rm(list = ls())
###############################input data
dir_path <- "D:\\2023\\2023_1_virus\\1_original_2_virus_for_SM-20230817\\3_sars-cov2-rdrp-followup-3\\"
dir_path_name <- dir(dir_path,pattern = "*.txt",full.names = T)
dir_path_name
## [1] "D:\\2023\\2023_1_virus\\1_original_2_virus_for_SM-20230817\\3_sars-cov2-rdrp-followup-3\\sars-cov2-rdrp-followup-3.txt"
data_1 <- read.delim2(grep("sars-cov2-rdrp-followup-3.txt",dir_path_name,value = T),header = T,stringsAsFactors = F)
dim(data_1) #[1] 128 117
## [1] 128 117
data_1$Max.Resp <- as.numeric(data_1$Max.Resp)
#str(data_1)
data_3 <- data_1$Sample.ID[data_1$Max.Resp < -50]
data_3 <- gsub("-.*", "", data_3)
#data_3
#########################################################
#INPUT DIAGRAM
dir_path_1 <- dir_path
dir.create(paste0(dir_path_1, "positive\\"))
## Warning in dir.create(paste0(dir_path_1, "positive\\")):
## 'D:\2023\2023_1_virus\1_original_2_virus_for_SM-20230817\3_sars-cov2-rdrp-followup-3\positive'
## already exists
library(magick)
## Linking to ImageMagick 6.9.12.3
## Enabled features: cairo, freetype, fftw, ghostscript, heic, lcms, pango, raw, rsvg, webp
## Disabled features: fontconfig, x11
#?dir
dir_path_name_1 <- dir(dir_path_1, pattern = "*.tif",full.names = T, recursive = T)
#dir_path_name_1
for (i in 1:length(unique(data_3))) {
tryCatch({
#i =3
print(i)
image_1 <- image_read(grep(unique(data_3)[i], dir_path_name_1, value = T))
print(image_1)
image_2 <- image_trim(image_1)
# Resize
#image_3 <- image_scale(image_2, "700") # width: 300px
#image_4 <- image_resize(image_2, "1000x1000")
#print(image_3)
image_write(image_2, path = paste0(dir_path_1, "positive\\",unique(data_3)[i], ".tiff"),
format="tiff",density = 1,quality = 100)
}, error = function(e) {
cat("ERROR :",conditionMessage(e), "\n")
cat("ERROR :", conditionMessage(e),"---",i,"---",gsub("\\:","-",Sys.time()),file = "error.txt", append = TRUE, "\n")
#cat(message('** ERR at ', Sys.time(), " **"),file = "test_1.txt", append = TRUE)
#print(e)
},
warning = function(w){
cat("Warning :", conditionMessage(w),"---",i,"---",gsub("\\:","-",Sys.time()),file = "warning.txt", append = TRUE, "\n")
# print(w)
})
}
## [1] 1
## format width height colorspace matte filesize density
## 1 TIFF 1347 957 sRGB FALSE 202184 1x1
## 2 TIFF 1347 957 sRGB FALSE 202184 1x1
## 3 TIFF 1347 957 sRGB FALSE 202184 1x1
## 4 TIFF 1417 1003 sRGB FALSE 51792 300x300
## [1] 2
## format width height colorspace matte filesize density
## 1 TIFF 1347 957 sRGB FALSE 184934 1x1
## 2 TIFF 1347 957 sRGB FALSE 184934 1x1
## 3 TIFF 1347 957 sRGB FALSE 184934 1x1
## 4 TIFF 1417 1003 sRGB FALSE 48436 300x300
## [1] 3
## format width height colorspace matte filesize density
## 1 TIFF 1347 957 sRGB FALSE 187466 1x1
## 2 TIFF 1347 957 sRGB FALSE 187466 1x1
## 3 TIFF 1347 957 sRGB FALSE 187466 1x1
## 4 TIFF 1417 1003 sRGB FALSE 47504 300x300
## [1] 4
## format width height colorspace matte filesize density
## 1 TIFF 1347 957 sRGB FALSE 209156 1x1
## 2 TIFF 1347 957 sRGB FALSE 209156 1x1
## 3 TIFF 1347 957 sRGB FALSE 209156 1x1
## 4 TIFF 1417 1003 sRGB FALSE 53738 300x300
## [1] 5
## format width height colorspace matte filesize density
## 1 TIFF 1347 957 sRGB FALSE 201254 1x1
## 2 TIFF 1347 957 sRGB FALSE 201254 1x1
## 3 TIFF 1347 957 sRGB FALSE 201254 1x1
## 4 TIFF 1417 1003 sRGB FALSE 51138 300x300
## [1] 6
## format width height colorspace matte filesize density
## 1 TIFF 1347 957 sRGB FALSE 178016 1x1
## 2 TIFF 1347 957 sRGB FALSE 178016 1x1
## 3 TIFF 1347 957 sRGB FALSE 178016 1x1
## 4 TIFF 1417 1003 sRGB FALSE 45068 300x300
## [1] 7
## format width height colorspace matte filesize density
## 1 TIFF 1347 957 sRGB FALSE 185972 1x1
## 2 TIFF 1347 957 sRGB FALSE 185972 1x1
## 3 TIFF 1347 957 sRGB FALSE 185972 1x1
## 4 TIFF 1417 1003 sRGB FALSE 48770 300x300
## [1] 8
## format width height colorspace matte filesize density
## 1 TIFF 1347 957 sRGB FALSE 193016 1x1
## 2 TIFF 1347 957 sRGB FALSE 193016 1x1
## 3 TIFF 1347 957 sRGB FALSE 193016 1x1
## 4 TIFF 1417 1003 sRGB FALSE 49138 300x300
## [1] 9
## format width height colorspace matte filesize density
## 1 TIFF 1347 957 sRGB FALSE 195320 1x1
## 2 TIFF 1347 957 sRGB FALSE 195320 1x1
## 3 TIFF 1347 957 sRGB FALSE 195320 1x1
## 4 TIFF 1417 1003 sRGB FALSE 50788 300x300
## [1] 10
## format width height colorspace matte filesize density
## 1 TIFF 1347 957 sRGB FALSE 211730 1x1
## 2 TIFF 1347 957 sRGB FALSE 211730 1x1
## 3 TIFF 1347 957 sRGB FALSE 211730 1x1
## 4 TIFF 1417 1003 sRGB FALSE 53018 300x300
## [1] 11
## format width height colorspace matte filesize density
## 1 TIFF 1347 957 sRGB FALSE 180110 1x1
## 2 TIFF 1347 957 sRGB FALSE 180110 1x1
## 3 TIFF 1347 957 sRGB FALSE 180110 1x1
## 4 TIFF 1417 1003 sRGB FALSE 46700 300x300
## [1] 12
## format width height colorspace matte filesize density
## 1 TIFF 1347 957 sRGB FALSE 182540 1x1
## 2 TIFF 1347 957 sRGB FALSE 182540 1x1
## 3 TIFF 1347 957 sRGB FALSE 182540 1x1
## 4 TIFF 1417 1003 sRGB FALSE 46298 300x300
## [1] 13
## format width height colorspace matte filesize density
## 1 TIFF 1347 957 sRGB FALSE 71176 1x1
## [1] 14
## format width height colorspace matte filesize density
## 1 TIFF 1347 957 sRGB FALSE 197882 1x1
## 2 TIFF 1347 957 sRGB FALSE 197882 1x1
## 3 TIFF 1347 957 sRGB FALSE 197882 1x1
## 4 TIFF 1417 1003 sRGB FALSE 51388 300x300
## [1] 15
## format width height colorspace matte filesize density
## 1 TIFF 1347 957 sRGB FALSE 202694 1x1
## 2 TIFF 1347 957 sRGB FALSE 202694 1x1
## 3 TIFF 1347 957 sRGB FALSE 202694 1x1
## 4 TIFF 1417 1003 sRGB FALSE 51490 300x300
## [1] 16
## format width height colorspace matte filesize density
## 1 TIFF 1347 957 sRGB FALSE 188648 1x1
## 2 TIFF 1347 957 sRGB FALSE 188648 1x1
## 3 TIFF 1347 957 sRGB FALSE 188648 1x1
## 4 TIFF 1417 1003 sRGB FALSE 48172 300x300