Release 2017.05.17 · catmaid/CATMAID

2017.05.17

Contributors: Andrew Champion, Tom Kazimiers

A virtualenv upgrade is required. To correctly install one updated dependency, the django-rest-swagger Python package has to be removed first from from the virtualenv, before the virtualenv is updated:

pip uninstall django-rest-swagger
pip install -r requirements.txt

Widget state saving:

Infrastructure has been added to store widget configuration client side in a browser cookie. This makes it easy to update widgets to support automatic saving and loading of state information. The automatic saving and loading behavior can be configured in the General Settings section of the Settings Widget. To explicitly save the state in a supported widget, the respective button available through the "Window Configuration" title bar icon can be used as well.
State saving support has been added for the 3D Viewer and the Connectivity Widget.

Generic node filtering:

A generic user interface for filtering nodes is now available to widgets. If a widget supports it, the filtering user interface is available through the filter icon in the widget's title bar.
The user interface has a "Filters" tab which lists all active filters for a widget and a "Add filter" tab, which can be used to create new filter rules.
Filter rules select nodes that are kept, i.e. the filter application results in a list of nodes that match the filter expression.
Different filter types are available at the moment: Only end nodes, only tagged nodes, only nuclei, only a sub-arbor starting from a tag, tag defined region, created by user(s), node creation/edite time, binary split, axon, dendrite, synaptic connectivity and volumes. Some come with own user input elements, but all can optionally be applied to only a subset of skeletons.
Multiple filters can be combined, e.g. all branch nodes with a particular tag and end nodes. All filter rules are combined in a left-associative fashion and union and intersection can be used as operators.

Connectivity widget:

Support for node filtering has been added, it can be configured through the filter icon in the title bar. All features listed under Generic Node Filters are supported. If a node of a skeleton from the top list doesn't match the filter expression, synaptic connections involving it will not be respected.

Review widget:

Whether detailed review colors should be used is now persisted.
The checkbox "Save review updates" allows to disable sending review updates to the server. Ending review or closing the widget will cause all review updates to be lost. If disabled, a warning is displayed. This is useful to only use the "navigational" features of the review widget.
Support for node filtering has been added, it can be configured through the filter icon in the title bar. All features listed under Generic Node Filters are supported. If nodes are filtered, all percentages are relative to the filtered set of nodes.

3D viewer:

The color of custom tag spheres can now be adjusted through a "color" button right next to the custom tag pattern.
The color of the floor can now be adjusted though a "color" button next after the "Floor" checkbox.
Skeleton coloring can now be set to not interpolate between different vertex colors and instead use always child colors for an edge.
The color and whether to display mesh faces of individual volumes can now be adjusted more easily. A color selector is available right next to the checkbox of each visible volume in the volume drop-down menu. The global color controls are used as default for newly displayed volumes.
Support for node filtering has been added, which can be configured through the filter icon in the title bar. All features listed under Generic Node Filters are supported.

Tracing layer:

When inserting a new node between two existing nodes, the new node's user will now be the logged in user as long as the skeleton is not locked. This makes it easier for reviewers to make corrections, because the new node can now be moved (instead of only initially placed). If the neuron is locked, it is only possible to create a collinear node between parent and child with the child's user (e.g. through tagging a virtual node).

Miscellaneous:

When a node is selected a minimal node status line is now shown again using information already available in the client. If the "Show extended status bar information" setting is the Settings Widget is checked, additional information is fetched from the back-end.
The SWC export by default now maps real node IDs to incremental IDs starting with 1 from the root node, which is something some SWC tools expect. To disable this uncheck "Linearize IDs" in the SWC export dialog.
Neuron Navigator: It is now possible to delete multiple neurons from a neuron listing.
The importer widget now allows to allow multiple SWC files at the same time.

Export widget: The SWC export link works again.
Tracing tool: using the personal tag set doesn't remove existing tags anymore when added or removed.
Fix catmaid_insert_example_projects management command.
Review widget: it is possible again to use Q/W to move along already reviewed segments (re-review of nodes).
Fix some accidental key mapping collisions of some special keys and media keys.
Connector nodes can be deleted again right after they were created.
3D viewer: connector links are displayed again if connector restrictions are in use.
Radius creation works now in orthogonal views as expected.

POST /{project_id}/skeletons/connectivity:
If the new "with_nodes" parameter is true, the involved treenode links are
also returned for each partner.