Ecosyste.ms: Issues

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GitHub / alan-turing-institute/affinity-vae issues and pull requests

#282 - Post processing notebook

Pull Request - State: open - Opened by marjanfamili 9 months ago - 1 comment

#280 - Differentiable Gaussian splat decoder

Pull Request - State: open - Opened by marjanfamili 9 months ago - 1 comment

#279 - [WIP] Pytorch lightning

Pull Request - State: open - Opened by crangelsmith 9 months ago

#277 - Flexible installation

Pull Request - State: closed - Opened by crangelsmith 9 months ago

#276 - Eval flag in input file not registered

Issue - State: open - Opened by marjanfamili 10 months ago
Labels: bug

#275 - Error when pose_vis_class is not specified

Issue - State: open - Opened by marjanfamili 10 months ago
Labels: bug

#274 - Affinity error in evaluation mode

Issue - State: open - Opened by marjanfamili 10 months ago
Labels: bug

#274 - Affinity error in evaluation mode

Issue - State: open - Opened by marjanfamili 10 months ago
Labels: bug

#273 - new_out produces error if file full path not declared

Issue - State: open - Opened by marjanfamili 10 months ago
Labels: bug

#272 - Type hints

Pull Request - State: closed - Opened by crangelsmith 10 months ago

#272 - Type hints

Pull Request - State: open - Opened by crangelsmith 10 months ago

#271 - Updated toml file for different systems

Issue - State: closed - Opened by crangelsmith 10 months ago

#270 - Napari for pose dimentions > 3

Issue - State: open - Opened by crangelsmith 10 months ago

#269 - Add more comprehensive unit tests

Pull Request - State: closed - Opened by jolaem 10 months ago - 1 comment

#268 - Per-class pose visualisation fails when `VIS_POSE_CLASS` is `None`

Issue - State: closed - Opened by jolaem 10 months ago
Labels: bug

#267 - Evaluation should check if data dimension is compatible with model

Issue - State: open - Opened by jolaem 10 months ago
Labels: bug

#266 - Evaluation incorrectly picks out pose dim from model name

Issue - State: open - Opened by jolaem 10 months ago - 1 comment
Labels: bug

#265 - New interpolation plot fails with pose=0

Issue - State: closed - Opened by jolaem 10 months ago
Labels: bug

#264 - Napari widget

Pull Request - State: closed - Opened by crangelsmith 10 months ago - 1 comment

#263 - Typo in Tutorial (---new_out)

Issue - State: closed - Opened by moi-taiga 10 months ago - 1 comment

#262 - bug when vis_all : False

Issue - State: open - Opened by marjanfamili 10 months ago - 4 comments

#261 - Umap embedding fails due to uninitialised variable

Issue - State: closed - Opened by jolaem 10 months ago - 3 comments
Labels: bug

#260 - remove batch processing from visualisation functions

Issue - State: closed - Opened by marjanfamili 10 months ago

#259 - removed grid processing from pose_class_disentanglement_plot

Pull Request - State: closed - Opened by marjanfamili 10 months ago - 1 comment

#258 - Napari plugin

Issue - State: closed - Opened by crangelsmith 10 months ago

#257 - MNIST tutorial

Pull Request - State: closed - Opened by crangelsmith 10 months ago - 4 comments

#256 - specific frequencies to overwrite freq_all

Issue - State: closed - Opened by marjanfamili 11 months ago
Labels: enhancement

#255 - Second interpolation plot

Pull Request - State: closed - Opened by marjanfamili 11 months ago - 3 comments

#254 - Update README.md

Pull Request - State: closed - Opened by NikJur 11 months ago

#253 - Abstract model

Pull Request - State: closed - Opened by crangelsmith 11 months ago - 1 comment

#252 - Unify models

Pull Request - State: closed - Opened by jolaem 11 months ago

#251 - Pydantic config

Pull Request - State: closed - Opened by crangelsmith 11 months ago - 2 comments

#250 - Warnings

Issue - State: open - Opened by crangelsmith 11 months ago

#249 - Move installation to toml based.

Pull Request - State: closed - Opened by crangelsmith 11 months ago - 2 comments

#248 - Reduce logging

Pull Request - State: closed - Opened by crangelsmith 11 months ago - 3 comments

#247 - Affinity matrix plot has white space

Issue - State: open - Opened by marjanfamili 11 months ago
Labels: bug

#246 - Visualisations don't always check if plots directory exists

Issue - State: closed - Opened by jolaem 11 months ago
Labels: bug

#245 - test

Pull Request - State: closed - Opened by crangelsmith 11 months ago

#244 - Consolidate embedding code

Issue - State: open - Opened by jolaem 11 months ago

#243 - Add pose space visualisation

Pull Request - State: closed - Opened by jolaem 11 months ago

#242 - Add model summary to logging info

Pull Request - State: closed - Opened by jolaem 11 months ago

#241 - Update disentanglement interpolation

Pull Request - State: open - Opened by jolaem 11 months ago

#240 - Abstract encoder - decoder

Issue - State: closed - Opened by crangelsmith 12 months ago

#239 - Implement type hints

Issue - State: closed - Opened by crangelsmith 12 months ago

#238 - Move to toml based setup

Issue - State: closed - Opened by crangelsmith 12 months ago

#235 - Fix failing default pose class disentanglement settings

Pull Request - State: closed - Opened by jolaem 12 months ago

#234 - Per-class pose visualisation fails when using default value from config

Issue - State: closed - Opened by jolaem 12 months ago
Labels: bug

#233 - Config accepts parameters that do not exist

Issue - State: closed - Opened by jolaem 12 months ago - 2 comments
Labels: good first issue

#232 - Accuracy for KNN fails with smaller number of samples

Issue - State: open - Opened by jolaem 12 months ago
Labels: bug, good first issue

#231 - Enable 2D input in model B and associated tests

Pull Request - State: closed - Opened by jolaem 12 months ago

#230 - Fix per-class pose visualisation and associated tests

Pull Request - State: closed - Opened by jolaem 12 months ago

#229 - [Draft] 228 fix per class pose disentanglement

Pull Request - State: closed - Opened by jolaem 12 months ago - 1 comment

#228 - Pose class disentanglement plot not working

Issue - State: closed - Opened by jolaem 12 months ago - 3 comments
Labels: bug

#227 - Adapt model B to 2D data

Pull Request - State: closed - Opened by jolaem 12 months ago - 2 comments

#226 - 2D image preview in dynamic plots fix

Pull Request - State: closed - Opened by jolaem 12 months ago - 4 comments

#225 - 2D image preview in dynamic plots is incorrectly summed

Issue - State: closed - Opened by jolaem 12 months ago
Labels: bug

#224 - Fix for unconditional rescale

Pull Request - State: closed - Opened by jolaem 12 months ago

#223 - Channels hyperparameter is hardcoded in model A

Issue - State: closed - Opened by jolaem 12 months ago - 1 comment
Labels: bug

#222 - Update loss to use long indices

Pull Request - State: closed - Opened by quantumjot 12 months ago - 1 comment
Labels: bug

#221 - Can we sort the F1 scores in the plot?

Issue - State: open - Opened by jolaem 12 months ago

#220 - Rescale always applied and causing issues

Issue - State: closed - Opened by crangelsmith 12 months ago
Labels: bug

#219 - Early stopping

Pull Request - State: open - Opened by crangelsmith almost 1 year ago - 1 comment

#218 - Example dataset to run affinity VAE

Issue - State: closed - Opened by crangelsmith about 1 year ago - 1 comment
Labels: documentation

#217 - Create a directory for configs

Pull Request - State: closed - Opened by jolaem about 1 year ago

#216 - Can we suppress this NN classifier warning?

Issue - State: open - Opened by jolaem about 1 year ago

#215 - Add rescale option to transforms

Pull Request - State: closed - Opened by jolaem about 1 year ago

#214 - Add gamma to text feedback

Pull Request - State: closed - Opened by jolaem about 1 year ago

#213 - Disabling VIS_CON flag

Pull Request - State: closed - Opened by jolaem about 1 year ago

#212 - Metadata file independent of dynamic plots

Pull Request - State: closed - Opened by crangelsmith about 1 year ago

#211 - Pose per class

Pull Request - State: closed - Opened by crangelsmith about 1 year ago

#210 - Kld loss

Pull Request - State: closed - Opened by crangelsmith about 1 year ago - 3 comments

#209 - Configurable choice for latent space visualisation

Issue - State: open - Opened by crangelsmith about 1 year ago

#208 - F1 bugfix

Pull Request - State: closed - Opened by crangelsmith about 1 year ago

#207 - F1 eval fix

Pull Request - State: closed - Opened by crangelsmith about 1 year ago - 1 comment

#206 - Warning repeatedly appearing in output

Issue - State: open - Opened by marjanfamili about 1 year ago

#205 - F1 underestimated in evaluation

Issue - State: closed - Opened by crangelsmith about 1 year ago
Labels: bug

#204 - Fix bug in batch print and clean up execution feedback.

Pull Request - State: closed - Opened by jolaem about 1 year ago

#203 - Bug in logging where batch iterator is outside the batch loop

Issue - State: closed - Opened by jolaem about 1 year ago

#202 - Correct kld loss

Pull Request - State: closed - Opened by crangelsmith about 1 year ago - 1 comment

#201 - Consider using pydantic for configuration

Issue - State: closed - Opened by quantumjot about 1 year ago

#200 - Error in Evaluation mode when using .npy files

Issue - State: closed - Opened by marjanfamili about 1 year ago - 2 comments
Labels: bug

#199 - Revert "Embedding colours"

Pull Request - State: closed - Opened by marjanfamili about 1 year ago

#198 - Pose interpolation for each class

Pull Request - State: closed - Opened by marjanfamili about 1 year ago - 1 comment

#197 - Embedding colours

Pull Request - State: closed - Opened by marjanfamili about 1 year ago

#196 - Bugfix

Pull Request - State: closed - Opened by crangelsmith about 1 year ago

#195 - Bug fixes

Pull Request - State: closed - Opened by crangelsmith about 1 year ago

#194 - Embedding and reconstruction plots broken

Issue - State: closed - Opened by crangelsmith about 1 year ago
Labels: bug

#193 - Reduce logging + CI fix

Pull Request - State: closed - Opened by crangelsmith about 1 year ago

#192 - Out-of-memory error

Issue - State: closed - Opened by crangelsmith about 1 year ago
Labels: bug

#191 - Logging is slowing down run

Issue - State: closed - Opened by crangelsmith about 1 year ago

#190 - Create subtomo

Pull Request - State: closed - Opened by marjanfamili about 1 year ago - 4 comments

#189 - Update .gitignore to exclude DS_Store

Pull Request - State: closed - Opened by quantumjot about 1 year ago

#188 - Mixture between prints and logging

Issue - State: closed - Opened by crangelsmith about 1 year ago - 2 comments

#187 - Refactoring run.py + new_out option + logging

Pull Request - State: closed - Opened by crangelsmith about 1 year ago

#186 - added tensorboard

Pull Request - State: closed - Opened by chris-soelistyo about 1 year ago

#185 - Add a preprocessing script to augment mrc files.

Pull Request - State: closed - Opened by jolaem about 1 year ago

#184 - Add preprocessing augment mrcs script

Issue - State: closed - Opened by jolaem about 1 year ago