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2.4.6
* Fix building with boost-1.65
2.4.5
* Fix that mia-3dsegment-local-cmeans would fail when the number of
slices N was relatwed to the grid size G according to k*G+1
(k integer)
* Reduce the amount of template instanciations created by the *ncc cost
functions. This should reduce the memory requirements during build time.
2.4.4
Issues fixed:
#129: Move all optional parts to addon
#167: Add alternative FastICA implementation and
move IT++ based version to addons
#191: Use C11 integer data types for consistent sizes
#192_ Replace lazy copy by move semantics
#193: Make documentation creation and nipype interfaces compatible
with python3
#194: Create a complete facate for XML handling
- remove dependency from libxml++ (use libxml directly)
#195: Correct errors in Nifti s-form handlig
Additional changes:
* New SO-version
* Add tools for localized c-means segmentation
* Add fluid-symetric registration
* Fix lots of coverity reported problems
* Make VTKIO compatible with VTK-7
* Add Sobel and Scharr filters
* Improve test coverage
2.4.3
* m/c/utils.cc: Always define PATH_MAX when it is not defined by
system headers
* Correct spellings
* Replace use of boost::regex by std::regex
2.4.2
* correct installed headers
2.4.1
* Add additional search path for MathJax
* Correct type in VistaIO
* Change file load handling to throw when file is not available
2.4.0
* Add support for a repeatable command line option; Closes: #183
* Add interface for pixel type filter conversion test; Closes: #5
* Work on enabling compiling against DCMTK that requires ICONV
* Make it compile on FreeBSD
* Add new filters
* Add tests and improve code coverage
* Improve fuzzy-segmentation algorithms by using tested code
(kmeans, probability estimation)
* Add support for piping through the vista plugin interface
* correct type of sparse histogram bin value
* Add new program that applies a 2D local cmeans segmentaion
* Correct Coverity issues
* Clean up code of similarity_profiles and add test
* Add test for 2D image comparison
* Add a sparse histogram implementation
* Remove the code for the so-called auto-ICA estimation
* install lxml in travis via pip to work around travis-ci/travis-ci#4948
* Remove need to use a dummy file for plug-in and test creation
* disable unused registration code in build
* Prepare mia for compilation with boost-1.60
* Correct compilation with g++-6
* Correct copyright
* remove obsolete create_2dinterpolation_factory function
* remove the create_XXinterpolation_factory functions
* Correct reading of 24-bit RGB BMP images
* Update bmp image io to support compressed 4bit pixel reading
* Correct critical point and matrix eigenvalue/vector handlinG
* Remove all optimization from coverage build
* Remove the src/ directory from coveralls check, can't be tested in time
* Add possibility to use installed mathjax files
* Add generic get_minmax function to images
* Correct code to prepare for auto-threshholding
* Enable compilation with libxml++3.0 and libxml-2.6
* Start implementing switchable ICA implementations.
* Use c++11 threads as default, instead of TBB
* Change reading nifti oriention
* Update CXDBitImage to not use vector<bool>
* Read nifti files without applying the slope transformation
* Add SpacingBetweenSlices Attribute to DCMTK IO
* More code parallelization
* Add const-correctnes to the gsl::matrix class and its iterators. Closes [tickets:#169]
2.2.7
* Correct tests that fail on arm64, armhf and ppc64el
* Make the m/2d/mlv use always the same random seed
2.2.6
* Correct pkg-config dependencies
* Change label type in fifof to unsigned int
2.2.5
Bug Fixes:
* Fix SSE2 alignment bugs on 32 bit x86
* Correct test to use BOOST_CHECK_CLOSE for floating point numbers
* Fix a series of Coverity reported bugs
- Change the CXMLElement to track ist children
- fix past-end access in histograms
- check for empty histogram in new CMeans implementation
* Correct explicite instanciation of 3diterator, clang++ needed this
Other fixes
* Remove outdate documentation files
* Correct licenses
2.2.4
New features:
* Add programs for
- cmeans on sparse input data
- combining an abitrary number of images with an comutative operation
- estimating a bounding box around the data in an image
- applying a deformabale model to a mesh
- evaluating statistics in a masked area of an 3d image
* Add mesh filters
- remove triangles based on normal direction
- select largest connected mesh part
- add a scale value taken from a 3D image to each vertex
* enable use of parallel gzip/xz in IO if available
* Add image filters
- 3D labelmap filter
- 3D re-orientation filter re-enabled
- 2D maxflow/mincut segmentation filter
- 2D sobel filter
* Cleanups
- remove eigen3 from public interface
- remove libxml++ from public interface (Closes: #178)
- remove boost/filesystem from public interface (Closes: #177)
* Coverity fixes
* Implement 2d gradient normalized cross correlation
* Parallize some filter for speedup
* Add new bounded parameter type that replaces ranged parameter
* Add cmeans class with different initializers given by plug-ins
* correct evaluation of normalization filter in nonlinearregistration
(Closes #185)
* Remove cost name test from s/2dmany-to-one.cc (Related to #186)
* Add a 3D to image drawtool
* remove time stamp from man pages for reproducible builds
* Lots of minor changes and fixes (see git log for details)
2.2.3
New features:
* Add some more speceliyed 3D image transformations
* Install the documentation tools
* Add nipype interfaces to all command line tools
* Add (localized) normalized cross correlation as cost function
2.2.2
Fixes:
* #165 throw exception where "exit" was used before
* Add boost_system to required link libraries in *.pc files
* Reduce the number of explicitely libraries used from VTK
* vtkmash.cc: Add explicit cast to make it compile with clang++
* test_cmdlineparser: Correct failing test if NDEBUG is defined
2.2.1
* fixes for potential bugs discovered by Coverity
* src/2dmyoica-full.cc: fixes and error in the order of
parameters passed
2.2.0
New features:
* Major ABI changes
* Add support for HDF5 and NIFTI1 IO
* Support for masked cost functions in voxel based image registration
* Use Eigen3 for the 3D matrix eigenvalue/eigenvector evaluation
* More C++11, minimal requirement is now g++ >= 4.7
* Keep track of orientations
* Add perfusion motion compensation programs that are specifically
designed to use a global reference even if the algorithm doesn't
dictate this
* automatically set C++11 compiler flag by cmake
Fixes for tracked issues:
* #4 add 2D/3D filters that actually run a combiner,
* #12 add basic support for loading and stroring nifti
* #14 load and store ImageOrientationPatient and ImagePositionPatient related
* #19 Add positional information to C3DTransform::const_iterator
* #49 Parallize the 3D scale filter
* #57 Add parameter type that can take a vector of coma separated values.
* #76 Remove the old divcurl penalty interface in 2D Closes
* #90 Add voxel/pixel size attribute to vector field
* #100 Make the 3D image combiner similar to the 2D combiner
* #108 Change segmentation set IO to possible make use of plug-ins
* #117 Add support to query minimal image size for transformations
* #123 Correct handling of ica instance when RV/LV classification fails in all cases,
* #124 Add attribute to indicate the pixel size is from the imager
* #125 Make slicelocation and slicespacing non-obligatory
* #126 Correct plug-in file suffix mapping for 2D and 3D images.
* #127 Correct documentation and output to refer to 2D data.
* #128 Add program to convert multi-record 2D image to 3D image
* #129 Move plug-ins that are configurable to the addons source tree
* #132 add 2D normalized local cross correaltion, see
* #135 Read from created file name instead of in_filename.
* #136 Add a normalization parameter to the spline penalty,
* #138 Handle compressed file extension properly when selecting the IO plugin.
* #139 Do not throw when opening the HDF5 file fails
* #140 add property flag for IO piping
* #141 Add attribute IO to the available 2d/3d transform IO backends
* #143 Fix zero boundary condition handling
* #144 Parallelize the prefiltering in the 3D interpolator
* #145 make sure the interpolator output range always includes zero
* #147 Add function to override interpolator once.
* #152 add 3 label-voting downscale filter
* #153 Add traits for the range iterators
* #156 add additional flags to to the XML document creation CStringParameter,
* #157 split range iterator in version with and without boundary flags.
* #158 Consistently implement the lncc metric for masked and unmasked images
* #159 Add option to chain filters into one entity.
* #160 Add a new gradient descent implementation with some step adjustment
Additional fixes:
* make all source files lowercase
* correct compilation with visibility=hidden
* handles signed and unsigned pixel values in DICOM
* let the xml-help write to a file instead of stdout
* Correct default suffix for 2D transforms.
* add attributes to boost::serialization transform IO
* Add the _1 quaternion that corresponds to no rotation
* Add printing of CAttributedData for testing
* Add an affine matrix with OpenGL like layout
* add a program to evaluate the pixel wise maximum intensity of number of images
* add support for setting the minimum number of digits in the output file names.
* Add SSD cost function with automasking baswed on intensity thresholds.
* Add xz to the possible compressors/decompressors that can be invoked on the fly.
* Add a 3D distance transform filter
* add label distance evaluation program
* add a min-frequency parameter to the classifier in the ICA perfusion analysis
* update to use supprt VTK >= 6.0
* add photometric interpretation and correct acquisition time saving in DICOM
2.0.13
Fixes for tracked bugs:
* #138 Handle compressed file extension properly when selecting the IO plugin.
* #143 Fix zero-fill boundary condition handling
* #144 Parallelize the prefiltering in the 3D interpolator
* 2dimageregistration: Exit if no cost functions are given
* 3dgetimage: add support for setting the minimum number of
digits in the output file names.
* factoryplugins: throw error if a factory plugin is not found
* make the basic interpolator operator in 3D thread save
2.0.12
Fixes for tracked bugs:
* #49: Parallize the 3D scale filter
* #125: Make slicelocation and slicespacing non-obligatory
* #127: Correct documentation and output to refers to 2D data.
* #128: Add program to convert multi-record 2D image to 3D image
Partial fixes:
* #126: (partially) add override for do_get_preferred_suffix()
* #129: (partial) move optional plug-ins that depend on external
libraries to /addons
Additional fixes:
* Fix 147 issues reported by Coverty http://scan.coverity.com
* Dissmiss 37 issues reported by Coverty als intentional or false positive
* wavelet slope statistics will now throw an exception if the slope is too short
* set the C++11 flag correctly in UNIX
* Correct strides when writing to the 2D output tensor field.
2.0.11
Fixes of tracked bugs:
* #106: mia-2dmyomilles - save feature images also when no segmentation is requested
* #122: boundary-condition plug-ins - remove width parameters since it is set internally
* #123: Correct handling of ICA instance when RV/LV classification fails for all numbers of components
Partial fixes:
* #104: improve some of the command line parameter descriptions
2.0.10
Fixes of tracked bugs:
* #3 add a image load plugins to filters
* #11 make the author information for the programs a possible program specific parameter
* #79 (experimental) remove the need to provide "<>" delimiters when reading 2d/3d vectors and don't write them
* #28 Add a filter that applies a transformation (2d/3d)
* #91 Fix regression by reintroducing the parameter 's' in the scale filter
* #93 Properly interpret the pixel value signedness when loading DICOM images
* #94 3d crop filter: change the parameter 'begin' to 'start' to conform with the 2D implementation
* #96 Add functions to TDelayedParameter to check key availability
* #97 Propper filling of output image in scale filters
* #98 (experimental) Dicomio: add support for reading multiframe dicom images
* #102 Correct a race condition in the image filtering when downscaling.
* #114 mia/3d/transform/rigid.cc lock access to m_matrix_valid, making code thread save
* #116 src/2dmyopgt-nonrigid.cc Add a missing coma in the transform creation.
Partial fixes:
* #14 core: add patient position enum and string-enum translator
* #89 (experimental) vtkio: change the method of storing vector field data from structured grid to structured points
* #101 [23]d/transform/spline.cc Check for the range/c-rate ratio in spline transfromations and give better error messages
* #103 2dimagefilterstack.cc: Add options to select first and last image of the series of images to be filtered
* #106 2dmyomilles.cc save the coefficient matrix also if no segmentation was requested
* #113 (needs testing): correct race conditions in parallel code
Additional fixes:
* 3D filters: correct buggy string in morphometric shape definition
* 3D transform: deduct the output image size from the deformation field range instead of the input image size
* Dicom: Remove required flag from the MediaStorageSOPClassUID tag
* 3D datafield: add functions to test whether the data hold by a field is unique (required for parallelization)
* Add mia/core/statistics.hh to the installed files.
* check precicion of pixel values in jpg and throw if it is larger than 8.
* remove some attribute translators that don't make sense
new image filters
* 2D load, transform
* 3D load, transform, morphological thinning
new notable command line tools
* mia-3dcrispsegment - evaluate a segmentation by first using fuzzy-cmeans and then classify based on the highest class probability
* mia-3dlandmarks-distance (experimental) evaluate the Euclidean distance between corresponding 3D landmarks
* mia-3dlandmarks-transform (experimental) transform landmarks by applying some 3D transform
2.0.9
Fixes of tracked bugs:
* fix 58: mia-fluid3d: Add parallelization
* fix 52,59,60,61,62: Add 2D Rotation only transformation and centerparameter to rigid and rotation
* fix 74: Tests: Fix failing tests on PowerPC
* fix 82: core: Add padding to the arrays in splineparzenmo
* fix 83: core: Add more tests to the Array-vector wrapper to ensure its proepr working
* fix 84: AnalyzeIO: Discard voxel-offset bytes when reading the image data.
* fix 85: IO: Add MetaImage IO support based on VTK.
* fix 86: Build: Test for Altivec and SSE and discard modules that require it
if not available, Closes Debian Bug #705384
* fix 87: core: Set default numbers of threads to 1 on powerpc is the Intel threading building blocks
version is < 4.1u2 (Interface version 6101), and warn user if she sets it higher
This is a workaround for Debian Bug #705385
* fix 88: core: add the --threads option to the options that are always provided
Additional fixes and changes:
* add a program to binarily combine two 3d images
* correct the evalation of the gradient-from vectorfield evaluation
* correct the gradient from vector field translation
* correct the handling of zero-argument flags to satisfy the address sanitizer of LLVM
* Parallelize some more code
* Correct the libinclude path in the pkg-config files
* Relax some tests that compare floating point evaluation to pass tests on i386 were
the limited amount of available registers results in a lower accuracy.
Closes Debian Bug #705383
2.0.8
Fixes of tracked bugs:
* fix #69: GSL simplex optimizer now interprets parameter epsilon as simplex size termination parameter
* fix #68: Add obtion to revert the triangle winding at surface creation.
* fix #65 #66, #67: Store the transformation vector field as transformation in fluid registration
* fix #55: isoscale filter now scales to the exact requested voxel size
* fix #54: Call cost.reinit() before evaluating the value.
* fix #53: make handler initialization thread save,
* fix #51: proper relebaling in stack filters
* fix #50: correct test for changed coefficient field size
* fix #46: Spline transformation now takes the penalty term as parameter (experimental)
* fix #41: correct tensor file header.
* fix #39: vtk-IO (exterimental): images (XML and legacy), mesh, and vector field
* fix #8: Add the interface to store attributes with transformations
Additional fixes and changes:
* fix compiling with clang-3.2
* fix error in voxel size scaling when (down)scaling 3D
* fix the transform upscaling to be based on the reference image size
* Fix the preferred suffix specification for vector field storing
* fix dependecies in miacore.pc to include TBB and BLAS
* fix comparison of entries and reading of the histogram.
* fix test for required option to use the method 'is_required()' instead of the enum 'required'.
* fix compilation errors with clang 3.2 that enforce more standard conformance
* fix stackfilter label join map evaluation, distance evaluation, label remap evaluation
* add xml scheme for xml-help output
* add test to make sure the scaling is to a positive size, even if the voxel size carries negative values.
* add initial implementation of voxel-to-isometric scaling
* add support for unsigned short and unsigned int to vistaio
* DICOM change the dicom loading interface, to allow default values for entries that should be
in the DICOM file and are needed for slice sorting in 3D data
* DICOM reading: When the locations show a negative Z-scale, then flip the output image to have a positive scale.
* DICOM also read the instance number for slice sorting
* update copyright year
* update BLAS handling
* update filter help for meshes
* enable section name based file names for userref
* remove empty option groups from --help-xml output
* remove obsolete VTK imageio implementation
* remove the requirement of equal-sized images in rigid registration, because it is not needed
* rename mesh distance program for consitency
* remove the vistaio files and always use the system provided version
2.0.7
* change build dependencies to cmake 2.8.5 because of GNUInstallDirs
* change installation directories to support multiarch
* add test for STRICT_DEPENDENCIES to nlopt and xsltproc
2.0.6
* move to new vistaio interface, minimum required external vistaio is now
version 2.1.14
* add a new 3D rotation only transformation
* fix regressions introduced with 2.0.4
2.0.4
* Intrusive changes
- change file nameing scheme of the 2D and 3D files
- change program description type and adapt all programs
- change the virtual method interface of 2D and 3D transformations
- eliminate fatcost related classes and plug-ins, use Fullcost
- remove the THROW macro in favour of the variadic template based create_exception function
- library SO version bump
* Added programs and functions:
- evaluate 2D and 3D transformation quantities
- 2D/3D transformation to strain matrix program
- mesh-to-mask distance for out-of core mask processing
- distance transform evaluation function
- add RGB image output (jpg, bmp, png)
- 3D trackpoint class
- new segmentation XML format and drawing method
- mesh filtering program
- program for out-of-core distance evaluation between masks
- program to create a norm image of the cost function gradient after translating it by means of a transformation
- estimating of percetual range reduction of histogram
- filter facility for meshes and a scaling filter
- gray scale jpeg support
- io handler links to parameter descriptions
- missing header to installation
- more tests for 3D point tracking
- option to spline based mutual infomation to eliminate outliers at the extrems of the histogram
- plugin for RGB<unsigned char> image saving
- possibility to store a prefered reference index and - tests accordingly
- program to combine three gray scale 8-bit images to one color image
- program to extract an iso-surface from a stack of images
- program to get a volume from a segmentation series
- program to track 2D pixel movement defined by a 2D transform
- some parallelization
- storing the prefered_reference parameter to the series registration programs
- support for plug-in hints in string parameters
- support for the attributes in the segmentation set version 2
- support for writing information about the supported file types for IO plugins
- supported data types and file extensions to IO plugin docu
- test case for 3d derivative at abitrary point
- test cases for more weights?
- test drawing version 2 segmentations and correct for closed/open line sections
- test for derivative_at and correct code
- test for distance from real function
- test for moving the pixels
- test for reading
- test for reading version 2 segmentation
- test for reading/writing version 2 segmentation
- test to see if all attributes are reordered
- tests for base class of new penalty model
- 2D trackpoint implementation
- algorithm for evaluating distances without getting the whole distance slice
- marching triangles mesh extraction program
- mesh filter
- C2DTransform: add derivative evaluation at abitrary coordinates, closes #2
- for vector based command line parameters: if the input size != 0, then expect exatly the corresponding number of coma separated values
- slopestatistics: add test for avarage level change
* Bug fixes:
- correct install filess: meanvar.hh
- 3d/image.cc: evaluating the cost at lower resolutions would actually deform the high resolution image
- Correct bug in normal evaluation on meshes
- Make most of the code compile with clang++ 3.1, g++-4.6.3 stdc++ std::atomic still conflicts, now uses tbb::atomic
- SegFrame: correct section test to set is_open properly
- cost correction to the iso-surface extraction
- to correct the number of output slices in FIFO filter
- correct bad mapping in label joining
- correct build order and tests
- correct build with clang and g++ 4.6.3
- correct gradient evaluation at the image boundaries
- correct mesh colorization to use dot product correctly
- correct plugin-path search for new locations
- correct preferred suffix for some IO plug-ins
- correct spline transform initialization to fix #22
- correct test for evaluating gradinet along the boundaries
- correct type of C3DTransformMock
- correct upper boundary for default unsigned short intensity range for histograms
- histogram: correct off-by-one error in histogram tail cutting function
- make test-history pass when compiling with -DNDEBUG
- mia/2d/iterator.cxx correct postfix increment of range iterator
- mia/3d/iterator.cxx correct postfix increment of range iterator
* Other changes:
- Change default of histogram tail cutting.
- Correct to wavelet slope classifier to account for stronger RV enhancement and handle free-breathing
and initial free breathing + later breathhold equally.
- Move the estimation of LV and RV peak to the first ICA.
- unified class to combine 2D images to 3D volumes
- add base class for spline penalty model
- 2D/3D transformation: add derivative_at for non-grid points
- assert that the generic load_image function is not instanciated
- avoid some missing return values warning by turning asserts into exceptions on release build
- change the plugin search path type
- clean up the load/save functions for transforms
- code cleanup: replace THROW by variadic template and review asserts
- copy attributes in syntetic reference creation based on ICA
- disable gsl error handler in release builds
- make studyid not needed when reading DICOM
- move from anonymous enummerates to static const for pixel type traits
- make the io-plugin know about its own suffixes
- make the slice counter short, this should suffice for stack based distances
* Documentation
- Sort members in Doxygen documentation
- myocard intensity curve estimation: Update the reference frame help and allow that the frame
is selected as the LV peak from the registered set. As a fallback the last frame may be used.
- IO plugin hint to command line parameters
- add a xml scheme for the segmentation sets
- docu about supported extensions and data types
- more internal linking of documentation
- correct output for non-parameter taking plugins (i.e. IO plugins)
- correct plug-in descriptions
- correct the help for IO options that use the plugin-hint
2.0.3
* version bump to reflect API changes in 3D transform
* add more vector field conversion programs
* remove save function and add vector field transformation
* add a creator string to the output PNG file
* correct bugs in the the fifo filter (thanks Matt Skinner for pointing it out)
* add a program to track pixel movement
* add a convertor from a 3D transform to an according vector field
* correct docu
* revise the error message and handling of output file type
* properly install miamesh-*.pc
2.0.2
* correct code to work on 32 bit
* Correct implementation of landmarklistio test
* Add non-SSE implementation of Divcurl
* turn off sse implementation on non-64 bit arch
* remove some unneeded sse code
* update docu
* correct bad handling of missing argument in command line parser
* add the preferred suffix for analyze files
* add infrastruture for axamples and a first example
* remove StudyID from required 3D reading parameters, since it may not be available
* add loading and saving the landmarks
* add run_filters based on variadic templates
* add a resize filter that can also enlarge the image and uses the center of the data as reference point
2.0.1
* update installation of files
* test proper reset of parameters and correct it
* add support for 64 bit integer on 64 bit platforms
* 2dseries2sets: correct bug that would result in empty files if output directory is the same as location of the input files
* correct passing of attributes in filters
* add a pc file for the mesh library
* correct installation of pkg-config files
* correct attribute handling in ICA reference image creation
* Add insertion of a range of attributes
* update build system to silence warnings
* update icons and desktop files
* add menu entries for the documentation
* add a specific boolean option
* fix race condition in the build process
* correct the doc installation path and remove GZIP from man page compression
* make watch test more tolerant (still a shaky test that depends on the system load)
2.0.0
* docu: update doxygen generated docu
* docu: add support for building all the documentation
2.0_pre20120305
* library: correct compile errors with g++4.6
2.0_pre20120302 is considered to be the initial release
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