News

nat.templatebrains 0.9

• 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

nat.templatebrains 0.8

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)

nat.templatebrains 0.7

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.

nat.templatebrains 0.6.4

• 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!

nat.templatebrains 0.6.3

• 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 / mirroing between template brains (#21).

nat.templatebrains 0.6.2

• fix issues with git repository cloning on Windows

nat.templatebrains 0.6.1

• fix bug in mirror_brain for non-zero origin (#14)

nat.templatebrains 0.6

• 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.

nat.templatebrains 0.5

• 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

nat.templatebrains 0.4.1

• 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

nat.templatebrains 0.4

• 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

nat.templatebrains 0.3

• 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.

nat.templatebrains 0.2

• 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

Reference manual