view macros.xml @ 0:81b0ca76435d draft default tip

"planemo upload for repository https://gitlab.com/eetun-tiimi/EODIE commit c4a5672398bc878dd2bc0bf4f3a26f59b3f6395c"

<macros>
    <token name="@VERSION@">1.0.2</token>
    <xml name="edam_ontology">
        <edam_topics>
            <edam_topic>topic_0610</edam_topic>
            <edam_topic>topic_3050</edam_topic>
        </edam_topics>
    </xml>
    <xml name="configfiles">
        <configfiles>
            <configfile name="config_tif"><![CDATA[
platform: tif

##the first that is found is used
datepattern: '20[1-2][0-9][0-1][0-9][0-3][0-9]'

##name to write into output statistics filename
name: 'testrgb'
        ]]>            </configfile>
            <configfile name="config_s2"><![CDATA[
####

## Configuration file for the use of Sentinel-2 ##

## Know what you do before you change anything here ##

####

platform: 's2'

## Mask conditions are stored as values, not as bitflags
bitmask: 0
## Values to be to be included in cloudmask
## default [9,8,3,10,0,1]
tobemaskedlist: 
  - 9 ## cloud high probability
  - 8 ## cloud medium probability
  - 3 ## cloud shadow
  - 10 ## cirrus
  - 0 ## no data
  - 1 ## saturated and defective

##pattern to find all data files
filepattern: 'S2[A-C]_MSIL2A_\d{8}T\d{6}_N\d{4}_R\d{3}_T\d{2}[A-Z]{3}_\d{8}T\d{6}.SAFE$'

## Sentinel-2 bands
red : 'B04'
green: 'B03'
blue: 'B02'
nir: 'B08'
r_edge: 'B05'
swir1: 'B11'
swir2: 'B12'

## some part of the products file name that identifies them as product to be used
productnameidentifier: 'S2*.SAFE'

## parts to build path towards bands
bandlocation: ['.','*','*','IMG_DATA']

## path building set after imgpath to get the bandfile
pathbuildinglist: ['R', 'pixelsize' , 'm','*', 'bandname', '_' , 'pixelsize' ,'m.jp2']

##indicator for cloudfile
cloudfilename: 'SCL'

tilepattern: '(?<=T)[0-9]{2}[A-Z]{3}'

##the first that is found is used
datepattern: '20[1-2][0-9][0-1][0-9][0-3][0-9]'

band_designation: 'B[0-1]?\dA?'

## Quantification value used to multiple the reflectance to get DN
## This could be read from metadata but for now at least is here
quantification_value: 10000

## available resolutions per band
B01: [60]
B02: [10,20,60]
B03: [10,20,60]
B04: [10,20,60]
B05: [20,60]
B06: [20,60]
B07: [20,60]
B08: [10]
B8A: [20,60]
B09: [60]
B11: [20,60]
B12: [20,60]
SCL: [20,60]
AOT: [10,20,60]
TCI: [10,20,60]
WVP: [10,20,60]
     ]]>            </configfile>
            <configfile name="config_ls8"><![CDATA[
platform: 'ls8'

## Process only files with less than xx % cloudcover
maxcloudcover: 10


## Mask conditions are not stored as values, but as individual 0/1 flags in bits
bitmask: 1
## Bits to be to be included in cloudmask
## https://prd-wret.s3.us-west-2.amazonaws.com/assets/palladium/production/atoms/files/LSDS-1328_Landsat8-9-OLI-TIRS-C2-L2-DFCB-v6.pdf
tobemaskedlist: 
  - 0 ## Fill data
  - 1 ## Dilated cloud
  - 2 ## Cirrus
  - 3 ## Cloud
  - 4 ## Cloud shadow
  - 5 ## Snow 
  - 9 ## Cloud medium to high confidence
  - 11 ## Cloud shadow high confidence
  - 13 ## Snow/Ice high confidence
  - 15 ## Cirrus high confidence


##pattern to find all data files
filepattern: 'LC08_L\d.._\d{6}_\d{8}_\d{8}_02_[TR][12T]$'  

##all bands are located in parent directory directly
bandlocation: ['.']

##indicator for cloudfile
cloudfilename: 'QA_PIXEL'

## LS8 bands
## https://www.usgs.gov/media/images/landsat-8-band-designations
red : 'B4'
green: 'B3'
blue: 'B2'
nir: 'B5'
swir1: 'B6'
swir2: 'B7'

tilepattern: '[0-9]{6}'

## the first that is found is used
datepattern: '20[1-2][0-9][0-1][0-9][0-3][0-9]'

band_designation: 'B\d?\d'

##???????????
## Quantification value used to multiple the reflectance to get DN
## This could be read from metadata but for now at least is here
quantification_value: 65535

## available resolutions per band
B1: [30]
B2: [30]
B3: [30]
B4: [30]
B5: [30]
B6: [30]
B7: [30]
QA_PIXEL: [30]
## to be continued

##upsampling (converting to higher resolution/smaller cells) / downsampling (converting to lower resolution/larger cellsize)
##available: ‘nearest’, ‘bilinear’, ‘cubic’, ‘cubic_spline’, ‘lanczos’, ‘average’, ‘mode’, and ‘gauss’,
## from https://rasterio.readthedocs.io/en/latest/api/rasterio.enums.html#rasterio.enums.Resampling

resampling_method: 'bilinear'


## path building set *after inpath* to get the bandfile

pathbuildinglist: ['*', 'bandname', '*' , '.TIF']
     ]]>            </configfile>
            <configfile name="user_config"><![CDATA[
####

## Configuration file for adjusting the process/results and give paths ##

####

## Process only files with less than xx % cloudcover
maxcloudcover: 99

## Extract files with xx m pixel size 
## options: 10,20 (for Sentinel-2)
## options: 30 (for Landsat8)

#if str($input_type.platform) == 'ls8'
pixelsize: 30
#else
pixelsize: 10
#end if

##resampling (converting to higher/lower resolution/smaller cells)
##available: 'biliner','nearest','cubic','average', ...
## from https://rasterio.readthedocs.io/en/latest/api/rasterio.enums.html#rasterio.enums.Resampling

resampling_method: 'bilinear'

##location of the shapefile with tiles (Sentinel2-tiles-world in case of Sentinel-2, WRS2_descending in case of Landsat 8)
#if str($input_type.platform) == 's2'
tileshp: './sentinel2_tiles_world/sentinel2_tiles_world'
#elif str($input_type.platform) == 'ls8'
tileshp: './WRS2_descending/WRS2_descending'
#end if

##name of field where tilenames are stored in shapefile ('Name' in case of sentinel2_tiles_world, 'PR' in case of WRS2_descending )
#if str($input_type.platform) == 'ls8'
fieldname: 'PR'
#else
fieldname: 'Name'
#end if

## Lookup table for storing the tiles and the IDs they include for every tile processed by EODIE with --array_out
## Table needed for array plotting
lookup: './postprocesses/lookuptable.txt'
    ]]>            </configfile>
        </configfiles>
    </xml>
    <xml name="citations">
        <citations>
            <citation type="doi">10.5281/zenodo.4762323</citation>
        </citations>
    </xml>
</macros>