Mercurial > repos > ecology > srs_spectral_indices
diff indices_spectral.xml @ 0:a8dabbf47e15 draft
planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
| author | ecology |
|---|---|
| date | Mon, 09 Jan 2023 13:39:08 +0000 |
| parents | |
| children | b40aba3d9e5c |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/indices_spectral.xml Mon Jan 09 13:39:08 2023 +0000 @@ -0,0 +1,270 @@ +<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="${input_indice} plot"> + <discover_datasets pattern="(?P<designation>.+)\.png" visible="false" format="png"/> + </collection> + <collection type="list" name="output_raster" label="${input_indice} raster"> + <discover_datasets pattern="(?P<designation>.+)" directory="SpectralIndices/" visible="false" recurse="true" format="bil,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>