ivadomed/ivadomed issues and pull requests

#1316 - Consider intensity-based soft labeling with geodesic loss

Issue - State: open - Opened by jcohenadad 7 months ago
Labels: Good intership project

#1315 - Update `CHANGES.md` and `version.txt` for ivadomed `2.9.10` release

Pull Request - State: closed - Opened by joshuacwnewton 11 months ago - 2 comments
Labels: documentation

#1313 - Fix edge case bug where grayscale image has an alpha channel, minor rtd fix

Pull Request - State: closed - Opened by mathieuboudreau about 1 year ago - 15 comments
Labels: bug

#1312 - convert_file_to_nifti bug for ADS SEM test data

Issue - State: closed - Opened by mathieuboudreau about 1 year ago - 16 comments
Labels: bug

#1311 - issue with two-class segmentation: ValueError: operands could not be broadcast together with shapes (744,1154,2) (4,)

Issue - State: closed - Opened by chennyyuee about 1 year ago - 1 comment

#1309 - Use Implicit Functions for SC/Lesion Segmentation

Issue - State: open - Opened by naga-karthik about 1 year ago
Labels: Good intership project

#1308 - Test upgrades for pinned dependencies to improve downstream compatibility

Pull Request - State: closed - Opened by joshuacwnewton about 1 year ago - 5 comments
Labels: dependencies, installation

#1307 - Update changelog and version.txt for v2.9.9

Pull Request - State: closed - Opened by joshuacwnewton about 1 year ago - 6 comments

#1306 - How do I pass something to the ChatOpenAI class at all??

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

#1305 - Hi, I encounter an issue: 'RuntimeError: Derivatives not found.'

Issue - State: open - Opened by zwb0 about 1 year ago - 2 comments
Labels: bug

#1304 - Test out newer versions of PyTorch (`torch>=2.0.0`) for compatibility with downstream projects (SCT, ADS)

Pull Request - State: closed - Opened by joshuacwnewton over 1 year ago - 6 comments
Labels: installation, maintenance

#1303 - Test out `torch==2.0.0` (base branch: `master`)

Pull Request - State: closed - Opened by joshuacwnewton over 1 year ago - 1 comment

#1302 - ivadomed_segment_image RuntimeError: 'PixelSizeUnits' is missing from metadata

Issue - State: closed - Opened by GrimmSnark over 1 year ago - 2 comments

#1299 - Fix path bug for windows

Pull Request - State: closed - Opened by mathieuboudreau over 1 year ago - 1 comment

#1298 - chore: remove ubuntu-18.04 and python 3.7 from `run_tests` workflow

Pull Request - State: closed - Opened by kanishk16 over 1 year ago
Labels: CI, maintenance

#1297 - chore: Dependency Maintenance (imageio 2->3, pyBIDS<0.15.6, readthedocs.yml v2, Python 3.7->3.8)

Pull Request - State: closed - Opened by kanishk16 over 1 year ago - 49 comments
Labels: bug

#1296 - Fix 2D image conversion to 8 bit

Pull Request - State: closed - Opened by mathieuboudreau over 1 year ago - 9 comments
Labels: bug

#1295 - BIDS parsing error for ADS user on Windows

Issue - State: closed - Opened by mathieuboudreau over 1 year ago - 1 comment

#1294 - Issue training models ( raise source.error("bad escape %s" % escape, len(escape)) re.error: bad escape \m at position 10)

Issue - State: closed - Opened by GrimmSnark over 1 year ago - 2 comments

#1292 - Fix deprecated feature call due to newest imageio release

Pull Request - State: closed - Opened by mathieuboudreau almost 2 years ago - 8 comments
Labels: bug

#1291 - imageio "as_gray" option deprecated as of 2.28.0

Issue - State: closed - Opened by mathieuboudreau almost 2 years ago
Labels: bug

#1290 - Update doc for segment_image.py

Pull Request - State: closed - Opened by jcohenadad almost 2 years ago
Labels: documentation

#1288 - feat: integrate wandb sweeps for hyperparameter optimization

Pull Request - State: open - Opened by kanishk16 about 2 years ago

#1287 - ASPP-based model (Perone et al. 2018)

Issue - State: open - Opened by hermancollin about 2 years ago - 3 comments

#1286 - Remove tabs in all configs files and add unit test to test this

Pull Request - State: open - Opened by konantian about 2 years ago
Labels: bug, feature

#1285 - How to do ensemble with ivadomed?

Issue - State: open - Opened by jcohenadad about 2 years ago - 6 comments
Labels: card:DESIGN_DISCUSSION

#1284 - Confusion between `fname_split` and `random_seed`

Issue - State: closed - Opened by jcohenadad about 2 years ago - 2 comments
Labels: card:DESIGN_DISCUSSION

#1283 - Clarified usage for `fname_split`

Pull Request - State: closed - Opened by jcohenadad about 2 years ago
Labels: documentation

#1282 - Do we want to parametrize the type of optimizer?

Issue - State: open - Opened by jcohenadad about 2 years ago - 1 comment
Labels: enhancement, card:DESIGN_DISCUSSION

#1281 - Point to the URL specific to the learning rate

Pull Request - State: closed - Opened by jcohenadad about 2 years ago
Labels: documentation

#1280 - Shouldn't RandomReverse be applied to both `im` and `gt`?

Issue - State: open - Opened by jcohenadad about 2 years ago - 3 comments
Labels: documentation

#1279 - Strange behaviour when `filter_empty_mask` is True for 2D training

Issue - State: open - Opened by naga-karthik about 2 years ago - 1 comment

#1278 - Match location of `object_detection` in the template config file and in the documentation

Pull Request - State: closed - Opened by jcohenadad about 2 years ago
Labels: documentation

#1277 - Expose parameters for losses

Issue - State: open - Opened by jcohenadad about 2 years ago - 2 comments

#1276 - Convenient way to visualize predictions at test time

Issue - State: open - Opened by jcohenadad about 2 years ago - 4 comments
Labels: card:DESIGN_DISCUSSION, feature

#1275 - 2D microscopy tutorial broken: No subject files found.

Issue - State: open - Opened by hermancollin about 2 years ago - 5 comments

#1274 - fix: update the default file for the log file

Pull Request - State: open - Opened by kanishk16 about 2 years ago
Labels: bug

#1273 - Add flipping for proper visualization on wandb

Pull Request - State: open - Opened by naga-karthik about 2 years ago - 5 comments

#1272 - WandB visualization shows flipped images even with no data augmentation

Issue - State: open - Opened by naga-karthik about 2 years ago - 3 comments

#1271 - Resolve the discrepancies

Pull Request - State: closed - Opened by konantian about 2 years ago
Labels: documentation

#1270 - Improving the `segment_image` CLI

Issue - State: open - Opened by naga-karthik about 2 years ago

#1269 - Visualisation of multi-class training

Issue - State: open - Opened by jcohenadad about 2 years ago

#1268 - Can ground truth labels be in another folder than `derivatives/labels`?

Issue - State: open - Opened by jcohenadad about 2 years ago

#1267 - Fix NormalizeInstance for uniform samples

Pull Request - State: closed - Opened by mariehbourget about 2 years ago - 1 comment
Labels: bug

#1266 - Harmonize get_item in MRI2D dataset and MRI3D dataset

Pull Request - State: closed - Opened by mariehbourget about 2 years ago - 1 comment
Labels: refactoring

#1265 - Clarify usage of --no-patch for 2D only

Pull Request - State: closed - Opened by mariehbourget about 2 years ago - 1 comment
Labels: documentation

#1264 - Confusing usage for `keep_largest`

Issue - State: open - Opened by jcohenadad about 2 years ago

#1263 - The Terminal output does not show all the testing data, which can be confusing

Issue - State: open - Opened by jcohenadad about 2 years ago - 2 comments

#1262 - Consider changing the variable name

Issue - State: open - Opened by jcohenadad about 2 years ago

#1261 - Confusion about the use of `"slice_axis"` and image orientation

Issue - State: open - Opened by jcohenadad about 2 years ago - 2 comments

#1260 - Release v2.9.8

Pull Request - State: closed - Opened by mariehbourget about 2 years ago - 1 comment

#1259 - Possible to input segmentation to constrain model training/inference?

Issue - State: open - Opened by jcohenadad about 2 years ago - 7 comments

#1258 - Clarify what goes under "debugging"

Issue - State: open - Opened by jcohenadad about 2 years ago
Labels: documentation

#1257 - Design feature: Consider automatically running testing after training

Issue - State: open - Opened by jcohenadad about 2 years ago
Labels: card:DESIGN_DISCUSSION

#1256 - IndexError: list index out of range when testing model

Issue - State: open - Opened by jcohenadad about 2 years ago - 1 comment

#1255 - Is `ivadomed --segment --no-patch` also applicable to 3D?

Issue - State: open - Opened by jcohenadad about 2 years ago - 5 comments
Labels: documentation

#1254 - Introduce `segment_image` CLI

Pull Request - State: closed - Opened by jcohenadad about 2 years ago - 4 comments
Labels: feature

#1253 - Do not use wandb if not specified in the config file

Pull Request - State: closed - Opened by jcohenadad about 2 years ago - 4 comments
Labels: enhancement, wandb

#1252 - Do not use wandb if not specified in the config file

Issue - State: closed - Opened by jcohenadad about 2 years ago - 4 comments
Labels: wandb

#1251 - Create individual group/run in WanDB when using `ivadomed_automate_training`

Issue - State: open - Opened by jcohenadad about 2 years ago
Labels: feature, wandb

#1250 - Confusing doc for `ivadomed_automate_training`

Issue - State: open - Opened by jcohenadad about 2 years ago
Labels: documentation

#1249 - Initial prototype for wandb sweep

Pull Request - State: open - Opened by jcohenadad about 2 years ago - 2 comments
Labels: feature

#1248 - Confusing default `stride_3D` parameter for architecture `Modified3DUNet`

Issue - State: open - Opened by jcohenadad about 2 years ago - 15 comments

#1247 - wandb: What is displayed for 3D kernels?

Issue - State: closed - Opened by jcohenadad about 2 years ago - 5 comments

#1246 - chore: remove numpy related deprecations in support of v1.24.0

Pull Request - State: closed - Opened by kanishk16 about 2 years ago - 1 comment
Labels: dependencies, CI

#1245 - NotImplementedError: Got <class 'NoneType'>, but numpy array, torch tensor, or caffe2 blob name are expected.

Issue - State: closed - Opened by jcohenadad about 2 years ago - 15 comments
Labels: bug

#1244 - Clarify testing output files

Pull Request - State: closed - Opened by mariehbourget about 2 years ago - 2 comments
Labels: documentation, refactoring

#1241 - More details needed on the `NumpyToTensor` field in config file

Issue - State: open - Opened by jcohenadad about 2 years ago - 1 comment
Labels: documentation

#1240 - Implementation of the new data loader v2 architecture.

Pull Request - State: open - Opened by kaidalisohaib about 2 years ago

#1239 - Introducing FilesDataset, Files3DDataset, FileDatasetGroup, and AllDatasetGroups with their tests.

Pull Request - State: open - Opened by kaidalisohaib about 2 years ago

#1237 - fix/feat: update the path for wandb logs

Pull Request - State: closed - Opened by kanishk16 about 2 years ago - 1 comment
Labels: enhancement

#1236 - Update configuration_file.rst

Pull Request - State: open - Opened by jcohenadad about 2 years ago - 1 comment
Labels: documentation

#1235 - Consider renaming `slice_filter_params` and `patch_filter_params`

Issue - State: closed - Opened by jcohenadad about 2 years ago - 4 comments
Labels: documentation

#1234 - Unclear if `patch_filter_params` also applies to 3D kernels

Issue - State: closed - Opened by jcohenadad about 2 years ago - 1 comment
Labels: documentation

#1232 - How is `filter_empty_mask` interpreted for 3D kernels?

Issue - State: closed - Opened by jcohenadad about 2 years ago - 1 comment
Labels: documentation, feature

#1231 - Can we do cropping after applying data augmentation transformations?

Issue - State: open - Opened by jcohenadad about 2 years ago - 5 comments

#1230 - Discrepancies in config file fields from the documentation

Issue - State: closed - Opened by jcohenadad about 2 years ago
Labels: documentation

#1229 - Confusion around testing outputs `_pred` and `_pred_painted`

Issue - State: closed - Opened by jcohenadad about 2 years ago - 3 comments
Labels: documentation

#1228 - FutureWarning: The frame.append method is deprecated and will be removed from pandas in a future version. Use pandas.concat instead.

Issue - State: open - Opened by jcohenadad about 2 years ago

#1227 - wandb: Network error (SSLError), entering retry loop.

Issue - State: closed - Opened by kiristern about 2 years ago - 10 comments

#1225 - Introducing mocker for bids strutures.

Pull Request - State: open - Opened by kaidalisohaib about 2 years ago - 1 comment
Labels: enhancement, priority:medium

#1224 - Introduced generalized_loader_configuration with a test, tests for loading files, and some base for future steps.

Pull Request - State: open - Opened by kaidalisohaib about 2 years ago - 1 comment
Labels: enhancement, priority:medium

GitHub / ivadomed/ivadomed issues and pull requests