siibra 1.0.1a0__py3-none-any.whl → 1.0.1a2__py3-none-any.whl

siibra/features/feature.py

@@ -1,4 +1,4 @@
-# Copyright 2018-2024
+# Copyright 2018-2025
 # Institute of Neuroscience and Medicine (INM-1), Forschungszentrum Jülich GmbH
 
 # Licensed under the Apache License, Version 2.0 (the "License");
@@ -14,12 +14,6 @@
 # limitations under the License.
 """Handles multimodal data features and related queries."""
 
-from . import anchor as _anchor
-
-from ..commons import logger, InstanceTable, siibra_tqdm, __version__
-from ..core import concept, space, region, parcellation, structure
-from ..volumes import volume
-
 from typing import Union, TYPE_CHECKING, List, Dict, Type, Tuple, BinaryIO, Any, Iterator
 from hashlib import md5
 from collections import defaultdict
@@ -28,6 +22,11 @@ from abc import ABC, abstractmethod
 from re import sub
 from textwrap import wrap
 
+from . import anchor as _anchor
+from ..commons import logger, InstanceTable, siibra_tqdm, __version__
+from ..core import concept, space, region, parcellation, structure
+from ..volumes import volume
+
 if TYPE_CHECKING:
     from ..retrieval.datasets import EbrainsDataset
     TypeDataset = EbrainsDataset
@@ -53,7 +52,7 @@ _README_TMPL = """
 Downloaded from siibra toolsuite.
 siibra-python version: {version}
 
-All releated resources (e.g. doi, web resources) are categorized under publications.
+All related resources (e.g. doi, web resources) are categorized under publications.
 
 Name
 ----
@@ -130,23 +129,22 @@ class Feature:
         # allows subclasses to implement lazy loading of an anchor
         return self._anchor_cached
 
-    def __init_subclass__(cls, configuration_folder=None, category=None, do_not_index=False, **kwargs):
+    def __init_subclass__(cls, configuration_folder=None, category=None, **kwargs):
 
         # Feature.SUBCLASSES serves as an index where feature class inheritance is cached. When users
         # queries a branch on the hierarchy, all children will also be queried. There are usecases where
         # such behavior is not desired (e.g. ProxyFeature, which wraps livequery features id to capture the
         # query context).
-        # do_not_index flag allow the default index behavior to be toggled off.
-
-        if do_not_index is False:
+        if "ProxyFeature" in cls.__name__:
+            return
 
-            # extend the subclass lists
-            # Iterate over all mro, not just immediate base classes
-            for BaseCls in cls.__mro__:
-                # some base classes may not be sub class of feature, ignore these
-                if not issubclass(BaseCls, Feature):
-                    continue
-                cls._SUBCLASSES[BaseCls].append(cls)
+        # extend the subclass lists
+        # Iterate over all mro, not just immediate base classes
+        for BaseCls in cls.__mro__:
+            # some base classes may not be sub class of feature, ignore these
+            if not issubclass(BaseCls, Feature):
+                continue
+            cls._SUBCLASSES[BaseCls].append(cls)
 
         cls._live_queries = []
         cls._preconfigured_instances = None
@@ -156,6 +154,9 @@ class Feature:
             cls._CATEGORIZED[category].add(cls.__name__, cls)
         return super().__init_subclass__(**kwargs)
 
+    def __repr__(self) -> str:
+        return f"<{self.__class__.__name__}(id='{self.id}', name='{self.name}')>"
+
     @classmethod
     def _get_subclasses(cls):
         return {Cls.__name__: Cls for Cls in cls._SUBCLASSES}
@@ -199,9 +200,9 @@ class Feature:
     @property
     def authors(self):
         return [
-            contributer['name']
+            contributor['name']
             for ds in self.datasets
-            for contributer in ds.contributors
+            for contributor in ds.contributors
         ]
 
     @property
@@ -256,7 +257,7 @@ class Feature:
         concept: Union[structure.BrainStructure, space.Space],
     ) -> bool:
         """
-        Match the features anatomical anchor agains the given query concept.
+        Match the features anatomical anchor against the given query concept.
         Record the most recently matched concept for inspection by the caller.
         """
         # TODO: storing the last matched concept. It is not ideal, might cause problems in multithreading
@@ -509,7 +510,7 @@ class Feature:
         This will
         - call Feature.match(concept) for any registered preconfigured features
         - run any registered live queries
-        The preconfigured and live query instances are merged and returend as a list.
+        The preconfigured and live query instances are merged and returned as a list.
 
         If multiple feature types are given, recurse for each of them.
 
@@ -519,7 +520,7 @@ class Feature:
         concept: AtlasConcept
             An anatomical concept, typically a brain region or parcellation.
         feature_type: subclass of Feature, str
-            specififies the type of features ("modality")
+            specifies the type of features ("modality")
         """
         if isinstance(feature_type, list):
             # a list of feature types is given, collect match results on those
@@ -604,7 +605,7 @@ class Feature:
                 if inst.id == feature_id
             ]
             if len(candidates) == 0:
-                raise NotFoundException(f"No feature instance wth {feature_id} found.")
+                raise NotFoundException(f"No feature instance with {feature_id} found.")
             if len(candidates) == 1:
                 return candidates[0]
             else:
@@ -625,7 +626,9 @@ class Feature:
 
         See docstring of serialize_query_context for further context.
         """
-        class ProxyFeature(feature.__class__, do_not_index=True):
+
+        # if you change the name of this class, change the string in Feature.__init_subclass__
+        class ProxyFeature(feature.__class__):
 
             # override __class__ property
             # some instances of features accesses inst.__class__
@@ -719,7 +722,7 @@ class Compoundable(ABC):
         """
         Compute the merge data and create a merged instance from a set of
         elements of this class. This will be used by CompoundFeature to
-        create the aggegated data and plot it. For example, to compute an
+        create the aggregated data and plot it. For example, to compute an
         average connectivity matrix from a set of subfeatures, we create a
         RegionalConnectivty feature.
         """
@@ -728,7 +731,7 @@ class Compoundable(ABC):
 
 class CompoundFeature(Feature):
     """
-    A compound aggregating mutliple features of the same type, forming its
+    A compound aggregating multiple features of the same type, forming its
     elements. The anatomical anchors and data of the features is merged.
     Features need to subclass "Compoundable" to allow aggregation
     into a compound feature.

siibra/features/image/__init__.py

@@ -1,4 +1,4 @@
-# Copyright 2018-2024
+# Copyright 2018-2025
 # Institute of Neuroscience and Medicine (INM-1), Forschungszentrum Jülich GmbH
 
 # Licensed under the Apache License, Version 2.0 (the "License");
@@ -22,6 +22,8 @@ from .volume_of_interest import (
     XPCTVolumeOfInterest,
     LSFMVolumeOfInterest,
     DTIVolumeOfInterest
-    # SegmentedVolumeOfInterest
 )
-from .sections import CellbodyStainedSection
+from .sections import (
+    CellbodyStainedSection,
+    BigBrain1MicronPatch
+)

siibra/features/image/image.py

@@ -1,4 +1,4 @@
-# Copyright 2018-2024
+# Copyright 2018-2025
 # Institute of Neuroscience and Medicine (INM-1), Forschungszentrum Jülich GmbH
 
 # Licensed under the Apache License, Version 2.0 (the "License");
@@ -14,15 +14,13 @@
 # limitations under the License.
 """Base type of features in volume format and related anatomical anchor."""
 
+from typing import List, TYPE_CHECKING
 from zipfile import ZipFile
-from .. import feature
 
+from .. import feature
 from .. import anchor as _anchor
-
 from ...volumes import volume as _volume
 
-from typing import List, TYPE_CHECKING
-
 if TYPE_CHECKING:
     from ...locations.boundingbox import BoundingBox
     from ...volumes.providers import provider
@@ -44,7 +42,7 @@ class ImageAnchor(_anchor.AnatomicalAnchor):
         if self._location_cached is None:
             self._location_cached = self.volume.get_boundingbox(
                 clip=False
-            )  # use unclipped to preseve exisiting behaviour
+            )  # use unclipped to preserve existing behaviour
         return self._location_cached
 
     @property

siibra/features/image/sections.py

@@ -1,4 +1,4 @@
-# Copyright 2018-2024
+# Copyright 2018-2025
 # Institute of Neuroscience and Medicine (INM-1), Forschungszentrum Jülich GmbH
 
 # Licensed under the Apache License, Version 2.0 (the "License");
@@ -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

@@ -1,4 +1,4 @@
-# Copyright 2018-2024
+# Copyright 2018-2025
 # Institute of Neuroscience and Medicine (INM-1), Forschungszentrum Jülich GmbH
 
 # Licensed under the Apache License, Version 2.0 (the "License");
@@ -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

@@ -1,4 +1,4 @@
-# Copyright 2018-2024
+# Copyright 2018-2025
 # Institute of Neuroscience and Medicine (INM-1), Forschungszentrum Jülich GmbH
 
 # Licensed under the Apache License, Version 2.0 (the "License");
@@ -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

@@ -1,4 +1,4 @@
-# Copyright 2018-2024
+# Copyright 2018-2025
 # Institute of Neuroscience and Medicine (INM-1), Forschungszentrum Jülich GmbH
 
 # Licensed under the Apache License, Version 2.0 (the "License");
@@ -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

@@ -1,4 +1,4 @@
-# Copyright 2018-2024
+# Copyright 2018-2025
 # Institute of Neuroscience and Medicine (INM-1), Forschungszentrum Jülich GmbH
 
 # Licensed under the Apache License, Version 2.0 (the "License");
@@ -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):
@@ -60,7 +59,7 @@ class PolyLine:
         return sum(self.lengths)
 
     def sample(self, d: Union[Iterable[float], np.ndarray, float]):
-        # if d is interable, we assume a list of sample positions
+        # if d is iterable, we assume a list of sample positions
         try:
             iter(d)
         except TypeError:

siibra/features/tabular/cortical_profile.py

@@ -1,4 +1,4 @@
-# Copyright 2018-2024
+# Copyright 2018-2025
 # Institute of Neuroscience and Medicine (INM-1), Forschungszentrum Jülich GmbH
 
 # Licensed under the Apache License, Version 2.0 (the "License");
@@ -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):
@@ -37,7 +37,7 @@ class CorticalProfile(tabular.Tabular, Compoundable):
     Optionally, the depth coordinates of layer boundaries can be specified.
 
     Most attributes are modelled as properties, so dervide classes are able
-    to implement lazy loading instead of direct initialiation.
+    to implement lazy loading instead of direct initialization.
 
     """
 
@@ -151,7 +151,7 @@ class CorticalProfile(tabular.Tabular, Compoundable):
 
     @property
     def _layers(self):
-        """List of layers assigned to each measurments,
+        """List of layers assigned to each measurements,
         if layer boundaries are available for this features.
         """
         if self.boundaries_mapped:

siibra/features/tabular/gene_expression.py

@@ -1,4 +1,4 @@
-# Copyright 2018-2024
+# Copyright 2018-2025
 # Institute of Neuroscience and Medicine (INM-1), Forschungszentrum Jülich GmbH
 
 # Licensed under the Apache License, Version 2.0 (the "License");
@@ -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

@@ -1,4 +1,4 @@
-# Copyright 2018-2024
+# Copyright 2018-2025
 # Institute of Neuroscience and Medicine (INM-1), Forschungszentrum Jülich GmbH
 
 # Licensed under the Apache License, Version 2.0 (the "License");
@@ -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

@@ -1,4 +1,4 @@
-# Copyright 2018-2024
+# Copyright 2018-2025
 # Institute of Neuroscience and Medicine (INM-1), Forschungszentrum Jülich GmbH
 
 # Licensed under the Apache License, Version 2.0 (the "License");
@@ -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

@@ -1,4 +1,4 @@
-# Copyright 2018-2024
+# Copyright 2018-2025
 # Institute of Neuroscience and Medicine (INM-1), Forschungszentrum Jülich GmbH
 
 # Licensed under the Apache License, Version 2.0 (the "License");
@@ -13,17 +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 ... import commons, vocabularies
-from ...retrieval import requests
-
-import pandas as pd
-import numpy as np
 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
+
 
 class ReceptorDensityFingerprint(
     tabular.Tabular,
@@ -34,7 +35,7 @@ class ReceptorDensityFingerprint(
     DESCRIPTION = (
         "Fingerprint of densities (in fmol/mg protein) of receptors for classical neurotransmitters "
         "obtained by means of quantitative in vitro autoradiography. The fingerprint provides average "
-        "density measurments for different receptors measured in tissue samples from different subjects "
+        "density measurements for different receptors measured in tissue samples from different subjects "
         "together with the corresponding standard deviations. "
     )
 
@@ -75,9 +76,9 @@ class ReceptorDensityFingerprint(
         # Likely ill-formed tsv's
         return [
             "{} ({})".format(
-                vocabularies.RECEPTOR_SYMBOLS[t]['neurotransmitter']['label'],
-                vocabularies.RECEPTOR_SYMBOLS[t]['neurotransmitter']['name'],
-            ) if t in vocabularies.RECEPTOR_SYMBOLS else
+                RECEPTOR_SYMBOLS[t]['neurotransmitter']['label'],
+                RECEPTOR_SYMBOLS[t]['neurotransmitter']['name'],
+            ) if t in RECEPTOR_SYMBOLS else
             f"{t} (undeciphered)"
             for t in self.receptors
         ]
@@ -107,7 +108,7 @@ class ReceptorDensityFingerprint(
             std = [data[_]["density (sd)"] for _ in labels]
         except KeyError as e:
             print(str(e))
-            commons.logger.error("Could not parse fingerprint from this dictionary")
+            logger.error("Could not parse fingerprint from this dictionary")
         return {
             'unit': next(iter(units)),
             'labels': labels,
@@ -124,9 +125,11 @@ class ReceptorDensityFingerprint(
         if backend == "matplotlib":
             try:
                 import matplotlib.pyplot as plt
-            except ImportError:
-                commons.logger.error("matplotlib not available. Plotting of fingerprints disabled.")
-                return None
+            except ImportError as e:
+                logger.error(
+                    "matplotlib not available. Please install matplotlib or use or another backend such as plotly."
+                )
+                raise e
             from collections import deque
 
             # default args
@@ -187,6 +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

@@ -1,4 +1,4 @@
-# Copyright 2018-2024
+# Copyright 2018-2025
 # Institute of Neuroscience and Medicine (INM-1), Forschungszentrum Jülich GmbH
 
 # Licensed under the Apache License, Version 2.0 (the "License");
@@ -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