diff --git a/.gitignore b/.gitignore index 1c12553..9075af1 100644 --- a/.gitignore +++ b/.gitignore @@ -180,3 +180,4 @@ lightning_logs/ # Project /data +playground.ipynb diff --git a/.mypy.ini b/.mypy.ini index 1c6f44e..abd4983 100644 --- a/.mypy.ini +++ b/.mypy.ini @@ -2,4 +2,5 @@ strict = True ignore_missing_imports = True disallow_untyped_calls = False -disable_error_code = no-any-return \ No newline at end of file +disable_error_code = no-any-return +exclude = scripts \ No newline at end of file diff --git a/configs/base.yaml b/configs/base.yaml new file mode 100644 index 0000000..94c880e --- /dev/null +++ b/configs/base.yaml @@ -0,0 +1,7 @@ +defaults: + - hydra: default + - logger: mlflow + - _self_ + +metadata: + experiment_name: Ulcerative Colitis diff --git a/configs/dataset/raw/ftn.yaml b/configs/dataset/raw/ftn.yaml new file mode 100644 index 0000000..59b9d69 --- /dev/null +++ b/configs/dataset/raw/ftn.yaml @@ -0,0 +1,10 @@ +institution: ftn +folder: /mnt/data/FTN/colon/IBD_AI +# [0-9]{1,6} - case ID (1 to 6 digits) (in year scope) +# _ - underscore separator +# 2[0-5] - year (2020 to 2025) +# .czi - file extension +regex_pattern: ^[0-9]{1,6}_2[0-5]\.czi$ +labels: + - IBD_AI_FTN.xlsx + - IBD_AI_FTN_doplnek.xlsx \ No newline at end of file diff --git a/configs/dataset/raw/ikem.yaml b/configs/dataset/raw/ikem.yaml new file mode 100644 index 0000000..4ae65db --- /dev/null +++ b/configs/dataset/raw/ikem.yaml @@ -0,0 +1,14 @@ +institution: ikem +folder: /mnt/data/IKEM/colon/IBD_AI/20x +# [0-9]{1,5} - case ID (1 to 5 digits) (in year scope) +# _ - underscore separator +# 2[1-4] - year (2021 to 2024) +# _ - underscore separator +# HE - stain type +# (?:_0[1-6])? - optional underscore and slide number (01 to 06) +# .czi - file extension +regex_pattern: ^[0-9]{1,5}_2[1-4]_HE(?:_0[1-6])?\.czi$ +labels: + - Fab_IBD_AI_12_2024.csv + - IBD_AI_2.xlsx + - missing.xlsx \ No newline at end of file diff --git a/configs/dataset/raw/knl_patos.yaml b/configs/dataset/raw/knl_patos.yaml new file mode 100644 index 0000000..450ee36 --- /dev/null +++ b/configs/dataset/raw/knl_patos.yaml @@ -0,0 +1,17 @@ +institution: knl_patos +folder: /mnt/data/KNL_PATOS/colon/IBD_AI +# [0-9]{1,5} - case ID (1 to 5 digits) (in year scope) +# _ - underscore separator +# 25 - year 2025 +# _ - underscore separator +# [A-F] - block identifier (A to F) +# _ - underscore separator +# HE - stain type +# (0[1-9]|1[0-2]) - slide number (01 to 12) +# .czi - file extension +regex_pattern: ^[0-9]{1,5}_25_[A-F]_HE(0[1-9]|1[0-2])\.czi$ +labels: + - IBD_AI_Liberec.xlsx + - IBD_AI_Liberec_02.xlsx + - IBD_AI_Liberec_10_2025.xlsx + - IBD_AI_Liberec_28_10_2025.xlsx \ No newline at end of file diff --git a/configs/default.yaml b/configs/default.yaml deleted file mode 100644 index 20eabdd..0000000 --- a/configs/default.yaml +++ /dev/null @@ -1,20 +0,0 @@ -defaults: - - hydra: default - - logger: mlflow - - _self_ - -seed: ${random_seed:} -mode: ??? -checkpoint: null - -trainer: {} - -data: {} - -model: {} - -metadata: - experiment_name: ??? - run_name: ??? - description: ??? - hyperparams: {} diff --git a/configs/preprocessing.yaml b/configs/preprocessing.yaml new file mode 100644 index 0000000..08a0372 --- /dev/null +++ b/configs/preprocessing.yaml @@ -0,0 +1,9 @@ +# @package _global_ + +defaults: + - base + - _self_ + +dataset: ??? + +project_dir: /mnt/projects/inflammatory_bowel_disease/ulcerative_colitis diff --git a/configs/preprocessing/create_dataset.yaml b/configs/preprocessing/create_dataset.yaml new file mode 100644 index 0000000..154709e --- /dev/null +++ b/configs/preprocessing/create_dataset.yaml @@ -0,0 +1,5 @@ +# @package _global_ + +metadata: + run_name: "📂 Dataset Creation: ${dataset.institution}" + description: "Create dataset for ${dataset.institution} institution" diff --git a/preprocessing/create_dataset.py b/preprocessing/create_dataset.py new file mode 100644 index 0000000..af2ef37 --- /dev/null +++ b/preprocessing/create_dataset.py @@ -0,0 +1,108 @@ +import re +import tempfile +from pathlib import Path + +import hydra +import pandas as pd +from omegaconf import DictConfig +from rationai.mlkit import autolog, with_cli_args +from rationai.mlkit.lightning.loggers import MLFlowLogger + + +def get_labels(folder_path: Path, labels: list[str]) -> pd.DataFrame: + dfs = [] + for labels_file in labels: + labels_path = folder_path / labels_file + + if labels_path.suffix == ".csv": + # One labels file is in CSV format + df = pd.read_csv(labels_path, index_col=0) + else: + df = pd.read_excel(labels_path, index_col=0) + + df.columns = df.columns.str.lower() + dfs.append(df) + + labels_df = pd.concat(dfs) + # id is in format [case_id]/YY (e.g., 01234/24 or 1234/24) + labels_df.index = labels_df.index.str.lstrip("0") + labels_df.index = labels_df.index.str.strip() + labels_df.index = labels_df.index.str.replace("/", "_", regex=False) + + return labels_df + + +def get_slides(folder_path: Path, pattern: re.Pattern) -> pd.DataFrame: + slides = [] + for slide_path in folder_path.iterdir(): + if not pattern.fullmatch(slide_path.name): + continue + case_id = "_".join(slide_path.stem.split("_")[:2]) + + slides.append( + {"slide_id": slide_path.stem, "case_id": case_id, "path": str(slide_path)} + ) + + slides_df = pd.DataFrame(slides).set_index("slide_id") + return slides_df + + +def create_dataset( + folder: str, labels: list[str], institution: str, pattern: re.Pattern +) -> tuple[pd.DataFrame, list[str], list[str]]: + folder_path = Path(folder) + labels_df = get_labels(folder_path, labels) + slides_df = get_slides(folder_path, pattern) + + # IKEM has only case-level labels (FTN has one slide per case) + on = "case_id" if institution == "ikem" else "slide_id" + dataset_df = slides_df.join(labels_df, on=on, how="outer") + dataset_df.index.name = "slide_id" + + if institution == "ikem": + # IKEM has 'Lokalita' and 'Diagnóza' columns + # Slides inside ileum are not used + dataset_df = dataset_df[dataset_df["lokalita"] != "ileum"] + # Columns 'Lokalita' and 'Diagnóza' are no longer needed + + missing_labels = dataset_df[dataset_df["nancy"].isna()].index.to_list() + missing_slides = dataset_df[dataset_df["path"].isna()][on].to_list() + + dataset_df = dataset_df[["case_id", "path", "nancy"]] + dataset_df = dataset_df.dropna() + dataset_df["nancy"] = dataset_df["nancy"].astype(int) + + return dataset_df, missing_slides, missing_labels + + +@with_cli_args(["+preprocessing=create_dataset"]) +@hydra.main(config_path="../configs", config_name="preprocessing", version_base=None) +@autolog +def main(config: DictConfig, logger: MLFlowLogger) -> None: + dataset, missing_slides, missing_labels = create_dataset( + config.dataset.folder, + config.dataset.labels, + config.dataset.institution, + re.compile(config.dataset.regex_pattern), + ) + + with tempfile.TemporaryDirectory() as tmpdir: + tmpdir_path = Path(tmpdir) + + output_path = tmpdir_path / "dataset.csv" + dataset.to_csv(output_path, index=True) + logger.log_artifact(str(output_path)) + + def _log_missing_items(items: list[str], filename: str) -> None: + if not items: + return + file_path = tmpdir_path / filename + file_path.write_text("\n".join(items) + "\n") + logger.log_artifact(str(file_path)) + + _log_missing_items(missing_slides, "missing_slides.txt") + _log_missing_items(missing_labels, "missing_labels.txt") + + +if __name__ == "__main__": + main() diff --git a/scripts/preprocessing/create_dataset.py b/scripts/preprocessing/create_dataset.py new file mode 100644 index 0000000..245eb97 --- /dev/null +++ b/scripts/preprocessing/create_dataset.py @@ -0,0 +1,17 @@ +from kube_jobs import storage, submit_job + + +submit_job( + job_name="ulcerative-colitis-dataset-creation-...", + username=..., + public=False, + cpu=2, + memory="4Gi", + script=[ + "git clone https://github.com/RationAI/ulcerative-colitis.git workdir", + "cd workdir", + "uv sync --frozen", + "uv run -m 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