turagalab/decode issues and pull requests

#241 - Sample training data takes tens of minutes one epoch on Linux with an A800

Issue - State: open - Opened by GuohuaQiu1999 12 days ago

#119 - disable network outputs for disabled_attributes

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

#117 - Errors while saving emitter as csv

Issue - State: closed - Opened by cleterrier over 3 years ago - 5 comments

#115 - Add auto-restart to Colab

Issue - State: closed - Opened by Haydnspass over 3 years ago - 1 comment
Labels: enhancement

#114 - Polishing the documentations

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

#113 - Using device='cuda' does not work in Renderer2DIndividual

Issue - State: closed - Opened by Haydnspass over 3 years ago - 1 comment
Labels: bug

#112 - Updated docs

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

#111 - fix restart after finished training

Pull Request - State: closed - Opened by ASpeiser over 3 years ago - 1 comment

#110 - Training restarts after max epochs has been reached

Issue - State: closed - Opened by Haydnspass over 3 years ago - 1 comment
Labels: bug, important

#109 - Update package_1

Issue - State: closed - Opened by Haydnspass over 3 years ago - 1 comment
Labels: documentation

#108 - Notebook changes

Issue - State: closed - Opened by Haydnspass over 3 years ago - 8 comments

#107 - Doc changes after v0.10.0 rc

Issue - State: closed - Opened by Haydnspass over 3 years ago
Labels: documentation, publication

#106 - Instructions for Testers and Collection of Feedback / Bugs for DECODE v0.10.rc.2

Issue - State: closed - Opened by Haydnspass over 3 years ago - 19 comments
Labels: publication, tests, deployment, important

#105 - Change semantic versioning scheme after full release

Issue - State: closed - Opened by Haydnspass over 3 years ago - 1 comment
Labels: deployment

#104 - Dev docs

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

#103 - Dev render clip

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

#102 - Checklist v0.10 release

Issue - State: closed - Opened by Haydnspass over 3 years ago
Labels: deployment

#100 - Doc changes

Issue - State: closed - Opened by Haydnspass over 3 years ago - 14 comments
Labels: documentation

#99 - Add intermediate flag for transpose plotting

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

#98 - additional comments to Training, change plotting in Fit

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

#97 - Failed to download assets

Issue - State: closed - Opened by github-actions[bot] over 3 years ago

#96 - Failed to download assets

Issue - State: closed - Opened by github-actions[bot] over 3 years ago

#95 - Failed to download assets

Issue - State: closed - Opened by github-actions[bot] over 3 years ago

#94 - Failed to download assets

Issue - State: closed - Opened by github-actions[bot] over 3 years ago

#93 - add total sig properties

Pull Request - State: closed - Opened by ASpeiser over 3 years ago - 2 comments

#92 - Failed to download assets

Issue - State: closed - Opened by github-actions[bot] over 3 years ago

#91 - Failed to download assets

Issue - State: closed - Opened by github-actions[bot] over 3 years ago

#90 - Failed to download assets

Issue - State: closed - Opened by github-actions[bot] over 3 years ago

#89 - Failed to download assets

Issue - State: closed - Opened by github-actions[bot] over 3 years ago

#88 - Failed to download assets

Issue - State: closed - Opened by github-actions[bot] over 3 years ago

#87 - Failed to download assets

Issue - State: closed - Opened by github-actions[bot] over 3 years ago

#86 - Failed to download assets

Issue - State: closed - Opened by github-actions[bot] over 3 years ago

#85 - import warning

Issue - State: closed - Opened by Haydnspass over 3 years ago - 3 comments
Labels: bug

#84 - Fix Clipping, Update Renderer

Pull Request - State: closed - Opened by ASpeiser over 3 years ago - 2 comments

#81 - Add method to frame processing that transforms emitters accordingly

Issue - State: open - Opened by Haydnspass over 3 years ago
Labels: enhancement

#80 - Simple way to automatically submit trainings to cluster

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

#79 - Uncaught warning during training

Issue - State: closed - Opened by Haydnspass over 3 years ago - 2 comments
Labels: enhancement, wontfix

#78 - Pip Build with python version matrix (like unit tests)

Issue - State: closed - Opened by Haydnspass over 3 years ago - 2 comments
Labels: enhancement, deployment

#77 - Add workshop video to the repo

Issue - State: closed - Opened by Haydnspass over 3 years ago - 1 comment
Labels: documentation, enhancement

#76 - automated build/upload

Pull Request - State: closed - Opened by olbris over 3 years ago - 1 comment

#70 - Update Google Colab to latest version and notebooks

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

#69 - Problem getting DECODE to work with an sCMOS camera (no EM gain)

Issue - State: closed - Opened by cleterrier over 3 years ago - 5 comments
Labels: question

#68 - Test current SMAP plugin for creating a .yaml file

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

#67 - Markdown table not working in docs

Issue - State: closed - Opened by Haydnspass over 3 years ago - 1 comment
Labels: bug, documentation

#66 - Add details for lower-end hardware

Issue - State: closed - Opened by Haydnspass over 3 years ago - 2 comments
Labels: documentation, important

#65 - Fix unstable rendering when using slightly different clip percentiles

Issue - State: closed - Opened by Haydnspass over 3 years ago - 1 comment
Labels: bug

#64 - Failed to download assets

Issue - State: closed - Opened by github-actions[bot] over 3 years ago - 1 comment

#63 - Dev checkpt load

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

#62 - Segmentation fault on testing the train implementation

Issue - State: closed - Opened by Haydnspass over 3 years ago - 2 comments
Labels: bug, help wanted, tests

#61 - Failed to download assets

Issue - State: closed - Opened by github-actions[bot] over 3 years ago

#60 - add 3D renderer

Pull Request - State: closed - Opened by ASpeiser over 3 years ago
Labels: enhancement

#59 - Document logic for mirroring in Notebooks and documentation

Issue - State: closed - Opened by Haydnspass over 3 years ago - 1 comment
Labels: documentation, important

#56 - Make Emitter compatible to None attributes

Issue - State: closed - Opened by Haydnspass almost 4 years ago - 1 comment
Labels: enhancement

#55 - Sync CSV i/o signature and return to HDF5 / torch signature,return

Issue - State: closed - Opened by Haydnspass almost 4 years ago - 1 comment
Labels: enhancement, tests, change

#54 - add functionality to restart training automatically

Pull Request - State: closed - Opened by ASpeiser almost 4 years ago - 2 comments

#53 - Abstract logger implementation to allow for other loggers

Issue - State: open - Opened by Haydnspass almost 4 years ago
Labels: enhancement

#52 - add comparison of photon/background fits with simulation ranges

Pull Request - State: closed - Opened by ASpeiser almost 4 years ago

#51 - Python 3.6 dependency solving fails for conda, but works for mamba

Issue - State: closed - Opened by Haydnspass almost 4 years ago - 1 comment
Labels: bug

#50 - Dev remove warnings

Pull Request - State: closed - Opened by ASpeiser almost 4 years ago

#47 - Add all relevant (hyper)params to tensorboard

Issue - State: open - Opened by Haydnspass almost 4 years ago - 1 comment
Labels: enhancement

#42 - Change x/y axis

Issue - State: open - Opened by Haydnspass almost 4 years ago - 2 comments
Labels: change

#41 - Change parameter file logic because it breaks sometimes

Issue - State: open - Opened by Haydnspass almost 4 years ago
Labels: bug

#40 - Pad to Size instead of center crop

Issue - State: closed - Opened by Haydnspass almost 4 years ago - 1 comment
Labels: enhancement

#39 - Failed to download assets

Issue - State: closed - Opened by github-actions[bot] almost 4 years ago

#38 - Failed to download assets

Issue - State: closed - Opened by github-actions[bot] almost 4 years ago

#37 - Failed to download assets

Issue - State: closed - Opened by github-actions[bot] almost 4 years ago

#36 - Failed to download assets

Issue - State: closed - Opened by github-actions[bot] almost 4 years ago

#35 - Failed to download assets

Issue - State: closed - Opened by github-actions[bot] almost 4 years ago

#34 - Failed to download assets

Issue - State: closed - Opened by github-actions[bot] almost 4 years ago

#33 - Failed to download assets

Issue - State: closed - Opened by github-actions[bot] almost 4 years ago - 1 comment

#32 - Add python 3.9 support and update to latest pytorch

Issue - State: closed - Opened by Haydnspass almost 4 years ago - 1 comment

#31 - Dummy Issue

Issue - State: closed - Opened by Haydnspass almost 4 years ago

#30 - Failed to download assets

Issue - State: closed - Opened by github-actions[bot] almost 4 years ago - 1 comment

#29 - Failed to download assets

Issue - State: closed - Opened by github-actions[bot] almost 4 years ago - 1 comment

#28 - Automatic Batch Size

Issue - State: closed - Opened by Haydnspass almost 4 years ago - 2 comments
Labels: enhancement, publication

#27 - Batch Folder processing

Issue - State: open - Opened by Haydnspass almost 4 years ago
Labels: enhancement

#26 - Automatic Learning Rate setter

Issue - State: closed - Opened by Haydnspass almost 4 years ago - 3 comments
Labels: enhancement, important

#24 - Multiprocessing / multiple workers on Windows

Issue - State: open - Opened by Haydnspass almost 4 years ago - 2 comments
Labels: bug, enhancement, wontfix, tests

#23 - Filter warnings when no emitter is found

Issue - State: closed - Opened by Haydnspass almost 4 years ago
Labels: enhancement

#22 - SMAP prefit .yaml does not conform with DECODE

Issue - State: closed - Opened by Haydnspass almost 4 years ago
Labels: bug

#21 - On the fly tiff loader

Issue - State: closed - Opened by Haydnspass almost 4 years ago - 1 comment
Labels: enhancement

#20 - Add verification to the end of fitting (notebook)

Issue - State: closed - Opened by Haydnspass almost 4 years ago
Labels: enhancement

#19 - Move example package caching to user-level cache

Issue - State: closed - Opened by Haydnspass about 4 years ago - 2 comments
Labels: enhancement

#18 - Robust EM Gain tag read from .tiff

Issue - State: open - Opened by Haydnspass about 4 years ago
Labels: enhancement

#17 - Logging training at the end of the epoch can take quite some time.

Issue - State: open - Opened by Haydnspass about 4 years ago
Labels: enhancement

#16 - Memory leak when training in notebook directly

Issue - State: closed - Opened by Haydnspass about 4 years ago - 1 comment
Labels: bug, help wanted

#15 - Implement checkpoint loading in codebase

Issue - State: closed - Opened by Haydnspass about 4 years ago
Labels: enhancement

#14 - Output an all-in-one decode.pt file for model, param (logging)

Issue - State: closed - Opened by Haydnspass about 4 years ago - 1 comment
Labels: enhancement

#13 - Seperate parameter magic from load param

Issue - State: open - Opened by Haydnspass about 4 years ago
Labels: enhancement

#12 - Tensorboard from conda not working

Issue - State: closed - Opened by Haydnspass about 4 years ago - 1 comment
Labels: bug

#11 - NoArch build of DECODE

Pull Request - State: closed - Opened by Haydnspass about 4 years ago

#10 - Can we make DECODE a conda 'noarch'?

Issue - State: closed - Opened by Haydnspass about 4 years ago
Labels: enhancement, deployment

#9 - (Soon) Deprecated oepration in post-processing

Issue - State: closed - Opened by Haydnspass about 4 years ago
Labels: deprecation

#8 - Replace paths in tests by pkg resources

Issue - State: open - Opened by Haydnspass about 4 years ago
Labels: bug, tests

#7 - Replace paths in decode tests

Issue - State: closed - Opened by Haydnspass about 4 years ago

#6 - Modify model save to store also parameters

Issue - State: closed - Opened by Haydnspass about 4 years ago - 1 comment
Labels: enhancement

#5 - Clean up Metrics in Tensorboard logging

Issue - State: closed - Opened by Haydnspass about 4 years ago - 3 comments
Labels: documentation, enhancement, publication

#4 - Implementation of EmitterSet does not always follow pythonic indexing

Issue - State: closed - Opened by Haydnspass about 4 years ago
Labels: enhancement

#3 - Version tag should be automatically imported by conda and setup.py.

Issue - State: closed - Opened by Haydnspass about 4 years ago - 2 comments
Labels: enhancement, publication

#2 - XYZ_sigma of EmitterSet does not convert as xyz does

Issue - State: closed - Opened by Haydnspass about 4 years ago - 1 comment
Labels: bug, enhancement

GitHub / turagalab/decode issues and pull requests