ZooImage1, Change log: ---------------------- version 1.2-1: -------------- - Partial size spectra bars (red bars on the graph) are now only displayed when the value is higher than zero (previously, small red dots were displayed and it was difficult to differentiate low values from missing data on the graph). - The program now prompts for a conversion (biomass calculation) file. One can use the default file, or select another one during processing of the samples. Conversion file must be named as: [xxxx_]Conversion.txt, with the content in the square bracket optional (for instance, ZooplanktonNorthSea_Conversion.txt) The default file is 'Conversion.txt', located in the /bin/R/R-2.4.1/library/ zooimage/etc subdirectory of the Zoo/PhytoImage installation directory. - When a process using ImageMagick is required, Zoo/PhytoImage now check if it is correctly installed, and prompt for (re)installing it otherwise. - In the 'Macrophoto Gray16' ImageJ plugin, the diameter of the rolling ball is now 250, as it is for 'Scan Gray16' (was 50, a too small value). - Bug correction: at first use, if keys were not defined yet in the registry under Windows, the program failed to start - Bug correction: images in Scan16G-example were incorrectly placed in the _raw subdirectory during importation of the data - Bug correction: the directories were not always cleaned after image processing (the original data are placed in the _raw subdirectory) and only .zid files should remain in the original directory. - Bug correction: when trying to plot a graph of a variable that does not contain any data, the program exited with a cryptic error message. Now, the graph is drawn, with the indication "No data!" in the middle version 1.2-0: -------------- - ImageJ is updated to version 1.38r. - A new version of FIT-IMS is provided, and FIT-VIS (for importing data coming from the VisualSpreadsheet program) is now provided too. - PlanktonJ, a separate open source program to visualize, manually measure and classify plankton image in the same format as used by Zoo/PhytoImage is now added. Start ImageJ and go to Plugins -> PlanktonJ menu - The metaeditor (SC1.exe) is updated to version 1.73. - Vuescan is upgraded to version 8.4.23. - Many R packages are updated to their current version as on CRAN on 2007-05-25. - Biomasses are now computed from the file 'Conversion.txt' in the \etc subdir of the zooimage R package (see the manual). A special entry '_other_' is used to specify conversion formula for all groups that are not otherwise explicitly specified in the table. - Zoo/PhytoImage now optionally exports also identification and contribution to the biomass for each particle in the sample (files _Bio.txt) during sample processing. - Bug correction: If the default directory is deleted between two sessions, Zoo/PhytoImage was unable to start and issued an error. - Bug correction: When loading a ZIClass object, the required package(s) were not loaded automatically. Consequently, the predict method did not work well. Now, the corresponding package is loaded in memory as soon as predict is called. version 1.1-0: -------------- - A new function, RawConvert() is now available to convert RAW images files into TIFF images - Several bugs are corrected for the conversion of RAW images to tif, including in the elimination of the blank field. - A bug is corrected in the FIT-IMS plugin (FlowCAM ImageJ plugin): the label of objects was incorrectly assigned label + item value. - The default directory is now saved between sessions and it is moved to the Options menu, the choice of the decimal separator is also moved to the Options menu. - There is now an option to specify decimal separator used for input/output (. or ,). It is applied for all files (.zim, .zis, output tables, etc.). The option is saved between sessions - ImageJ upgraded to version 1.38j (memory leak with some plugins in version 1.37). - Clean up of the working directory and moving zim files to raw directory after successful building of .zid files - Option to build .zid files without vignettes - R upgraded to version 2.4.1. - ImageJ processes reworked to take [Calibration] data into account - Examples are not distributed any more with the program. They are in separate files (one for each sample) version 1.0-0beta3: ------------------- - Further bug corrections in the FIT IMS plugin. version 1.0-0beta2: ------------------- - The FIT IMS plugin is updated to a new version with correction of some bugs. version 1.0-0beta1: ------------------- - A big jump in version number for a small number of improvements. It is indeed a feature freeze version (meaning we will make further changes in version 1.x-x compatible with this one). It is important for developers to make sure that the software will not change radically from one version to the other (well, at least in the version 1.x-x familly). This feature freeze was planned for November 2006 at the ZooImage meeting held in San Sebastian in November 2005. So, one year has elapsed between version 0.3-1 and this one... enough time for developers to make comments and suggestions. So now is time to freeze its features! - ImageJ is upgraded to version 1.37v. - R is upgraded to version 2.4.0 and additional packages are updated with latest versions available on CRAN at 28 November 2006. - XnView is upgraded to version 1.82.4. - SciTe is upgraded to version 1.71. - Vuescan is upgraded to version 8.3.82. - DeepBurner is upgraded to version 1.8.0.224. - Filzip is upgraded to version 3.06. - Color24bits 600dpi plugin and example set are renammed, respectively, 'Scanner Color' and 'ScannerColor' - Gray16bits 2400dpi is renammed 'Scanner Gray16'. - Gray16bits digicam is renammed 'Macrophoto Gray16'. - Color24bits Microscope is renammed 'Microscope Color'. - All plugins (in ZooImage and PhytoImage subdirectories) are collected together in the ZooPhytoImage subdirectory of ImageJ/Plugins. - A new plugin is provided in ImageJ/FIT/Fit IMS to process FlowCAM images, thanks to the Bigelow Lab team (especially, M. Sieracki and B. Tupper). - ZooImageManual.pdf and PhytoImageManual.pdf are edited to reflect changes introduced in this version. version 0.4-0: -------------- - ZooImage is now 'skinnable'. For instance, the phytoimage R package transforms it into PhytoImage! - New plugins for analysis of digical and digital reflex cameras are added in the Plugins -> ZooImage/PhytoImage menus of ImageJ - There is now a mechanism to add extensions (with .zie files). Currently, an importation extension (Import_*.zie) is supported. It allows importing images and creating associated metafiles (*.zim) automatically, by processing the .zie file. - Another method to import images and metadata is also added. It takes a table (Excel file, for instance) and a .zie template, and it make the whole image importation, using these information. - A better process of RAW digicam and digital reflex camera images is now provided, using dc_raw.exe. - A PhytoImage-example dataset is included. - R is updated to version 2.3.1, and many additional R package have been added or upgraded (R is up-to-date with CRAN on 2006-07-20). - Scite (\bin\MetaEditor\Sc1.exe) is update to version 1.70. - ImageJ is upgraded to version 1.35i (version compatible with ZooProcess). - DcRaw 8.05 and ppmtopgm from the NetPBM library (free software) in .\bin\RAW for converting digital camera's raw files. version 0.3-3: -------------- - Scite (\bin\MetaEditor\Sc1.exe) is updated to version 1.67. - Vuescan is updated from 8.1.26 to 8.3.23. - XnView updated from 1.80.1 to 1.80.3. - R updated from 2.2.0 to 2.2.1, and many additional packages are also updated. version 0.3-2: -------------- This is the first prerelease of ZooImage1 made available on the zooimage web site (http://www.sciviews.org/zooimage). - There is an experimental FlowCAM images import filter (files must be zipped with a .zfc extension). There is no ImageJ specific process plugin yet (but it will be available in the next version). - There is now a first version of the user's manual... but you have to look at http://zooimage.sciviews.org/wiki (it is not compiled into PDF yet). - Attribution of names for objects ZIClass (a manual training set) and ZITrain (a classifier) is not logical. The two names are now inverted (ZITrain for the manual training set & ZIClass for the classifier). WARNING: if you saved such objects in version 0.3-1, they are now not compatible any more with this and all future versions of ZooImage. Do recreate all your objects with this version! - print.ZITrain is reworked: 4 significant digits in the output and error rate per class is now sorted in increasing order. - confu.map() now draws the confusion map in the same orientation as it is printed on the R console. - progress() is renamed Progress() to avoid confusion with the corresponding function in svMisc package. - setwd() is renamed Setwd() to avoid confusion with the equivalent base R function. - A bug in ZIClass() function is corrected: sometimes the calc.vars() function was not found. - get.ZITrain() returned either a correct ZITrain object, or an old and uncompatible one, depending on the presence of .RData in the training set root dir. So, no error was issued if the old object was create, but it was unusable. Now, explicit error and warning messages are issued and a valid ZITrain object is always returned. - The installer is reworked. Secondary apps are now in \Apps and \Apps\More... subdirectories. The initial working dir of the ImageJ plugin was incorrect and caused an error when started from its icon. Filzip was not correctly associated with .zid files. This bug is also corrected now. - A bug prevented correct update of statusbar text and progression bar in the ZooImage1 assistant when a long process was running. This bug is now corrected and the progression status is now reported correctly both in the R Console and in the ZooImage1 assistant (so, user that minimize either of these windows now still gets feedback about long running processes). version 0.3-1: -------------- First public release. Made available at the ZooImage meeeting, 1-3 November, San Sebastian, Spain.