[WIP] Attempt on validator

examples/plot_validator.py

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+import os.path as op
+
+from mne_bids.validator import validate_meg
+
+# test an _meg.json file:
+json_fname = op.join('.', 'sub-01_task-audiovisual_meg.json')
+
+validate_meg(json_fname)
+
+# test an _fid.json file:
+json_fname = op.join('.', 'sub-testme01_meg_fid.json')
+
+validate_meg(json_fname)

examples/sub-01_task-audiovisual_meg.json

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+{
+    "TaskName": "audiovisual",
+    "SamplingFrequency": 600.614990234,
+    "Manufacturer": "Elekta",
+    "ManufacturerModelName": "Neuromag Vectorview 306",
+    "TaskDescription": "In this experiment, checkerboard patterns were presented to the subject into the left and right visual field, interspersed by tones to the left or right ear. The interval between the stimuli was 750 ms. Occasionally a smiley face was presented at the center of the visual field. The subject was asked to press a key with the right index finger as soon as possible after the appearance of the face.",
+    "MEGChannelCount": 306,
+    "MEGREFChannelCount": 0,
+    "EEGChannelCount": 60,
+    "EOGChannelCount": 1,
+    "ECGChannelCount": 0,
+    "EMGChannelCount": 0,
+    "MiscChannelCount": 0,
+    "TriggerChannelCount": 9,
+    "PowerLineFrequency": 60,
+    "HLCFrequency": [],
+    "EEGReference": "nose",
+    "MEGPosition": "upright",
+    "OnlineFilters": "0.10000000149 Hz high-pass, 172.176300049 Hz low-pass",
+    "RecordingType": "continuous",
+    "EyesClosed": "false",
+    "ContinuousHeadLocalization": "false",
+    "DigitizedLandmarks": "true",
+    "DigitizedHeadPoints": "true",
+    "SubjectArtefactDescription": "false"
+}

examples/sub-testme01_meg_fid.json

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+{
+    "MEGCoordinateSystem": "not_empty",
+    "MEGCoordinateUnits": "not_empty",
+    "MEGCoordinateSystemDescription": "",
+    "EEGCoordinateSystem": "not_empty",
+    "EEGCoordinateUnits": "not_empty",
+    "EEGCoordinateSystemDescription": "",
+    "IntendedFor": "not_empty",
+    "AnatomicalMRICoordinateSystem": "not_empty",
+    "AnatomicalMRICoordinateUnits": "not_empty",
+    "AnatomicalMRICoordinateSystemDescription": "",
+    "CoilCoordinates": "not_empty",
+    "CoilCoordinateSystem": "not_empty",
+    "CoilCoordinateUnits": "not_empty",
+    "CoilCoordinateSystemDescription": "",
+    "LandmarkCoordinates": "not_empty",
+    "LandmarkCoordinateSystem": "not_empty",
+    "LandmarkCoordinateUnits": "not_empty",
+    "LandmarkCoordinateSystemDescription": "",
+    "DigitizedHeadPoints": "",
+    "DigitizedHeadPointsCoordinateSystem": "",
+    "DigitizedHeadPointsCoordinateUnits": "",
+    "DigitizedHeadPointsCoordinateSystemDescription": ""
+}

mne_bids/jsonschemas/schema_meg.json

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+{
+        "type": "object",
+        "properties": {
+                "TaskName": {"type": "string","minLength": 1},
+                "Manufacturer": {"type": "string","minLength": 1},
+                "ManufacturerModelName": {"type": "string"},
+                "TaskDescription": {"type": "string"},
+                "Instructions": {"type": "string"},
+                "SamplingFrequency": {"type": "number"},
+                "CogAtlasID": {"type": "string"},
+                "CogPOID": {"type": "string"},
+                "InstitutionName": {"type": "string"},
+                "InstitutionAddress": {"type": "string"},
+                "DeviceSerialNumber": {"type": "string"},
+                "MEGChannelCount": {"type": "integer"},
+                "MEGREFChannelCount": {"type": "integer"},
+                "EEGChannelCount": {"type" : "integer"},
+                "EOGChannelCount": {"type" : "integer"},
+                "ECGChannelCount": {"type" : "integer"},
+                "EMGChannelCount": {"type" : "integer"},
+                "MiscChannelCount": {"type" : "integer"},
+                "TriggerChannelCount": {"type" : "integer"},
+                "PowerLineFrequency": {"type" : "number"},
+                "EEGPlacementScheme": {"type" : "string"},
+                "EEGReference": {"type" : "string"},
+                "DewarPosition": {"type" : "string"},
+                "SoftwareFilters": {"type" : "string"},
+                "RecordingDuration": {"type" : "number"},
+                "RecordingType": {"type" : "string"},
+                "EpochLength": {"type" : ["number","string"]},
+                "DeviceSoftwareVersion": {"type" : "string"},
+                "ContinuousHeadLocalization": {"type" : "string"},
+                "CoilFrequency": {"type" : "number"},
+                "MaxMovement": {"type" : "number"},
+                "SubjectArtefactDescription": {"type" : "string"},
+                "DigitizedLandmarks": {"type" : "string"},
+                "DigitizedHeadPoints": {"type" : "string"}
+                    },
+        "required": [   "TaskName",
+                        "Manufacturer",
+                        "SamplingFrequency",
+                        "MEGChannelCount",
+                        "MEGREFChannelCount",
+                        "EEGChannelCount",
+                        "EOGChannelCount",
+                        "ECGChannelCount",
+                        "EMGChannelCount",
+                        "MiscChannelCount",
+                        "TriggerChannelCount"]
+}

mne_bids/jsonschemas/schema_meg_fid.json

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+{
+        "type": "object",
+        "properties": {
+                "MEGCoordinateSystem": {"type": "string","minLength": 1},
+                "MEGCoordinateUnits": {"type": "string","minLength": 1},
+                "MEGCoordinateSystemDescription": {"type": "string"},
+                "EEGCoordinateSystem": {"type": "string","minLength": 1},
+                "EEGCoordinateUnits": {"type": "string","minLength": 1},
+                "EEGCoordinateSystemDescription": {"type": "string"},
+                "IntendedFor": {"type": "string","minLength": 1},
+                "AnatomicalMRICoordinateSystem": {"type": "string","minLength": 1},
+                "AnatomicalMRICoordinateUnits": {"type": "string","minLength": 1},
+                "AnatomicalMRICoordinateSystemDescription": {"type": "string"},
+                "CoilCoordinates": {"type": "string","minLength": 1},
+                "CoilCoordinateSystem": {"type": "string","minLength": 1},
+                "CoilCoordinateUnits": {"type": "string","minLength": 1},
+                "CoilCoordinateSystemDescription": {"type": "string"},
+                "LandmarkCoordinates": {"type": "string","minLength": 1},
+                "LandmarkCoordinateSystem": {"type": "string","minLength": 1},
+                "LandmarkCoordinateUnits": {"type": "string","minLength": 1},
+                "LandmarkCoordinateSystemDescription": {"type": "string"},
+                "DigitizedHeadPoints": {"type": "string"},
+                "DigitizedHeadPointsCoordinateSystem": {"type": "string"},
+                "DigitizedHeadPointsCoordinateUnits": {"type": "string"},
+                "DigitizedHeadPointsCoordinateSystemDescription": {"type": "string"}
+                },
+        "required": ["MEGCoordinateSystem",
+                    "MEGCoordinateUnits",
+                    "EEGCoordinateSystem",
+                    "EEGCoordinateUnits",
+                    "IntendedFor",
+                    "AnatomicalMRICoordinateSystem",
+                    "AnatomicalMRICoordinateUnits",
+                    "CoilCoordinates",
+                    "CoilCoordinateSystem",
+                    "CoilCoordinateUnits",
+                    "LandmarkCoordinates",
+                    "LandmarkCoordinateSystem",
+                    "LandmarkCoordinateUnits"
+                  ]
+}

mne_bids/validator.py

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+import os.path as op
+import inspect
+
+import json
+from jsonschema import validate
+
+FILE = inspect.getfile(inspect.currentframe())
+base_dir = op.join(op.dirname(op.abspath(FILE)), 'jsonschemas')
+
+
+def validate_meg(fname):
+    # get the correct schema
+    if fname.endswith('_meg.json'):
+        schema_fname = 'schema_meg.json'
+    elif fname.endswith('_fid.json'):
+        schema_fname = 'schema_meg_fid.json'
+
+    # open the schema
+    with open(op.join(base_dir, schema_fname)) as json_data:
+        schema = json.load(json_data)
+
+    # open the BIDS json file to validate
+    with open(fname) as json_data:
+        test_json = json.load(json_data)
+
+    # validate it
+    validate(test_json, schema)