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Timeline

Below is a simplified timeline of DICOMautomaton development, broken down by month.

Note: this list is periodically updated and is likely to be out-of-date!

202206

  • CI: added custom gitlab runner tags.
  • CI: add wait-and-retry when dealing with (most) package managers.
  • ExportFITSImages: notify user how many images are being exported.
  • FITS: support full metadata encoding. FITS images are now an option for lossless image transfer.
  • FITS: upgrade support from single-image to multi-image for both reader/writer.
  • WIP documentation for forthcoming network protocol.

202205

  • Add operation for decomposing images using SVD (i.e., 'eigenfaces').
  • Add TabulateImageMetadata operation.
  • SDL_Viewer: contours: garbage-collect entries for removed ROIs.
  • SDL_Viewer: support hot-keys (open, quit, help).

202204

  • Add grid-like test meshes to test simplification.
  • Address operation parameter compiler warning (unused parameters).
  • Always expose SimplifySurfaceMeshes and QueryUserInteractively operations.
  • AppImage: proceed if git commit hash not available.
  • CMakeLists: enable optimization for memory-constrained builds.
  • ConvertContoursToMeshes: add convex hull method.
  • QueryUserInteractively: include header.
  • ReduceNeighbourhood: add geometric mean reduction method.
  • SDL_Viewer: address minor compiler warnings.
  • SDL_Viewer: add tooltip 'advertising' drag-and-drop.
  • SDL_Viewer: support file drag-and-drop loading.
  • SimplifySurfaceMeshes: add Ygor 'flat' mesh simplification method.
  • SimplifySurfaceMeshes: disregard option for disengaged functionality.
  • SimplifySurfaceMeshes: expose Ygor MinAlignAngle threshold criteria.
  • SimplifySurfaceMeshes: fix documentation layout typo.
  • Workaround for git CVE-2022-24765 on Arch.

202203

  • Added Time and Sleep operations.
  • Added file selector helper script.
  • Add libnotify as optional (runtime) dependency.
  • Add transform file reader and expand writer.
  • AnalyzePicketFence: consolidate CSV output files.
  • Bug fix: replace numeric_limits::min --> lowest.
  • check_syntax: auto-enable Eigen, if available.
  • DICOM image loading: provide better message if rows/columns data missing.
  • DICOM metadata: add optional pixel extrema.
  • DICOM reader: add optional metadata.
  • DICOM: support multi-frame images.
  • Ensure alignment classes can be in-place constructed from a stream.
  • ExportWarps: ensure file has consistent extension.
  • Expose Orthogonal Procrustes (SVD) point set alignment.
  • ModelIVIM: replace placeholder image metadata.
  • OrderImages: ensure the default variant is provided.
  • OrderImages: support stable image array sorting.
  • OrthogonalProcrustes: confirm solution validity.
  • OrthogonalProcrustes: disable use of SVDBase.
  • OrthogonalProcrustes: parametrize mirroring and isotropic scaling.
  • Pixel mapping: clamp rescale for good measure.
  • Pixel mapping: protect against degenerate cases.
  • ReduceNeighbourhood: label neighbourhood arg examples as exhaustive.
  • Re-introduce previous resample-less WarpImages.
  • Rename 'TPlan' to 'RTPlan' for clarity.
  • RTIMAGE: explicitly apply top-level LUT.
  • Script: add img sort after partitioning.
  • SDL_Viewer: image feature matching: default to SVD-based solver.
  • SDL_Viewer: image feature matching: visualize transformed points.
  • SDL_Viewer: implement manual image feature selector.
  • SDL_Viewer: loading bar: decouple wave speed from frame rate.
  • SDL_Viewer: meshes: expose yaw, pitch, and roll angles.
  • SDL_Viewer: plot viewer: display ordinate and abscissa, if available.
  • SDL_Viewer: show loading animation.
  • SDL_Viewer: shrink script editor button width.
  • SDL_Viewer: speed up loading bar wave speed.
  • Surface_Meshes: add missing CGAL header.
  • Time: explicitly include stringstream header.
  • WarpImages: support resampling warped images.

202202

  • Add AnyOf/FirstOf/AllOf/NoneOf operations or aliases.
  • Added Eigen support to syntax checking script.
  • Add Ignore operation.
  • Add NotifyUser operation.
  • Add ValidateTPlan example script.
  • Dispatcher: lengthen pause time for error messages on Windows.
  • Documentation: remove duplicated DICOM RT warnings.
  • Harmonize control flow meta-operations.
  • ModelIVIM: add example script.
  • ModelIVIM: fix bi-exp model matrix coeff access bug.
  • ModelIVIM: rewrite script filtering steps.
  • Notifications: powershell: switch to blocking notifications.
  • NotifyUser: assume powershell is always available.
  • PFD: increase result buffer.
  • README: update Zenodo DOI for previous release
  • SDL_Viewer: add rudimentary RTPLAN viewer.
  • SDL_Viewer: avoid drawing scale bar when changing colour map.
  • SDL_Viewer: avoid RTPLAN metadata window overlap.
  • SDL_Viewer: contouring: standardize contour metadata.
  • SDL_Viewer: default to wider table view.
  • SDL_Viewer: explicitly check coordinate map validity.
  • Tray_Notification: re-order powershell commands.
  • Valgrind and TSAN bug fixes.
  • ValidateTPlan: add is_VMAT and collimator angle degeneracy checks.
  • ValidateTPlan: add minimum jaw-defined field size check.

202201

  • Add support for RTPLAN-based grouping.
  • Add WIP TPlan checking operation.
  • DroverDebug: provide more granular control over verbosity.
  • ForEachDistinct: make N/A partition accessible.
  • Partitioning: support partitioning tables.
  • SDL_Viewer: account for viewer aspect ratio.
  • SDL_Viewer: add keyword-based cell highlighting for tables.
  • SDL_Viewer: add minimal keyboard positioning for meshes.
  • SDL_Viewer: add toggleable face smoothing.
  • SDL_Viewer: flip vertical screen axis.
  • SDL_Viewer: force deprecation of pre-3.0 OpenGL functionality.
  • SDL_Viewer: more aggressively strip chars from GLSL version string.
  • SDL_Viewer: OpenGL: switch to shader-based rendering.

202112

  • Add basic table operations (Delete, Copy, Generate).
  • Added constructive solid geometry functionality using signed distance functions (CSG-SDF).
  • Add ExportTables operation.
  • Add MakeMeshes example script.
  • Add minimal 'table' class.
  • AnalyzeHistograms: use OS-dependent tmp dir.
  • CSG: add poly chain shape.
  • CSG-SDF: add 2D->3D extrusion operation.
  • CSG-SDF: add extrusion example.
  • CSG: SDF: add rotations and more Boolean ops.
  • CSG-SDF: add text primitive.
  • CSG: SDFs: add chamfer Boolean variants.
  • CSG-SDF: support asymmetric SDFs.
  • Expand CSG-SDF operation examples.
  • Move README content to wiki.
  • parse_functions: added nested function support.
  • Remove non-critical FUNCERRs in operations.
  • SDL_Viewer: always ensure mesh number is valid.
  • SDL_Viewer: enable mesh metadata viewer.
  • SDL_Viewer: fix table expansion ID issue.
  • SDL_Viewer: force reload of OpenGL meshes after script execution
  • SDL_Viewer: integrate table and table metadata editor
  • Surface_Meshes: support marching cubes with oracle functor.
  • Tables: implement CSV write.

202111

  • Added a position-based image sorter.
  • Added a position-based image sorter.
  • Added de-EQD2 standard script.
  • Added ModifyParameters operation.
  • Add LoadFilesInteractively, which uses recently-added dialog functionality.
  • Add QueryUserInteractively operation.
  • Add read support for (proprietary) XIM format images.
  • Always prospectively rebuild Ygor on Debian.
  • Avoid std::filesystem::absolute on Windows.
  • CMake: replace large macro (stringified standard scripts) with generated file.
  • ConvertContoursToMeshes: expose marching-cubes extractor.
  • Dialogs: disable prospective pfd::kill().
  • Dialogs: try to accept more Windows-like systems.
  • ExtractRadiomicFeatures: use DCMA marching cubes for speed-up.
  • FITS images: imbue minimal DICOM metadata in images.
  • OrderImages: add spatial ordering option.
  • OrderImages: add spatial ordering option.
  • PFD: remove OS version check, which seemingly fails for no discernable reason?
  • Replace large macro with generated file.
  • Scripts: support quotation escapes.
  • SDL_Viewer: add native dialog support via PFD.
  • SDL_Viewer: disable optional parameters in stringified scripts.
  • SDL_Viewer: handle empty metadata tags.
  • SDL_Viewer: isolate dialogs into separate library.
  • SDL_Viewer: limit default script open dialog to script extensions.
  • SDL_Viewer: rely on select_files defaults.
  • SDL_Viewer: simplify file loading.
  • SDL_Viewer: simplify script optional parameters.
  • Standard_Scripts: generator: disable verbose mode
  • Windows: delay for longer when terminating abnormally.
  • Windows: provide a new icon.

202110

  • Add ConvertWarpToMeshes operation.
  • Add MingW-specific winsock libs for Asio/Boost.
  • Added ConvertImageToWarp to pair with ConvertWarpToImage.
  • CI: GitHub: add aarch64 and x86_64 static builds.
  • ConvertWarpToMeshes: provide means to disregard rigid component.
  • ConvertWarpTo*: inject user-provided metadata.
  • De-CGALify marching cubes implementation.
  • Explicitly link imebrashim.
  • Fallback to previous wstring offload when needed.
  • Imbue converted warps with DICOM-style metadata.
  • Imebra_Shim: def reg reading: swap spatial dimensions.
  • Img Reg: add an example of accessing images and voxels.
  • Img Reg: added placeholder write_to and apply_to functions.
  • Img Reg: support reading whole directories of FITS files.
  • Musl: Fallback to an identity conversion if iconv does not support required conversion.
  • Properly differentiate fv_surface_mesh and Polyhedron meshes.
  • Documented current state of GUI intefaces via screenshots in GitHub issue.
  • Roughed in field-based deformations.
  • SDL_Viewer: add 3D Gaussian brush.
  • SDL_Viewer: add custom mesh colouring with alpha support.
  • SDL_Viewer: add image auto-advance.
  • SDL_Viewer: add rudimentary lighting for meshes.
  • SDL_Viewer: cleanup OpenGL textures when re-assigning.
  • SDL_Viewer: encapsulate mesh loading and rendering in a class.
  • SDL_Viewer: fix clipping bug.
  • SDL_Viewer: honour minimizing the script window.
  • SDL_Viewer: maintain aspect ratio in model space.
  • SDL_Viewer: normalize soft brushes and add tanh{2D,3D}.
  • SDL_Viewer: release OpenGL resources while context valid.
  • SDL_Viewer: simplify placeholder script.
  • SDL_Viewer: support light mode.
  • SDL_Viewer: support mesh selection, rotation, and precession.
  • SDL_Viewer: tighten range for tanh brushes.
  • SDL_Viewer: embed raw opengl mesh in imgui window.
  • Script: list exhaustive arguments in debug feedback.
  • Scripts: map parent directory to category.
  • Split point cloud and image registration working directories.
  • Surface_Meshes: accelerate marching cubes.
  • Surface_Meshes: face re-orientation: allow unorientable faces.
  • Surface_Meshes: implement orientation normalizer.
  • Surface_Meshes: marching cubes: track per-component orientation.
  • Surface_Meshes: use a faster vertex de-duplication method.
  • Swap long int --> int64_t to appease mingw64 ygor linking issue (and some arm archs).
  • Support reading and visualizing deformation fields.
  • Add minimal Affine registration DICOM read support.
  • deformation_field: conceal a spatial index.
  • deformation_field: implement basic apply_to().

202109

  • Add 'standard' scripts.
  • Add an operation to add noise to an image array.
  • Add script to build statically-linked DCMA binaries.
  • Added extremely minimal terminal-based image viewer.
  • Address upstream Boost bind placeholder de-escalation.
  • AppImage: manually set rpath for binaries.
  • Arm: also avoid clobbering user-provided mcpu and mtune.
  • Arm: avoid clobbering user-provided march flag.
  • CI: GitHub: WIP: add armv7 static build + test.
  • CI: github: be more forceful with artifact sync.
  • Common_Plotting: when forking, use std::exit() rather than std::quick_exit().
  • Cross compiling: more clearly state which configurations work.
  • Cross compiling: remove BUILD_SHARED_LIBS="ON" override.
  • Cross-compiling: more tinkering to get armv8 to cross-compile with zig-cc or musl toolchain.
  • DCMA: check that CWD is valid, else make it valid.
  • DICOM loader: warn when modality cannot be assessed.
  • Dispatcher: load command-line script operations before command-line operations.
  • Docker: Alpine: add X and OpenGL-related packages.
  • Docker: Alpine: add aarch64 and x86_64 build_bases.
  • Docker: Alpine: add builders to complement build_bases.
  • Docker: Alpine: add note wrt mesa/OpenGL support.
  • Docker: Alpine: avoid failing if unable to delete directory.
  • Docker: Alpine: fix arm64 --> amd64 typo.
  • Docker: Alpine: follow MXE build_base and defer building DCMA.
  • Docker: Alpine: make use of GSL and Eigen.
  • Docker: CI: ensure patchelf is available.
  • Docker: add Alpine armv7 container build_base.
  • GenerateSyntheticImages: provide UIDs that parse correctly.
  • Metadata: bug fix: to_seconds() string replacement.
  • Metadata: generalize metadata evaluation and macro replacement.
  • Metadata: implement WIP DICOM module-based metadata coalescers.
  • Metadata: provide helper for key-value modifying operations.
  • NormalizePixels: add PET SUVbw normalization.
  • Remove vestigial getopts.h include.
  • Scripts: bundle scripts during builds.
  • SDL_Viewer: WIP: support modifying image pixels.
  • SDL_Viewer: add 2D median filter brushes.
  • SDL_Viewer: add 3D median brushes.
  • SDL_Viewer: contouring: handle case with multiple overlapping images.
  • SDL_Viewer: display contour metadata as a tooltip.
  • SDL_Viewer: drawing: added full complement of 2D and 3D rigid/mean/median brushes.
  • SDL_Viewer: hoist image drawing from contouring.
  • SDL_Viewer: improve metadata handling for line samples.
  • SDL_Viewer: proactively set LIBGL_ALWAYS_SOFTWARE=1 within AppImages.
  • SDL_Viewer: provide a way to directly run scripts as actions.
  • SDL_Viewer: use bounding box to speed drawing.
  • SDL_Viewer: use imgui table for image metadata viewer.
  • Terminal_Viewer: add bare-bones shade glyphs display option.
  • Terminal_Viewer: add displays for non-ansi, non-unicode terminals.
  • Terminal_Viewer: allow user to override display settings.
  • Terminal_Viewer: disable use of terminal control codes for completely portable display option.

202108

  • ModifyImageMetadata: support macro expansion and time extraction.
  • GroupImages: add note about de-grouping.
  • Address LGTM static analysis concerns.
  • SYCL: switch to triSYCL.
  • Operations: separate Drover updates from return/exit.
  • Support loading scripts from files.
  • Add control flow meta-operations for programming scripts.
  • Provide conditional (if-then-else) control flow meta-operation.
  • Debian: continue with buster (now oldstable) for now.
  • Documentation: do not clobber inline paragraphs.
  • Regex_selectors: add compliment to 'numerous': 'fewest'.
  • Regex_Selectors: add undocumented image selector (numerous).
  • GroupImages: provide automated partition key selection.
  • ModelIVIM: support Siemens CSA b-values
  • Imebra_Shim: switch pixel extraction to metadata.
  • Imebra_Shim: added ad-hoc support Siemens private DICOM tag 'CSA2' binary blob decoding.
  • Dispatcher: default to SDL_Viewer.
  • Dispatcher: added workaround for AppImageKit chdir() call.
  • Replace boost::filesystem with std::filesystem.
  • check_syntax: document libraries needed for linkage.
  • File_Loader: verbosely report unloadable files.
  • File_Loader: attempt to resolve relative paths.
  • File_Loader: add a few more short-circuit extensions.
  • File_Loader: only FUNCINFO notice when loader is invoked.
  • Load_Files: bug fix: let user override extension filtering.
  • Dispatcher: disable file checking logic.
  • Scripts: check for shebang and provide compilation feedback to stdout.
  • Script_Loader: merely suggest non-expected arguments.
  • SDL_Viewer: expose abscissa for time courses.
  • SDL_Viewer: default to 'dt' metadata element for time courses.
  • SDL_Viewer: WIP time course viewing.
  • SDL_Viewer: display aliases in add-to=script menu.
  • SDL_Viewer: support saving generated contours.
  • SDL_Viewer: plots: give buttons unique IDs.
  • SDL_Viewer: plots: allow legend to be disabled.
  • SDL_Viewer: plots: more tooltip weidth tweaking.
  • SDL_Viewer: Plots: adjust column widths.
  • SDL_Viewer: attempt to widen plot hover metadata.
  • SDL_Viewer: Plots: view metadata and add on-the-fly normalization.
  • SDL_Viewer: plot selection bug fix.

202107

  • Dispatcher: permit directory file command line arguments.
  • Testing: report verbose results before summary.
  • CI: provide verbose feedback for integration test failures.
  • TAR loader: attempt to use file extensions from the archive.
  • DICOM: add (ad-hoc) proprietary CSA header tag parser.
  • check_syntax: optionally check YAML files.
  • DCMA-Dump: support printing beyond null bytes.
  • File_Loader: recursively find files when directories provided.
  • File_Loader: disable reprioritization when extension missing.
  • File_Loader: switch from constexpr lambda to regular function.
  • File_Loader: switch to priority-based file loading via file extension.
  • Load_Files: provide more insight into which loaders are being used.
  • ContourWholeImages: only allocate space when creating contours.
  • Scripts: accept up to 500 feedback notifications.
  • Add single-thread worker FIFO queue class.
  • ModelIVIM: use fuzzy key-value lookup for b-values.
  • Docker: avoid unnecessary costly rebuilds (Debian stable).
  • Add support for shellcheck-based checks.
  • Provide better support for remote aarch64 compilation.
  • CI: attempt to add armhf CI builds.
  • CI: GitLab: use a loopback swapfile for all builders.
  • Script_Editor: make variable replacement exhaustion an error.
  • Script_Loader: support variable replacements.
  • Script_Editor: recursively parse operations and variables.
  • Script_Editor: imbue characters with basic parsing metadata.
  • Script_Editor: expand script validation feedback.
  • Script_Editor: validate parentheses and quotations.
  • SDL_Viewer: bug-fix: honour user image view setting.
  • SDL_Viewer: Script_Editor: provide line numbers.
  • SDL_Viewer: added rudimentary script parser.
  • SDL_Viewer: make auto-scaler aware of multi-channel images.
  • SDL_Viewer: script editor: emphasize active script file better.
  • SDL_Viewer: continue to display previous image texture without locking.
  • SDL_Viewer: used timed mutex to skip locked data access.
  • SDL_Viewer: compartmentalize sub-operations.
  • SDL_Viewer: roughed-in worker offload thread.
  • SDL_Viewer: roughed-in script support.

202106

  • CI: add binutils explicitly.
  • CI: adjust rpath for aarch64 dynamic linked binaries and libraries.
  • CI: mitigate AppImage naming differences on aarch64.
  • CI: GitHub: account for chroot-nested AppImage.
  • CI: altogether disable Wt for CI builds.
  • CI: switch to CMake '-B' option.
  • CI: more Wt compilation wrangling.
  • CI: adjust Wt optimization level.
  • CI: speed up Wt compilation.
  • CI: GitHub: lengthen timeout for aarch64 AppImahe building.
  • CI: AppImage: fallback to linuxdeploy for x86_64.
  • CI: permit longer aarch64 builds.
  • CI: Debian: add script to make aarch64 chroot.
  • AppImage: switch to appimagetool directly.
  • CellularAutomata: added simplistic 'gravity' mode for voxel values.
  • Added 2D cellular automata operation.
  • ModelIVIM: Fixed bugs for Kurtosis model fitting
  • ModelIVIM: utilize multiple model params as separate channels
  • WIP: ModelIVIM: add bounds checks for debugging.
  • WIP: ModelIVIM: Bayesian kurtosis model with noise floor (CSample)
  • HighlightROIs: use r*-tree for faster spatial lookups.
  • HighlightROIs: rely on modified upstream Mutate_Voxels() for contour overlap
  • HighlightROIs: added integration test.
  • HighlightROIs: expose receding-squares method
  • HighlightROIs: add WIP marching-squares-inverse algorithm
  • ContourViaThreshold: consistently handle contour orientation
  • ContourViaThreshold: support marching-sqaure lower and upper thresholds
  • ContourViaThreshold: make marching-squares handle boundaries
  • ContourViaThreshold: add marching squares option.
  • SDL_Viewer: support 3D contour brushes.
  • SDL_Viewer: add snapping distance measuring tool.
  • SDL_Viewer: provide colour map scale bar.
  • SDL_Viewer: provide visual cue of contouring brush
  • SDL_Viewer: avoid double-counting overlapping line segments.
  • SDL_Viewer: support gapless contouring.
  • SDL_Viewer: added square rigid brush.
  • SDL_Viewer: add channel selector.
  • SDL_Viewer: support erosion and dilation (margins)
  • SDL_Viewer: contouring respects image aspect ratio
  • SDL_Viewer: use public ContourViaThreshold interface
  • SDL_Viewer: support multi-plotting
  • SDL_Viewer: contouring: notify user of contour deletion
  • SDL_Viewer: marching squares: switch to grid-based representation.
  • SDL_Viewer: contouring: implemented marching squares
  • SDL_Viewer: provide contouring fallback method.
  • SDL_Viewer: give user control of contouring resolution.

202105

  • Added diffusion MR DICOM attributes.
  • CI: GitLab: Fedora: workaround LD_PRELOAD issues, explicitly preload libs, add gmp-c++ dependency.
  • CI: remove Travis.ci.
  • CI: upload artifacts to GitHub.
  • Docker: added Ubuntu build_base.
  • ModelIVIM: account for extra voxel value.
  • ModelIVIM: bug fix: log-transform MR intensities
  • ModelIVIM: expose model selection flag.
  • ModelIVIM: merge pull request from samplecm (biexponential model)
  • Regex_Selectors: add simplistic regex inversion mechanism.
  • Regex_Selectors: provide basic missing key selector.
  • SDL_Viewer: WIP asynchronous contours overlay
  • SDL_Viewer: WIP contours overlay
  • SDL_Viewer: WIP mask-based contouring.
  • SDL_Viewer: add image coordinates tooltip.
  • SDL_Viewer: add realtime row and column profile viewer
  • SDL_Viewer: add realtime-updating image metadata window.
  • SDL_Viewer: add simple linesample plots.
  • SDL_Viewer: add voxel intensity probe.
  • SDL_Viewer: allow contour line thickness adjustment, provide per-contour display toggle
  • SDL_Viewer: cache filesystem queries.
  • SDL_Viewer: disable default OpenGL word-alignment.
  • SDL_Viewer: expose window/level and colour maps.
  • SDL_Viewer: generate mipmaps and use nearest pixel sampling.
  • SDL_Viewer: improve file opener edge cases.
  • SDL_Viewer: load files asynchronously.
  • SDL_Viewer: protect against empty root paths.
  • SDL_Viewer: provide rudimentary file loader.
  • SDL_Viewer: report DICOM position.
  • SDL_Viewer: retain custom window and level
  • SDL_Viewer: revert mipmaps, keep nearest pixel sampling.
  • SDL_Viewer: support contour colour adjustment
  • SDL_Viewer: support mouse zoom and pan, zooming and panning images, keyboard image navigation
  • SDL_Viewer: support multiple file selections.
  • SDL_Viewer: support synchronized low-high and window-level.
  • SDL_Viewer: use shared_mutexes for contour threads
  • SDL_Viewer: workaround wstring/wchar.
  • Support remote AppImage builds.

202104

  • SDL: provide explicit format strings.

202103

  • Perfusion: implement a single-compartment model

202102

  • SDL_Viewer: make specific views toggleable.
  • SDL_Viewer: added basic operation documentation menu.
  • Convert version macro to extern variable.
  • CI: GitHub: support manual launch.
  • Merge pull requests/branches from anthonyho.

202101

  • Simple_Meshing: accept disoriented contours.
  • PurgeContours: expand functionality.
  • Expose Drover partitioning backend.
  • Merge pull requests/branches from mojanjz and ceringstrom
  • Provide version information.
  • CI: use GitHub actions to deploy CI to GitHub page.
  • Add no-op operation.
  • Bug fix: properly document Repeat operation.
  • Support fuzzy operation names and explicit aliases.
  • Clean up and similarity threshold
  • Rearranged includes and fixed a lot of warning and added more parameters
  • ContourViaThreshold: enable partial support without CGAL.
  • Added DeleteContours operation.
  • Avoid running tests when functionality unavailable.
  • Add a non-trivial example (double-threaded screw).
  • ConvertContoursToMeshes: contour selection bug fix.
  • CGAL: use exact-exact kernel for boolean operations.
  • CopyContours: rely on metadata update member.
  • CopyContour: added missing contour duplication operation.
  • WarpImages: test spatial mirroring.
  • GenerateTransform: rely on upstream affine factories.

202012

  • Enable rigid and affine registration implementation
  • Improve compatibility with older Boost::Serialization versions.
  • Support for Boost::Serialization 1.74.
  • Support loading point clouds and surface meshes from both ASCII and binary PLY files.
  • Added support for vertex normals (surface meshes, point clouds).
  • Added basic support for vertex colours (surface meshes, point clouds).
  • Partial migration from Travis CI to GitHub actions.
  • Added explicit support surface mesh export in (ASCII+binary) PLY, OBJ, OFF, and (ASCII+binary) STL formats.

202011

  • Support loading point clouds from OBJ and OFF files.
  • Added ConvertMeshesToPoints operation with vertex extraction and random surface sampling.
  • SYCL: added test file generation program, SCDI perfusion model minor bug fixes.
  • Nix: overhaul of all nix files, slightly more idiomatic file hierarchy.
  • SDL_Viewer: make image array viewing optional, but still a WIP.
  • CI: ensure all systems provide libOpenGL.so.
  • Docker: added WIP debian:oldstable support. Might have to wait for next oldstable.

202010

  • Reworked EQDx operation to also provide BED conversion, added tests.
  • Simplified very old code (contours_with_meta class).
  • Simplified ROI operation parameter selectors and documentation.
  • Webserver: relocate config directory, simplify parameter selection when exmaples are exhaustive.
  • Add SDL2 and Glew dependencies on all platforms.
  • SFML_Viewer: provide cross-platform partial replacements for Zenity dialogs.
  • Explicator: provide built-in lexicon, default to most generic lexicon provided by Explicator (if available).
  • ContourSimilarity: sync documentation with current implementation.
  • Documentation: indicate version in online documentation.
  • Added mock-up starting point for deformable registration algorithm development.

202009

  • Added development log.
  • Modernized use of 'new' for Contour_Data and Image_Data unique_ptr/shared_ptr allocations.
  • Added support for nested operations and meta-operations, Repeat and ForEachDistinct. These can be used to partition data, analyze group-wise, or implement control flow at the level of operations.
  • Nix: nix files reconfigured to use git master branches rather than commit pinning.

202008

  • Successfully ported DCMA to Windows.
  • CI: added MXE cross compilation and expose build artifacts.
  • CI: expanded number of builds and test matrix, added nightly scheduled builds.

202007

  • CI: updateCI scripts and AppImage creation, switched base image to Debian for greater stability.
  • Docker: separated setup scripts from Dockerfiles for easier re-use.
  • Docker: parameterized multi-part builds.
  • Addressed some static analysis warnings (memcpy, localtime, if(false), std::bind, ...).
  • CI: publish AppImage artifacts.
  • CMake: better support for ARM builds.

202006

  • ReduceNeighbourhood: support statistical standarization.
  • ReduceNeighbourhood: support adaptive renormalization.
  • CMake: easier support for sanitizer builds.
  • TPS-RPM: report bending energy, support for alternative solver methods, support double-sided outlier handling, added tolerance-based Sinkhorn normalization for adaptive refinement, finalize user-interface.
  • IO: normalize floating-point precision to maximum for exact round-trips.
  • AnalyzeHistograms: fix conversion typo (cm^3^ to mm^3^).
  • Added Transform3 as first-class object to support registrations.

202005

  • Preliminary TPS-RPM implementation for deformable registration.
  • Many small tweaks throughout code base (UID generation, debugging features, IO
  • Added test files for meshing.
  • Simple_Meshing: force manifoldness at edges.
  • Added Simple_Meshing routine to quickly stitch together well-behaved contours. It is experimental, but has limited support for N-to-M contour connections, holes, and nested contours. Meshes produced this way are extremely unreliable, except in well-constrained situations!
  • Support for explicit DVH Line_Sample files.

202004

  • Attempted WASM compilation, but SFML and few others are currently blocking such a port. Will likely have to move to SDL at some point, probably with a more functional interface.
  • Added script to generate AppImages.
  • Added minimal Nix scripts for building with Nix and integrating into NixOS.
  • Overhauled entire histogram sub-system.
  • Docker: added X-passthrough script for distributing full DICOMautomaton builds, including graphical parts.
  • Added Linux live-cd distribution method, which provides full DICOMautomaton builds and all requirements. Also provides a script to download all sources for all packages. This distribution method is rock-solid, but fairly inconvenient. Best for archival or offline distribution.
  • Support reading and writing of gzipped-TAR files.
  • File_Loader: support (uncompressed) TAR files.
  • DICOMExportImagesAsCT: upstream class name change.
  • Support writing TAR archives when exporting multiple files (e.g., CT images).

202003

  • SimulateRadiograph: faster ray marching, smarter ray pruning, optimized code hot-paths, and truncate rays to bounding volumes.
  • Upstream (Ygor) planar_image_adjacency change: switched from map to linear lookups for int-to-images, which will significantly speed-up ray-casting through rectilinearly voxelized geometries.
  • Added basic treatment plan analysis routine. Basically just a shell to build on later (e.g., for automated plan checks).

202002

  • Address excessive Docker build memory consumption.
  • Added small collection of test files of various kinds, mostly for development and testing.
  • Added support for reading STL files.
  • Added TransformContours operation.
  • Meshing: prune irrelevant candidate vertices (Marching Cubes) to speed-up large meshing operations.
  • Added Fuzzing Docker container for easier fuzzing with AFL.
  • EQDConvert: typo fix: conversions mistakenly always used a non-pinned conversion scheme.

202001

  • Added documentation for fuzz testing, expanded Termux documentation.
  • PointSeparation: reduce to constant memory usage.
  • PointSeparation: report Hausdorff distance.
  • Added operation to compute extreme distances between point clouds (PointSeparation).
  • Improved linking, dependency tracking, and invalid flags when clang is used.
  • Switched to C++17 to expand compiler compatibility (wrt std::experimental).

201912

  • portable_dcma: provide default lexicon for all wrapper scripts.
  • Provide an embedded fallback font.
  • PartitionContours: ensure sub-segment ordering when some are omitted.
  • Added operation to partition ROIs (PartitionContours).
  • SubsegmentContours: provide means of re-ordering cleaves.
  • Extracted sub-segmentation operation from earlier segment+analyze operation.
  • AnalyzeDoseVolumeHistograms: hoist macro expansion routine into Ygor for broader use.
  • DeDuplicateImages: add simple means of de-duplicating image arrays.
  • ContourBooleanOperations: ensure at least one contour has been selected.
  • DCMA_DICOM: Provide a custom DICOM writer.

201911

  • Imebra: extract DICOM tag writing sub-routines.
  • Optional external dependencies: support conditional compilation for major external dependencies. This will eventually be needed for increasing portability to other Linuxes, Windows, and WebAssembly.

201910

  • Joint_Pixel_Sampler: rely on Mutate_Voxels img_refw.
  • Joint_Pixel_Sampler: eliminate racy static logging.
  • AlignPoints: provide implementation of exhaustive ICP.

201909

  • AlignPoints: handle cases of 2D and 1D degeneracy for PCA alignment.
  • ConvertContoursToPoints: provide an operation to extract vertices from contours as a point cloud.
  • Added an operation for registration of point clouds (AlignPoints).
  • XYZ loading: load each file as a separate point cloud.
  • Moved point cloud implementation to Ygor.
  • AnalyzeDoseVolumeHistograms: increased support for literals, sig. figs., and unrecognized constraints.
  • Added support for Line_Samples as first-class objects. This will be used for DVH handling and possibly some tabular data applications.

201908

  • Provide a routine to deal with non-manifold meshes.
  • EvaluateDoseVolumeHistograms: switch to more sophisticated backend.
  • Supersampling: clean up metadata and intermediate images.
  • Interpolate_Image_Slices: exploit rectilinearity to interpolate slices much more quickly.
  • Experimental support for treatment plans.
  • Docker: Added Void Linux Docker (musl) build. Note that this container still builds dynamic artifacts.
  • Generalized compilation convenience scripts wrt which Linux distribution is being called and whether to delegate to Docker.
  • Surface_Meshes: specify image traversal order.
  • SimulateRadiograph: WIP: added path integration, parameterized more image characteristics.

201907

  • Added operation for exporting images in FITS format.
  • Added operation for convolution, correlation, and pattern-matching with two images.
  • Added support for reading DOSXYZnrc 3ddose files.
  • Added operation for rigid mesh transformations.
  • Added mesh processing routines (remeshing, subdivision, and simplification).
  • Added preliminary support for first-class surface meshes.
  • ContourSimilarity: revamped earlier quick implementation.
  • Added runtime ELF patching for portable dcma binary.
  • DumpImageSurfaceMeshes: added user-facing interpolative surface mesher.
  • VolumetricNeighbourhoodSampler: clarify exception when images overlap.
  • ContourViaThreshold: support non-binary marching cubes contouring.
  • DrawGeometry: added solid sphere pattern.

201906

  • Docker: Arch: use dynamic mirrorlist to avoid timeouts or reliance on any one mirror.
  • PresentationImage: expose window and level configuration, permit not specifying any window/level.
  • DumpROISurfaceMeshes: expose contour interprettation options.
  • Expose contour inclusivity for mesh generation.
  • DumpImageMeshes: simplify specification of output base and expose more options, including normalization.
  • SFML_Viewer: added explicit window/level entry, replace DB contour export with local export.
  • DrawGeometry: added a wireframe cube shape.
  • DumpImageMeshes: added image export as 3D OBJ and MTL models.
  • SubtractImages: support more advanced image selection.
  • BoostSerializeDrover: support export of inidividual components.

201905

  • ReduceNeighbourhood: explicitly mention 'erosion' and 'dilation'.
  • ReduceNeighbourhood: add fixed isotropic spherical neighbourhoods.
  • DetectGrid3D: WIP tweaks for improving image intensity-based detection of regular grids (RANSAC, reporting, Procrustes and algorithmic tweaks).
  • FVPicketFence: hide parameters from picket fence web interface, use whitelist for exposing parameters.
  • Added operation implementing Otsu thresholding.
  • Add a volumetric spatial blur operation.
  • ImprintImages: update image description.
  • Added conservative filter for speckle reduction.
  • DumpROISurfaceMeshes: generate more precise surfaces by default (CGAL).
  • Ensure Gram-Schmidt orthogonalization retains unit vector magnitudes.
  • ContourViaGeometry: pre-filter degenerate contours.
  • Added operation for making volumetric contours from 3D shape primitives.
  • SFML_Viewer: added a simple DICOM distance measurement tool, factored common coordinate transformations.
  • ScalePixels: added operation for scaling pixel/voxel intensities.
  • VirtualGenerators: correct invalid PatientOrientation metadata.
  • ModifyImageMetadata: allow modification of image spatial characteristics.
  • GenerateSyntheticImages: bug fix: make metadata optional.
  • Avoid null deference when no contours are loaded.
  • GenerateSyntheticImages: bug fix: stringify metadata ints.
  • LoadFiles: added operation for on-the-fly file loading.
  • VolumetricSpatialDerivative: switch to pre-indexed trilinear interpolation.
  • VolumetricSpatialDerivative: added non-maximum suppression for 3D derivatives.
  • VolumetricSpatialDerivative: separate end-user-callable operation from implementation.
  • DetectGrid3D: added support for PLY file writing.

201904

  • Added operation to imprint images with point clouds.
  • Added read support for ASCII XYZ point cloud file format.
  • Added routine for more easily creating test images.
  • Structs: enable point_data copying for Drover class.
  • DroverDebug: add image modality and min/max pixel values.
  • DroverDebug: add point clouds to debug operation.
  • WebServer: improve clarity of user-facing parameters.
  • Add a customized reduced-memory CMake option.
  • Hide shared template functions rather than expose them directly.
  • ConvertPixelsToPoints: added routine for generating point clouds from images.
  • Docker: base/archlinux -> archlinux/base.
  • Add support for CI (Travis).
  • Partial switch from std::regex() to more homogeneous Compile_Regex().
  • Recognize RTRECORD file signatures.
  • Breaking change: removed Dose_Arrays in favour of Image_Arrays.
  • SupersampleImageGrid: support for 3D supersampling.
  • CompareVoxels: elaborate DTA and discrepancy computations.
  • ComparePixels: support for multipe types of discrepancy.
  • PresentationImage: allow specification of colour map.
  • Added operation for image slice interpolation.

201903

  • Added ability to mimic planes with planar contours.
  • Explicitly indicate Drover serialization version.
  • Break-out operations created for image detection functionality.
  • Added script for easy syntax checking.
  • Added operation for generating calibration curves.
  • ReduceNeighbourhood: added NaN replacement variants.

201902

  • ReduceNeighbourhood: support for logical filters (is_min, is_max).
  • Added 3D voxel neighbourhood sampler.
  • Added an isotropic remeshing routine.
  • MarchingCubes: handle inconsistent contour orientation and spacing.
  • Surface Dose Sampler: switch to Surface_Meshes Marching Cubes implementation.
  • Added a Marching Cubes surface generator.
  • CompareImages: Migrate to Ygor image 3D adjacency routines.
  • CompareImages: replace R*-tree approach with grid-traversal.
  • ThresholdImages: fix threshold inclusivity.
  • Added basic man page render of reference guide.
  • Added script to compile documentation to pdf and html.
  • Added html and pdf versions of documentation.
  • Added snapshot of documentation.
  • Revamp runtime documentation.

201901

  • Added rudimentary shell tab completion.
  • RankPixels: added operation for ranking pixel values.
  • Added script for bundling dispatcher binary and necessary shared libraries.
  • Added routine for negating image pixel values.
  • Boost Serialization: switch from binary to XML by default.
  • DetectShapes3D: add WIP clustered RANSAC detector for planes and spheres.
  • WebServer streamlining.
  • DoseDecay: switch to planar inclusive catchment by default.
  • DoseDecay: add a mask channel to avoid re-decay in multi-pass workflows.
  • OrderImages: added a robust image sorter.
  • GroupImages: added two logic-based grouping options.
  • Added regex selector inversion.
  • RTDOSE export: ensure UIDs do not have leading zeros.

201812

  • ThresholdImages: reduce verbosity.
  • Increased flexibility in image selection.
  • Added image thresholding operation.
  • Edge-detection: added non-maximum suppression to thin edges.

201811

  • Added support for upstream vertex collapse contour simplification.
  • Radiomics: add a simplified interface for web.
  • Gracefully handle REG-modality DICOM files.

201810

  • Surface Meshing: default to reasonable criteria to avoid ambiguities.
  • Added contour simplification operation.
  • Radioimics: added additional morphology features based on surface meshed ROIs.

201809

  • Added perimeter-based contour features.
  • Validation of select distribution-based statistical radiomic features.
  • Limit number of concurrent build jobs to reduce memory usage.
  • Honour TreatAsEmpty regex selector option.
  • Added convenience script for remote building.
  • Added 3D surface-based inset, outset, and shell operations.
  • Static beam optimizer: switch from hypersphere-constrained parameters to direct hyperplane parameters, constrain beam weights to the coordinate n-sphere cartesian coordinate sector, improve transparency and reporting.
  • Field-weight optimization: permit run-time parameter tweaking.

201808

  • Switch docker base from Debian to Arch Linux to access newer upstream packages.
  • Support subtraction of arbitrary images, if necessary.
  • Support for surface mesh processing.

201807

  • Switch from deprecated CGAL routine.
  • Protect against incomplete data and when zero junctions detected.

201806

  • Permit inexact decimation factors.
  • Added partial support for Boolean negation.
  • Expose EQD2Convert operation to web server.
  • FVPicketFence: swap autocrop and pixel crop.
  • AutoCrop: account for non-identity SAD-to-SID scaling.
  • Protect against degenerate contours.
  • Added dual operation to TrimROIDose.
  • Only show hover info on parameter name column.
  • Added image array subtraction operation.
  • Added operation to delete image arrays.

201805

  • Respect the tag element count.
  • Added TemporalPositionIndex DICOM tag to dictionary.
  • Renamed default PACS file store location.
  • Support for non-default DB store locations.
  • Added an operation for static beam optimization.
  • Simplified ROI dose trimming operation.

201804

  • Added multi-stage Picket Fence analysis operation.
  • Added centroid-based selectors for ContourVote operation.
  • Sub-segmentation: permit specification of bisection stopping parameters.
  • More clearly documented OBJ/MTL contour export operation.
  • Picket Fence: provide threshold boundaries as a contour, added contours for detected peak locations.
  • Picket fence: added a summary file for quick inspection.
  • Picket fence: project analysis results onto isoplane.
  • Added image grouping operation.
  • WebServer: layout updates using CSS animations, exposed operation descriptions.
  • Translated in-source operation descriptions to runtime documentation functions.
  • Plumbing for RTIMAGEs with z!=0 and dz!=0.
  • Disallow explicit rescaling for RTDOSE exports.
  • More clearly differentiate anonymization levels in the source.
  • Default to more obviously phony date for missing/anonymized RTDOSEs.
  • Feed Imebra correct FrameIncrementPointer value.
  • Basic support for concealing parameters from user-facing interfaces.
  • Added explicit dependencies for building.
  • Added additional boost library dependencies.

201803

  • Added temp file suffixes.
  • Picket fence: explicitly colour junction contour lines to avoid colour clash, crop line contours to the provided image.
  • Remove unnecessary termination points and irrelevant metadata lookups.
  • Fix infinite loop when loading a bad DICOM image file.
  • Fix setColor() SFML deprecations.
  • Harden against missing contour metadata.
  • Added a slew of named colours.
  • Refined MLC model selection for picket fence analysis.
  • Added contour metadata injection operation.
  • Added simplistic screenshot extractor.
  • Handle special case where all voxels are exactly zero.
  • Added an operation to apply arbitrary calibration curves.
  • Genericized HighlightROIs YgorFunctor.
  • Mass header cleaning using include-what-you-use.
  • Workaround for libc++'s std::optional::swap.
  • Fixed UB in old Imebra code.
  • Removed several unnecessary std::move (-Wpessimizing-move).
  • Let the user opt-out of interactive plots.
  • Added sanity check for images with volume.
  • Added light-rad analysis edge visualization.
  • Added basis spline peak-finding.
  • Light-rad field coincidence analysis operation completed.
  • Added autocrop operation using per-image metadata to crop.
  • DICOM reading: added support for nested sequence items.
  • Added free-form image cropping operation.
  • Added percentile-based contour thresholding.
  • Added multi-sequence metadata support for deeply nested DICOM tags.
  • Split edge detection routine into two parts.
  • Indicate invalid plots more clearly.
  • Added an operation for selecting a contour via various criteria.

201802

  • Completed percentage-based contouring.
  • Added relative contour by threshold capabilities.
  • Added a cyclic colour map for viewing gradient orientation angles.
  • Support for 5x5 variants of the Sobel and Scharr derivative estimators.
  • Reoriented gradient orientations for consistency.
  • Added pixel sharpening operator.
  • Imbued LogScale operation with an image selector.
  • Exposed new upstream blur convolution-based estimators.
  • SFML_Viewer: indicate where the mouse is in sub-plots.
  • Overhauled row, column profiles in the SFML-based viewer.
  • Permit selection of first image in an array.
  • Support additional upstream derivative estimators for edge detection.
  • Auto-compile without CMakeCache invalidation.
  • Removed audio from SFML-based viewer.
  • Generalized partial derivative imaging functor for edge detection.
  • Added WIP edge detection operation.
  • Removed hard-coded gcc-isms.
  • Added image metadata insertion operation.
  • Added contour simplification pass.
  • Permit display of contours that extend beyond image bounds.
  • Added metadata to generated contours.
  • Many clang-tidy modernizations.
  • Patched in-tree Imebra to rid auto_ptrs.
  • Added a new, standalone DVH routine.
  • Migrated to libWt v4.
  • Updated CGAL header name changes.

201712

  • BED: added a longer description for an alpha/beta parameter.
  • Removed BED from TCP/NTCP evaluation operations.

201711

  • Added explicit EQD2 conversion operation.
  • Added image sampling routine to the SFML_Viewer.
  • Protect against empty dose arrays.
  • Added UserComment column to all recent evaluation operations.
  • Avoid NaN contamination in LKB NTCP model.
  • Exposed dose melding operation.
  • Webserver displays generated CSV files.
  • Added mimetypes to file OptArgDocs.
  • Added a from-scratch window update routine.
  • Added a routine to read standard (uint8_t-typed) FITS images.
  • Added operation for reporting dose-volume statistics.
  • Changed behaviour for missing ROI NormalizedROINames in Boolean operation.
  • Added support for new YgorImages voxel iteration wrapper routine.
  • WIP implementation for direct contour growth.
  • Added a routine for explicit contour seaming.
  • Webserver: added support for multi-pass operations.
  • Added a 'paranoia' mode for dose export.
  • Added a virtual dose data generator.
  • Added paranoid mode for RTDOSE export.
  • Bug fix: erroneously used hypothetical course 2 fractionation for course 1 BED conversion.

201710

  • Implemented a NTCP models operation.
  • Added the Fenwick TCP model.
  • Added a contour-based Boolean function operation using CGAL.
  • Added CMake-sanctioned pthreads flags.
  • Added image --> dose conversion routine.
  • Added two temporal dose decay models for re-irradiation dose estimates.
  • Added utility file for dose <--> BED conversion.
  • Recognize but skip over RTPLAN files and emit warning.

201708

  • Strip executables and shared libraryies for Debian packages to reduce excessive binary sizes.
  • Improved support for foreign FITS files.
  • Added option for voxel inclusivity tweaking.
  • Bump from c++14 --> c++17.
  • Capped dose_scaling.
  • Dead code elimination.
  • Completed simplistic, constrained RTDOSE export routine.

201707

  • Extended functionality of Highlight images functor and created standalone operation for it.
  • Added gnuplot optional dependency.
  • Added font dependencies.

201704

  • Clarified that YgorClustering is a header-only library dependency.
  • Cleaned up PKGBUILD.
  • Removed some auxiliary analysis files.
  • Small changes for segmentation visualization.

201703

  • Added a backup font found on a Debian installation.
  • Added Debian packaging scripts (via CPack).
  • Added ROI exclusion capability.
  • Added pixel stats reporting for the working contour ROI.

201702

  • Fixed race condition.
  • Made ContourWholeImages operation tolerant of spatially overlapping images.
  • Added whole-image ROI generation.
  • Added a custom colour map.
  • Added on-the-fly colour mapping.
  • Toned down NaN colouring.
  • Added empty image_array pruning operation.
  • Added a no-op option for easier script tweaking.
  • Use contour colour to convey contour orientation.
  • Added rudimentary contour-via-pixel-threshold operation.
  • Added SNR computations for comparison purposes.

201701

  • Fully pruned CSVTools dependency.
  • Removed old, unused code causing unspecified custom library dependencies.
  • Added output file options for surface-based ray casting operation.
  • Added safer internal-to-ROI check for surface seed point.
  • Exposed surface-based ray casting operation options to the user.
  • Added trilinear interpolation to surface-based ray casting computation.
  • Surface-based ray casting: only consider a single ray intersection.
  • Made pacs_ingress safer to use on duplicate files.
  • Added a rudimentary pop-out realtime plotting window.

201612

  • Additional ROI topological/morphological data in dumps.
  • Disabled non-critical computations in surface mesh dump operation.

201611

  • Added a voxel stats dump operation.
  • IVIM/ADC tweaks.
  • Operationalized many existing sub-operations.

201610

  • Added sub-segment area logging for sub-segmentation routine.

201609

  • Provided an option to forgo dumping of voxel distributions.
  • Moved 'usemtl' specification prior to vertices to accomodate evrtex colouring.
  • Converted ROI contour dumping to export Wavefront OBJ files.
  • Added a routine for dumping ROI contours.
  • Purged old CSVTools, Demarcator, and Distinguisher references from modern executables.
  • Added supersampling and blurring to raster grid surface map.
  • Added a standalone FITS file loader for easier viewing.
  • Decoupled grid-based ray casting surface raster grid voxel size from ray source/detector grid size.
  • Added an ROI-based cropping routine. Added to van Luijk script.
  • Added supersampling pre-processing step to sub-segmentation script.
  • Separated bisection and sub-segmentation to more easily switch sub-segmentation schedule.
  • Improved bisection reporting and added a script for viewing multiple sub-segmentations.
  • Improved stewardship of file-based loaders.
  • Added additional sub-segmentation to van Luijk operation.
  • Added a boost.thread and asio based thread pool to improve grid-based ray casting throughput.

201608

  • Converted grid-based surface mask construction to use simple parallel for-loop.
  • Converted ray-casting to use simple parallel for-loop.
  • Separated surface mask grid creation from ray casting source+detector creation.
  • Added a routine for generating a surface mask (and interior mask) over an image grid.
  • Made 'van Luijk' subsegmentation selection extents less sensitive to numerical issues.
  • Reverted PACS_Loader to load dose files as Dose_Arrays, not Image_Arrays.
  • Added basic DICOM file loader based on PACS loader.
  • Added a lexicon building operation.
  • Fixed bug in which clustered surface mesh facets' clusters were not reported correctly.

201607

  • Added runtime parameters to control fast, approximate Chebyshev multiplication.
  • Updated post-computation model evaluation for 1C2I model Reduced3Param.
  • Added CXX_FLAGS needed for CGAL (-frounding-math) and others to improve compiler optimization.
  • Another hierarchial rename. Added Reduced3Param variant of 1C2I model (no gradient yet!).
  • Hoisted a deserialization outside of a loop.
  • Added a post-modeling parameter dumping routine.
  • Added a Levenberg-Marquardt-based direct linear interpolation variant of the 1Compartment2Input_5Param model.
  • Exposed B-spline and Chebyshev coefficient totals as runtime parameters for level-of-detail adjustment.
  • Added B-spline interpolation for AIF and VIF approximation.
  • Basic support for storing model state with parameter maps.
  • Streamlined pre-pharmacokinetic modeling AIF & VIF plotting.
  • Factored some similar plotting routines together.
  • Added pre-pharmacokinetic modeling AIF and VIF plot popup.
  • Added runtime ROI selection for Cheby-based pharmacokinetic modeling.
  • Added runtime plotting specification to pharmacokinetic modeling operation.
  • Clean-up of GSL modeling routine.
  • Completed 5Param Chebyshev Least-Squares modeling via Levenberg-Marquardt in GSL.
  • Improved linear (non-Chebyshev) perfusion model optimization stopping criteria.
  • Wrapped plotting calls with fork() to improve stability.
  • Added another optimization criteria.
  • Removed possibly misleading vestigial code.
  • Added an ROI-based slice selector for pruning image slices.
  • Made example values more explicit for disabling pre-analysis decimation.

201606

  • DVSM: updated minetest skeleton location.

201605

  • Added a dry-run mode for the ingress tool.
  • Migrated CGAL code to CGAL>=4.8, addressing breaking API changes.

201604

  • Decoupled contour resolution from image pixel size, fixed is-cursor-in-contour bug.
  • Added dependencies to the PKGBUILD.

201603

  • Added support for computing centroids for CGAL surface mesh polyhedra.
  • Added per-ROI dose info dumping.
  • Changed regex type from grep to extended POSIX throughout code base.
  • Attempted to improve surface meshes by emulating planar contour extrusion with point set techniques.
  • Added CGAL Scale-Space Surface Reconstruction operation.
  • Added standalone operations for Max-Min pixel filtering, ROI time course plotting, and image copying.
  • Added workaround for reading NaN and +-Inf in Boost.Serialization text and xml formats.
  • Completed support for Boost.Serialization of the Drover class.
  • Replaced Protobufs with Boost.Serialization.
  • Created stubs for serialization, separated into a new file.
  • Renamed 'Analyses' to 'Operations' where applicable to be more accurate.
  • Added a default, reasonable .clang-format file.
  • Major refactoring to decouple invocation handling, file loading, analysis dispatch, and analysis.
  • Removed rarely-used but pervasive verbosity mechanism using awkward global state.
  • Added support for image modality 3D rotation.
  • Added explicit image reordering after modeling for improved viewing.
  • Applied tweaks from 3-parameter testing to the 5-parameter perfusion modeling routine.
  • Partially converted many image processing tasks to parallel execution.
  • Added a work-around for recurring inconvenience regarding DICOM pixel mapping.
  • Optimizer tweaking and transparency improvements.

201602

  • Added plotting capabilities to perfusion modeled pixels for in-situ inspection.
  • Incorporated pixel decimation into the CT liver perfusion modeling routine.
  • Added pharmacokinetic modeling library sources.
  • Added pixel decimation to do block-wise spatial pixel aggregation.
  • Bug fix. Supersampled pixel 3D offset was not properly set.
  • Split (some) pharmacokinetic modeling into separate library.
  • Removed vestigial files from years ago.
  • Added a more focused metadata dumper for image registration and non-DICOM image viewers.

201601

  • Added ability to call a modified Minetest for contouring purposes ("DVSM")
  • Tweaked orthogonal view defaults; added filters for new data; added an executable.

201511

  • Simplified YgorImage_Functor image description and window centre/width updating and Liver Perfusion map generation.
  • Added support for custom display window centre and level.
  • Added a proper orthogonal slice functor. Required modifications in Ygor.
  • Implementation error: incorrect integral manipulation fixed.
  • Migrated from hand-made Makefiles to CMake.
  • Liver perfusion functionality enhancements.
  • Migration to git.