nat 1.8.24 ========== * workaround for a small regression in igraph 2.0.1 dfs function * test error reported by CRAN (BDR) * replace deprecated igraph functions * add nvertices.igraph method nat 1.8.23 ========== * fix bug in handling of numeric versions in . r-devel now refuses to compare a number with a numeric_version * reported by CRAN (Kurt Hornik, who also kindly pointed out the precise error) nat 1.8.22 ========== * version bump owing to package archival nat 1.8.21 ========== * tweaks to the news file format picked up on cran linux pretest (but strangely not win-devel etc) nat 1.8.20 ========== * replace deprected rgl functions * update igraph test for compatability nat 1.8.18 ========== * Fix errors in `neurons-intro` vignette when pandoc is missing nat 1.8.17 ========== * Suggest webshot2 to cope with changes in rgl snapshot behaviour (at the request of BDR for CRAN) * Fix URLs nat 1.8.16 ========== * Fix further failing URLs from CRAN pre-test nat 1.8.15 ========== * Fix failing test on CRAN for R 4.1 (thanks to KH, #444). nat 1.8.14 ========== * Fix failing test on CRAN when Rvcg unavailable (thanks to BDR). nat 1.8.13 ========== * backports a few urgent fixes to the 1.8 branch * 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) * also updates URLs to point to nat's new home organisation on GitHub https://github.com/natverse. 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) nat 1.8.11 ========== * 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 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) 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 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) nat 1.8.7 ========= * This release includes some bug fixes and significantly improved online package documentation visible at http://natverse.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) 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 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)