These functions are usually not called directly by the user, but they are interesting for developers.
sampleInfo(filename, type = c("sample", "fraction", "image", "scs",
"date", "id", "frac", "imgnbr"), ext = "_dat[135][.]zim$")underscoreToSpace(string)
trimString(string)
listSamples(ZIobj)
makeId(ZIDat)
addClass(ZIDat, ZIobj)
calcVars(x, drop.vars = NULL, drop.vars.def = dropVars())
dropVars()
ecd(area, cells = 1)
parseIni(data, label = "1")
calibrate(ODfile)
getDec()
zipNoteAdd(zipfile, zimfile)
zipNoteGet(zipfile, zimfile = NULL)
makeZIVignettes(orig.dir = getwd(), target.dir = dirname(orig.dir), clean.work = FALSE)
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.
the type of data to extract (see examples) for
sampleInfo(), or the type of file to select in selectFile().
the pattern to use (regular expression) to eliminate file extension from the 'filename'.
a character string to rework, or a vector of character strings.
a ZooImage object (here, a 'ZIDat', 'ZIDesc', 'ZITrain' or
'ZITest' object; most probably one of the last two for addClass()).
a 'ZIDat' object, or a data frame with correct column labels.
a data frame, but most probably, a 'ZIDat' object.
a character vector with names of variables to drop, or
NULL (by default) to keep them all.
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).
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).
the number of cells in the particle (colony). If different from 1, the area is first divided by the number of cells bevore calculating the cell individual ECD.
a vector containing the data to parse.
a label to include for the parsed data.
an image file of O.D. calibrated items that can be used to calibrate grayscales.
a zip archive.
a .zim file to use, or to create. If NULL (default)
in zipNoteGet(), the data are not written in a file, but returned.
the directory containing the data (current directory by default)
where to place the results, by defaut, the parent directory
of orig.dir
should we clean intermediary items (FALSE, by default)
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.
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 |
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.
# NOT RUN {
# 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)
ecd(1:10, cells = 2)
ecd(1:10, cells = 1:10)
### TODO: addClass(), calibrate(), calcVars(), parseIni(), zipNoteAdd() and zipNoteGet() examples
# }
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