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"data\\Lung_Patient_17\\Beams\\Beam_5_Data.h5", "data\\Lung_Patient_17\\Beams\\Beam_6_Data.h5"], "beam_metadata_paths": ["data\\Lung_Patient_17\\Beams\\Beam_0_MetaData.json", "data\\Lung_Patient_17\\Beams\\Beam_1_MetaData.json", "data\\Lung_Patient_17\\Beams\\Beam_2_MetaData.json", "data\\Lung_Patient_17\\Beams\\Beam_3_MetaData.json", "data\\Lung_Patient_17\\Beams\\Beam_4_MetaData.json", "data\\Lung_Patient_17\\Beams\\Beam_5_MetaData.json", "data\\Lung_Patient_17\\Beams\\Beam_6_MetaData.json"], "optimization_voxels_data": "data\\Lung_Patient_17\\OptimizationVoxels_Data.h5", "optimization_voxels_metadata": "data\\Lung_Patient_17\\OptimizationVoxels_MetaData.json", "planner_beams": "data\\Lung_Patient_17\\PlannerBeams.json", "rt_dose_echo_imrt": "data\\Lung_Patient_17\\rt_dose_echo_imrt.dcm", "rt_plan_echo_imrt": "data\\Lung_Patient_17\\rt_plan_echo_imrt.dcm"} +{"patient_id": "Lung_Patient_18", "ct_data": "data\\Lung_Patient_18\\CT_Data.h5", "ct_metadata": "data\\Lung_Patient_18\\CT_MetaData.json", "structureset_data": "data\\Lung_Patient_18\\StructureSet_Data.h5", "structureset_metadata": "data\\Lung_Patient_18\\StructureSet_MetaData.json", "beam_data_paths": ["data\\Lung_Patient_18\\Beams\\Beam_0_Data.h5", "data\\Lung_Patient_18\\Beams\\Beam_1_Data.h5", "data\\Lung_Patient_18\\Beams\\Beam_2_Data.h5", "data\\Lung_Patient_18\\Beams\\Beam_3_Data.h5", "data\\Lung_Patient_18\\Beams\\Beam_4_Data.h5", "data\\Lung_Patient_18\\Beams\\Beam_5_Data.h5"], "beam_metadata_paths": ["data\\Lung_Patient_18\\Beams\\Beam_0_MetaData.json", "data\\Lung_Patient_18\\Beams\\Beam_1_MetaData.json", "data\\Lung_Patient_18\\Beams\\Beam_2_MetaData.json", "data\\Lung_Patient_18\\Beams\\Beam_3_MetaData.json", "data\\Lung_Patient_18\\Beams\\Beam_4_MetaData.json", "data\\Lung_Patient_18\\Beams\\Beam_5_MetaData.json"], "optimization_voxels_data": "data\\Lung_Patient_18\\OptimizationVoxels_Data.h5", "optimization_voxels_metadata": "data\\Lung_Patient_18\\OptimizationVoxels_MetaData.json", "planner_beams": "data\\Lung_Patient_18\\PlannerBeams.json", "rt_dose_echo_imrt": "data\\Lung_Patient_18\\rt_dose_echo_imrt.dcm", "rt_plan_echo_imrt": "data\\Lung_Patient_18\\rt_plan_echo_imrt.dcm"} +{"patient_id": "Lung_Patient_19", "ct_data": "data\\Lung_Patient_19\\CT_Data.h5", "ct_metadata": "data\\Lung_Patient_19\\CT_MetaData.json", "structureset_data": "data\\Lung_Patient_19\\StructureSet_Data.h5", "structureset_metadata": "data\\Lung_Patient_19\\StructureSet_MetaData.json", "beam_data_paths": ["data\\Lung_Patient_19\\Beams\\Beam_0_Data.h5", "data\\Lung_Patient_19\\Beams\\Beam_1_Data.h5", "data\\Lung_Patient_19\\Beams\\Beam_2_Data.h5", "data\\Lung_Patient_19\\Beams\\Beam_3_Data.h5", "data\\Lung_Patient_19\\Beams\\Beam_4_Data.h5", "data\\Lung_Patient_19\\Beams\\Beam_5_Data.h5"], "beam_metadata_paths": ["data\\Lung_Patient_19\\Beams\\Beam_0_MetaData.json", "data\\Lung_Patient_19\\Beams\\Beam_1_MetaData.json", "data\\Lung_Patient_19\\Beams\\Beam_2_MetaData.json", "data\\Lung_Patient_19\\Beams\\Beam_3_MetaData.json", "data\\Lung_Patient_19\\Beams\\Beam_4_MetaData.json", "data\\Lung_Patient_19\\Beams\\Beam_5_MetaData.json"], "optimization_voxels_data": "data\\Lung_Patient_19\\OptimizationVoxels_Data.h5", "optimization_voxels_metadata": "data\\Lung_Patient_19\\OptimizationVoxels_MetaData.json", "planner_beams": "data\\Lung_Patient_19\\PlannerBeams.json", "rt_dose_echo_imrt": "data\\Lung_Patient_19\\rt_dose_echo_imrt.dcm", "rt_plan_echo_imrt": "data\\Lung_Patient_19\\rt_plan_echo_imrt.dcm"} diff --git a/dataset.py b/dataset.py new file mode 100644 index 0000000000000000000000000000000000000000..b630cc980ccfa10584cb76c7463f6bf25a83f387 --- /dev/null +++ b/dataset.py @@ -0,0 +1,54 @@ +import os +import json +from datasets import DatasetInfo, GeneratorBasedBuilder, SplitGenerator, Split, Value, Features + +class TestGJ(GeneratorBasedBuilder): + def _info(self): + return DatasetInfo( + description="PortPy radiotherapy dataset. Each entry corresponds to a patient listed in datainfo.jsonl.", + features=Features({ + "patient_id": Value("string"), + "ct_data": Value("string"), + "ct_metadata": Value("string"), + "structureset_data": Value("string"), + "structureset_metadata": Value("string"), + "beam_data_paths": Value("string"), # Semicolon-separated list + "beam_metadata_paths": Value("string"), # Semicolon-separated list + "optimization_voxels_data": Value("string"), + "optimization_voxels_metadata": Value("string"), + "planner_beams": Value("string"), + "rt_dose_echo_imrt": Value("string"), + "rt_plan_echo_imrt": Value("string") + }), + ) + + def _split_generators(self, dl_manager): + return [ + SplitGenerator( + name=Split.TRAIN, + gen_kwargs={"data_dir": self.config.data_dir} + ) + ] + + def _generate_examples(self, data_dir): + datainfo_path = os.path.join(data_dir, "data_info.jsonl") + with open(datainfo_path, "r") as f: + lines = f.readlines() + + for idx, line in enumerate(lines): + entry = json.loads(line) + + yield idx, { + "patient_id": entry["patient_id"], + "ct_data": entry["ct_data"].replace("\\", "/"), + "ct_metadata": entry["ct_metadata"].replace("\\", "/"), + "structureset_data": entry["structureset_data"].replace("\\", "/"), + "structureset_metadata": entry["structureset_metadata"].replace("\\", "/"), + "beam_data_paths": ";".join(p.replace("\\", "/") for p in entry["beam_data_paths"]), + "beam_metadata_paths": ";".join(p.replace("\\", "/") for p in entry["beam_metadata_paths"]), + "optimization_voxels_data": entry["optimization_voxels_data"].replace("\\", "/"), + "optimization_voxels_metadata": entry["optimization_voxels_metadata"].replace("\\", "/"), + "planner_beams": entry["planner_beams"].replace("\\", "/"), + "rt_dose_echo_imrt": entry["rt_dose_echo_imrt"].replace("\\", "/"), + "rt_plan_echo_imrt": entry["rt_plan_echo_imrt"].replace("\\", "/"), + } \ No newline at end of file