def get_regional_map_info(atlas_id: str,
parcellation_id: str,
region_id: str,
space_id: Optional[str] = None):
"""
Returns information about a regional map for given region name.
"""
validate_and_return_atlas(atlas_id)
parcellation = validate_and_return_parcellation(parcellation_id)
region = validate_and_return_region(region_id, parcellation)
region.get_regional_map("mni152", siibra.MapType.CONTINUOUS)
roi, space_of_interest = parse_region_selection(atlas_id, parcellation_id,
region_id, space_id)
query_id = f'{atlas_id}{parcellation_id}{roi.name}{space_id}'
cached_fullpath = get_path_to_regional_map(query_id, roi,
space_of_interest)
import nibabel as nib
import numpy as np
nii = nib.load(cached_fullpath)
data = nii.get_fdata()
return {
'min': np.min(data),
'max': np.max(data),
}
def get_parcellation_by_id(atlas_id: str, parcellation_id: str,
request: Request):
"""
Returns one parcellation for given id.
"""
atlas = validate_and_return_atlas(atlas_id)
parcellation = validate_and_return_parcellation(parcellation_id,
atlas=atlas)
result = __parcellation_result_info(parcellation, atlas_id, request)
return jsonable_encoder(result, custom_encoder=siibra_custom_json_encoder)
def get_global_features_rest(atlas_id: str, parcellation_id: str,
request: Request):
"""
Returns all global features for a parcellation.
"""
validate_and_return_atlas(atlas_id)
validate_and_return_parcellation(parcellation_id)
result = {
'features': [
{
m.modality():
'{}atlases/{}/parcellations/{}/features/{}'.format(
get_base_url_from_request(request),
atlas_id.replace('/', '%2F'),
parcellation_id.replace('/', '%2F'), m.modality())
} for m in siibra.features.
modalities # TODO siibra.get_features(parcellation, 'all') - too slow at the moment
]
}
return jsonable_encoder(result)
def get_all_regions_for_parcellation_id(atlas_id: str,
parcellation_id: str,
space_id: Optional[str] = None):
"""
Returns all regions for a given parcellation id.
"""
parcellation = validate_and_return_parcellation(parcellation_id)
if not space_id is None:
space = validate_and_return_space(space_id)
else:
space = None
return [
region_encoder(region, space=space)
for region in parcellation.regiontree.children
]
def parse_region_selection(atlas_id: str, parcellation_id: str, region_id: str,
space_id: str):
if space_id is None:
raise HTTPException(
status_code=400,
detail='space_id is required for this functionality')
space_of_interest = validate_and_return_space(space_id)
validate_and_return_atlas(atlas_id)
parcellation = validate_and_return_parcellation(parcellation_id)
region = validate_and_return_region(region_id, parcellation)
if region is None:
raise HTTPException(status_code=404,
detail=f'cannot find region with spec {region_id}')
# if len(region) > 1:
# raise HTTPException(
# status_code=400,
# detail=f'found multiple region withs pec {region_id}')
return region, space_of_interest
def get_all_features_for_region(request: Request, atlas_id: str,
parcellation_id: str, region_id: str):
"""
Returns all regional features for a region.
"""
validate_and_return_atlas(atlas_id)
parcellation = validate_and_return_parcellation(parcellation_id)
region = validate_and_return_region(region_id, parcellation)
result = {
'features': [{
m:
'{}atlases/{}/parcellations/{}/regions/{}/features/{}'.format(
get_base_url_from_request(request),
atlas_id.replace('/', '%2F'),
parcellation_id.replace('/', '%2F'),
region_id.replace('/', '%2F'), m)
} for m in siibra.get_features(region, 'all')]
}
return jsonable_encoder(result)
def get_spatial_features(atlas_id,
space_id,
modality_id,
feature_id=None,
detail=False,
parc_id=None,
region_id=None):
if modality_id not in siibra.features.modalities:
raise HTTPException(status_code=400,
detail=f'{modality_id} is not a valid modality')
# TODO: Why only spatial features
if not issubclass(
# feature_classes[modality_id],
# feature_export.SpatialFeature):
siibra.features.modalities[modality_id]._FEATURETYPE,
siibra.features.feature.SpatialFeature):
# modality_id is not a global feature, return empty array
return []
atlas = validate_and_return_atlas(atlas_id)
space_of_interest = validate_and_return_space(space_id, atlas)
# TODO not working at the moment. Space_of_interest is never in atlas.spaces
# if space_of_interest not in atlas.spaces:
# raise HTTPException(404, detail=f'space {space_id} not in atlas {atlas}')
# TODO: No Selection of parcellation and region is needed - TODO: How to provide parcellation/region
if parc_id is None:
raise HTTPException(status_code=400, detail='Parc id is needed')
parc = validate_and_return_parcellation(parc_id, atlas)
roi = validate_and_return_region(region_id, parc)
logger.debug(
f'get_spatial_features: {str(atlas)}, {str(space_of_interest)}, {str(parc)}, {str(roi)}'
)
try:
# spatial_features=atlas.get_features(modality_id)
spatial_features = siibra.get_features(roi,
modality_id,
space=space_of_interest)
except Exception as e:
logger.warn(e, str(space_of_interest), space_id)
raise HTTPException(404, detail=f'Could not get spatial features.')
shaped_features = None
if siibra.features.modalities[
modality_id] == siibra.features.ieeg.IEEG_SessionQuery:
shaped_features = [{
'summary': {
'@id': hashlib.md5(str(feat).encode("utf-8")).hexdigest(),
'name': f'{feat.dataset.name} sub:{feat.sub_id}',
'description': str(feat.dataset.description),
'origin_datainfos': [{
'urls': feat.dataset.urls
}]
},
'get_detail':
lambda ft: get_ieeg_session_detail(ft,
region=roi,
parcellation=parc,
space=space_of_interest,
atlas=atlas),
'instance':
feat
} for feat in spatial_features]
if shaped_features is None:
raise HTTPException(501, detail=f'{modality_id} not yet implemented')
if feature_id is not None:
shaped_features = [
f for f in shaped_features if f['summary']['@id'] == feature_id
]
return [{
**f['summary'],
**(f['get_detail'](f['instance']) if detail else {}),
} for f in shaped_features]
def get_regional_feature(atlas_id,
parcellation_id,
region_id,
modality_id,
detail=True,
feature_id=None,
gene=None):
if not siibra.modalities.provides(modality_id): #feature_classes:
# modality_id not found in feature_classes
raise HTTPException(status_code=400,
detail=f'{modality_id} is not a valid modality')
# TODO - check for subclass
# if not issubclass(
# feature_classes[modality_id],
# feature_export.RegionalFeature):
# # modality_id is not a global feature, return empty array
# return []
atlas = validate_and_return_atlas(atlas_id)
parcellation = validate_and_return_parcellation(parcellation_id)
# region = atlas.get_region(region_id, parcellation)
region = validate_and_return_region(region_id, parcellation)
# TODO: validate region
# raise HTTPException(status_code=404,
# detail=f'Region with id {region_id} not found!')
try:
got_features = siibra.get_features(region, modality_id)
except:
raise HTTPException(
status_code=500,
detail=f'Could not get features for region with id {region_id}')
shaped_features = None
if siibra.features.modalities[
modality_id] == siibra.features.ebrains.EbrainsRegionalFeatureQuery:
shaped_features = [{
'summary': {
'@id': kg_rf_f.id,
'src_name': kg_rf_f.name,
},
'get_detail': lambda kg_rf_f: {
'__detail': kg_rf_f.detail
},
'instance': kg_rf_f,
} for kg_rf_f in got_features]
if siibra.features.modalities[
modality_id] == siibra.features.genes.AllenBrainAtlasQuery:
shaped_features = [{
'summary': {
'@id': hashlib.md5(str(gene_feat).encode("utf-8")).hexdigest(),
},
'get_detail': lambda gene_feat: {
'__donor_info': gene_feat.donor_info,
'__gene': gene_feat.gene,
'__probe_ids': gene_feat.probe_ids,
'__mri_coord': gene_feat.mri_coord,
'__z_scores': gene_feat.z_scores,
'__expression_levels': gene_feat.expression_levels
},
'instance': gene_feat,
} for gene_feat in got_features]
if siibra.features.modalities[
modality_id] == siibra.features.connectivity.ConnectivityProfileQuery:
shaped_features = [
{
'summary': {
"@id": conn_pr._matrix.id,
"src_name": conn_pr.name,
"src_info": conn_pr.description,
"kgSchema": conn_pr._matrix.type_id,
"kgId": conn_pr._matrix.id,
},
'get_detail': lambda conn_pr: {
"__column_names": list(conn_pr.regionnames
), #TODO: where to get the names?
"__profile": conn_pr.profile.tolist(),
},
'instance': conn_pr,
} for conn_pr in got_features
]
if siibra.features.modalities[
modality_id] == siibra.features.receptors.ReceptorQuery:
shaped_features = [
{
'summary': {
"@id":
receptor_pr.name,
"name":
receptor_pr.name,
"info":
receptor_pr.info,
"origin_datainfos": [{
'name': receptor_pr.name,
'description': receptor_pr.info,
'urls': [{
'doi': receptor_pr.url
}]
}]
},
'get_detail': lambda receptor_pr: {
"__receptor_symbols": siibra.features.receptors.
RECEPTOR_SYMBOLS,
"__files": [
], #receptor_pr.files, # TODO where to get files
"__data": {
"__profiles": receptor_pr.profiles,
"__autoradiographs": {
key: {
"content_type":
"application/octet-stream",
"content_encoding":
"gzip; base64",
"x-width":
np.transpose(value, axes=[1, 0, 2]).shape[0],
"x-height":
np.transpose(value, axes=[1, 0, 2]).shape[1],
"x-channel":
np.transpose(value, axes=[1, 0, 2]).shape[2],
"content":
base64.b64encode(
zlib.compress(
np.transpose(value, axes=[1, 0, 2]).
tobytes(order="F"))),
}
for key, value in receptor_pr.autoradiographs.
items()
},
"__fingerprint": receptor_pr.fingerprint,
# "__profile_unit": receptor_pr.profile_unit, TODO check where to get units
},
},
'instance': receptor_pr,
} for receptor_pr in got_features
]
if siibra.features.modalities[
modality_id] == siibra.features.cells.RegionalCellDensityExtractor:
shaped_features = [{
'summary': {
"@id": '...',
'regionspec': conn_pr.regionspec,
'species': conn_pr.species,
'cells': conn_pr.cells.to_dict(),
'section': conn_pr.section,
'patch': conn_pr.patch
},
'get_detail': lambda conn_pr: {
'regionspec': conn_pr.regionspec,
'species': conn_pr.species,
'cells': conn_pr.cells.to_dict(),
'section': conn_pr.section,
'patch': conn_pr.patch
},
'instance': conn_pr,
} for conn_pr in got_features]
if shaped_features is None:
raise HTTPException(
status_code=501,
detail=f'feature {modality_id} has not yet been implmented')
if feature_id is not None:
shaped_features = [
f for f in shaped_features if f['summary']['@id'] == feature_id
]
return [{
**f['summary'],
**(f['get_detail'](f['instance']) if detail else {})
} for f in shaped_features]