Making use of LightningDataModule and simplification of data loading

This merge request adds LightningDataModule to better organize the code and make better use of lightning's features. This centralizes common tasks such as DataLoader creation and application of transforms into a base class to be inherited from.

Data loading was also simplified by removing custom Sample classes and maker functions, and the addition of RuntimeDataset and CachedDataset.

Remaining tasks:

• (@dcarron) Create a common/default DataModule for the shenzhen dataset that takes protocols and transforms as parameters to avoid copying code for each protocol configuration
• (@dcarron) Add typehints to ShenzenDataModule
• (@dcarron) Investigate issue where training a new model with ElasticDeformation as a transform converges more slowly if the data is not cached.
• (@andre.anjos) Update documentation on ShenzenDataModule
• (@biosignal) Update all datasets, using Shenzhen as a reference
  • (@mdelitroz) Montgomery
  • (@mdelitroz) Hivtb
  • (@andre.anjos) Indian
  • (@andre.anjos) Padchest
  • (@mdelitroz) Tbpoc
  • (@andre.anjos) tbx11_simplified -> renamed as tbx11k, protocol v1 (uses original dataset organisation)
  • (@andre.anjos) tbx11_simplified_v2 -> renamed as tbx11k, protocol v2 (uses original dataset organisation)
  • (@andre.anjos) mc_ch -> renamed as montgomery-shenzhen
  • (@andre.anjos) mc_ch_in -> renamed as montgomery-shenzhen-indian
  • (@andre.anjos) mc_ch_in_11k -> renamed as montgomery-shenzhen-indian-tbx11k-v1
  • (@andre.anjos) mc_ch_in_11k_v2 -> renamed as montgomery-shenzhen-indian-tbx11k-v2
  • (@andre.anjos) mc_ch_in_pc -> renamed as montgomery-shenzhen-indian-padchest
  • (@andre.anjos) nih_cxr14_re -> renamed as nih-cxr14 (n.b.: multi-class dataset, radiological findings)
  • (@andre.anjos) nih_cxr14_re_pc -> renamed as nih-cxr14-padchest
• (@dcarron) Update models
• (@dcarron) Update evaluation scripts
• (@dcarron) Update support for extra_validation datasets
• (@biosignal) Update full documentation
• (@biosignal) Update unit tests

Addresses the following issues:

• Closes #14 (closed)
• Closes #18 (closed)
• Closes #19 (closed)
• Closes #21 (closed)
• Closes #29 (closed)

src/ptbench/data/indian/datamodule.py

@@ -21,9 +21,10 @@ def make_split(basename: str) -> DatabaseSplit:
 class DataModule(CachingDataModule):
     """Indian collection dataset for computer-aided diagnosis.
 
-    The Indian collection database has been established to foster research
-    in computer-aided diagnosis of pulmonary diseases with a special
-    focus on pulmonary tuberculosis (TB).
+    The Indian collection database has been established to foster research in
+    computer-aided diagnosis of pulmonary diseases with a special focus on
+    pulmonary tuberculosis (TB).  This database is also known as the "Database
+    A/Database B" database.
 
     * Original images PNG, 8-bit grayscale, 1024 x 1024 pixels
     * Split reference: [INDIAN-2013]_ with 20% of train set for the validation set
@@ -54,5 +55,5 @@ class DataModule(CachingDataModule):
     def __init__(self, split_filename: str):
         super().__init__(
             database_split=make_split(split_filename),
-            raw_data_loader=RawDataLoader(),
+            raw_data_loader=RawDataLoader(config_variable="datadir.indian"),
         )