-
Notifications
You must be signed in to change notification settings - Fork 71
New issue
Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.
By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.
Already on GitHub? Sign in to your account
🎨 New EngineABC
Design for Patches
#635
🎨 New EngineABC
Design for Patches
#635
Conversation
- Refactor base code from IOSegmentorConfig to IOConfigABC
- No need for a separate function
- Enable git workflow on this PR
- Add missing variable
- Move `to_baseline` code to ABC
- Move `to_baseline` code to ABC
- Fix incorrect calculations for output_resolutions
- Update `PatchPredictor` to use `ModelIOConfigABC` Signed-off-by: Shan E Ahmed Raza <[email protected]>
- Define `ModelIOConfigABC` as a dataclass Signed-off-by: Shan E Ahmed Raza <[email protected]>
- Remove kwargs. - Define dataclass attributes. Signed-off-by: Shan E Ahmed Raza <[email protected]>
- Add `IOInstanceSegmentorConfig` Signed-off-by: Shan E Ahmed Raza <[email protected]>
- Update yaml for `IOInstanceSegmentorConfig` Signed-off-by: Shan E Ahmed Raza <[email protected]>
- Update yaml for `IOInstanceSegmentorConfig` Signed-off-by: Shan E Ahmed Raza <[email protected]>
- Update `to_baseline` for `IOInstanceSegmentorConfig` Signed-off-by: Shan E Ahmed Raza <[email protected]>
- Update IOInstanceSegmentorConfig in test_nucleus_instance_segmentor.py Signed-off-by: Shan E Ahmed Raza <[email protected]>
- Update cli for IOInstanceSegmentorConfig Signed-off-by: Shan E Ahmed Raza <[email protected]>
- Remove unnecessary test after kwargs removal Signed-off-by: Shan E Ahmed Raza <[email protected]>
- Move ioconfigs to io_config.py Signed-off-by: Shan E Ahmed Raza <[email protected]>
- Fix circular import Signed-off-by: Shan E Ahmed Raza <[email protected]>
- Refactor to reduce code in inheriting class Signed-off-by: Shan E Ahmed Raza <[email protected]>
- Fix deepsource errors Signed-off-by: Shan E Ahmed Raza <[email protected]>
- Fix ioconfig import to avoid circular imports Signed-off-by: Shan E Ahmed Raza <[email protected]>
- Fix missing input arguments Signed-off-by: Shan E Ahmed Raza <[email protected]>
- Improve error catching Signed-off-by: Shan E Ahmed Raza <[email protected]>
- Default configuration is not correct Signed-off-by: Shan E Ahmed Raza <[email protected]>
- Fix error check Signed-off-by: Shan E Ahmed Raza <[email protected]>
- Fix typo Signed-off-by: Shan E Ahmed Raza <[email protected]>
- Fix unnecessary update Signed-off-by: Shan E Ahmed Raza <[email protected]>
…ueImageAnalytics/tiatoolbox into dev-redefine-patchpredictor
Review comments addressed and pushed. I've only made changes to engine_abc and test_engine_abc. The |
There was a problem hiding this comment.
Choose a reason for hiding this comment
The reason will be displayed to describe this comment to others. Learn more.
Thanks, Shan and collaborators for working on this. Looks like to is in good shape. I only made a couple of suggestions to consider.
num_postproc_workers (int): | ||
Number of workers to postprocess the results of the model. default = 0 | ||
verbose (bool): | ||
Whether to output logging information. |
There was a problem hiding this comment.
Choose a reason for hiding this comment
The reason will be displayed to describe this comment to others. Learn more.
Actually, it would be nice to give the user option set the path to save engine logs for a specific run.
Shan: let's do it in a separate PR.
Abishek: EngineABC's verbose option displays the progress bar. Should we really have an option to save this to a file?
________________________________________________________________ test_engine_run_with_verbose _________________________________________________________________
-------------------------------------------------------------------- Captured stderr call ---------------------------------------------------------------------
100%|#############################################| 2/2 [00:00<00:00, 5.37it/s]
progress_bar = None
if self.verbose:
progress_bar = tqdm.tqdm(
total=int(len(data_loader)),
leave=True,
ncols=80,
ascii=True,
position=0,
)
570615d
to
122e114
Compare
…-redefine-patchpredictor # Conflicts: # tests/test_utils.py # tiatoolbox/utils/misc.py
for more information, see https://pre-commit.ci
…ueImageAnalytics/tiatoolbox into dev-redefine-patchpredictor
for more information, see https://pre-commit.ci
…ueImageAnalytics/tiatoolbox into dev-redefine-patchpredictor
for more information, see https://pre-commit.ci
…ueImageAnalytics/tiatoolbox into dev-redefine-patchpredictor
There was a problem hiding this comment.
Choose a reason for hiding this comment
The reason will be displayed to describe this comment to others. Learn more.
Thanks @AbishekRajVG Looks good!
EngineABC
designPatchPredictor
based on the new designmodel_to
fromutils.misc
tomodel_abc
load_torch_model
inmodel_abc