Remove browser() command left over from debugging
Merge branch 'master' of jgit:AnalysisSuite

* 'master' of jgit:AnalysisSuite: (22 commits)
  Update README now that hand editing of R/Startup.R is unnecessary
  Use prune.dotprops in subset.dotprops (and add roxygen docs)
  Add prune.dotprops function to prune down to points near another dotprops
  subset.neuronlist - drop missing indices with a warnings
  Add arithmetic functions for neuron coordinates & scale.neuron
  roxygen @example->@examples
  Make MyNeurons inherit from neuronlist (and make sure elements are neurons)
  Don't require a space after roxygen comments (#')
  Give function name correctly in error messages
  restrict to roxygen comments
  Fix bugs in handling of params with . and roxygen comments
  Add option to print arguments
  Tidy up hlp help
  Find the nearest point in a neuron to a query point
  Add INDICES option to subset.neuronlist - much faster for large neuronlists
  WriteIGSRegistrationFolder(): Use floating_study in studylist if model_study is NA
  Help for NrrdMinMax
  Add roxygen help for VTKIO functions
  Startup.R: Allow user to specify RootDir before start up
  ignore vim files
  ...
Merge branch 'master' of jgit:AnalysisSuite

* 'master' of jgit:AnalysisSuite:
  Teach RunCmdForNewerInput to cope with multiple output files
  Fix inaccurate status message in RunCmdForNewerInput
  Add tests for RunCmdForNewerInput
Improved guessing of path to AnalysisSuite
Merge branch 'master' of jgit:AnalysisSuite

* 'master' of jgit:AnalysisSuite: (56 commits)
  Change default ColormapAlpha from 0.5 to 0.35
  Add tests for CMTKStatistics function
  Cope with malformed statistics headers by ignoring them on error
  Teach CMTKStatistics to handle mask files
  Add transform.dotprops fn
  Factor out voxdims code from Read3DDensityFromNrrd
  Docs in NrrdResample
  Teach NrrdVoxDims to parse a list and cope with off diag terms in space dirs
  Factor out new NrrdVoxDims function to read voxel dimensions
  Source recursively now that code is in subdirs
  Subfolders for AnalysisSuite source code
  STY: Remove all explicit calls to source in source code
  spelling fix
  Implement CRC check for detached headers as well
  Move Test data out of main Data folder into a new Tests/Data folder
  Avoid re-opening connection when reading ASCII hxskeletonize amiramesh
  Test for any connections left over
  Avoid leaving open connections
  Tests for reading gzipped amiramesh neurons
  Allow opening of gzipped ASCII amiramesh skeletonize 3d files
  ...
Merge branch 'master' of jgit:AnalysisSuite

* 'master' of jgit:AnalysisSuite:
  Fix syntax error (due to spurious char)
  Add a test for parsing of complex Materials from Amiramesh Label fields
  Fix bug in reading Parameters of labelfield .am file
Merge branch 'master' of jgit:AnalysisSuite

* 'master' of jgit:AnalysisSuite: (31 commits)
  Make ReformatImage use whatever reformatx is in the path by default
  Avoid copying neuronlist in read.neurons
  plot3d.neuronlist - rainbow colours by default
  Bug in nlapply - should always make a neuronlist
  bug in as.neuronlist - should make neuronlist be first not last class entry
  Add nlapply function (returned object is neuronlist)
  Fix very slow subsets of neuronlists
  Fix errors with transformedPoints/TransformNeuron when warp file is missing
  Handling of rds files for saving/loading dotprops objects
  Add write.neuron and write.neuronlist functions
  Fixes to RerootNeuron (also recalculates core Neuron fields inc SegList)
  Fix refactoring of ParseSWC now that input is called swc (not MySWCTree)
  remove redefinition of intersect function
  Recalculate SWC data from SegList
  Replace calls to deprecated ParseSWCTree with SWC2Neuron
  Deprecate ParseSWCTree
  Add new SWC2Neuron (which actually makes a neuron) and ParseSWC (core parsing)
  New RerootNeuron function + test for GraphTheory
  Make ParseSWCTree return an object with class neuron
  New function to extract the crc checksum from a gzip file
  ...
Give NrrdProject a kernel option
Merge branch 'master' of jgit:AnalysisSuite

* 'master' of jgit:AnalysisSuite:
  Fix typo (syntax error)
  Better install instructions, including Easy Install
  Handle installation from expanded zip file
  More information in WebInstall
  Handle situation when there are no new or existing packages
  Add simple WebInstall.R designed to be sourced from a stable http url
  Don't reinstall up to date packages
  Move Install.R script to R root
  Add an easy installation script
  Rename README to README.md to keep github happy
  Update README to mention Amira installation
  Add install script and instructions for amira code
  Update README with download link for zipped source files
  Fix: Ensure consistent handling of filename suffixes
  Teach write.neuronlist to use variables in attached dataframe to specify subdirs
  Fix bug in choosing correct suffix in write.neuron
Add gamma option to nrrd project

* not used by default
blind8 error
note about gamma
New function NrrdMerge
New file rglexts adding open3dgj() -> rgl window with panning
Add documentation for read.neurons