Test coverage imporovement

config/augmentations_test/linear-roads-bin-seg-test.yaml

@@ -0,0 +1,9 @@
+defaults:
+  - /augmentations/preprocessing:
+      - standard_images
+  - /augmentations/combined:
+      - none
+  - /augmentations/position:
+      - none
+  - /augmentations/color:
+  - /augmentations/postprocessing:

config/augmentations_train/linear-roads-bin-seg-test.yaml

@@ -0,0 +1,15 @@
+defaults:
+    - /augmentations/preprocessing:
+        - standard_images
+    - /augmentations/combined:
+        - none
+    - /augmentations/position:
+        - flip
+        - rotate90
+        - transpose
+        - grid_distortion
+    - /augmentations/color:
+        - random_gamma
+        - blur
+    - /augmentations/postprocessing:
+        - to_tensor

config/augmentations_val/linear-roads-bin-seg-test.yaml

@@ -0,0 +1,9 @@
+defaults:
+  - /augmentations/preprocessing:
+      - standard_images
+  - /augmentations/combined:
+      - none
+  - /augmentations/position:
+      - none
+  - /augmentations/color:
+  - /augmentations/postprocessing:

config/datasets/regression/table_regression.yaml

@@ -1,3 +1,4 @@
+_target_: innofw.core.datamodules.pandas_datamodules.RegressionPandasDataModule
 target_col: Index
 train:
   source: tests/data/tabular/bmi/bmi_prep.csv

config/datasets/semantic-segmentation/segmentation_arable.yaml

@@ -1,3 +1,4 @@
+_target_: innofw.core.datamodules.lightning_datamodules.segmentation_dir.DirSegmentationLightningDataModule
 task:
   - image-segmentation
 

config/datasets/semantic-segmentation/segmentation_arable_full.yaml

@@ -1,3 +1,4 @@
+_target_: innofw.core.datamodules.lightning_datamodules.segmentation_dir.DicomDirSegmentationLightningDataModule
 task:
   - image-segmentation
 

config/datasets/semantic-segmentation/segmentation_landslides.yaml

@@ -1,3 +1,4 @@
+_target_: innofw.core.datamodules.lightning_datamodules.HDF5LightningDataModule
 task:
   - image-segmentation
 

config/datasets/token_classification_drugprot.yaml

@@ -1,4 +1,4 @@
-task:
+task: 
   - text-ner
 
 name: Drugprot

config/datasets/water_erosion_segmentation.yaml

@@ -1,3 +1,4 @@
+_target_: innofw.core.datamodules.lightning_datamodules.semantic_segmentation.tiff.SegmentationDM
 task:
   - image-segmentation
 

config/experiments/classification/DS_190423_8dca23dc_ucmerced.yaml

@@ -22,7 +22,7 @@ models:
 project: "ucmerced_classification"
 task: "image-classification"
 random_seed: 42
-original_work_dir: ${hydra:runtime.cwd}
+# original_work_dir: ${hydra:runtime.cwd}
 weights_freq: 1
 batch_size: 256
 epochs: 30

config/experiments/classification/NP_010423_concatenated_classification.yaml

@@ -1,8 +1,9 @@
 # @package _global_
 defaults:
-  - /datasets@_dataset_dict.classification_mnist1: classification/classification_mnist
-  - /datasets@_dataset_dict.classification_mnist2: classification/classification_mnist
-  - override /models: resnet.yaml
+  # - /datasets@_dataset_dict.classification_mnist1: classification/classification_mnist
+  # - /datasets@_dataset_dict.classification_mnist2: classification/classification_mnist
+  - override /datasets: classification/classification_mnist
+  - override /models: classification/resnet.yaml
   - override /augmentations_train: none #classification.yaml
   - override /augmentations_val: none
   - override /augmentations_test: none
@@ -12,7 +13,7 @@ defaults:
 project: "mnist_classification"
 task: "image-classification"
 random_seed: 42
-original_work_dir: ${hydra:runtime.cwd}
+# original_work_dir: ${hydra:runtime.cwd}
 weights_freq: 1
 batch_size: 8
 stop_param: 1

config/experiments/classification/SK_010822_jvslrmvk_resnet.yaml

@@ -12,7 +12,7 @@ defaults:
 project: "mnist_classification"
 task: "image-classification"
 random_seed: 42
-original_work_dir: ${hydra:runtime.cwd}
+# original_work_dir: ${hydra:runtime.cwd}
 weights_freq: 1
 batch_size: 8
 stop_param: 1

config/experiments/detection/KA_031122_invalid_experiment.yaml

@@ -1,6 +1,6 @@
 # @package _global_
 defaults:
-  - override /models: linear_regression
+  - override /models: regression/linear_regression
   - override /datasets: osl_faces
 
 

config/experiments/detection/KA_120722_8adfcdaa_yolov5.yaml

@@ -1,9 +1,10 @@
 # @package _global_
 batch_size: 32
 defaults:
+- override /models: detection/yolov5
 - override /datasets: detection_lep
 - override /optimizers: sgd
-- override /models: detection/yolov5x.yaml
+
 epochs: 500
 project: lep
 random_seed: 42

config/experiments/detection/KA_120722_8adfcdaa_yolov5_non_pretrained.yaml

@@ -2,11 +2,12 @@
 batch_size: 2
 ckpt_path: /home/qazybek/pmi_tatneft/innofw/dui/logs/something/20240122-082640/weights/best.pt
 defaults:
-- override /models: detection/yolov5
-- override /datasets: detection_lep.yaml
-- override /initializations: random
-epochs: 5
-project: lep
+  - override /models: detection/yolov5
+  - override /datasets: detection_lep
+  - override /initializations: random
+
+project: "lep"
+task: "image-detection"
+
 random_seed: 42
-task: image-detection
 weights_freq: 1

config/experiments/detection/KA_120722_8adfcdaa_yolov5_pretrained.yaml

@@ -1,7 +1,7 @@
 # @package _global_
 defaults:
   - override /models: detection/yolov5
-  - override /datasets: detection/lep
+  - override /datasets: detection_lep
 
 
 project: "lep"

config/experiments/detection/KG_190124_wpiig1_ttpla.yaml

@@ -1,7 +1,7 @@
 # @package _global_
 defaults:
   - override /models: detection/yolov5
-  - override /datasets: detection/detection_ttpla
+  - override /datasets: detection/ttpla
   - override /optimizers: sgd
 
 project: "ttpla"

config/experiments/detection/NP_210523_yolov8_insects.yaml

@@ -1,6 +1,7 @@
 # @package _global_
 defaults:
-  - override /models: ultralytics
+  # - override /models: ultralytics
+  - override /models: detection/yolov8
   - override /datasets: detection/detection_ar_tax_or
   - override /loggers: wandb
   - override /optimizers: sgd

config/experiments/regression/GR_070922_jLqZn8Wh_catboost_regressor_mcl1.yaml

@@ -7,4 +7,4 @@ defaults:
 project: "mcl1"
 task: "qsar-regression"
 random_seed: 42
-original_work_dir: ${hydra:runtime.cwd}
+# original_work_dir: ${hydra:runtime.cwd}

config/experiments/regression/KA_081122_df82ds8_defaults.yaml

@@ -1,6 +1,7 @@
 # @package _global_
 defaults:
-  - override /datasets: regression_house_prices
+  - override /datasets: regression/regression_house_prices
+  - override /models: regression/linear_regression
 
 project: "check_defaults"
 task: "table-regression"

config/experiments/regression/KA_280722_ba099979_catboost_regressor.yaml

@@ -1,7 +1,7 @@
 # @package _global_
 defaults:
   - override /models: regression/catboost_regression
-  - override /datasets: regression_house_prices
+  - override /datasets: regression/regression_house_prices
 #  - override /callbacks: regression
 
 

config/experiments/regression/SK_010822_infer_kdsr_linear_regression.yaml

@@ -1,7 +1,7 @@
 # @package _global_
 defaults:
   - override /models: regression/linear_regression
-  - override /datasets: regression_house_prices
+  - override /datasets: regression/regression_house_prices
 
 project: "house_prices"
 ckpt_path:

config/experiments/semantic-segmentation/AS_151123_oks.yaml

@@ -1,8 +1,6 @@
+# @package _global_
 accelerator: gpu
 batch_size: 20
-datasets:
-- batch_size: 20
-- num_workers: 42
 defaults:
 - override /models: semantic-segmentation/deeplabv3plus
 - override /datasets: semantic-segmentation/oks_151123
@@ -13,11 +11,11 @@ defaults:
 devices: 1
 epochs: 1
 models:
-- in_channels: 3
-- classes: 1
-- encoder_name: resnet101
-- encoder_depth: 5
-- decoder_channels: 256
+  in_channels: 3
+  classes: 1
+  encoder_name: resnet101
+  encoder_depth: 5
+  decoder_channels: 256
 num_workers: 42
 project: oks
 random_seed: 42

config/experiments/semantic-segmentation/DA_230922_sdgh32lk_deeplab.yaml

@@ -18,6 +18,6 @@ weights_freq: 1
 batch_size: 16
 epochs: 50
 accelerator: gpu
-gpus: [2]
+gpus: 2 #[2]
 models:
   in_channels: 4

config/experiments/semantic-segmentation/DN_051923stroke.yaml

@@ -16,7 +16,7 @@ accelerator: gpu
 random_seed: 42
 epochs: 50
 batch_size: 64
-original_work_dir: ${hydra:runtime.cwd}
+# original_work_dir: ${hydra:runtime.cwd}
 weights_freq: 1
 override hydra/job_logging: stdout
 metrics:

config/experiments/semantic-segmentation/KA_250123_439erfks_basic_water_erosion_segmentation.yaml

@@ -1,13 +1,13 @@
 # @package _global_
 defaults:
   - override /models: semantic-segmentation/deeplabv3plus.yaml
-  - override /datasets: segmentation_arable_full.yaml
+  - override /datasets: semantic-segmentation/segmentation_arable_full.yaml
   - override /optimizers: adam.yaml
   - override /losses: segmentation_losses # triple_segmentation_loss
-  - override /augmentations: segmentation_satellite_imagery
+  - override /augmentations_train: none #segmentation_satellite_imagery
   # - override /initializations: he
   - override /callbacks: segmentation_2
-  - override /wandb: qb
+  - override /wandb: default
 
 optimizers:
   implementations:
@@ -24,8 +24,7 @@ models:
 
 accelerator: gpu
 devices: 1
-gpus:  
-  - 1  # use second gpu
+gpus: 1  # use second gpu
 
 
 wandb:

config/experiments/semantic-segmentation/SK_180822_qwefnew31_yolov5_lungs_seg.yaml

@@ -1,6 +1,6 @@
 # @package _global_
 defaults:
-  - override /models: semantic-segmentation/yolov5_segmentation
+  - override /models: detection/yolov5_segmentation
   - override /datasets: detection/detection_lungs
 
 

config/experiments/semantic-segmentation/landslides-kanopus/baseline.yaml

@@ -5,7 +5,7 @@ defaults:
   - override /datasets: semantic-segmentation/landslides-kanopus/270223-hdf5
   - override /losses: semantic-segmentation/triple_loss_old_pipe
   - override /optimizers: adam
-  - override /schedulers: custom_old_pipeline
+  - override /schedulers: cosine_annealing
   - override /augmentations_train: landslides-kanopus
   - override /augmentations_val: landslides-kanopus
   # - override /metrics: basic

config/experiments/semantic-segmentation/water-erosion-kanopus/baseline.yaml

@@ -1,11 +1,11 @@
 # @package _global_
 defaults:
   - _self_
-  - override /models: semantic-segmentationdeeplabv3plus
+  - override /models: semantic-segmentation/deeplabv3plus
   - override /datasets: semantic-segmentation/water-erosion-kanopus/220223-hdf5
   - override /losses: semantic-segmentation/triple_loss_old_pipe
   - override /optimizers: adam
-  - override /schedulers: custom_old_pipeline
+  - override /schedulers: cosine_annealing
   - override /augmentations_train: water-erosion-bin-seg
   - override /augmentations_val: water-erosion-bin-seg
   # - override /metrics: basic

config/ui.yaml

@@ -31,4 +31,4 @@ accelerator: gpu
 #devices: 1
 gpus: 1
 
-original_work_dir: ${hydra:runtime.cwd}
+# original_work_dir: ${hydra:runtime.cwd}

examples/infer_contrasting_ct_dicom_brain.sh

@@ -1 +1 @@
-python3 /innofw/utils/data_utils/preprocessing/CT_hemorrhage_contrast.py
+python3 ./innofw/utils/data_utils/preprocessing/CT_hemorrhage_contrast.py

innofw/core/active_learning/datamodule.py

@@ -3,6 +3,8 @@
 
 import numpy as np
 import pandas as pd
+from abc import abstractmethod 
+
 
 
 class DataContainer(TypedDict):
@@ -34,14 +36,14 @@ class DataModuleI(Protocol):
     setup():
         returns Nothing.
     """
-
-    def test_dataloader(self) -> DataContainer:
+    @abstractmethod
+    def test_dataloader(self) -> DataContainer: # pragma: no cover
         ...
-
-    def train_dataloader(self) -> DataContainer:
+    @abstractmethod
+    def train_dataloader(self) -> DataContainer: # pragma: no cover
         ...
-
-    def setup(self) -> None:
+    @abstractmethod
+    def setup(self) -> None: # pragma: no cover
         ...