parseini() -> type.convert(..., as.is = TRUE) = argument added to avoid spurious warnings.
zidDatMake(): make sure Label column is character, not factor.
getTrain(): make sure Class is factor.
Define auxiliary programs for Linux.
Bug correction in selectFile(): now filters are correct.
Bug correction in saveObjects(): multiple= is not an argument for the Unix version of the dlgOpen() dialog box + filters corrected.
Bugs corrected in zidToZidb(), zidbMake() and sampleInfo() that prevented to convert old (zooimage v.1) .zid files to .zidb files.
Change import() to importFrom() in NAMESPACE for many dependencies for a more robust management of these dependencies.
importImg(), zieCompile() and zieCompileFlowCAM() are adapted to detect if a "regular" set of images, or FlowCAM data are compiled.
In makeZIVignettes(), scale bars are now recalculated and regenerated according to PixelSize/PixelUnit metadata.
Two new functions to help visualize the content of .zidb files: zibdSummary() displays all numerical data and all the metadata, and zidbPlotPage() plots the vignettes page by page (by 25 items on each page).
In zidDatMake(), only the two last image metadata was kept. This bug is corrected now.
zidbPlotPage() has now two more arguments: method & class to use validated data and define the class to filter before displaying vignettes.
Vignettes can now be created from within R, using the new makeZIVignettes()
function.
zidbMake()
and makeZidb()
are updated to handle the new 'ZI5' format with tinted vignettes created directly from within R.
sampleInfo()
now can process _dat3.zim
and _dat5.zim
files as well as the original _dat1.zim
files.
checkFirstLine()
can now deal with ZI1 - ZI5 files.
zimDatList()
now recognizes _dat1.zim
, _dat3.zim
and _dat5.zim
files.
zidDatMake()
now creates ZI5 files.
zisRead()
now tries to convert date, but if it fails, it continues leaving the unmodified string and issues a warning.
zidbMake()
now creates ZI5 files and can replace <<<SMP>>>
in label, <<<DATE>>>
in date, and <<<TIME>>>
in time metadata fields with appropriate values. Note that time must be provided in the new smptime =
argument. In case CellPart
is missing, the default value of 0.73
is assumed. Similarly, if Replicates
is missing, a value of 1
is assumed by default. The check.vignettes =
is now FALSE
by default, since we may generate them on the fly.
A bug in errorCorrection()
led to fail with message telling it is impossible to replace GpFPDiff
because replacement has 0 rows and data has xxx.
Plankton sorter pages used /planktonSorter.html?v=xxxx, but the argument v= is falsely interpretted as part of the file path in Linux. So, the version information of the page is now dropped.
Function imported from grDevices, graphics and stats are now declared in NAMESPACE.
A bug in processSamplesWithCells()
failed to select another "cells.rds" file when a default one is recorded.
recode.ZITrain()
and recode.ZITest()
mangled completely the classes when depth =
argument was provided. Corrected.
Warnings were issued when zieCompile()
did not found calibration images. Corrected.
The processSamples()
function was not able to deal with .zid
files any more. Now, it can use both .zid
and .zidb
files, but not a mix of them simultaneously.
A regression prevented zieMake()
to finialize the .zim
files from a .zie
template. Corrected.
In errorCorrection()
, a table with items not sorted alphabetically led to a mix in the correction/validation of the vignettes. Corrected.
Correction of a bug that prevented the calculation of cells per colonies to work (changes in cellCompute()
not taken into account here).
The calibration()
function to calibrate grayscale for flat-bed scanner is rewritten to use only R code.
A wrong default argument in makeZidb()
is replaced with a more sensible value.
processSample()
and processSampleAll()
: new defaults for keep =
and detail =
arguments (takes classes with uppercase first character), and a couple of minor bug corrections.
Several bugs corrected in viewResults()
and exportResults()
.
External executables (Vuescan, Fiji or ImageJ, XnView and metadata editor) are not distributed any more with zooimage because this is not allowed by CRAN. The routine to detect those programs is more robust for Mac (should be in the Applications folder), and under Windows where it looks for a /Zooimage/bin
folder into the Program Files (64bit first, then 32bit).
Correction of a bug in zidbMake()
in the computation of the .zidb
file name.
dropVars()
function now also drops "MinFeret", "AR" and "Round" that make problems between old and new samples.activeLearing()
function prevented to use data and/or classifiers build with versions of zooimage older than 5.4-x. Corrected.Cells counting per colonies (per particles) is now provided.
processSamples()
now look for .zidb
files instead of .zid
files.
Correction of one bug in the function addVigsToTrain()
.
The functions activeLearning()
and viewFrenchManual()
were not exported in the NAMESPACE
, but are required for the menus. Fixed.
Functions to count cells in a particle (colony): countCells()
and the corresponding countCellsGUI()
function for an access through the menu.
Function to build predictive models for cells in particles (colonies) after counting: cellModel()
.
Function to compute the number of cells in particles in a new sample: cellCompute()
.
Function to make .zidb
file for FlowCAM data through the menu: makeZidbMakeFlowCAM()
.
Correct makeClass()
function in the menu (missing formula).
Functions to process active learning: contextSelection()
, the associated addItemsToTrain()
and dropItemsToTrain()
functions to complete the training set with validated items, and the corresponding activeLearningGUI()
function for an access through the menu. Integration in the classification process.
Function compTrain()
to compare two training sets and highlight differences.
Translation of the user manual in French and update to include all changes.
Adaptation of menus to include also the new features.
calcVarsVIS()
now included in calcVars()
and not accessible any more as top function (to avoid duplicate code).
ecd()
and ecdCell()
are now merged in ecd()
using arguments cells = 1
.
errorCorrection()
and planktonSorterPage()
functions now use the new interface to get R httpd server port, for R svn rev >= 67550.
In the shiny app, dataTableOutput is now called from the DT package. Dependency to DT is now added.
The planktonSorter html page was sometimes too small, with the last group being wrapped consequently. Solved by increasing the page by 1 pixel * groups.
A bug in processSample()
prevented for calculation with both keep =
and a data frame for biomass =
provided simultaneously.
importFlowCAM()
now can deal with color FlowCAM images (but they are first converted into grayscale because background calibration images are recorded as grayscale by Visual Spreadsheet -at least, the tested version 3.2.3-, hence we cannot subtract the background of the vignettes in color mode)!
importFlowCAM()
now iterates a message to indicate progression of vignettes importation.
For importFlowCAM()
, the default value of the argument rgb.vigs =
is changed from TRUE
to FALSE
.
Functions to count cells in a particle (colony): cellCount()
and the corresponding cellCountGUI()
function for an access through the menu.
New utility function ecdCell()
to calculate the ECD for one cell in a colony.
Functions to build predictive models for cells in particles (colonies) after counting: cellModel()
.
Function to compute the number of cells in particles in a new sample: cellCompute()
.
Function to make zidb file for FlowCAM data through the menu: zidbMakeFlowCAMGUI()
.
Correct makeClass()
function in the menu (missing formula).
calcVars()
/calcVarsVIS()
and dropVars()
are reworked to use only FIT_xxx
variables in case of FlowCAM data (and to calculated many derived vars from there). This way, there is no need any more of a second image analysis in ImageJ.
A new UI for error correction using shiny.
importFlowCAM()
and readFlowCAMlst()
are reworked to create complete .zidb
files using all metadata from various version of Fluid Imaging's Visual Spreadsheet software.correctError()
has now a mode argument allowing to run the analysis in 'demo' and 'stat' mode, in addition to the default 'validation' mode
The internal errorCorrection()
function did not intialized ntrusted and nsuspect in 'demo' mode
New version of the user manual (explanations of the new functions).
errorCorrection()
in demo or stat mode. Corrected.Error correction functions added: correctError()
.
Plankton sorter interface to manual validation added.
New dependency on the digest package.
A new menu entry, Validate classification...
, is added for validation and error correction.
readFlowCAMlst()
can now read Visual Spreadsheet .lst
file format 017 where the name of the columns is explicitly provided in the header of the file.
zimDatMakeFlowCAM()
now uses readFlowCAMlst()
instead of the hidden function .lstRead()
to avoid duplicated code.
zidVerify()
now builds automatically the _dat1.zim
file from FlowCAM data if it is not there, but corresponding .lst
and .zim
files are found in the parent directory.
zidUncompress()
unzipped files in current directory, ignoring its path =
argument. Solved now.
zidUncompressAll()
now computes full names for .zid
files argument by default.
calcVarsVIS()
added. Specific function to calculate derived variables from FlowCAM's Visual Spreadsheet software.
Added the extraction of RGB vignettes when importing FlowCAM data.
dropVars()
: adding a few items, including 'Skew', 'Kurt' and 'Solidity' that produce NAs in ImageJ for multiple ROIs objects..GlobalEnv
is strictly restricted to GUI operations, and only following direct request by the end-user through an explicit dialog box. The internal function .assignGlobal()
is used for that purpose.getTrain()
was not able to collect data when attributes measured on samples mixed in training set differ slightly. Now, data are more carefully merged.
Meaningless FIT_xxx
attributes from the FlowCAM are now excluded by default in dropVars()
.
The GUI function vignettesClass()
, and thus, the corresponding menu entry were not implemented (the function prepareTest() that is called internally was working properly, but was not reacheable through the menu). Done now.
The GUI function analyzeClass()
and the corresponding menu entry listed old (version 2) items. The list is now updated with new plots available in zooimage 3 and mlearning 1.
All the java code (ImageJ + zooimage plugins) are now moved to zooimageJ.
This is a major refactoring of code from zooimage 1.x and 2.X. NEWS file now.
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