- shortest_bridging_seq complains if template brain does not exist in graph (#34)
- xform_brain does not transform when sample and reference are identical (#33)
- templatebrain constructor does not need all boundingbox/origin etc fields to be specified (#24)
- as.templatebrain.im3d should not need an im3d made from a file (#25)
- Fix unstated dependencies in ‘tests’ error noted by CRAN r-devel for 0.8.2
This is another major version bump since there is significant new/changed behaviour in xform_brain brain and friends which will now tag transformed objects with a registration template space. This means that nat functions will typically not be need to told the space of an object such as a neuron list in many cases, but some objects will have a new regtemplate attribute.
- xform_brain should tag objects with their space (#16)
- add regtemplate function as part of this
- fix xform_brain should give better error when sample unknown (#29)
- fix: teach plot3d.templatebrain to work with regtemplate (#32)
- fix: add_reglist should not return anything (visibly) (#30)
This is the first public release since 0.6.2 and there are some significant changes under the hood, hence the major version bump.
- fix inversion of reglist objects read from disk (so that xform_brain calls depending on reglist objects work in both directions).
- add support for memoisation of shortest_bridging_seq so that we do not need to rescan registration directories / reload on disk reglist objects.
- Add regtemplate function and integrate it with xform_brain and mirror_brain. It will often no longer be necessary to specify the initial space of objects to be transformed - you’ll still need to specify your target space though!
- add support for reglist objects containing one or more arbitrary transforms as bridging or mirroring registrations. A function add_reglist makes it easy to add new in memory reglist objects to those that can be used for bridging / mirroring between template brains (#21).
- fix issues with git repository cloning on Windows
- fix bug in mirror_brain for non-zero origin (#14)
- add functions to download new registrations from git repositories: add_reg_folder, download_reg_repo, local_reg_dir_for_url, update_reg_repos.
- add tests and documentation for new git functionality.
- downloaded registrations are automatically made available on package load.
- xform_brain can now find the best available path from one template to another automatically.
- this uses new functions bridging_graph, shortest_bridging_seq and allreg_dataframe
- xform_brain now has an imagedata argument (to set sensible defaults for handling of inverse registrations, which are very slow for image data)
- add doi field to templatebrain object
- fix: mirror_brain passes on transform argument
- dev: now imports igraph
- dev: requires nat >=1.7.0
- fix handling of regName in templatebrain
- fix as.templatebrain.im3d (completely broken due to variable name error)
- better defaults in as.templatebrain.im3d / as.templatebrain.character (both name and short name will be take from file name)
- print.templatebrain now includes short name
- prepare for CRAN release
- fix export of is.templatebrain
- give mirror_brain explicit transform argument
- full examples in mirror_brain and xform_brain functions and templatebrain-meths.
- add FCWB.demo as data object that can be loaded
- dev: integrate with nat.flybrains build on travis
- add bridging_sequence function to return a bridging registrations sequence that may span more than 2 template brains.
- xform_brain can apply compound registrations in one streamxform call (but depends on nat >=1.5.9 and CMTK >= 3.2.2)
- add is.templatebrain and as.character.templatebrain utility functions.
- switch to single option regdirs for all paths
- no longer suggests nat.flybrains but includes basic tests with internal data.
- move all generic functionality from nat.flybrains (which is now a data only package).
- give xform_brain a via option
- add options for directories containing bridging and mirroring registrations nb these can accept multiple dirs, but registration names must be globally unique.
- suggest nat.flybrains for tests
- package docs and tests