added feature information

SPIDER.py

@@ -23,6 +23,7 @@ from typing import Dict, List, Mapping, Optional, Set, Sequence, Tuple, Union
 import numpy as np
 
 import datasets
+from datasets import Image
 import SimpleITK as sitk
 
 # Define functions
@@ -135,18 +136,123 @@ class SPIDER(datasets.GeneratorBasedBuilder):
         This method specifies the datasets.DatasetInfo object which contains 
         informations and typings for the dataset.
         """
-        features = datasets.Features(
-            {
-                "patient_id": datasets.Value("string"),
-                "scan_type": datasets.Value("string"),
-                "raw_image": datasets.Value(sitk.Image),
-                "numeric_array": datasets.Value(np.array),
-                "metadata": datasets.Value(dict),
-                "rad_gradings": datasets.Value(dict),
-
-                # These are the features of your dataset like images, labels ...
+        features = datasets.Features({
+            "patient_id": datasets.Value("string"),
+            "scan_type": datasets.Value("string"),
+            "raw_image": datasets.Value("object"),
+            "numeric_array": datasets.Value("numpy", dtype="int16", shape=(512, 512, 17)),
+            "metadata": {
+                "num_vertebrae": datasets.Value(dtype="string"),
+                "num_discs": datasets.Value(dtype="string"),
+                "sex": datasets.Value(dtype="string"),
+                "birth_date": datasets.Value(dtype="string"),
+                "AngioFlag": datasets.Value(dtype="string"),
+                "BodyPartExamined": datasets.Value(dtype="string"),
+                "DeviceSerialNumber": datasets.Value(dtype="string"),
+                "EchoNumbers": datasets.Value(dtype="string"),
+                "EchoTime": datasets.Value(dtype="string"),
+                "EchoTrainLength": datasets.Value(dtype="string"),
+                "FlipAngle": datasets.Value(dtype="string"),
+                "ImagedNucleus": datasets.Value(dtype="string"),
+                "ImagingFrequency": datasets.Value(dtype="string"),
+                "InPlanePhaseEncodingDirection": datasets.Value(dtype="string"),
+                "MRAcquisitionType": datasets.Value(dtype="string"),
+                "MagneticFieldStrength": datasets.Value(dtype="string"),
+                "Manufacturer": datasets.Value(dtype="string"),
+                "ManufacturerModelName": datasets.Value(dtype="string"),
+                "NumberOfPhaseEncodingSteps": datasets.Value(dtype="string"),
+                "PercentPhaseFieldOfView": datasets.Value(dtype="string"),
+                "PercentSampling": datasets.Value(dtype="string"),
+                "PhotometricInterpretation": datasets.Value(dtype="string"),
+                "PixelBandwidth": datasets.Value(dtype="string"),
+                "PixelSpacing": datasets.Value(dtype="string"),
+                "RepetitionTime": datasets.Value(dtype="string"),
+                "SAR": datasets.Value(dtype="string"),
+                "SamplesPerPixel": datasets.Value(dtype="string"),
+                "ScanningSequence": datasets.Value(dtype="string"),
+                "SequenceName": datasets.Value(dtype="string"),
+                "SeriesDescription": datasets.Value(dtype="string"),
+                "SliceThickness": datasets.Value(dtype="string"),
+                "SoftwareVersions": datasets.Value(dtype="string"),
+                "SpacingBetweenSlices": datasets.Value(dtype="string"),
+                "SpecificCharacterSet": datasets.Value(dtype="string"),
+                "TransmitCoilName": datasets.Value(dtype="string"),
+                "WindowCenter": datasets.Value(dtype="string"),
+                "WindowWidth": datasets.Value(dtype="string"),
+            },
+            "rad_gradings": {
+                "IVD1": {
+                    "Modic": datasets.Value(dtype="string"),
+                    "UP endplate": datasets.Value(dtype="string"),
+                    "LOW endplate": datasets.Value(dtype="string"),
+                    "Spondylolisthesis": datasets.Value(dtype="string"),
+                    "Disc herniation": datasets.Value(dtype="string"),
+                    "Disc narrowing": datasets.Value(dtype="string"),
+                    "Disc bulging": datasets.Value(dtype="string"),
+                    "Pfirrman grade": datasets.Value(dtype="string"),
+                },
+                "IVD2": {
+                    "Modic": datasets.Value(dtype="string"),
+                    "UP endplate": datasets.Value(dtype="string"),
+                    "LOW endplate": datasets.Value(dtype="string"),
+                    "Spondylolisthesis": datasets.Value(dtype="string"),
+                    "Disc herniation": datasets.Value(dtype="string"),
+                    "Disc narrowing": datasets.Value(dtype="string"),
+                    "Disc bulging": datasets.Value(dtype="string"),
+                    "Pfirrman grade": datasets.Value(dtype="string"),
+                },
+                "IVD3": {
+                    "Modic": datasets.Value(dtype="string"),
+                    "UP endplate": datasets.Value(dtype="string"),
+                    "LOW endplate": datasets.Value(dtype="string"),
+                    "Spondylolisthesis": datasets.Value(dtype="string"),
+                    "Disc herniation": datasets.Value(dtype="string"),
+                    "Disc narrowing": datasets.Value(dtype="string"),
+                    "Disc bulging": datasets.Value(dtype="string"),
+                    "Pfirrman grade": datasets.Value(dtype="string"),
+                },
+                "IVD4": {
+                    "Modic": datasets.Value(dtype="string"),
+                    "UP endplate": datasets.Value(dtype="string"),
+                    "LOW endplate": datasets.Value(dtype="string"),
+                    "Spondylolisthesis": datasets.Value(dtype="string"),
+                    "Disc herniation": datasets.Value(dtype="string"),
+                    "Disc narrowing": datasets.Value(dtype="string"),
+                    "Disc bulging": datasets.Value(dtype="string"),
+                    "Pfirrman grade": datasets.Value(dtype="string"),
+                },
+                "IVD5": {
+                    "Modic": datasets.Value(dtype="string"),
+                    "UP endplate": datasets.Value(dtype="string"),
+                    "LOW endplate": datasets.Value(dtype="string"),
+                    "Spondylolisthesis": datasets.Value(dtype="string"),
+                    "Disc herniation": datasets.Value(dtype="string"),
+                    "Disc narrowing": datasets.Value(dtype="string"),
+                    "Disc bulging": datasets.Value(dtype="string"),
+                    "Pfirrman grade": datasets.Value(dtype="string"),
+                },
+                "IVD6": {
+                    "Modic": datasets.Value(dtype="string"),
+                    "UP endplate": datasets.Value(dtype="string"),
+                    "LOW endplate": datasets.Value(dtype="string"),
+                    "Spondylolisthesis": datasets.Value(dtype="string"),
+                    "Disc herniation": datasets.Value(dtype="string"),
+                    "Disc narrowing": datasets.Value(dtype="string"),
+                    "Disc bulging": datasets.Value(dtype="string"),
+                    "Pfirrman grade": datasets.Value(dtype="string"),
+                },
+                "IVD7": {
+                    "Modic": datasets.Value(dtype="string"),
+                    "UP endplate": datasets.Value(dtype="string"),
+                    "LOW endplate": datasets.Value(dtype="string"),
+                    "Spondylolisthesis": datasets.Value(dtype="string"),
+                    "Disc herniation": datasets.Value(dtype="string"),
+                    "Disc narrowing": datasets.Value(dtype="string"),
+                    "Disc bulging": datasets.Value(dtype="string"),
+                    "Pfirrman grade": datasets.Value(dtype="string"),
+                },
             }
-        )
+        })
 
         return datasets.DatasetInfo(
             # This is the description that will appear on the datasets page.
@@ -297,10 +403,13 @@ class SPIDER(datasets.GeneratorBasedBuilder):
         grades_data = import_csv_data(paths_dict['gradings'])
         
         # Convert overview data list of dicts to dict of dicts
+        exclude_vars = ['new_file_name', 'subset'] # Original data only lists train and validate
         overview_dict = {}
         for item in overview_data:
             key = item['new_file_name']
-            overview_dict[key] = item
+            overview_dict[key] = {
+                k:v for k,v in item.items() if k not in exclude_vars
+            }
         
         # Merge patient records for radiological gradings data
         grades_dict = {}