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Complete re-write of tifftags2df (only internal changes).

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No changes in input or output of this function, only of the internal
mechanism with which tags are chosen and formatted for output.
init.R contains the sourceDir() function which is necessary for sourcing
all .R files in a directory.
master
Taha Ahmed 13 years ago
parent b55af5d478
commit 4fff82be0c
2 changed files with 91 additions and 87 deletions
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165
LEO1550/tifftags2df.R
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@ -1,5 +1,3 @@
source("/home/taha/chepec/chetex/common/R/common.R")
################################################## ##################################################
################ tifftags2df ##################### ################ tifftags2df #####################
################################################## ##################################################
@ -20,10 +18,10 @@ tifftags2df <- function(tiffimage) {
substrate.id <- strsplit(basename(tiffimage), "\\.")[[1]][1] substrate.id <- strsplit(basename(tiffimage), "\\.")[[1]][1]
tifftags <- system(paste("tiffinfo", tiffimage, sep = " "), tifftags <- system(paste("tiffinfo", tiffimage, sep = " "),
intern = TRUE, ignore.stderr = TRUE) intern = TRUE, ignore.stderr = TRUE)
# The first 47 rows of tifftags contains info about
# the image itself, and is not interesting # Clean certain special characters from the tiff tags strings
# The last row of tifftags is the empty string # If these strings are left untreated, they cause all sorts of weird errors later
trimtags <- tifftags.clean <-
sub("[ ]+$", "", #trim trailing spaces, if any sub("[ ]+$", "", #trim trailing spaces, if any
sub("\\r$", "", #remove trailing \r sub("\\r$", "", #remove trailing \r
gsub("\\xb9", "", #remove special character gsub("\\xb9", "", #remove special character
@ -35,7 +33,7 @@ tifftags2df <- function(tiffimage) {
gsub("\\xb3", "", #remove special character gsub("\\xb3", "", #remove special character
gsub("\\xb2", "", #remove special character gsub("\\xb2", "", #remove special character
gsub("\\xb1", "", #remove special character gsub("\\xb1", "", #remove special character
gsub("\\xb0", "", tifftags[48:length(tifftags) - 1], gsub("\\xb0", "", tifftags,
useBytes=T), useBytes=T),
useBytes=T), useBytes=T),
useBytes=T), useBytes=T),
@ -46,85 +44,78 @@ tifftags2df <- function(tiffimage) {
useBytes=T), useBytes=T),
useBytes=T), useBytes=T),
useBytes=T))) useBytes=T)))
oddtags <- trimtags[seq(1, length(trimtags), by = 2)]
eventags <- trimtags[seq(2, length(trimtags), by = 2)]
tmp.tagsdf <-
data.frame(stringsAsFactors = FALSE, # These are the tags we are looking for
sampleid = substrate.id, tags.df <- data.frame(stringsAsFactors = FALSE, substrate.id, matrix(#
tag = oddtags, # Name # REGEXP # splitchar # unit
value = eventags) c("EHT", "AP\\_ACTUALKV", " = ", "\\kilo\\volt",
# A vector of displayed tags "High current", "DP\\_HIGH\\_CURRENT", " = ", "",
displaytags <- "WD", "AP\\_WD", " = ", "\\milli\\metre",
c("AP_ACTUALKV", # EHT = 5.00 kV "Magnification", "AP\\_MAG", " = ", "", # could warrant special treatment
"DP_HIGH_CURRENT", # High Current = Off # commonly used for EDS analysis "Brightness", "AP\\_BRIGHTNESS", " = ", "\\percent",
"AP_WD", # WD = 4.1 mm "Contrast", "AP\\_CONTRAST", " = ", "\\percent",
"AP_MAG", # Mag = 15.00 K X "Signal A", "DP\\_DETECTOR\\_CHANNEL", " = ", "",
"AP_BRIGHTNESS", # Brightness = 49.0 % "SCM status", "DP\\_SCM\\_STATUS", " = ", "",
"AP_CONTRAST", # Contrast = 32.4 % "Specimen current", "AP\\_SCM", " = ", "\\femto\\ampere",
"DP_DETECTOR_CHANNEL", # InLens # Beam
"DP_SCM_STATUS", # SCM Status = Off #"Filament curent", "AP\\_ACTUALCURRENT", " = ", "\\ampere",
"AP_SCM", # Specimen I = 0 fA # zero if SCM Status = Off "Stigmation Y", "AP\\_STIG\\_Y", " = ", "\\percent",
# Beam "Stigmation X", "AP\\_STIG\\_X", " = ", "\\percent",
#notrelevant#"AP_ACTUALCURRENT", # Fil I = 2.370 A "Aperture align Y", "AP\\_APERTURE\\_ALIGN\\_Y", " = ", "\\percent",
"AP_STIG_Y", # Stigmation Y = -0.2 % "Aperture align X", "AP\\_APERTURE\\_ALIGN\\_X", " = ", "\\percent",
"AP_STIG_X", # Stigmation X = 1.9 % "Aperture size", "AP\\_APERTURESIZE", " = ", "\\micro\\metre",
"AP_APERTURE_ALIGN_Y", # Aperture Align Y = -1.5 % "Beam shift Y", "AP\\_BEAMSHIFT\\_Y", " = ", "\\percent",
"AP_APERTURE_ALIGN_X", # Aperture Align X = -2.4 % "Beam shift X", "AP\\_BEAMSHIFT\\_X", " = ", "\\percent",
"AP_APERTURESIZE", # Aperture Size = 30.00 m #"Beam offset Y", "AP\\_BEAM\\_OFFSET\\_Y", " = ", "\\nano\\metre",
"AP_BEAMSHIFT_Y", # Beam Shift Y = 0.1% #"Beam offset X", "AP\\_BEAM\\_OFFSET\\_X", " = ", "\\nano\\metre",
"AP_BEAMSHIFT_X", # Beam Shift X = 0.1% # Stage
#notrelevant#"AP_BEAM_OFFSET_Y", # Beam Offset Y = 13.89 nm "Track Z", "DP\\_TRACK\\_Z", " = ", "",
#notrelevant#"AP_BEAM_OFFSET_X", # Beam Offset X = 9.13 nm "Stage at Z", "AP\\_STAGE\\_AT\\_Z", " = ", "\\milli\\metre",
# Stage "Stage at Y", "AP\\_STAGE\\_AT\\_Y", " = ", "\\milli\\metre",
"DP_TRACK_Z", # Track Z = On "Stage at X", "AP\\_STAGE\\_AT\\_X", " = ", "\\milli\\metre",
"AP_STAGE_AT_Z", # Stage at Z = 25.857 mm # Tilt
"AP_STAGE_AT_Y", # Stage at Y = 49.0708 mm "Stage tilted?", "DP\\_STAGE\\_TILTED", " = ", "",
"AP_STAGE_AT_X", # Stage at X = 50.0753 mm "Tilt angle", "AP\\_TILT\\_ANGLE", " = ", "",
# Tilt "Tilt axis", "AP\\_TILT\\_AXIS", " = ", "",
"DP_STAGE_TILTED", # Stage Tilt = In Y # Image
"AP_TILT_ANGLE", # Tilt Angle = 0.0 "Scan speed", "DP\\_SCANRATE", " = ", "",
"AP_TILT_AXIS", # Tilt Axis = 0.0 "Cycle time", "AP\\_FRAME\\_TIME", " = ", "\\second",
# Image "Freeze on", "DP\\_FREEZE\\_ON", " = ", "",
"DP_SCANRATE", # Scan Speed = 10 "Dwell time", "DP\\_DWELL\\_TIME", " = ", "\\nano\\second",
"AP_FRAME_TIME", # Cycle Time = 48.7 Secs "Noise reduction", "DP\\_NOISE\\_REDUCTION", " = ", "",
"DP_FREEZE_ON", # Freeze on = End Frame "Frames to integrate", "AP\\_FRAME\\_INT\\_COUNT", " = ", "",
"DP_DWELL_TIME", # Dwell time = 100 ns "Frames to average", "AP\\_FRAME\\_AVERAGE\\_COUNT", " = ", "",
"DP_NOISE_REDUCTION", # Noise Reduction = Pixel Avg. #"Profile width", "AP\\_PROFILE\\_W", " = ", "\\micro\\metre",
"AP_FRAME_INT_COUNT", # Frames to integrate = 0 "Pixel size", "AP\\_PIXEL\\_SIZE", " = ", "\\nano\\metre",
"AP_FRAME_AVERAGE_COUNT", # Frames to average = 1 # System
#notrelevant#"AP_PROFILE_W", # Profile Width = 71.79 m "Gun vacuum", "AP\\_COLUMN\\_VAC", " = ", "\\milli\\bar",
"AP_PIXEL_SIZE", # Pixel Size = 23.96 nm "System vacuum", "AP\\_SYSTEM\\_VAC", " = ", "\\milli\\bar",
# System "Filament age", "AP\\_FILAMENT\\_AGE", " = ", "\\hour",
"AP_COLUMN_VAC", # Gun Vacuum = 1.74e-009 mbar # Misc
"AP_SYSTEM_VAC", # System Vacuum = 2.32e-006 mbar "Photo no.", "AP\\_PHOTO\\_NUMBER", " = ", "",
"AP_FILAMENT_AGE", # Filament Age = 1378.35 Hours "Date", "AP\\_DATE", " :", "",
# Misc "Time", "AP\\_TIME", " :", ""),
"AP_PHOTO_NUMBER", # Photo No. = 9069 ncol = 4, byrow = T))
"AP_DATE", # Date :23 Mar 2011 names(tags.df) <- c("sampleid", "name", "regexp", "splitchar", "unit")
"AP_TIME") # Time :19:10:46
#
extracted.tagsdf <- data.frame() for (i in 1:dim(tags.df)[1]) {
for (i in 1:length(displaytags)) { current.tag <- which(regexpr(tags.df$regexp[i], tifftags.clean) == 1) + 1
rows.extract <- which(displaytags[i] == tmp.tagsdf$tag) value.tmp <- strsplit(tifftags.clean[current.tag], split = tags.df$splitchar[i])[[1]][2]
extracted.tagsdf <- rbind(extracted.tagsdf, # Remove leading spaces from tags.df$value
data.frame(stringsAsFactors = FALSE, tags.df$value[i] <- sub("^\\s+", "", value.tmp, useBytes = T)
tmp.tagsdf[rows.extract, ])) if (tags.df$unit[i] != "") {
} tags.df$value[i] <- paste("\\SI{", strsplit(tags.df$value[i], split = " ")[[1]][1], "}{", tags.df$unit[i], "}", sep = "")
# Fix split of time and date fields
splittags <- strsplit(extracted.tagsdf$value, " = ")
for (i in 1:length(splittags)) {
if (length(splittags[[i]]) == 1) {
splittags[[i]] <- strsplit(splittags[[i]], " :")[[1]]
}
} }
tagsdf <- data.frame() }
for (i in 1:length(splittags)) {
tagsdf <- rbind(tagsdf,
data.frame(stringsAsFactors = FALSE, tags <- data.frame(stringsAsFactors = FALSE,
sampleid = extracted.tagsdf$sampleid[i], sampleid = tags.df$sampleid,
parameter = splittags[[i]][1], parameter = tags.df$name,
value = splittags[[i]][2])) value = tags.df$value)
}
# return(tags)
return(tagsdf)
} }

13
init.R
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@ -0,0 +1,13 @@
# To source a bunch of files in the same directory
sourceDir <- function(path, trace = TRUE) {
for (nm in list.files(path, pattern = "\\.[Rr]$")) {
if(trace) {
cat(nm,":")
}
source(file.path(path, nm))
if(trace) {
cat("\n")
}
}
}
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