change.log

### CATMAID to Blender Import Script - Version History:

### V7.1 11/07/2023:
    - allow importing skeletons above a given node count

### V7.0 04/10/2021:
    - re-write to work with Blender 2.9x (possibly also 2.8x)
    - dropped support for Blender 2.7x
    - moved plugin to sidebar of 3d view
    - dropped a bunch of functions

### V6.2 26/02/2018:
    - use requests library if possible to prevent SSL handshake errors due to outdated OpenSSL version in Blender 2.79
    - add option to disable SSL (untested and won't help with handshake)

### V6.1.0 07/11/2018:
    - followed a change in CATMAID's volume API

### V5.84 28/02/2018:
    - fixed a bug in export connectors that caused only the first export of connectors to svg to succeed

### V5.83 11/08/2017:
    - added option to restrict to specific sources and targets when importing connectors for a set of neurons

### V5.82 10/06/2017:
    - added option to filter minimum node contribution if loading neurons by user
    - added requests per second to addon-preferences: useful when getting errors while retrieving large numbers of neurons
    - fixed bugs in animate.history
    - made randomise color use color range
    - fixed a bug with using .lower() at urlencoding

### V5.81 31/05/2017:
    - performance improvements and bug fixes for animate history

### V5.8 30/05/2017:
    - added basic history plot (similar to CATMAID's 3D viewer)

### V5.74 05/05/2017:
    - added option to color connectors by neuron color

### V5.73 03/05/2017:
    - bugfixes
    - made plotting of dendrogram using pylab optional

### V5.72 19/04/2017:
    - added import of tags

### V5.71 19/04/2017:
    - added import of volumes by name (enables import of multiple volumes at a time)
    - imported volumes are now smoothed

### V5.7 30/03/2017:
    - added import of gap junctions and abutting connectors

### V5.64 20/03/2017:
    - list of available volumes is now only updated upon initially connecting with CATMAID server

### V5.63 28/02/2017:
    - added invert_colors and change_bevel to color_by_strahler

### V5.62 15/02/2017:
    - added optional usage of SciPy.spatial.distance for clustering -> about 2 fold increase in speed

### V5.61 01/02/2017:
    - UI improvements
    - code clean up

### V5.6 14/11/2016:
    - added minimal node count as parameter for import
    -> if this is the only paramter provided, all neurons in the data set larger than this will be loaded
    - neurons will now be imported as chunks of 100 to reduce the number of open threads at a time

### V5.51 03/11/2016:
    - added export and import of meshes to/from CATMAID
    - minor improvements in UI

### V5.5 28/10/2016:
    - combined 'retrieve by annotation' and 'retrieve by skeleton id' into single button -> now called 'Import Neuron(s)'
        - added search by tag (=neuron name)
        - added option for partial match (works for names and annotations)
        - added option to intersect between annotations and/or names
    - changed width of all property pop ups to 500 -> they had been too small e.g. on Macs
    - added check for CATMAID server version!

### V5.4 02/08/2016:
    - added 'color by strahler index
    - added option use node radius as thickness for neuron in Blender

### V5.31 16/06/2016:
    - fixed bug with grouping in connector to svg export
    - also, added error handling in case neurons had no connectors to export

### V5.3 10/06/2016:
    - added on-screen messages and area header messages for reporting progress:
        - on-screen msg has hick-ups if used at high frequency -> use area header
        - also refresh does not seem to work when scene is more crowded
    - made similarity calculations threaded -> major speed-up for most but not for morphology

### V5.211 01/05/2016:
    - fixed a bug that led to an error with retrieve_paired when 'paired with #' annotation had invalid skid

### V5.21 26/04/2016:
    - greatly improved speed when importing/exporting connectors by pooling requests to server
    - use mesh color will now also affect the order of export such that same colors are grouped
    - added perspective brain outline to connector to svg export
    - fixed a bug when importing connector spheres
    - fixed a bug that ignored project_id when requesting skeleton data

### V5.2 19/04/2016:
    - combined all threaded skeleton data retrieval into one function and added a timeout variable

### V5.1 13/04/2016:
    - added coloring by similarity in connectivity and paired connectivity
    - added relative synapse count to color by synapse count
    - improved tooltips
    - bugfixes

### V5 12/04/2016:
    - separated requests to server into multiple threads (not for all operators): results in 6X increased import speed!
    - other improvements
    - bugfixes

### V4.33 02/04/2016:
    - made sure Addon doesnt crash if numpy is not installed
      -> will instead throw error when not found

### V4.32 01/04/2016:
    - added option to unify materials
    - changed 'Retrieve Weighted Connectors' to also retrieve non-weighted connectors
    - fixed bug that caused layer to be ignored
    - cleaned up connector retrieval

### V4.31 25/03/2016:
    - added select by annotation feature
    - fixed bug in dendrogram export

### V4.3 23/03/2016:
    - changed addon name to CATMAIDImport - needs to be the same as bl_label of Addon preference class
    - added Addon Settings for credentials and server url
    - added self.report() to all error messages -> will show error message at cursor loc
    - connecting to CATMAID now does a test call by asking for user list
    - improved prepare 4 blender functionality
    - added advanced tooltip to some functions
    - added 'Active/Selected/All neurons' option to remaining functions
    - optimized function icons

### V4.21 15/03/2016:
    - added option to export dendrogram svg of similarity clustering

### V4.2 14/03/2016:
    - added option to export barplot to SVG export- this will export distribution of pre-, postsynaptic sites or node count along vertical
      and horizontal axis
    - various bug fixes

### V4.1 21/12/2015:
    - added Token System to replace catmaid user+pw

### V4.01 17/11/2015:
    - had to change get_connectivity_url due to changes in CATMAID API to skeletons/connectivity and postdata to source_skeleton_ids

### V4.0 10/11/2015:
    - added import of neurons in given volume
    - added clustering (coloring) of neurons based on morphological similarity (after Kohl et al., 2013)
    - added option to import only longest neurite up to given length for all ways to import neurons
    - added missing descriptions to import/export options -> just hover over checkbox/drop-down/textfield/etc.

### V3.94 9/11/2015:
    - had to change the way neurons with given annotation are retrieved: both url and postdata changed!

### V3.93 20/10/2015
    - fixed some bugs due to changes in CATMAID API:
        - changed annotations url to skeleton/annotationlist
        - changed url to get list of all annotations to /annotations/

### V3.92 15/10/2015
    - fixed color by synapses lut calculation:
        * values needed to be reduced by 1, such that range for calculation is 0 to (max_value-1)
    - fixed get_annotations_from_list -> CATMAID returns now a list of dictionaries for each neuron:
      {'skeletons' : { 'skeleton ID' : [{'id': annotation id, 'uid' : dont know what this is}] , [....]}
       'annotations': {'annotation_id':'annotation_name', ... }
      }
    - added option to apply threshold when importing synaptic partners to single connections instead of the
      sum of all connections
    - added option to change project ID when logging into CATMAID (default = 1)

### V3.91 28/08/2015
    - added option to color by annotation

### V3.9 04/08/2015
    - had to compensate for new format of connectivity data: now contains list of synapses with confidences 0-5
        old: {'incoming': { 'neuronXY': {'skids': { 'upstream_neuronZ' : 5 } } }
        new: {'incoming': { 'neuronXY': {'skids': { 'upstream_neuronZ' : [0,0,2,1,2] } } }

### V3.81 14/07/2015
    - adjusted annotation import to fix new layout of received dict

### V3.8 29/06/2015
    - added option to color_by_pairs and load_paired: will color/load neurons based on given annotation
      'paired with #skid'

### V3.73 17/05/2015
    - added option to color_by_synapses: if 'shift color' is set, the color will only be changed
      by given value RELATIVE to it's current color
    - added option to filter by annotation when importing partners
        -> works only with a single annotation and has to be exact
    - added option to also adopt bevel_depth when coloring by synapse count
    - added option to use curve's bevel_depth when exporting morphology

### V3.72 26/03/2015
    - soma radius is now based on node radius in CATMAID
    - also applies for exports to svg: soma radius is multiplied by basic_radius (default = 1)

### V3.71 20/03/2015
    - added option to import weighted connectors from selected neurons
    - added option to export connectors to SVG and give them mesh color (will apply to inputs AND outputs)

### V3.7 10/01/2015
    - fixed bug in export morphology that would cause neuron names to be created at the same location if exporting multiple neurons
    - added option to randomize grayscale colors
    - added option to SVG exports to color by density of given CURVE object (e.g. DCV tracings)
        - alternatively: choose 'Synapses' as density object and it will load connectors
        -> added filter option: -'incoming' or 'outgoing' will include only post/presynaptic sites. If no filter is given, both are processed
                                -any other filter will be applied to the connected neurons' names!
    - added option to SVG morphology export to color arbors by ratio between post- and presynaptic sites
        - Keep in mind that the subdivision into arbors can be misleading, especially for very large arbors
    - added option to choose which views should be exported
    - added perspective to connector-to-svg export
    - added new perspective 'Perspective-Dorsal' and made it standard:
        - looks at the brain from behind at an elevated angle - comparable to squeeze mounting
    - added option to filter for synapse threshold when exporting connectors by using e.g. '>3'
    - fixed bug that occured when exporting connectors and a treenode has more than one connector upstream and led to all but one connectors be ignored

### V3.6 16/12/2014
    - fixed bugs in connector export

### V3.6 09/12/2014
    - added license information

### V3.6 20/10/2014
    - added option to color neurons by #of synapses with given partner(s)
    - added option to export to svg using the colors from Blender
    - fixed bug in version check: was called to early when not __main__:
      - version check is now done manually via button OR whenever 'Connect 2 Catmaid' is
        called

### V3.52 09/09/2014
    - added check for latest version (update.txt at Github repository)

    V3.51 05/09/2014
    - changed server url to 'https://...'
    - removed subtype 'PASSWORD' from CATMAID Login as this seems to be bugged in Blender 2.71
      -> forces you to enter passwords in reverse


### V3.5 23/07/14
    - added orthographic perspective for export

### V3.4 13/07/14
    - added resampling option for importing and updating neurons
    - added option to skip connectors when importing

### V3.31 07/07/14
    - exchanged compact-json url for compact-skeleton url to retrieve morphology/connectors
    -> compact-json doesn't work anymore!!!
    -> neuron's names now have to be retrieved by separate get_neuronnames() function
    - fixed 'Retrieve Partners' (wouldn't check thresholds before)
    - minor clean ups

### V3.3 28/06/14
    - added function to also export neuron's morphology when exporting it's connectors to svg
    - fixed some bugs in legend creation of connector export (still quite some left)

### V3.22 26/06/2014
    - changed Blender operators polls to check if connection to CATMAID was successful
    -> buttons will be greyed out until connected to CATMAID server
    - newly imported neurons will have 'name', 'skeleton_id' and 'date_imported' assigned as custom properties

### V3.21 23/06/2014
    - changed request of skeleton name via ancestry to neuronnames -> requests a list instead of single names (MAJOR speed up!)
    -> removed progress bar for cursor
    - credentials will be read from txt file - if no file is found credentials will be empty

### V3.2 18/06/2014
    - added filter option to export connectors
    - added poll function to all Blender operators to gray out buttons if not connected to CATMAID server
        Note: just checks whether connection has been attempted, not if successfull
    - improved creation of legends for export connectors (probably still some glitches here)
    - added progress bar for cursor

### V3.1 16/06/2014
    - added color by spatial position (soma-based)

### V3.0 03/06/14
    - added Import by Annotation
    - added 'Reload Neurons'

### V2.22 28/05/14
    - removed Import from TXT/neuroML as they are no longer needed
    - added 'Setup 4 Render' that sets up Materials for Rendering
    - removed 'Render All' button

### V2.21 27/05/14
    - adjusted data format to changes in CATMAID
    - added option to export outlines of ring gland as well
    - added masked pw entry to 'Connect' button
    - fixed export for brain shapes: if multiple neurons are processed only one brain shape will be created

### V2.2
    - added lateral view
    - added option for scaled presynapse export

### V2.1
    - changed the way data is imported from CATMAID - should be almost as fast as CATMAIDs'
      3D viewer now
    - added connector retrieval from CATMAID to Blender and a SVG file:
        - both options require connecting to CATMAID!!!
        - will retrieve number of targets for all downstream connectors and resize
          nodes relative to that
        - won't affect upstream nodes as there is always only one presynaptic source

### V2.0
    - implemented support for CATMAID API to directly interact with database

### V1.2
    - changed NeuroML Import according to CATMAID Export changes (complete names exported)

### V1.1
    - made Import from NeuroML read data line-by-line instead of importing all at once
        -> didn't speed things up, but made it more stable and more reactive if necessary
    - added better monitoring of progress in system console while importing
    - NOTE: Creation of the Neurons seems to be the bottleneck
    - added 'Render All Function'. What it does:
        - Creates Cameras if neccessary and then does single neuron renders of all neurons