catmaid_query_connected() now returns stats for all connections but also allows a confidence threshold to be set. The default threshold of 1 is a new more permissive behaviour (#113). Thanks to Sebastian Cachero / @schlegelp for the bug report.
- Fix bug in
catmaid_connection_getenv() and friends in getting environment variables on some OSes. It turns out that we should switch to recommending variables of the form
catmaid_* (#110). Thanks to @SridharJagannathan for detective work and a PR with a fix.
read.neurons.catmaid() an optional fetch.annotations argument that adds a second metadata data.frame as an attribute to the resultant
neuronlist() object (#18).
- Fix handling of CATMAID version string (#103)
catmaid_get_connector_table() returning duplicate rows when there are multiple connections between the same partner neurons at a given connector. Thanks to Shanice Bailey and Istvan Taisz for the bug report (#106).
- Pass on pid in
catmaid_skids(), thereby fixing an issue with
read.neurons.catmaid() with annotation queries when project id is not 1. Thanks to Marta Costa for the bug report (#105)
- workaround for bug in
catmaid_version() (#103). Still waiting on changes in CATMAID for more permanent fix.
- fix import error with jsonlite version >=1.6
- Add catmaid_get_labels, catmaid_set_labels, catmaid_remove_labels to manipulate labels (aka tags) on treenodes and connectors (#95)
- Add catmaid_get_all_labels
- Add nsoma function to return number of somata (#96)
- Add catmaid_get_treenodes_detail to get location and other information for many nodes at once (#94)
- Teach catmaid_get_connectors_between to find names for pre/post skids (optional, #93)
- Teach catmaid_get_neuronnames to handle duplicate requests efficiently (#91)
- Teach catmaid_login to accept arguments in a list (#91)
This version is synced with the upcoming release of nat v1.9.0 which streamlines some functionality but has some breaking changes in behaviour. It must be used with nat >=188.8.131.520 from github.
- switch to Ops.catmaidneuron to match nat 1.9.0 in prep (and add version requirement)
- Simple search for skids with exact annotation match (#89) Now you can do: catmaid_skids(“ORN”) or read.neurons.catmaid(“ORN”)
- Fix bug in catmaid_skids error message when looking for one skid (#90)
- Add function to get volumes from catmaid (#82)
- Add functions to read/write catmaid json selection files
- make catmaid_neuronnames returns NA for NA skids
This is a major version update because of the new support (and recommendation) to use environment variables for login (.Rprofile is still supported).
- support fetching login information from environment variables (#80)
- catmaid_get_compact_skeleton now returns list of vectors (#79) (used to be a list of lists, but this was less convenient and not helpful)
- fix query_by_neuron_or_annotation adding empty annotations attribute
- Add catmaid_get_label_stats (use it to find neurons with soma)
- Add copy_tags_connectors (bring over tags/connector info)
- improve summary.catmaidneuron (#78)
- plot3d bugfix when there are NA points (and soma=T) (#77)
- only plot soma when explicitly tagged (rather than plotting a sphere at the root of the neuron if not tagged) (#62)
- only plot3d connectors if they exist (#73)
- Ensure nodes do not normally plot for catmaidneurons (#74)
- doc fix for catmaid_get_treenode_table (#75)
This is a substantial release with many new functions/enhancements, changes to match the API defined by the 2016.10.18 CATMAID release, support for token-based authentication and numerous bug fixes.
- support for CATMAID token-based authentication (#35)
- Add catmaid_get_connectors_between to return connections between (multiple) pre and postsynaptic partners - thanks to Zhihao Zheng (#53, #56)
- Add function to parse CATMAID urls e.g. to extract xyz position (#55)
- Add rename_neuron function (#54)
- Add catmaid_version function (#58)
- Add catmaid_user_history function (#57)
- Add catmaid_get_annotations_for_skeletons function (#38)
- Add catmaid_remove_annotations_for_skeletons function (#43)
Add catmaid_add_volume to add 3D meshes to catmaid (#69)
- catmaid_get_connector_table can now accept multi skid specifications (#49)
catmaid_get_connectors_between returns more informative errors (#51)
- fix “No encoding supplied: defaulting to UTF-8.” warning (#59)
- stop catmaid_skids returning duplicates when there are multiple matching annotations (#44)
- ensure that connectors are also scaled when xforming neurons (#47)
- catmaid_query_by_annotation returns neuron column as character vector (#46)
- catmaid_get_connector_table returns partner_skid columns as an integer (#48)
- fix bug in url for catmaid_get_review_status function (#45)
- Give sensible name to 1st column of connector data.frame (#42)
- ensure neurons without connectors scale properly (#41)
- fix bug in catmaid_connection_setenv() when some elements are null (#50)
- catmaid_get_annotations_for_skeletons - fix bug in skid order (#39)
- ensure catmaid_get_contributor_stats passes on connection (#37)
- ensure all functions pass on connection to catmaid_fetch (#60)
- connectors.neuronlist should handle neurons without connectors (#29)
- catmaid_skids should pass on pid (#64)
- fix catmaid_get_connector_table to reflect 2016.09.01-65 API change (#65)
fix bug in catmaid_user_history with small queries (#70)
- support for upcoming httr 1.0 release
- fix: ensure catmaid connection objects are passed to all downstream functions e.g. so that you can you use different servers in the same session.
- fix queries that match multiple annotations when using a defined connection object
- fix: ensure that catmaid_fetch works even if server does not have a terminal / and remote path is also missing a slash
- fix: servers don’t have to be https
- check for http status errors in catmaid (in case there is trouble connecting to site, bad URL etc)
- … and errors in returned JSON when request is invalid
- export funcs to get/set login details as environment variables
- … and clear those env vars (all useful for testing)
This release significantly enhances functionality for querying for neurons by annotation or name, while also simplifying a number of plotting/analysis tasks involving connectors (synapses).
- catmaid_query_by_neuronname was renamed to catmaid_query_by_name (since it can query by both neuron or annotation name as well as returning both annotations and neurons)
- read.catmaid.neurons has richer attached metadata (see https://github.com/jefferis/rcatmaid/issues/9)
- read.catmaid.neurons can make simple queries (see https://github.com/jefferis/rcatmaid/issues/9)
- add catmaid_query_by_annotation to fetch objects tagged with a matching annotation (rather than searching by object name).
- add connectors to get connector (synapse) information from a neuron
- add catmaid_catmaid_get_connector_table to see a list of incoming/outgoing connections for a given neuron.
- add plot3d.catmaidneuron to enable convenient plotting of synapses
- fix catmaid_get_neuronnames should return names in the same order as passed skids (see https://github.com/jefferis/rcatmaid/issues/6)
- the catmaid skeleton_id is consistently referred to as skid in argument names and return values
- depend on nat (and therefore rgl). Import rather than depend on jsonlite.
- minor doc fixes
- cache login credentials for automatic reuse
- option to set/get environment variables for passwords etc
- Add catmaid_query_connected, catmaid_get_annotationlist, catmaid_query_by_neuronname
- low level catmaid_fetch function covers GET and POST requests