batchgenerators 0.25.1__tar.gz → 0.25.2__tar.gz

batchgenerators-0.25.2/PKG-INFO

@@ -0,0 +1,400 @@
+Metadata-Version: 2.4
+Name: batchgenerators
+Version: 0.25.2
+Summary: Data augmentation toolkit
+Author-email: "Division of Medical Image Computing, German Cancer Research Center AND Applied Computer Vision Lab, Helmholtz Imaging Platform" <f.isensee@dkfz-heidelberg.de>
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+           Copyright [2021] [Division of Medical Image Computing, German Cancer Research Center (DKFZ), Heidelberg, Germany
+           AND Applied Computer Vision Lab, Helmholtz Imaging Platform]
+        
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+Project-URL: Homepage, https://github.com/MIC-DKFZ/batchgenerators
+Keywords: data augmentation,deep learning,image segmentation,image classification,medical image analysis,medical image segmentation
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: pillow>=7.1.2
+Requires-Dist: numpy>=1.10.2
+Requires-Dist: scipy
+Requires-Dist: scikit-image
+Requires-Dist: scikit-learn
+Requires-Dist: future
+Requires-Dist: pandas
+Requires-Dist: unittest2
+Requires-Dist: threadpoolctl
+Dynamic: license-file
+
+# batchgenerators by MIC@DKFZ
+
+Copyright German Cancer Research Center (DKFZ) and contributors.
+Please make sure that your usage of this code is in compliance with its
+[`license`](https://github.com/MIC-DKFZ/batchgenerators/blob/master/LICENSE).
+
+batchgenerators is a python package for data augmentation. It is developed jointly between the Division of
+Medical Image Computing at the German Cancer Research Center (DKFZ) and the Applied Computer 
+Vision Lab of the Helmholtz Imaging Platform.
+
+It is not (yet) perfect, but we feel it is good enough to be shared with the community. If you encounter bug, feel free
+to contact us or open a github issue.
+
+If you use it please cite the following work:
+```
+Isensee Fabian, Jäger Paul, Wasserthal Jakob, Zimmerer David, Petersen Jens, Kohl Simon, 
+Schock Justus, Klein Andre, Roß Tobias, Wirkert Sebastian, Neher Peter, Dinkelacker Stefan, 
+Köhler Gregor, Maier-Hein Klaus (2020). batchgenerators - a python framework for data 
+augmentation. doi:10.5281/zenodo.3632567
+```
+
+batchgenerators also contains the following application-specific augmentations:
+* **Anatomy-informed Data Augmentation**  
+Proposed at [MICCAI 2023](https://arxiv.org/abs/2309.03652) for simulation of soft-tissue deformations. Implementation details can be found [here](https://github.com/MIC-DKFZ/anatomy_informed_DA).
+* **Misalignment Data Augmentation**  
+Proposed in [Nature Scientific Reports 2023](https://www.nature.com/articles/s41598-023-46747-z)
+for enhancing model's adaptability to diverse misalignments\
+between multi-modal (multi-channel) images and thereby ensuring robust performance. Implementation details can be found [here](https://github.com/MIC-DKFZ/misalignment_DA).
+
+If you use these augmentations please cite them too.
+
+[![Build Status](https://travis-ci.com/MIC-DKFZ/batchgenerators.svg?branch=master)](https://travis-ci.com/github/MIC-DKFZ/batchgenerators)
+
+## Supported Augmentations
+We supports a variety of augmentations, all of which are compatible with **2D and 3D input data**! (This is something
+that was missing in most other frameworks).
+
+* **Spatial Augmentations**
+  * mirroring
+  * channel translation (to simulate registration errors)
+  * elastic deformations
+  * rotations
+  * scaling
+  * resampling
+  * multi-channel misalignments
+* **Color Augmentations**
+  * brightness (additive, multiplivative)
+  * contrast
+  * gamma (like gamma correction in photo editing)
+* **Noise Augmentations**
+  * Gaussian Noise
+  * Rician Noise
+  * ...will be expanded in future commits
+* **Cropping**
+  * random crop
+  * center crop
+  * padding
+* **Anatomy-informed Augmentation**
+
+Note: Stack transforms by using batchgenerators.transforms.abstract_transforms.Compose. Finish it up by plugging the
+composed transform into our **multithreader**: batchgenerators.dataloading.multi_threaded_augmenter.MultiThreadedAugmenter
+
+
+## How to use it
+
+The working principle is simple: Derive from DataLoaderBase class, reimplement generate_train_batch member function and
+use it to stack your augmentations!
+For simple example see `batchgenerators/examples/example_ipynb.ipynb`
+
+A heavily commented example for using SlimDataLoaderBase and MultithreadedAugmentor is available at:
+`batchgenerators/examples/multithreaded_with_batches.ipynb`. 
+It gives an idea of the interplay between the SlimDataLoaderBase and the MultiThreadedAugmentor.
+The example uses the MultiThreadedAugmentor for loading and augmentation on mutiple processes, while 
+covering the entire dataset only once per epoch (basically sampling without replacement).
+
+We also now have an extensive example for BraTS2017/2018 with both 2D and 3D DataLoader and augmentations: 
+`batchgenerators/examples/brats2017/`
+
+There are also CIFAR10/100 datasets and DataLoader available at `batchgenerators/datasets/cifar.py`
+
+## Data Structure
+
+The data structure that is used internally (and with which you have to comply when implementing generate_train_batch)
+is kept simple as well: It is just a regular python dictionary! We did this to allow maximum flexibility in the kind of
+data that is passed along through the pipeline. The dictionary must have a 'data' key:value pair. It optionally can
+handle a 'seg' key:vlaue pair to hold a segmentation. If a 'seg' key:value pair is present all spatial transformations
+will also be applied to the segmentation! A part from 'data' and 'seg' you are free to do whatever you want (your image
+classification/regression target for example). All key:value pairs other than 'data' and 'seg' will be passed through the
+pipeline unmodified.
+
+'data' value must have shape (b, c, x, y) for 2D or shape (b, c, x, y, z) for 3D!
+'seg' value must have shape (b, c, x, y) for 2D or shape (b, c, x, y, z) for 3D! Color channel may be used here to
+allow for several segmentation maps. If you have only one segmentation, make sure to have shape (b, 1, x, y (, z))
+
+## How to install locally
+
+Install batchgenerators
+```
+pip install --upgrade batchgenerators
+```
+
+Import as follows
+```
+from batchgenerators.transforms.color_transforms import ContrastAugmentationTransform
+```
+
+## Windows Support is very experimental!
+Batchgenerators makes heavy use of python multiprocessing and python multiprocessing on windows is different from linux. 
+To prevent the workers from freezing in windows, you have to guard your code with `if __name__ == '__main__'` and use multiprocessing's [`freeze_support`](https://docs.python.org/3/library/multiprocessing.html#multiprocessing.freeze_support). The executed script may then look like this:
+
+```
+# some imports and functions here
+
+def main():
+    # do some stuff
+
+if __name__ == '__main__':
+    from multiprocessing import freeze_support
+    freeze_support()
+    main()
+```
+
+This is not required on Linux.
+
+
+## Release Notes
+(only highlights, not an exhaustive list)
+- 0.23.2:
+  - Misalignment data augmentation added
+- 0.23.1:
+  - Anatomy-informed data augmentation added
+- 0.23: 
+  - fixed the import mess. `__init__.py` files are now empty. This is a breaking change for some users! 
+  Please adapt your imports :-)
+  - local_transforms are now a thing, check them out!
+  - resize_segmentation now uses 'edge' mode and no longer takes a cval argument. Resizing segmentations with constant
+  border values (previous default) can cause problems and should not be done.
+- 0.20.0: 
+  - fixed an issue with MultiThreadedAugmenter not terminating properly after KeyboardInterrupt; Fixed an error 
+  with the number and order of samples being returned when pin_memory=True; Improved performance by always hiding 
+  process-process communication bottleneck through threading
+- 0.19.5: 
+  - fixed OMP_NUM_THREADS issue by using threadpoolctl package; dropped python 2 support (threadpoolctl is not 
+  available for python 2)
+- 0.19:
+   - There is now a complete example for BraTS2017/8 available for both 2D and 3D. Use this if you would like to get 
+   some insights on how I (Fabian) do my experiments
+   - Windows is now supported! Thanks @justusschock for your support!
+   - new, simple parametrization of elastic deformation. Use SpatialTransform_2!
+   - CIFAR10/100 DataLoader are now available for your convenience
+   - a bug in MultiThreadedAugmenter that could interfere with reproducibility is now fixed
+
+- 0.18:
+    - all augmentations (there are some exceptions though) are implemented on a per-sample basis. This should make it 
+    easier to use the augmentations outside of the Transforms of batchgenerators 
+    - applicable Transforms now have a keyword p_per_sample with which the user can specify a probability with which this
+     transform is applied to a sample. Before, this was handled by RndTransform and applied to the whole batch (so 
+     either all samples were augmented or none). Now this decision is made on a per-sample basis and increases 
+     variability by a lot.
+    - following the previous point, RndTransform is now deprecated
+    - AlternativeMultiThreadedAugmenter is now deprecated as well (no need to have this anymore)
+    - pytorch users can now transform numpy arrays to pytorch tensors within batchgenerators (NumpyToTensor). For some 
+    reason, inter-process communication is faster with tensors (~factor 4), so this is recommended!
+    - if numpy arrays were converted to pytorch tensors, MultithreadedAugmenter now allows to pin the memory as well 
+    (pin_memory=True). This will happen in a background thread (inspired by pytorch DataLoader). pinned memory can be 
+    copied to the GPU much faster. My (Fabian) classification experiment with Resnet50 got a speed boost of 12% from just 
+    that.
+
+
+-------------------------
+
+<img src="DKFZ_Logo.png" width="512px" />
+
+<img src="HIP_Logo.png" width="512px" />
+
+batchgenerators is developed by the [Division of Medical Image Computing](https://www.dkfz.de/en/mic/index.php) of the 
+German Cancer Research Center (DKFZ) and the Applied Computer Vision Lab (ACVL) of the
+[Helmholtz Imaging Platform](https://helmholtz-imaging.de).

batchgenerators-0.25.2/README.md

@@ -0,0 +1,178 @@
+# batchgenerators by MIC@DKFZ
+
+Copyright German Cancer Research Center (DKFZ) and contributors.
+Please make sure that your usage of this code is in compliance with its
+[`license`](https://github.com/MIC-DKFZ/batchgenerators/blob/master/LICENSE).
+
+batchgenerators is a python package for data augmentation. It is developed jointly between the Division of
+Medical Image Computing at the German Cancer Research Center (DKFZ) and the Applied Computer 
+Vision Lab of the Helmholtz Imaging Platform.
+
+It is not (yet) perfect, but we feel it is good enough to be shared with the community. If you encounter bug, feel free
+to contact us or open a github issue.
+
+If you use it please cite the following work:
+```
+Isensee Fabian, Jäger Paul, Wasserthal Jakob, Zimmerer David, Petersen Jens, Kohl Simon, 
+Schock Justus, Klein Andre, Roß Tobias, Wirkert Sebastian, Neher Peter, Dinkelacker Stefan, 
+Köhler Gregor, Maier-Hein Klaus (2020). batchgenerators - a python framework for data 
+augmentation. doi:10.5281/zenodo.3632567
+```
+
+batchgenerators also contains the following application-specific augmentations:
+* **Anatomy-informed Data Augmentation**  
+Proposed at [MICCAI 2023](https://arxiv.org/abs/2309.03652) for simulation of soft-tissue deformations. Implementation details can be found [here](https://github.com/MIC-DKFZ/anatomy_informed_DA).
+* **Misalignment Data Augmentation**  
+Proposed in [Nature Scientific Reports 2023](https://www.nature.com/articles/s41598-023-46747-z)
+for enhancing model's adaptability to diverse misalignments\
+between multi-modal (multi-channel) images and thereby ensuring robust performance. Implementation details can be found [here](https://github.com/MIC-DKFZ/misalignment_DA).
+
+If you use these augmentations please cite them too.
+
+[![Build Status](https://travis-ci.com/MIC-DKFZ/batchgenerators.svg?branch=master)](https://travis-ci.com/github/MIC-DKFZ/batchgenerators)
+
+## Supported Augmentations
+We supports a variety of augmentations, all of which are compatible with **2D and 3D input data**! (This is something
+that was missing in most other frameworks).
+
+* **Spatial Augmentations**
+  * mirroring
+  * channel translation (to simulate registration errors)
+  * elastic deformations
+  * rotations
+  * scaling
+  * resampling
+  * multi-channel misalignments
+* **Color Augmentations**
+  * brightness (additive, multiplivative)
+  * contrast
+  * gamma (like gamma correction in photo editing)
+* **Noise Augmentations**
+  * Gaussian Noise
+  * Rician Noise
+  * ...will be expanded in future commits
+* **Cropping**
+  * random crop
+  * center crop
+  * padding
+* **Anatomy-informed Augmentation**
+
+Note: Stack transforms by using batchgenerators.transforms.abstract_transforms.Compose. Finish it up by plugging the
+composed transform into our **multithreader**: batchgenerators.dataloading.multi_threaded_augmenter.MultiThreadedAugmenter
+
+
+## How to use it
+
+The working principle is simple: Derive from DataLoaderBase class, reimplement generate_train_batch member function and
+use it to stack your augmentations!
+For simple example see `batchgenerators/examples/example_ipynb.ipynb`
+
+A heavily commented example for using SlimDataLoaderBase and MultithreadedAugmentor is available at:
+`batchgenerators/examples/multithreaded_with_batches.ipynb`. 
+It gives an idea of the interplay between the SlimDataLoaderBase and the MultiThreadedAugmentor.
+The example uses the MultiThreadedAugmentor for loading and augmentation on mutiple processes, while 
+covering the entire dataset only once per epoch (basically sampling without replacement).
+
+We also now have an extensive example for BraTS2017/2018 with both 2D and 3D DataLoader and augmentations: 
+`batchgenerators/examples/brats2017/`
+
+There are also CIFAR10/100 datasets and DataLoader available at `batchgenerators/datasets/cifar.py`
+
+## Data Structure
+
+The data structure that is used internally (and with which you have to comply when implementing generate_train_batch)
+is kept simple as well: It is just a regular python dictionary! We did this to allow maximum flexibility in the kind of
+data that is passed along through the pipeline. The dictionary must have a 'data' key:value pair. It optionally can
+handle a 'seg' key:vlaue pair to hold a segmentation. If a 'seg' key:value pair is present all spatial transformations
+will also be applied to the segmentation! A part from 'data' and 'seg' you are free to do whatever you want (your image
+classification/regression target for example). All key:value pairs other than 'data' and 'seg' will be passed through the
+pipeline unmodified.
+
+'data' value must have shape (b, c, x, y) for 2D or shape (b, c, x, y, z) for 3D!
+'seg' value must have shape (b, c, x, y) for 2D or shape (b, c, x, y, z) for 3D! Color channel may be used here to
+allow for several segmentation maps. If you have only one segmentation, make sure to have shape (b, 1, x, y (, z))
+
+## How to install locally
+
+Install batchgenerators
+```
+pip install --upgrade batchgenerators
+```
+
+Import as follows
+```
+from batchgenerators.transforms.color_transforms import ContrastAugmentationTransform
+```
+
+## Windows Support is very experimental!
+Batchgenerators makes heavy use of python multiprocessing and python multiprocessing on windows is different from linux. 
+To prevent the workers from freezing in windows, you have to guard your code with `if __name__ == '__main__'` and use multiprocessing's [`freeze_support`](https://docs.python.org/3/library/multiprocessing.html#multiprocessing.freeze_support). The executed script may then look like this:
+
+```
+# some imports and functions here
+
+def main():
+    # do some stuff
+
+if __name__ == '__main__':
+    from multiprocessing import freeze_support
+    freeze_support()
+    main()
+```
+
+This is not required on Linux.
+
+
+## Release Notes
+(only highlights, not an exhaustive list)
+- 0.23.2:
+  - Misalignment data augmentation added
+- 0.23.1:
+  - Anatomy-informed data augmentation added
+- 0.23: 
+  - fixed the import mess. `__init__.py` files are now empty. This is a breaking change for some users! 
+  Please adapt your imports :-)
+  - local_transforms are now a thing, check them out!
+  - resize_segmentation now uses 'edge' mode and no longer takes a cval argument. Resizing segmentations with constant
+  border values (previous default) can cause problems and should not be done.
+- 0.20.0: 
+  - fixed an issue with MultiThreadedAugmenter not terminating properly after KeyboardInterrupt; Fixed an error 
+  with the number and order of samples being returned when pin_memory=True; Improved performance by always hiding 
+  process-process communication bottleneck through threading
+- 0.19.5: 
+  - fixed OMP_NUM_THREADS issue by using threadpoolctl package; dropped python 2 support (threadpoolctl is not 
+  available for python 2)
+- 0.19:
+   - There is now a complete example for BraTS2017/8 available for both 2D and 3D. Use this if you would like to get 
+   some insights on how I (Fabian) do my experiments
+   - Windows is now supported! Thanks @justusschock for your support!
+   - new, simple parametrization of elastic deformation. Use SpatialTransform_2!
+   - CIFAR10/100 DataLoader are now available for your convenience
+   - a bug in MultiThreadedAugmenter that could interfere with reproducibility is now fixed
+
+- 0.18:
+    - all augmentations (there are some exceptions though) are implemented on a per-sample basis. This should make it 
+    easier to use the augmentations outside of the Transforms of batchgenerators 
+    - applicable Transforms now have a keyword p_per_sample with which the user can specify a probability with which this
+     transform is applied to a sample. Before, this was handled by RndTransform and applied to the whole batch (so 
+     either all samples were augmented or none). Now this decision is made on a per-sample basis and increases 
+     variability by a lot.
+    - following the previous point, RndTransform is now deprecated
+    - AlternativeMultiThreadedAugmenter is now deprecated as well (no need to have this anymore)
+    - pytorch users can now transform numpy arrays to pytorch tensors within batchgenerators (NumpyToTensor). For some 
+    reason, inter-process communication is faster with tensors (~factor 4), so this is recommended!
+    - if numpy arrays were converted to pytorch tensors, MultithreadedAugmenter now allows to pin the memory as well 
+    (pin_memory=True). This will happen in a background thread (inspired by pytorch DataLoader). pinned memory can be 
+    copied to the GPU much faster. My (Fabian) classification experiment with Resnet50 got a speed boost of 12% from just 
+    that.
+
+
+-------------------------
+
+<img src="DKFZ_Logo.png" width="512px" />
+
+<img src="HIP_Logo.png" width="512px" />
+
+batchgenerators is developed by the [Division of Medical Image Computing](https://www.dkfz.de/en/mic/index.php) of the 
+German Cancer Research Center (DKFZ) and the Applied Computer Vision Lab (ACVL) of the
+[Helmholtz Imaging Platform](https://helmholtz-imaging.de).

{batchgenerators-0.25.1 → batchgenerators-0.25.2}/batchgenerators/dataloading/nondet_multi_threaded_augmenter.py

@@ -15,7 +15,7 @@
 
 import traceback
 from copy import deepcopy
-from typing import List, Union
+from typing import List, Union, Callable
 import threading
 from builtins import range
 from multiprocessing import Process
@@ -37,9 +37,15 @@ except ImportError:
 
 def producer(queue: Queue, data_loader, transform, thread_id: int, seed,
              abort_event: Event, wait_time: float = 0.02):
+    if torch is not None:
+        torch.set_num_threads(1)
+        if seed is not None:
+            torch.manual_seed(seed)
+
+    np.random.seed(seed)
+
     # the producer will set the abort event if something happens
     with threadpool_limits(1, None):
-        np.random.seed(seed)
         data_loader.set_thread_id(thread_id)
         item = None
 
@@ -139,7 +145,7 @@ class NonDetMultiThreadedAugmenter(object):
     """
 
     def __init__(self, data_loader, transform, num_processes, num_cached=2, seeds=None, pin_memory=False,
-                 wait_time=0.02):
+                 wait_time=0.02, results_loop_fn: Callable = results_loop):
         self.pin_memory = pin_memory
         self.transform = transform
         self.num_cached = num_cached
@@ -151,6 +157,7 @@ class NonDetMultiThreadedAugmenter(object):
 
         self._queue = None
         self._processes = []
+        self.results_loop_fn = results_loop
         self.results_loop_thread = None
         self.results_loop_queue = None
         self.abort_event = None
@@ -208,18 +215,13 @@ class NonDetMultiThreadedAugmenter(object):
             if isinstance(self.generator, DataLoader):
                 self.generator.was_initialized = False
 
-            if torch is not None:
-                torch_nthreads = torch.get_num_threads()
-                torch.set_num_threads(1)
-            with threadpool_limits(limits=1, user_api=None):
-                for i in range(self.num_processes):
-                    self._processes.append(Process(target=producer, args=(
-                        self._queue, self.generator, self.transform, i, self.seeds[i], self.abort_event, self.wait_time
-                    )))
-                    self._processes[-1].daemon = True
-                _ = [i.start() for i in self._processes]
-            if torch is not None:
-                torch.set_num_threads(torch_nthreads)
+
+            for i in range(self.num_processes):
+                self._processes.append(Process(target=producer, args=(
+                    self._queue, self.generator, self.transform, i, self.seeds[i], self.abort_event, self.wait_time
+                )))
+                self._processes[-1].daemon = True
+            _ = [i.start() for i in self._processes]
 
             if torch is not None and torch.cuda.is_available():
                 gpu = torch.cuda.current_device()
@@ -228,7 +230,7 @@ class NonDetMultiThreadedAugmenter(object):
 
             # in_queue: Queue, out_queue: thrQueue, abort_event: Event, pin_memory: bool, worker_list: List[Process],
             # gpu: Union[int, None] = None, wait_time: float = 0.02
-            self.results_loop_thread = threading.Thread(target=results_loop, args=(
+            self.results_loop_thread = threading.Thread(target=self.results_loop_fn, args=(
                 self._queue, self.results_loop_queue, self.abort_event, self.pin_memory, self._processes, gpu,
                 self.wait_time)
                                                         )