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)

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

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.

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

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)

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)