v1.1.1

Feature changes

• Correct error in formula for Compactness1. N.B. Baseline updated! #218
• Remove feature Roundness, as this feature is identical to feature sphericity, but uses different implementation for surface area calculation (all implemented in SimpleITK) #218

Documentation

Restructure documentation #216

• Split package documentation into "Pipeline Modules" (all non-feature-class modules) and "Feature Definitions" (feature class modules)
• Add developers section with documentation on how to implement new filters, feature and feature classes.
• Add FAQ section with some trouble shooting tips
• Rename some GLSZM features, this is to make them more consistent with GLRLM features, which are similar, but calculated on a different matrix
• Add documentation for Elongation and Flatness
• Document mathematical correlation between various Shape features.
• The version specific documentation is available here.

Bugfixes

• Add some missing python 3 compatibility lines to the supporting script addClassToBaseline and command line script pyradiomicsbatch #210 #214
• Fix bug when loading image as file path and mask as SimpleITK object. #211
• Add sphinx_rtd_theme to requirements (needed to build documentation). #222
• Change location of parameter schema files. These files are otherwise not included in the wheel distribution. #221

Enhancements

• Update logging with more extensive debug logging and more informative info log messages. #220
• Replace parameter verbose with output printing implemented in logging. Control verbosity level to output (stderr) by calling radiomics.setVerbosity(level), where level determines the verbosity level (as defined in python logging). This prints out the requested levels of the log messaging, where process reports with parameter verbose are now classified as INFO-level messages (i.e. specify INFO or DEBUG to enable these). N.B. parameter verbose is not longer supported and will throw an error if passed in the parameter file #220
• Add feature class and input image type checks in featureextractor when changing these settings. #213
• Remove usage of eval (replaced by implementations of getattr), this is a more secure approach. #216
• Change handling of cases where max(X) mod binwidth = 0 during image discretization. These used to be assigned to topmost bin, but this produces unexpected behaviour (i.e. in range 1, 2, 3, 4, 5 with binwidth 1, value 5 would be discretized to 4 in stead of 5). Value now assigned is topmost bin + 1 (in concordance with default behavior of numpy.digitize) #219
• Add forced 2D extraction (as alternative to resampling for handling anisotropy in voxels spacing) #215
• Enable specification of distances between neighbors for texture matrices. #215
• Change default value for voxelArrayShift (from 2000 to 0), this is to prevent unknowingly using a too large shift when not necessary. Document effect of this parameter in the first order formulas affected. #219

Style

• Remove unused variable (self.provenance_on in featureextractor, this value is now replaced by a customizable setting)
• Define default settings in featureextractor in a separate function. This is to ensure consistency in applied default settings, as well as make them easily available outside of featureextractor #224 216
• Update reference in documentation. #224