nat - v1.10.4

What's Changed

• xyzmatrix<- can now set list columns containing coordinates in forms like `list(c(1,2,3), c(4,5,6)) (#485)
• a new function xyzmatrix2list() is added to achieve this output format directly
• xyzmatrix() can now extract coordinates from a 3-vector like c(1,3,5) (#486)

Full Changelog: https://github.com/natverse/nat/compare/v1.10.3...v1.10.4

- R
Published by jefferis about 4 years ago

nat - nat 1.10.3

nat 1.10.3

Some new features, speed-ups and bug fixes including from @dokato and @jonmarty. Thanks to @PostPreAndCleft and @artxz for bug reports.

• xyzmatrix can now get and set character columns containing coordinates in forms like "(1, 6, 3)" or "1 6 3" (#449)
• also a bug fix for the same (#451)
• Improve reading of Simple Neurite Tracer fills (#448)
• Fix bug pan3d() not found (#447)
• Added support for multi material binary Amira surface files while fixing "Bad triangle numbers" error in read.hxsurf() (#445)
• reroot function added with support for neuronlist (#463, @dokato).
• Add xform() and xyzmatrix<-() methods for mesh3d objects
• Don't clean mesh3d objects read from ply files by default
• summary.neuron now prints number of subtrees (#462, @dokato)
• fixes in xyzmatrix.list() (#484)
• new c.hxsurf() method (#482, @dokato
• Teach write.neuron() and write.neurons() to put metadata in SWC header
• switch to GitHub actions
• speed-ups for simplify_neuron() in part through new natcpp package (#472,#473,#474)
• Fix Strahler order fails on a simplified neuron with no branches (#464 @dokato)
• add function for rerooting neuron reroot.neuron() and reroot.neuronlist() (#463, @dokato)
• New neuronlistz() fast access to neuronlists stored as zip files (#456)
• print method for neuronlistz() (#468, #466 @dokato)
• pointsinside: defer check for Rvcg until committed to use it (#455,454)
• Zip command line character limit error fix (#452 @jonmarty)

https://github.com/natverse/nat/issues?q=closed%3A2020-09-11..2021-09-20+

nat 1.10.2

This release brings support for reading, plotting and writing 3D surface meshes of neurons into line with the skeleton support. It also includes an essential fix requested by CRAN.

https://github.com/natverse/nat/issues?q=closed%3A2020-02-23..2020-09-11+

• Fix test failure on R-devel (R 4.1) for c.neuronlist (#444)
• Add print.neuron(), print.neuronlist(),print.dotprops() methods #443
• Better support for reading / plotting neuron meshes (#441, #442)
• Bug in xyzmatrix() for 0 row data.frames (#433)
• Updated parameter for toggling grid lines in plotly (#432)
• Add support for Amira hxsurf binary format to read.hxsurf() (#431)
• improve error message for cmtk.version() (#430)
• Remaining items to move from elmr (#428)
• Turn off grid lines when using plotly engine (#427)
• Move features to nat from other packages (#423)
• Add support for thin plate spine transformations via tpsreg() (#289)

New Contributors

• @jonmarty made their first contribution in https://github.com/natverse/nat/pull/452
• @dokato made their first contribution in https://github.com/natverse/nat/pull/459

Full Changelog: https://github.com/natverse/nat/compare/v1.10.1...v1.10.3

- R
Published by jefferis about 4 years ago

nat - nat 1.8.13

This release backports a few urgent fixes to the 1.8 branch. It should be the last release of the nat v.1.8.x series and was prepared to satisfy a quick turnaround from CRAN to fix a test error that has recently appeared. Note that all fixes in this release are also present in current master, which we would recommend for most users.

• Fix very slow loading of neurons in neuronlistfh() objects. Apparently due to a change in behaviour in R 3.6.0 (#402). Thanks to Shanice Bailey and Lisa Marin for the bug report.
• Fix ndigest check error on CRAN (#411)

It also updates URLs to point to nat's new home organisation on GitHub (https://github.com/natverse/).

- R
Published by jefferis over 6 years ago

nat - nat 1.9.1

• Fix very slow loading of neurons in neuronlistfh() objects. Apparently due to a change in behaviour in R 3.6.0 (#402). Thanks to Shanice Bailey and Lisa Marin for the bug report.

- R
Published by jefferis over 6 years ago

nat - nat 1.9.0

We are bumping a whole version point because of some changes in the default behaviour of nat. We do not expect to submit this first version in the 1.9.x series to CRAN without further testing, but it is our current recommended version for general use.

Significant changes:

• read.neurons will name neurons in the neuronlist that it returns by their filename after removing the file extension. So the neuron read from file "n1.swc" will now be named "n1" not "n1.swc". (#383)

• write.swc normalises SWC files to maximise external compatibility. The canonical SWC form gives each point a numbered identifier increasing from 1 to the number of points. However many SWC files in the wild do not respect such an ordering. The new behaviour will result in cases where SWC files will be written out with a different point ordering from earlier versions of nat; nevertheless we prefer this behaviour since it is a source of confusion for new users since many external programs cannot read SWC files where this is not the case. The original behaviour can still be requested (#358).

• The use of operators e.g. adding or multiplying neurons by a constant is now provided by the Ops approach (see ?groupGeneric in main R help). This is a fairly large change under the hood, but should not have any user visible effects other than the fact that it is now possible to use the same functionality for hxsurf and mesh3d objects.

New vignettes:

• Working with Individual Neurons as Graph Structures
• NeuroGeometry: Analysing 3D Morphology of Neurons

Additional changes:

• Support for CMTK deformation fields
• Always pass on ... for reglists in xform() and friends. This ensures that nat.templatebrains::xform_brain can fall back to an affine registration when a non-rigid registration fails (#365)
• Fix thinko in re-ordering vertex ids for SWC files (#366)
• Add makeboundingbox() for constructing a boundingbox explicitly rather than from an object. This allows boundingbox() to work for matrices of 3D points (#222)
• Export nrrd.datafiles() + nrrd doc fixes (#316)
• Teach materials() to return col for amiramesh/im3d (#284)
• Fix nview3d() "oblique_right"
• Pass ... on to spheres3d to plot somata with alpha transparency (#370)
• as.data.frame.neuronlist() makes autonames when none present (#371)
• Check that ngraph() edgelist references valid vertices to avoid segfaults in igraph library (#363)
• Fix bug in constructing im3d() with image bounds (#205)
• Allow dotprops objects to be plotted in 2D (#112)
• Speed up spine() by only considering endpoints (#372)
• Export graph.nodes() and improve docs for root points (#373)
• Speed up pointsinside() by checking if inside bounding box of surface mesh (progress on #353)
• Teach read.neurons() to read remote zip file (#381)
• Fix invert_reglist() for mix of swapped/unswapped regs
• Fix bug in write.im3d()/write.nrrd() for raw detached nrrd (#384)
• Export is.im3d()

- R
Published by jefferis about 7 years ago

nat - nat 1.8.12

nat 1.8.12

• Speed up (2-3x) summary.neuron(list) by faster calculation of total cable length. Note that this may cause some changes in the reported cable length because all cable is now included (as it should always have been). (#361)
• fix bug: dotprops do not get resampled labels bug (#360)
• Add nview3d function to set anatomical viewpoints (#359)

- R
Published by jefferis about 8 years ago

nat - nat 1.8.11

nat 1.8.11

Fixes * pointsinside fails for points >1e5 from mesh (#354) * as.neuron should work for an igraph made from an ngraph (#356) this is helpful if you e.g. delete nodes/edges from an ngraph object * breaking change with testthat v2 (#355)

- R
Published by jefferis about 8 years ago

nat - nat v1.8.10

nat 1.8.10

• pointsinside now works with alpha shape (ashape3d) objects directly (#350)
• On windows add cygwin binary directory to path if not present (fixes errors with missing cygwin DLLs)
• workaround for some functions (eg those using CMTK registration folders) that were affected by file.exists("/some/real/registration.list/") returning FALSE on Windows
• Fix cmtk.reformatx under Cygwin - output NRRD file path (but not other paths) must be munged for reformatx - not sure why this isn't handled internally.
• Fix as.mesh3d.ashape3d messing up the order of triangle vertices which was giving problems with pointsinside (#349)
• Fix pointsinside to return TRUE for vertices defining mesh (with distance=0) (#348)
• Switch pointsinside to use Rvcg::vcgClostKD, thereby fixing some cases where points were incorrectly reported to be inside a surface. (#352)

- R
Published by jefferis over 8 years ago

nat - nat 1.8.7

nat 1.8.7

This release includes some bug fixes and significantly improved online package documentation visible at http://jefferis.github.io/nat/ including two vignettes.

• Teach xform and friends to transform soma positions (#206)
• Copy attributes (including templatebrains) of neuronlists when subsetting (#310)
• Fix error in read.amiramesh for RLE encoded files. (#317) (reported by K. Hornik)
• replace nat::trim with base::trimws (#313)

- R
Published by jefferis almost 9 years ago

nat - nat 1.8.8

nat 1.8.8

• add xyzmatrix<-.neuronlist so that we can replace the vertices of a set of objects in one go (#328)
• add as.mesh3d.ashape3d thereby adding support for 3D alpha surfaces generated by the alphashape3d package (#337)
• add as.hxsurf to convert surfaces (#332)
• add nvertices as generic method to find the number of vertices in an object (#329)
• add plot3d.cmtkreg to visualise domain of CMTK registration (#333)
• speed up resample function (and seglist2swc) (#336)
• add an option to override default progress bar behaviour for nlapply (and many other functions that use it) (#322)
• make plot3d more forgiving of colour specification (#331)
• fix overwrite=T option for landmarks files (#319)
• fix prune_edges for paths with opposing edge directions (#320)
• make read.amiramesh cope with different NA values (#324)
• fix crashing bug in read.neuron.hxlineset for malformed files (#325)
• only warn if xform.neuronlist fails to transform soma positions (#326)

- R
Published by jefferis almost 9 years ago

nat - nat v1.8.9

nat 1.8.9

• fix reading of neurons when origin is not an endpoint (#342) nb this bug was introduced in 1.8.8
• fix edge case for is.neuron when applied to tibbles (#338)
• add PlotSubTrees option for plot.neuron (#339) thanks to Zhihao Zheng

- R
Published by jefferis almost 9 years ago

nat - nat 1.8.6

• Add xform.data.frame method (#309)
• Add invert_reglist function (#308)
• Fix bug in imslice storing position of new singleton dim (#306)
• Fix namespace issues for smooth_neuron

- R
Published by jefferis over 9 years ago

nat - nat 1.8.5

nat 1.8.5

The main feature of this release is improved support for nat+CMTK on Windows. - teach voxdims.character to get voxel dimensions straight from image file on disk enhancement (#303) - teach coord2ind to accept nat.templatebrains objects for imdims (#302) - add simple smooth_neuron function (#300) - fix bug reading amira surfaces when Color precedes Id (#305) - cmtk.reformatx needs to use system2 (#301) - Don't use shell features on Windows (#295)

- R
Published by jefferis over 9 years ago

nat - nat v1.8.4

• fix build failures with testthat >=0.12 (#293)
• ensure that nat still works with igraph <1.0 (#298)
• fix read.hxsurf failure when a region is not listed in the Parameters section (#291)
• Protect find.neuron from trying to filter with a neuronlist (#299)
• Fix simplification of reglist containing one cmtkreg (#297)
• Don't lose swap attribute when >1 cmtk registrations in reglist (#296)
• Documentation improvements for neurons and file formats

- R
Published by jefferis over 9 years ago

nat - nat 1.8.2

• roll back rgl NULL mode changes from 1.8.0 in favour of less invasive approach of marking the majority of rgl based plotting examples as donttest (#274)

- R
Published by jefferis almost 10 years ago

nat - nat 1.8.3

• nat now handles compound registrations via reglist objects (#286). These can contain homogeneous affine, CMTK registrations (in disk or in memory) and R functions (which can be used to wrap arbitrary registration types not directly supported by nat). NB xformimage.reglist will currently only work for CMTK compatible registrations.
• add mask(.im3d) function to zero out parts of an image (#285) Looks after im3d attributes and material name to integer pixel level mapping.
• add read.ngraph.swc which can be used to read even malformed SWC files (such as those containing cycles) (#282). This is exposed by giving read.neuron an argument class, which can be set to 'ngraph' instead of 'neuron'. Inspired by https://github.com/BigNeuron/BigNeuron-Wiki/wiki/BigNeuron-Imperial-College-London-Hackathon-Discussion-Notes
• add prune_edges to delete by specifying neuron edges rather than vertices (#280)
• Give give spine an invert option (#279) using prune_edges
• Teach spine to return point ids (#278)
• fix bug in pointsinside for distant points (#290)
• fix subsetting neuronlists with a single column data.frame drops column name (#276)
• Fix invert option of subset/prune_vertices returns an error with igraph::dfs points (#288)
• Fix fileformats(, rval='info') to return a well-formatted data.frame
• The idiom neuronlist[,] will never drop columns (since it is a useful shortcut for as.data.frame(neuronlist)) (#277)

- R
Published by jefferis almost 10 years ago

nat - nat 1.8.1

nat 1.8.1

• fix non-canonical URLs to CRAN packages (thanks to Uwe Ligges)

- R
Published by jefferis about 10 years ago

nat - nat 1.8.0

nat 1.8.0

This is tagged as a major release because of a change in behaviour that (by default) suppresses interactive rgl windows when running in batch (non-interactive) mode. See ?nat "rgl Package" section for details. - nat will only activate an rgl display in interactive mode, otherwise defaulting to rgl's NULL mode display. This should help run nat in batch mode situations including knitr runs, the CRAN build server etc. (#272) - Add summary.neuron(list) functions to calculate tree statistics such as number of nodes and cable length for neurons/neuronlists (#269) - Automate progress bar in nlapply - this will always show in interactive mode when there are more than 10 neurons being processed. (#271) - Fix bug in c.neuronlist when combining more than 2 neuronlists (#270) - Fix bug in read.neuronlistfh on Windows (#268) - Fix bug when constructing an ngraph with a single node (#267) - Fix bug in [<-.neuronlist when assigning a whole data.frame using (#256) - Fix bug in bounding box with input = "bounds" (#273) - Documentation improvements (especiall package overview - see ?nat)

- R
Published by jefferis about 10 years ago

nat - nat 1.7.2

• new function subset.neuron can keep/remove individual vertices from a neuron based on internal variables such as position, width, vertex number etc while still producing a valid neuron with an appropriate graph structure (#261)
• this depends on a new low level function prune_vertices that can remove specified vertices
• this has also enabled the prune.neuron method to be defined for the first time enabling pruning by spatial proximity (#258)
• teach mirror to work with image data (#265) and enable better handling of the mirrorAxisSize by allowing this to be supplied as a bounding box (#254)
• teach as.im3d.matrix to use an im3d object to specify the desired space (#263) This enables for example a set or tracings to be turned into volume data that exactly matches a specific template brain.
• fix bug: seglengths fails for neurons with multiple trees bug (#257)
• fix bug: xformpoint.cmtkreg fails for in memory registration lists (#259)

- R
Published by jefferis about 10 years ago

nat -

• new functions strahlerorder and prunestrahler to calculate the Strahler order of points in a neuron and to remove lower order (terminal) branches (see #253)
• fix is.cmtkreg for non-existent files (and better handling of status messages)
• export segmentgraph function for end users
• enable segmentgraph to return segment ids

- R
Published by jefferis over 10 years ago

nat - nat 1.7.0

CRAN release - implement extraction/replacement of the data.frame attached to a neuronlist using the [ operator (#217) - fix xform of image data (#143, #199) - implement handling of inverted (swapped i.e. reference to sample) registrations in xform(image) (#199) - normalise handling of registration sequences and inversion in xform/image/points (all 3 expect reg to be in sample to ref order and for any individual registration to be marked with swap=T if it is ref->sample) - read.nrrd no longer returns an im3d (use read.im3d) (#238) - teach write.nrrd to handle more diverse inputs (including #242) - add reading of detached nrrds (#236, #237) - add ability to write detached nrrds - add ability to make a detached nrrd from a compatible amira file on disk (#243) - new function is.im3d - fix cmtk.targetvolume for templatebrain objects (#241) - fix cmtk.targetvolume for --target-grid specification (#240) - fix names for [.neuronlistfh with null df (#250) - plot.neuron can cope with some NA coordinates - teach plot.neuron(list) to cope with NA points (#247) - boundingbox has an na.rm argument (#246) - teach droplevels.neuronlist to use extra arg (#249) - teach plot.neuron to plot soma (#245) - fix cmtk.call for numeric args (#235) - set read.hxsurf RegionChoice="both" by default - document return values of cmtk.statistics in more detail (#252) - support for igraph 1.0 (#248)

- R
Published by jefferis over 10 years ago

nat - nat 1.6.6

• Fixes description capitalisation/quoting for CRAN
• Adds ability to write dotprops neuron objects to SWC format (#233)
• fixes bug in xyzmatrix.neuron for single point neurons (#234)
• likewise for xyzmatrix.default for 1-row >3-col matrices

- R
Published by jefferis over 10 years ago

nat - nat 1.6.5

This release includes a host of small enhancements and bug fixes - add xyzmatrix get/set methods for class mesh3d along with xform.shape3d. This should enable rgl::mesh3d objects (used in a number of other packages) to be transformed using CMTK registrations. - add tail.neuronlist - add as.data.frame.neuronlist for convenient generation of a data.frame from a neuronlist - add help topics for generics subset and plot3d so that e.g. ?subset will give the option to see our documentation as well as base docs. - subset.hxsurf drops unused vertices by default - add sample surface object of mushroom body - teach cmtk.statistics to handle imagetype == 'label' (#221) - plot.neuronlist sets axes based on boundingbox of all plotted neurons, not just the first neuron (#223) - plot.neuron(,AxisDirections) argument is re-implemented (#224) - don't warn when read.neuronlistfh changes the directory location on disk (#157) - remove superimposed plots in mirror example (hope this will fix build on macosx snowleopard) - teach read.neurons to OmitFailures when reading in a neuronlistfh object. - fix handling of default colours in plot.neuronlist and plot3d.neuronlist (#230) - fix plot3d.neuronlist returns one element per neuron - fix bug in xformpoints.cmtkreg when some points could not be transformed - now give NAs as expected (#227) - fix bug when xform(na.action='drop') dropped dimensions when only 1 valid point resulted (#228) - teach xyz.matrix<- to work for bare 3 column matrices (i.e. without colnames) - fix bug in xformimage where input image was not being passed on when transforming with a matrix. - read.hxsurf can accept RegionChoices='both' (see ?read.hxsurf) - fix: unary -.neuronlist behaves - docs: numerous minor doc/example improvements - dev: improvements in test coverage (up to 84%) catching numerous small bugs in the process.

- R
Published by jefferis almost 11 years ago

nat - NeuroAnatomy Toolbox v1.6.4

Released to CRAN. Changes since the last github release (v1.5.3) are itemised below.

nat 1.6.4

• Edits to package description for CRAN

nat 1.6.3

• fix invalid url in README.md noticed by r-devel/BDR

nat 1.6.2

• add as.im3d.matrix which allows conversion of a Nx3 matrix of coordinates into a volume representation
• add ability to use a neuron's StartPoint in the spine function that finds the longest path (aka backbone or spine) of a neuron
• fix xformimage's handling of in-memory registrations
• fix bug in read.hxsurf docs
• dev: add coveralls code coverage support
• dev: fix use of require in package code (a new note from r-devel)
• dev: fix a cmtk-dependent test that was not guarded against cmtk's absence

nat 1.6.1

• add ability to transform images (specified as path to a file)
• register image file formats to use with read/write.im3d
• register amira types including linesets, surfaces and landmarks
• add ability to read neurons from remote url
• add support for applying multiple registrations in xform.neuronlist, as well as vectorisation (where each registration is applied to a different object)

nat 1.6.0

• Add support for reading NeuroML and Fiji Simple Neurite Tracer neurons
• recognise SWC neurons by content (rather than just file extension)
• can write a set of neurons to a zip archive (?write.neurons)
• getformatreader returns name of identified format
• Give find.soma and find.neuron invert arguments
• internal function normalise_swc sets sensible defaults for column values (and these can be overridden from some user functions).
• fix resample.neuron so that it keeps all subtrees and handles width and labels
• fix seglist2swc when receiving flat seglist
• ngraph attaches vertex data to each point and now includes diameter
• fix is.nrrd for raw input
• fix node colours in plot3d.neuron when WithAllPoints=TRUE

nat 1.5.14

• add nlscan function to review a set of neurons, optionally selecting a subset
• add find.soma function to select neurons whose cell bodies fall within an rgl seelection box (thanks to Ben Sutcliffe).
• add setdiff, intersect and union generics with implementations for neuronlist objects (note this is done in more or less identical fashion to generics defined in the dplyr package).
• give write.neurons a format argument to make it more obvious that this is an option rather than pointing people to the write.neuron docs (suggestion from Ben Sutcliffe)
• teach as.neuronlist to handle inputs with empty (rather than NULL names)
• simplify calculation of inertia in dotprops
• minor doc fixes and clarifications

nat 1.5.13

• mat2dof output gets descriptive rownames
• ndigest.neuronlistfh only uses 2 key fields (keyfilemap and df)
• fix bug in locating cmtk when only the cmtk wrapper script is in the path (spotted on neurodebian with /usr/bin/cmtk)
• fix bug in compound registrations when CMTK <3.2.2
• fix rgl import errors on r-devel
• switch from RANN to nabor package for finding nearest neighbours
• dev: update help to roxygen2 4.0.2

nat 1.5.12

• fix bug in updating neuronlistfh objects from remote url
• nlapply now has options for progress bars and parallelisation by using the plyr package under the hood.
• c.neuronlist can now join lists with attached data.frames with different columns (missing values are filled with NAs). This also applies when some neuronlists have no attached data.frame at all.
• read.neurons can read neuronlist files from disk
• cmtk.statistics now has a Verbose argument
• warn if resmapling a neuron with multiple subtrees that only the main subtree will be kept.

nat 1.5.11

• add cmtk.statistics function
• fix infinite recursion in cmtk.targetvolume

nat 1.5.10

• fix: write.neurons subdir argument can accept a column of the attached data.frame (unquoted)
• fix: write.neuron(s) can add an extension to an output filename that does not have one
• write.neurons now has an explicit files argument
• cmtk.targetvolume (and therefore cmtk.reformatx) can accept e.g. templatebrains (as contained in nat.flybrains package) to specify target image for registration.

nat 1.5.9

• fix transformation of points using compound CMTK registrations (this was broken for CMTK<3.2.2, so a workaround is required).
• Add cmtk.version function.
• xyzmatrix can cope with lower case x,y,z for column names
• doc: fixes in xform
• dev: fix test for winbuilder

nat 1.5.8

• Add boundingbox.list method to find boundingbox for neurons, surfaces etc
• nmapply and nlapply get OmitFailures arguments
• nlapply also gets a subset argument
• both arguments are also added to xform/mirror.neuronlist
• dotprops.neuronlist also gets the OmitFailures argument.
• fix subset.neuronlist handling of numeric indices
• minor bug/doc fixes

nat 1.5.7

• teach plot3d.neuronlist and friends to plot soma locations.
• add npop3d function to remove last plotted neurons (identical to flycircuit::pop3dfc, except that it works with any neurons plotted by plot3d.neuronlist, rather than only those plotted by plot3dfc)

nat 1.5.6

• give mirror/xform.neuronlist subset arguments
• add plot3d.boundingbox
• give plot(3d).neuronlist a SUBSTITUTE argument that can be used to control non-stadard evaluation. This is useful for people who wish to incoroporate these funcitons inside other user-defined functions. See ?subset.neuronlist for details.
• fix: write.neurons into subdirs when df=NULL

nat 1.5.5

• fix bug in reading swc files with many decimal places specific to R 3.1.0
• fix bug in header when writing swc files [ajdm]
• read.im3d now adds file as an attribute to output
• read.im3d can now add amiramesh files without the standard file extension
• doc: minor improvements to read.im3d docs and examples

nat 1.5.4

• remove internal is.gzip function and depend on nat.utils >=0.4.2

- R
Published by jefferis almost 11 years ago

nat - NeuroAnatomy Toolbox v1.5.3

nat v1.5.3

This is the current stable release on github. Changes since the last stable release on CRAN (v1.4.10) are detailed below.

Changes in version 1.5.3:

• new function pointsinside to determine if points (e.g. neuron) are inside a closedd surface
• resample.neuron implemented (no support for interpolating widths or multiple) subtrees
• dotprops.neuron can resample to a consistent segment length
• consistent return values for as.seglist and seglengths when all subtrees are returned
• seglengths can return lengths for each edge as well as the sum for each neurite segment (the default)
• suppress remote tests if flybrain unreachable
• zenodo DOI for package

Changes in version 1.5.2:

• add seglengths function for neurons
• add segmentgraph function to produced a simplified graph representation of neurons with one edge per segment
• add potential_synapses.dotprops method
• add as.seglist.neuron method
• teach plot3d.hxsurf and subset.hxsurf to accept regexes
• always drop unused vertices in as.mesh3d.hxsurf
• fix bug in write.neurons when subdir not specified
• fix colouring of vectors by plot3d.dotprops
• dev: switch to roxygygen2 v4

Changes in version 1.5.1:

• add potential_synapses (from nat.as)
• surfaces: add subset.hxsurf and as.mesh3d
• Teach read.im3d to read Vaa3d raw format
• add plot.neuronlist (for 2d plotting)
• add c.neuronlist function to combine neuronlists
• add db argument to plot3d.character
• make WithNodes=FALSE the default for plot3d.neuronlist
• make asp=1 the default for image.im3d
• write.cmtkreg warns if versions specified by cmtkreg attribute and argument differ (to avoid writing old registrations as if they were new or vice versa)
• fix: prune.neuronlist method signature (and therefore dispatch)

- R
Published by jefferis over 11 years ago

nat - NeuroAnatomy Toolbox v1.5.2

nat v1.5.2

This is the current stable release on github. Changes since the last stable release on CRAN (v1.4.10) are detailed below.

Changes in version 1.5.2:

• add seglengths function for neurons
• add segmentgraph function to produced a simplified graph representation of neurons with one edge per segment
• add potential_synapses.dotprops method
• add as.seglist.neuron method
• teach plot3d.hxsurf and subset.hxsurf to accept regexes
• always drop unused vertices in as.mesh3d.hxsurf
• fix bug in write.neurons when subdir not specified
• fix colouring of vectors by plot3d.dotprops
• dev: switch to roxygygen2 v4

Changes in version 1.5.1:

• add potential_synapses (from nat.as)
• surfaces: add subset.hxsurf and as.mesh3d
• Teach read.im3d to read Vaa3d raw format
• add plot.neuronlist (for 2d plotting)
• add c.neuronlist function to combine neuronlists
• add db argument to plot3d.character
• make WithNodes=FALSE the default for plot3d.neuronlist
• make asp=1 the default for image.im3d
• write.cmtkreg warns if versions specified by cmtkreg attribute and argument differ (to avoid writing old registrations as if they were new or vice versa)
• fix: prune.neuronlist method signature (and therefore dispatch)

- R
Published by jefferis over 11 years ago