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Created LEO1550.R: created tifftags2df() function.

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In common.R: marked LinearBaseline() as deprecated.
master
Taha Ahmed 14 years ago
parent 8e0733d03e
commit fd62a103c8
3 changed files with 161 additions and 3 deletions
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4
CHI.R
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@ -369,13 +369,13 @@ cv2df <- function(datafilename, wearea = 1) {
for (s in 1:length(starts)) {
zz <- textConnection(chifile[starts[s]:ends[s]], "r")
ff <- rbind(ff,
data.frame(sampleid, segment = s, cycle = as.integer(ceiling(s/2)),
data.frame(sampleid, cycle = as.integer(ceiling(s/2)), segment = s,
matrix(scan(zz, what = numeric(), sep = ","),
ncol = 3, byrow = T)))
close(zz)
}
# Column names after initial assignment
names(ff) <- c("sampleid", "segment", "cycle", "potential", "current", "charge")
names(ff) <- c("sampleid", "cycle", "segment", "potential", "current", "charge")
# Calculate current density
currentdensity <- ff$current / wearea
ff <- cbind(ff[, 1:5], currentdensity = currentdensity, charge = ff[, 6])

158
LEO1550.R
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@ -0,0 +1,158 @@
# LEO1550.R
# Functions to read and manipulate data from the LEO1550 scanning electron microscope
# Taha Ahmed, March 2011
# CONTENTS
source("/home/taha/chepec/chetex/common/R/common.R")
# >>>> tifftags2df
##################################################
################ tifftags2df #####################
##################################################
tifftags2df <- function(tiffimage) {
## Description:
## Extracts all tags from a TIFF image file
## using the tiffinfo tool and stores
## a selection of the tags in a dataframe.
## Usage:
## tifftags2df(fulltiffpath)
## Arguments:
## tiffimage: character string, the full filename
## (with path) to one TIFF file.
## Value:
## A dataframe with three columns:
## sampleid, parameter, value.
#
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 <-
sub("[ ]+$", "", #trim trailing spaces, if any
sub("\\r$", "", #remove trailing \r
gsub("\\xb9", "", #remove special character
gsub("\\xb8", "", #remove special character
gsub("\\xb7", "", #remove special character
gsub("\\xb6", "", #remove special character
gsub("\\xb5", "", #remove special character
gsub("\\xb4", "", #remove special character
gsub("\\xb3", "", #remove special character
gsub("\\xb2", "", #remove special character
gsub("\\xb1", "", #remove special character
gsub("\\xb0", "", tifftags[48:length(tifftags) - 1],
useBytes=T),
useBytes=T),
useBytes=T),
useBytes=T),
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,
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]]
}
}
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)
}

2
common.R
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@ -3,7 +3,7 @@
# Taha Ahmed, Jan 2011
# CONTENTS
# >>>> LinearBaseline
# >>>> LinearBaseline (deprecated)
# >>>> int2padstr
# >>>> It2charge
# >>>> ProvideSampleId

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