name of a file from which to extract information. It is
supposed to be spelled as: SCS.xxxx-xx-xx.SS+Fnn.ext where 'SCS' is the
series-cruise-station code, 'xxxx-xx-xx' is the date of collection
(year-month-day), 'SS' is the unique sample identifier, 'F' is the fraction,
'nn' is the image number (when there are several images per fraction) or
'nn.mmm' when there are 'mmm' pictures taken to cover a bigger area of cell
'nn', and 'ext' is the file extension.
type
the type of data to extract (see examples) for
sampleInfo(), or the type of file to select in selectFile().
ext
the pattern to use (regular expression) to eliminate file
extension from the 'filename'.
string
a character string to rework, or a vector of character strings.
ZIobj
a ZooImage object (here, a 'ZIDat', 'ZIDesc', 'ZITrain' or
'ZITest' object; most probably one of the last two for addClass()).
ZIDat
a 'ZIDat' object, or a data frame with correct column labels.
x
a data frame, but most probably, a 'ZIDat' object.
drop.vars
a character vector with names of variables to drop, or
NULL (by default) to keep them all.
drop.vars.def
a second list of variables to drop contained in a
character vector. That list is supposed to match the name of variables that
are obviously non informative and that are dropped by default. It can be
gathered automatically using dropVars(). That list includes Id,
Label, Dil, ... (see details, variables with an asterisk).
area
a numerical vector with areas from which ECDs are calculated
(Equivalent Circular Diameter, a more suitable term for 2D images than ESD,
Equivalent Spherical Diameter).
data
a vector containing the data to parse.
label
a label to include for the parsed data.
ODfile
an image file of O.D. calibrated items that can be used to
calibrate grayscales.
zipfile
a zip archive.
zimfile
a .zim file to use, or to create. If NULL (default)
in zipNoteGet(), the data are not written in a file, but returned.
Details
As these functions are not made to be directly used by end-users, We don't
give more details here. Developers interested to use these functions are
encouraged to look at their code in the zooimage package source!
Here is the list of all variables you got after running the standard version
of calcVars() on ZIDat objects made by one of the ZooImage ImageJ
plugins (you can provide your own version for, e.g., calculating
more features):
Variable
Description
Origin
Area
Area of the region of interest (ROI)
ImageJ
Mean
Average gray value of the ROI
ImageJ
StdDev
Standard deviation of the gray values
ImageJ
Mode
Most frequent gray value within the ROI
ImageJ
Min
Minimum gray value within the ROI
ImageJ
Max
Maximum gray value within the ROI
ImageJ
X*
X coordinate of the centroid of the ROI in the image
ImageJ
Y*
Y coordinate of the centroid of the ROI in the image
ImageJ
XM*
X coordinate of the center of mass of the ROI in the image
ImageJ
YM*
Y coordinate of the center of mass of the ROI in the image
ImageJ
Perim.
Perimeter of the ROI
ImageJ
BX*
X coordinate of the upper left corner of the bounding rectangle (BR)
ImageJ
BY*
Y coordinate of the upper left corner of the BR
ImageJ
Width*
Width of the rectangle enclosing the ROI
ImageJ
Height*
Height of the rectangle enclosing the ROI
ImageJ
Major
Length of the longest axis of the ellipse fitted to the ROI
ImageJ
Minor
Length of the smallest axis of ellipse fitted to the ROI
ImageJ
Angle*
Angle between longest axis and an horizontal line
ImageJ
Circ.
Circularity of the ROI
ImageJ
Feret
Longest Feret diameter
ImageJ
IntDen
Sum of the gray values within the ROI
ImageJ
Median
Median value of the gray values within the ROI
ImageJ
Skew
Third order moment for the gray value
ImageJ
Kurt
Fourth order moment for the gray value
ImageJ
XStart*
X coordinate of initial point for the outline of the ROI
ImageJ
YStart*
Y coordinate of initial point for the outline of the ROI
ImageJ
Id*
Unique identifier of the ROI (Label_Item)
zooimage
Label*
Unique name of the image
zooimage
Item*
Name of the ROI
zooimage
ECD
Equivalent circular diameter of the ROI
zooimage
Dil*
Dilution coefficient to use for that ROI
zooimage
AspectRatio
Aspect ratio of the ROI
zooimage
CentBoxD
Distance between the centroid and the center of the BR
zooimage
GrayCentBoxD
Distance between the center of mass and the center of the BR
zooimage
CentroidsD
Distance between the centroid and the center mass
zooimage
Range
Range of the gray values in the ROI
zooimage
MeanPos
Position of mean gray value in the range of gray values
zooimage
SDNorm
Normalized standard deviation of the gray values
zooimage
CV
Coefficient of variation of gray values
zooimage
MeanDia
Mean diameter calculated on Major and Minor
zooimage
MeanFDia
Mean diameter calculated on Feret and Minor
zooimage
Transp1
Transparency calculated using ECD and MeanDia
zooimage
Transp2
Transparency calculated using ECD and MeanFDia
zooimage
Elongation
Elongation of the ROI
zooimage
Compactness
Compactness of the ROI
zooimage
Roundness
Roundness of the ROI
zooimage
Class*
Manual identification of the vignette for that ROI
zooimage
Predicted*
Automatic identification of the vignette for that ROI
zooimage
Predicted2*
Second automatic identification of the vignette for that ROI
zooimage
For the origin, ImageJ = measured during image ananlysis plugin in ImageJ,
zooimage = calculated either during importation of data, or by
calcVars(). Variables whose name ends with an asterisk are dropped by
default.
Value
A string or vector of strings for sampleInfo(), listSamples()
and makeId(). For those functions, character(0) is returned to
indicate a problem (usually with a warning issued to explain it), while
an empty string ("") is returned in case there is no corresponding
element found.
The data.frame with additional columns for calculated variables with
calcVars(). Variables to drop are gathered using dropVars(),
altogether with a list provided explicitly in the drop.vars = argument.
The list of variable names to drop automatically and silently can be stored in
a variable named ZI.dropVarsDef or in
options(ZI.dropVarsDef = ....).
A vector of numerical values for ecd().
Transformed strings for trimstring() and underscoreToSpace()
parseIni() reads the data and creates a list of data frames. Each
entry in the list maps one section in the ini file (with the same name). For
'key=value' pairs, a one line data frame containing values and with keys as
column names. The first column of these data frames is named label and get the
corresponding value passed by the 'label' argument. That way, one can easily
keep track of entries when data frames originated from various different ini
files are merged together.
calibrate() returns a vector of two numbers with white and black point
calibration (gray levels corresponding, respectively to O.D. = 0 and
O.D. = 1.024), plus a "msg" attribute with some explanation in case of problem.
zipNoteAdd() returns TRUE or FALSE depending if the data
from the zimfile was successfully added to the zip archive or not. Problem is
returned in a warning.
zipNoteGet() returns the comment included in the zip archive
(invisibly if 'zimfile' is not NULL), character(0) if no comment
if found, or NULL in case of a problem. The problem is detailled in a
warning.
Author(s)
Philippe Grosjean <Philippe.Grosjean@umons.ac.be>
See Also
noExtension, selectObject
Examples
# Given a correct ZooImage name for a sample, return parts of it
smp__ <- "MTLG.2010-03-15.H1+A1.03_dat1.zim"
sampleInfo(smp__, "sample")
sampleInfo(smp__, "fraction")
sampleInfo(smp__, "image")
sampleInfo(smp__, "scs")
sampleInfo(smp__, "date")
sampleInfo(smp__, "id")
sampleInfo(smp__, "frac")
sampleInfo(smp__, "imgnbr")
rm(smp__)
sampleInfo(c("ScanG16.2004-10-20+A1.tif", "ScanG16.2004-10-20+B1.tif"),
type = "sample", ext = extensionPattern("tif"))
# Character strings manipulation functions
underscoreToSpace("Some_string_to_convert")
trimString(" \tString with\textra spaces \t")
# Variables calculation utilities
df__ <- data.frame(Label = c("Alabel", "AnotherLabel"), Item = c("01", "02"))
makeId(df__)
rm(df__)
ecd(1:10)
### TODO: addClass(), calibrate(), calcVars(), parseIni(), zipNoteAdd() and zipNoteGet() examples