NEWS.md

In jefferis/rcatmaid: R access to the API for the CATMAID web image annotation tool

catmaid 0.10.1

• Fix bug in pid handling for meshes (#144)
• Pass on pid / conn in catmaid_get_annotations_for_skeleton (#147)
• Fix bug in catmaid_query_connected when no outputs at all (#148) Thanks to Shanice Bailey
• Always pass on conn in catmaid_version calls (#150) Thanks to Rob Turnbull
• Fix test baseline in catmaid_get_annotations_for_skeletons
• Switch from deprecated as_data_frame to as_tibble
• Fix NA types in tibble (#153, @SridharJagannathan)
• Fix HTTP/2 call failures in catmaid server (#158, @SridharJagannathan)
• Fix problem in elmr::unspike when only one tag (#163, #164)
• Add vfbcatmaid() convenience function
• Add print.catmaid_connection method to give a nice summary of connection properties in the console.
• Fix bug in setting label field for soma (#167) Thanks to @Robbie1977
• Fix copy_tags_connectors

catmaid 0.10.0

• New functions for handling meta annotations (i.e. annotations of annotations): catmaid_get_meta_annotations(), catmaid_query_meta_annotations(), catmaid_set_meta_annotations(), catmaid_remove_meta_annotations() thanks to @alexanderbates for the PR (#130).
• New functions for (un)locking neurons: catmaid_lock_neurons(), catmaid_unlock_neurons() thanks to @alexanderbates for the PR (#130).
• New functions to fetch soma information from neurons in a neuronlist: 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).
• Set the SWC Label column inside neurons to identify the soma (#143).
• Fix catmaid_get_volumelist() and catmaid_get_volume() when the project (pid) is not 1 (#144).

catmaid 0.9.9

• 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.

catmaid 0.9.8

• Fix bug in 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 0.9.7

• New catmaid_userids() function converts user login names to ids.
• catmaid_connection() gets a new config argument to allow curl options to be set (#108).
• Return format and documentation fix: tree node ids in catmaid_get_connector_table() always refer to the query skeleton and not the partner neuron (#107)

catmaid 0.9.6

• Give 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 0.9.5

• Stop 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)

catmaid 0.9.4

• write_catmaid_selection() accepts annotations/name specs

catmaid 0.9.3

• 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

catmaid 0.9.2

• Teach catmaid_get_volumelist() about new API return format (#102)
• Sync catmaid_get_treenode_table() with API (#101)
• make catmaid_query_by_name() treat query as regex (#100)
• Fix bug in metadata for read_catmaid_selection (#99)
• Sort tags for neurons so that they are always returned in the same order (#98)
• Add catmaid_get_node_count() to get the number of nodes per skeleton
• Teach catmaid_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.
• Fix bug in nsoma() for duplicate skids; also speed-up
• Make catmaid_login() explain why passing server directly doesn't work
• Add name|nodes to results of catmaid_get_connector_table()
• Speed-up in catmaid_get_compact_skeleton()/read.neuron.catmaid()
• Teach catmaid_get_node_count() to handle NAs/dupes

catmaid 0.9.1

• 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)

catmaid 0.9.0

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 >=1.8.12.900 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)

catmaid 0.8.1

• 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

catmaid 0.8

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

catmaid 0.7.2

• 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)

catmaid 0.7.1

• 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)

catmaid 0.7

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)

catmaid 0.6

• 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

catmaid 0.5

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)

catmaid 0.4

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

catmaid 0.3

• 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

jefferis/rcatmaid documentation built on Aug. 16, 2022, 8:52 p.m.