Mercurial > repos > ecology > interpolation_run_idw_interpolation
changeset 0:d07fcc660f3c draft
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/interpolation commit 450e4496f243d6e94d5238358873bbc014fe2f08
| author | ecology |
|---|---|
| date | Mon, 08 Jan 2024 10:32:25 +0000 |
| parents | |
| children | b4b9edf9ea27 |
| files | run_idw_interpolation.R run_idw_interpolation.xml test-data/run_idw_interpolation_test_input1.csv test-data/run_idw_interpolation_test_input2.geojson test-data/run_idw_interpolation_test_output.png |
| diffstat | 5 files changed, 1218 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/run_idw_interpolation.R Mon Jan 08 10:32:25 2024 +0000 @@ -0,0 +1,100 @@ +library("getopt") +library("sf") +library("tmap") +library("RColorBrewer") +library("raster") +library("gstat") + +args = commandArgs(trailingOnly=TRUE) +option_specification = matrix(c( + 'observationsCsv', 'i1', 1, 'character', + 'latitudeColumn', 'i2', 1, 'double', + 'longitudeColumn', 'i3', 1, 'double', + 'observationsColumn', 'i4', 1, 'double', + 'studyArea', 'i5', 1, 'character', + 'idwPower', 'i6', 1, 'double', + 'samplePoints', 'i7', 1, 'double', + 'sampleType', 'i8', 1, 'character', + 'legendLabel', 'i9', 1, 'character', + 'legendPosition', 'i10', 1, 'character', + 'numberClasses', 'i11', 1, 'double', + 'dotSize', 'i12', 1, 'double', + 'colorType', 'i13', 1, 'character', + 'testCase', 'i14', 1, 'character', + 'outputData', 'o', 2, 'character' +), byrow=TRUE, ncol=4); +options = getopt(option_specification); + +obsData <- read.csv(file=options$observationsCsv, sep = ',', header = TRUE) +latitudeColumn <- options$latitudeColumn +longitudeColumn <- options$longitudeColumn +observationsColumn <- options$observationsColumn +studyArea <- options$studyArea +idwPower <- options$idwPower +samplePoints <- options$samplePoints +sampleType <- options$sampleType +legendLabel <- options$legendLabel +legendPosition <- options$legendPosition +numberClasses <- options$numberClasses +dotSize <- options$dotSize +colorType <- options$colorType +testCase <- options$testCase + +#cat("\n observationsCsv", options$observationsCsv) +cat("\n latitudeColumn", latitudeColumn) +cat("\n longitudeColumn", longitudeColumn) +cat("\n observationsColumn", observationsColumn) +#cat("\n studyArea", studyArea) +cat("\n idwPower", idwPower) +cat("\n samplePoints", samplePoints) +cat("\n sampleType", sampleType) +cat("\n legendLabel", legendLabel) +cat("\n legendposition", legendPosition) +cat("\n numberClasses", numberClasses) +cat("\n dotSize", dotSize) +cat("\n colorType", colorType) +cat("\n testCase", testCase) +#cat("\n outputData: ", options$outputData) + +coordinates(obsData) <- c(colnames(obsData)[longitudeColumn], colnames(obsData)[latitudeColumn]) +sf_obsData <- as_Spatial(st_as_sf(obsData)) + +polygon <- as_Spatial(st_read(studyArea)) +sf_obsData@bbox<-polygon@bbox + +runInterpolation <- function(points, values, interpolation_power, sample_points, sample_type){ + if (testCase == "true") { + cat("\n set seed!") + set.seed(123) + } + grd <- as.data.frame(spsample(points, sample_type, n=sample_points)) + names(grd) <- c("X", "Y") + coordinates(grd) <- c("X", "Y") + gridded(grd) <- TRUE + fullgrid(grd) <- TRUE + + proj4string(points) <- proj4string(points) + proj4string(grd) <- proj4string(points) + return(gstat::idw(values ~ 1, points, newdata=grd, idp=interpolation_power)) +} + +plotInterpolationMap <- function(raster, points, legend_label){ + plot <- tm_shape(raster) + + tm_raster(n=numberClasses,palette = rev(brewer.pal(7, colorType)), auto.palette.mapping = FALSE, + title=legend_label) + + tm_shape(points) + tm_dots(size=dotSize) + + tm_legend(legend.outside=legendPosition) + return(plot) +} + +sf_obsData.idw <- runInterpolation(sf_obsData, obsData$measurement, idwPower, samplePoints, sampleType) + +raster_object <- raster(sf_obsData.idw) +raster_object.mask <- mask(raster_object, polygon) + +idw <- plotInterpolationMap(raster_object.mask, sf_obsData, legendLabel) +idw + +png(options$outputData) +idw +dev.off() \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/run_idw_interpolation.xml Mon Jan 08 10:32:25 2024 +0000 @@ -0,0 +1,102 @@ +<tool id="interpolation_run_idw_interpolation" name="Run interpolation" version="1.0" profile="22.05"> + <description>based on Inverse Distance Weighting (IDW)</description> + <requirements> + <requirement type="package" version="1.20.4">r-getopt</requirement> + <requirement type="package" version="3.3_4">r-tmap</requirement> + <requirement type="package" version="3.6_26">r-raster</requirement> + <requirement type="package" version="2.1_1">r-gstat</requirement> + </requirements> + <command detect_errors='exit_code'><![CDATA[ + Rscript '$__tool_directory__/run_idw_interpolation.R' + --observationsCsv '$observations_csv' + --latitudeColumn '$latitude_column' + --longitudeColumn '$longitude_column' + --observationsColumn '$observations_column' + --studyArea '$study_area' + --idwPower '$idw_power' + --samplePoints '$sample_points' + --sampleType '$sample_type' + --legendLabel '$legend_label' + --legendPosition '$legend_position' + --numberClasses '$number_classes' + --dotSize '$dot_size' + --colorType '$color_type' + --testCase '$test_case' + --outputData '$output' + ]]></command> + <inputs> + <param type="data" format="csv" name="observations_csv" label="Select the .csv file including the observations"/> + <param type="data" format="geojson" name="study_area" label="Select the .geojson containing the study area"/> + <param name="latitude_column" type="data_column" data_ref="observations_csv" label="In which column are the latitude coordinates?"/> + <param name="longitude_column" type="data_column" data_ref="observations_csv" label="In which column are the longitude coordinates?"/> + <param name="observations_column" type="data_column" data_ref="observations_csv" label="In which column are the observation values?"/> + <param value="2" min="0.1" max="5" type="float" name="idw_power" label="Select the interpolation power of the IDW method"/> + <param value="50000" min="1000" max="100000" type="integer" name="sample_points" label="Select the number of sample points"/> + <param type="select" name="sample_type" label="Select a sample type"> + <option value="regular">Regular</option> + <option value="random">Random</option> + <option value="stratified">Stratified</option> + <option value="nonaligned">Nonaligned</option> + </param> + <param type="text" name="legend_label" label="Enter a label for the legend"/> + <param type="select" name="legend_position" label="Should the legend be displayed inside or outside the frame?"> + <option value="false">Inside</option> + <option value="true">Outside</option> + </param> + <param value="0.2" min="0.1" max="2" type="float" name="dot_size" label="Select the dot size of the points shown on the map"/> + <param value="10" min="1" max="100" type="integer" name="number_classes" label="Number of classes" help="Note: Not all values are possible. tmap tries to generate a number of classes which are as close to the indicated value as possible"/> + <param type="select" name="color_type" label="Select a color palette"> + <option value="RdBu">RdBu</option> + <option value="Blues">Blues</option> + <option value="BuGn">BuGn</option> + <option value="BuPu">BuPu</option> + <option value="GnBu">GnBu</option> + <option value="Greens">Greens</option> + <option value="Greys">Greys</option> + <option value="Oranges">Oranges</option> + <option value="OrRd">OrRd</option> + <option value="PuBu">PuBu</option> + <option value="PuBuGn ">PuBuGn</option> + <option value="PuRd">PuRd</option> + <option value="Purples">Purples</option> + <option value="RdPu">RdPu</option> + <option value="Reds">Reds</option> + <option value="YlGn">YlGn</option> + <option value="YlGnBu">YlGnBu</option> + <option value="YlOrBr">YlOrBr</option> + <option value="YlOrRd">YlOrRd</option> + </param> + <param type="boolean" name="test_case" label="Should a seed be set?" truevalue="true" falsevalue="false" /> + </inputs> + <outputs> + <data name="output" format="png" /> + </outputs> + <tests> + <!-- Run test with: planemo test - -biocontainers plotInterpolationMap.xml - -test_output=plotInterpolationMap.html --> + <test> + <param name="observations_csv" value="run_idw_interpolation_test_input1.csv"/> + <param name="latitude_column" value="3"/> + <param name="longitude_column" value="4"/> + <param name="observations_column" value="5"/> + <param name="study_area" value="run_idw_interpolation_test_input2.geojson"/> + <param name="idw_power" value="2"/> + <param name="sample_points" value="50000"/> + <param name="sample_type" value="regular"/> + <param name="legend_label" value="Legend"/> + <param name="legend_position" value="false"/> + <param name="number_classes" value="10"/> + <param name="dot_size" value="1"/> + <param name="color_type" value="RdBu"/> + <param name="test_case" value="true"/> + <output name="output" file="run_idw_interpolation_test_output.png" compare="sim_size" delta_frac="0.1"/> + </test> + </tests> + <help><![CDATA[ + IDW stands for Inverse Distance Weighting. The .csv file contains the observations and the .geojson file the study area. The plot is stored as a .png file. + ]]></help> + <citations> + <citation type="doi">10.32614/RJ-2018-009</citation> + <citation type="doi">10.18637/jss.v084.i06</citation> + <citation type="doi">10.32614/RJ-2016-014</citation> + </citations> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/run_idw_interpolation_test_input1.csv Mon Jan 08 10:32:25 2024 +0000 @@ -0,0 +1,11 @@ +sensor_id,attribute,latitude,longitude,measurement,accuracy,unit,date,quality_level,data_processing +1,waterTemp,51.95690094,7.61361456,10.428,0.002,celsius,03.04.2023 10:00,checked,adjusted +2,waterTemp,51.9558893,7.616701107,10.181,0.1,celsius,03.04.2023 10:00,checked,adjusted +3,waterTemp,51.95355062,7.606799142,11.653,0.1,celsius,03.04.2023 10:00,checked,raw +4,waterTemp,51.95258302,7.608679928,10.619,0.002,celsius,03.04.2023 10:00,unchecked,adjusted +5,waterTemp,51.95078585,7.604339653,10.124,0.002,celsius,03.04.2023 10:00,checked,adjusted +6,waterTemp,51.94994044,7.605288084,10.834,0.1,celsius,03.04.2023 10:00,checked,raw +7,waterTemp,51.94679837,7.596725189,11.244,0.002,celsius,03.04.2023 10:00,checked,adjusted +8,waterTemp,51.94552117,7.600045848,20.575,0.002,celsius,03.04.2023 10:00,unchecked,raw +9,waterTemp,51.94244725,7.594818813,10.669,0.002,celsius,03.04.2023 10:00,checked,adjusted +10,waterTemp,51.94294707,7.597031164,10.702,0.1,celsius,03.04.2023 10:00,checked,adjusted
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