Chris Oswald
commited on
Commit
•
b31174f
1
Parent(s):
a23ca77
added description of dataset
Browse files
SPIDER.py
CHANGED
@@ -81,8 +81,7 @@ _CITATION = """\
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}
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"""
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#
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# You can copy an official description
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_DESCRIPTION = """\
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This is a large publicly available multi-center lumbar spine magnetic resonance \
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imaging (MRI) dataset with reference segmentations of vertebrae, intervertebral \
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@@ -114,7 +113,11 @@ following degenerative changes:
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7. Pfirrman grade (grade 1 to 5).
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All radiological gradings are provided per IVD level.
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_HOMEPAGE = "https://zenodo.org/records/10159290"
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@@ -165,7 +168,8 @@ class CustomBuilderConfig(datasets.BuilderConfig):
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class SPIDER(datasets.GeneratorBasedBuilder):
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"""
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# Class attributes
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DEFAULT_WRITER_BATCH_SIZE = 16 # PyArrow default is too large for image data
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@@ -183,19 +187,6 @@ class SPIDER(datasets.GeneratorBasedBuilder):
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]
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DEFAULT_CONFIG_NAME = "default"
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# def __init__(
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# self,
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# *args,
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# scan_types: List[str] = DEFAULT_SCAN_TYPES,
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# resize_shape: Tuple[int, int, int] = DEFAULT_RESIZE,
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# shuffle: bool = True,
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# **kwargs,
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# ):
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# super().__init__(*args, **kwargs)
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# self.scan_types = self.scan_types
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# self.resize_shape = self.resize_shape
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# self.shuffle = self.shuffle
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def _info(self):
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"""Specify datasets.DatasetInfo object containing information and typing
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for the dataset."""
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@@ -211,46 +202,6 @@ class SPIDER(datasets.GeneratorBasedBuilder):
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k:datasets.Value(v) for k,v in
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self.config.var_types['metadata'].items()
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},
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# {
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# "num_vertebrae": datasets.Value("int16"),
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# "num_discs": datasets.Value("int16"),
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# "sex": datasets.Value("string"),
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# "birth_date": datasets.Value("string"),
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# "AngioFlag": datasets.Value("string"),
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# "BodyPartExamined": datasets.Value("string"),
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# "DeviceSerialNumber": datasets.Value("string"),
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# "EchoNumbers": datasets.Value("float32"),
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# "EchoTime": datasets.Value("float32"),
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# "EchoTrainLength": datasets.Value("float32"),
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# "FlipAngle": datasets.Value("float32"),
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# "ImagedNucleus": datasets.Value("string"),
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# "ImagingFrequency": datasets.Value("float32"),
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# "InPlanePhaseEncodingDirection": datasets.Value("string"),
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# "MRAcquisitionType": datasets.Value("string"),
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# "MagneticFieldStrength": datasets.Value("float32"),
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# "Manufacturer": datasets.Value("string"),
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# "ManufacturerModelName": datasets.Value("string"),
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# "NumberOfPhaseEncodingSteps": datasets.Value("int32"),
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# "PercentPhaseFieldOfView": datasets.Value("float64"),
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# "PercentSampling": datasets.Value("float64"),
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# "PhotometricInterpretation": datasets.Value("string"),
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# "PixelBandwidth": datasets.Value("int32"),
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# "PixelSpacing": datasets.Sequence(datasets.Value("float32")),
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# "RepetitionTime": datasets.Value("float64"),
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# "SAR": datasets.Value("float64"),
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# "SamplesPerPixel": datasets.Value("int32"),
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# "ScanningSequence": datasets.Value("string"),
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# "SequenceName": datasets.Value("string"),
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# "SeriesDescription": datasets.Value("string"),
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# "SliceThickness": datasets.Value("float32"),
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# "SoftwareVersions": datasets.Sequence(datasets.Value("string")),
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# "SpacingBetweenSlices": datasets.Value("float32"),
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# "SpecificCharacterSet": datasets.Value("string"),
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# "TransmitCoilName": datasets.Value("string"),
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# "WindowCenter": datasets.Value("float32"),
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# "WindowWidth": datasets.Value("float32"),
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# "OrigSubset":datasets.Value("string"),
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# },
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"rad_gradings": {
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"IVD label": datasets.Sequence(datasets.Value("string")),
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"Modic": datasets.Sequence(datasets.Value("string")),
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}
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"""
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+
# Official description
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_DESCRIPTION = """\
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This is a large publicly available multi-center lumbar spine magnetic resonance \
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imaging (MRI) dataset with reference segmentations of vertebrae, intervertebral \
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7. Pfirrman grade (grade 1 to 5).
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All radiological gradings are provided per IVD level.
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+
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Repository: https://zenodo.org/records/10159290
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Paper: https://www.nature.com/articles/s41597-024-03090-w
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"""
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_HOMEPAGE = "https://zenodo.org/records/10159290"
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class SPIDER(datasets.GeneratorBasedBuilder):
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"""Resized/rescaled 3-dimensional volumetric arrays of lumbar spine MRIs \
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with corresponding scanner/patient metadata and radiological gradings."""
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# Class attributes
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DEFAULT_WRITER_BATCH_SIZE = 16 # PyArrow default is too large for image data
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]
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DEFAULT_CONFIG_NAME = "default"
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def _info(self):
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"""Specify datasets.DatasetInfo object containing information and typing
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for the dataset."""
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k:datasets.Value(v) for k,v in
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self.config.var_types['metadata'].items()
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},
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"rad_gradings": {
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"IVD label": datasets.Sequence(datasets.Value("string")),
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"Modic": datasets.Sequence(datasets.Value("string")),
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