specchio ch Please use this database for the tutorial exercise and all other tests you would like to carry out To change you database connection to the test database select Database Connect to data base from the main menu Connect to the test database by entering specchio test in the database connection dialog cf Figure 114 Note that the user name and password you received when creating a SPECCHIO account are identical for both the productive and the test databases specchio resp spec chio test Connect to database Sele Known connections db specchio ch 4406 4Hueni specchio Server db specchio ch Port 4406 Database specchio best Username AHueni Password du d4 4g Connect Cancel Figure 114 Connecting to the specchio test database SPECCHIO_UserGuide_V2 1 1 docx Version 2 1 1 02 11 2010 SPECCHIO Page 81 User Guide of 103 6 1 2 Creating Campaigns on the Test Database In order
99. ne Plot Space no 1 Spectral plot Spectral plot 1000 Wavelength nm Wavelength nm Figure 156 Spectral plots of radiance and calculated reflectance SPECCHIO_UserGuide_V2 1 1 docx Version 2 1 1 02 11 2010 SPECCHIO Page 98 User Guide of 103 The calculated reflectances show the typical features of a vegetation spectrum green peak red edge water absorption features The high reflectance in the UV Blue of the first few bands is an artefact of the instrument and indicates an unreliable calibration of the according channels 6 5 2 Data Queries Data set all campaigns loaded to the database If you worked through the whole tutorial a total of three new campaigns should now be loaded to the database Note that you have access to campaigns other persons entered in the database Queries on the database can thus return more rows than you might expect Open the Query Builder and switch to the Query conditions tab In the wildcard field of the Campaign name type in your first or last name followed by the percent age sign e g hueni Alternatively select your name from the investigators list The number of resulting rows should be 154 if all 3 tutorial data sets were loaded Select Directional as measurement type The number of rows should drop to 70 and the autobuilt SQL statement looks similar to SELECT count FROM Spectrum campaign WHERE name like hueni AND spectrum measurement type id 2
100. new campaign for goniometer data and load the campaign data SPECCHIO_UserGuide_V2 1 1 docx Version 2 1 1 02 11 2010 SPECCHIO Page 93 User Guide of 103 If you explore the data in the Metadata Editor you will find that the Measurement unit has been set to Radiance and the FOV to 3 degrees Use a group update to set the Measurement type of all spectra of this campaign to Directional In the Metadata Editor select the special function Link targets to references cf 5 2 6 2 10 2 In the Link Target to Reference dialog select the target and reference directories of the goniometer campaign as inputs cf Figure 143 and press Link The datalinks have now been created In the Metadata Editor explore the datalink settings cf Figure 142 You should find that the tar gets triticaa 001 triticaa 005 are referencing the triticaa 000 white reference spectrum Target triticaa 007 references triticaa 006 and so on and so forth The linking mechanism is based on the spectrum capture time and does not depend on the spectrum file name Link Target to Reference Targets References specchio best specchio test Andy veg example Campaign Andy veg example Campaign amp Andy GER example Campaign Andy GER example Campaign Andy_Gonio_example Campaign Andy Gonio example Campaign Gonio_example E Gonio_example E reference w GGG cAERESME target Target hierarchy lare Reference hierarchy scs
101. ng calibrations 5 2 11 5 2 Reference Panel Administration The reference data tab allows adding editing and removing reference panels and related meta data in particular panel calibration data Figure 101 Page 73 of 103 Current Reference RSL Field Spectralon 10 HH Reference Data Insert new reference Delete reference Instrument Data _ Reference Data Reference Data Reference name RSL Field Spectralon 10 Reference owner RSL University of Zurich E3 Serial number RSL 003 SRT 99 100 Spectralon Reference brand Calibrations Cal Date 2004 12 28 Calibration number 4411021 Comments Purchase Order 2413606 Pictures Pictures Field spectralon panel pa uu Cal Factors v u c s 9 1 0 v oc un e o Spectral plot Figure 101 Reference data tab of the instrumentation administration window To edit or remove a reference panel select the reference in the reference list first Cal Uncertai Removing a reference is achieved by clicking Delete reference A confirmation dialog will be dis played SPECCHIO_UserGuide_V2 1 1 docx Version 2 1 1 02 11 2010 SPECCHIO Page 74 User Guide of 103 eoo Delete reference m f Do you really want to delete the reference Foobar reference panel Cancel Co Figure 102 Reference deletion confirmation dialog A reference panel cannot be deleted while still being refe
102. ng for data Figure 71 Space Processing Network for the panel correction and delta calculation 1000 2000 1000 2000 1000 2000 Wavelength nm Wavelength nm Wavelength nm Figure 72 Spectral plots of input spectrum left panel corrected spectrum middle and delta spectrum left 5 2 10 4 5 Waveband Filter Waveband filtering is used to cut wavelengths regions from spectra A typical example is the re moval of noisy wavebands caused by water vapour absorption The wavebands are freely configurable The Configure menu brings up the Filter configuration dialog Figure 73 00 Filter configuration Filter regions nm New Cancel 1400 0 1500 0 Modify Remove Figure 73 Filter configuration window SPECCHIO_UserGuide_V2 1 1 docx Version 2 1 1 02 11 2010 SPECCHIO Page 61 User Guide of 103 To add a new filter region click New and enter the upper and lower wavelengths in nanometres in the Filter Definition dialog Figure 74 ANDO Filter Definition Lower wvl nm 1700 OK Upper wvl nm 1800 Cancel Figure 74 Filter definition dialog To remove an existing filter region select the region in the list and click Remove 5 2 10 4 6 Broadband and Narrowband Filters The filters act on the element type of sensor elements They are useful to process data of sensors that contain bands widely differing spectral resolutions An example is the MF
103. ngle Calculation dialog 1 If there are any gaps specify the positions of the gaps in the Gaps input text field The gap numbers must be separated with commas Then click the Insert gaps button and the total number of spectra plus inserted gap dummies will be shown in the read only field Spectra dummies Note that positions start with 0 O Click Calculate This fills the listbox one the right side of the dialog with a preview of the calculated angles The line format is lt position gt lt azimuth gt lt zenith gt lt filename gt O Click OK to insert the calculated angles into the database SPECCHIO_UserGuide_V2 1 1 docx Version 2 1 1 02 11 2010 SPECCHIO Page 42 User Guide of 103 ICMDSVYUI uUi taricc IMUNAN UIDLAILe Calc Gonio Angles Calc Sun Angles jJ Spectrum Data ANDO Goniometer Angle Calculation e Reset 3 Selected hierarchy target v E hem c 0 75 hem c r 001 k incoming No of spectra 66 0 60 hem c r 002 v reflected T M 2 0 45 hem c r 003 gt B reference a ae v MILES Spectra dummies hem_c_ L hem c 4 Insert gaps hem c I nt hem c I hem c I OK Cancel hem c I ee ne hem c I Figure 43 Goniometer angle calculation dialog 5 2 6 2 10 2 Linking Targets to References This dialog can be used to automatically create a datalink of the type Spectralon between target spectra and white re
104. ngles can be calculated for a spectrum if the spatial position in latitude longitude and the capture time in UTC are known Select the spectra to be processed in the spectral data browser of the metadata editor see Figure 46 Note that any selection single spectra hierarchy and mixed cases is possible The sun angle calculation dialog opens and the number of spectra is displayed Click OK to calcu late the sun angles and store the results in the database SPECCHIO_UserGuide_V2 1 1 docx Version 2 1 1 02 11 2010 SPECCHIO Page 44 User Guide of 103 Sampling geometry Data Vegetation Example Campaign v Vegetation example Sensor zenith 0 Illumination zenith v Blackf MEME ase Sensor azimuth Illumination azimuth v Ge sitel Sensor distance Illumination distance Calc Gonio Angles Calc Sun Angles 3 bfern 00s Mamas 3 bfern 006 Bil5 ern 007 1 URS No of spectra 8 bfern 009 bfern 010 OK Cancel bfern 011 So 31 bfern 012 Figure 46 Sun Angle Calculation dialog 5 2 6 2 10 4 Direct Irradiance Calculation The calculation of direct irradiances applies to photometers where the total and diffuse irradiance are known Total and diffuse spectra must be stored in separate hierarchies see Figure 47 Furthermore all spectra need to have a defined sun zenith angle The calculation cannot be carried out on hierarchies already containing a direct hierarchy If a recal
105. nit id l AND spectrum illumination source id 1 AND spectrum instrument id 1 AND spectrum campaign id campaign campaign id AND spectrum user id spec chio user user id AND spectrum position id position position id AND spec trum sampling geometry id sampling geometry sampling geometry id AND cam paign user id specchio user user 1d AND specchio user user id posi tion user id AND specchio user user id sampling geometry user id SPECCHIO_UserGuide_V2 1 1 docx Version 2 1 1 02 11 2010 SPECCHIO Page 49 User Guide of 103 Campaign Campaign name All Investigator All Md spe Description Landcover Level IIl Deciduous forest HH Position Latitude 40 Buffer size 10 Longitude Buffer size Altitude 50 Buffer size 20 Sampling geometry Sensor zenith Buffer size Sensor azimuth Buffer size Sensor_distance Buffer size Illumination zenith 45 Buffer size 5 Illumination azimuth Buffer size Figure 53 Query conditions tab part 1 SPECCHIO_UserGuide_V2 1 1 docx Version 2 1 1 02 11 2010 SPECCHIO Page 50 User Guide of 103 General settings Measurement type All incl none B illumination source Sun H Measurement unit Reflectance 1 Target homogeneity All incl none 1 Sampling environment All incl none H Goniometer All incl none A Sensor and instrument data Sensor All incl none HB Instrument INR ASD HH Foreoptic All incl none H4 Spectru
106. nvironment where the sampling took place field laboratory hdrf to brf or model model stands for simulated data using a computational model of some sort Target homogeneity Defines the possible values of homogeneity Homogenous or Mixed O Goniometer FIGOS or LAGOS Sampling Geometry Data Numbers in this group can all be entered as floating point numbers O Sensor zenith angle in degrees where 0 degrees is equal to nadir O Sensor azimuth angle in degrees measured relative to the principal plane l e 0 de grees the principal plane opposite of illumination source Sensor distance distance of sensor to target in metres Illumination zenith angle in degrees where 0 degrees is equal to nadir Illumination azimuth absolute angle in degrees Illumination distance distance from source to target Two action buttons for the automatic calculation of goniometer and sun angles EXISTE Spectrum Names O A list of spectrum names Two name types are currently supported Latin and Common ENVI Hdr is used internally for data read from ENVI spectral libraries Further name types can be defined by the administrator Use the Add Edit and Remove buttons next to the list to change to contents of the list To edit or remove an existing name selected it in the list and then click the appropriate button Target Type Defines the target type and the abundance of this target type in the sampled object cf also 4 5 3 Further target types can
107. of Goniometer Angles RSL uses a standard protocol for the capturing of directional data using a goniometer FIGOS LAGOS The sensor zenith and azimuth are given by the capturing sequence Figure 42 Figure 42 Data collection sequence of the RSL FIGOS LAGOS system A full directional set consists of 66 spectra The routine expects a maximum number of 66 spectra i e excessive spectra like white reference readings must be removed before the angles are calcu lated The function can deal with gaps in the data provided that the user can specify them See Figure 43 for a screenshot of the dialog with the metadata editor in the background The following user actions are needed O Inthe spectral data browser of the metadata editor select a hierarchy that contains the spectrodirectional measurements cf Figure 43 where the target hierarchy has been selected in the metadata editor O Click the Calc Gonio Angles button in the Sampling Geometry section of the meta data editor This will open the Goniometer Angle Calculation dialog The selected hier archy and the number of spectra is displayed in the according fields in the middle sec tion of the dialog If the wrong hierarchy was selected in the metadata editor you can redefine your selection in the metadata editor while leaving the Goniometer Angle Cal culation dialog opened Changes in the spectral data browser of the metadata editor will be reflected within the Goniometer A
108. omated loading of spectra into the database including the structure infor mation Typically the operations carried out for each campaign are 1 Creation of anew campaign 2 Loading of spectra 3 Entering of metadata 4 Repeated data query visualisation processing and file output New data can be added to ongoing campaigns by a storing them first in the already existing cam paign data structure on the file system and be invoking the SPECCHIO loading operation for the respective campaign again Only new spectra will be added to the database in this case 5 2 SPECCHIO Application 5 2 1 Look and Feel SPECCHIO is written in Java and has been setup to use the native operating system look and feel The screenshots provided in the following sections have been taken on Windows XP and MacOS X Depending on your system the windows and widgets will look differently The functionality of the GUI is generally identical on all tested operating systems There is however a minor difference in the selection of directory pathnames under UNIX As a filename is required in the Open dialog enter a dot in the filename box cf Figure 8 Alternatively on some UNIX ma chines just click the folder but do not double click in this fashion the folder will be selected and no has to be inserted in the filename box Open on terra Enter path or folder name jhomejrsI ahueni Filter Files NES Y Folders Enter file name OK Update
109. on 5 2 7 Your data are now ready to be visualised and exported Open the Query Builder by selecting Data Processing amp Output gt Build query In the Spectral Data Browser the tree like display on the left side of the dialog select your campaign tick the box Show only my data to restrict the displayed campaigns to your own and explore the structure Note that the database has stored the hierarchi cal structure of the campaign folder and displays it accordingly cf Figure 121 Also note that as you click around the tree selecting folders or files the SQL query and the number of resulting rows on the right side are updated simultaneously You can also use Ctrl and Shift keys to do multiple selections Now select the first 6 spectra of the Blackfern site1 the number of resulting rows should be 6 and click on Show report A new window will appear looking similar to Figure 122 Note that a scrollable list containing the metadata is associated with every spectrum Have a look at the meta data and note the data filled in automatically filename capture date spatial position measurement unit sensor name number of spectral channels instrument name owner and serial number The strong noise in the water bands is due to the generally high humidity found in New Zealand maritime climate coupled with high yearly rainfall up to 10 metres in Fjordland SPECCHIO_UserGuide_V2 1 1 docx Version 2 1 1 02 11 2010 SPECC
110. orial data download page 6 2 Part 1 Loading Editing and Retrieving Data Data set Vegetation example 6 2 1 Examine the Folder and File Structure Relevant sections 3 2 3 3 Open a filing system window and browse the directory structure of the Vegetation example folder It contains three species folders Blackfern Cabbage tree and Lemonwood Open each of these species folders and examine the contents of the site directories contained in them Blackfern has only one sample site while Lemonwood and Cabbage tree have three resp two Also browse inside the site directories to find the ASD binary files cf Figure 116 SPECCHIO_UserGuide_V2 1 1 docx Version 2 1 1 02 11 2010 SPECCHIO Page 82 User Guide of 103 Folders x Name Size Type C Vegetation example Slicabbage 000 3KB 000 File amp 3 Blackfern E cabbage 001 9KB 001 File sitet E cabbage 002 9KB 002 File 3 C3 Cabbage tree f cabbage 003 9KB 003 File C3 sitel f cabbage 004 OKB 004 File site2 E cabbage 005 9KB 005 File amp Lemonwood E cabbage 006 9KB O06 File sitet Ej cabbage 007 9KB 007 File site2 E cabbage 008 9KB 008 File site3 E cabbage 009 9KB 009 File Figure 116 Folder and file structure of the Vegetation example campaign 6 2 2 Creating a new Campaign and Loading the Spectra Relevant sections 5 2 4 5 2 5 Create a new campaign by selecting Data Input gt Create new campaign In the
111. ory Note that when using a UNIX system you may have to enter a dot as filename cf 5 2 1 A base name must be specified This name should contain no characters that are not allowed in filenames depending on the operating system The base name is used to build the real filenames Filenames use one of the following patterns base name sensor name file extension base name instrument name cal calibration sequence number file extension If no instrument has been defined the sensor name will be used If an instrument has a defined calibration then the calibration sequence number is added to the filename If the spectra being written have been captured with different instruments or different calibrations then for each combination of instrument and calibration a separate file will be written E g consider a campaign containing spectra captured with O An ASD instrument belonging to the Institute of Natural Resources Massey University named INR ASD with calibration sequence number 1 O An ASD instrument belonging to the Remote Sensing Laboratories University of Zurich named RSL ASD 1 with no calibrations entered in the database O AGER 3700 instrument belonging to the Remote Sensing Laboratories University of Zurich named RSL GER 3700 with no calibrations entered in the database A CSV file output of this campaign with the option Split header and body results in the following files Bal mixed instr INR ASD_cal1_BO
112. owing target and reference spectra right Targets and references are linked internally by a datalink on spectrum level cf 4 4 Open the Metadata Editor and display the spectrum data for one of the GER target spectra Note that a link referring to the reference spectrum of the type Spectralon has been created cf Figure 142 These datalinks are used during radiance to reflectance conversion Datalink Datalinks GRO83005 080 Spectralon data v Figure 142 Automatically created link between target and reference spectra 6 4 Part 3 Directional Data Data set Gonio example Relevant sections 5 2 4 5 2 5 5 2 6 This exercise uses FIGOS goniometer data FIGOS is used at RSL to acquire spectrodirectional measurements in 66 points arranged on a hemisphere For more information please refer to Schopfer et al 2007 Goniometer data is provided in the Gonio example folder It contains two subfolders one holding the targets and one the references The spectra of targets and references have been manually moved to these folders This separation should be carried out before the data is loaded into SPECCHIO alternatively all data can be loaded and the unwanted spectra removed using the Data Remover tool It must also be noted that any surplus measurements must also be removed i e the system expects 66 directional measurements maximum SPECCHIO can however deal with gaps in the data as will be demonstrated hereafter Create a
113. ows Figure 58 19 CO wN On Go ho 32 33 ee EE eee GINNNNN Number Comment Capture date Loading date Filename Internal no of avg Is reference Latitude Longitude Altitude Location Campaign name Campaign desc Landcover Cloud cover octas Ambient temp C Air pressure Rel humidity Wind direction Wind speed Sensor zenith Sensor azimuth Illumination zenith Illumination azimuth Sensor distance Illumination distance Measurement unit Measurement type Illumination source Sampling environment Spectrum names Target types 350 351 352 353 354 355 1 2 2005 09 11 23 09 50 2005 09 11 23 09 54 2005 09 11 23 09 58 2006 12 11 18 23 03 2006 12 11 18 23 03 2006 12 11 18 23 03 bfern 001 10 false 40 3849 175 622 52 Vegetation Example Deciduous forest 0 18 calm 0 47 7073 21 975 Reflectance Single Sun Field 0 0251693 0 026092373 0 026704058 0 026678136 0 025368243 0 02532748 bfern 002 10 false 40 3849 175 622 54 2 Vegetation Example Deciduous forest 47 7025 21 9535 Reflectance 0 02180227 0 022058768 0 02304296 0 023551108 0 022222875 0 022796206 Figure 58 CSV file example loaded into Excel SPECCHIO_UserGuide_V2 1 1 docx bfern 003 false Vegetation Example Deciduous forest calm Reflectance Single Sun Field Page 53 of 103 10 40 3849 175 621 49 2 0 47 6981 21 9333 1 Blackfern Com
114. pectroradiometer is configured to acquire radiances the irradiance will commonly be charac terised indirectly by measuring the radiance reflected by a reference panel This may be preferable to the direct acquisition of reflectance data as information about the irradiance can be retrieved from the dataset The structure must therefore hold target and reference radiance spectra A possible structure is shown in Figure 3 v ref target example v Planta plant_a 000 plant a 001 plant a 002 gt 3 Plant B gt L3 PlantC v L3 Reference ref 000 m ref 001 m ref 002 Figure 3 A possible structure for the storage of target and reference radiance spectra SPECCHIO_UserGuide_V2 1 1 docx Version 2 1 1 02 11 2010 SPECCHIO Page 13 User Guide of 103 4 SPECCHIO Concepts 4 1 Modelling of Hierarchies in the SPECCHIO Database and GUI The hierarchical structure of a campaign is stored in the database using three tables O campaign O hierarchy level Spectrum The hierarchy level table recursively models the folder structure of the campaign i e any depth of a tree structure can be stored in only one table The data hierarchy is used in the GUI to build the contents of a component called Spectral Data Browser This browser shows the structure as defined on the file system and adds a campaign node to the top of the structure Figure 4 shows a Spectral Data Browser component that visualises the directory structure of the
115. pixels width or height respectively Names Ciddi spectrum_name Add Lemonwood Common Edit er Remove _ a Target type a N target type Add Tree 10058 E LL Remove _ a Associated Measurements assoc measurement Water content 50 5 Figure 26 Spectrum data tab part 3 SPECCHIO_UserGuide_V2 1 1 docx Version 2 1 1 02 11 2010 SPECCHIO Page 34 User Guide of 103 Sensor and Instrument Data Sensor ASD FS FR 3 He FOV deg 25 Name NR ASD Show Instrument Info ntl Instrument Settings instrument setting Integration time 17 Gain SWIR1 500 Gain SWIR2 500 Reference Data Reference name INR Spectralon 44110 B Show Reference Info Pictures Pictures Add Lemonwood near Atawhai Village Figure 27 Spectrum data tab part 4 Instrument name RSL ASD FS3 1 Instrument owner RSL University of Zurich Instrument number 16006 Sensor name ASD FS FR 3 Description ASD FieldSpec FR or FieldSpec3 type No of bands 2151 Wavelength range 350 0 2500 0 Manufacturer Analytical Spectral Devices Inc ASD ASD FieldSpec 3 Manufacturer WWW www asdi com Figure 28 Instrument information window SPECCHIO_UserGuide_V2 1 1 docx Version 2 1 1 02 11 2010 SPECCHIO Page 35 User Guide of 103 Reference name RSL Field Spectralon 10 Serial number RSL 003 SRT 99 100 Comments Owner University of Zurich RS
116. plication Files The SPECCHIO application is contained in a Java archive file SPECCHIO App V lt x xx gt jar lt x xx gt stands for the version tag e g 1 0c i e the jar file would be named SPECCHIO App V1 0Oc jar The file db config txt contains database connection configurations SPECCHIO_UserGuide_V2 1 1 docx Version 2 1 1 02 11 2010 SPECCHIO Page 10 User Guide of 103 2 2 2 2 Java Library Extensions The following files are needed to run SPECCHIO jcommon 1 0 5 jar jfreechart 1 0 2 jar jgraph jar mysql connector java 3 1 13 bin jar qcchart3djava jar E T E TE The extensions are supplied in the same folder as the SPECCHIO application file 2 2 3 Microsoft Windows Copy the whole content of the ZIP file SPECCHIO Application jar the db config txt and the libraries to some new directory on your machine It is recommended to create a new folder in C Program Files and copy the above files to this folder O To start the SPECCHIO Application double click the SPECCHIO App V lt x xx gt jar icon 2 2 4 UNIX The described installation procedure installs the software in a user directory This implies that only users with access to this user account can run the software For the installation on a server with access for every system user you need administrator rights on the concerned machine or have it installed by the system administrator Copy the whole content of the ZIP file SPECCHIO Application jar the db conf
117. r Instrument Foreoptic Landcover Target homogeneity Measurement unit Sampling environment Measurement type Ex deg dps epp Ep ses pn Position Latitude Longitude Altitude Exp dr det Environmental condition O Cloud cover Sampling geometry O Sensor zenith O Sensor azimuth Oo Illumination zenith O Illumination azimuth Target type O Target type SPECCHIO_UserGuide_V2 1 1 docx Version 2 1 1 02 11 2010 SPECCHIO Page 15 User Guide of 103 4 4 Data Links Data links have been introduced as a means of defining relations between data sets or single spec tra l e data links are 1 1 relationships between either two hierarchies or two spectra Data links are of a defined type Implemented types are a Photometer data b Spectralon data and c Radiance data Data links are in some cases set up automatically during campaign data loading E g GER signa ture files include the spectra of both target and white reference For more information on data links see 5 2 5 1 and 5 2 6 2 10 2 SPECCHIO uses data link information for e g the automatic calculation of reflectance from target and reference radiances 4 5 Metadata A number of metadata parameters are detailed hereafter For more information on the metadata parameters supported by SPECCHIO please refer to the Metadata Editor section and to Huni et al 2007 4 5 1 Cloud Cover Description of the cloudiness of the sky by octas For the total cloud amo
118. r M 2007 SPECCHIO a system for storing and sharing spectroradiom eter data SPIE Newsroom December 2007 DOI 10 1117 2 1200711 0956 Online at http spie org x18220 xml PDF 0956 2007 11 29 pdf H ni A Nieke J Schopfer J Kneub hler M amp Itten K 2007 Metadata of Spectral Data Col lections 5th EARSeL Workshop on Imaging Spectroscopy Bruges Belgium H ni A Nieke J Schopfer J Kneub hler M amp Itten K 2007 2nd Generation of RSL s Spec trum Database SPECCHIO ISMPSRS Davos Switzerland Hueni A amp Tuohy M 2006 Spectroradiometer Data Structuring Pre Processing and Analysis An IT Based Approach Journal of Spatial Science 51 2 93 102 Hueni A 2006 Field Spectroradiometer Data Acquisition Organisation Processing and Analy sis on the Example of New Zealand Native Plants Institute of Natural Resources Palmerston North Massey University SPECCHIO_UserGuide_V2 1 1 docx Version 2 1 1 02 11 2010 SPECCHIO Page 9 User Guide of 103 2 Installation and Configuration 2 1 Database 2 1 1 MySQL Instance SPECCHIO runs on version 5 of MySQL database An online instance of the database is available on the db specchio ch database server The SPECCHIO database can as well be installed locally MySQL is available from www mysql com A SPECCHIO system installation package allowing local installation is available from RSL RSL distributes the SPECCHIO system package free
119. reCA HR1024 Instrument owner Imaging Centre CA H4 Serial number 0761008 Sensor SVC HR 1024 B ImagingCentreCA HR1024 Instrument Data HR 1024 on tripod Reset 3 Update l l Calibration Data Calibrations Insert new instrument j 4 Spectral plot Delete instrument p p p AJ Cal Date Calibration number Cal Factors E Cal Uncert Comments Wavelength calibration by SVC 1000 2000 gth Spectral plot Figure 96 Instrument data tab of the instrumentation administration window SPECCHIO_UserGuide_V2 1 1 docx Version 2 1 1 02 11 2010 SPECCHIO Page 72 User Guide of 103 To edit or remove an instrument select the instrument in the instrument list first Removing an instrument is achieved by clicking Delete instrument A confirmation dialog will be displayed Figure 97 BOM Delete instrument 4 Do you really want to delete the instrument Another ASD Figure 97 Instrument deletion confirmation dialog An instrument cannot be deleted while still referenced by one or more spectra in the database An according message will be shown if the delete action failed Figure 98 e e Message vA Error while deleting instrument some spectra still reference this instrument Gon Figure 98 Instrument deletion error The currently selected instrument will only be removed if no database constraints are v
120. renced by one or more spectra in the database An according message will be shown if the delete action failed Figure 102 The cur rently selected reference will only be removed if no database constraints are violated AOO Message S Error while deleting reference some spectra still reference this reference panel C Figure 103 Panel deletion error To insert a new reference click Insert new reference A new record is created in the database and the reference name is set to dummy Figure 104 Reference Data dummy Reference name dummy Reference Data Reference owner NIL Reset gt Serial number Reference brand 4 Insert new reference Delete reference J Figure 104 New dummy reference The reference can now be renamed and it s metadata filled accordingly To add a new calibration to a reference click the menu button over the Calibrations section of the Instrumentation Metadata Editor and choose Add calibration Figure 105 Calibrations Add calibration Remove calibration Figure 105 Popup menu for the reference calibrations Use the file browser to select a calibration file see below for a description of the file format and click Open Figure 106 SPECCHIO_UserGuide_V2 1 1 docx Version 2 1 1 02 11 2010 SPECCHIO Page 75 User Guide of 103 a OO Open E Spectralon HB Date Modified RSL 001 SRT 99 100 jpg Thursday De
121. rganised in a structured way in order to allow the automated import into the spectral database Section 3 2 explains the background of the structure used and section 3 3 gives a practical example of a directory and file structure that should be adopted for data collection Preferably sampling experiments should be designed to include some form of data structuring from the beginning Alternatively existing data can be arranged to meet the requirements 3 2 Hierarchical Structure The concept of hierarchical data structure has been adapted from SpectraProc Hueni 2006 SpectraProc was built on a fixed hierarchy of three levels The following example is based on the sampling design used for SpectraProc campaigns A hierarchical data structure that reflects the real world and the setup of sampling campaigns for vegetation is used This structure is derived from the following conditions 1 Reflectances of several different species are captured 2 In order to describe the in species variation several specimens of a species are sampled 3 The variability of the specimens is described by several measurements per specimen The spatial extent where a specimen is sampled is termed a sample site thus a species contains a number of sample sites The sites are numbered in the order of sampling At each site several readings are taken to capture the variation exhibited by the specimen in question A site therefore contains a number of spectra This leads to a hi
122. s the panel correction factors and plots using a spectral line plot Figure 67 Proc module Get Panel Correction Factors J Ref panel com factors Vis module Spectral Line Plot i Settings f Type Spectral Space Settings D 2151 i D 2281 Status Waiting for data Status Waiting for data Vectors 66 Vectors 1 0 Type Sensor instrument Space Figure 66 Processing chain selecting the correction factors and plotting them as a spectrum SPECCHIO_UserGuide_V2 1 1 docx Version 2 1 1 02 11 2010 SPECCHIO Page 58 User Guide of 103 1 5 1 0 MM M Reflectance 0 5 0 0 0 1000 2000 3000 Wavelength nm Figure 67 Reference panel correction factors 5 2 10 4 3 Correct for Reference Panel Non Idealness This module applies calibration factors to correct spectra for the reference panel non idealness These correction factors are selected from the database using the Reference Panel Correction Factors module The module requires two inputs the spectra to be corrected and the correction factors The input space selection dialog offers the according choices Figure 68 _ Input Space Selection Primary Spectra Correction Factors Y OK 2 Cancel Figure 68 Input space selection for the Correct for Panel module Note that the dimensions of the spaces holding the spectra and correction factors must be identical a check on the wavelengths is not carried out In the example show
123. set Schopfer 2008 SPECCHIO_UserGuide_V2 1 1 docx Version 2 1 1 02 11 2010 SPECCHIO Page 65 User Guide of 103 Hemispherical Radiance Plot Spectral plot Spectrum Statistics Mean 0 00409 Min O0 Max 0 00844 Stddev 0 064 Sampling Point Information Filename hem_a 001 Azimuth O Zenith 75 Band 1 431 861 1291 1721 2151 Wvl nm 628 0 Figure 82 Gonio Hemisphere Explorer window The explorer window comprises a number of components interacting with each other as described hereafter The hemispherical plot Figure 83 displays an interpolated surface of a specific wavelength Click ing the icon in the top left of the plot brings up a control panel for plot adjustments rotations Hemispherical Radiance Plot OO Roue QGZHUAOAND Ll Chart Rotation Control Z Axis X Axis LE ORGE Light Le ES gt 100 GD CD Gan A Figure 83 Interpolated 3D plot for a chosen wavelength left and rotation toolbox to manipulate the 3D plot SPECCHIO_UserGuide_V2 1 1 docx Version 2 1 1 02 11 2010 SPECCHIO Page 66 User Guide of 103 Use the band selection slider to select a spectral band for display Figure 84 The wavelength text field below is reflecting the wavelength of the chosen band Selecting a band triggers a re plotting of both hemispherical plot and spectral plot Band 1 431 861 1291 1721 2151 Wvl nm 1342 0 Figure 84 Band selection slider and wavelengt
124. shows showing the direct irradi ance over time for an MFR sunphotometer band with centre wavelength 496 4nm The channel to be plotted can be chosen in the list below the plot Time information is retrieved from the sampling time of the spectra SPECCHIO_UserGuide_V2 1 1 docx Version 2 1 1 02 11 2010 SPECCHIO Page 67 User Guide of 103 e 00 Time Line Plot Space noO Temporal Spectral Plot 11 00 13 00 15 00 17 00 Time Figure 87 Time Line Plot showing the direct irradiance over time for centre wavelength 496 4nm 5 2 10 5 6 Time Line Explorer The time line explorer consists of a time line plot and a spectral plot Figure 88 The red bar in the time plot indicates what spectrum is plotted in the spectral plot i e the spectral plot shows the spectrum taken at a certain time The red bar in the spectral plot shows the currently selected in strument channel which is plotted versus time in the time line plot ADO Time Line Explorer Space no 1 Temporal Spectral Plot Spectral plot 11 00 13 00 15 00 17 00 Time Instrument Channels 413 7 496 4 0 612 7 ES 671 3 v Figure 88 Time Line Explorer window The example given in Figure 88 is using MFR sunphotometer data A removal of the broadband channel is needed for the spectral plot to work properly The according processing chain is shown in Figure 89 SPECCHIO_UserGuide_V2 1 1 docx Version 2 1 1 02 11 2010 SPECCHIO Page 68 User Guide of
125. space are transformed to an output space The algorithm of the processing module defines the dimensionality of the resulting space This is illustrated in Figure 6 with an input space of di mensionality N being transformed into another discrete space of dimensionality M Although pro cessing modules tend to have singular input output in most cases they may have multiple inputs and generate multiple outputs SPECCHIO_UserGuide_V2 1 1 docx Version 2 1 1 02 11 2010 SPECCHIO Page 18 User Guide of 103 5 Operation 5 1 Overview 5 1 1 Dataflow A typical dataflow is illustrated in Figure 7 A spectroradiometer is used to capture the radiance of field objects Optionally a GPS connected to the field laptop where supported by the capturing software records the spatial position of the field object This is a recommended setup as the spa tial position can later be automatically loaded into the database Spectral and metadata are auto matically saved on the field laptop These files are transferred to a laboratory computer where they are read by the SPECCHIO appli cation and stored in the relevant tables in the spectral database GPS device B So Wty e Reflectance Spectral data Radiance Radiance DN C Data file amp metadata Absobens ERES BEI MES Ssorpance Field object Spectroradiometer Field laptop Lab computer SPECCHIO DB Figure 7 Dataflow and involved hardware 0 1 2 File System Interfaces
126. the data capturing The level A is foreseen to also include some quality measure for the spectral data Metadata quality levels are implemented and enforced by so called metadata policies These poli cies define the mandatory metadata fields for each database table Quality levels are managed on spectrum level i e each spectrum can have its own required quality Required quality is a user defined level It defines what metadata quality level the spectrum is supposed to reach at some point in time Once all metadata required for the specified level are entered the attained quality level of the spectrum will be updated to reflect the required level When new data are loaded they have no required quality level defined and thus no metadata poli cies are enforced Currently the following levels have been defined or foreseen Level A not implemented yet the exact specification is to be defined Reserved for spectra of high quality probably requiring some pre processing like atmospheric noise removal and smoothing Level B defines the minimal set of metadata that must be entered to reach a metadata quality level of B Level B should make spectral data useable by third persons who were not directly involved in the capturing process and are thus not familiar with the sampling circumstances The required metadata fields are detailed hereafter grouped by metadata groups as found in the metadata edi tor Campaign O Investigator Spectrum Senso
127. ther test Campaign gt Gj export test 1 Campaign gt stefan problem Campaign Figure 91 Data Remover dialog 5 2 11 2 Campaign Export The campaign export functionality is used to write all data of a campaign to an xml file while retain ing the relational structure These xml files can then be used to import the campaign into another SPECCHIO database instance AOO Campaign Export l Campaign name Vegetation Example A All relational data of this campaign will be exported to an xml file Target directory Users andyhueni Downloads Export Cancel Figure 92 Campaign Export Dialog The xml file structure contains all table entries that are required to reproduce the exported cam paign in its relational structure Entries are ordered by their inserting sequence i e the campaign import will carry out the inserts in the order given by the file 5 2 11 3 Campaign Import The Campaign import function is only available for users that have the rights equal to the SPECCHIO database administrator user sdb admin The import function requires an xml file cre ated by the SPECCHIO campaign export function The import will create an exact copy of the ex ported campaign and will insert new system table entries if required e g new sensor definitions SPECCHIO_UserGuide_V2 1 1 docx Version 2 1 1 02 11 2010 SPECCHIO Page 70 User Guide of 103 eoo0o Campaign Import Import source file ers andyhueni Downlo
128. tiated when a new campaign is created To load data into a new campaign use the function load campaign data Create new campaign Campaign name Main directory Figure 14 New campaign dialog My Recent Documents File name 3 Studies RSL SPECCHIO Project Campaigns GP5_Position My Network Figure 15 Directory selection dialog 0 2 5 Loading Campaign Data To automatically load the spectral data files of a campaign select Data Input gt Load campaign data Figure 16 Note that if different file types e g ASD binary files and GER signature files are occurring in the same campaign hierarchies must contain only one file type This restriction is due to two reasons a the file loading process is instantiating one concrete file loader class and ap plies it to all files in a directory and b it is against common sense to put files from different instru ments sensors into one directory Consider a case where one species is being sampled with ASD and GER A logical folder setup would be a species folder with two subfolders for ASD and GER These subfolders then contain the spectral files SPECCHIO_UserGuide_V2 1 1 docx Version 2 1 1 02 11 2010 SPECCHIO Page 23 User Guide of 103 Data Input Ig T4 Data Output Create new campaign Load campaign data Edit metadata Figure 16 Loading campaign data menu entry All names of the available campaigns of the current d
129. to keep things organised always include your name in the campaign name by using the following template lt your name gt _ lt campaign name gt e g Andy_veg_example This will make it easier to find your campaigns in the Query Builder where you can see all campaigns of the other users as well Note that the Query Browser includes a switch that will show only your own data 6 1 3 Downloading Test Data Sets The data sets used in this tutorial are available on the internet http specchio ch tutorial_data php The following data sets are provided as ZIP archives vegetation example zip ger example zip gonio example zip To download the ZIP files click on the links and select Save to Disk in the web browser dialog see Figure 115 Unzip the ZIP files to some working directory on your machine e g create a new folder called SPECCHIO data and unzip all datasets into this directory Opening vegetation_example zip Home i You have chosen to open Tutorial Data Download vegetation_example zip Create database account The following data sets are used in the tutorial which is a Compressed zipped Folder User Guides from ftp ftp geo unizh ch Download application p M Tutorial data Vegetation example What should Firefox do with this file Publications GER example CompressedFolder default LUST oject RSL Gonio_example Do this automatically for files like this from now on Figure 115 Tut
130. tomatically containing to output of the Radiance to Reflectance Transformation module Figure 154 0 Type Sensor instrument Space D 647 Vectors 10 Proc module Radiance to Reflectance 1 Settings Automatic selection from DB Type Spectral Space D Status Waiting for data Vectors Figure 154 Input and output spaces of the Radiance to Reflectance Transformation module Now we would like to see what this transformation is actually doing by plotting the input and output spectra Add two new modules of the type Visualisation Module to the processing plane configure them as Spectral Line Plot and connect them with the input space space 0 and the output space space 1 respectively Your Space Processing Network should now be similar to the one shown in Figure 155 0 Type Sensor Instrument Space D 647 Vectors 10 Vis module Spectral Line Plot Settings Status Waiting for data Proc module Radiance to Reflectance 1 Settings Automatic selection from DB Type Spectral Space Status Waiting for data sd it Vectors 10 Vis module Spectral Line Plot Settings Status Waiting for data Figure 155 Space Processing Network for radiance to reflectance transformation and visualisation Press the Run button of the Space Network Processor and two spectral plots should appear Figure 156 Spectral Line Plot Space no 0 Spectral Li
131. ty area of the processing plane This brings up the context sensitive menu shown in Figure 60 Select Add Module and a selection of the available modules will appear Figure 63 Select one of the modules click OK and a new module will be added to the processing plane To connect the module with an input space click the menu button over the module This displays the popup menu of the module Figure 64 Select Set Input Spaces and in the Input Space Se lection dialog select the number of the space to connect and click OK Figure 64 Note that all spaces are given a unique number which is located on the top left of each space Connecting an input space automatically generates an output space which is added to the processing plane and connected with the module 6 00 Module Selection Modules Radiance to Reflectance Transformation Ref Panel Corr Factors Correct for Ref Panel Delta Waveband Filter Broadband Filter Cancel Narrowband Filter Visualisation Module File Export Module Proof of Concept Figure 63 Module selection dialog SPECCHIO_UserGuide_V2 1 1 docx Version 2 1 1 02 11 2010 SPECCHIO Page 57 User Guide of 103 S Configure me PO Input space S tic 4 sen Spaces Input Space 0 Be Cancel Figure 64 Popup menu of a module left and the input space selection dialog right 5 2 10 3 Configuration of Modules Some modules may need configuratio
132. uld be upgraded by the database administrator using the Upgrade function see 5 2 11 6 BOLT Message vA Attention Database version is too old Version 2 0 is required Co Figure 12 Database version warning message 5 2 4 Creating a new Campaign To create a new Campaign select Data Input gt Create new campaign Figure 13 This brings up the new campaign dialog Figure 14 B 2 Bir 148 Data Output Create new al S Load campaign data Edit metadata Figure 13 Create New Study menu entry Enter a campaign name of 45 characters maximum length The main directory path is a file system pathname pointing to the directory that contains all hier archies and spectra of this study To set the path select the Browse button to display a directory tree Figure 15 and select the appropriate directory Note that when using a UNIX system you may have to enter a dot as filename see 5 2 1 Click Create to create the new empty campaign on the database Note that there is no check if a campaign of the same name already exists It is technically feasible to have two campaigns named the same However it is suggested to check on existing campaigns to avoid multiple campaigns with identical names SPECCHIO_UserGuide_V2 1 1 docx Version 2 1 1 02 11 2010 SPECCHIO Page 22 User Guide of 103 A message box will appear once the campaign has been successfully created No automatic loading of spectral files is ini
133. unt codes 0 to 8 show the fraction in octas of the celestial dome covered by all clouds An octa is one eighth of the celestial dome so we estimate how many eighths of the celestial dome are covered up by clouds University of Washington undated Code Definition 0 Clear 1 1 octa or less but not zero 2 6 2 6 octas T 7 octas or more but not 8 octas 8 8 octas Table 1 Cloud cover definition in octas Source University of Washington undated 4 5 2 Measurement Types Three measurement types are currently distinguished O Single The standard case when single measurements are taken Single measure ments are not grouped with other spectra by geometric or temporal conditions O Directional Applies to goniometer measurements A spectrum is part of a hemisphere and has a specific position given by its sampling geometry settings Temporal Applies to photometer data Spectra have a specific capturing time on a common timeline SPECCHIO_UserGuide_V2 1 1 docx Version 2 1 1 02 11 2010 SPECCHIO Page 16 User Guide of 103 4 5 3 Target Types Target types are predefined in the database and can only be edited by the SPECCHIO administra tor Target types should always be chosen with the goal to help the search and selection of spectra for e g image classification tasks The target types should therefore not be too detailed It is foreseen that target types can be grouped into categories This might be implemented in future when the
134. user by using the Connect to database dialog To start this dialog select Database Connect to database cf Figure 10 eee Data Input Dal Connect to database Figure 10 Connect to database menu entry All connections that are configured in the db config txt file are listed in a list box Known connec tions To change the current connection either select a preconfigured connection from the list box or alternatively enter the server that hosts the MySQL instance you want to connect to the listening port of the database port 3306 by default the database instance name the user name and pass word this is the database user name and password which is different from your local network ac count in the relevant text entry fields Press Connect to connect to the specified database user SPECCHIO_UserGuide_V2 1 1 docx Version 2 1 1 02 11 2010 SPECCHIO Page 21 User Guide of 103 Connect to database Known connections Server db specchio ch Port 4406 Database specchio Username AHueni Password Wd de x n Connect Cancel Figure 11 Connect to a database dialog Starting from version 2 0 a database version check is carried out If a database with the wrong version is connected a warning message is shown Figure 12 The connection will still be set up however some functions will not work on older database versions Old databases sho
135. uses vae Doi uisi e beaenteniasa dss 70 5 2 11 5 strutmentatloncAdmaatstEdtlOE aod ood nest eso t es erae oi uideo Dette Du o icu Ortus 71 S 2 DE 5 T Tnsttumetit AGHIDISIEALOD eode nod oodd ases tese tum uuu dais andi neath ude tub e aeui tbid 71 JaA Jdeererence Panel Administrations osson a a a aa 73 S16 Database Upri dE a E a tci ue du tu Um buda 75 52 12 LINKING to a GIS System 224 a a eee eae 76 5 2 12 1 Setting up the SPECCHIO DB as a Data Source ssssesseeeeeesetee esee nenne nnne nnno 76 5 2 12 2 Establishing a Database Connection in ArcCatalog ccccccccccccccccceeceeceeeeeeeeeeeeeeeeeeeeaseeaaaaas 77 52 123 Adding Table Data 10 3 Maps etti o erases Om uin rete 78 CU regen 80 SPECCHIO_UserGuide_V2 1 1 docx Version 2 1 1 02 11 2010 SPECCHIO Page 7 User Guide of 103 MEE O01 ene eae gM an ROREM 80 6 1 1 SPECCHIO Online Test Database ut vocet oae oec a uy ET Chus cute Cea eoa Debe ados 80 6 1 2 Creating Campaigns on the Test Database ssssessssseeeeeereenee nennen 81 6 1 3 Downloading Test Data Sets ccc ccccsscceceeeeeseceeeceeceeeeseecaeeseeesueceeeseeeeeeseeneeeneees 81 6 2 Part 1 Loading Editing and Retrieving Data seseeseeeeeeneer 81 6 2 1 Examine the Folder and File Structure essseseeen mmm meme nens 81 6 2 2 Creating a new Campaign and Loading the Spectra eseeeeeeseeeeeeeeee 82 62 3 Gebto
136. ySQL Browser BEICEBUEIDICGHERNISIE Help Remove data Export campaign Import campaign Load sensor definition Instrumentation admin Upgrade DB SPECCHIO_UserGuide_V2 1 1 docx Version 2 1 1 02 11 2010 SPECCHIO Page 69 User Guide of 103 5 2 11 1 Removing data Spectra hierarchies and campaigns can be removed from the database using the Data Remover cf Figure 91 Users can only remove their own data from the database The spectral database administrator can remove all datasets irrespective of their owner Use the spectral data browser to select the nodes that should be removed and click the Remove button There is no further prompt to warn you All data that is below the selected node will be de leted E g if a campaign is selected then all hierarchies and spectra belonging to this campaign will be deleted In addition all metadata that has been entered for an object will be removed along with this object Removing data can take a long time the progress report shows which hierarchy is currently being removed ADO Data Remover gt 3 Martins vegies Campaign gt test Campaign E nd Vegetation Example Campaign S nd rheinau test Campaign gt 3 gonio Campaign gt 3 photometer readings Campaign gt Bj dir test Campaign gt CH GER dir Campaign Remove J h another test Campaign z Cancel Y 39 Vegetation example PS gt 3j Blackfern gt Cabbage tree gt 3j Lemonwood gt 0 ano

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