R/annotateDTA.R
In jbrzusto/sensorgnome-R-package: Tools for the sensorgnome project.
Defines functions
annotateDTA
## annotate a DTA file with information from the tag filtering process
## write the output to the same file with "_annotated.txt" appended,
## and optionally to an html file with a bit of navigation chrome.
annotateDTA = function(
DTAfile,
tagDB,
show=TRUE,
html=FALSE,
confirm = 3,
maxMiss = 20,
slop = 4,
slopExpand = 0) {
DTAfile = chooseDTAFile(DTAfile)
tagDB = chooseDBFile(tagDB)
dtalines = readLines(DTAfile)
dtaout = readDTA(lines=dtalines)
out = filterTags(dtaout, tagDB, confirm, maxMiss, slop, slopExpand)
extra = rep("", length(dtalines))
extra[out$tags$DTAline] = sprintf(" Run %6d: %6d/%6d Tag: %s", out$tags$runID, out$tags$posInRun, out$tags$runLen, out$tags$id)
txt = file(paste(DTAfile, "_annotated.txt", sep=""), "w")
if (html) {
htmlname = paste(DTAfile, "_annotated.html", sep="")
htmlf = file(htmlname, "w")
cat(sprintf('
<html>
<head>
<title>%s - filtered and annotated
</title>
<style>
.DTA_annotation { color: rgb(0, 200, 0); }
.line0 { background-color: rgb(225, 255, 200);}
.line1 { background-color: rgb(200, 255, 225);}
</style>
</head>
<body>
<pre>
', basename(DTAfile)), file=htmlf)
}
info = sprintf('
This annotated Lotek .DTA file was created by annotateDTA() in R package sensorgnome
from http://sensorgnome.org.
Filtering Parameters
====================
tag database = %s
confirm = %4d : minimum number of bursts required in a run; need not be consecutive
maxMiss = %4d : maximum number of consecutive missed bursts; detected bursts
separated by more than this number of missing bursts are placed in separate runs.
slop = %6.1f: maximum deviation from registered burst interval between consecutive bursts,
in milliseconds
slopExpand = %4d : amount permitted deviation increases for each missed burst, in milliseconds
Filtering is performed by looking for maximal runs of each tag ID in the database.
The bursts in a run must satisfy the filtering parameters. In particular, the time gap
between them must be reasonably compatible with the burst interval in the database.
In the ID only and ID + GPS sections below, detections surviving the filtering are grouped
into runs, which are indicated to the right of the original table. The annotation
looks like this:
Slop: -1.6 ms Run 1: 3/ 263 Proj: LHSP2013
where:
- Slop is the difference between the observed burst interval and the one registered
in the database.
- Run is the run identifier; detections with the same run ID are linked together
by compatible time gaps.
- i/N the index and total number of detections in this run; here, the
detection is the third out of 263 for run #1.
- Proj is the inferred project for this tag, based on antenna frequency and
burst interval. Tags having the same ID but different burst interval
can be distinguished, and are placed in different runs. The project code
is from the master database.
',
basename(tagDB),
confirm,
maxMiss,
slop,
slopExpand)
cat(info, file=txt)
if (html) {
cat (info, file=htmlf)
}
annotation = sprintf(' Slop: %5.1f ms Run %6d: %6d/%6d Tag: %s',
out$tags$burstSlop * 1000,
out$tags$runID,
out$tags$posInRun,
out$tags$runLen,
out$tags$id)
extra[out$tags$DTAline] = paste('<span class="DTA_annotation">', annotation, '</span>', sep="")
if (html) {
prefix = sprintf('<span class="line%d">', seq(along=dtalines) %% 2)
suffix = '</span>'
## class names of file pieces
pn = names(dtaout$pieces)
## numbered class names of file pieces
pn2 = rep("", length(pn))
tapply(seq(along=pn), pn, function(i) pn2[i] <<- sprintf("%s_%d", pn[i], 1:length(i)))
## a back to TOC link for each table piece
prefix[dtaout$piece.lines.before] = paste(prefix[dtaout$piece.lines.before],
sprintf('<a name="%s"></a><br><a href="#TOC">Back to TOC</a><br>', pn2), sep="")
cat('
</pre><h3>
<a name="TOC">Table of Contents</a>
</h3>\n', file=htmlf)
tapply(seq(along=pn), pn,
function(i) {
cat(paste(sprintf("<li>%s: %s</li>", pn[i][1],
paste(sprintf('<a href="#%s">%d</a>', pn2[i], seq(along=i)), collapse=", ")
), collapse="\n"),
file=htmlf)})
cat("</ul><hr><br><pre>\n", file=htmlf)
cat(paste(prefix, dtalines, extra, suffix, sep="", collapse="\r\n"), file=htmlf)
cat("</pre></body></html>\r\n", file=htmlf)
close(htmlf)
}
## bare text version
dtalines[out$tags$DTAline] = paste(dtalines[out$tags$DTAline], annotation)
cat(paste(dtalines, collapse="\r\n"), file=txt)
close(txt)
## browse to the annotated HTML version
if (html && show) {
if (.Platform$OS.type == "unix" && substr(htmlname, 1, 1) != "/")
htmlname = file.path(getwd(), htmlname)
browseURL(paste("file:///", htmlname, sep=""))
}
}
jbrzusto/sensorgnome-R-package documentation built on May 18, 2019, 9:19 p.m.
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Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Defines functions annotateDTA
## annotate a DTA file with information from the tag filtering process
## write the output to the same file with "_annotated.txt" appended,
## and optionally to an html file with a bit of navigation chrome.
annotateDTA = function(
DTAfile,
tagDB,
show=TRUE,
html=FALSE,
confirm = 3,
maxMiss = 20,
slop = 4,
slopExpand = 0) {
DTAfile = chooseDTAFile(DTAfile)
tagDB = chooseDBFile(tagDB)
dtalines = readLines(DTAfile)
dtaout = readDTA(lines=dtalines)
out = filterTags(dtaout, tagDB, confirm, maxMiss, slop, slopExpand)
extra = rep("", length(dtalines))
extra[out$tags$DTAline] = sprintf(" Run %6d: %6d/%6d Tag: %s", out$tags$runID, out$tags$posInRun, out$tags$runLen, out$tags$id)
txt = file(paste(DTAfile, "_annotated.txt", sep=""), "w")
if (html) {
htmlname = paste(DTAfile, "_annotated.html", sep="")
htmlf = file(htmlname, "w")
cat(sprintf('
<html>
<head>
<title>%s - filtered and annotated
</title>
<style>
.DTA_annotation { color: rgb(0, 200, 0); }
.line0 { background-color: rgb(225, 255, 200);}
.line1 { background-color: rgb(200, 255, 225);}
</style>
</head>
<body>
<pre>
', basename(DTAfile)), file=htmlf)
}
info = sprintf('
This annotated Lotek .DTA file was created by annotateDTA() in R package sensorgnome
from http://sensorgnome.org.
Filtering Parameters
====================
tag database = %s
confirm = %4d : minimum number of bursts required in a run; need not be consecutive
maxMiss = %4d : maximum number of consecutive missed bursts; detected bursts
separated by more than this number of missing bursts are placed in separate runs.
slop = %6.1f: maximum deviation from registered burst interval between consecutive bursts,
in milliseconds
slopExpand = %4d : amount permitted deviation increases for each missed burst, in milliseconds
Filtering is performed by looking for maximal runs of each tag ID in the database.
The bursts in a run must satisfy the filtering parameters. In particular, the time gap
between them must be reasonably compatible with the burst interval in the database.
In the ID only and ID + GPS sections below, detections surviving the filtering are grouped
into runs, which are indicated to the right of the original table. The annotation
looks like this:
Slop: -1.6 ms Run 1: 3/ 263 Proj: LHSP2013
where:
- Slop is the difference between the observed burst interval and the one registered
in the database.
- Run is the run identifier; detections with the same run ID are linked together
by compatible time gaps.
- i/N the index and total number of detections in this run; here, the
detection is the third out of 263 for run #1.
- Proj is the inferred project for this tag, based on antenna frequency and
burst interval. Tags having the same ID but different burst interval
can be distinguished, and are placed in different runs. The project code
is from the master database.
',
basename(tagDB),
confirm,
maxMiss,
slop,
slopExpand)
cat(info, file=txt)
if (html) {
cat (info, file=htmlf)
}
annotation = sprintf(' Slop: %5.1f ms Run %6d: %6d/%6d Tag: %s',
out$tags$burstSlop * 1000,
out$tags$runID,
out$tags$posInRun,
out$tags$runLen,
out$tags$id)
extra[out$tags$DTAline] = paste('<span class="DTA_annotation">', annotation, '</span>', sep="")
if (html) {
prefix = sprintf('<span class="line%d">', seq(along=dtalines) %% 2)
suffix = '</span>'
## class names of file pieces
pn = names(dtaout$pieces)
## numbered class names of file pieces
pn2 = rep("", length(pn))
tapply(seq(along=pn), pn, function(i) pn2[i] <<- sprintf("%s_%d", pn[i], 1:length(i)))
## a back to TOC link for each table piece
prefix[dtaout$piece.lines.before] = paste(prefix[dtaout$piece.lines.before],
sprintf('<a name="%s"></a><br><a href="#TOC">Back to TOC</a><br>', pn2), sep="")
cat('
</pre><h3>
<a name="TOC">Table of Contents</a>
</h3>\n', file=htmlf)
tapply(seq(along=pn), pn,
function(i) {
cat(paste(sprintf("<li>%s: %s</li>", pn[i][1],
paste(sprintf('<a href="#%s">%d</a>', pn2[i], seq(along=i)), collapse=", ")
), collapse="\n"),
file=htmlf)})
cat("</ul><hr><br><pre>\n", file=htmlf)
cat(paste(prefix, dtalines, extra, suffix, sep="", collapse="\r\n"), file=htmlf)
cat("</pre></body></html>\r\n", file=htmlf)
close(htmlf)
}
## bare text version
dtalines[out$tags$DTAline] = paste(dtalines[out$tags$DTAline], annotation)
cat(paste(dtalines, collapse="\r\n"), file=txt)
close(txt)
## browse to the annotated HTML version
if (html && show) {
if (.Platform$OS.type == "unix" && substr(htmlname, 1, 1) != "/")
htmlname = file.path(getwd(), htmlname)
browseURL(paste("file:///", htmlname, sep=""))
}
}
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