experimental: control siibra-explorer

siibra/explorer/README.md

@@ -0,0 +1,24 @@
+# (experimental) Explorer extension
+
+```python
+from siibra.explorer.plugin import Explorer
+explorer = Explorer()
+explorer.start()
+
+# Open the link specified in the console
+# And click "OK" to open the companion plugin
+
+explorer.navigate(position=(1e7,1e7,1e7)) # in nm
+
+explorer.overlay(url="nifti://https://data-proxy.ebrains.eu/api/v1/public/buckets/d-d69b70e2-3002-4eaf-9c61-9c56f019bbc8/probabilistic_maps_pmaps_175areas/Area-hOc1/Area-hOc1_pmap_l_N10_nlin2ICBM152asym2009c_4.2_public_258e8c1d846f92be76922b20287344ae.nii.gz") # TODO a bit buggy, and does not yet work
+
+from siibra.locations import Point
+import siibra
+
+p1 = Point([1,2,3], space=siibra.spaces['mni152'])
+p2 = Point([2,3,4], space=siibra.spaces['mni152'])
+ps = p1.union(p2)
+
+explorer.annotate(points=ps) # maximize perspective view for best effect
+
+```

siibra/explorer/api/broadcast/allRegions/request/__init__.py

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+# generated by datamodel-codegen:
+#   filename:  sxplr.on.allRegions__fromSxplr__request.json
+#   timestamp: 2023-12-07T15:40:35+00:00
+
+from __future__ import annotations
+
+from dataclasses import dataclass, field
+from typing import Any, List, Optional, Union
+
+
+@dataclass
+class VocabModel:
+    field_vocab: str
+
+
+@dataclass
+class QuantitativeOverlapItem:
+    value: float
+    field_context: Optional[VocabModel] = field(
+        default_factory=lambda: {'@vocab': 'https://openminds.ebrains.eu/vocab/'}
+    )
+    typeOfUncertainty: Optional[Any] = None
+    uncertainty: Optional[List[float]] = None
+    unit: Optional[Any] = None
+
+
+@dataclass
+class QuantitativeOverlapItem1:
+    maxValue: float
+    minValue: float
+    field_context: Optional[VocabModel] = field(
+        default_factory=lambda: {'@vocab': 'https://openminds.ebrains.eu/vocab/'}
+    )
+    maxValueUnit: Optional[Any] = None
+    minValueUnit: Optional[Any] = None
+
+
+@dataclass
+class ApiModelsOpenmindsSANDSV3AtlasParcellationEntityVersionCoordinates:
+    value: float
+    field_context: Optional[VocabModel] = field(
+        default_factory=lambda: {'@vocab': 'https://openminds.ebrains.eu/vocab/'}
+    )
+    typeOfUncertainty: Optional[Any] = None
+    uncertainty: Optional[List[float]] = None
+    unit: Optional[Any] = None
+
+
+@dataclass
+class RelationAssessmentItem:
+    inRelationTo: Any
+    qualitativeOverlap: Any
+    field_context: Optional[VocabModel] = field(
+        default_factory=lambda: {'@vocab': 'https://openminds.ebrains.eu/vocab/'}
+    )
+    criteria: Optional[Any] = None
+
+
+@dataclass
+class RelationAssessmentItem1:
+    inRelationTo: Any
+    quantitativeOverlap: Union[QuantitativeOverlapItem, QuantitativeOverlapItem1]
+    field_context: Optional[VocabModel] = field(
+        default_factory=lambda: {'@vocab': 'https://openminds.ebrains.eu/vocab/'}
+    )
+    criteria: Optional[Any] = None
+
+
+@dataclass
+class BestViewPoint:
+    coordinateSpace: Any
+    coordinates: List[
+        ApiModelsOpenmindsSANDSV3AtlasParcellationEntityVersionCoordinates
+    ]
+    field_context: Optional[VocabModel] = field(
+        default_factory=lambda: {'@vocab': 'https://openminds.ebrains.eu/vocab/'}
+    )
+
+
+@dataclass
+class HasAnnotation:
+    criteriaQualityType: Any
+    internalIdentifier: str
+    field_context: Optional[VocabModel] = field(
+        default_factory=lambda: {'@vocab': 'https://openminds.ebrains.eu/vocab/'}
+    )
+    bestViewPoint: Optional[BestViewPoint] = None
+    criteria: Optional[Any] = None
+    displayColor: Optional[str] = None
+    inspiredBy: Optional[List] = None
+    laterality: Optional[List] = None
+    visualizedIn: Optional[Any] = None
+
+
+@dataclass
+class PTRegion:
+    field_type: str
+    field_id: str
+    versionIdentifier: str
+    field_context: Optional[VocabModel] = field(
+        default_factory=lambda: {'@vocab': 'https://openminds.ebrains.eu/vocab/'}
+    )
+    hasAnnotation: Optional[HasAnnotation] = None
+    hasParent: Optional[List] = None
+    lookupLabel: Optional[str] = None
+    name: Optional[str] = None
+    ontologyIdentifier: Optional[List[str]] = None
+    relationAssessment: Optional[
+        Union[RelationAssessmentItem, RelationAssessmentItem1]
+    ] = None
+    versionInnovation: Optional[str] = None
+
+
+@dataclass
+class Model:
+    jsonrpc: str = '2.0'
+    method: str = 'sxplr.on.allRegions'
+    params: Optional[List[PTRegion]] = None

siibra/explorer/api/broadcast/atlasSelected/request/__init__.py

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+# generated by datamodel-codegen:
+#   filename:  sxplr.on.atlasSelected__fromSxplr__request.json
+#   timestamp: 2023-12-07T15:40:36+00:00
+
+from __future__ import annotations
+
+from dataclasses import dataclass
+from typing import List, Optional
+
+
+@dataclass
+class SiibraAtIdModel:
+    field_id: str
+
+
+@dataclass
+class PTAtlas:
+    field_type: str
+    field_id: str
+    name: str
+    spaces: List[SiibraAtIdModel]
+    parcellations: List[SiibraAtIdModel]
+    species: str
+
+
+@dataclass
+class Model:
+    jsonrpc: str = '2.0'
+    method: str = 'sxplr.on.atlasSelected'
+    params: Optional[PTAtlas] = None

siibra/explorer/api/broadcast/parcellationSelected/request/__init__.py

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+# generated by datamodel-codegen:
+#   filename:  sxplr.on.parcellationSelected__fromSxplr__request.json
+#   timestamp: 2023-12-07T15:40:36+00:00
+
+from __future__ import annotations
+
+from dataclasses import dataclass, field
+from typing import Any, Dict, List, Optional
+
+
+@dataclass
+class EbrainsDsPerson:
+    field_type: str
+    field_id: str
+    schema_org_shortName: str
+    identifier: str
+    shortName: str
+    name: str
+
+
+@dataclass
+class EbrainsDsUrl:
+    field_type: str
+    url: str
+
+
+@dataclass
+class SiibraAtIdModel:
+    field_id: str
+
+
+@dataclass
+class VocabModel:
+    field_vocab: str
+
+
+@dataclass
+class EbrainsDatasetModel:
+    field_type: str
+    field_id: str
+    name: str
+    urls: List[EbrainsDsUrl]
+    contributors: List[EbrainsDsPerson]
+    custodians: List[EbrainsDsPerson]
+    description: Optional[str] = None
+    ebrains_page: Optional[str] = None
+
+
+@dataclass
+class SiibraParcellationVersionModel:
+    field_type: str
+    name: str
+    deprecated: Optional[bool] = None
+    prev: Optional[SiibraAtIdModel] = None
+    next: Optional[SiibraAtIdModel] = None
+
+
+@dataclass
+class Copyright:
+    holder: List
+    year: str
+    field_context: Optional[VocabModel] = field(
+        default_factory=lambda: {'@vocab': 'https://openminds.ebrains.eu/vocab/'}
+    )
+
+
+@dataclass
+class HasTerminologyVersion:
+    hasEntityVersion: List
+    field_context: Optional[VocabModel] = field(
+        default_factory=lambda: {'@vocab': 'https://openminds.ebrains.eu/vocab/'}
+    )
+    definedIn: Optional[List] = None
+    ontologyIdentifier: Optional[List[str]] = None
+
+
+@dataclass
+class OtherContribution:
+    contributionType: List
+    contributor: Any
+    field_context: Optional[VocabModel] = field(
+        default_factory=lambda: {'@vocab': 'https://openminds.ebrains.eu/vocab/'}
+    )
+
+
+@dataclass
+class BrainAtlasVersionModel:
+    field_type: str
+    field_id: str
+    accessibility: Dict[str, Any]
+    coordinateSpace: Dict[str, Any]
+    fullDocumentation: Dict[str, Any]
+    hasTerminologyVersion: HasTerminologyVersion
+    license: Dict[str, Any]
+    releaseDate: str
+    shortName: str
+    versionIdentifier: str
+    versionInnovation: str
+    field_context: Optional[VocabModel] = field(
+        default_factory=lambda: {'@vocab': 'https://openminds.ebrains.eu/vocab/'}
+    )
+    abbreviation: Optional[str] = None
+    atlasType: Optional[Dict[str, Any]] = None
+    author: Optional[List] = None
+    copyright: Optional[Copyright] = None
+    custodian: Optional[List] = None
+    description: Optional[str] = None
+    digitalIdentifier: Optional[Dict[str, Any]] = None
+    fullName: Optional[str] = None
+    funding: Optional[List] = None
+    homepage: Optional[Dict[str, Any]] = None
+    howToCite: Optional[str] = None
+    isAlternativeVersionOf: Optional[List] = None
+    isNewVersionOf: Optional[Dict[str, Any]] = None
+    keyword: Optional[List] = None
+    ontologyIdentifier: Optional[List[str]] = None
+    otherContribution: Optional[OtherContribution] = None
+    relatedPublication: Optional[List] = None
+    repository: Optional[Dict[str, Any]] = None
+    supportChannel: Optional[List[str]] = None
+
+
+@dataclass
+class PTParcellation:
+    field_type: str
+    field_id: str
+    name: str
+    datasets: List[EbrainsDatasetModel]
+    brainAtlasVersions: List[BrainAtlasVersionModel]
+    modality: Optional[str] = None
+    version: Optional[SiibraParcellationVersionModel] = None
+    shortname: Optional[str] = None
+
+
+@dataclass
+class Model:
+    jsonrpc: str = '2.0'
+    method: str = 'sxplr.on.parcellationSelected'
+    params: Optional[PTParcellation] = None