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Commits on Oct 5, 2018
  1. Upgrade Django from v1.11.14 to v1.11.16

    tomka committed Oct 5, 2018
    This fixes a security vulnerabiliy (CVE-2018-14574) in
    `CommonMiddleware` and a race condition in
    QuerySet.update_query_create(). See more details here:
    Thanks to @aschampion for making me aware of this.
Commits on Aug 30, 2018
  1. 3D viewer: make synapse cluster connector shading more robust

    tomka committed Aug 30, 2018
    The Synapse Clusters shading mode for connectors won't consider nodes to
    be synaptic if there is not an actual pre->post connection. Connector
    nodes however are still displayed at these locations and need a color.
    Without returning a "not computable" color, an error was raised for
    treenodes linked to connectors without a full connection.
  2. Reconstruction sampler: fix leaf node list data access

    tomka committed Aug 30, 2018
  3. Reconstruction sampler: don't try to load leaf details without leaf n…

    tomka committed Aug 30, 2018
  4. Improve robustness of get_request_list()

    tomka committed Aug 30, 2018
    Depending on what type of request dict is provided, the 'getlist'
    method might not be available. Only call the method if it is there.
  5. Reconstruction sampler: add leaf node table to "Synapse" step

    tomka committed Aug 28, 2018
    This shows all leaf nodes of an interval in a separate table in the
    Synapse step, which makes it easier to find places where to continue a
    started interval.
    See #1784
  6. Reconstruction sampler: improve robustness of ignored leaf segment li…

    tomka committed Aug 30, 2018
    So far the skeleton traversal to find ignored leaf segments didn't
    expect valid intervals after a node without interval was found. While
    this shouldn't happen, in older samplers this can in fact occur. To get
    better estimates for ignored leaf fragments for those samplers, the
    traversal algorithm doesn't make such an assumption anymore.
  7. 3D viewer: fix computation of synapse counts

    tomka committed Aug 30, 2018
    Regular node vertices don't store their node ID anymore in the vertex.
    Instead a metadata store is used or, for connector links, the connector
    vertex can be used to find node IDs. This also fixes shading modes like
    flow centrality or synapse free chunks.
  8. 3D viewer: fix typo (minor)

    tomka committed Aug 30, 2018
Commits on Aug 25, 2018
  1. Connector list: show relation name of link

    tomka committed Aug 25, 2018
    This adds a relation name column to the connector list widget, which is
    used when filtering connectors by volume.
Commits on Aug 24, 2018
  1. Volume widget: fix skeleton constraint source select element update

    tomka committed Aug 24, 2018
    The ID of the select element wasn't set correctly.
  2. Volume manager: use skeleton constraints also for connector listing

    tomka committed Aug 23, 2018
    If a skeleton source is selected as skeleton constraint in the Volume
    Manager and a user clicks the "List connectors" action for a particular
    volume, the opened Connector List will now only show connectors that are
    are connected to skeletons in the selected source.
  3. Connector list: fix treenode column double click

    tomka committed Aug 23, 2018
    A double click on the treenode column should take the user to that
    treenode. Due to an index mismatch this wasn't working anymore, which is
    fixed with this commit.
Commits on Aug 21, 2018
  1. Tracing overlay: fix annotation assignment after swapped merge

    tomka committed Aug 21, 2018
    When merging two skeleton A into skeleton B, skeleton A won't exist
    anymore afterwards (it "loses"). The merge dialog provides a button to
    swap the current merge order, i.e. to merge skeleton B into A. The merge
    dialog also suggests to keep the name of the losing skeleton as an
    annotation on the winning skeleton. When swapping the merge order, this
    reference is updates as well. However, while the visual representation
    was correct, the actual merge used to the unswapped reference
    annotation. This means when after a merge order swap skeleton B would be
    merged into skeleton A, the reference annotation kept would still be A.
    This is fixed now by updating the merge handler. It was always
    referencing the original merge dialog, even after a swap (which creates
    a new dialog). It now uses the calling dialog.
    Thanks to Katharina Eichler, who noticed this bug.
Commits on Aug 16, 2018
  1. Back-end: fix parsing of 0 values in get_request_list()

    tomka committed Aug 16, 2018
    If a value was zero, it was removed from the list parsing code. This is
    fixed now and a test has been updated to reflect this.
Commits on Aug 13, 2018
  1. Skeleton shading: fix sampler-interval shading when nodes where added

    tomka committed Aug 13, 2018
    If a sampler added nodes, the sampler-interval shading would throw an
    error. The problem was the CATMAID.Sampling.intervalEdges() function is
    in this case allowed to modify the passed arbor (as sort of cache). So
    far only the arbor was updated, but not the location dictionary. This
    caused an error on location lookup for newly added nodes. This is fixed
    now by caching the position dictionary.
  2. Reconstruction sampler: improve interval creation preview colors

    tomka committed Aug 13, 2018
    Two different colors are now used for ignored leaf segments and the rest
    of the skeleton. The rest of the skeleton is now only shown very
  3. 3D viewer: remove unneeded sampler domain check code

    tomka committed Aug 13, 2018
    This is an older version of the code right below it and was accidentally
    left in there.
  4. Tests: fix treenode table API tests

    tomka committed Aug 13, 2018
  5. 3D viewer: add per-skeleton X/Y/Z rainbow coloring modes

    tomka committed Aug 13, 2018
    In addition to the stack normalized X/Y/Z color modes, a per-skeleton
    normalized version can now be used.
  6. 3D viewer: allow selecting specific sampler domains/intervals for sha…

    tomka committed Aug 13, 2018
    This adds the options "Sampler domain IDs" and "Sampler interval IDs" to
    the "Shading parameters" tab. It allows to only show specific domains
    and intervals rather than all available.
  7. Detail dialog: use non-breaking space for detail space replacement

    tomka committed Aug 13, 2018
    This prevents some rendering problems due to line breaks.
  8. Detail dialog: print error whitespace with correct length

    tomka committed Aug 13, 2018
    This makes tracebacks easier to read.
  9. Error dialog: fix printing detail information multiple times

    tomka committed Aug 13, 2018
    The wrong variable was referenced in the loop.
Commits on Aug 11, 2018
  1. Reconstruction sampler: add button to show ignored leaf fragment info

    tomka committed Aug 10, 2018
    The dialog shown when the "Uncovered domain parts" button is pressed in
    the Interval step of the Sampler, shows a histogram of the lengths of
    all leaf fragments that are not covered by intervals but that are part
    of the domain. It uses Plotly.js for this, so the histogram is
    interactive by default. When histogram bins are clicked, a Treenode
    Table is opened with the respective treenodes listed, which makes it
    easier to inspect those sites. The dialog also provides an option to
    download the list of all measured leaf fragment lengths.
  2. Move treenode table endpoint into skeletonexport module

    tomka committed Aug 10, 2018
    Also give it a more reasonable name and add basic documentation.
  3. Upgrade plotly.js from v1.30.0 to v1.39.4

    tomka committed Aug 10, 2018
    This is needed because of some histogram improvements that provide more
    data on clicked bins.
Commits on Aug 8, 2018
  1. Reconstruction sampler: make more columns sortable

    tomka committed Aug 8, 2018
    And compare strictly against 0 to make JSHint happy.
  2. Reconstruction sampler: mark interval of domain start node

    tomka committed Aug 8, 2018
  3. Client: add support for URLs without XYZ and only node/skeleton IDs

    tomka committed Aug 8, 2018
    If only a node is given in the URL, move to this node and select it. If
    only a skeleton ID passed in, move to the skeleton's root node and
    select it.