Chris Oswald
commited on
Commit
·
f2ef76c
1
Parent(s):
81b3fb4
added original subset indicator
Browse files
SPIDER.py
CHANGED
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@@ -73,8 +73,37 @@ _CITATION = """\
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# TODO: Add description of the dataset here
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# You can copy an official description
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_DESCRIPTION = """\
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This
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_HOMEPAGE = "https://zenodo.org/records/10159290"
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@@ -106,7 +135,7 @@ class CustomBuilderConfig(datasets.BuilderConfig):
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class SPIDER(datasets.GeneratorBasedBuilder):
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"""TODO: Short description of my dataset."""
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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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@@ -174,6 +203,7 @@ class SPIDER(datasets.GeneratorBasedBuilder):
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"TransmitCoilName": datasets.Value(dtype="string"),
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"WindowCenter": datasets.Value(dtype="string"),
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"WindowWidth": datasets.Value(dtype="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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@@ -319,6 +349,7 @@ class SPIDER(datasets.GeneratorBasedBuilder):
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overview_dict[key] = {
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k:v for k,v in item.items() if k not in exclude_vars
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}
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# Merge patient records for radiological gradings data
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grades_dict = {}
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# TODO: Add description of the dataset here
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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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discs (IVDs), and spinal canal. The dataset includes 447 sagittal T1 and T2 \
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MRI series from 218 studies of 218 patients with a history of low back pain. \
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The data was collected from four different hospitals. There is an additional \
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hidden test set, not available here, used in the accompanying SPIDER challenge \
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on spider.grand-challenge.org. We share this data to encourage wider \
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participation and collaboration in the field of spine segmentation, and \
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ultimately improve the diagnostic value of lumbar spine MRI.
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This file also provides the biological sex for all patients and the age for \
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the patients for which this was available. It also includes a number of \
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scanner and acquisition parameters for each individual MRI study. The dataset \
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also comes with radiological gradings found in a separate file for the \
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following degenerative changes:
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1. Modic changes (type I, II or III)
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2. Upper and lower endplate changes / Schmorl nodes (binary)
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3. Spondylolisthesis (binary)
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4. Disc herniation (binary)
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5. Disc narrowing (binary)
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6. Disc bulging (binary)
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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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class SPIDER(datasets.GeneratorBasedBuilder):
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"""TODO: Short description of my dataset.""" #TODO
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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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"TransmitCoilName": datasets.Value(dtype="string"),
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"WindowCenter": datasets.Value(dtype="string"),
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"WindowWidth": datasets.Value(dtype="string"),
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"OrigSubset":datasets.Value(dtype="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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overview_dict[key] = {
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k:v for k,v in item.items() if k not in exclude_vars
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}
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overview_dict[key]['OrigSubset'] = item['subset'] # Change name to original subset
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# Merge patient records for radiological gradings data
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grades_dict = {}
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