HTEP - Water Quality Application

Transcription

1 HTEP - Water Quality Application Prepared by: Joël Hogeveen Delft University of Technology 2 March 2017 This document provides information about the Water Quality application of the Hydrology Thematic Exploitation Platform (HTEP) and comes together with a tutorial covering the features and functionalities of the application in combination with HTEP. Access to HTEP Community Portal: Content 1. HTEP Water Quality Application: Water Quality of the Red River About EOMAP s Water Quality Application Water Quality Application Input Water Quality Application Output Tutorial: Producing a Water Quality Map of My Area of Interest Accessing the Water Quality Thematic Application An Overview of The Water Quality Application Geobrowser Functionalities Water Quality Thematic Application Processing Services

2 1. HTEP Water Quality Application: Water Quality of the Red River It is of essential importance to be able to monitor temporal and spatial dynamics of inland water quality in order to obtain improved understanding of aquatic ecosystems. Making use of remote sensing (RS) earth observation data is an efficient and cost-effective method to assess a variety of physical and biological parameters in aquatic ecosystems over large areas. The thematic application Water Quality developed by EOMAP is a good tool to map these aquatic ecosystems. Combining this application with the features and functionalities of the Hydrology Thematic Exploitation Platform (HTEP) ensures RS data can be easily accessed, processed, reproduced and shared with the hydrology community. In this tutorial the functionalities and features of HTEP, specifically those of EOMAP s Water Quality app, are covered. Before the actual tutorial, the most important information of EOMAP s Water Quality application is discussed in an about section: the advantages of using RS data over conventional measurement methods and the currently available in- and outputs for the application. Afterwards, in Chapter 2, a hands-on tutorial shows how to use this application on HTEP About EOMAP s Water Quality Application RS satellite data for monitoring of water quality yields a wide variety of advantages compared to conventional insitu measurements. The usage of RS data yields low costs and low labour intensity, easy mapping of large areas and a high spatial resolution in contrary to the conventional in-situ measurements. Furthermore near real-time monitoring is possible using satellites with high temporal resolution and physically inaccessible areas can be covered. Besides the accuracies are high, typically 20-30% deviation from in-situ measurements. Figure 1: Red River, Vietnam Water Quality Application Input As input for the Water Quality application, there is RS data available of multiple satellite sensors, with varying spatial, temporal and spectral resolution. Currently there is RS data available from three satellites: Sentinel-3: Medium Spatial, High Temporal Resolution The spatial resolution of the output products of EOMAP s Water Quality application that can be achieved using Sentinel-3 data products is approximately 500 meters [1]. This means that one pixel in the results of EOMAP s Water Quality application represents an area of approximately 500mx500m. Sentinel-3 provides an almost daily temporal resolution as it records about 15 times a month [1]. Data from Sentinel-3 is therefore highly recommended for near real-time (daily) monitoring of water quality in coastal areas and large lakes. The spectral bands of Sentinel-3 s sensors range from 400 to 1020 nm [2]. However, the output parameters of EOMAP s Water Quality application (discussed in Section 1.1.2), are determined by measurements of backscattering of light between nm. This is within the visible spectrum, which has some implications as those wavelengths cannot properly penetrate obstructions such as clouds. These implications are discussed after the specifications of the other available satellites are discussed, Sentinel-2 and Landsat-8. [1] EOMAP Information Booklet: [2] P. Regner, Sentinel-3, ESA-ESRIN, Frascati Italy: 1

3 Sentinel-2 and Landsat-8: High Spatial, Weekly Temporal Resolution The spatial resolution of the output products of EOMAP s Water Quality application that can be achieved using Sentinel-2 data products is approximately 30 meters [1]. Sentinel-2 has a monthly revisit of approximately 5 times, meaning a weekly temporal resolution. Landsat-8 yields a similar spatial resolution and has a temporal resolution of 16 days [1]. Therefore both Sentinel-2 and Landsat-8 data is ideal for large scale monitoring of most relevant lake and river sizes. The spectral bands of Sentinel-2 s sensors range between 490 and 1375 nm and Landsat-8 s sensors range between 433 and 2300 nm [3] [4]. However, the output parameters of EOMAP s Water Quality app are based on backscattering of light between nm, which is in the visible spectrum. Influence of obstructions such as clouds The output parameters of the Water Quality app are determined based on backscattering of light within the visible spectrum. The wavelengths in the visible spectrum cannot properly penetrate obstructions such as clouds and haze, meaning that those kind of obstructions sometimes result in difficult measuring conditions. Also cloud shadows, disturbances by floating materials and mixed landwater pixels can result in ambiguous measurement results. Those pixels are flagged in the results. Therefore it is important that data images are as clear as possible. There are no guidelines for allowed cloud cover percentage, but a reduction in cloud coverage will improve the quality of the output products. In earlier water quality assessment research by Kloiber comparing Landsat s RS data with insitu measurements, images with a cloud percentage of 10% and less were used and considered suitable for accurate analysis [5]. To avoid ambiguous results from mixed land-water pixels the minimum extension of a water body should not be less than 5 times the spatial resolution of a product [1]. This means that for instance in case of a 30m spatial resolution -meaning that one pixel in the output product represents an area of 30mx30m-, the minimal extension of the water body should be 120m. Figure 2: Landsat-8 Observations of Hoa Binh Reservoir Capture of HTEP Geobrowser Water Quality Application Output The available output products that can currently be created from the input data using EOMAP s Water Quality application, consists of the following four main water quality parameters: TSS Total suspended solids The total suspended solid is the dry-weight of scattered particles in the water column. The influence of TSS on aquatic ecology is for example the negative effects on plants and animals due to a reduction of available light. [3] C. Lloyd, Putting Landsat 8 s bands to work, NASA Landsat Science, 14 June 2013: 8/landsat-8-bands/ [4] ESA Sentinel-2 User Guide, Spatial Resolutions and Spectral Bands: msi/resolutions/spatial [5] S.M. Kloiber, P. L. Brezonik, L. G. Olmanson, M. E. Bauer, A procedure for regional lake water clarity assessment using Landsat multispectral data., Remote Sensing of Environment, 2002, 82 (1), pp:

4 CHL Chlorophyll A pigment included in phytoplankton cells that serves as a proxy for algae in natural waters. The amount of chlorophyll is a measure for water quality, as it relates to algae biomass which can for instance result in decreased levels of dissolved oxygen. CDOM Colored Dissolved Organic Matter CDOM absorbs light at the blue end of the visible spectrum, therefore being responsible for the water colour. Increasing CDOM, primarily caused by tannin due to decaying detritus, causes the water colour to go from blue, green to brown. The amount of CDOM importantly affects aqua systems: an overdose of CDOM may for instance result in a lack of available light for phytoplankton populations to grow, while phytoplankton is the basic of oceanic food chains and important for atmospheric oxygen. SST Water Surface Temperature SST stands for Sea Surface Temperature, but using EOMAPS s Water Quality application the temperature at the surface of each water body can be determined. Water surface temperature knowledge is important in aquatic ecosystems to better determine and predict for instance wind streams introduced by temperature differences. >>>IMPLEMENT PICTURE OF PROCESSED HTEP WATER QUALITY PRODUCT HERE<<< 3

5 2. Tutorial: Producing a Water Quality Map of My Area of Interest This chapter contains a tutorial showing how to work with EOMAP s Water Quality application on HTEP. The hands-on tutorial shows and explains step-by-step the different features of HTEP and the actions to be taken in order to create a Water Quality map of (one of) the output parameters discussed in the introduction for your area of interest. For this tutorial, the area of interest is AREA IN VIETNAM Accessing the Water Quality Thematic Application 1. Enter the HEP portal and sign in with your HEP community user account. There is no preferred internet browser. However, for this specific tutorial, Google Chrome is used as the internet browser. Do you not have an account yet? Then first register on the platform. To register at the platform, it is advised to follow the steps in the Quick Start manual I want to become a new user of the HEP platform, which can be found under the Quick Start-tab in the menu of the HEP portal. Figure 3: Step 1 - HEP Portal 2. Open the list of existing Thematic Applications. Right now there are only 4 Thematic Apps available, this number will increase in the future. Open the list of existing thematic applications by clicking on View Apps below the 4 Thematic Apps-icon. Figure 4: Step 2 - Entering the thematic applications 4

6 3. A list of available Thematic Applications is shown. For this tutorial use is made of the Water Quality App. This application can be opened by clicking on the Open App button on the right side. When clicking on the title of the app, Water Quality, a pop-up appears containing information about this application and the corresponding keywords. The Water Quality application can also be directly accessed by using the following URL: Figure 5: Step 3 and 4 - Available applications and your selections 4. Filter your application of interest by using the Your selections column on the left side of the Thematic Applications page: Search text allows you to use keywords to find a corresponding thematic application, Date begins after and Date ends before allows you to search for applications within a certain timeframe and the Extent map allows you to specify a global area of interest, thereby filtering only those apps with available data and/or processing services in the defined area of interest. Currently this feature is not needed, as there is only a limited amount of thematic applications available. However, you might need this feature to find your application of interest once the number of available applications has increased to an indistinct amount. 5

7 2.2. An Overview of The Water Quality Application Geobrowser Functionalities Once the Water Quality application has been accessed, you see the Geobrowser on your screen. This part of the tutorial provides an overview of the features and functions of the Geobrowser. After accessing the Water Quality application, the default map shown is of Central Africa. This is the default map because of earlier HTEP testing in this part of the world, but the default map shown upon opening the Water Quality app may change in the future. 1. You can zoom in and zoom out by clicking on the + and icons on the left side of the Geobrowser, encircled in red, and by clicking on the map and dragging your mouse you can shift the displayed map from Central Africa to any desired area. For this Tutorial the focus is set on the Red River area in Northern Vietnam. 1a 1b 1c Figure 6: Step 1,2 and 3 - The water quality application geobrowser 2. If you are correctly logged onto the HEP platform, on the top-right of the Geobrowser your username should be displayed (1a). If you need any further clarification regarding the HEPplatform, a Help Guide can be accessed by clicking on the book-icon next to the -icon (1b). If you would like to sign out, this can also be done within the Geobrowser by clicking the exit-icon (1c). 6

8 3. Also on the top-right of the Geobrowser, you can select the RS data you would like to make use of. By clicking on EO Data a dropdown menu appears showing all available RS data. EO stands for Earth Observation. As such RS and EO are different abbreviations for the same data. As discussed in Section 1.1.1, the Water Quality application has currently data available from the following three satellites: Landsat-8, Sentinel-2 and Sentinel-3. The RS data to be selected depends on your requirements and research purposes, as each satellite has its own specifications suiting different requirements. Sentinel-3 for instance has a spatial resolution of about 500m. Hence the RS data from this satellite should be picked if water quality of coastal areas or other large water bodies needs to be monitored. Sentinel-3 is also suitable for near real-time water quality monitoring, as it has an almost daily temporal resolution. On the other hand Landsat-8 and Sentinel-2 have a higher spatial resolution of 30m, meaning these satellites are more suitable for monitoring of water quality in for example rivers and small lakes. For this tutorial, Sentinel-2 data is selected. 4. Once RS data from a certain satellite is selected, you can search for specific data images within the available database from the selected satellite. To filter the desired data out of the complete database, the following actions can be performed. The actions can also be combined for an even more specific data search. Search Field (4a): On the top-left of the Geobrowser, you see a search field. In this field, you can search for specific RS data. By clicking on the magnifying glass below the search field, also a product type can be assigned. The product type says something about the level of processing and acquisition mode of the data: The acquisition mode says something about the method used by the satellite to measure the data. The data can be measured in four ways: Stripmap (SM), Interferometric Wide swath (IW), Extra-Wide swath (EW) and Wave (WV), each illustrated in Figure 7. Figure 7: Step 4 - Different data acquisition modes [6] [6] ESA User Guide, Data Products: ttps://sentinels.copernicus.eu/web/sentinel/missions/sentinel-1/data-products 7

9 The data obtained by the satellite sensors have different processing levels: Level-0 is raw data (RAW) and usually not made available for data users. Level-1 and Level-2 data is pre-processed data by applying algorithms and calibration data. Level-1 and -2 data is made available for data users. If images are further processed using for instance the applications on HTEP, the level of processing increases even further. Available product types which can be chosen in the search field are for instance Single Look Complex (SLC) and Ground Range Detected (GRD). These data products are, as described by ESA created by the following RS measurement techniques [6] : Single Look Complex (SLC): This Level-1 data product, obtained through SM, IW, EW or WV data acquisition, consists of focused Synthetic Aperture Radar (SAR) data, georeferenced using orbit and attitude data from the satellite, and provided in slantrange geometry. Ground Range Detected (GRD): This Level-1 data product, obtained through SM, IW or EW data acquisition, consists of focused SAR data that has been detected, multilooked and projected to ground range using an Earth ellipsoid model. Phase information is lost. The resulting product has approximately square resolution pixels and square pixel spacing with reduced speckle at the cost of reduced geometric resolution. GRD data products can be obtained by processing SLC products. SLC products are primarily used for interferometric applications, for other applications usually GRD products are used for analysis. Although this tutorial makes use of GRD data products, for now the Search Field is left blank. Bear in mind that the Search Field cannot search geographic places: this feature in non-existent in the Geobrowser. Spatial Filter (4b): The data can also be selected based on a spatial search. A polygon, rectangle, marker and well-known text (WKT) search can be applied. For this tutorial, a rectangle polygon (pink circumference) is applied to select the Hoa Binh water reservoir. The screenshot below is zoomed out, hence the rectangle is not very clear. Time Filter (4c): At the bottom of the map a time filter can be applied by sliding the begin and end date to the desired time range within data is needed. For now, a time interval from the 1 st of August until the 31 st of August 2016 is selected. [6] ESA User Guide, Data Products: ttps://sentinels.copernicus.eu/web/sentinel/missions/sentinel-1/data-products 8

10 4a 4b 4c 5b 5a Figure 8: Step 4 and 5 - Searching and sharing data products 5. The current search results, based on the selected satellite and the applied filters, are displayed on the bottom left of the Geobrowser (5a). Those products are also displayed on the map of the Geobrowser (by means of orange rectangles). If you would like to share your search results with other users of the HEP community or even with visitors (people that are not yet member of the HEP community), this can be done by clicking on the blue icon above the search results (5b). The link can be copied and pasted or be directed posted through social media (i.e. Facebook and Twitter) by clicking on the corresponding icon. 6. By clicking on the RS data product in the current search results, the specific product becomes blue in the current search results. In the Geobrowser map the spatial area covered by the selected product is displayed by a red rectangle and a pop-up appears. In the pop-up information about this specific product is displayed, amongst others the product type, orbit, cloud cover percentage and the date of monitoring. In Section it is discussed why the cloud cover percentage is of importance for the quality of the output products of the Water Quality application. The picked data products have a cloud coverage of 11 and 66% respectively, in order to demonstrate the influence of cloud cover on the output products. 9

11 Figure 9: Step 6 and 7 - Product information and (de)selection of data products 7. To easily select/deselect (multiple) products or show/hide (multiple) products on the map of the Geobrowser, you can click on the icon next to the orange square as shown in Figure 9 and select your desired options. 8. The data products of interest for your research can be selected and transferred to the features basket. All current (selected) search results can be transferred at once to the features basket by clicking the corresponding arrow indicated by the red rectangle below. It is also possible to drag and drop the selected data products from the search results to the features basket. Figure 10: Step 8 - Transfer search results to features basket For the purpose of this tutorial, two data products are selected and transferred to the features basket: a Sentinel-2 product from the 7 th of August 2016 and another Sentinel-2 product covering the same spatial area but dating from the 27 th of August The products in the features basket can also be selected, then again the spatial covered area is displayed in the Geobrowser map and a pop-up appears with further details about the 10

12 product. However, in contrary to the products in the search results, spatial area covered by a product in the features basket is displayed by a blue rectangle instead of a red rectangle. Figure 11: Step 9, 10 and 11 - Data products in the features basket 10c 10a 10b 10. The products in the features basket can be easily selected/deselected and/or removed using the options on the top-right of the features basket (10a). Furthermore all data products dropped in the features basket, can together be saved as a single Data Package by clicking on the Save button (10b). Upon clicking Save, the following screen pops up and a name can be assigned to the Data Package, in this case Hoa Binh Reservoir August Click on Save to save the Data Package. Figure 12: Step 10 - Saving a data package 11. By clicking the Data Packages tab (10c), a list of available public and private Data Packages is shown including the newly created Data Package. 12. The advantage of a Data Package, is that basically all steps applied to getting that Data Package can be easily reobtained. By clicking on Set as current search all products obtained from the applied filters in Step 4 are reloaded in the search basket. By clicking on load, the products from the features basket belonging to that Data Package will be reloaded and, equally as for the search results explained in Step 5, the Data Package can be easily shared through for instance social media by clicking the blue Share-icon. 11

13 Figure 13: Step 11 and 12 - Available private and public data packages In addition to the previous two steps, if you save products from the features basket in a Data Package, this Data Package is by default private and therefore only visible for the current user. By clicking on the puppet-icon, encircled in red in Figure 13, you can manage to whom your Data Package is visible. A screen as shown in Figure 14 pops up, where you can change the settings of your private Data Package from private to public (visible to everyone, even visitors) or to certain specified user groups. Figure 14: Step 12 - Visibility of data packages 13. Additional features to manage Geobrowser map lay-out: On the top-right of the Geobrowser the lay-out manager-icon, indicated by the red rectangle in Figure 15, can be selected: a list of options will drop down to manage the Geobrowser map lay-out. The background of the map can be changed from default to for example Google Maps or Natural Earth. In the dropdown menu it can also be defined which products should be shown on the map: for instance the products from the related search, the products from the features basket or the data results after processing, which will be discussed in the following. Figure 15: Step 13 - Additional features to manage Geobrowser lay-out 2.3. Water Quality Thematic Application Processing Services Section 2.2 provided an overview of the Geobrowser features and functionalities once the Water Quality application is accessed. Having the relevant data selected and saved, it is now time to process this data to obtain the desired product output. 1. The processing services can be accessed from within the Geobrowser, but they are initially hidden. Open the available processing services by clicking on the processing services tab. 12

14 Figure 16: Step 1, 2 and 3 - Accessing processing services 2. On top of the processing services, three options are displayed: Services, Jobs and a Search Field. Services: Clicking this tab yields a list of available processing services (basically the different models/algorithms within the application). At the moment only the Water Quality processing service is available, but this will increase in the future. Search Field: If in the future the number of available processing services has increased to an indistinct amount, the Search Field Filter Services can be used to filter only those processing services of interest. Jobs: Clicking the Jobs-tab, yields a list of existing jobs. The jobs shown are the privately created jobs by the user or jobs publicly shared by other HEP users. More information about (creating) jobs will follow in a later stadium of this tutorial. 13

15 3. For now, click on the process service Water Quality to access the Water Quality processing service. A screen as shown in Figure 17 appears. 4. To process data and create output, a Job needs to be created. A job can be created by filling in all the fields as shown in Figure 17: Job title: Give your Job a title, for instance Hoa Binh Reservoir Water Quality August Any other name with arbitrary length and symbols is also allowed. Select Input Files: Here you define which products should be analysed. To provide the processing service with your to-be-analysed - products of interest, simply drag and drop your product from the features basket (or straight from the search results) to the field. Multiple products for analysis can be selected by clicking on the -icon next to the field. As an alternative, you can also click on the arrow on the left of the field: a menu will drop down, where one can choose between current geometry, current bbox (bounding box) from geometry or current bounding box. The products that cover the area of your pick (this area is based on the defined spatial filter applied in Step 4 of Section 2.1), are then automatically defined. Figure 17: Step 3 and 4 - Water quality processing service For now the two products in your features basket will be selected for analysis by dragging them from the features basket to the Select input files fields in the processing service. If desired, you can share your processing service on social media with the Share-icon above Job Title. The last step is to Select (output) Products: The default output product is TSS-Total Suspended Solids. By clicking on this field, a dropdown menu appears with available Water Quality parameter output products that can be generated using this processing service (currently TSS, CHL, CDOM and SST). Multiple output parameters can be selected by clicking the -icon. Figure 18: Step 4 - Available output products 14

16 For now TSS and CHL are selected. 5. Lastly you need to select the result. By default Result Files Distribution Package is selected, which means that the results will be shown within the Geobrowser (and in xml-format) after the job-analysis is finished. Therefore this option is kept as default. 6. Click on Run Job to run the job. >>>GETTING A JOB SUBMIT ERROR, HENCE CANNOT CONTINUE FROM THIS POINT TO SHOW JOBS FEATURES AND HOW TO ACCESS JOB RESULTS AFTER FINISHING ANALYSIS<<< 15