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  <main id="main" class="col-md-9"><div class="page-header">
      <img src="../logo.png" class="logo" alt=""><h1>Running the tool in Interactive Mode: the MODIStsp GUI</h1>
            
      
      <small class="dont-index">Source: <a href="https://github.com/ropensci/MODIStsp/blob/HEAD/vignettes/interactive_execution.Rmd" class="external-link"><code>vignettes/interactive_execution.Rmd</code></a></small>
      <div class="d-none name"><code>interactive_execution.Rmd</code></div>
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<p>The easiest way to use <a href="https://docs.ropensci.org/MODIStsp">MODIStsp</a> is to use its powerful
GUI (Graphical User Interface) for selection of processing options, and
then run the processing.</p>
<p>To open the GUI, load the package and launch the
<a href="https://docs.ropensci.org/MODIStsp">MODIStsp</a> function, with no parameters:</p>
<div class="sourceCode" id="cb1"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://docs.ropensci.org/MODIStsp">MODIStsp</a></span><span class="op">)</span></span>
<span><span class="fu"><a href="../reference/MODIStsp.html">MODIStsp</a></span><span class="op">(</span><span class="op">)</span></span></code></pre></div>
<p>This <strong>opens a GUI</strong> from which processing options can
be specified and eventually saved (or loaded from a previously saved
file).</p>
<p>The GUI allows selecting all processing options required for the
creation of the desired MODIS time series. The GUI uses a dashboard
structure, divided in the following tabs. The available processing
options configurable in each tab are described in the following.</p>
<hr>
<div class="section level2">
<h2 id="selecting-processing-parameters">
<i class="fa fa-arrow-circle-o-right" aria-hidden="true"></i>
<strong>Selecting Processing Parameters</strong><a class="anchor" aria-label="anchor" href="#selecting-processing-parameters"></a>
</h2>
<p><br></p>
<div class="section level3">
<h3 id="product-and-layers-tab">
<em>Product and Layers Tab</em><a class="anchor" aria-label="anchor" href="#product-and-layers-tab"></a>
</h3>
<p><img src="interactive_execution_files/figure-html/GUIfig-1.png" width="960" style="display: block; margin: auto;"></p>
<p>The top-most tab allow to specify details of the desired MODIS
Product and Layers to be processed:</p>
<ol style="list-style-type: decimal">
<li>
<strong>“Category”</strong> and <strong>“Product”</strong>: selects
the MODIS product of interest;</li>
<li>
<strong>MODIS platform(s)</strong>: selects if only TERRA, only AQUA
or Both MODIS platforms should be considered for download and creation
of the time series;</li>
<li>
<strong>MODIS layers to be processed</strong>: the user
<strong>must</strong> select which MODIS original layers and/or derived
Quality Indexes (QI) and Spectral Indexes (SI) layers should be
processed:
<ul>
<li>the left-hand selector allows to select which <em>original MODIS
layers</em> should be processed;</li>
<li>the central selector allows to select which <em>Quality Indicators
should be extracted</em> from the original MODIS Quality Assurance
layers;</li>
<li>for MODIS products containing surface reflectance data, the
right-hand selector allows selecting which additional <em>Spectral
Indexes should be computed</em>.</li>
</ul>
</li>
</ol>
<p>The following commonly used Spectral Indexes are available for
computation by default:</p>
<p><br></p>
<div class="datatables html-widget html-fill-item-overflow-hidden html-fill-item" id="htmlwidget-261b5d08c8b0ef47779c" style="width:100%;height:auto;"></div>
<script type="application/json" data-for="htmlwidget-261b5d08c8b0ef47779c">{"x":{"style":"bootstrap","filter":"none","vertical":false,"data":[["NDVI","EVI","SR","NDFI","NDII6 (NDWI6)","NDII7 (NDWI7)","SAVI","NDSI","GNDVI","RGRI","GRVI"],["Normalized Difference Vegetation Index (Rouse, 1973)","Enhanced Vegetation Index (Huete, 2002)","Simple Ratio[@Tucker1979]","Normalized Difference Flood Index (Boschetti, 2014)","Normalized Difference Infrared Index - Band 6 (Hunt, 1989)","Normalized Difference Infrared Index - Band 7 (Hunt, 1989)","Soil Adjusted Vegetation Index  (Huete, 1988)","Normalized Difference Snow Index (Hall, 2002)","Green Normalized Difference Vegetation Index (Gitelson, 1998)","Red Green Ratio Index (Gamon, 1999)","Green-Red ratio Vegetation Index  (Tucker, 1979)"],["(NIR - RED)/(NIR + RED)","2.5 * (NIR - RED)/(NIR + 6 * RED - 7.5 * BLUE + 1","NIR / RED","(NIR - SWIR1) / (NIR + SWIR1)","(NIR - SWIR1) / (NIR + SWIR1)","(NIR - SWIR2) / (NIR + SWIR2)","((NIR - RED) / (NIR + RED + 0.5)) * (1 + 0.5)","(GREEN - SWIR1) / GREEN + SWIR1)","(NIR - GREEN)/(NIR + GREEN)","RED / GREEN","(RED - GREEN) / (RED + GREEN)"]],"container":"<table class=\"table table-striped table-hover row-border order-column display\">\n  <thead>\n    <tr>\n      <th>Acronym<\/th>\n      <th>Index Name and reference<\/th>\n      <th>Index Formula<\/th>\n    <\/tr>\n  <\/thead>\n<\/table>","options":{"dom":"tip","pageLength":11,"columnDefs":[],"order":[],"autoWidth":false,"orderClasses":false,"lengthMenu":[10,11,25,50,100]}},"evals":[],"jsHooks":[]}</script><p>You can however <strong>specify other SIs to be computed without
modifying MODIStsp source code</strong> by clicking on the
<em><strong>“Add New Spectral Index”</strong></em> button, which allow
providing info related to the new desired SI using a simple GUI
interface.</p>
<p><img src="interactive_execution_files/figure-html/indexfig-1.png" width="576" style="display: block; margin: auto;"></p>
<p>Provided information (e.g., correct band-names, computable formula,
etc…) is automatically checked upon clicking “Set New Index”. On
success, the new index is added in the list of available ones for all
products allowing its computation. Clicking “Done!” returns to the
main.</p>
<p><strong>Note:</strong> all custom defined indexes can be removed by
using the <code><a href="../reference/MODIStsp_resetindexes.html">MODIStsp_resetindexes()</a></code> function.</p>
</div>
<div class="section level3">
<h3 id="spatialtemporal-options-tab">
<em>Spatial/Temporal Options Tab</em><a class="anchor" aria-label="anchor" href="#spatialtemporal-options-tab"></a>
</h3>
<p>The middle tab allow specifying details about the temporal and
spatial extent of the analysis.</p>
<p><img src="interactive_execution_files/figure-html/unnamed-chunk-2-1.png" width="960" style="display: block; margin: auto;"></p>
<div class="section level4">
<h4 id="temporal-extent">
<em>Temporal Extent</em><a class="anchor" aria-label="anchor" href="#temporal-extent"></a>
</h4>
<p>Specify the starting and ending dates to be considered for the
creation of the time in the series corresponding fields.</p>
<p>The <strong>Date Range Type</strong> drop-down menu allows to choose
between two options:</p>
<ol style="list-style-type: decimal">
<li><p><strong>full</strong>: all available images between the starting
and ending dates are downloaded and processed;</p></li>
<li><p><strong>seasonal</strong>: data is downloaded only for one part
of the year, but for multiple years. For example, if the starting date
is 2005-03-01 and the ending is 2010-06-01, only the images of March,
April and May for the years between 2005 and 2010 will be downloaded.
This allows to easily process data concerning a particular season of
interest.</p></li>
</ol>
</div>
<div class="section level4">
<h4 id="output-projection">
<em>Output Projection</em><a class="anchor" aria-label="anchor" href="#output-projection"></a>
</h4>
<p>Specify the options to be used for reprojecting and resizing the
MODIS images.</p>
<ul>
<li><p><strong>“Output Projection”</strong>: select either the Native
MODIS projection (Default) or specify a user-defined one. To specify a
user selected projection, select “Change” and then insert a valid “EPSG”
code or WKT string in the pop-up window. Validity of the new projection
string is automatically checked, and error messages issued if the check
fails.</p></li>
<li><p><strong>“Output Resolution”</strong>, <strong>“Pixel
Size”</strong> and <strong>“Resampling Method”</strong>: specify whether
output images should inherit their spatial resolution from the original
MODIS files, or be resampled to a user-defined resolution. In the latter
case, output spatial resolution must be specified in the measure units
of the selected output projection. Resampling method can be chosen among
the ones available for the “gdalwarp” routine. <strong>Note:</strong>
resampling methods different than Nearest Neighbour” and “Mode” (Useful
for down-sampling purposes) should used carefully. Other resampling
methods (e.g., bilinear, cubic) i) cannot be used for resampling of
categorical variables such as the QA and QI layers, and ii) using them
on continuous variable (e.g., reflectance, VI values) without performing
an a-priori data cleaning would risk to contaminate the values of
high-quality observations with those of low-quality ones.</p></li>
</ul>
</div>
<div class="section level4">
<h4 id="spatial-extent">
<em>Spatial Extent</em><a class="anchor" aria-label="anchor" href="#spatial-extent"></a>
</h4>
<p>Allows defining the area of interest for the processing. Four main
options are possible, and can be selected using a dropdown menu.</p>
<ol style="list-style-type: decimal">
<li>
<p><strong>Select Tiles</strong>: specify which MODIS tiles need to
be processed either by:</p>
<ol style="list-style-type: lower-alpha">
<li>Using the “Start” and “End” horizontal and vertical sliders in the
<em>Required MODIS Tiles</em> frame.<br>
</li>
<li>Selecting the <strong>“From Map”</strong> option in the dropdown and
clicking on “change selection”. A map will open, allowing interactive
selection of the required tiles</li>
</ol>
</li>
</ol>
<p>Note that during processing, data from the different tiles is
mosaicked, and a single file covering the total area is produced for
each acquisition date. For this reason, selected tiles must cover a
rectangular area.</p>
<ol start="2" style="list-style-type: decimal">
<li><p><strong>Select Bounding Box</strong>: manually insert the
coordinates of the Upper Left and Lower Right corners of the area of
interest in the <strong>Bounding Box</strong> frame. <em>Coordinates of
the corners must be provided in the coordinate system of the selected
output projection</em>.</p></li>
<li><p><strong>Load From File</strong>: click the
<strong>“Browse”</strong> button and select a raster or vector spatial
file that will be used to compute the required bounding box in output
projection coordinates.</p></li>
<li><p><strong>Draw on Map</strong>: click the <strong>“Draw
Extent”</strong> button a map will open in a<br>
window, allowing interactive selection of the spatial extent using the
tools on the left.</p></li>
</ol>
</div>
</div>
<div class="section level3">
<h3 id="output-format-options-and-folders-tab">
<em>Output Format, Options and Folders Tab</em><a class="anchor" aria-label="anchor" href="#output-format-options-and-folders-tab"></a>
</h3>
<p>The last tab allows specifying some options concerning processing,
and the output folders.</p>
<p><img src="interactive_execution_files/figure-html/unnamed-chunk-3-1.png" width="960" style="display: block; margin: auto;"></p>
<div class="section level4">
<h4 id="download-method">
<em>Download Method</em><a class="anchor" aria-label="anchor" href="#download-method"></a>
</h4>
<p>Select the method to be used for download. Available choices are:</p>
<ol style="list-style-type: decimal">
<li><p><strong>http</strong>: download through http from NASA lpdaac
http archive (<a href="http://e4ftl01.cr.usgs.gov" class="external-link uri">http://e4ftl01.cr.usgs.gov</a>). This requires providing a
user name and password, which can be obtained by registering an account
at the address <a href="https://urs.earthdata.nasa.gov/profile" class="external-link">https://urs.earthdata.nasa.gov/profile</a>;</p></li>
<li><p><strong>offline</strong>: this option allows to process/reprocess
HDF files already available on the user’s PC without downloading from
NASA – useful if the user already has an archive of HDF images, or to
reprocess data already downloaded via <code><a href="../reference/MODIStsp.html">MODIStsp()</a></code> to create
time series for an additional layer (<em>it is fundamental that the HDFs
are those directly downloaded from NASA servers</em>; see <a href="https://docs.ropensci.org/MODIStsp/articles/faq.html#working-with-already-downloaded-hdf-files">here</a>
for additional details).</p></li>
</ol>
<p>A second dropdown menu allows selecting if using standard http
download to access NASA servers, or using the <strong>aria2c</strong>
downloader, which may speed-up the download. This requires however that
that the “aria2c” software is installed in your system. To download and
install it, see <a href="https://aria2.github.io/" class="external-link">aria2.github.io</a>.</p>
</div>
<div class="section level4">
<h4 id="output-options">
<em>Output Options</em><a class="anchor" aria-label="anchor" href="#output-options"></a>
</h4>
<p>Several processing options can be set using
check-boxes/dropdowns:</p>
<ul>
<li><p><strong>Output Files Format</strong>: two of the most commonly
formats used in remote sensing applications are available at the moment:
ENVI binary and GeoTiff. If GeoTiff is selected, the type of file
compression can be also specified among “None”, “PACKBITS”, “LZW” and
“DEFLATE”.</p></li>
<li><p><strong>Save Time Series as</strong>: specify if virtual
multitemporal files should be created. These virtual files allow access
to the entire time series of images as a single file without the need of
creating large multitemporal raster images. Available virtual files
formats are “R” rasterStacks, ENVI meta-files and GDAL “vrt” files. In
particular, <code>R</code> RasterStacks may be useful in order to easily
access the preprocessed MODIS data within <code>R</code> scripts (see
also <a href="output.html">here</a>).</p></li>
<li><p><strong>Apply Scale/Offset</strong>: specify if scale and offset
values of the different MODIS layers should be applied. If selected,
outputs are appropriately rescaled on the fly, and saved in the true
“measure units” of the selected parameter (e.g., spectral indexes are
saved as floating point values; Land Surface Temperature is saved in
degrees Kelvin, etc.).</p></li>
<li><p><strong>Modify No Data Values</strong>: specify if NoData values
of MODIS layers should be kept at their original values, or changed to
those specified within the <code>MODIStsp_Products_Opts</code> XML file.
By selecting “Yes” in the “Change Original NoData values” check-box,
NoData of outputs are set to the largest integer value possible for the
data type of the processed layer (e.g., for 8-bit unsigned integer
layers, NoData is set always to 255, for 16-bit signed integer layers to
32767, and for 16-bit unsigned integer layers to 65535). Information
about the new NoData values is stored both in the output rasters, and in
the XML files associated with them. <strong>Note:</strong> some MODIS
layers have multiple NoData (a.k.a. <em>fill</em>) values. if <em>Modify
No Data</em> is set to “Yes”, <code><a href="../reference/MODIStsp.html">MODIStsp()</a></code> will convert all
<em>fill</em> values to a common output NoData value.</p></li>
</ul>
</div>
<div class="section level4">
<h4 id="output-folders">
<em>Output Folders</em><a class="anchor" aria-label="anchor" href="#output-folders"></a>
</h4>
<div class="section level5">
<h5 id="main-modistsp-output-folder">
<em>Main MODIStsp Output Folder</em><a class="anchor" aria-label="anchor" href="#main-modistsp-output-folder"></a>
</h5>
<p>Select the main folder where the pre-processed time series data will
be stored. All <code><a href="../reference/MODIStsp.html">MODIStsp()</a></code> outputs <strong>will be placed in
specific sub-folders of this main folder</strong> (see <a href="output.html">here</a> for details on <code>MODIStsp</code> naming
conventions).</p>
<p>The <strong>“Reprocess”</strong> selector allows to decide if images
already available should be reprocessed if a new run of
<code><a href="../reference/MODIStsp.html">MODIStsp()</a></code> is launched with the same output folder. If set
to “No”, <code><a href="../reference/MODIStsp.html">MODIStsp()</a></code> skips dates for which output files
following the <a href="https://docs.ropensci.org/MODIStsp">MODIStsp</a> naming conventions are already
present in the output folder. This allows to incrementally extend MODIS
time series without reprocessing already available dates.</p>
</div>
<div class="section level5">
<h5 id="output-folder-for-storage-of-original-modis-hdf">
<em>Output Folder for storage of original MODIS HDF</em><a class="anchor" aria-label="anchor" href="#output-folder-for-storage-of-original-modis-hdf"></a>
</h5>
<p>Select the folder where downloaded <strong>original MODIS HDF
files</strong> downloaded from NASA servers will be stored.</p>
<p>The <strong>“delete HDF”</strong> selector allows also to decide if
the downloaded images should be deleted from the file system at the end
of the processing. To avoid accidental file deletion, this is always set
to “No” by default, and a warning is issued before execution whenever
the selection is changed to “Yes”.</p>
<hr>
<p><br></p>
</div>
</div>
</div>
</div>
<div class="section level2">
<h2 id="saving-and-loading-processing-options">
<i class="fa fa-arrow-circle-o-right" aria-hidden="true"></i>
<strong>Saving and Loading Processing Options</strong><a class="anchor" aria-label="anchor" href="#saving-and-loading-processing-options"></a>
</h2>
<p><img src="interactive_execution_files/figure-html/unnamed-chunk-4-1.png" width="576" style="display: block; margin: auto;"></p>
<p>Specified processing parameters can be saved to a JSON file for later
use by clicking on the <em><strong>Save Options</strong></em> button in
the sidebar.</p>
<p>Previously saved options can be restored clicking on the
<em><strong>Load Options</strong></em> button and navigating to the
previously saved JSON file.</p>
<hr>
<p><br></p>
</div>
<div class="section level2">
<h2 id="starting-the-processing">
<i class="fa fa-arrow-circle-o-right" aria-hidden="true"></i>
<strong>Starting the processing</strong><a class="anchor" aria-label="anchor" href="#starting-the-processing"></a>
</h2>
<p>Once you are happy with your choices, click on <strong>Run
MODIStsp</strong>. <code><a href="../reference/MODIStsp.html">MODIStsp()</a></code> will start accessing NASA
servers to download and process the MODIS data corresponding to your
choices.</p>
<p>For each date of the specified time period, <code>MODIStp()</code>
downloads and preprocesses all HDF images required to cover the desired
spatial extent. Informative messages concerning the status of the
processing are provided on the console, as well as on a self-updating
progress window.</p>
<p>The processed time series are saved in specific subfolders of the
main selected output folder, as explained in detail <a href="output.html">here</a>.</p>
<hr>
</div>
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