10th Birthday

Happy birthday!

Today marks 10 years since the first code was committed to the ADAMS repository (back then still stored in an in-house subversion repository)!

Back then, ADAMS wasn't yet a standalone project, but merely the common code base between a project for processing GC-MS data and one for processing NIR data. The GC-MS research project never really took off, but the NIR one (whic started off as an unofficial side-project) was successfully turned into a commercial application. The code-based for this offshoot project was migrated to ADAMS data structures again over the last few years and a new version for processing NIR data has been successfully launched this year at Eurofins Agro in the Netherlands and Ravensdown/ARL here in New Zealand.

Recently, we embarked on better integrating deeplearning frameworks, such as Keras. These frameworks can (in theory) now be used as a regular Weka classifier thanks to the Pyro4 library which we use for exchanging data. You only need to implement the Python side of things for parsing the data and making use of it (predictions and/or training). This opens up doors for models that work better on certain domains, like data fusion, and still being able to integrate them with all the functionality within ADAMS.

Exciting times ahead!

Flow editor

The Flow editor, the heart of ADAMS, goes back further than the initial commit, has seen a constant evolution of features and appearance. But one thing that has never changed: never uses explicit connections between operators (or actors in ADAMS terms). It is more of a graphic programming language than other workflow engines, with flow control, variables and internal data storage. You could say that it is Scratch for Data Scientists. It leaves out the nitty-gritty details of the underlying APIs involved and allows you to concentrate on rapidly developing machine learning and data processing applications, which you can then deploy as Linux daemons or Windows services.

Flow editor from the (internal) 0.2.0 release (June 2011)

This version only allowed a single flow to be edited and only offered the list of actors as side panel.

/galleries/floweditor/0.2.0.thumbnail.png

Flow editor from the 18.12.0 release (Dec 2018)

Much has happened since then, multiple open flows, various context-sensitive tabs, locating of variables and storage items, much improved context-sensitive menus and object editor.

/galleries/floweditor/18.12.0.thumbnail.png

Powerful tools

Over the years, ADAMS has added its own set of tools to better support the users in their tasks. Below are some of them:

Weka Investigator

The Weka Investigator is a much more powerful tool than the vanilla Weka Explorer. It allows you to manage multiple sessions in one interface and each session can manage multiple files and multiple tabs for the same operation (e.g., classification). It allows you to predefine various outputs for evaluations (rather than manually requesting them via popup menus) and you can also compare them side by side.

/galleries/screenshots/weka_investigator.thumbnail.png

Preview browser

The Preview browser allows you to browse a directory and quickly display file content with various handlers. Inspect Weka models? Check! Display annotations for images? Check! Many more file types are supported.

/galleries/screenshots/previewbrowser-default.thumbnail.png

Spreadsheet file viewer

A built-in spreadsheet application that can handle many different types of file formats (depending on modules): CSV, fixed tabular, Gnumeric, ODF, MS Excel, ...

/galleries/screenshots/spreadsheet_file_viewer.thumbnail.png

Spreadsheet processor

You are performing the same operation on several spreadsheets all the time? You might want to check out the Spreadsheet processor, which allows you to extract, transform and load spreadsheets of various types.

/galleries/screenshots/spreadsheet-processor.thumbnail.png

SQL Workbench

Need to work with databases then you can use the SQL Workbench to connect to (theoretically) any database via JDBC and retrieve data from it.

/galleries/screenshots/sqlworkbench.thumbnail.png

File commander

Need a file manager that can handle 10s of thousands of files and doesn't need minutes to display them (like the Windows File Explorer) but mere seconds? Need to copy things from/to remote servers? Then the File commander tool might be for you. It sports a two-panel layout with optional filtering, that was inspired by similar tools (Norton Commander, Midnight Commander, Double Commander).

/galleries/screenshots/filecommander.thumbnail.png

Spectrum Explorer

For exploring spectral like NIR (near infrared), MIR (mid infrared), XRF (x-ray fluorescence), you can use the Spectrum explorer. It allows you to explore and filter the data and also apply PLS or PCA.

/galleries/screenshots/spectrum_explorer.thumbnail.png

3-way Heatmap Viewer

For multi-dimensional spectra, like 3D fluorescence spectra, you can use the 3-way heatmap viewer.

/galleries/screenshots/3way_heatmap_viewer.thumbnail.png

Updates 2019/07/10

It is not about quantity in this update, but more about the importance of the changes.

After several weeks of incremental development and testing, I have pushed out changes regarding random split and cross-validation fold generation. To avoid duplication of code, I implemented a general framework for such operations, which is now utilized across the board (which also fixes some bugs).

Fixes

  • The transformers BaseName and DirName now handle placeholder abbreviations ("${...}") correctly.
  • adams-weka and adams-weka-lts: by moving to the generalized framework for random split and cross-validation fold generation, a number of bugs in aligning additional attributes to predictions have been fixed.

Changes

  • upgraded jshell-scripting to 0.1.0.
  • upgraded pdfbox to 2.0.16 to address https://nvd.nist.gov/vuln/detail/CVE-2019-0228
  • adams-ml: the file-based dataset preparation schemes for train test split and cross-validation now make use of the new generalized framework for such operations.
  • adams-weka and adams-weka-lts: the random split and cross-validation fold generators (both default and grouped) now make use of the new generalized framework for such operations.

Additions

  • adams-ml: added a generalized framework for random split and cross-validation fold generation, to be utilized in other data domains. Makes use of the work implemented for binning algorithms.

Updates 2019/07/03

Been spending a lot of time lately on sorting out Debian package generation for Maven projects. The .deb packages available for download now make it easier to install ADAMS on Debian systems (and derivatives like Ubuntu). This includes installing them inside Docker containers. The MySQL JDBC driver is back to the old version due to a problem introduce with 6.x (my bug report is linked below).

Fixes

  • adams-weka and adams-weka-lts: The number of threads defined in the JobRunner used for cross-validation in the Classify tab of the Weka Investigator is no longer getting ignored.
  • adams-rats: fixed a race condition in the FileLister rat input scheme when used inside a Cron one, which occurred when the Cron was triggering faster than the file listing was moving the files, resulting in multiple outputs.

Changes

  • reverted MySQL driver back to 5.1.42, due to driver listing columns from table from any database that the database user has access to - file a bug report with MySQL regarding this https://bugs.mysql.com/bug.php?id=95717
  • upgraded processoutput4j to 0.0.10
  • upgraded jclasslocator to 0.0.14
  • obsolete provenance support has been completely removed.
  • The new ListSelectionValueDefinition class, to be used with the EnterManyValues source, is targed at pre-defined lists with a pre-selected default value (rather than just using the first list item as the DefaultValueDefinition only offers).
  • The SequentialDirectory, as used by the Sequence control actor (and therefore by a lot of other actors internally) has seen speed improvements for large sequences that contain multiple disabled/skipped actors. Code for storing output from last active actor in such a sequence has been optimized as well. In some cases, this reduced the actor execution overheads by 20 percent. NB: these overheads may be trivial to the other operations executed in the sequence itself. In order for this to work properly, variable support has been disabled for the skip option of actors.
  • introduced lenient flag in AbstractDataContainerDbReader which only outputs warnings instead of generating errors when containers cannot be loaded from DB.
  • Class names (ADAMS and JDK ones) are now better hyperlinked in the GUI help frame.
  • adams-video: updated vljc dependency to 3.12.1 (VLC player works again on Linux Mint 19.1).

Additions

  • The ArrayBinning statistic applies selected binning algorithm/postprocessing.
  • added module adams-scripts-debian for generic scripts to be used in debian packages
  • adams-applications: after forking the abandoned debian-maven project (http://debian-maven.sf.net/ to https://github.com/fracpete/debian-maven-plugin) and reworking the code base extensively, support for generating .deb install packages for Debian was added. and Ubuntu, using deb:package maven target.
  • adams-meta: The CurrentFlow source outputs the flow itself, with optional expansion of variables using their current state. Useful when trying to store the state of a flow at a certain time or when auto-generating flows.
  • adams-spreadsheet:
    • With the MakeJFreeChartDataset transformer, you can generate datasets for JFreeChart plots or file writers.
    • The StorageJFreeChartDataset transformer allows you to add data series to an existing JFreeChart dataset in storage, e.g., when combining plots from multiple spreadsheets.

Updates 2019/05/24

A big push towards support for distributing jobs from anywhere within ADAMS that make use of the JobRunner interface has been happened in the last few weeks. Thanks to the new module offering RabbitMQ functionality (adams-rabbitmq, https://www.rabbitmq.com/), it is now possible to send jobs to a job queue on a RabbitMQ server and slave machines running flows for processing jobs can poll this job queue. Since the RabbitMQ server does not need to know about any slaves, it makes it easy for scaling up, by simply adding more slaves that pull jobs off the queue. Encrypting the communication via SSL/TLS is posible as well.

Furthermore, (experimental) SSL/TLS support is now available in the adams-rest module thanks to the new adams-security module.

And finally, it is now possible to monitor the memory consumption from within a flow and send out notifications (eg emails) in case the available free memory gets low over prolonged periods of time (MemoryMonitor standalone). This is something that background flows should make use of.

Fixes

  • Pasting a flow from the clipboard as new flow now works again. Now handles plain text nested format, command-line and nodes format.
  • Graphical flow components (like interactive actors such as SelectArraySubset) now work again when execute via the active flow functionality, but not being visible.
  • The JVisualVM menu item under Help (displayed in Developer user mode or higher) now checks whether the JVisualVM binary is actually present (no longer bundled with JDK after Java 8).
  • adams-weka and adams-weka-lts: ClassificationViaRegressionD classifuer now sets the class value to missing at prediction time before pushing through the filter, as MakeIndicator is taking the class value into account generating an exception if the value is invalid.

Changes

  • Upgraded jclasslocator dependency to 0.0.13
  • Upgraded java-utils dependency to 0.0.2
  • Upgraded MySQL JDBC driver to 8.0.16
  • Positions and sizes of the main tool frames are now recorded and restored.
  • The FindInFiles tool can search compressed files now as well (as long as the module adams-compress is present).
  • The SetMapValue now offers a built-in conversion for converting the value into the appropriate type, if necessary (eg string into integer).
  • The MemoryUsage source now also outputs init and max for heap and non-heap.
  • JMap and JDeps now support inline variables in the additional options parameter.
  • adams-rest:
    • experimental SSL/TLS support (only tested on self-signed certificates so far).
    • expanded all the missing sections in the manual.
  • adams-weka and adams-weka-lts:
    • The Weka Investigator now allows the definition of a JobRunner instead of #threads to allow for remote execution, eg via RabbitMQ. #threads can be configured within the LocalJobRunner (the default setting).

Additions

  • Javadoc for all classes is now available at: Javadoc
  • The FindInFile transformer allows to search for a text string in files, using the same functionality as the FindInFiles tool.
  • The ColorPerRegExpGroup meta-data color scheme, allows coloring based on a group string extracted from a label using a regular expression (eg parts of a sample ID).
  • Added enclose/pull up menu items in the GenericObjectEditor's popup menu for boolean conditions, conversions, spreadsheet row/column finders.
  • Added simple class hierarchy for sending notifications via SendNotification sink.
  • The MemoryMonitor standalone sends out a notification if the heap usage exceeds the specified threshold, making use of the new notification scheme class hierarchy.
  • Added support for generating heapdumps from within ADAMS, via main menu or through the HeapDump control actor.
  • The CollectionSubset transformer allows you to generate a subset collection, with only the elements from the specified indices.
  • Added a multi-page action to the Flow editor for comparing two flows with each other.
  • adams-meta: added actor for executing the actor passing through: ExecuteActor.
  • adams-security: new module for providing security related support, like SSL context.
  • adams-rabbitmq: new module for making use of the RabbitMQ message broker (https://www.rabbitmq.com/). Also includes a job runner for distributing jobs and actors for executing sub-flows remotely.
  • adams-rabbitmq-rats: new module for adding RabbitMQ consume/publish functionality to the RATS framework.
  • adams-weka and adams-weka-lts: Added enclose/pull up menu items in the GenericObjectEditor's popup menu for row/column finders working on Instances.
  • adams-spreadsheet: The Spreadsheet processor now has a Passthrough processor, if nothing needs to be done to the data and a Database target for storing the processed data back in a database table.

Updates 2019/04/30

Well, I didn't quite manage to get this post out the door before going on holiday over Easter. Collection handling is much improved in the flow, a new tool for handling spreadsheets, the Spreadsheet processor, has been added, a new merge transformer for spreadsheets added (SpreadSheetMethodMerge), and lots of little fixes and improvements.

Fixes

  • Added the -close-connection option to the DatabaseConnection standalone, which closes the connection one the flow wraps up. This is required for SQLite to release the database file properly. Otherwise ADAMS has to be restarted.
  • Errors and warnings that occur when processing the first line in the compact flow format are now being propagated properly, i.e., displayed in the user interface. External actors cano now report these errors again.
  • Pasting actors in the Flow editor now updates the display again to show the modified state.
  • The Debug execution listener in the flow now ensures that it is visible when a breakpoint is triggered.
  • The Find usages action from the Flow editor's popup menu now also finds nested variables and storage names. It also allows jumping to actors now that are in external flows, which don't have a root Flow actor and therefore miss a UI parent component context.
  • adams-imaging: The additionalObject option of the ImageObjectOverlap transformer now works when no label key was provided.
  • adams-spreadsheet: charts used by the Spreadsheet file viewer now plot all the data points with differing X/Y pairs, not just with differing X.
  • adams-weka and adams-weka-lts:
    • The Multi-Experimenter now handles the split generators correctly in the user interface, the train/test split experiment now works again, some minor user interface bugs fixed.
    • Hermione now stops the run if there are no optimization handlers defined, e.g., when loading invalid classnames.
    • In the Preprocess tab of the Weka Investigator, you can now filter the attribute names using the provided filter text field.

Changes

  • added flow_start_timestamp programmatic variable
  • upgraded RSyntaxTextArea dependency to 2.6.1
  • upgraded matrix-algorithms dependency to 0.0.15
  • removed the Quick edit tab in the Flow editor, due to strange lockups in the GenericObjectEditor.
  • The ReportHandler in the Preview browser now allows the report file reader to be configured, to display a wider range of report file formats.
  • adams-spreadsheet:
    • The DefaultXY JFreeChart dataset now allows X to be empty, uses row index for X in this case.
    • The SpreadSheetDisplay now accepts objects implementing the SpreadSheetSupporter interface as well.
  • adams-weka and adams-weka-lts:
    • The Instance tab in the Weka Investigator now allows the selection of an attribute to use for coloring instances (each unique value represents a color).
    • On the Preprocess tab in the Weka Investigator, you can now select the menu item Use selected as class from the split button of the attribute selection panel. Batch-filtering now only works if the datasets are actually compatible. The table listing the attribute names now also lists their types in a separate column.
    • Any GOE panel handling Weka classifiers now has an additional popup menu item called Enclose, which allows you to enclose the current classifier within a SingleClassifierEnhancer scheme (eg FilteredClassifier).
  • adams-heatmap:
    • The Heatmap class now implements SpreadSheetSupporter;
    • The HeatmapToSpreadSheet conversion now simply calls the toSpreadSheet() method.

Additions

  • Added the ProgrammaticTokenListener transformer for hooking into flow with non-flow code, allowing the listening to the data flowing through, e.g., for updating Swing user interface components.
  • Added the ArrayCovariance array statistic.
  • Added jshell-scripting dependency and JShell menu item (you need to switch to Developer mode). In order to execute a script it needs to be saved first.
  • Added ArrayToCollection transformer for turning an array into a collection.
  • Added CollectionAppend transformer to append a collection in storage with the one passing through.
  • Added CollectionProcess control actor for processing collections similar to ArrayProcess.
  • adams-imaging:
    • added the ColorProvider transformer which outputs a Color object whenever a token passes through.
    • added PngIsComplete file in use check scheme (looks for IEND end of file marker).
  • adams-spreadsheet:
    • The SpreadSheetMethodMerge transformer allows merging of spreadsheets via a class hierarchy of merge algorithms, similar to the SpreadSheetMerge transformer.
    • The Spreadsheet processor tool allows you to easily load spreadsheet data (file, database, clipboard), process it (query, flow) and output it (file, chart, clipboard). It also allows you to save configurations to easily re-use processing in certain scenarios.
  • adams-pdf: The PDFGenerate transformer allows PDF generation using specified generator scheme. Similar to PDFCreate, but depending on the generator, is not limited to processing files.
  • adams-heatmap: added conversions for computing correlation and covariance between columns of a spreadsheet: ColumnCorrelationToHeatmap and ColumnCovarianceToHeatmap.
  • adams-weka and adams-weka-lts:
    • The Classify tab of the Weka Investigator now has tree visualization output and GraphML output using the JGraphT library.
    • Added MSLE (mean squared logarithmic error) evaluation metric.
    • Added MSLE to Hermione as measure to be used for evaluation.
    • Added evaluation post-processors to remove worst predictions: RemoveWorst (using percentage), RemoveWorstStdDev (based on mean and stdev of actual class values).
  • adams-spectral-2dim-core:
    • added the DeleteDbSampleDataValue transformer for removing specific fields from the database for a sample ID.
    • added the SampleDataValueDbWriter transformer for writing specific sample data fields to the database.

Updates 2019/03/15

Fixed a bunch of little bugs and also worked on many minor improvements in the user interface.

A new Weka classifier got added: XGBoost, though currently only available for Linux/Mac.

The database backend within ADAMS has been further abstracted and now allows mirroring (ie replicating the queries on another server). Useful when trying to use a backup database server.

Fixes

  • Pasting of actors no longer generates long name suffixes consisting of (x) (y) (z) ...
  • EnterManyValues: date types now get inserted with their string representation into a map.
  • Histoy lists, like used in the Weka Investigator, now prompt the user when selecting Remove all from the popup menu, whether they really want to remove X entries.
  • The generates() method of the StringConstants source now outputs the class that the selected conversion generates (proper compatibility check).
  • The Close/cleanup and Remove graphical output actions in the Flow editor now close any Debug views as well.
  • Row plots in spreadsheet tables (eg Spreadsheet file viewer) no longer sub-sample points if the same number of points was selected.
  • Fixed incorrect path handling when placeholders present: Command, Exec, Java, SimpleStringReplace, StringInsert, StringReplace.
  • Command source now launches the commands again.
  • adams-python: fixed incorrect path handling when placeholders present: PipExec, PythonExec, PythonVenvExec.
  • adams-spreadsheet:
    • fixed incorrect path handling when placeholders present: SpreadSheetInsertColumn, SpreadSheetInsertRow, SpreadSheetReplaceCellValue.
    • entering multiple values through the GenericArrayEditor now works again in the Spreadsheet file viewer (Java decided to place the dialog behind all other windows).
  • adams-rats: fixed incorrect path handling when placeholders present: Exec (rat input and output).
  • adams-weka and adams-weka-lts: Row plots in instances tables (eg Weka Investigator) no longer sub-sample points if the same number of points was selected.

Changes

  • Changed the Compare actors menu item in the Flow editor's tree popup menu into a sub-menu with Just actors (original functionality) and Sub-flows (additional) as menu items.
  • Added support for unordered ranges: adams.core.UnorderedRange
  • External actor files are now being monitored and reloaded/reexpanded if necessary through the GenericObjectEditor.
  • The ArrayProcess control actor now has an optional variable for storing the index of the current element being processed (1-based index).
  • Added FILE_FORWARD_SLASHES variable type, which generates a filename with forward slashes. Affects transformers/standalones: SetVariable, SetManyVariables.
  • The Switch control now has a lenient option, which drops the requirement of the token having a payload (eg the Start source generates a null token, simply to kick off things).
  • Removed module adams-phmm4weka.
  • adams-spreadsheet:
    • Added support for unordered ranges: adams.data.spreadsheet.SpreadSheetUnorderedColumnRange
    • The SpreadSheetReorderColumns transformer now uses SpreadSheetUnorderedColumnRange for its order option.
    • The SpreadSheetJoinColumns conversion now uses SpreadSheetUnorderedColumnRange for its columns option, allowing for out-of-order joins.
    • Disabled Spreadsheet Explorer in the menu for the time being.
    • Added support for overlaying a diagonal in the scatter plot (via a second data series): enable addDiagonalSeries in the DefaultXY dataset. Affects JFreeChartPlot and JFreeChartFileWriter.
    • Added History button to the Query tab.
  • adams-weka and adams-weka-lts:
    • Added support for unordered attribute ranges: adams.data.weka.WekaUnorderedAttributeRange
    • The Weka Investigator now allows moving its tabs (like Preprocessing and Classify) via the Move tab to submenu in the tab's popup menu.
  • adams-spectral-2dim-core:
    • added ability to Update Sample data dialog to work off sample IDs obtained from a spreadsheet.
    • SpectrumT and SampleDataT are no longer directly accessed, but through facades, which allows swapping out of backend (e.g., introduce mirroring).
  • adams-rats:
    • The RatControl actor now has a Console button in the user interface, which allows the display of the last X lines that occurred in the console.
    • The type of log object generated from errors and sent to the log actor (if available) is now defined via the AbstractLogObjectGenerator class hierarchy.
  • adams-cntk-weka and adams-cntk-weka-lts: moved CNTKPyroProxy classifier from into new module adams-python-weka(-lts) and renamed it to PyroProxy, as it is framework-agnostic.
  • adams-pdf: The PDF Viewer switched from multi-tab layout to multi-page.

Additions

  • Added the DeleteVariable and DeleteStorageValue standalones.
  • Added the Configure option handler tool (developer mode) that allows configuring any option handler.
  • adams-weka and adams-weka-lts: i
    • added the GraphSource serialized object preview handler for weka.core.Drawable objects, which outputs the graph source code (dot or XML BIF).
    • added the GraphSource output for the Investigator's Classify/Cluster tabs, which outputs the graph source (dot or XML BIF) for weka.core.Drawable classifiers/clusterers.
    • added WekaDatasetsMerge transformer, an alternative to WekaInstancesMerge for merging multiple Weka Instances objects into one (side-by-side). This transformer can be selected in the Weka Investigator now as well for merging datasets (Preprocess panel, data table actions).
    • The XGBoost classifier got added (using https://github.com/dmlc/xgboost) - currently only for Linux/Mac.
    • The Weka Multi-Experimenter now has a table-based results panel as well.
  • adams-spectral-2dim-core:
    • added List Sample data dialog which lists all sample data for the selected spectra in a single table.
    • added Delete Sample data dialog which allows removal of specified sample data values from the selected spectra.
    • no longer storing Dummy report flag in sample data table.
  • adams-spreadsheet:
    • spreadsheet tables now allow sorting on multiple columns using via the Sort... menu item of the table's popup menu.
    • added query panel for meta-data to the SQL Workbench tool

Updates 2019/01/30

A lot of minor UI improvements and dependency refreshments happened since the release in December last year. New in the flow is EXIF tag support and communication with Python processes across the network using Pyro4 (Python Remote Object, https://github.com/irmen/Pyro4).

Fixes

  • Multi page panes are now showing border again when focused, to make it easier to see which widget has the focus.
  • The Preview browser did not maintain correctly its internal list of content handlers, resulting in apparently random preview handlers getting selected.
  • The SQL Workbench now disables the user interface while a query is being executed.
  • Chooser panels (eg for dates, files or colors) now change the font color to RED if the entered value is not in a valid format and will revert to the default value when opening the dialog via the ... button. The Use default menu item was added to allow the user to revert back to the default value.
  • EnterManyValues now shows the tool tip of the underlying component if there was no explicit help string entered.
  • The sources EnterValue, EnterManyValues, SelectDirectory and SelectFile now honor any information recovered from restoration files during non-interactive and/or headless operation.
  • adams-weka and adams-weka-lts: the transformers WekaFilter, WekaClassifying and WekaClustering are now threadsafe when using the internally used Weka object (previously, when using a shared model in storage in concurrent situations, it could end up in an unsuable state).
  • adams-net: upgraded tika-core to 1.20 due to https://nvd.nist.gov/vuln/detail/CVE-2018-17197
  • adams-ml: The CrossValidation scheme for preparing file-based datasets now generates correct leave-one-out datasets.
  • adams-groovy: Upgraded Groovy to 2.5.5 to make the Groovy Console work with Java versions 9 and later.
  • adams-video: fixed user interface issues in VLCjPlayer and Annotator

Changes

  • Retired the obsolete NamedSetup framework.
  • The Find in files tool now has all its operations in a button with a drop-down list, using a class hierarchy. New actions are: Copy to... and Move to.... The View... action now uses the Preview browser.
  • How graphical actors are being displays is now handled by a class hierarchy, replacing the displayInEditor option. The default scheme (appropriately named Default) just displaying it on top of all windows. With DisplayInEditor, the window gets displayed in Flow editor window. NoDisplay suppresses the display completely and Background displays behind all other windows. The ChangeDisplayType actor processor allows you to change the type(s) to a new one.
  • The menu item MakeInteractive of the Flow editor tree popup allows one to turn one or more SetVariable standalones into an interactive sub-flow (Trigger/EnterManyValues/MapToVariables).
  • The DefaultValueDefinition used by EnterManyValues now offers an option to output paths (file or directory) with forward slashes.
  • All value definitions, as used by EnterManyValues can be now disabled/enabled, which makes it easier to maintain testing/production ones side by side.
  • The LocalScopeTransformer and LocalScopeTrigger control actors now add the programmatic variables to their local scope when using EMPTY for variable propagation: flow_filename_long, flow_filename_short, flow_filename_restore, flow_dir, flow_id, is_headless, has_gui, project_name, project_home, project_modules
  • The JsonFileReader can now enforce output type (OBJECT or ARRAY) if know beforehand, default is ANY (no enforcement)
  • Added ability to flag a flow as active and manage that one through the Active menu and the buttons in the toolbar that have the little A in the bottom right corner. This is useful when editing external flows, as the switching back to the main flow is now no longer necessary.
  • The pause/resume and stop buttons are now also available through a debug flow perspective.
  • Removed the Run/Debug flow notification area actions.
  • adams-spreadsheet: the sinks JFreeChartFileWriter and JFreeChartPlot now allow the selection of shapes for the data point markers, the background color is now white (aligned with other ADAMS plots) and the plot color can be selected as well.
  • adams-weka and adams-weka-lts:
    • The WekaEvaluationSummary transformer now has options for custom titles for summary, confusion matrix and class details.
    • Updated Weka dependencies to 3.9.3-fork-0.0.4 and 3.9.0-fork-0.0.9 respectively (fixes duplicate output when using Logback or log4j; AbstractClassifier.forName no longer casts to AbstractClassifier, but Classifier).
  • adams-jython: upgraded Jython to 2.7.1b3.

Additions

  • adams-imaging:
    • added image reader/writer using the Apache Commons Imaging library, added preview handlers for images and meta-data using this library as well. This will eventually replace the Sanselan-based classes.
    • The ExifTagOperation transformer allows you to work on the EXIF data in files, e.g., read/write/remove fields or check for fields. The HasExifTag boolean condition checks whether the specified tag is present.
  • adams-python:
  • adams-maps: added GPSDistance conversion for computing distance (in meters) between two GPS points.

Updates 2018/12/20

Just a short list of updates, due to upcoming release. Main new feature is an SQL workbench for running SELECT, UPDATE, DELETE queries from within ADAMS.

Fixes

  • adams-rest: added missing Maven dependencies to make it work with Java 9+.

Changes

  • Added button to the control panel for debugging flows, to highlight the current actor in the editor window.
  • adams-weka: upgraded Weka dependency to 3.9.3-fork-0.0.3, fixes duplicate output in console for LogBack and log4j
  • adams-weka-lts: upgraded Weka dependency to 3.9.0-fork-0.0.8, fixes duplicate output in console for LogBack and log4j

Additions

  • adams-weka and adams-weka-lts: added menu item for Weka's SimpleCLI
  • adams-spreadsheet: added SQL Workbench for running SQL queries on SQL databases.

Updates 2018/12/07

A fair amount of work was going on in the Weka-related modules, with a new Compare tab getting introduced to the Weka Investigator and a number of new filters. The content handlers in the Preview browser can be customized now, provided they have customizable options.

Fixes

  • When swapping SetVariable transformer with standalone (and vice versa), the transfer for variable of variableValue now works. Also added transfer for expandValue, valueType properties.
  • String content on the clipboard is now only parsed in the Flow editor when performing an actual paste. This is to avoid lengthy wait times when switching between flows or generating popup menu when the clipboard content is large.
  • Pasting from clipboard in file or directory chooser panels now updates the history as well.
  • adams-rats: meta ratinput/output schemes now call the base initReception/Transmission methods; the Cron input scheme now installs the cronjob in the initReception method (to avoid race conditions), DeQueue configures queue in initReception, Socket sets up server socket in initReception, Subscribe configures subscription in initReception.
  • Updating a value using a field with a different data type as currently stored in a report didn't update the field itself, the old key was kept instead. Problematic when updating reference data for spectra, attempting to fix the data type of values.
  • adams-spreadsheet: fixed the quick info of the SpreadSheetAddRowID conversion.
  • adams-spectral-2dim-core: the Preview browser now handles simple spectrum files (.spec) again.
  • adams-weka and adams-weka-lts:
    • fixed setting of numZeroes in RemoveWithZeroes filter.
    • the WekaFileChooser now lists all loaders/savers again
  • adams-net: fixed generation of output file name in SFTPGet transformer.
  • adams-rats: bulk actions now only get applied to checked ones, not all; checking/unchecking RatControl panel now uncheckings the RatsControl panel.

Changes

  • NumericStringCompare, as used by the Sort transformer, now providers better error messages when regexp replacement fails.
  • Content handlers in the Preview browser can be customized now (only some offer cutomizable options)
  • The Flow editor now has an Actors help menu item, which brings up class help just for actors. Additional copy operations got movied into Copy... sub-menu to keep menu cleaner, also added the Copy acto name action to sub-menu.
  • adams-spreadsheet: The spreadsheet table now has menu items in the header popup menu for setting column width/widths manually.
  • adams-spectral-3way-core: added option to the SimpleEEMReader to denormalize the amplitudes using the stored normalization factor.
  • adams-python: PythonEnvironment now allows updating the PYTHONPATH environment variable (append, prepend, replace).
  • adams-imaging:
    • The Grid scheme of the SubImages BufferedImageTransformer algorithm now offers options for overlaps on x and y axis, to avoid cutting through objects of interest.
    • Renamed transformer ImageReader to ImageFileReader and sink ImageWriter to ImageFileWriter to make them consistent with other actors that read/write files.
  • adams-weka and adams-weka-lts:
    • added dataset-weights-weka-package 2015.6.16 dependency
    • SimpleArffLoader and SimpleArffSaver now handle instance weights
    • The Weka Investigator now has a popup menu on tabs (right-click) and also allows saving/loading of parameters of individual tabs. Data tab can display extra column with instance weights now. Closing tabs no longer prompts a dialog, as closing can be undone now (via Tab menu).

Additions

  • Added InList boolean condition for checking whether incoming string is in list of strings.
  • The CollectionToArray transformar turns any collection (eg java.util.List or java.util.Set) into an array.
  • The StorageCollectionInsert transformer updates a collection object in storage with the object(s) passing through.
  • The Find in files interface allows you to search for files in a directory that contain a certain search string. Search text can be either a simple string or a regular expression.
  • adams-ml: added the CrossValidation scheme to the file-based dataset generation for generating cross-validation folds.
  • adams-weka and adams-weka-lts:
    • The WeightsBasedResample filter (package weka.filters.unsupervised.instance) allows you to resample a dataset using its weights.
    • The AccumulatedLWLWeights filter (package weka.filters.unsupervised.instance) generates weights for dataset using LWL-based approach, accumulating them and normalizing them to [0;1].
    • The RemoveWithWeights filter (package weka.filters.unsupervised.instance) removes instances outside the specified range.
    • The new Compare tab in the Weka Investigator allows you to compare two datasets via a common ID attribute (string or nominal): lists common IDs and ones that are only in first or second dataset, visual comparison of internal numeric values in separate tab (mainly aimed at spectral data).
  • adams-imaging: added simple framework for generating negative regions (regions without annotations) using annotated images as input for automating negative region generation: NegativeRegions transformer and class hierarchy of schemes.