diff --git a/BCCasebook_binary.py b/BCCasebook_binary.py new file mode 100644 index 0000000000000000000000000000000000000000..e92410fd43be0037e9f1be88f9523bb10c5cd067 --- /dev/null +++ b/BCCasebook_binary.py @@ -0,0 +1,127 @@ +import pandas as pd +from pathlib import Path +from datasets import Features, Value, Sequence +from datasets import DatasetInfo, GeneratorBasedBuilder, SplitGenerator, Split +import pickle +import pyarrow as pa +import pyarrow.parquet as pq + + +class FcsParquetIO: + """A class including all methods to write and read parquets transformed from one fcs by FileTransformer.fcs_to_parquet. + """ + @staticmethod + def read_parquets(read_dir: Path) -> tuple[dict, pd.DataFrame]: + """A method to read a group of parquets, which are transformed and partitioned from one fcs by FileTransformer.fcs_to_parquet, from the given directory. + + Args: + read_dir (Path): The directory including all parquets transformed and partitioned from one fcs. + + Returns: + tuple[dict, pd.DataFrame]: The tuple includes two elements. The first one is the meta data from the original fcs. The second one is the event data from the original fcs. + """ + parquet_filepaths = list(read_dir.glob("*.parquet")) + table = {"meta": None, "event": pd.DataFrame()} + for parquet_filepath in parquet_filepaths: + table = pq.read_table(parquet_filepath) + + parquet_filename = str( + parquet_filepath.name).replace(".parquet", '') + if "part_001" in parquet_filename: + raw_meta = table.schema.metadata or {} + table["meta"] = {k.decode('utf8'): v.decode('utf8') + for k, v in raw_meta.items()} + + table["event"] = pd.concat( + [table["event"], table.to_pandas()], axis=0, ignore_index=True) + + return table["meta"], table["event"] + + +feature_fields = { + "flow_id": Value("string"), + "original_id": Value("string"), + "specimen": Value("string"), + "purpose": Value("string"), + "site": Value("string"), + "machine": Value("string"), + "color_counts": Value("int32"), + "sampling_date": Value("date32"), + "measuring_date": Value("date32"), + "panel": Value("string"), + "label": Value("string"), + "sublabel": Sequence(Value("string")), + "RDP": Value("float32"), + + "tube_counts": Value("int32"), + "tube_event_counts": Value("string"), + "tube_channels": Value("string"), + + "data": Value("binary") +} +features = Features(feature_fields) + + +class BCCasebook_binary(GeneratorBasedBuilder): + def _info(self): + return DatasetInfo( + features=features, + description="This dataset is a project of BC Casebook data labeled for Malignant and Non-malignant.", + homepage="", + citation="", + license="" + ) + + def _split_generators(self, dl_manager): + data_dir = Path(self.base_path) / "fcs" + return [ + SplitGenerator( + name=Split.TRAIN, + gen_kwargs={"data_dir": data_dir}, + ) + ] + + def _generate_examples(self, data_dir: Path): + sample_metas = pd.read_csv(Path(self.base_path) / "sample_metas.csv") + + for column in sample_metas.columns.to_list(): + if column in feature_fields.keys(): + feature_field = column + feature_type = feature_fields[feature_field] + if feature_type is Value("int32"): + sample_metas[feature_field] = sample_metas[feature_field].astype( + "Int32") + elif feature_type is Value("float32"): + sample_metas[feature_field] = sample_metas[feature_field].astype( + "float32") + elif feature_type is Value("date32"): + sample_metas[feature_field] = pd.to_datetime( + sample_metas[feature_field], format="%m/%d/%Y").dt.date + elif feature_type is Value("string"): + sample_metas[feature_field] = sample_metas[feature_field].astype( + "string") + + for column in feature_fields.keys(): + if column not in sample_metas.columns.to_list(): + sample_metas[column] = None + + sublabel_columns = [ + column for column in sample_metas.columns.to_list() if "sublabel" in column] + if len(sublabel_columns) > 0: + sample_metas["sublabel"] = sample_metas.apply( + lambda row: [str(row[col]) for col in sublabel_columns], axis=1) + sample_metas = sample_metas.drop(columns=sublabel_columns) + + for sample_index, sample_dir in enumerate(sorted(list(data_dir.glob('*')))): + if sample_dir.is_dir(): + sample_meta = sample_metas[sample_metas["flow_id"] + == str(sample_dir.name)].to_dict(orient="records")[0] + sample_tubes = {} + for tube_dir in sorted(list(sample_dir.glob('*'))): + if tube_dir.is_dir(): + meta, event = FcsParquetIO.read_parquets(tube_dir) + sample_tubes[tube_dir.name] = { + "meta": meta, "event": event} + sample_meta["data"] = pickle.dumps(sample_tubes) + + yield sample_index, sample_meta diff --git a/README.md b/README.md new file mode 100644 index 0000000000000000000000000000000000000000..5c8e6f85c2e001bd78608e797cab6196d0dc4848 --- /dev/null +++ b/README.md @@ -0,0 +1,13 @@ +--- +language: +- en +tags: +- flow cytometry +- fcs +- BC +- malignant +- binary + +--- + +This dataset is a project of BC Casebook data labeled for Malignant and Non-malignant. \ No newline at end of file diff --git a/fcs/case01/000035/000035_part_001.parquet b/fcs/case01/000035/000035_part_001.parquet new file mode 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Lymphoma +case07,PB,BC_Navios(EX),ClearLLab 10C,Malignant,Chronic Lymphocytic Leukemia/ Small Lymphocytic Lymphoma +case08,BM,BC_Navios(EX),ClearLLab 10C,Malignant,Mantle cell lymphoma +case09,BM,BC_Navios(EX),ClearLLab 10C,Malignant,Plasma Cell Myeloma +case10,BM,BC_Navios(EX),ClearLLab 10C,Malignant,Follicular Lymphoma +case11,BM,BC_Navios(EX),ClearLLab 10C,Malignant,B cell lymphoma of germinal center origin +case12,BM,BC_Navios(EX),ClearLLab 10C,Malignant,Mature B-cell lymphoma +case13,BM,BC_Navios(EX),ClearLLab 10C,Malignant,Mature B-cell lymphoma +case14,LN,BC_Navios(EX),ClearLLab 10C,Malignant,T Lymphoblastic Leukemia/ T Lymphoblastic Lymphoma +case15,PB,BC_Navios(EX),ClearLLab 10C,Malignant,T Lymphoblastic Leukemia/ T Lymphoblastic Lymphoma +case16,PB,BC_Navios(EX),ClearLLab 10C,Malignant,T–Cell Lymphoproliferative Disorder +case17,BM,BC_Navios(EX),ClearLLab 10C,Malignant,T–cell lymphoproliferative Disorder +case18,BM,BC_Navios(EX),ClearLLab 10C,Malignant,Acute Myeloid Leukemia +case19,BM,BC_Navios(EX),ClearLLab 10C,Malignant,Acute Monocytic Leukemia +case20,PB,BC_Navios(EX),ClearLLab 10C,Malignant,Acute Myeloid-NOS Leukemia +case21,BM,BC_Navios(EX),ClearLLab 10C,Malignant,Acute Promyelocytic Leukemia +case22,BM,BC_Navios(EX),ClearLLab 10C,Malignant,Acute Monocytic Leukemia +case23,BM,BC_Navios(EX),ClearLLab 10C,Malignant,Myelodysplastic Syndrome +case24,BM,BC_Navios(EX),ClearLLab 10C,Malignant,Myelodysplastic Syndrome