Merging Latest Development Branch #7
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Owner
rg2
commented
Aug 1, 2021
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rg2
commented
- AVFoundation is used to write videos on MacOS when ffmpeg is not found,
- Single-view pelvis registration example now has option to skip log remap - useful when running on projection data that has already been remapped, such as conventional radiographs (e.g. not intraoperative fluoroscopy),
- Adding readers for data formats from the Ljubljana 2D/3D datasets (.rad/.raw and .sta/.raw),
- Adding general utility function and a command line tool for converting planar radiography DICOM files (such as fluoroscopy or portable X-ray imaging) into the xReg projection data structure - this replaces any need for specific CIOS Fusion convertors,
- Adding some more options to the tool for adding landmarks to projection data HDF5,
- DICOM metadata reader updates:
- Fix bug with failed assertion on convolution kernel from Siemens CT scanner,
- Using boost::optional for optional fields instead of an additional boolean variable,
- Adding many more fields, mostly those used with fluoroscopy or radiographs,
- Adding HDF5 (de)serialization of DICOM fields - useful for storing original metadata in HDF5 projection data files,
- Updates to the DICOM volume converter and resampled program:
- More options for determining output file names,
- Ability to exclude input series based on derived, secondary, or modality,
- In tool for extracting NIFTI from xReg HDF5 projection data file, added an option for discarding geometry information,
- Adding tool for creating a video from a directory of 2D images,
- Fixing bugs in 2D/3D registration replay tool:
- Always use even frame dimensions - required by ffmpeg,
- Fixed issue where view border thickness was at most 1 pixel,
- Fixed border thickness bug in projection data tile and remap tool,
- Adding a tool for batch remapping a directory of DICOM files to a collection of 2D images - e.g. PNG or JPEG,
- In DICOM metadata report tool, can now skip printing all fields verbatim and also added ability to print out the DICOM fields as parsed into the xReg DICOM struct,
- Updated boost source URLs in build scripts,
- Added support for terminals with zero width or height to the program options utility,
- Adding some new combinatorial utility functions (e.g. binomial coefficient, sampling random combinations, brute-forcing all choices of 3 or 4 objects),
- Fixing a bug when writing zero-length (empty) strings to HDF5,
- Adding routine for fitting a 2D circle from points using RANSAC,
- Various other miscellaneous updates.
* ReadDICOMFileBasicFields() will return an instance of a populated
info struct instead of populating a struct passed via pointer
* optional fields of DICOMFIleBasicFields no longer use separate bool
valid flags, but are now boost::optional's
* not asserting when the conv. kernel field has more than 1 element,
but now printing a warning and discarding values after the first
* patient id may be excluded
* patient name may be used
* naming conventions may now be combined instead of only allowing a
single, e.g. can now name using both series desc. and conv. kernel.
HDF5 proj. data files
* useful for testing registration of 2D radiographs which typically "already have bone bright"
fixing a bug with computing border width minor grammar fix
or a directory of images
collection of images
the pixel spacing values were explicitly provided by the source metadata or whether they were guessed
separate FCSV pixel spacing value when pixel spacings are not provided by the image metadata
no program usage formatting is performed in these cases any longer (previously triggered an assert)
created using a NIFTI extracted from a proj. data H5 file which had estimated geometries
* this is now superceded by the DICOM metadata
* This has been replaced by the more general routines that process 2D
radiographs stored as DICOM
* it caused some linker warnings when building on Big Sur * for targeting 10.14, we can just build in a 10.14 VM
* now handles updates to ffmpeg version number * updated boost URL
* updating custom cmake directory * using quotes around xreg directory to handle a directory with spaces
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