/
dataStitchR.R
315 lines (262 loc) · 14.9 KB
/
dataStitchR.R
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
#!/usr/bin/env Rscript
#Caitlin Casar
#github.com/caitlincasar
#19 March 2020
#DataStitchR stitches panoramic images of SEM images coupled to x-ray energy dispersive spectroscopy.
# usage: ./dataStitchR. -f "/Users/Caitlin/Desktop/dataStitcher/example_dataset" -b "/Users/Caitlin/Desktop/dataStitcher/example_dataset/SEM_images" -c "/Users/Caitlin/Desktop/dataStitcher/coordinates.txt" -z ".tif" -m ".tif" -a "Unknown|Os|SEM" -d "overview" -y "overview" -p TRUE -o "example" -n "example"
# usage Rscript dataStitchR.R -f "/Users/Caitlin/Desktop/dataStitcher/example_dataset" -b "/Users/Caitlin/Desktop/dataStitcher/example_dataset/SEM_images" -c "/Users/Caitlin/Desktop/dataStitcher/coordinates.txt" -z ".tif" -m ".tif" -a "Unknown|Os|SEM" -d "overview" -y "overview" -p TRUE -o "example" -n "example"
message("
##### ######
##### ## ##### ## # # ##### # ##### #### # # # #
# # # # # # # # # # # # # # # # #
# # # # # # # ##### # # # # ###### ######
# # ###### # ###### # # # # # # # # #
# # # # # # # # # # # # # # # # # #
##### # # # # # ##### # # # #### # # # #
")
message("DataStitchR was created by Caitlin Casar and is maintained at github.com/CaitlinCasar/dataStitchR.
")
message("DataStitchR stitches panoramic images of SEM images coupled to x-ray energy dispersive spectroscopy.
")
message("For help, run 'dataStitchR.R --help'.
")
suppressPackageStartupMessages(require(optparse))
option_list = list(
make_option(c("-f", "--file"), action="store", default=getwd(), type='character',
help="Input parent directory with subdirectories of element xray data to be stitched. The element names should be abbreviated, i.e. 'Ca' for calcium."),
make_option(c("-o", "--out"), action="store", default=NA, type='character',
help="Output file directory. This is where your x-ray raster brick and output figures will be saved."),
make_option(c("-n", "--name"), action="store", default=NA, type='character',
help="Optional name for output files."),
make_option(c("-b", "--base-images"), action="store", default=NA, type='character',
help="SEM image file directory."),
make_option(c("-c", "--coords"), action="store", default=NA, type='character',
help="Tab-delimited file of xy coordinates for each image. A third column should denote stitching positions that correspond to the file names for each image."),
make_option(c("-u", "--use-positions"), action="store", default="-?(?<![Kα1||Kα1_2])\\d+", type='character',
help="Optional regex pattern to extract position IDs from each file name that corresponds to positions in the xy file. The default searches for numbers that appear after 'Kα1' or 'Kα2'. Numbers can include signs, i.e. -1 is acceptable."),
make_option(c("-z", "--z-format"), action="store", default="*", type='character',
help="Optional regex pattern of x-ray image formats to select for stitching, i.e. '.tif'."),
make_option(c("-m", "--make"), action="store", default="*", type='character',
help="Optional regex pattern of SEM image formats to select for stitching, i.e. '.tif'. You do not need to specify this unless you are generating a PDF output."),
make_option(c("-a", "--all-exclude"), action="store", default=NA, type='character',
help="Optional regex pattern of x-ray file directories to exclude from stitiching, i.e. the element your sample was coated with."),
make_option(c("-d", "--drop"), action="store", default=NA, type='character',
help="Optional regex pattern of files to exclude from x-ray data stitching."),
make_option(c("-y", "--y-exclude"), action="store", default=NA, type='character',
help="Optional regex pattern of files to exclude from SEM image stitiching. You do not need to specify this unless you are generating a PDF output."),
make_option(c("-v", "--verbose"), action="store_true", default=TRUE,
help="Print updates to console [default %default]."),
make_option(c("-q", "--quiet"), action="store_false", dest="verbose",
help="Do not print anything to the console."),
make_option(c("-p", "--pdf"), action="store", default=FALSE,
help="Generate PDF of x-ray brick colored by element superimposed on the SEM image, default is TRUE [default %default].")
)
opt = parse_args(OptionParser(option_list=option_list))
#load dependencies
suppressPackageStartupMessages(require(pacman))
pacman::p_load(raster, magick, tidyverse, rasterVis, ggnewscale, Hmisc, cowplot)
#create list all sub-directories within main directory
directories <- list.dirs(opt$f, full.names = T , recursive =F)
if(!is.na(opt$a)){
directories <- directories[!str_detect(directories, opt$a)]
}
#set image coordinates
xy <- read_delim(opt$c, delim = "\t", col_types = cols())
positions <- xy %>%
select(-x, -y)
# stitch xray images ------------------------------------------------------
#stitch xray images into panoramas and store in raster brick
xray_brick_list <- list()
xray_data <- list()
for(j in 1:length(directories)){
path = directories[j]
files <- list.files(path, full.names = T, pattern = opt$z)
if(!is.na(opt$d)){
files <- files[!str_detect(files, opt$d)]
}
if(length(files) >0){
xray_data[[j]] <- str_extract(path, "([^/]+$)")
message(paste0("Stitching ",xray_data[[j]], " data (element ", j, " of ", length(directories), ")..."))
xy_id <- which(positions[[1]] %in% str_extract(files, opt$u))
panorama <- list()
for(i in 1:length(files)){
message(paste0("Processing image ", i, " of ", length(files), "..."))
image <- files[i] %>% image_read() %>%
image_quantize(colorspace = 'gray') %>%
image_equalize()
temp_file <- tempfile()
image_write(image, path = temp_file, format = 'tiff')
image <- raster(temp_file) %>%
cut(breaks = c(-Inf, 150, Inf)) - 1
image <- aggregate(image, fact=4)
image_extent <- extent(matrix(c(xy$x[xy_id[i]], xy$x[xy_id[i]] + 1024, xy$y[xy_id[i]], xy$y[xy_id[i]]+704), nrow = 2, ncol = 2, byrow = T))
image_raster <- setExtent(raster(nrows = 704, ncols = 1024), image_extent, keepres = F)
values(image_raster) <- values(image)
panorama[[xy_id[i]]] <- image_raster
}
empty_xy_id <- which(!positions[[1]] %in% str_extract(files, opt$u))
if(length(empty_xy_id) > 0){
for(k in 1:length(empty_xy_id)){
empty_raster_extent <- extent(matrix(c(xy$x[empty_xy_id[k]], xy$x[empty_xy_id[k]] + 1024, xy$y[empty_xy_id[k]], xy$y[empty_xy_id[k]]+704), nrow = 2, ncol = 2, byrow = T))
empty_raster <- setExtent(raster(nrows = 704, ncols = 1024), empty_raster_extent, keepres = F)
values(empty_raster) <- 0
panorama[[empty_xy_id[k]]] <- empty_raster
}
}
panorama_merged <- do.call(merge, panorama)
xray_brick_list[[j]] <- panorama_merged
}
}
message("Stitching complete. Creating x-ray brick...")
xray_brick <- do.call(brick, xray_brick_list)
names(xray_brick) <- unlist(xray_data)
message("...complete.")
#write the brick
message("Writing brick...")
if(!is.na(opt$o)){
dir.create(opt$o)
if(!is.na(opt$n)){
out_brick <- writeRaster(xray_brick, paste0(opt$o, "/", opt$n,"_brick.grd"), overwrite=TRUE, format="raster")
x <- writeRaster(xray_brick, paste0(opt$o, "/", opt$n,"_brick.tif"), overwrite=TRUE, format="GTiff",options=c("INTERLEAVE=BAND","COMPRESS=LZW"))
}else{
out_brick <- writeRaster(xray_brick, path = opt$o, "brick.grd", overwrite=TRUE, format="raster")
x <- writeRaster(xray_brick, path = opt$o, "brick.tif", overwrite=TRUE, format="GTiff",options=c("INTERLEAVE=BAND","COMPRESS=LZW"))
}
}else{
if(!is.na(opt$n)){
out_brick <- writeRaster(xray_brick, paste0(opt$n,"_brick.grd"), overwrite=TRUE, format="raster")
x <- writeRaster(xray_brick, paste0(opt$n,"_brick.tif"), overwrite=TRUE, format="GTiff",options=c("INTERLEAVE=BAND","COMPRESS=LZW"))
}else{
out_brick <- writeRaster(xray_brick, "brick.grd", overwrite=TRUE, format="raster")
x <- writeRaster(xray_brick, "brick.tif", overwrite=TRUE, format="GTiff",options=c("INTERLEAVE=BAND","COMPRESS=LZW"))
}
}
message("...complete.")
#flush everything we don't need from memory
remove(list = c("x", "xray_brick_list", "xray_data", "empty_raster", "empty_raster_extent",
"i", "j", "k", "path", "positions", "xy_id",
"panorama_merged", "panorama", "empty_xy_id", "files", "directories"))
# create base SEM image ---------------------------------------------------
if(opt$p){
if(!is.na(opt$b)){
SEM_images <- list.files(opt$b, full.names = T, pattern = opt$m)
}else{
message("Please provide a file path for your SEM images to stitch. For help, see 'dataStitchR.R --help.'")
break
}
if(!is.na(opt$y)){
SEM_images <- SEM_images[!str_detect(SEM_images , opt$y)]
}
SEM_panorama <- list()
message("Stitching SEM images into panorama...")
for(i in 1:length(SEM_images)){
image <- SEM_images[i] %>% image_read() %>%
image_quantize(colorspace = 'gray') %>%
image_equalize()
temp_file <- tempfile()
image_write(image, path = temp_file, format = 'tiff')
image <- raster(temp_file)
image_extent <- extent(matrix(c(xy$x[i], xy$x[i] + 1024, xy$y[i], xy$y[i]+704), nrow = 2, ncol = 2, byrow = T))
image_raster <- setExtent(raster(nrows = 704, ncols = 1024), image_extent, keepres = F)
values(image_raster) <- values(image)
SEM_panorama[[i]] <- image_raster
}
SEM_panorama_merged <- do.call(merge, SEM_panorama)
message("...complete.")
#flush everything we don't need from memory
remove(list = c("SEM_panorama", "SEM_images", "image", "image_extent", "image_raster"))
#optinal plot to check if SEM image merge looks correct
#plot(SEM_panorama_merged, col = gray.colors(10, start = 0.3, end = 0.9, gamma = 2.2, alpha = NULL))
# plot the data -----------------------------------------------------------
message("Generating plot...")
# Set color palette
#palette source: https://sciencenotes.org/molecule-atom-colors-cpk-colors/
element_colors <- c("#FFFFFF", "#D9FFFF", "#CC80FF", "#C2FF00", "#FFB5B5", "#909090", "#3050F8",
"#FF0D0D", "#90E050", "#B3E3F5", "#AB5CF2", "#8AFF00", "#BFA6A6", "#F0C8A0",
"#FF8000", "#FFFF30", "#1FF01F", "#80D1E3", "#8F40D4", "#3DFF00", "#E6E6E6",
"#BFC2C7", "#A6A6AB", "#8A99C7", "#9C7AC7", "#E06633", "#F090A0", "#50D050",
"#C88033", "#7D80B0", "#C28F8F", "#668F8F", "#BD80E3", "#FFA100", "#A62929",
"#5CB8D1", "#702EB0", "#00FF00", "#94FFFF", "#94E0E0", "#73C2C9", "#54B5B5",
"#3B9E9E", "#248F8F", "#0A7D8C", "#006985", "#C0C0C0", "#FFD98F", "#A67573",
"#668080", "#9E63B5", "#D47A00", "#940094", "#429EB0", "#57178F", "#00C900",
"#70D4FF", "#FFFFC7", "#D9FFC7", "#C7FFC7", "#A3FFC7", "#8FFFC7", "#61FFC7",
"#45FFC7", "#30FFC7", "#1FFFC7", "#00FF9C", "#00E675", "#00D452", "#00BF38",
"#00AB24", "#4DC2FF", "#4DA6FF", "#2194D6", "#267DAB", "#266696", "#175487",
"#D0D0E0", "#FFD123", "#B8B8D0", "#A6544D", "#575961", "#9E4FB5", "#AB5C00",
"#754F45", "#428296", "#420066", "#007D00", "#70ABFA", "#00BAFF", "#00A1FF",
"#008FFF", "#0080FF", "#006BFF", "#545CF2", "#785CE3", "#8A4FE3", "#A136D4",
"#B31FD4", "#B31FBA", "#B30DA6", "#BD0D87", "#C70066", "#CC0059", "#D1004F",
"#D90045", "#E00038", "#E6002E", "#EB0026")
names(element_colors) <- c("H", "He", "Li", "Be", "B", "C", "N", "O", "F", "Ne", "Na", "Mg", "Al", "Si",
"P", "S", "Cl", "Ar", "K", "Ca", "Sc", "Ti", "V", "Cr", "Mn", "Fe", "Co", "Ni",
"Cu", "Zn", "Ga", "Ge", "As", "Se", "Br", "Kr", "Rb", "Sr", "Y", "Zr", "Nb", "Mo",
"Tc", "Ru", "Rh", "Pd", "Ag", "Cd", "In", "Sn", "Sb", "Te", "I", "Xe", "Cs", "Ba",
"La", "Ce", "Pr", "Nd", "Pm", "Sm", "Eu", "Gd", "Tb", "Dy", "Ho", "Er", "Tm", "Yb",
"Lu", "Hf", "Ta", "W", "Re", "Os", "Ir", "Pt", "Au", "Hg", "Tl", "Pb", "Bi", "Po",
"At", "Rn", "Fr", "Ra", "Ac", "Th", "Pa", "U", "Np", "Pu", "Am", "Cm", "Bk", "Cf",
"Es", "Fm", "Md", "No", "Lr", "Rf", "Db", "Sg", "Bh", "Hs", "Mt")
xray_frame <- as.data.frame(xray_brick, xy=TRUE)
xray_frame <- gather(xray_frame, element, value, colnames(xray_frame)[3]:colnames(xray_frame)[ncol(xray_frame)])
element_plotter<-function(coord_frame, brick, SEM_image, colors){
p <-rasterVis::gplot(SEM_image) +
geom_tile(aes(fill = value)) +
scale_fill_gradient(low = 'black', high = 'white') +
ggnewscale::new_scale_fill()
for(i in names(brick)){
message(paste0("Adding ", names(brick[[i]]), " to plot..."))
element_coords <- coord_frame %>%
filter(element == names(brick[[i]]) & value!=0)
p <- p+geom_raster(element_coords, mapping = aes(x, y, fill = element, alpha = value)) +
scale_fill_manual(values = colors) +
ggnewscale::new_scale_fill()
}
message("Writing plot...")
suppressWarnings(print(p +
coord_fixed() +
theme(axis.title = element_blank(),
axis.text = element_blank(),
legend.position = "none")))
}
element_plot <- element_plotter(xray_frame, xray_brick, SEM_panorama_merged, element_colors)
element_plot_legend <- data.frame(element = unique(xray_frame$element)) %>%
rownames_to_column() %>%
ggplot(aes(element, rowname, fill=element)) +
geom_bar(stat= "identity") +
scale_fill_manual(values = element_colors) +
guides(fill=guide_legend(nrow=2)) +
theme(legend.title = ggplot2::element_blank(),
legend.text = ggplot2::element_text(size = 8))
element_plot_with_legend <- plot_grid(
element_plot,
plot_grid(get_legend(element_plot_legend),
ncol = 1),
nrow = 2,
rel_heights = c(8,2)
)
# generate PDF ------------------------------------------------------------
if(!is.na(opt$n)){
if(!is.na(opt$o)){
pdf(paste0(opt$o, "/", opt$n, "_element_plot.pdf"),
width = 13.33,
height = 7.5)
}else{
pdf(paste0(opt$n, "_element_plot.pdf"),
width = 13.33,
height = 7.5)
}
}else{
if(!is.na(opt$o)){
pdf(paste0(opt$o, "/", "element_plot.pdf"),
width = 13.33,
height = 7.5)
}else{
pdf("element_plot.pdf",
width = 13.33,
height = 7.5)
}
}
print(element_plot_with_legend)
dev.off()
message("...complete.")
remove(list = ls())
}