Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Segment counts #360

Draft
wants to merge 61 commits into
base: master
Choose a base branch
from
Draft

Segment counts #360

wants to merge 61 commits into from

Commits on Oct 4, 2019

  1. Add support for datasets relative to project directory. 

    Note that this does not work for label Paintera datasets (yet)
    @hanslovsky
    hanslovsky committed Oct 4, 2019
    Configuration menu
    Copy the full SHA
    5efb5ab View commit details
    Browse the repository at this point in the history

  2. Kotlinify n5 meta code

    @hanslovsky
    hanslovsky committed Oct 4, 2019
    Configuration menu
    Copy the full SHA
    11e6e17 View commit details
    Browse the repository at this point in the history

  3. WIP: Start writing relative label source state

    @hanslovsky
    hanslovsky committed Oct 4, 2019
    Configuration menu
    Copy the full SHA
    dcd263e View commit details
    Browse the repository at this point in the history

  4. Fix compilation errors (hopefully)

    @hanslovsky
    hanslovsky committed Oct 4, 2019
    Configuration menu
    Copy the full SHA
    09c44e1 View commit details
    Browse the repository at this point in the history

  5. Uncomment onShutDown

    @hanslovsky
    hanslovsky committed Oct 4, 2019
    Configuration menu
    Copy the full SHA
    a005d0a View commit details
    Browse the repository at this point in the history

  6. Continue updating label source state

    @hanslovsky
    hanslovsky committed Oct 4, 2019
    Configuration menu
    Copy the full SHA
    33aec29 View commit details
    Browse the repository at this point in the history

Commits on Oct 7, 2019

  1. Add single scale n5 backend

    @hanslovsky
    hanslovsky committed Oct 7, 2019
    Configuration menu
    Copy the full SHA
    ae1dca5 View commit details
    Browse the repository at this point in the history

  2. Create first simple single-scale n5 label backend

    @hanslovsky
    hanslovsky committed Oct 7, 2019
    Configuration menu
    Copy the full SHA
    4b0ae55 View commit details
    Browse the repository at this point in the history

  3. Make flood fill available in new ConnectomicsLabelState

    @hanslovsky
    hanslovsky committed Oct 7, 2019
    Configuration menu
    Copy the full SHA
    209df81 View commit details
    Browse the repository at this point in the history

  4. Add multi-scale group backend

    @hanslovsky
    hanslovsky committed Oct 7, 2019
    Configuration menu
    Copy the full SHA
    a264f08 View commit details
    Browse the repository at this point in the history

  5. Start adding Paintera dataset backend

    @hanslovsky
    hanslovsky committed Oct 7, 2019
    Configuration menu
    Copy the full SHA
    f34e25e View commit details
    Browse the repository at this point in the history

Commits on Oct 8, 2019

  1. Do not serialize id service

    @hanslovsky
    hanslovsky committed Oct 8, 2019
    Configuration menu
    Copy the full SHA
    ada8e0a View commit details
    Browse the repository at this point in the history

  2. Serialize only non-backend specific data 

    The actual type of the FragmentSegmentAssignment does not need to be specified. This makes relative datasets a lot easier!
    @hanslovsky
    hanslovsky committed Oct 8, 2019
    Configuration menu
    Copy the full SHA
    ae9a05f View commit details
    Browse the repository at this point in the history

  3. Remove unused functions

    @hanslovsky
    hanslovsky committed Oct 8, 2019
    Configuration menu
    Copy the full SHA
    86e151f View commit details
    Browse the repository at this point in the history

  4. Add unifying N5Backend interface with factory method

    @hanslovsky
    hanslovsky committed Oct 8, 2019
    Configuration menu
    Copy the full SHA
    d5341f8 View commit details
    Browse the repository at this point in the history

  5. Use ConnectomicsLabelState when adding sources from CLI

    @hanslovsky
    hanslovsky committed Oct 8, 2019
    Configuration menu
    Copy the full SHA
    5e8ccbc View commit details
    Browse the repository at this point in the history

  6. Add meta information to UI 

    Add remarks to add UI configuration for offset/resolution in the future
    @hanslovsky
    hanslovsky committed Oct 8, 2019
    Configuration menu
    Copy the full SHA
    d6ba5db View commit details
    Browse the repository at this point in the history

Commits on Oct 9, 2019

  1. Make next Id shortcut work for new ConnectomicsLabelState

    @hanslovsky
    hanslovsky committed Oct 9, 2019
    Configuration menu
    Copy the full SHA
    0c4bce3 View commit details
    Browse the repository at this point in the history

  2. Pass binding keys into handlers instead of using static members of de… 

    …precated class
    @hanslovsky
    hanslovsky committed Oct 9, 2019
    Configuration menu
    Copy the full SHA
    7a768ad View commit details
    Browse the repository at this point in the history

  3. Ensure that the intersecting source state works with ConnectomicsLabe… 

    …lState as well
    @hanslovsky
    hanslovsky committed Oct 9, 2019
    Configuration menu
    Copy the full SHA
    8010e47 View commit details
    Browse the repository at this point in the history

  4. Bump label-utilities-n5 dependency version to use relative lookups

    @hanslovsky
    hanslovsky committed Oct 9, 2019
    Configuration menu
    Copy the full SHA
    965efce View commit details
    Browse the repository at this point in the history

Commits on Oct 10, 2019

  1. Serialize arbitrary meshes relative to project

    @hanslovsky
    hanslovsky committed Oct 10, 2019
    Configuration menu
    Copy the full SHA
    8ff358b View commit details
    Browse the repository at this point in the history

Commits on Nov 1, 2019

  1. Update label-utilities-n5 dependency

    @hanslovsky
    hanslovsky committed Nov 1, 2019
    Configuration menu
    Copy the full SHA
    faacd98 View commit details
    Browse the repository at this point in the history

  2. Start working on converting LabelSourceState into ConnectomicsLabelState

    @hanslovsky
    hanslovsky committed Nov 1, 2019
    Configuration menu
    Copy the full SHA
    a207961 View commit details
    Browse the repository at this point in the history

Commits on Nov 21, 2019

  1. Only serialize mesh settings if not managed

    @hanslovsky
    hanslovsky committed Nov 21, 2019
    Configuration menu
    Copy the full SHA
    5b398a9 View commit details
    Browse the repository at this point in the history

Commits on Nov 22, 2019

  1. Separate backend from state for raw data as well

    @hanslovsky
    hanslovsky committed Nov 22, 2019
    Configuration menu
    Copy the full SHA
    56d87e5 View commit details
    Browse the repository at this point in the history

  2. Repaint on contrast or alpha change

    @hanslovsky
    hanslovsky committed Nov 22, 2019
    Configuration menu
    Copy the full SHA
    8409f48 View commit details
    Browse the repository at this point in the history

Commits on Nov 25, 2019

  1. Re-implement channel source states with backend as well.

    @hanslovsky
    hanslovsky committed Nov 25, 2019
    Configuration menu
    Copy the full SHA
    978e1bd View commit details
    Browse the repository at this point in the history

  2. Fix constructor bug for channel state 

    The number of channels is not the same as the number of mipmap levels!
    @hanslovsky
    hanslovsky committed Nov 25, 2019
    Configuration menu
    Copy the full SHA
    202277a View commit details
    Browse the repository at this point in the history

Commits on Nov 26, 2019

  1. WIP add fallback deserializer

    @hanslovsky
    hanslovsky committed Nov 26, 2019
    Configuration menu
    Copy the full SHA
    1533142 View commit details
    Browse the repository at this point in the history

  2. Also convert actions

    @hanslovsky
    hanslovsky committed Nov 26, 2019
    Configuration menu
    Copy the full SHA
    b080937 View commit details
    Browse the repository at this point in the history

  3. Add fall-back deserialization for LabelSourceState

    @hanslovsky
    hanslovsky committed Nov 26, 2019
    Configuration menu
    Copy the full SHA
    ba6d928 View commit details
    Browse the repository at this point in the history

  4. Add fall-back serializers for RawSourceState

    @hanslovsky
    hanslovsky committed Nov 26, 2019
    Configuration menu
    Copy the full SHA
    a6f5aa8 View commit details
    Browse the repository at this point in the history

Commits on Nov 27, 2019

  1. WIP Refactor responsibilities of backend and state 

    The backend should not hold on to the source. Instead, it should create it on demand.

WIP because of weird compilation error.
    @hanslovsky
    hanslovsky committed Nov 27, 2019
    1 Configuration menu
    Copy the full SHA
    7c5c5e9 View commit details
    Browse the repository at this point in the history

Commits on Dec 2, 2019

  1. Fix compilation

    @hanslovsky
    hanslovsky committed Dec 2, 2019
    Configuration menu
    Copy the full SHA
    68147f6 View commit details
    Browse the repository at this point in the history

  2. Use correct interfaces for deserializers

    @hanslovsky
    hanslovsky committed Dec 2, 2019
    Configuration menu
    Copy the full SHA
    98d106e View commit details
    Browse the repository at this point in the history

  3. Fix method keywords

    @hanslovsky
    hanslovsky committed Dec 2, 2019
    Configuration menu
    Copy the full SHA
    02f6888 View commit details
    Browse the repository at this point in the history

  4. Deserialize custom colors when converting from LabelSourceState

    @hanslovsky
    hanslovsky committed Dec 2, 2019
    Configuration menu
    Copy the full SHA
    0a7c855 View commit details
    Browse the repository at this point in the history

  5. Convert n5-filesystem to n5-filesystem-relative when opening Paintera… 

    … dataset

To make datasets really relative to project directory, label-block lookup has to be relative to containing Paintera dataset.
    @hanslovsky
    hanslovsky committed Dec 2, 2019
    Configuration menu
    Copy the full SHA
    13ab982 View commit details
    Browse the repository at this point in the history

Commits on Dec 3, 2019

  1. Add fallback deserializer for channel sources as well.

    @hanslovsky
    hanslovsky committed Dec 3, 2019
    Configuration menu
    Copy the full SHA
    21bbdfc View commit details
    Browse the repository at this point in the history

  2. Merge branch 'master' into relative-data-location

    @hanslovsky
    hanslovsky committed Dec 3, 2019
    Configuration menu
    Copy the full SHA
    fe9e1be View commit details
    Browse the repository at this point in the history

  3. Skip JavaDoc generation

    @hanslovsky
    hanslovsky committed Dec 3, 2019
    Configuration menu
    Copy the full SHA
    7a0ad44 View commit details
    Browse the repository at this point in the history

Commits on Dec 6, 2019

  1. Start working on fragment counts

    @hanslovsky
    hanslovsky committed Dec 6, 2019
    Configuration menu
    Copy the full SHA
    54c0fb9 View commit details
    Browse the repository at this point in the history

  2. Save WIP smallest segment count node

    @hanslovsky
    hanslovsky committed Dec 6, 2019
    Configuration menu
    Copy the full SHA
    576ec32 View commit details
    Browse the repository at this point in the history

Commits on Dec 9, 2019

  1. Center viewer at fragment upon request

    @hanslovsky
    hanslovsky committed Dec 9, 2019
    Configuration menu
    Copy the full SHA
    8829506 View commit details
    Browse the repository at this point in the history

Commits on Dec 10, 2019

  1. Refactor segment count feature to use caches 

    Even on a small CREMI dataset, extracting count features is pretty slow already. Use caches instead.
    @hanslovsky
    hanslovsky committed Dec 10, 2019
    Configuration menu
    Copy the full SHA
    fbc8100 View commit details
    Browse the repository at this point in the history

Commits on Dec 11, 2019

  1. Ask user to convert deprecated datasets 

    It is important that the user to make this decision instead of automatic, implicit conversion
    @hanslovsky
    hanslovsky committed Dec 11, 2019
    Configuration menu
    Copy the full SHA
    1677d47 View commit details
    Browse the repository at this point in the history

  2. Fix bugs in channel state fallback deserializer 

     - channels not deserialized correctly
 - channelIndex not deserialized correctly
 - converter not deserialized correctly
 - checked for wrong source class
    @hanslovsky
    hanslovsky committed Dec 11, 2019
    Configuration menu
    Copy the full SHA
    d80fbba View commit details
    Browse the repository at this point in the history

  3. Do not deserialize label block lookup in fallback deserializer 

    The lookup is always provided in the Paintera dataset backend, no need to deserialize when converting.
    @hanslovsky
    hanslovsky committed Dec 11, 2019
    Configuration menu
    Copy the full SHA
    5cedc81 View commit details
    Browse the repository at this point in the history

  4. Create backup files for converted attributes files

    @hanslovsky
    hanslovsky committed Dec 11, 2019
    Configuration menu
    Copy the full SHA
    4464911 View commit details
    Browse the repository at this point in the history

  5. Merge branch 'master' into relative-data-location

    @hanslovsky
    hanslovsky authored Dec 11, 2019
    Configuration menu
    Copy the full SHA
    87e40bd View commit details
    Browse the repository at this point in the history

Commits on Dec 17, 2019

  1. Add mnemonic to remember choice check box

    @hanslovsky
    hanslovsky committed Dec 17, 2019
    Configuration menu
    Copy the full SHA
    2eb51e9 View commit details
    Browse the repository at this point in the history

  2. Merge branch 'master' into relative-data-location

    @hanslovsky
    hanslovsky committed Dec 17, 2019
    Configuration menu
    Copy the full SHA
    3b41462 View commit details
    Browse the repository at this point in the history

  3. Merge branch 'relative-data-location' into fragment-count

    @hanslovsky
    hanslovsky committed Dec 17, 2019
    Configuration menu
    Copy the full SHA
    b2051a9 View commit details
    Browse the repository at this point in the history

Commits on Dec 18, 2019

  1. Add some JavaDoc to ConnectomicsLabelState

    @hanslovsky
    hanslovsky committed Dec 18, 2019
    Configuration menu
    Copy the full SHA
    eff9285 View commit details
    Browse the repository at this point in the history

  2. Save WIP: use min/max size filter instead of best N 

    Currently, there is still concurrent exceptions. Fix those, then get this ready for discussion!
    @hanslovsky
    hanslovsky committed Dec 18, 2019
    Configuration menu
    Copy the full SHA
    bf8897d View commit details
    Browse the repository at this point in the history

  3. Put UI elements inside titled pane

    @hanslovsky
    hanslovsky committed Dec 18, 2019
    Configuration menu
    Copy the full SHA
    27a2237 View commit details
    Browse the repository at this point in the history

  4. Make tasks actually cancellable 

    Still experiencing concurrent modification exceptions
    @hanslovsky
    hanslovsky committed Dec 18, 2019
    Configuration menu
    Copy the full SHA
    8ab5ba6 View commit details
    Browse the repository at this point in the history

  5. Do not sort by column 

    Before adding the data to the table, it is sorted already at the moment
    @hanslovsky
    hanslovsky committed Dec 18, 2019
    Configuration menu
    Copy the full SHA
    e3dff4e View commit details
    Browse the repository at this point in the history

Commits on Jan 9, 2020

  1. Extract SegmentVoxelCountStore into separate class and expose in labe… 

    …l state
    @hanslovsky
    hanslovsky committed Jan 9, 2020
    Configuration menu
    Copy the full SHA
    f0c7f4e View commit details
    Browse the repository at this point in the history

Commits on Jan 13, 2020

  1. Save WIP 

    Navigate to next smallest segment that intersects with at least one synapse.

Does not work as of now, will probably require a more well-thoughtout feature store.
    @hanslovsky
    hanslovsky committed Jan 13, 2020
    Configuration menu
    Copy the full SHA
    6d671ac View commit details
    Browse the repository at this point in the history