Changelog¶
All notable changes to this project will be documented in this file.
The format is based on Keep a Changelog and this project adheres to Semantic Versioning
3.0.0 - 2019-05-08¶
Added¶
Now ported to Python3.6+ (Python 2 is no longer supported!). Thereby also to fastr3.
Compatibility for Windows. Some small changes in functions, as some packages behaviour differently under Windows. Also, adjusted sink and source paths to use OS file separator.
Config is now also a sink.
Changed¶
PCE and DTI node removed, as they were not open source.
Pinfo file can now also be a csv. Txt is still supported.
Use fastr as default for hyperparameter search parallelization instead of Joblib, as this is much more flexible.
When the conffidence interval cannot be computed, just use the mean.
Fixed¶
WORC_config.py was not correctly copied in Windows due to incorrect path separation.
Source creation for the config was only for Linux.
In numpy 1.15>, booleans cannot be subtracted. Fixed an error due to this in segmentix by using bitwise_xor instead.
Bug when using masks, but not for all images, and segmentix.
Cardinality of classify node was incorrect.
2.1.3 - 2019-04-08¶
Changed¶
PREDICT was updated, so had to update the requirements. Changed it to a minimum of PREDICT to prevent these issues in the future.
2.1.2 - 2019-04-02¶
Added¶
Dummy workflow in segmentix and calcfeatures PREDICT tools.
Added several new PREDICT parameters.
Slicer tool.
Changed¶
Memory for elastix tool is now larger.
Fixed¶
-Evaluate framework now correctly adopts the name you give it.
2.1.1 - 2019-02-15¶
Added¶
Several new PREDICT variables to the config.
Multilabel classification workflow.
New oversampling strategy.
RankedSVM multilabel classification and Relief feature selection.
Changed¶
Major reduction in memory usage, especially due to PREDICT updates.
Only use first configuration in the classify config.
Outputs are now in multiple subfolders instead of one big folder.
Fixed¶
Minor bug in test workflow: needed str of label in appending to classify.
There was a bug in using a .ini file as a config.
2.1.0 - 2018-08-09¶
Added¶
Feature imputation settings in WORC config.
PCA settings in WORC config.
Dummy file, which can generally be accepted by WORC.
Preprocessing is now a separate node before the calcfeatures node.
Started working on a RTStructReader tool.
Added EditElastixTransformFile node to set FinalBSplineInterpolationOrder to 0 in Elastix. Neccesary for transforming segmentations.
Registred image is also saved as a sink.
Tex, Zip and PNG Datatypes
Plot ROC tool for PREDICT
Plot SVM tool for PREDICT
Plot Barchart tool for PREDICT
Plot Ranked Scores tool for PREDICT
Plot statistical test tool for PREDICT
Tools: Evaluation network. Can currently be run only serparately: future work includes the optional addition of the Evaluate network to the WORC network.
Settings for PREDICT General, which contains the joblib Parallel settings and whether a temporary save will be made after each cross validation.
Changed¶
Separate sinks for the output segmentations of the elastix and segmentix nodes.
Switched from using PXCastConvert to WORCCastConvert, hence ITK is not anymore required as well as ITK tools.
Fixed¶
Patientclass ID was used for both test and training. Now given separate names.
When elastix is used but segmentix isn’t, there was a bug.
DataFile dataype is now a TypeGroup instead of an URLType.
Last transformation output from elastix is passed further to the network.
Set FinalBSplineInterpolationOrder to 0 before transforming segmentation with transformix.
Bug: when giving multiple feature sources, only the first was used.
2.0.0 - 2018-02-13¶
Added¶
Elastix and transformix as separate workflow in the tools folder. Can be used through the WORC.Tools attribute.
Example data for elastix and transformix tool.
Workflow for separate training and testing set
FASTR tool for applying ttest to all features. Works similar to the trainclassifier tool in terms of inputs and outputs.
Changed¶
Option for multiple modalities. Supports infinitely many inputs per object.
Moved many PREDICT parameters to the configuration file.
When using a multimodal workflow with only a single segmentation, Elastix will automatically be used for registration. Note that you have to put the reference segmentation on the first modality!
Fixed¶
Proper combining of features from multiple modalities to classify tool.
Minor bugs in segmentix tool.
For multiple modalities, add only optional sources like metadata when present.
1.0.0rc1 - 2017-05-08¶
First release