deepdraw merge requestshttps://gitlab.idiap.ch/biosignal/software/deepdraw/-/merge_requests2024-03-27T21:25:03Zhttps://gitlab.idiap.ch/biosignal/software/deepdraw/-/merge_requests/72CXR8 Raw Data Loader Function Fix2024-03-27T21:25:03ZMatheus Armani RenzoCXR8 Raw Data Loader Function FixCloses #28Closes #28André AnjosAndré Anjoshttps://gitlab.idiap.ch/biosignal/software/deepdraw/-/merge_requests/71Use hatch and versioningit for modern project management2024-03-18T10:32:28ZAndré AnjosUse hatch and versioningit for modern project managementAndré AnjosAndré Anjoshttps://gitlab.idiap.ch/biosignal/software/deepdraw/-/merge_requests/69Remove detect2023-05-02T14:36:42ZMaxime DELITROZRemove detectRemoved object detection part
Moved all common part into source code for binary segmentation
Replaced all references to binseg by deepdrawRemoved object detection part
Moved all common part into source code for binary segmentation
Replaced all references to binseg by deepdrawhttps://gitlab.idiap.ch/biosignal/software/deepdraw/-/merge_requests/67Adding xtests for ground truth crop configs2023-03-30T16:36:41ZMatheus RENZOAdding xtests for ground truth crop configsAndré AnjosAndré Anjoshttps://gitlab.idiap.ch/biosignal/software/deepdraw/-/merge_requests/66Ground Truth Box Crop Transform2023-03-16T11:29:35ZMatheus Armani RenzoGround Truth Box Crop TransformCreates a new transform function that crops all images using the ground truth mask as reference. Can also take an additional parameter extra_area that increases the dimensions of the resulting square before cropping images.Creates a new transform function that crops all images using the ground truth mask as reference. Can also take an additional parameter extra_area that increases the dimensions of the resulting square before cropping images.André AnjosAndré Anjoshttps://gitlab.idiap.ch/biosignal/software/deepdraw/-/merge_requests/65Resolves Gaussian-blur test is failing2023-03-15T18:48:13ZMatheus Armani RenzoResolves Gaussian-blur test is failingCloses #25Closes #25André AnjosAndré Anjoshttps://gitlab.idiap.ch/biosignal/software/deepdraw/-/merge_requests/62Move from bob group and cookiecuter usage2023-03-07T15:53:47ZDaniel CARRONMove from bob group and cookiecuter usageThis merge request updates the codebase after the move from the bob to the biosignal group and makes use of the cookiecutter template.
- Project has been moved from bob/ip/binseg to biosignal/software/deepdraw
- Paths in the projects ha...This merge request updates the codebase after the move from the bob to the biosignal group and makes use of the cookiecutter template.
- Project has been moved from bob/ip/binseg to biosignal/software/deepdraw
- Paths in the projects have been replaced accordingly
- Tests have been moved at the root of the repository
- The project now uses the template from cookiecutter-idiap-pypackage and the new CI pipeline
- SPDX headers have been added and updated
- Data files are now tracked with LFS, even if they are not using too much space
Closes #20https://gitlab.idiap.ch/biosignal/software/deepdraw/-/merge_requests/63Fix documentation2023-03-02T10:08:10ZDaniel CARRONFix documentationMoved the documentation from bob.ip.binseg to deepdraw, fixing imports and warningsMoved the documentation from bob.ip.binseg to deepdraw, fixing imports and warningsMigration to new infrastructure (phase 1)https://gitlab.idiap.ch/biosignal/software/deepdraw/-/merge_requests/61Update chexphoto (3000 labels)2023-01-23T13:02:52ZMatheus Armani RenzoUpdate chexphoto (3000 labels)André AnjosAndré Anjoshttps://gitlab.idiap.ch/biosignal/software/deepdraw/-/merge_requests/60Changes detection2023-01-17T14:39:11ZMatheus Armani RenzoChanges detectionAndré AnjosAndré Anjoshttps://gitlab.idiap.ch/biosignal/software/deepdraw/-/merge_requests/58[script.dataset] Fixes dataset script to account to changes in the base...2022-11-25T10:46:04ZAndré Anjos[script.dataset] Fixes dataset script to account to changes in the base...[script.dataset] Fixes dataset script to account to changes in the base representation of configuration[script.dataset] Fixes dataset script to account to changes in the base representation of configurationAndré AnjosAndré Anjoshttps://gitlab.idiap.ch/biosignal/software/deepdraw/-/merge_requests/57Object Detection2022-10-20T10:45:46ZMatheus Armani RenzoObject DetectionAndré AnjosAndré Anjoshttps://gitlab.idiap.ch/biosignal/software/deepdraw/-/merge_requests/56Allows GPU logging in multi-GPU systems; Fixes DRIVE download link2022-09-23T08:45:52ZTan XiaoAllows GPU logging in multi-GPU systems; Fixes DRIVE download linkThis MR includes the following changes:
* GPU information logging will now work in single or multi-GPU systems (closes #18)
* The DRIVE download link is fixed (closes #17)This MR includes the following changes:
* GPU information logging will now work in single or multi-GPU systems (closes #18)
* The DRIVE download link is fixed (closes #17)André AnjosAndré Anjoshttps://gitlab.idiap.ch/biosignal/software/deepdraw/-/merge_requests/53Implements option to pass one or more extra validation datasets2022-06-20T13:04:05ZAndré AnjosImplements option to pass one or more extra validation datasetsThis MR:
* Implements option to pass one or more extra validation datasets that do not affect checkpointing (closes #16)
* Deprecates `SmoothedValue`, and makes loss logging a bit more explicit
* Updates tests and analysis to accomodate...This MR:
* Implements option to pass one or more extra validation datasets that do not affect checkpointing (closes #16)
* Deprecates `SmoothedValue`, and makes loss logging a bit more explicit
* Updates tests and analysis to accomodate changesAndré AnjosAndré Anjoshttps://gitlab.idiap.ch/biosignal/software/deepdraw/-/merge_requests/50WIP:Add CXR8 Dataset, Improves resource logging, Deprecates SSL, Adds tensors...2022-04-14T11:46:08ZMatheus Armani RenzoWIP:Add CXR8 Dataset, Improves resource logging, Deprecates SSL, Adds tensorsboard supportThis MR contains some important additions:
* Adds the CXR8 dataset and segmentations as input source for training lung segmentation on CXR, including specific versions for Idiap usage
* Fixes CPU logging (missing `recurse=True` setting)...This MR contains some important additions:
* Adds the CXR8 dataset and segmentations as input source for training lung segmentation on CXR, including specific versions for Idiap usage
* Fixes CPU logging (missing `recurse=True` setting)
* Improves CPU/GPU logging by consulting devices in a parallel process, during the whole epoch
* Fine-tunes `train-analysis` plot, adds a plot for hardware utilisation through training
* Deprecates Semi-supervised Learning (SSL) approaches due to changes in the overall re-design and infrastructural changes
* Added plumbery to support tensorboard logging
* Parallelises the evaluation procedure so it may be faster on very large datasets
* Change the flag `--multiproc-data-loading` to `--parallel` as it now can be used through the whole experiment
* Implements plot axes limits for the compare (portion of the experiment) script
* Adjusts the root of lung segmentation datasets (Montgomery, Shenzhen, JSRT) to make running a bit easier to reproduce remotely
* Fixes the loading of Montgomery and Shenzhen datasets to avoid resizing distortionsAndré AnjosAndré Anjoshttps://gitlab.idiap.ch/biosignal/software/deepdraw/-/merge_requests/52Fix error in trainer function2022-03-23T16:14:20ZDriss KHALILFix error in trainer functionThis MR fixes #14.This MR fixes #14.André AnjosAndré Anjoshttps://gitlab.idiap.ch/biosignal/software/deepdraw/-/merge_requests/43Improve trainer function2022-03-22T14:11:39ZDriss KHALILImprove trainer functionSplit the trainer run function into different steps in order to make it easier to use the different part of the code again in case of a different type of training (example : Multi task learning) where we will need to work with multiple l...Split the trainer run function into different steps in order to make it easier to use the different part of the code again in case of a different type of training (example : Multi task learning) where we will need to work with multiple losses.
The function is now split to :
- **check_gpu(device)** : Where we check the device type and the availability of GPU.
- **save_model_summary(output_folder, model)** : Save summary of the model in a txt file.
- **static_information_to_csv(static_logfile_name, device, n)** : Save the static information in a csv file.
- **check_exist_logfile(logfile_name, arguments)** : Check existence of logfile (trainlog.csv),
If the logfile exist the and the epochs number are still 0, The logfile will be replaced.
- **create_logfile_fields(valid_loader, device)** : Creation of the logfile fields that will appear in the logfile.
- **train_sample_process(samples, model, optimizer, losses, device, criterion)** : Processing the training inputs (Images, ground truth, masks) and apply the backprogration to update the training losses.
- **valid_sample_process(samples, model, valid_losses, device, criterion)** : Processing the validation inputs (Images, ground truth, masks) and update validation losses.
- **checkpointer_process(checkpointer, checkpoint_period, valid_losses, lowest_validation_loss, arguments, epoch, max_epoch,)** : Process the checkpointer, save the final model and keep track of the best model.
- **write_log_info(epoch, current_time, eta_seconds, losses, valid_losses, optimizer, logwriter, logfile, device,)** : Write log info in trainlog.csv
-André AnjosAndré Anjoshttps://gitlab.idiap.ch/biosignal/software/deepdraw/-/merge_requests/51Add baselines results2022-03-01T09:57:22ZDriss KHALILAdd baselines resultshttps://gitlab.idiap.ch/biosignal/software/deepdraw/-/merge_requests/49Add baselines results2022-01-20T13:14:49ZDriss KHALILAdd baselines results- Baselines results
- New Combined protocols- Baselines results
- New Combined protocolshttps://gitlab.idiap.ch/biosignal/software/deepdraw/-/merge_requests/48Resolve "Blur test is not passing anymore"2021-12-15T14:04:16ZMatheus Armani RenzoResolve "Blur test is not passing anymore"Closes #10Closes #10André AnjosAndré Anjos