Created LEO1550.R: created tifftags2df() function.

In common.R: marked LinearBaseline() as deprecated.

CHI.R

@@ -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])

LEO1550.R

@@ -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)
+}
+
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common.R

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