Mercurial > repos > ecology > otb_mean_shift_smoothing

comparison OTB_MeanShiftSmoothing.R @ 0:6c6e8b16dba6 draft

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planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/interpolation commit bd6f07bf29bad450af2e552f2524f23277edfef5-dirty
author ecology
date Wed, 13 Mar 2024 19:12:46 +0000
parents
children dd397752ad21
comparison
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-1:000000000000 0:6c6e8b16dba6
1 # Run with Rscript ./OTB_MeanShiftSmoothing.R
2 #--file otb_band_math_test_input.txt
3 #--fOut float --fOutpos float --processingMemory 1024 --spatialR 5 --rangeR 15
4 #--thresHold 0.1 --maxIter 100 --rangeRamp 0 --modeSearch False
5 #--outputType png
6 #--outputFormat download --outputData test1.png
7
8 library("httr2")
9 library("jsonlite")
10 library("getopt")
11
12 args <- commandArgs(trailingOnly = TRUE)
13 option_specification <- matrix(c(
14 "file", "i1", 1, "character",
15 "fOut", "i2", 1, "character",
16 "fOutpos", "i3", 1, "character",
17 "processingMemory", "i4", 1, "integer",
18 "spatialR", "i5", 2, "integer",
19 "rangeR", "i6", 2, "double",
20 "thresHold", "i7", 2, "double",
21 "maxIter", "i8", 2, "integer",
22 "rangeRamp", "i9", 2, "double",
23 "modeSearch", "i10", 1, "character",
24 "outputType", "i11", 1, "character",
25 "outputFormat", "i12", 1, "character",
26 "outputData", "o", 1, "character"
27 ), byrow = TRUE, ncol = 4)
28 options <- getopt(option_specification)
29
30 file <- options$file
31 fout <- options$fOut
32 foutpos <- options$fOutpos
33 processing_memory <- options$processingMemory
34 spatialr <- options$spatialR
35 ranger <- options$rangeR
36 threshold <- options$thresHold
37 maxiter <- options$maxIter
38 rangeramp <- options$rangeRamp
39 modesearch <- options$modeSearch
40 output_type <- paste0("image/", options$outputType)
41 output_format <- options$outputFormat
42 output_data <- options$outputData
43
44 cat("\n file: ", file)
45 cat("\n fout: ", fout)
46 cat("\n foutpos: ", foutpos)
47 cat("\n processing_memory: ", processing_memory)
48 cat("\n spatialr: ", spatialr)
49 cat("\n ranger: ", ranger)
50 cat("\n threshold: ", threshold)
51 cat("\n maxiter: ", maxiter)
52 cat("\n rangeramp: ", rangeramp)
53 cat("\n modesearch: ", modesearch)
54 cat("\n output_type: ", output_type)
55 cat("\n output_format: ", output_format)
56
57 base_url <- "https://ospd.geolabs.fr:8300/ogc-api/"
58 execute <- "processes/OTB.MeanShiftSmoothing/execution"
59 get_status <- "jobs/"
60 get_result <- "/results"
61
62 file_urls <- readLines(file, warn = FALSE)
63
64 il_list <- lapply(file_urls, function(url) {
65 list("href" = url)
66 })
67
68 json_data <- list(
69 "inputs" = list(
70 "in" = il_list,
71 "fout" = fout,
72 "foutpos" = foutpos,
73 "ram" = processing_memory,
74 "spatialr" = spatialr,
75 "ranger" = ranger,
76 "thres" = threshold,
77 "maxiter" = maxiter,
78 "rangeramp" = rangeramp,
79 "modesearch" = modesearch
80 ),
81 "outputs" = list(
82 "fout" = list(
83 "format" = list(
84 "mediaType" = output_type
85 ),
86 "transmissionMode" = "reference"
87 ),
88 "foutpos" = list(
89 "format" = list(
90 "mediaType" = output_type
91 ),
92 "transmissionMode" = "reference"
93 )
94 )
95 )
96
97 make_response_body_readable <- function(body) {
98 hex <- c(body)
99 int_values <- as.integer(hex)
100 raw_vector <- as.raw(int_values)
101 readable_output <- rawToChar(raw_vector)
102 json_object <- jsonlite::fromJSON(readable_output)
103 return(json_object)
104 }
105
106 tryCatch({
107 # Request 1
108 resp1 <- request(paste0(base_url, execute)) %>%
109 req_headers(
110 "accept" = "/*",
111 "Prefer" = "respond-async;return=representation",
112 "Content-Type" = "application/json"
113 ) %>%
114 req_body_json(json_data) %>%
115 req_perform()
116 response <- make_response_body_readable(resp1$body)
117 status_code1 <- resp1$status_code
118 if (status_code1 == 201) {
119 status <- "running"
120 attempt <- 1
121 while (status == "running") {
122 # Request 2
123 resp2 <- request(paste0(base_url, get_status, response$jobID)) %>%
124 req_headers(
125 "accept" = "application/json"
126 ) %>%
127 req_perform()
128 status_code2 <- resp2$status_code
129 if (status_code2 == 200) {
130 response2 <- make_response_body_readable(resp2$body)
131 cat("\n", response2$status)
132 if (response2$status == "successful") {
133 status <- "successful"
134 # Request 3
135 resp3 <- request(paste0(
136 base_url,
137 get_status, response2$jobID, get_result
138 )) %>%
139 req_headers(
140 "accept" = "application/json"
141 ) %>%
142 req_perform()
143 status_code3 <- resp3$status_code
144 if (status_code3 == 200) {
145 response3 <- make_response_body_readable(resp3$body)
146 if (output_format == "download") {
147 options(timeout = 600)
148 download.file(response3$fout$href,
149 destfile = paste0("output1.", options$outputType),
150 mode = "wb"
151 )
152 download.file(response3$foutpos$href,
153 destfile = paste0("output2.", options$outputType),
154 mode = "wb"
155 )
156 } else if (output_format == "getUrl") {
157 writeLines(paste(response3$fout$href, response3$foutpos$href,
158 sep = "\n"
159 ), con = "output.txt")
160 }
161 } else if (status_code3 == 404) {
162 print("The requested URI was not found.")
163 } else if (status_code3 == 500) {
164 print("A server error occurred.")
165 } else {
166 print(paste("HTTP", status_code3, "Error:", resp3$status_message))
167 }
168 } else if (response2$status == "failed") {
169 status <- "failed"
170 }
171 } else {
172 status <- "failed"
173 print(paste("HTTP", status_code2, "Error:", resp2$status_message))
174 }
175 Sys.sleep(3)
176 }
177 print(status)
178 } else if (status_code1 == 400) {
179 print("A query parameter has an invalid value.")
180 } else if (status_code1 == 404) {
181 print("The requested URI was not found.")
182 } else if (status_code1 == 500) {
183 print("The requested URI was not found.")
184 } else {
185 print(paste("HTTP", status_code1, "Error:", resp1$status_message))
186 }
187 })