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+ # Copyright 2022 for msynth dataset
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+ #
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+ # Licensed under the Apache License, Version 2.0 (the "License");
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+ # you may not use this file except in compliance with the License.
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+ # You may obtain a copy of the License at
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+ #
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+ # http://www.apache.org/licenses/LICENSE-2.0
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+ #
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+ # Unless required by applicable law or agreed to in writing, software
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+ # distributed under the License is distributed on an "AS IS" BASIS,
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+ # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
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+ # See the License for the specific language governing permissions and
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+ # limitations under the License.
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+ '''
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+ Custom dataset-builder for msynth dataset
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+ '''
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+
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+ import os
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+ import datasets
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+ import glob
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+ import re
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+
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+ logger = datasets.logging.get_logger(__name__)
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+
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+ _CITATION = """\
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+ @article{sizikova2023knowledge,
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+ title={Knowledge-based in silico models and dataset for the comparative evaluation of mammography AI for a range of breast characteristics, lesion conspicuities and doses},
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+ author={Sizikova, Elena and Saharkhiz, Niloufar and Sharma, Diksha and Lago, Miguel and Sahiner, Berkman and Delfino, Jana G. and Badano, Aldo},
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+ journal={Advances in Neural Information Processing Systems},
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+ volume={},
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+ pages={16764--16778},
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+ year={2023}
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+ """
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+
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+
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+ _DESCRIPTION = """\
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+ M-SYNTH is a synthetic digital mammography (DM) dataset with four breast fibroglandular density distributions imaged using Monte Carlo x-ray simulations with the publicly available Virtual Imaging Clinical Trial for Regulatory Evaluation (VICTRE) toolkit.
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+ Curated by: Elena Sizikova, Niloufar Saharkhiz, Diksha Sharma, Miguel Lago, Berkman Sahiner, Jana Gut Delfino, Aldo Badano
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+ License: Creative Commons 1.0 Universal License (CC0)
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+ """
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+
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+
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+ _HOMEPAGE = "link to the dataset description page (FDA/CDRH/OSEL/DIDSR/VICTRE_project)"
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+
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+ _REPO = "https://huggingface.co/datasets/didsr/msynth/resolve/main/data"
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+
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+ # satting parameters for the URLS
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+ _LESIONDENSITY = ["1.0","1.06", "1.1"]
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+ _DOSE = ["20%","40%","60%","80%","100%"]
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+ _DENSITY = ["fatty", "dense", "hetero","scattered"]
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+ _SIZE = ["5.0","7.0", "9.0"]
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+ _DETECTOR = 'SIM'
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+
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+ _DOSETABLE = {
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+ "dense": {
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+ "20%": '1.73e09',
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+ "40%": '3.47e09',
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+ "60%": '5.20e09',
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+ "80%": '6.94e09',
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+ "100%": '8.67e09'
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+ },
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+ "hetero": {
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+ "20%": '2.04e09',
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+ "40%": '4.08e09',
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+ "60%": '6.12e09',
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+ "80%": '8.16e09',
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+ "100%": '1.02e10'
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+ },
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+ "scattered": {
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+ "20%": '4.08e09',
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+ "40%": '8.16e09',
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+ "60%": '1.22e10',
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+ "80%": '1.63e10',
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+ "100%": '2.04e10'
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+ },
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+ "fatty": {
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+ "20%": '4.44e09',
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+ "40%": '8.88e09',
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+ "60%": '1.33e10',
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+ "80%": '1.78e10',
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+ "100%": '2.22e10'
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+ }
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+ }
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+ # Links to download readme files
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+ _URLS = {
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+ "meta_data": f"{_REPO}/metadata/bounds.zip",
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+ "read_me": f"{_REPO}/README.md"
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+ }
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+
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+
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+
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+ # Define the labels or classes in your dataset
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+ #_NAMES = ["raw", "mhd", "dicom", "loc"]
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+
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+ DATA_DIR = {"all_data": "SIM", "seg": "SIM", "info": "bounds"}
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+
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+ class msynthConfig(datasets.BuilderConfig):
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+ """msynth dataset"""
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+ lesion_density = _LESIONDENSITY
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+ dose = _DOSE
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+ density = _DENSITY
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+ size = _SIZE
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+ def __init__(self, name, **kwargs):
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+ super(msynthConfig, self).__init__(
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+ version=datasets.Version("1.0.0"),
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+ name=name,
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+ description="msynth",
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+ **kwargs,
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+ )
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+
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+ class msynth(datasets.GeneratorBasedBuilder):
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+ """msynth dataset."""
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+
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+ DEFAULT_WRITER_BATCH_SIZE = 256
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+ BUILDER_CONFIGS = [
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+ msynthConfig("device-data"),
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+ msynthConfig("segmentation-mask"),
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+ msynthConfig("metadata"),
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+ ]
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+
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+ def _info(self):
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+ if self.config.name == "device-data":
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+ # Define dataset features and keys
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+ features = datasets.Features(
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+ {
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+ "Raw": datasets.Value("string"),
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+ "mhd": datasets.Value("string"),
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+ "loc": datasets.Value("string"),
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+ "dcm": datasets.Value("string"),
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+ "density": datasets.Value("string"),
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+ "mass_radius": datasets.Value("float32")
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+ }
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+ )
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+ #keys = ("image", "metadata")
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+ elif self.config.name == "segmentation-mask":
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+ # Define features and keys
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+ features = datasets.Features(
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+ {
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+ "Raw": datasets.Value("string"),
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+ "mhd": datasets.Value("string"),
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+ "loc": datasets.Value("string"),
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+ "density": datasets.Value("string"),
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+ "mass_radius": datasets.Value("float32")
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+ }
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+ )
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+
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+ elif self.config.name == "metadata":
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+ # Define features and keys
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+ features = datasets.Features(
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+ {
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+ "fatty": datasets.Value("string"),
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+ "dense": datasets.Value("string"),
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+ "hetero": datasets.Value("string"),
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+ "scattered": datasets.Value("string")
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+ }
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+ )
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+
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+ return datasets.DatasetInfo(
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+ description=_DESCRIPTION,
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+ features=features,
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+ supervised_keys=None,
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+ homepage=_HOMEPAGE,
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+ citation=_CITATION,
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+ )
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+
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+ def _split_generators(
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+ self, dl_manager: datasets.utils.download_manager.DownloadManager):
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+ # Setting up the **config_kwargs parameters
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+ if self.config.lesion_density == "all":
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+ self.config.lesion_density = _LESIONDENSITY
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+
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+ if self.config.dose == "all":
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+ self.config.dose = _DOSE
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+
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+ if self.config.density == "all":
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+ self.config.density = _DENSITY
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+
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+ if self.config.size == "all":
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+ self.config.size = _SIZE
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+
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+
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+ if self.config.name == "device-data":
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+ file_name = []
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+ for ld in self.config.lesion_density:
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+ for ds in self.config.dose:
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+ for den in self.config.density:
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+ value = _DOSETABLE[den][ds]
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+ for sz in self.config.size:
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+ temp_name = []
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+ temp_name = (
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+ "device_data_VICTREPhantoms_spic_"
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+ + ld
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+ + "/"
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+ + value
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+ + "/"
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+ + den
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+ + "/2/"
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+ + sz
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+ + "/"
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+ + _DETECTOR
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+ + ".zip"
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+ )
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+ file_name.append(_REPO +"/"+ temp_name)
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+
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+ # Downloading the data files
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+ # data_dir = dl_manager.download_and_extract(file_name)
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+ data_dir = []
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+ for url in file_name:
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+ try:
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+ temp_down_file = []
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+ # Attempt to download the file
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+ temp_down_file = dl_manager.download_and_extract(url)
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+ data_dir.append(temp_down_file)
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+
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+ except Exception as e:
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+ # If an exception occurs (e.g., file not found), log the error and add the URL to the failed_urls list
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+ logger.error(f"Failed to download {url}: {e}")
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+
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+ return [
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+ datasets.SplitGenerator(
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+ name="device-data",
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+ gen_kwargs={
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+ "files": [data_dir_t for data_dir_t in data_dir],
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+ "name": "all_data",
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+ },
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+ ),
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+ ]
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+
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+ elif self.config.name == "segmentation-mask":
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+ seg_file_name = []
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+ for den in self.config.density:
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+ for sz in self.config.size:
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+ temp_name = []
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+ temp_name = (
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+ "segmentation_masks"
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+ + "/"
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+ + den
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+ + "/2/"
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+ + sz
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+ + "/"
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+ + _DETECTOR
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+ + ".zip"
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+ )
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+ seg_file_name.append(_REPO+ "/" + temp_name)
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+
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+ # Downloading the files
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+ seg_dir = []
248
+ #seg_dir = dl_manager.download_and_extract(seg_file_name)
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+
250
+ for url in seg_file_name:
251
+ try:
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+ # Attempt to download the file
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+ temp_down_file = []
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+ temp_down_file = dl_manager.download_and_extract(url)
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+ seg_dir.append(temp_down_file)
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+
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+ except Exception as e:
258
+ # If an exception occurs (e.g., file not found), log the error and add the URL to the failed_urls list
259
+ logger.error(f"Failed to download {url}: {e}")
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+
261
+ return [
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+ datasets.SplitGenerator(
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+ name="segmentation-mask",
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+ gen_kwargs={
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+ "files": [data_dir_t for data_dir_t in seg_dir],
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+ "name": "seg",
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+ },
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+ ),
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+ ]
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+
271
+ elif self.config.name == "metadata":
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+ meta_dir = dl_manager.download_and_extract(_URLS['meta_data'])
273
+ return [
274
+ datasets.SplitGenerator(
275
+ name="metadata",
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+ gen_kwargs={
277
+ "files": meta_dir,
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+ "name": "info",
279
+ },
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+ ),
281
+ ]
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+
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+
284
+ def get_all_file_paths(self, root_directory):
285
+ file_paths = [] # List to store file paths
286
+
287
+ # Walk through the directory and its subdirectories using os.walk
288
+ for folder, _, files in os.walk(root_directory):
289
+ for file in files:
290
+ if file.endswith('.raw'):
291
+ # Get the full path of the file
292
+ file_path = os.path.join(folder, file)
293
+ file_paths.append(file_path)
294
+ return file_paths
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+
296
+ def get_support_file_path(self, raw_file_path, ext):
297
+ folder_path = os.path.dirname(raw_file_path)
298
+ # Use os.path.basename() to extract the filename
299
+ raw_file_name = os.path.basename(raw_file_path)
300
+ # Use os.path.splitext() to split the filename into root and extension
301
+ root, extension = os.path.splitext(raw_file_name)
302
+ if ext == "dcm":
303
+ supp_file_name = f"000.{ext}"
304
+ file_path = os.path.join(folder_path,"DICOM_dm",supp_file_name)
305
+ else:
306
+ supp_file_name = f"{root}.{ext}"
307
+ file_path = os.path.join(folder_path, supp_file_name)
308
+
309
+ if os.path.isfile(file_path):
310
+ return file_path
311
+ else:
312
+ return "Not available for this raw file"
313
+
314
+
315
+
316
+ def _generate_examples(self, files, name):
317
+ if self.config.name == "device-data":
318
+ key = 0
319
+ data_dir = []
320
+ for folder in files:
321
+ tmp_dir = []
322
+ tmp_dir = self.get_all_file_paths(os.path.join(folder, DATA_DIR[name]))
323
+ data_dir = data_dir + tmp_dir
324
+
325
+ for path in data_dir:
326
+ res_dic = {}
327
+ for word in _DENSITY:
328
+ if word in path:
329
+ breast_density = word
330
+ pattern = rf"(\d+\.\d+)_{word}"
331
+ match = re.search(pattern, path)
332
+ matched_text = match.group(1)
333
+ break
334
+
335
+ # Get image id to filter the respective row of the csv
336
+ image_id = os.path.basename(path)
337
+ # Use os.path.splitext() to split the filename into root and extension
338
+ root, extension = os.path.splitext(image_id)
339
+ # Get the extension without the dot
340
+ image_labels = extension.lstrip(".")
341
+ res_dic["Raw"] = path
342
+ res_dic["mhd"] = self.get_support_file_path(path, "mhd")
343
+ res_dic["loc"] = self.get_support_file_path(path, "loc")
344
+ if self.config.name == "device-data":
345
+ res_dic["dcm"] = self.get_support_file_path(path, "dcm")
346
+ res_dic["density"] = breast_density
347
+ res_dic["mass_radius"] = matched_text
348
+
349
+ yield key, res_dic
350
+ key += 1
351
+
352
+
353
+ if self.config.name == "segmentation-mask":
354
+ key = 0
355
+ data_dir = []
356
+ for folder in files:
357
+ tmp_dir = []
358
+ tmp_dir = self.get_all_file_paths(os.path.join(folder, DATA_DIR[name]))
359
+ data_dir = data_dir + tmp_dir
360
+
361
+ for path in data_dir:
362
+ res_dic = {}
363
+ for word in _DENSITY:
364
+ if word in path:
365
+ breast_density = word
366
+ pattern = rf"(\d+\.\d+)_{word}"
367
+ match = re.search(pattern, path)
368
+ matched_text = match.group(1)
369
+ break
370
+
371
+ # Get image id to filter the respective row of the csv
372
+ image_id = os.path.basename(path)
373
+ # Use os.path.splitext() to split the filename into root and extension
374
+ root, extension = os.path.splitext(image_id)
375
+ # Get the extension without the dot
376
+ image_labels = extension.lstrip(".")
377
+ res_dic["Raw"] = path
378
+ res_dic["mhd"] = self.get_support_file_path(path, "mhd")
379
+ res_dic["loc"] = self.get_support_file_path(path, "loc")
380
+ res_dic["density"] = breast_density
381
+ res_dic["mass_radius"] = matched_text
382
+
383
+ yield key, res_dic
384
+ key += 1
385
+
386
+ if self.config.name == "metadata":
387
+ key = 0
388
+ examples = list()
389
+ meta_dir = os.path.join(files, DATA_DIR[name])
390
+
391
+ res_dic = {
392
+ "fatty": os.path.join(meta_dir,'bounds_fatty.npy'),
393
+ "dense": os.path.join(meta_dir,'bounds_dense.npy'),
394
+ "hetero": os.path.join(meta_dir,'bounds_hetero.npy'),
395
+ "scattered": os.path.join(meta_dir,'bounds_scattered.npy')
396
+ }
397
+ yield key, res_dic
398
+ key +=1