siibra 1.0.1a1__py3-none-any.whl → 1.0.1a2__py3-none-any.whl

siibra/features/image/sections.py

@@ -14,13 +14,92 @@
 # limitations under the License.
 """Multimodal data features in 2D section."""
 
+from typing import TYPE_CHECKING
+
 from . import image
 
+if TYPE_CHECKING:
+    from ...locations import AxisAlignedPatch, Contour
+    from ...features.anchor import AnatomicalAnchor
+
 
 class CellbodyStainedSection(
     image.Image,
-    configuration_folder='features/images/sections/cellbody',
-    category="cellular"
+    configuration_folder="features/images/sections/cellbody",
+    category="cellular",
 ):
     def __init__(self, **kwargs):
         image.Image.__init__(self, **kwargs, modality="cell body staining")
+
+
+class BigBrain1MicronPatch(image.Image, category="cellular"):
+
+    _DESCRIPTION = """Sample approximately orthogonal cortical image patches
+    from BigBrain 1 micron sections, guided by an image volume
+    in a supported reference space providing. The image
+    volume is used as a weighted mask to extract patches
+    along the cortical midsurface with nonzero weights in the
+    input image.
+    An optional lower_threshold can be used to narrow down
+    the search. The weight is stored with the resulting features."""
+
+    def __init__(
+        self,
+        patch: "AxisAlignedPatch",
+        profile: "Contour",
+        section: CellbodyStainedSection,
+        vertex: int,
+        relevance: float,
+        anchor: "AnatomicalAnchor",
+    ):
+        self._patch = patch
+        self._profile = profile
+        self._section = section
+        self.vertex = vertex
+        self.relevance = relevance
+        image.Image.__init__(
+            self,
+            name=f"Cortical patch in {section.name}",
+            modality=section.modality,
+            space_spec=section._space_spec,
+            providers=list(section._providers.values()),
+            region=None,
+            datasets=section.datasets,
+            bbox=patch.boundingbox,
+            id=None,
+        )
+        self._anchor_cached = anchor
+        self._description_cached = self._DESCRIPTION
+
+    def __repr__(self):
+        return (
+            f"<{self.__class__.__name__}(space_spec={self._space_spec}, "
+            f"name='{self.name}', "
+            f"section='{self._section.get_boundingbox().minpoint.bigbrain_section()}', "
+            f"vertex='{self.vertex}', providers={self._providers})>"
+        )
+
+    @property
+    def section(self) -> CellbodyStainedSection:
+        return self._section
+
+    def get_boundingbox(self, **fetch_kwargs):
+        """Enforce that the bounding box spans the full section thickness."""
+        bbox_section = self._section.get_boundingbox(**fetch_kwargs)
+        bbox = self._patch.boundingbox
+        bbox.minpoint[1] = bbox_section.minpoint[1]
+        bbox.maxpoint[1] = bbox_section.maxpoint[1]
+        return bbox
+
+    @property
+    def profile(self) -> "Contour":
+        return self._profile
+
+    @property
+    def bigbrain_section(self):
+        return self.get_boundingbox().minpoint.bigbrain_section()
+
+    def fetch(self, flip: bool = False, resolution_mm: float = -1, **kwargs):
+        assert len(kwargs) == 0
+        p = self._patch.flip() if flip else self._patch
+        return p.extract_volume(self._section, resolution_mm=resolution_mm).fetch()

siibra/features/image/volume_of_interest.py

@@ -78,11 +78,3 @@ class LSFMVolumeOfInterest(
 ):
     def __init__(self, modality, **kwargs):
         image.Image.__init__(self, **kwargs, modality=modality)
-
-# class SegmentedVolumeOfInterest(
-#     image.Image,
-#     configuration_folder="features/images/vois/segmentation",
-#     category="segmentation"
-# ):
-#     def __init__(self, **kwargs):
-#         image.Image.__init__(self, **kwargs, modality="segmentation")

siibra/features/tabular/__init__.py

@@ -15,7 +15,7 @@
 """Multimodal data features in tabular formats."""
 
 from .bigbrain_intensity_profile import BigBrainIntensityProfile
-from .cell_density_profile import CellDensityProfile
+from .cell_density_profile import CellDensityProfile, cell_reader, layer_reader
 from .gene_expression import GeneExpressions
 from .layerwise_bigbrain_intensities import LayerwiseBigBrainIntensities
 from .layerwise_cell_density import LayerwiseCellDensity

siibra/features/tabular/bigbrain_intensity_profile.py

@@ -13,9 +13,10 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
+from typing import List, TYPE_CHECKING
+
 from . import cortical_profile
 
-from typing import List, TYPE_CHECKING
 if TYPE_CHECKING:
     from ...features.anchor import AnatomicalAnchor
 

siibra/features/tabular/cell_density_profile.py

@@ -13,19 +13,18 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
-from . import cortical_profile
-
-from .. import anchor as _anchor
-from ...commons import logger
-from ...retrieval import requests
+from io import BytesIO
+from typing import Union, Tuple, Iterable
 
-from skimage.draw import polygon
-from skimage.transform import resize
 import numpy as np
 import pandas as pd
+from skimage.draw import polygon
+from skimage.transform import resize
 
-from io import BytesIO
-from typing import Union, Tuple, Iterable
+from . import cortical_profile
+from .. import anchor as _anchor
+from ...commons import logger
+from ...retrieval import requests
 
 
 def cell_reader(bytes_buffer: bytes):

siibra/features/tabular/cortical_profile.py

@@ -13,15 +13,15 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
-from . import tabular
-from ..feature import Compoundable
-
-from .. import anchor as _anchor
-
-import pandas as pd
 from typing import Union, Dict, Tuple, List
+
 from textwrap import wrap
 import numpy as np
+import pandas as pd
+
+from . import tabular
+from .. import anchor as _anchor
+from ..feature import Compoundable
 
 
 class CorticalProfile(tabular.Tabular, Compoundable):

siibra/features/tabular/gene_expression.py

@@ -13,11 +13,6 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
-from .. import anchor as _anchor
-from . import tabular
-from ...retrieval.datasets import GenericDataset
-
-import pandas as pd
 from textwrap import wrap
 from typing import List
 try:
@@ -25,6 +20,12 @@ try:
 except ImportError:
     from typing_extensions import TypedDict
 
+import pandas as pd
+
+from . import tabular
+from .. import anchor as _anchor
+from ...retrieval.datasets import GenericDataset
+
 
 class GeneExpressions(
     tabular.Tabular,

siibra/features/tabular/layerwise_bigbrain_intensities.py

@@ -13,13 +13,14 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
-from . import cortical_profile
-from . import tabular
+from typing import TYPE_CHECKING
 
 import pandas as pd
 import numpy as np
 
-from typing import TYPE_CHECKING
+from . import tabular
+from . import cortical_profile
+
 if TYPE_CHECKING:
     from ...features.anchor import AnatomicalAnchor
 

siibra/features/tabular/layerwise_cell_density.py

@@ -13,17 +13,15 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
+import numpy as np
+import pandas as pd
+
 from . import cortical_profile
+from . import tabular, cell_reader, layer_reader
 from .. import anchor as _anchor
-from . import tabular
-from ..tabular.cell_density_profile import cell_reader, layer_reader
-
 from ... import commons
 from ...retrieval import requests
 
-import pandas as pd
-import numpy as np
-
 
 class LayerwiseCellDensity(
     tabular.Tabular,

siibra/features/tabular/receptor_density_fingerprint.py

@@ -13,18 +13,18 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
-from .. import anchor as _anchor
-from . import tabular
+from textwrap import wrap
+from typing import List
+
+import numpy as np
+import pandas as pd
 
+from . import tabular
+from .. import anchor as _anchor
 from ...commons import logger
 from ...vocabularies import RECEPTOR_SYMBOLS
 from ...retrieval import requests
 
-import pandas as pd
-import numpy as np
-from textwrap import wrap
-from typing import List
-
 
 class ReceptorDensityFingerprint(
     tabular.Tabular,
@@ -190,6 +190,31 @@ class ReceptorDensityFingerprint(
         else:
             raise NotImplementedError
 
-    def plot(self, *args, **kwargs):
+    def plot(
+        self,
+        *args,
+        receptors: List[str] = None,
+        backend: str = "matplotlib",
+        **kwargs
+    ):
+        """
+        Create a bar plot of receptor density fingerprint.
+
+        Parameters
+        ----------
+        receptors : List[str], optional
+            Plot a subset of receptors.
+        backend: str
+            "matplotlib", "plotly", or others supported by pandas DataFrame
+            plotting backend.
+        **kwargs
+            takes Matplotlib.pyplot keyword arguments
+        """
         kwargs['xlabel'] = ""
-        return super().plot(*args, **kwargs)
+        kwargs["backend"] = backend
+        og_data = self.data
+        if receptors is not None:
+            self._data_cached = og_data.loc[receptors]
+        fig = super().plot(*args, **kwargs)
+        self._data_cached = og_data
+        return fig

siibra/features/tabular/receptor_density_profile.py

@@ -13,9 +13,8 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
-from .. import anchor as _anchor
 from . import cortical_profile
-
+from .. import anchor as _anchor
 from ... import vocabularies
 from ...commons import create_key
 from ...retrieval import requests

siibra/features/tabular/regional_timeseries_activity.py

@@ -13,19 +13,19 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
+from typing import Callable, List, Union
+
+import numpy as np
+import pandas as pd
+
 from . import tabular
+from .. import anchor as _anchor
 from ..feature import Compoundable
-
 from ...core import region as _region
-from .. import anchor as _anchor
 from ...commons import QUIET, siibra_tqdm
 from ...locations import pointcloud
-from ...retrieval.repositories import RepositoryConnector
 from ...retrieval.requests import HttpRequest
-
-from typing import Callable, List, Union
-import pandas as pd
-import numpy as np
+from ...retrieval.repositories import RepositoryConnector
 
 
 class RegionalTimeseriesActivity(tabular.Tabular, Compoundable):

siibra/features/tabular/tabular.py

@@ -15,15 +15,14 @@
 """Base type of features in tabular formats."""
 
 from zipfile import ZipFile
-from .. import feature
-
-from .. import anchor as _anchor
-
-from ...commons import logger
 
 import pandas as pd
 from textwrap import wrap
 
+from .. import feature
+from .. import anchor as _anchor
+from ...commons import logger
+
 
 class Tabular(feature.Feature):
     """

siibra/livequeries/allen.py

@@ -14,21 +14,21 @@
 # limitations under the License.
 """Query Allen Human Brain Atlas microarray data in specified volume."""
 
-from .query import LiveQuery
+from typing import List
+from xml.etree import ElementTree
+import json
 
-from ..core import space as _space, structure
+import numpy as np
+
+from . import query as _query
+from ..core import structure
 from ..features import anchor as _anchor
 from ..features.tabular.gene_expression import GeneExpressions
 from ..commons import logger, Species
-from ..locations import point, pointcloud
+from ..locations import pointcloud
 from ..retrieval import HttpRequest
 from ..vocabularies import GENE_NAMES
 
-from typing import List
-from xml.etree import ElementTree
-import numpy as np
-import json
-
 
 BASE_URL = "http://api.brain-map.org/api/v2/data"
 
@@ -51,7 +51,7 @@ class InvalidAllenAPIResponseException(Exception):
     pass
 
 
-class AllenBrainAtlasQuery(LiveQuery, args=['gene'], FeatureType=GeneExpressions):
+class AllenBrainAtlasQuery(_query.LiveQuery, args=['gene'], FeatureType=GeneExpressions):
     """
     Interface to Allen Human Brain Atlas microarray data.
 
@@ -117,7 +117,7 @@ class AllenBrainAtlasQuery(LiveQuery, args=['gene'], FeatureType=GeneExpressions
         will be tested against the region mask in ICBM space
         to produce a table of outputs.
         """
-        LiveQuery.__init__(self, **kwargs)
+        _query.LiveQuery.__init__(self, **kwargs)
         gene = kwargs.get('gene')
 
         def parse_gene(spec):
@@ -144,27 +144,25 @@ class AllenBrainAtlasQuery(LiveQuery, args=['gene'], FeatureType=GeneExpressions
                 'https://github.com/FZJ-INM1-BDA/siibra-python/issues/636.'
             )
 
-        mnispace = _space.Space.registry().get('mni152')
-
         # Match the microarray probes to the query mask.
         # Record matched instances and their locations.
-        measurements = []
-        coordinates = []
-        for measurement in self:
-            pt = point.Point(measurement['mni_xyz'], space=mnispace, sigma_mm=LOCATION_PRECISION_MM)
-            if pt in concept:
-                measurements.append(measurement)
-                coordinates.append(pt)
-
-        if len(coordinates) == 0:
+        all_measurements = list(self)
+        all_mes_points = pointcloud.PointCloud(
+            [measurement['mni_xyz'] for measurement in all_measurements],
+            space='mni152',
+            sigma_mm=LOCATION_PRECISION_MM
+        )
+        intersecting_points = concept.intersection(all_mes_points)
+        if intersecting_points is None:
             logger.info(f"No probes found that lie within {concept}")
             return []
+        measurements = [all_measurements[index] for index in intersecting_points.labels]
 
         # Build the anatomical anchor and assignment to the query concept.
         # It will be attached to the returned feature, with the set of matched
         # MNI coordinates as anchor's location.
         anchor = _anchor.AnatomicalAnchor(
-            location=pointcloud.from_points(coordinates),
+            location=intersecting_points,
             species=self.species
         )
         explanation = f"MNI coordinates of tissue samples were filtered using {concept}"