siibra 0.5a2__py3-none-any.whl → 1.0.0a1__py3-none-any.whl

siibra/features/tabular/gene_expression.py

@@ -1,4 +1,4 @@
-# Copyright 2018-2021
+# Copyright 2018-2024
 # Institute of Neuroscience and Medicine (INM-1), Forschungszentrum Jülich GmbH
 
 # Licensed under the Apache License, Version 2.0 (the "License");
@@ -15,6 +15,7 @@
 
 from .. import anchor as _anchor
 from . import tabular
+from ...retrieval.datasets import GenericDataset
 
 import pandas as pd
 from textwrap import wrap
@@ -46,6 +47,114 @@ class GeneExpressions(
     as specified at https://alleninstitute.org/legal/terms-use/.
     """
 
+    DATASET = GenericDataset(
+        name="An anatomically comprehensive atlas of the adult human brain transcriptome",
+        contributors=[
+            'Michael J. Hawrylycz',
+            'Ed S. Lein',
+            'Angela L. Guillozet-Bongaarts',
+            'Elaine H. Shen',
+            'Lydia Ng',
+            'Jeremy A. Miller',
+            'Louie N. van de Lagemaat',
+            'Kimberly A. Smith',
+            'Amanda Ebbert',
+            'Zackery L. Riley',
+            'Chris Abajian',
+            'Christian F. Beckmann',
+            'Amy Bernard',
+            'Darren Bertagnolli',
+            'Andrew F. Boe',
+            'Preston M. Cartagena',
+            'M. Mallar Chakravarty',
+            'Mike Chapin',
+            'Jimmy Chong',
+            'Rachel A. Dalley',
+            'Barry David Daly',
+            'Chinh Dang',
+            'Suvro Datta',
+            'Nick Dee',
+            'Tim A. Dolbeare',
+            'Vance Faber',
+            'David Feng',
+            'David R. Fowler',
+            'Jeff Goldy',
+            'Benjamin W. Gregor',
+            'Zeb Haradon',
+            'David R. Haynor',
+            'John G. Hohmann',
+            'Steve Horvath',
+            'Robert E. Howard',
+            'Andreas Jeromin',
+            'Jayson M. Jochim',
+            'Marty Kinnunen',
+            'Christopher Lau',
+            'Evan T. Lazarz',
+            'Changkyu Lee',
+            'Tracy A. Lemon',
+            'Ling Li',
+            'Yang Li',
+            'John A. Morris',
+            'Caroline C. Overly',
+            'Patrick D. Parker',
+            'Sheana E. Parry',
+            'Melissa Reding',
+            'Joshua J. Royall',
+            'Jay Schulkin',
+            'Pedro Adolfo Sequeira',
+            'Clifford R. Slaughterbeck',
+            'Simon C. Smith',
+            'Andy J. Sodt',
+            'Susan M. Sunkin',
+            'Beryl E. Swanson',
+            'Marquis P. Vawter',
+            'Derric Williams',
+            'Paul Wohnoutka',
+            'H. Ronald Zielke',
+            'Daniel H. Geschwind',
+            'Patrick R. Hof',
+            'Stephen M. Smith',
+            'Christof Koch',
+            'Seth G. N. Grant',
+            'Allan R. Jones'
+        ],
+        url="https://doi.org/10.1038%2Fnature11405",
+        description='Neuroanatomically precise, genome-wide maps of transcript '
+            'distributions are critical resources to complement genomic '
+            'sequence data and to correlate functional and genetic brain '
+            'architecture. Here we describe the generation and analysis '
+            'of a transcriptional atlas of the adult human brain, '
+            'comprising extensive histological analysis and comprehensive '
+            'microarray profiling of ~900 neuroanatomically precise '
+            'subdivisions in two individuals. Transcriptional regulation '
+            'varies enormously by anatomical location, with different '
+            'regions and their constituent cell types displaying robust '
+            'molecular signatures that are highly conserved between '
+            'individuals. Analysis of differential gene expression and '
+            'gene co-expression relationships demonstrates that brain-'
+            'wide variation strongly reflects the distributions of major '
+            'cell classes such as neurons, oligodendrocytes, astrocytes '
+            'and microglia. Local neighbourhood relationships between '
+            'fine anatomical subdivisions are associated with discrete '
+            'neuronal subtypes and genes involved with synaptic '
+            'transmission. The neocortex displays a relatively '
+            'homogeneous transcriptional pattern, but with distinct '
+            'features associated selectively with primary sensorimotor '
+            'cortices and with enriched frontal lobe expression. Notably, '
+            'the spatial topography of the neocortex is strongly '
+            'reflected in its molecular topography— the closer two '
+            'cortical regions, the more similar their transcriptomes. '
+            'This freely accessible online data resource forms a high-'
+            'resolution transcriptional baseline for neurogenetic studies '
+            'of normal and abnormal human brain function.'
+            ""
+            "For retrieving microarray data, siibra connects to the web API of "
+            "the Allen Brain Atlas (© 2015 Allen Institute for Brain Science), "
+            "available from https://brain-map.org/api/index.html. Any use of the "
+            "microarray data needs to be in accordance with their terms of use, "
+            "as specified at https://alleninstitute.org/legal/terms-use/."
+    )
+
     class _DonorDict(TypedDict):
         id: int
         name: str
@@ -66,7 +175,7 @@ class GeneExpressions(
         genes: List[str],
         additional_columns: dict,
         anchor: _anchor.AnatomicalAnchor,
-        datasets: List = []
+        datasets: List = [DATASET]
     ):
         """
         Construct gene expression table.
@@ -130,15 +239,17 @@ class GeneExpressions(
         """
         wrapwidth = kwargs.pop("textwrap") if "textwrap" in kwargs else 40
         kwargs["title"] = kwargs.pop("title", None) \
-            or "\n".join(wrap(f"{self.modality} measured in {self.anchor._regionspec}", wrapwidth))
+            or "\n".join(wrap(f"{self.modality} measured in {self.anchor._regionspec or self.anchor.location}", wrapwidth))
         kwargs["kind"] = "box"
         if backend == "matplotlib":
             for arg in ['yerr', 'y', 'ylabel', 'xlabel', 'width']:
                 assert arg not in kwargs
-            passed_kwarg = {
-                "grid": True, "legend": False, 'by': "gene", 'column': ['level'], 'showfliers': False, 'ax': None, **kwargs
+            default_kwargs = {
+                "grid": True, "legend": False, 'by': "gene",
+                'column': ['level'], 'showfliers': False, 'ax': None,
+                'ylabel': 'expression level'
             }
-            return self.data.plot(*args, **passed_kwarg, backend=backend)
+            return self.data.plot(*args, **{**default_kwargs, **kwargs}, backend=backend)
         elif backend == "plotly":
             kwargs["title"] = kwargs["title"].replace('\n', "<br>")
             return self.data.plot(y='level', x='gene', backend=backend, **kwargs)

siibra/features/tabular/layerwise_bigbrain_intensities.py

@@ -1,4 +1,4 @@
-# Copyright 2018-2021
+# Copyright 2018-2024
 # Institute of Neuroscience and Medicine (INM-1), Forschungszentrum Jülich GmbH
 
 # Licensed under the Apache License, Version 2.0 (the "License");
@@ -19,6 +19,10 @@ from . import tabular
 import pandas as pd
 import numpy as np
 
+from typing import TYPE_CHECKING
+if TYPE_CHECKING:
+    from ...features.anchor import AnatomicalAnchor
+
 
 class LayerwiseBigBrainIntensities(
     tabular.Tabular,
@@ -31,7 +35,7 @@ class LayerwiseBigBrainIntensities(
         "'Wagstyl, K., et al (2020). BigBrain 3D atlas of "
         "cortical layers: Cortical and laminar thickness gradients diverge in sensory and "
         "motor cortices. PLoS Biology, 18(4), e3000678. "
-        "http://dx.doi.org/10.1371/journal.pbio.3000678'."
+        "http://dx.doi.org/10.1371/journal.pbio.3000678."
         "The data is taken from the tutorial at "
         "https://github.com/kwagstyl/cortical_layers_tutorial. Each vertex is "
         "assigned to the regional map when queried."
@@ -39,16 +43,10 @@ class LayerwiseBigBrainIntensities(
 
     def __init__(
         self,
-        regionname: str,
+        anchor: "AnatomicalAnchor",
         means: list,
         stds: list,
     ):
-
-        from ..anchor import AnatomicalAnchor
-        anchor = AnatomicalAnchor(
-            region=regionname,
-            species='Homo sapiens'
-        )
         data = pd.DataFrame(
             np.array([means, stds]).T,
             columns=['mean', 'std'],

siibra/features/tabular/layerwise_cell_density.py

@@ -1,4 +1,4 @@
-# Copyright 2018-2021
+# Copyright 2018-2024
 # Institute of Neuroscience and Medicine (INM-1), Forschungszentrum Jülich GmbH
 
 # Licensed under the Apache License, Version 2.0 (the "License");
@@ -16,13 +16,13 @@
 from . import cortical_profile
 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
-from io import BytesIO
 
 
 class LayerwiseCellDensity(
@@ -40,22 +40,14 @@ class LayerwiseCellDensity(
         "The cortical depth is estimated from the measured layer thicknesses."
     )
 
-    @classmethod
-    def CELL_READER(cls, b):
-        return pd.read_csv(BytesIO(b[2:]), delimiter=" ", header=0).astype(
-            {"layer": int, "label": int}
-        )
-
-    @classmethod
-    def LAYER_READER(cls, b):
-        return pd.read_csv(BytesIO(b[2:]), delimiter=" ", header=0, index_col=0)
-
     def __init__(
         self,
         segmentfiles: list,
         layerfiles: list,
         anchor: _anchor.AnatomicalAnchor,
         datasets: list = [],
+        id: str = None,
+        prerelease: bool = False,
     ):
         tabular.Tabular.__init__(
             self,
@@ -63,7 +55,9 @@ class LayerwiseCellDensity(
             modality="Cell body density",
             anchor=anchor,
             datasets=datasets,
-            data=None  # lazy loading below
+            data=None,  # lazy loading below
+            id=id,
+            prerelease=prerelease,
         )
         self.unit = "# detected cells/0.1mm3"
         self._filepairs = list(zip(segmentfiles, layerfiles))
@@ -73,8 +67,8 @@ class LayerwiseCellDensity(
         density_dict = {}
         for i, (cellfile, layerfile) in enumerate(self._filepairs):
             try:
-                cells = requests.HttpRequest(cellfile, func=self.CELL_READER).data
-                layers = requests.HttpRequest(layerfile, func=self.LAYER_READER).data
+                cells = requests.HttpRequest(cellfile, func=cell_reader).data
+                layers = requests.HttpRequest(layerfile, func=layer_reader).data
             except requests.SiibraHttpRequestError as e:
                 print(str(e))
                 commons.logger.error(f"Skipping to bootstrap a {self.__class__.__name__} feature, cannot access file resource.")
@@ -99,12 +93,3 @@ class LayerwiseCellDensity(
             )
             self._data_cached.index.name = 'layer'
         return self._data_cached
-
-    @property
-    def key(self):
-        assert len(self.species) == 1
-        return commons.create_key("{}_{}_{}".format(
-            self.dataset_id,
-            self.species[0]['name'],
-            self.regionspec
-        ))

siibra/features/tabular/receptor_density_fingerprint.py

@@ -1,4 +1,4 @@
-# Copyright 2018-2021
+# Copyright 2018-2024
 # Institute of Neuroscience and Medicine (INM-1), Forschungszentrum Jülich GmbH
 
 # Licensed under the Apache License, Version 2.0 (the "License");
@@ -42,7 +42,9 @@ class ReceptorDensityFingerprint(
         self,
         tsvfile: str,
         anchor: _anchor.AnatomicalAnchor,
-        datasets: list = []
+        datasets: list = [],
+        id: str = None,
+        prerelease: bool = False,
     ):
         """ Generate a receptor fingerprint from a URL to a .tsv file
         formatted according to the structure used by Palomero-Gallagher et al.
@@ -54,6 +56,8 @@ class ReceptorDensityFingerprint(
             anchor=anchor,
             data=None,  # lazy loading below
             datasets=datasets,
+            id=id,
+            prerelease=prerelease,
         )
         self._loader = requests.HttpRequest(tsvfile)
 
@@ -170,10 +174,11 @@ class ReceptorDensityFingerprint(
                             self.data["mean"] + self.data["std"]
                         ]
                     ),
-                    "cat":
-                        len(self.data) * ["mean"] +\
-                        len(self.data) * ["mean - std"] +\
-                        len(self.data) * ["mean + std"]
+                    "cat": (
+                        len(self.data) * ["mean"]
+                        + len(self.data) * ["mean - std"]
+                        + len(self.data) * ["mean + std"]
+                    )
                 }
             )
             return line_polar(

siibra/features/tabular/receptor_density_profile.py

@@ -1,4 +1,4 @@
-# Copyright 2018-2021
+# Copyright 2018-2024
 # Institute of Neuroscience and Medicine (INM-1), Forschungszentrum Jülich GmbH
 
 # Licensed under the Apache License, Version 2.0 (the "License");
@@ -41,7 +41,9 @@ class ReceptorDensityProfile(
         receptor: str,
         tsvfile: str,
         anchor: _anchor.AnatomicalAnchor,
-        datasets: list = []
+        datasets: list = [],
+        id: str = None,
+        prerelease: bool = False,
     ):
         """Generate a receptor density profile from a URL to a .tsv file
         formatted according to the structure used by Palomero-Gallagher et al.
@@ -52,8 +54,10 @@ class ReceptorDensityProfile(
             modality="Receptor density",
             anchor=anchor,
             datasets=datasets,
+            id=id,
+            prerelease=prerelease
         )
-        self.type = receptor
+        self.receptor = receptor
         self._data_cached = None
         self._loader = requests.HttpRequest(tsvfile)
         self._unit_cached = None
@@ -65,25 +69,18 @@ class ReceptorDensityProfile(
             self.id,
             create_key(self.species_name),
             create_key(self.regionspec),
-            create_key(self.type)
+            create_key(self.receptor)
         )
 
     @property
-    def receptor(self):
-        return "{} ({})".format(
-            self.type,
-            vocabularies.RECEPTOR_SYMBOLS[self.type]['receptor']['name'],
-        )
-
-    @property
-    def name(self):
-        return super().name + f" for {self.type}"
+    def receptor_fullname(self):
+        return vocabularies.RECEPTOR_SYMBOLS[self.receptor]['receptor']['name']
 
     @property
     def neurotransmitter(self):
         return "{} ({})".format(
-            vocabularies.RECEPTOR_SYMBOLS[self.type]['neurotransmitter']['label'],
-            vocabularies.RECEPTOR_SYMBOLS[self.type]['neurotransmitter']['name'],
+            vocabularies.RECEPTOR_SYMBOLS[self.receptor]['neurotransmitter']['label'],
+            vocabularies.RECEPTOR_SYMBOLS[self.receptor]['neurotransmitter']['name'],
         )
 
     @property

siibra/features/tabular/regional_timeseries_activity.py

@@ -1,4 +1,4 @@
-# Copyright 2018-2021
+# Copyright 2018-2024
 # Institute of Neuroscience and Medicine (INM-1), Forschungszentrum Jülich GmbH
 
 # Licensed under the Apache License, Version 2.0 (the "License");
@@ -16,13 +16,14 @@
 from . import tabular
 from ..feature import Compoundable
 
+from ...core import region as _region
 from .. import anchor as _anchor
-from ...commons import QUIET
-from ...locations import pointset
+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
+from typing import Callable, List, Union
 import pandas as pd
 import numpy as np
 
@@ -47,7 +48,9 @@ class RegionalTimeseriesActivity(tabular.Tabular, Compoundable):
         timestep: str,
         description: str = "",
         datasets: list = [],
-        subject: str = "average"
+        subject: str = "average",
+        id: str = None,
+        prerelease: bool = False,
     ):
         """
         """
@@ -57,7 +60,9 @@ class RegionalTimeseriesActivity(tabular.Tabular, Compoundable):
             description=description,
             anchor=anchor,
             datasets=datasets,
-            data=None  # lazy loading below
+            data=None,  # lazy loading below
+            id=id,
+            prerelease=prerelease,
         )
         self.cohort = cohort.upper()
         if isinstance(connector, str) and connector:
@@ -74,12 +79,12 @@ class RegionalTimeseriesActivity(tabular.Tabular, Compoundable):
 
     @property
     def subject(self):
-        """Returns the subject identifiers for which the matrix represents."""
+        """Returns the subject identifiers for which the table represents."""
         return self._subject
 
     @property
     def name(self):
-        return f"{super().name} with cohort {self.cohort} - subject {self.subject}"
+        return f"{self.subject} - " + super().name + f" cohort: {self.cohort}"
 
     @property
     def data(self) -> pd.DataFrame:
@@ -90,16 +95,61 @@ class RegionalTimeseriesActivity(tabular.Tabular, Compoundable):
             self._load_table()
         return self._table.copy()
 
+    @classmethod
+    def _merge_elements(
+        cls,
+        elements: List["RegionalTimeseriesActivity"],
+        description: str,
+        modality: str,
+        anchor: _anchor.AnatomicalAnchor,
+    ):
+        assert len({f.cohort for f in elements}) == 1
+        assert len({f.timestep for f in elements}) == 1
+        merged = cls(
+            cohort=elements[0].cohort,
+            regions=elements[0].regions,
+            connector=elements[0]._connector,
+            decode_func=elements[0]._decode_func,
+            filename="",
+            timestep=" ".join(str(val) for val in elements[0].timestep),
+            subject="average",
+            description=description,
+            modality=modality,
+            anchor=anchor,
+            **{"paradigm": "average"} if getattr(elements[0], "paradigm") else {}
+        )
+        if isinstance(elements[0]._connector, HttpRequest):
+            getter = lambda elm: elm._connector.get()
+        else:
+            getter = lambda elm: elm._connector.get(elm._filename, decode_func=elm._decode_func)
+        all_arrays = [
+            getter(elm)
+            for elm in siibra_tqdm(
+                elements,
+                total=len(elements),
+                desc=f"Averaging {len(elements)} activity tables"
+            )
+        ]
+        merged._table = elements[0]._arraylike_to_dataframe(
+            np.stack(all_arrays).mean(0)
+        )
+        return merged
+
     def _load_table(self):
         """
         Extract the timeseries table.
         """
-        array = self._connector.get(self._filename, decode_func=self._decode_func)
+        if isinstance(self._connector, HttpRequest):
+            array = self._connector.data
+        else:
+            array = self._connector.get(self._filename, decode_func=self._decode_func)
+        self._table = self._arraylike_to_dataframe(array)
+
+    def _arraylike_to_dataframe(self, array: Union[np.ndarray, pd.DataFrame]) -> pd.DataFrame:
         if not isinstance(array, np.ndarray):
-            assert isinstance(array, pd.DataFrame)
             array = array.to_numpy()
         ncols = array.shape[1]
-        self._table = pd.DataFrame(
+        table = pd.DataFrame(
             array,
             index=pd.TimedeltaIndex(
                 np.arange(0, array.shape[0]) * self.timestep[0],
@@ -120,7 +170,9 @@ class RegionalTimeseriesActivity(tabular.Tabular, Compoundable):
                 label - min(columnmap.keys()): region
                 for label, region in columnmap.items()
             }
-            self._table = self._table.rename(columns=remapper)
+            table = table.rename(columns=remapper)
+
+        return table
 
     def __str__(self):
         return self.name
@@ -151,14 +203,14 @@ class RegionalTimeseriesActivity(tabular.Tabular, Compoundable):
                 found = [r for r in region if r.name in all_centroids]
             assert len(found) > 0
             result.append(
-                tuple(pointset.PointSet(
+                tuple(pointcloud.PointCloud(
                     [all_centroids[r.name] for r in found], space=space
                 ).centroid)
             )
         return result
 
     def plot(
-        self, regions: List[str] = None, *args,
+        self, regions: List[Union[str, "_region.Region"]] = None, *args,
         backend="matplotlib", **kwargs
     ):
         """
@@ -166,13 +218,15 @@ class RegionalTimeseriesActivity(tabular.Tabular, Compoundable):
 
         Parameters
         ----------
-        regions: str, Region
+        regions: List[str or Region]
         subject: str, default: None
             If None, returns the subject averaged table.
         args and kwargs:
             takes arguments and keyword arguments for the desired plotting
             backend.
         """
+        if isinstance(regions, (str, _region.Region)):
+            regions = [regions]
         if regions is None:
             regions = self.regions
         indices = [self.regions.index(r) for r in regions]
@@ -181,7 +235,7 @@ class RegionalTimeseriesActivity(tabular.Tabular, Compoundable):
         return table.mean().plot(kind="bar", *args, backend=backend, **kwargs)
 
     def plot_carpet(
-        self, regions: List[str] = None, *args,
+        self, regions: List[Union[str, "_region.Region"]] = None, *args,
         backend="plotly", **kwargs
     ):
         """
@@ -189,7 +243,7 @@ class RegionalTimeseriesActivity(tabular.Tabular, Compoundable):
 
         Parameters
         ----------
-        regions: str, Region
+        regions: List[str or Region]
         subject: str, default: None
             If None, returns the subject averaged table.
         args and kwargs:
@@ -197,6 +251,8 @@ class RegionalTimeseriesActivity(tabular.Tabular, Compoundable):
         """
         if backend != "plotly":
             raise NotImplementedError("Currently, carpet plot is only implemented with `plotly`.")
+        if isinstance(regions, (str, _region.Region)):
+            regions = [regions]
         if regions is None:
             regions = self.regions
         indices = [self.regions.index(r) for r in regions]
@@ -235,4 +291,4 @@ class RegionalBOLD(
 
     @property
     def name(self):
-        return f"{super().name}, paradigm {self.paradigm}"
+        return super().name + f", paradigm: {self.paradigm}"

siibra/features/tabular/tabular.py

@@ -1,4 +1,4 @@
-# Copyright 2018-2021
+# Copyright 2018-2024
 # Institute of Neuroscience and Medicine (INM-1), Forschungszentrum Jülich GmbH
 
 # Licensed under the Apache License, Version 2.0 (the "License");
@@ -44,14 +44,18 @@ class Tabular(feature.Feature):
         modality: str,
         anchor: _anchor.AnatomicalAnchor,
         data: pd.DataFrame,  # sample x feature dimension
-        datasets: list = []
+        datasets: list = [],
+        id: str = None,
+        prerelease: bool = False,
     ):
         feature.Feature.__init__(
             self,
             modality=modality,
             description=description,
             anchor=anchor,
-            datasets=datasets
+            datasets=datasets,
+            id=id,
+            prerelease=prerelease
         )
         self._data_cached = data
 
@@ -59,8 +63,8 @@ class Tabular(feature.Feature):
     def data(self):
         return self._data_cached.copy()
 
-    def _export(self, fh: ZipFile):
-        super()._export(fh)
+    def _to_zip(self, fh: ZipFile):
+        super()._to_zip(fh)
         fh.writestr("tabular.csv", self.data.to_csv())
 
     def plot(self, *args, backend="matplotlib", **kwargs):
@@ -97,19 +101,24 @@ class Tabular(feature.Feature):
             kwargs["width"] = kwargs.get("width", 0.95)
             kwargs["ylabel"] = kwargs.get(
                 "ylabel",
-                f"{kwargs['y']}{yerr_label} {self.unit if hasattr(self, 'unit') else ''}"
+                f"{kwargs['y']}{yerr_label}" + f"\n{self.unit}" if hasattr(self, 'unit') else ""
             )
             kwargs["grid"] = kwargs.get("grid", True)
             kwargs["legend"] = kwargs.get("legend", False)
+            xticklabel_rotation = kwargs.get("xticklabel_rotation", 60)
             ax = self.data.plot(*args, backend=backend, **kwargs)
             ax.set_title(ax.get_title(), fontsize="medium")
-            ax.set_xticklabels(ax.get_xticklabels(), rotation=60, ha="right")
+            ax.set_xticklabels(
+                ax.get_xticklabels(),
+                rotation=xticklabel_rotation,
+                ha='center' if xticklabel_rotation % 90 == 0 else 'right'
+            )
             plt.tight_layout()
             return ax
         elif backend == "plotly":
             kwargs["title"] = kwargs["title"].replace("\n", "<br>")
             kwargs["error_y"] = kwargs.get("error_y", 'std' if 'std' in self.data.columns else None)
-            error_y_label = f" &plusmn; {kwargs.get('error_y')}" if kwargs.get('error_y') else ''
+            error_y_label = f" &plusmn; {kwargs.get('error_y')}<br>" if kwargs.get('error_y') else ''
             kwargs["labels"] = {
                 "index": kwargs.pop("xlabel", None) or kwargs.pop("index", ""),
                 "value": kwargs.pop("ylabel", None) or kwargs.pop(

siibra/livequeries/__init__.py

@@ -1,4 +1,4 @@
-# Copyright 2018-2021
+# Copyright 2018-2024
 # Institute of Neuroscience and Medicine (INM-1), Forschungszentrum Jülich GmbH
 
 # Licensed under the Apache License, Version 2.0 (the "License");
@@ -17,9 +17,3 @@
 from .allen import AllenBrainAtlasQuery
 from .bigbrain import LayerwiseBigBrainIntensityQuery, BigBrainProfileQuery
 from .ebrains import EbrainsFeatureQuery
-
-
-def warm_cache():
-    """Preload downloadable livequeries."""
-    from .bigbrain import WagstylProfileLoader
-    WagstylProfileLoader()