google-research/sofima issues and pull requests

#90 - Remove dependency on TensorFlow in favor of using gpathlib/pathlib for internal and external file access, respectively.

Pull Request - State: closed - Opened by copybara-service[bot] 2 days ago

#89 - Extract defaults for `reconcile_missing_flows` for 2D EM.

Pull Request - State: closed - Opened by copybara-service[bot] 2 days ago

#88 - Centralize `overlap` and `subvolume_size` into a JSON-SerDe dataclass used internally and externally.

Pull Request - State: closed - Opened by copybara-service[bot] 8 days ago

#87 - No public description

Pull Request - State: closed - Opened by copybara-service[bot] 13 days ago

#86 - SOFIMA rendering (warp) pipeline.

Pull Request - State: closed - Opened by copybara-service[bot] 13 days ago

#85 - jax.numpy.clip: update use of deprecated arguments.

Pull Request - State: closed - Opened by copybara-service[bot] about 1 month ago

#84 - Fix WarpByMap: old version was based on the behavior that `clip_to_volume` returned None for any box that was even partially outside the volume. `clip_box_to_volume` now returns a box in all instances, but can return zero-length boxes in one or more dimension. This was caught by this check when the box was completely outside the volume, but failed when one or more dimensions were still within the volume. Changing it to `any` now catches all invalid cases.

Pull Request - State: closed - Opened by copybara-service[bot] about 1 month ago

#83 - Update Python requirements to 3.11.

Pull Request - State: closed - Opened by copybara-service[bot] 2 months ago

#82 - Add default alignment configurations for 2D EM.

Pull Request - State: closed - Opened by copybara-service[bot] 2 months ago

#81 - Update references to JAX's GitHub repo

Pull Request - State: open - Opened by copybara-service[bot] 3 months ago

#80 - Update `calculate_flow` to use new configuration defaults.

Pull Request - State: closed - Opened by copybara-service[bot] 3 months ago

#79 - Move WarpByMap to external SOFIMA repository.

Pull Request - State: closed - Opened by copybara-service[bot] 3 months ago

#78 - Allow `flow_volinfos` in ReconcileAndFilterFlows.Config to be unspecified.

Pull Request - State: closed - Opened by copybara-service[bot] 3 months ago

#77 - Move default config registration and instantiation into connectomics.subvolume_processor.

Pull Request - State: closed - Opened by copybara-service[bot] 3 months ago

#76 - - Add default configurations for mesh relaxation for 2d EM

Pull Request - State: closed - Opened by copybara-service[bot] 4 months ago

#75 - - Rename processor configs from `ProcessorNameConfig` to `Config`.

Pull Request - State: closed - Opened by copybara-service[bot] 4 months ago

#74 - - Create `RelaxMesh` subvolume processor. Also adds private interfaces to SubvolumeProcessors for data paths supporting internal vs external data loading.

Pull Request - State: closed - Opened by copybara-service[bot] 4 months ago

#73 - Combine metadata.py's VolumeMetadata and Volume into a single class.

Pull Request - State: closed - Opened by copybara-service[bot] 5 months ago

#72 - Fix dataclass member names for masks. Mildly concerning these aren't caught by static type checking...?

Pull Request - State: closed - Opened by copybara-service[bot] 5 months ago

#71 - Remove explicit default instantiation from flow_config in favor of listing sane

Pull Request - State: closed - Opened by copybara-service[bot] 5 months ago

#70 - Add support for custom post patch starts and for progress reporting in flow_field().

Pull Request - State: closed - Opened by copybara-service[bot] 5 months ago

#69 - Add support for prefer_orig_order in 3d meshes.

Pull Request - State: closed - Opened by copybara-service[bot] 5 months ago

#68 - Add support for 3d stride in more functions.

Pull Request - State: closed - Opened by copybara-service[bot] 5 months ago

#67 - Add initial SOFIMA pipeline config.

Pull Request - State: closed - Opened by copybara-service[bot] 5 months ago

#66 - Add `EstimateMissingFlow` stage.

Pull Request - State: closed - Opened by copybara-service[bot] 5 months ago

#65 - Add ReconcileAndFilterFlows processor.

Pull Request - State: closed - Opened by copybara-service[bot] 5 months ago

#64 - Updates to `EstimateFlow` stages.

Pull Request - State: closed - Opened by copybara-service[bot] 5 months ago

#63 - Extend `build_mask` to support arbitrary data loading

Pull Request - State: closed - Opened by copybara-service[bot] 6 months ago

#62 - Request for Container image version

Issue - State: open - Opened by Kimyongmin1018 6 months ago

#61 - Make EstimateFlow's config class dataclasses_json compatible.

Pull Request - State: closed - Opened by copybara-service[bot] 6 months ago

#60 - - Convert EstimateFlow to use Dataclasses as a configuration parameter, and update pipelines to support.

Pull Request - State: closed - Opened by copybara-service[bot] 7 months ago

#59 - Add support for 3d maps in inner_box.

Pull Request - State: closed - Opened by copybara-service[bot] 8 months ago

#58 - Add tile masking for coarse offsets computation

Pull Request - State: closed - Opened by ganctom 8 months ago - 1 comment

#57 - Fix docstring.

Pull Request - State: closed - Opened by copybara-service[bot] 9 months ago

#56 - Add scale parameter to WarpCoordMap.

Pull Request - State: closed - Opened by copybara-service[bot] 12 months ago

#55 - Support setting mode and cval in WarpCoordMap.

Pull Request - State: closed - Opened by copybara-service[bot] 12 months ago

#54 - Support composing maps of different sizes.

Pull Request - State: closed - Opened by copybara-service[bot] about 1 year ago

#53 - Fix serialization issue in OptimFlow-decorator.

Pull Request - State: closed - Opened by copybara-service[bot] about 1 year ago

#52 - Add support for block interpolation in backward mode.

Pull Request - State: closed - Opened by copybara-service[bot] about 1 year ago

#51 - Adjust schema for virtual chunked.

Pull Request - State: closed - Opened by copybara-service[bot] about 1 year ago

#50 - Changes to schema adjustment utilities.

Pull Request - State: closed - Opened by copybara-service[bot] about 1 year ago

#49 - sofima.warp.render.tiles raise cv2.error: OpenCV(4.7.0) (-215:Assertion failed) dst.cols < SHRT_MAX && dst.rows < SHRT_MAX && src.cols < SHRT_MAX && src.rows < SHRT_MAX in function 'remap'

Issue - State: closed - Opened by youssefmys over 1 year ago - 4 comments

#48 - Support flow volumes with negative delta_z in reconcile_flows.

Pull Request - State: closed - Opened by copybara-service[bot] over 1 year ago

#47 - [LSC] Ignore incorrect type annotations related to jax.numpy APIs

Pull Request - State: closed - Opened by copybara-service[bot] over 1 year ago

#46 - Add .editorconfig.

Pull Request - State: closed - Opened by copybara-service[bot] over 1 year ago

#45 - Add pyink default settings.

Pull Request - State: closed - Opened by copybara-service[bot] over 1 year ago

#44 - Include the decorators submodule in the sofima package.

Pull Request - State: closed - Opened by copybara-service[bot] over 1 year ago

#43 - Add decorators.

Pull Request - State: closed - Opened by copybara-service[bot] over 1 year ago

#42 - Change OpenCV import.

Pull Request - State: closed - Opened by copybara-service[bot] over 1 year ago

#41 - Adding support for Zarr stitching/fusion

Pull Request - State: open - Opened by jwong-nd over 1 year ago - 2 comments