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comparison pca_raster.xml @ 0:79bcb8c6dff0 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 13:55:34 +0000
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children 9300a492b634
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-1:000000000000 0:79bcb8c6dff0
1 <tool id="srs_pca" name="Compute a PCA raster" version="@VERSION@" profile = "20.01">
2 <description>from remote sensing data</description>
3 <macros>
4 <import>macro.xml</import>
5 </macros>
6 <expand macro="SRS_requirements"/>
7 <command detect_errors="exit_code"><![CDATA[
8 #import re
9 #if $method.origin == 'envi_bil':
10 #set input_raster = $method.input_raster
11 #set input_raster_identifier = re.sub('[^\s\w\-]', '_', str($input_raster.element_identifier))
12 #set input_header = $method.input_header
13 #set input_header_identifier = re.sub('[^\s\w\-]+[^.hdr]', '_', str($input_header.element_identifier))
14 cp '${input_raster}' '${input_raster_identifier}' &&
15 cp '${input_header}' '${input_header_identifier}' &&
16 #end if
17 Rscript
18 '$__tool_directory__/pca_raster.r'
19 #if $method.origin == 'envi_bil':
20 '$input_raster_identifier'
21 '$input_header_identifier'
22 ''
23 #else:
24 ''
25 ''
26 '$method.input'
27 #end if
28 '$type'
29 '$__tool_directory__/functions.r'
30 '$output_raster'
31 '$output_pca'
32 '$plots'
33 ]]>
34 </command>
35 <inputs>
36 <conditional name="method">
37 <param name="origin" type="select" label="In which format are your data ?">
38 <option value="zipper">The data you are using are in a zip folder Reflectance</option>
39 <option value="envi_bil">Your already have the files ENVI BIL</option>
40 </param>
41 <when value="zipper">
42 <param name="input" type="data" format="zip" multiple="true" label="Input data"/>
43 </when>
44 <when value="envi_bil">
45 <param name="input_raster" type="data" format="bil" label="Input raster"/>
46 <param name="input_header" type="data" format="hdr" label="Input raster header"/>
47 </when>
48 </conditional>
49 <param name="type" type="select" label="Do you want to do a PCA or a SPCA ?" display="radio" help="If you choose PCA there is no rescaling of the data as oppposed as if you choose SPCA">
50 <option value="SPCA">SPCA</option>
51 <option value="PCA">PCA</option>
52 </param>
53 </inputs>
54 <outputs>
55 <collection type="list" name="output_raster" label="PCA raster">
56 <discover_datasets pattern="(?P&lt;designation&gt;.+)" directory="RESULTS/" visible="false" recurse="true" format="bil,hdr"/>
57 </collection>
58 <data name="output_pca" from_work_dir="PCA.tabular" format="tabular" label="PCA tabular"/>
59 <collection type="list" name="plots" label="PCA plot">
60 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.png" visible="false" format="png"/>
61 </collection>
62 </outputs>
63 <tests>
64 <test>
65 <param name="origin" value="envi_bil"/>
66 <param name="input_raster" value="S2A_Subset"/>
67 <param name="input_header" value="S2A_Subset.hdr"/>
68 <param name="type" value="PCA"/>
69 <output_collection name="output_raster" type="list" count="5"/>
70 <output name="output_pca">
71 <assert_contents>
72 <has_n_lines n="960435"/>
73 </assert_contents>
74 </output>
75 <output_collection name="plots" type="list" count="1"/>
76 </test>
77 </tests>
78 <help><![CDATA[
79 ========================================================================
80 Process satellite remote sensing data to produce biodiversity indicators
81 ========================================================================
82
83
84 **What it does**
85
86 Féret and Asner (2014) developed a method for **tropical forest** diversity mapping based on very high spatial resolution airborne imaging spectroscopy.
87
88 The goal of this tool using the package biodivMapR is to produce a Principal Components Analysis (PCA) based on (optical) images. Principal component analysis prepares for feature extraction in order to reduce noise in the image. It is performed on a random subset of the image to ensure computational efficiency for large images.
89
90 **Input description**
91
92 It expects an image file as input, with a specific data format. ENVI HDR image with BIL interleave required.
93 The image is an ENVI raster including :
94
95 - A binary file (which has no extension here).
96
97 - A header file (with .hdr extension).
98
99 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.
100
101 In order to get such input we advise to use the tool preprocessing sentinel 2 data.
102
103 +--------------+----------+
104 | BIL | ENVI HDR |
105 +==============+==========+
106 | raster stack | Metadata |
107 +--------------+----------+
108 | ... | ... |
109 +--------------+----------+
110
111 **Output**
112
113 - One tabular with 3 columns : longitude, latitude and pca.
114
115 - One png graph.
116
117 - One ENVI BIL files with the one file for the bil raster and one file for the hdr header.
118 ]]> </help>
119 <expand macro="SRS_BDMRref"/>
120 </tool>