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comparison indices_spectral.xml @ 0:a8dabbf47e15 draft

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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
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1 <tool id="srs_spectral_indices" name="Compute spectral indices" version="@VERSION@" profile = "20.01">
2 <description>as NDVI from remote sensing data</description>
3 <macros>
4 <import>macro.xml</import>
5 </macros>
6 <requirements>
7 <requirement type="package" version="4.2.2">r-base</requirement>
8 <requirement type="package" version="2.12.2">r-r.utils</requirement>
9 <requirement type="package" version="3.5_21">r-raster</requirement>
10 <requirement type="package" version="1.5_1">r-sp</requirement>
11 <requirement type="package" version="1.5_32">r-rgdal</requirement>
12 <requirement type="package" version="0.3.1">r-rasterdiv</requirement>
13 <requirement type="package" version="0.5_5">r-stars</requirement>
14 <requirement type="package" version="1.5.0">r-stringr</requirement>
15 <requirement type="package" version="2.4.2">r-pracma</requirement>
16 <requirement type="package" version="0.1_8">r-expint</requirement>
17 <requirement type="package" version="0.63.0">r-matrixstats</requirement>
18 <requirement type="package" version="3.4.0">r-ggplot2</requirement>
19 <requirement type="package" version="3.99_0.13">r-xml</requirement>
20 <requirement type="package" version="2.2.2">r-zip</requirement>
21 <requirement type="package" version="1.0.10">r-dplyr</requirement>
22 </requirements>
23 <command detect_errors="exit_code"><![CDATA[
24 #import re
25 #if $method.type == 'envi_bil':
26 #set input_raster = $method.input_raster
27 #set input_raster_identifier = re.sub('[^\s\w\-]', '_', str($input_raster.element_identifier))
28 #set input_header = $method.input_header
29 #set input_header_identifier = re.sub('[^\s\w\-]+[^.hdr]', '_', str($input_header.element_identifier))
30 cp '${input_raster}' '${input_raster_identifier}' &&
31 cp '${input_header}' '${input_header_identifier}' &&
32 #end if
33 Rscript
34 '$__tool_directory__/indices_spectral.r'
35 #if $method.type == 'envi_bil':
36 '$input_raster_identifier'
37 '$input_header_identifier'
38 ''
39 #else:
40 ''
41 ''
42 '$method.input'
43 #end if
44 '$__tool_directory__/prosail-master/R/Lib_PROSAIL.R'
45 '$__tool_directory__/prosail-master/R/Lib_SpectralIndices.R'
46 '$__tool_directory__/prosail-master/R/Lib_PROSAIL_HybridInversion.R'
47 '$input_indice'
48 '$__tool_directory__/functions.r'
49 '$choice'
50 '$output_indices'
51 '$plots'
52 '$output_raster'
53 ]]>
54 </command>
55 <inputs>
56 <conditional name="method">
57 <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'">
58 <option value="zipper">The data you are using are in a zip folder Reflectance</option>
59 <option value="envi_bil">You already have the files ENVI BIL</option>
60 </param>
61 <when value="zipper">
62 <param name="input" type="data" format="zip" multiple="true" label="Input data"/>
63 </when>
64 <when value="envi_bil">
65 <param name="input_raster" type="data" format="bil" label="Input raster"/>
66 <param name="input_header" type="data" format="hdr" label="Input raster header"/>
67 </when>
68 </conditional>
69 <param name="input_indice" type="select" label="Input the type of indice you want" multiple="true">
70 <option value="ARI1">ARI1</option>
71 <option value="ARI2">ARI2</option>
72 <option value="ARVI">ARVI</option>
73 <option value="BAI">BAI</option>
74 <option value="BAIS2">BAIS2</option>
75 <option value="CCCI">CCCI</option>
76 <option value="CHL_RE">CHL RE</option>
77 <option value="CRI1">CRI1</option>
78 <option value="CRI2">CRI2</option>
79 <option value="EVI">EVI</option>
80 <option value="EVI2">EVI2</option>
81 <option value="GRVI1">GRVI1</option>
82 <option value="GNDVI">GNDVI</option>
83 <option value="IRECI">IRECI</option>
84 <option value="LAI_SAVI">LAI SAVI</option>
85 <option value="MCARI">MCARI</option>
86 <option value="mNDVI705">mNDVI705</option>
87 <option value="MSAVI2">MSAVI2</option>
88 <option value="MSI">MSI</option>
89 <option value="mSR705">mSR705</option>
90 <option value="MTCI">MTCI</option>
91 <option value="nBR_RAW">nBR_RAW</option>
92 <option value="NDI_45">NDI_45</option>
93 <option value="NDII">NDII</option>
94 <option value="NDSI">NDSI</option>
95 <option value="NDVI">NDVI</option>
96 <option value="NDVI_G">NDVI_G</option>
97 <option value="NDVI705">NDVI705</option>
98 <option value="NDWI">NDWI</option>
99 <option value="NDWI1">NDWI1</option>
100 <option value="NDWI2">NDWI2</option>
101 <option value="PSRI">PSRI</option>
102 <option value="PSRI_NIR">PSRI_NIR</option>
103 <option value="RE_NDVI">RE_NDVI</option>
104 <option value="RE_NDWI">RE_NDWI</option>
105 <option value="S2REP">S2REP</option>
106 <option value="SAVI">SAVI</option>
107 <option value="SIPI">SIPI</option>
108 <option value="SR">SR</option>
109 <option value="CR_SWIR">CR_SWIR</option>
110 </param>
111 <param name="choice" type="select" label="Do you want the raster layer of the indice as an output ?" display="radio">
112 <option value="N">No</option>
113 <option value="Y">Yes</option>
114 </param>
115 </inputs>
116 <outputs>
117 <data name="output_indices" from_work_dir="Spec_Index.tabular" format="tabular" label="${input_indice} tabular"/>
118 <collection type="list" name="plots" label="${input_indice} plot">
119 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.png" visible="false" format="png"/>
120 </collection>
121 <collection type="list" name="output_raster" label="${input_indice} raster">
122 <discover_datasets pattern="(?P&lt;designation&gt;.+)" directory="SpectralIndices/" visible="false" recurse="true" format="bil,hdr"/>
123 <filter> choice == 'Y'</filter>
124 </collection>
125 </outputs>
126 <tests>
127 <test>
128 <param name="type" value="envi_bil"/>
129 <param name="input_raster" value="S2A_Subset"/>
130 <param name="input_header" value="S2A_Subset.hdr"/>
131 <param name="input_indice" value="NDVI"/>
132 <param name="choice" value="N"/>
133 <output name="output_indices">
134 <assert_contents>
135 <has_n_columns n="4"/>
136 <has_n_lines n="10001"/>
137 <has_text_matching expression="237\.25\t13.72\d*\t3.17\d*\t0.80\d*" />
138 </assert_contents>
139 </output>
140 <output_collection name="plots" type="list" count="1"/>
141 </test>
142 </tests>
143 <help><![CDATA[
144 =========================================================================
145 Computes biodiversity spectral indices from satellite remote sensing data
146 =========================================================================
147
148
149 **What it does**
150
151 This tool estimates vegetation properties (leaf and canopy) from sensor measurements. You can choose which vegetation property you want to compute.
152
153 **Input description**
154
155 It expects an image file as input, with a specific data format. ENVI HDR image with BIL interleave required.
156 The image is an ENVI raster including :
157
158 - A binary file (which has no extension here).
159
160 - A header file (with .hdr extension).
161
162 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.
163
164 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".
165
166 ⚠️ If you do not use this Reflectance folder make sure that your data are respectively in bil and hdr format in the datatypes.
167
168 Finally, you can choose whether or not you want to have the raster layer of your indice.
169
170 +--------------+----------+---------------+
171 | BIL | HDR |Spectral indice|
172 +==============+==========+===============+
173 | raster stack | Metadata | NDVI |
174 +--------------+----------+---------------+
175 | ... | ... | ... |
176 +--------------+----------+---------------+
177
178 **Output**
179
180 - One tabular with 3 columns : longitude, latitude and the chosen indice.
181
182 - One png plot for the vizualisation of the chosen indice.
183
184 - Opionnnal, the raster layer in a zip file.
185
186 **Additionnal informations**
187
188 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).
189
190 **Indices description**
191
192 +-------------------+---------------------------------------------------------+
193 | Abbreviation | Name |
194 +===================+=========================================================+
195 | ARI |Anthocyanin reflectance index |
196 +-------------------+---------------------------------------------------------+
197 | ARVI |Atmospherically Resistant Vegetation Index |
198 +-------------------+---------------------------------------------------------+
199 | BAI |Burn Area Index |
200 +-------------------+---------------------------------------------------------+
201 | BAIS2 |Burned Area Index for Sentinel 2 |
202 +-------------------+---------------------------------------------------------+
203 | CCCI |Canopy Chlorophyll Content Index |
204 +-------------------+---------------------------------------------------------+
205 | CHL_RE |Chlorophyll Red-Edge ? |
206 +-------------------+---------------------------------------------------------+
207 | EVI |Enhanced Vegetation Index |
208 +-------------------+---------------------------------------------------------+
209 | GRVI1 |Green Ratio Vegetation Index |
210 +-------------------+---------------------------------------------------------+
211 | GNDVI |Green Normalized Difference Vegetation Index |
212 +-------------------+---------------------------------------------------------+
213 | IRECI |Inverted Red-Edge Chlorophyll Index |
214 +-------------------+---------------------------------------------------------+
215 | LAI SAVI |Leaf Area Index Soil Adjusted Vegetation Index ? |
216 +-------------------+---------------------------------------------------------+
217 | MCARI |Modified Chlorophyll Absorption in Reflectance Index |
218 +-------------------+---------------------------------------------------------+
219 | mNDVI705 |Modified NDVI 705 |
220 +-------------------+---------------------------------------------------------+
221 | MSAVI2 |Modified Soil Adjusted Vegetation Index 2 |
222 +-------------------+---------------------------------------------------------+
223 | MSI |Moisture Stress Index |
224 +-------------------+---------------------------------------------------------+
225 | mSR705 |Modified Simple Ratio 705 |
226 +-------------------+---------------------------------------------------------+
227 | MTCI |MERIS Terrestrial Chlorophyll Index |
228 +-------------------+---------------------------------------------------------+
229 | NBR_RAW |Normalized Burn Ratio RAW |
230 +-------------------+---------------------------------------------------------+
231 | NDI_45 | |
232 +-------------------+---------------------------------------------------------+
233 | NDII |Normalized Difference 819/1600 NDII |
234 +-------------------+---------------------------------------------------------+
235 | NDSI |Normalized Difference Snow Index |
236 +-------------------+---------------------------------------------------------+
237 | NDVI |Normalized Difference Vegetation Index |
238 +-------------------+---------------------------------------------------------+
239 | NDVI_G | |
240 +-------------------+---------------------------------------------------------+
241 | NDVI705 |NDVI 705 |
242 +-------------------+---------------------------------------------------------+
243 | NDWI |Normalized Difference Water Index |
244 +-------------------+---------------------------------------------------------+
245 | NDWI1 |NDMI ? Normalized Difference Moisture Index ? |
246 +-------------------+---------------------------------------------------------+
247 | NDWI2 | |
248 +-------------------+---------------------------------------------------------+
249 | PSRI |Plant Senescing Reflectance Index |
250 +-------------------+---------------------------------------------------------+
251 | PSRI_NIR | |
252 +-------------------+---------------------------------------------------------+
253 | RE_NDVI |Red Edge NDVI ? |
254 +-------------------+---------------------------------------------------------+
255 | RE_NDWI |Red Edge NDWI |
256 +-------------------+---------------------------------------------------------+
257 | S2REP |Sentinel 2 Red-Edge Position |
258 +-------------------+---------------------------------------------------------+
259 | SAVI |Soil Adjusted Vegetation Index |
260 +-------------------+---------------------------------------------------------+
261 | SIPI |Structure Intensive Pigment Index 1 |
262 +-------------------+---------------------------------------------------------+
263 | SR |Simple Ratio ? |
264 +-------------------+---------------------------------------------------------+
265 | CR_SWIR |CR short wave infrared |
266 +-------------------+---------------------------------------------------------+
267
268 ]]> </help>
269 <expand macro="SRS_prosailref"/>
270 </tool>