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

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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