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ainuregAinur KarimovBarzaH
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Merging trk (#242)
* added new files * add files & fixes * fix * activ sigmoid * infer for lungs * tests * models uploaded, code readability * hemor_contrast old recover 1 * hemor_contrast old recover 2 * revert old test changes * refactor rtk to new files * restore old coco files * restore old test file * rename experiments * lung description check * fix tests * fix tests * tests removed * float comparison in tests * remove selfwritten iou * get test back * black * an attempt to pass tests * an attempt to pass tests * test back * Fixed gdcm error * Fixed gdcm error * fix path bug * more tests * fixes and more tests * argparse tests * tests more * remove redund comments --------- Co-authored-by: Ainur Karimov <ai.karimov@innopolis.ru> Co-authored-by: InnopolisU <i.mergaliev@innopolis.ru>
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‎config/datasets/classification/lung_description_decision_datamodule.yaml

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date_time: 13.09.2023
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_target_: innofw.core.datamodules.pandas_datamodules.lung_description_decision_datamodule.LungDescriptionDecisionPandasDataModule
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target_col: decision
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target_col: "decision"
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train:
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source: ./data/ainur/infer/labels.csv
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source: https://api.blackhole.ai.innopolis.university/public-datasets/rtk/labels.zip
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target: ./data/lung_description/train
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test:
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source: ./data/ainur/infer/labels.csv
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source: https://api.blackhole.ai.innopolis.university/public-datasets/rtk/labels.zip
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target: ./data/lung_description/test
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infer:
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source: ./data/ainur/infer/labels.csv
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source: https://api.blackhole.ai.innopolis.university/public-datasets/rtk/labels.zip
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target: ./data/lung_description/infer
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‎config/datasets/semantic-segmentation/segmentation_brain_complex.yaml

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_target_: innofw.core.datamodules.lightning_datamodules.coco_rtk.DicomCocoComplexingDataModule
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date_time: 30.09.2022
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description: stroke segmentation dataset
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markup_info: segmentation masks
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name: stroke segmentation
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task:
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- image-segmentation
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test:
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source: https://api.blackhole.ai.innopolis.university/public-datasets/stroke/test.zip
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target: ./data/stroke/test
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train:
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source: https://api.blackhole.ai.innopolis.university/public-datasets/stroke/train.zip
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target: ./data/stroke/train
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infer:
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source: https://api.blackhole.ai.innopolis.university/public-datasets/rtk/complex_infer.zip
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target: ./data/complex/infer

‎config/datasets/semantic-segmentation/segmentation_brain_rtk.yaml

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_target_: innofw.core.datamodules.lightning_datamodules.coco_rtk.DicomCocoDataModuleRTK
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date_time: 30.09.2022
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description: stroke segmentation dataset
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markup_info: segmentation masks
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name: stroke segmentation
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task:
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- image-segmentation
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test:
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source: https://api.blackhole.ai.innopolis.university/public-datasets/stroke/test.zip
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target: ./data/rtk/test
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train:
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source: https://api.blackhole.ai.innopolis.university/public-datasets/stroke/train.zip
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target: ./data/rtk/train
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infer:
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source: https://api.blackhole.ai.innopolis.university/public-datasets/rtk/infer.zip
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target: ./data/rtk/infer

‎config/experiments/semantic-segmentation/AK_081224_Yjc97FX_unet_brain_complex.yaml

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# @package _global_
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defaults:
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- override /models: semantic-segmentation/unet_brain
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- override /datasets: semantic-segmentation/segmentation_brain_complex.yaml
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- override /augmentations_train: none #segmentation_stroke.yaml
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- override /augmentations_val: none
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- override /augmentations_test: none
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- override /losses: segmentation_losses.yaml
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models:
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in_channels: 1
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project: "segmentation"
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task: "image-segmentation"
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random_seed: 42
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stop_param: 10
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epochs: 300
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weights_freq: 1
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batch_size: 10

‎config/experiments/semantic-segmentation/AK_081224_gwVOeQ_unet_brain_rtk.yaml

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# @package _global_
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defaults:
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- override /models: semantic-segmentation/unet_brain
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- override /datasets: semantic-segmentation/segmentation_brain_rtk.yaml
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- override /augmentations_train: none #segmentation_stroke.yaml
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- override /augmentations_val: none
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- override /augmentations_test: none
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- override /losses: segmentation_losses.yaml
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models:
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in_channels: 1
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project: "segmentation"
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task: "image-segmentation"
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random_seed: 42
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stop_param: 10
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epochs: 300
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weights_freq: 1
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batch_size: 10

‎config/models/classification/lung_description_decision.yaml

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- - "vectorizer"
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- _target_: sklearn.feature_extraction.text.TfidfVectorizer
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max_df: 1000
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stop_words:
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- russian
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# stop_words:
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# - russian
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min_df: 10
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- - "classifier"
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- _target_: sklearn.linear_model.LogisticRegression

‎config/models/semantic-segmentation/unet_brain.yaml

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_target_: segmentation_models_pytorch.FPN
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description: Base Unet segmentation model with 1 channel input
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name: FPN
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in_channels: 1
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classes: 4
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encoder_name: 'efficientnet-b7'
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encoder_weights:
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activation: sigmoid

‎examples/infer_contrasting_ct_dicom_brain.sh

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python3 ./innofw/utils/data_utils/preprocessing/CT_hemorrhage_contrast.py
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data_path=$1
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out_path=$2
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if [ -z "$data_path" ]; then
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data_path="https://api.blackhole.ai.innopolis.university/public-datasets/rtk/infer.zip"
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echo "Using default data path $data_path"
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fi
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python innofw/utils/data_utils/preprocessing/CT_hemorrhage_contrast_rtk.py --input "$data_path" --output "$out_path"

‎examples/infer_ct_brain_hemorrhage_detection.sh

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python infer.py experiments=semantic-segmentation/SK_180822_qmciwj41_unet_brain 'ckpt_path=https://api.blackhole.ai.innopolis.university/pretrained/segmentation_unet_brain.pt'
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data_path=$1
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experiments="semantic-segmentation/AK_081224_gwVOeQ_unet_brain_rtk"
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ckpt_path="https://api.blackhole.ai.innopolis.university/pretrained/segmentation_rtk_brain.pt"
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if [ -z "$data_path" ]
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then
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python infer.py experiments=$experiments \
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"ckpt_path=$ckpt_path"
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else
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python infer.py experiments=$experiments \
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"ckpt_path=$ckpt_path" \
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"++datasets.infer.target='$data_path'" \
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"++datasets.infer.source='$data_path'"
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fi

‎examples/infer_ct_brain_hemorrhage_segmentation.sh

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python infer.py experiments=semantic-segmentation/SK_180822_qmciwj41_unet_brain 'ckpt_path=https://api.blackhole.ai.innopolis.university/pretrained/segmentation_unet_brain.pt'
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data_path=$1
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experiments="semantic-segmentation/AK_081224_gwVOeQ_unet_brain_rtk"
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ckpt_path="https://api.blackhole.ai.innopolis.university/pretrained/segmentation_rtk_brain.pt"
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if [ -z "$data_path" ]
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then
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python infer.py experiments=$experiments \
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"ckpt_path=$ckpt_path"
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else
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python infer.py experiments=$experiments \
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"ckpt_path=$ckpt_path" \
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"++datasets.infer.target='$data_path'" \
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"++datasets.infer.source='$data_path'"
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fi

‎examples/infer_ct_mri_complexing.sh

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python infer.py experiments=semantic-segmentation/SK_100923_uner_brain_mri.yaml 'ckpt_path=https://api.blackhole.ai.innopolis.university/pretrained/segmentation_unet_brain_complex.pt'
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data_path=$1
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ckpt_path="https://api.blackhole.ai.innopolis.university/pretrained/segmentation_rtk_brain.pt"
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experiments="semantic-segmentation/AK_081224_Yjc97FX_unet_brain_complex.yaml"
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if [ -z "$data_path" ]
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then
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python infer.py experiments=$experiments \
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"ckpt_path=$ckpt_path"
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else
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python infer.py experiments=$experiments \
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"++datasets.infer.source='$data_path'" \
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"ckpt_path=$ckpt_path"
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fi

‎examples/infer_lung_description_decision.sh

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export HYDRA_FULL_ERROR=1
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export experiments="classification/AK_130923_fbFMFDe1_lung_description_decision.yaml"
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export model_weights="/home/ainur/Desktop/innopolis/text/pipe.pkl"
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export model_weights="https://api.blackhole.ai.innopolis.university/pretrained/lungs_description.pkl"
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export data_source=$1
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if [ -z "$data_source" ]
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then

‎examples/metrics_contrasting_ct_dicom_brain.sh

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output=$1
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if [ -z "$output" ]; then
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output="../innofw/logs/infer/contrast"
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output+="/$(ls $output -tr | tail -n 1)"
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output+="/$(ls $output -tr | tail -n 1)"
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fi
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python innofw/utils/data_utils/preprocessing/CT_hemorrhage_contrast_metrics.py -o "$output"

‎examples/metrics_ct_brain_hemorrhage_detection.sh

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data_path=$1
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out=$2
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if [ -z "$data_path" ]; then
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data_path="../innofw/data/rtk/infer/"
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echo "Using default data path $data_path"
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fi
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if [ -z "$output" ]; then
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output="../innofw/logs/infer/segmentation/semantic-segmentation/AK_081224_gwVOeQ_unet_brain_rtk/"
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output+="$(ls $output | tail -n 1)"
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echo "Using default output path $output"
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fi
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python innofw/utils/data_utils/rtk/CT_hemorrhage_metrics.py -i "$data_path" -o "$output" -t "detection"

‎examples/metrics_ct_brain_hemorrhage_segmentation.sh

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data_path=$1
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output=$2
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if [ -z "$data_path" ]; then
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data_path="../innofw/data/rtk/infer/"
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echo "Using default data path $data_path"
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fi
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if [ -z "$output" ]; then
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output="../innofw/logs/infer/segmentation/semantic-segmentation/AK_081224_gwVOeQ_unet_brain_rtk/"
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output+="$(ls $output -tr| tail -n 1)"
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echo "Using default output path $output"
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fi
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python innofw/utils/data_utils/rtk/CT_hemorrhage_metrics.py -i "$data_path" -o "$output" -t "segmentation"

‎examples/metrics_ct_mri_complexing.sh

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data_path=$1
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output=$2
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if [ -z "$data_path" ]; then
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data_path="../innofw/data/complex/infer"
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echo "Using default data path $data_path"
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fi
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if [ -z "$output" ]; then
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output="../innofw/logs/infer/segmentation/semantic-segmentation/AK_081224_Yjc97FX_unet_brain_complex.yaml/"
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output+="$(ls $output -tr | tail -n 1)"
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fi
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python innofw/utils/data_utils/rtk/CT_complexing_metrics.py -i $data_path -o $output

‎examples/metrics_lung_description_decision.sh

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data_path=$1
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if [ -z "$data_path" ]; then
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data_path="./data/lung_description/infer/labels.csv"
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echo "Using default data path $data_path"
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fi
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if [ -z "$output" ]; then
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output="./logs/infer/lung_description_decision/classification/AK_130923_fbFMFDe1_lung_description_decision.yaml/"
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output+="$(ls $output -tr| tail -n 1)/"
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output+="$(ls $output -tr| tail -n 1)"
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echo "Using default output path $output"
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fi
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python innofw/utils/data_utils/rtk/lungs_description_metrics.py -i "$data_path" -o "$output"

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