Ecosyste.ms: Issues

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GitHub / sjeknic/CellTK issues and pull requests

#115 - V043

Pull Request - State: closed - Opened by sjeknic over 2 years ago

#114 - V043b1

Pull Request - State: closed - Opened by sjeknic over 2 years ago

#113 - V043beta

Pull Request - State: closed - Opened by sjeknic over 2 years ago

#112 - Revert "V043beta (#111)"

Pull Request - State: closed - Opened by sjeknic over 2 years ago

#111 - V043beta

Pull Request - State: closed - Opened by sjeknic over 2 years ago

#110 - V042

Pull Request - State: closed - Opened by sjeknic over 2 years ago

#109 - V041 - Publishing

Pull Request - State: closed - Opened by sjeknic over 2 years ago

#108 - V040 - New typing, Track removed

Pull Request - State: closed - Opened by sjeknic over 2 years ago

#107 - V033

Pull Request - State: closed - Opened by sjeknic over 2 years ago

#106 - V032

Pull Request - State: closed - Opened by sjeknic over 2 years ago

#105 - `Pipeline` may try to open hdf5 files using `iio.mimread`

Issue - State: closed - Opened by sjeknic almost 3 years ago - 1 comment
Labels: bug

#104 - v0.3.1 - New Plotting API

Pull Request - State: closed - Opened by sjeknic almost 3 years ago

#103 - Better plotting API and Evaluator

Pull Request - State: closed - Opened by sjeknic almost 3 years ago

#102 - V023 patch

Pull Request - State: closed - Opened by sjeknic almost 3 years ago

#101 - V022 patch

Pull Request - State: closed - Opened by sjeknic almost 3 years ago

#100 - V0.2.1 Patch

Pull Request - State: closed - Opened by sjeknic almost 3 years ago

#99 - V020 patch

Pull Request - State: closed - Opened by sjeknic almost 3 years ago

#98 - Documentation Improvements

Pull Request - State: closed - Opened by sjeknic almost 3 years ago

#97 - Initial Documentation

Pull Request - State: closed - Opened by sjeknic almost 3 years ago

#96 - Renaming to CellTK

Pull Request - State: closed - Opened by sjeknic almost 3 years ago

#95 - added unit test workflow

Pull Request - State: closed - Opened by sjeknic almost 3 years ago

#94 - v0.1.0 patch

Pull Request - State: closed - Opened by sjeknic almost 3 years ago

#93 - v0.1.0 release - adding UPeak, Info theory, and plotting improvements

Pull Request - State: closed - Opened by sjeknic almost 3 years ago

#92 - Create groups within `Orchestrator` and `ExperimentArray`

Issue - State: open - Opened by sjeknic almost 3 years ago
Labels: enhancement

#91 - Handle positions with zero cells

Issue - State: closed - Opened by sjeknic almost 3 years ago - 1 comment
Labels: bug

#89 - rerunning jobs in `SlurmController` raises `ValueError`

Issue - State: open - Opened by sjeknic almost 3 years ago
Labels: bug

#88 - Add option to designate bad frames

Issue - State: closed - Opened by sjeknic almost 3 years ago - 1 comment
Labels: enhancement

#87 - Add low memory option for building `ExperimentArray` hdf5 files

Issue - State: open - Opened by sjeknic almost 3 years ago
Labels: bug

#86 - v0.0.1 patch

Pull Request - State: closed - Opened by sjeknic almost 3 years ago

#84 - v0.0.0 patch

Pull Request - State: closed - Opened by sjeknic about 3 years ago

#83 - `force_rerun` does not apply to stacks with multiple types

Issue - State: closed - Opened by sjeknic about 3 years ago - 1 comment
Labels: bug

#82 - add `keep_as` option to `Operation.add_function_to_operation`

Issue - State: open - Opened by sjeknic about 3 years ago
Labels: enhancement, good first issue

#81 - dtype of stacks can change in some circumstances

Issue - State: closed - Opened by sjeknic about 3 years ago - 2 comments
Labels: bug

#80 - `Pipeline` does not load `Array`

Issue - State: closed - Opened by sjeknic about 3 years ago - 1 comment
Labels: bug, good first issue

#79 - `Same` type should be more generally useful

Issue - State: closed - Opened by sjeknic about 3 years ago - 1 comment
Labels: enhancement

#78 - `ImageHelper` doesn't guarantee order for kwarg passed images

Issue - State: closed - Opened by sjeknic about 3 years ago - 1 comment
Labels: bug

#76 - `UNet` is broken compared to previous versions

Issue - State: closed - Opened by sjeknic about 3 years ago - 3 comments
Labels: bug

#75 - Pre-release changes

Pull Request - State: closed - Opened by sjeknic about 3 years ago - 2 comments

#74 - `Operation` input and output requests need to be more specific

Issue - State: closed - Opened by sjeknic about 3 years ago - 1 comment
Labels: bug

#73 - Add filtering cells to Extractor

Issue - State: closed - Opened by sjeknic about 3 years ago
Labels: enhancement

#72 - Derived metrics in Extractor must be numpy functions

Issue - State: open - Opened by sjeknic about 3 years ago - 1 comment

#71 - Running list of features that should be added for SLURM

Issue - State: open - Opened by sjeknic about 3 years ago - 1 comment
Labels: enhancement, good first issue

#70 - Add `bin` for using the command line

Issue - State: open - Opened by sjeknic about 3 years ago
Labels: enhancement

#69 - Improvements for submitting jobs to SLURM

Pull Request - State: closed - Opened by sjeknic about 3 years ago

#68 - Slurm updates

Pull Request - State: closed - Opened by sjeknic about 3 years ago

#67 - Updates to requirements

Pull Request - State: closed - Opened by sjeknic about 3 years ago

#66 - Adding BayesianTracker

Pull Request - State: closed - Opened by sjeknic about 3 years ago

#65 - Bump tensorflow from 2.0.0 to 2.5.2

Pull Request - State: closed - Opened by dependabot[bot] about 3 years ago - 2 comments
Labels: dependencies

#64 - Consistent import formatting

Pull Request - State: closed - Opened by sjeknic about 3 years ago

#63 - Adds cli, submission to slurm scheduler, and logging improvements

Pull Request - State: closed - Opened by sjeknic about 3 years ago

#62 - Bayesian tracking runs indefinitely for poorly formatted inputs

Issue - State: closed - Opened by sjeknic about 3 years ago - 1 comment
Labels: bug

#61 - Operation `__init__` should always use `BaseOperation` and allow inputs of all types

Issue - State: closed - Opened by sjeknic about 3 years ago - 1 comment
Labels: bug, enhancement

#60 - `UNetModel` does not properly pad some dimensions

Issue - State: closed - Opened by sjeknic about 3 years ago - 2 comments
Labels: bug

#59 - Add UNet training

Issue - State: open - Opened by sjeknic about 3 years ago
Labels: enhancement

#57 - `__call__` no longer works in `Operations`

Issue - State: closed - Opened by sjeknic about 3 years ago - 2 comments
Labels: bug

#56 - `Operations` with `save_name` is unclear how to save to `inputs`

Issue - State: closed - Opened by sjeknic about 3 years ago - 2 comments
Labels: bug

#55 - Logger gets duplicated in `Orchestrator` and/or in multiple `Pipeline`s

Issue - State: closed - Opened by sjeknic about 3 years ago - 1 comment
Labels: bug

#54 - Logger does not log errors or warnings

Issue - State: closed - Opened by sjeknic about 3 years ago
Labels: bug, good first issue

#53 - Add option to not re-run function if files are loaded

Issue - State: closed - Opened by sjeknic about 3 years ago
Labels: bug, enhancement

#52 - `Process` needs to be able to return multiple arrays

Issue - State: closed - Opened by sjeknic about 3 years ago - 1 comment
Labels: bug

#51 - Incorporate bottleneck where useful

Issue - State: closed - Opened by sjeknic about 3 years ago - 3 comments
Labels: enhancement, wontfix

#50 - Capture output from SLURM and log to file.

Issue - State: closed - Opened by sjeknic about 3 years ago - 1 comment
Labels: enhancement

#49 - Logger does not log where images are found if they came from outputs

Issue - State: closed - Opened by sjeknic about 3 years ago - 1 comment
Labels: bug

#48 - Running extract without mask or track runs indefinitely?

Issue - State: closed - Opened by sjeknic about 3 years ago - 1 comment
Labels: bug

#47 - Build from YAML

Pull Request - State: closed - Opened by sjeknic about 3 years ago

#46 - Add derived metrics

Issue - State: closed - Opened by sjeknic about 3 years ago
Labels: enhancement

#45 - Add command line calling of `Pipeline` and `Orchestrator`

Issue - State: closed - Opened by sjeknic about 3 years ago - 1 comment
Labels: enhancement

#44 - Adding logging of runs

Pull Request - State: closed - Opened by sjeknic about 3 years ago

#43 - Add automated testing for pull requests

Issue - State: closed - Opened by sjeknic about 3 years ago
Labels: enhancement, good first issue

#42 - Updates to kit_sch_ge tracking

Pull Request - State: open - Opened by sjeknic about 3 years ago

#41 - Files are not sorted in correct order

Issue - State: closed - Opened by sjeknic about 3 years ago - 1 comment

#40 - Define desired analysis with yaml files

Issue - State: closed - Opened by sjeknic about 3 years ago - 1 comment
Labels: enhancement

#39 - Multiprocessing added

Pull Request - State: closed - Opened by sjeknic about 3 years ago

#38 - Add alignment and background subtraction in `Process`

Issue - State: closed - Opened by sjeknic about 3 years ago - 1 comment
Labels: enhancement

#37 - Add information theory calculations

Issue - State: closed - Opened by sjeknic about 3 years ago - 1 comment
Labels: enhancement, good first issue

#36 - Add interactive pipeline segmentation

Issue - State: open - Opened by sjeknic about 3 years ago
Labels: enhancement

#35 - Add peak segmentation with UPeak CNN model

Issue - State: closed - Opened by sjeknic about 3 years ago - 1 comment
Labels: enhancement, good first issue

#34 - Documentation is poor

Issue - State: closed - Opened by sjeknic about 3 years ago - 1 comment
Labels: documentation

#32 - `CellArray` should be able to be made from an `np.ndarray`

Issue - State: open - Opened by sjeknic about 3 years ago
Labels: enhancement, good first issue

#31 - `Track` will only use one of `track` or `mask`

Issue - State: closed - Opened by sjeknic about 3 years ago - 1 comment

#30 - `Operation.save_arrays` needs to be deleted after completion

Issue - State: closed - Opened by sjeknic about 3 years ago

#29 - Make imports more consistent

Issue - State: closed - Opened by sjeknic about 3 years ago - 2 comments
Labels: enhancement

#28 - Add time axis to `CellArray` and `PositionArray`

Issue - State: closed - Opened by sjeknic about 3 years ago

#27 - Non-consecutive time steps

Issue - State: closed - Opened by sjeknic about 3 years ago - 1 comment
Labels: enhancement

#26 - Keep cell labels across multiple segmentation masks

Issue - State: closed - Opened by sjeknic about 3 years ago
Labels: bug, enhancement

#25 - `Track` should have the option to force sequential cell ids

Issue - State: open - Opened by sjeknic over 3 years ago
Labels: bug, enhancement

#24 - `Pipeline` should be able to save/load arrays

Issue - State: closed - Opened by sjeknic over 3 years ago

#22 - `Orchestrator` is currently non-functional

Issue - State: closed - Opened by sjeknic over 3 years ago

#20 - Lineage files should be able to be loaded

Issue - State: open - Opened by sjeknic over 3 years ago
Labels: enhancement, good first issue

#19 - `track_to_lineage` is slow and ineffective

Issue - State: closed - Opened by sjeknic over 3 years ago - 1 comment

#16 - cvxopt GLPK solver prints excessive messages

Issue - State: closed - Opened by sjeknic over 3 years ago - 2 comments

#14 - `Pipeline` searches for images in isolated locations

Issue - State: closed - Opened by sjeknic over 3 years ago - 2 comments

#13 - Add Tracking function

Pull Request - State: closed - Opened by sjeknic over 3 years ago

#12 - Improvements to segmentation

Pull Request - State: closed - Opened by sjeknic over 3 years ago

#5 - Import paths broken in subtrees

Issue - State: open - Opened by sjeknic over 3 years ago
Labels: wontfix

#4 - Rearrange files

Pull Request - State: closed - Opened by sjeknic over 3 years ago

#3 - Added CellSet

Pull Request - State: closed - Opened by sjeknic over 3 years ago