NEWS.md
catmaid server (#158,
@SridharJagannathan)vfbcatmaid() convenience functionprint.catmaid_connection method to give a nice
summary of connection properties in the console.catmaid_get_meta_annotations(),
catmaid_query_meta_annotations(),
catmaid_set_meta_annotations(),
catmaid_remove_meta_annotations() thanks to @alexanderbates
for the PR (#130).catmaid_lock_neurons(),
catmaid_unlock_neurons() thanks to @alexanderbates for the
PR (#130).soma() fetches the XYZ location of the soma.
somaindex() fetches the raw index of the skeleton node
associated with the soma (in range 1..N, number of vertices).
somaid() fetches the identifier of the skeleton node
associated with the soma thanks to @alexanderbates for the PR
(#128).Label column inside neurons to identify the
soma (#143).catmaid_get_volumelist() and
catmaid_get_volume() when the project (pid) is not 1
(#144).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.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.catmaid_get_connectors_between() when
getting neuron names. There was an off by one error for the postsynaptic
partner name (#109). Thanks to @mmc46 for the bug report.catmaid_userids() function converts user login
names to ids.catmaid_connection() gets a new config
argument to allow curl options to be set (#108).catmaid_get_connector_table() always refer to the query
skeleton and not the partner neuron (#107)read.neurons.catmaid() an optional
fetch.annotations argument that adds a second metadata data.frame as an
attribute to the resultant neuronlist() object (#18).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).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)write_catmaid_selection() accepts annotations/name
specscatmaid_version() (#103). Still
waiting on changes in CATMAID for more permanent fix.catmaid_get_volumelist() about new API return
format (#102)catmaid_get_treenode_table() with API (#101)catmaid_query_by_name() treat query as regex
(#100)catmaid_get_node_count() to get the number of nodes
per skeletoncatmaid_get_treenodes_detail() to search by
labels - can use this e.g. to find all nodes (regardless of neuron) with
a certain tag e.g. soma.nsoma() for duplicate skids; also
speed-upcatmaid_login() explain why passing server
directly doesn’t workcatmaid_get_connector_table()
catmaid_get_compact_skeleton()/read.neuron.catmaid()
catmaid_get_node_count() to handle NAs/dupesThis 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 >=1.8.12.900 from github.
This is a major version update because of the new support (and recommendation) to use environment variables for login (.Rprofile is still supported).
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)
This release * 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).