annotate indices_spectral.xml @ 1:b40aba3d9e5c draft default tip

planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit 0f331043178bbfbe5cda0e31d887971464b3071c

<tool id="srs_spectral_indices" name="Compute spectral indices" version="@VERSION@" profile = "20.01">
    <description>as NDVI from remote sensing data</description>
    <macros>
        <import>macro.xml</import>
    </macros>
    <requirements>
        <requirement type="package" version="4.2.2">r-base</requirement>
        <requirement type="package" version="2.12.2">r-r.utils</requirement>
        <requirement type="package" version="3.5_21">r-raster</requirement>
        <requirement type="package" version="1.5_1">r-sp</requirement>
        <requirement type="package" version="1.5_32">r-rgdal</requirement>
        <requirement type="package" version="0.3.1">r-rasterdiv</requirement>
        <requirement type="package" version="0.5_5">r-stars</requirement>
        <requirement type="package" version="1.5.0">r-stringr</requirement>
        <requirement type="package" version="2.4.2">r-pracma</requirement>
        <requirement type="package" version="0.1_8">r-expint</requirement>
        <requirement type="package" version="0.63.0">r-matrixstats</requirement>
        <requirement type="package" version="3.4.0">r-ggplot2</requirement>
        <requirement type="package" version="3.99_0.13">r-xml</requirement>
        <requirement type="package" version="2.2.2">r-zip</requirement>
        <requirement type="package" version="1.0.10">r-dplyr</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[ 
         #import re 
        #if $method.type == 'envi_bil': 
          #set input_raster = $method.input_raster
          #set input_raster_identifier = re.sub('[^\s\w\-]', '_', str($input_raster.element_identifier)) 
          #set input_header = $method.input_header
          #set input_header_identifier = re.sub('[^\s\w\-]+[^.hdr]', '_', str($input_header.element_identifier)) 
          cp '${input_raster}' '${input_raster_identifier}' &&
          cp '${input_header}' '${input_header_identifier}' &&
        #end if 
        Rscript
            '$__tool_directory__/indices_spectral.r'
             #if $method.type == 'envi_bil':
              '$input_raster_identifier' 
              '$input_header_identifier'
              ''
            #else:
              ''
              ''
              '$method.input'
            #end if
            '$__tool_directory__/prosail-master/R/Lib_PROSAIL.R'
            '$__tool_directory__/prosail-master/R/Lib_SpectralIndices.R'
            '$__tool_directory__/prosail-master/R/Lib_PROSAIL_HybridInversion.R'
            '$input_indice'
            '$__tool_directory__/functions.r'
            '$choice'
            '$output_indices'
            '$plots'
            '$output_raster'
        ]]>
    </command>
    <inputs>
        <conditional name="method">
            <param name="type" type="select" label="In which format are your data ?" help="You can directly take the Reflectance output from the tool 'Preprocessing sentinel 2 data'">
                <option value="zipper">The data you are using are in a zip folder Reflectance</option>
                <option value="envi_bil">You already have the files ENVI BIL</option>
            </param>
            <when value="zipper">
                <param name="input" type="data" format="zip" multiple="true" label="Input data"/>
            </when>
            <when value="envi_bil">
                <param name="input_raster" type="data" format="bil" label="Input raster"/>
                <param name="input_header" type="data" format="hdr" label="Input raster header"/>
            </when>
        </conditional>
        <param name="input_indice" type="select" label="Input the type of indice you want" multiple="true">
            <option value="ARI1">ARI1</option>
            <option value="ARI2">ARI2</option>
            <option value="ARVI">ARVI</option>
            <option value="BAI">BAI</option>
            <option value="BAIS2">BAIS2</option>
            <option value="CCCI">CCCI</option>
            <option value="CHL_RE">CHL RE</option>
            <option value="CRI1">CRI1</option>
            <option value="CRI2">CRI2</option>
            <option value="EVI">EVI</option>
            <option value="EVI2">EVI2</option>
            <option value="GRVI1">GRVI1</option>
            <option value="GNDVI">GNDVI</option>
            <option value="IRECI">IRECI</option>
            <option value="LAI_SAVI">LAI SAVI</option>
            <option value="MCARI">MCARI</option>
            <option value="mNDVI705">mNDVI705</option>
            <option value="MSAVI2">MSAVI2</option>
            <option value="MSI">MSI</option>
            <option value="mSR705">mSR705</option>
            <option value="MTCI">MTCI</option>
            <option value="nBR_RAW">nBR_RAW</option>
            <option value="NDI_45">NDI_45</option>
            <option value="NDII">NDII</option>
            <option value="NDSI">NDSI</option>
            <option value="NDVI">NDVI</option>
            <option value="NDVI_G">NDVI_G</option>
            <option value="NDVI705">NDVI705</option>
            <option value="NDWI">NDWI</option>
            <option value="NDWI1">NDWI1</option>
            <option value="NDWI2">NDWI2</option>
            <option value="PSRI">PSRI</option>
            <option value="PSRI_NIR">PSRI_NIR</option>
            <option value="RE_NDVI">RE_NDVI</option>
            <option value="RE_NDWI">RE_NDWI</option>
            <option value="S2REP">S2REP</option>
            <option value="SAVI">SAVI</option>
            <option value="SIPI">SIPI</option>
            <option value="SR">SR</option>
            <option value="CR_SWIR">CR_SWIR</option>
        </param>
        <param name="choice" type="select" label="Do you want the raster layer of the indice as an output ?" display="radio">
            <option value="N">No</option>
            <option value="Y">Yes</option>
        </param>
    </inputs>
    <outputs>
        <data name="output_indices" from_work_dir="Spec_Index.tabular" format="tabular" label="${input_indice} tabular"/>
        <collection type="list" name="plots" label="${input_indice} plot">
            <discover_datasets pattern="(?P&lt;designation&gt;.+)\.png" visible="false" format="png"/>
        </collection>
        <collection type="list" name="output_raster" label="${input_indice} raster">
            <discover_datasets pattern="(?P&lt;designation&gt;.+)" directory="SpectralIndices/" visible="false" recurse="true" format="bil"/>
                <filter> choice == 'Y'</filter>
            <discover_datasets pattern="(?P&lt;designation&gt;.+)" directory="SpectralIndices/" visible="false" recurse="true" format="hdr"/>
                <filter> choice == 'Y'</filter>
        </collection>
    </outputs>
    <tests>
        <test>
            <param name="type" value="envi_bil"/>
            <param name="input_raster" value="S2A_Subset"/>
            <param name="input_header" value="S2A_Subset.hdr"/>
            <param name="input_indice" value="NDVI"/>
            <param name="choice" value="N"/>
            <output name="output_indices">
                <assert_contents>
                    <has_n_columns n="4"/>
                    <has_n_lines n="10001"/>
                    <has_text_matching expression="237\.25\t13.72\d*\t3.17\d*\t0.80\d*" />
                </assert_contents>
            </output>
            <output_collection name="plots" type="list" count="1"/>
        </test>
    </tests>
    <help><![CDATA[
=========================================================================
Computes biodiversity spectral indices from satellite remote sensing data 
=========================================================================


**What it does**

This tool estimates vegetation properties (leaf and canopy) from sensor measurements. You can choose which vegetation property you want to compute.

**Input description**

It expects an image file as input, with a specific data format. ENVI HDR image with BIL interleave required.
The image is an ENVI raster including :

- A binary file (which has no extension here).

- A header file (with .hdr extension).

The header file is a text file including all necessary metadata which can be read with a text editor. It includes image dimensions, projection, and the name and central wavelength for each spectral band.

In order to get such input we advise to use the tool preprocessing sentinel 2 data. If you did so you can directly enter the "Reflectance" output from this tool and thus select the otpion "The data you are using are in a zip folder Reflectance". 

⚠️ If you do not use this Reflectance folder make sure that your data are respectively in bil and hdr format in the datatypes.

Finally, you can choose whether or not you want to have the raster layer of your indice.

+--------------+----------+---------------+
|      BIL     |    HDR   |Spectral indice|
+==============+==========+===============+
| raster stack | Metadata |     NDVI      |
+--------------+----------+---------------+
|      ...     |    ...   |      ...      |
+--------------+----------+---------------+

**Output**

- One tabular with 3 columns : longitude, latitude and the chosen indice. 

- One png plot for the vizualisation of the chosen indice.

- Opionnnal, the raster layer in a zip file.

**Additionnal informations**

This tools allows you to compute one of GEO BON EBV 'Canopy Chlorophyll Content' (https://portal.geobon.org/ebv-detail?id=13). This EBV is computed by GEO BON on the Netherlands, here you can compute it on which ever Sentinel 2 data you want by chosing to calculate the indice CCI. When you chose your data you have to select a cloud cover smaller than 10% (you can selct this character directly on the different platforms wher you can download Sentinel 2 data).

**Indices description**

+-------------------+---------------------------------------------------------+
|    Abbreviation   |                    Name                                 |
+===================+=========================================================+ 
|  ARI              |Anthocyanin reflectance index                            |
+-------------------+---------------------------------------------------------+
|  ARVI             |Atmospherically Resistant Vegetation Index               |
+-------------------+---------------------------------------------------------+
|  BAI              |Burn Area Index                                          |
+-------------------+---------------------------------------------------------+
|  BAIS2            |Burned Area Index for Sentinel 2                         |
+-------------------+---------------------------------------------------------+
|  CCCI             |Canopy Chlorophyll Content Index                         |
+-------------------+---------------------------------------------------------+
|  CHL_RE           |Chlorophyll Red-Edge ?                                   |
+-------------------+---------------------------------------------------------+
|  EVI              |Enhanced Vegetation Index                                |
+-------------------+---------------------------------------------------------+
|  GRVI1            |Green Ratio Vegetation Index                             |
+-------------------+---------------------------------------------------------+
|  GNDVI            |Green Normalized Difference Vegetation Index             |
+-------------------+---------------------------------------------------------+
|  IRECI            |Inverted Red-Edge Chlorophyll Index                      |
+-------------------+---------------------------------------------------------+
|  LAI SAVI         |Leaf Area Index Soil Adjusted Vegetation Index ?         |
+-------------------+---------------------------------------------------------+
|  MCARI            |Modified Chlorophyll Absorption in Reflectance Index     |
+-------------------+---------------------------------------------------------+
|  mNDVI705         |Modified NDVI 705                                        |
+-------------------+---------------------------------------------------------+
|  MSAVI2           |Modified Soil Adjusted Vegetation Index 2                |
+-------------------+---------------------------------------------------------+
|  MSI              |Moisture Stress Index                                    |
+-------------------+---------------------------------------------------------+
|  mSR705           |Modified Simple Ratio 705                                |
+-------------------+---------------------------------------------------------+
|  MTCI             |MERIS Terrestrial Chlorophyll Index                      |
+-------------------+---------------------------------------------------------+
|  NBR_RAW          |Normalized Burn Ratio RAW                                |
+-------------------+---------------------------------------------------------+
|  NDI_45           |                                                         |
+-------------------+---------------------------------------------------------+
|  NDII             |Normalized Difference 819/1600 NDII                      |
+-------------------+---------------------------------------------------------+
|  NDSI             |Normalized Difference Snow Index                         |
+-------------------+---------------------------------------------------------+
|  NDVI             |Normalized Difference Vegetation Index                   |
+-------------------+---------------------------------------------------------+
|  NDVI_G           |                                                         |
+-------------------+---------------------------------------------------------+
|  NDVI705          |NDVI 705                                                 |
+-------------------+---------------------------------------------------------+
|  NDWI             |Normalized Difference Water Index                        |
+-------------------+---------------------------------------------------------+
|  NDWI1            |NDMI ? Normalized Difference Moisture Index ?            |
+-------------------+---------------------------------------------------------+
|  NDWI2            |                                                         |
+-------------------+---------------------------------------------------------+
|  PSRI             |Plant Senescing Reflectance Index                        |
+-------------------+---------------------------------------------------------+
|  PSRI_NIR         |                                                         |
+-------------------+---------------------------------------------------------+
|  RE_NDVI          |Red Edge NDVI ?                                          |
+-------------------+---------------------------------------------------------+
|  RE_NDWI          |Red Edge NDWI                                            |
+-------------------+---------------------------------------------------------+
|  S2REP            |Sentinel 2 Red-Edge Position                             |
+-------------------+---------------------------------------------------------+
|  SAVI             |Soil Adjusted Vegetation Index                           |
+-------------------+---------------------------------------------------------+
|  SIPI             |Structure Intensive Pigment Index 1                      |
+-------------------+---------------------------------------------------------+
|  SR               |Simple Ratio ?                                           |
+-------------------+---------------------------------------------------------+
|  CR_SWIR          |CR short wave infrared                                   |
+-------------------+---------------------------------------------------------+

    ]]>    </help>
        <expand macro="SRS_prosailref"/>
</tool>