siibra 1.0a14__py3-none-any.whl → 1.0a19__py3-none-any.whl

siibra/features/image/image.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");
@@ -20,19 +20,19 @@ from .. import feature
 from .. import anchor as _anchor
 
 from ...volumes import volume as _volume
-from ...volumes.providers import provider
 
-from typing import List
+from typing import List, TYPE_CHECKING
+
+if TYPE_CHECKING:
+    from ...locations.boundingbox import BoundingBox
+    from ...volumes.providers import provider
 
 
 class ImageAnchor(_anchor.AnatomicalAnchor):
 
     def __init__(self, volume: _volume.Volume, region: str = None):
         _anchor.AnatomicalAnchor.__init__(
-            self,
-            species=volume.space.species,
-            location=None,
-            region=region
+            self, species=volume.space.species, location=None, region=region
         )
         self.volume = volume
 
@@ -42,7 +42,9 @@ class ImageAnchor(_anchor.AnatomicalAnchor):
         Loads the bounding box only if required, since it demands image data access.
         """
         if self._location_cached is None:
-            self._location_cached = self.volume.get_boundingbox(clip=False)  # use unclipped to preseve exisiting behaviour
+            self._location_cached = self.volume.get_boundingbox(
+                clip=False
+            )  # use unclipped to preseve exisiting behaviour
         return self._location_cached
 
     @property
@@ -60,10 +62,12 @@ class Image(feature.Feature, _volume.Volume):
         name: str,
         modality: str,
         space_spec: dict,
-        providers: List[provider.VolumeProvider],
+        providers: List["provider.VolumeProvider"],
         region: str = None,
         datasets: List = [],
-        id: str = None
+        bbox: "BoundingBox" = None,
+        id: str = None,
+        prerelease: bool = False,
     ):
         feature.Feature.__init__(
             self,
@@ -71,7 +75,8 @@ class Image(feature.Feature, _volume.Volume):
             description=None,  # lazy implementation below!
             anchor=None,  # lazy implementation below!
             datasets=datasets,
-            id=id
+            id=id,
+            prerelease=prerelease,
         )
 
         _volume.Volume.__init__(
@@ -80,6 +85,7 @@ class Image(feature.Feature, _volume.Volume):
             providers=providers,
             name=name,
             datasets=datasets,
+            bbox=bbox,
         )
 
         self._anchor_cached = ImageAnchor(self, region=region)
@@ -104,7 +110,6 @@ class Image(feature.Feature, _volume.Volume):
     def description(self):
         if self._description_cached is None:
             self._description_cached = (
-                f"Image feature with modality {self.modality} "
-                f"at {self.anchor}"
+                f"Image feature with modality {self.modality} " f"at {self.anchor}"
             )
         return self._description_cached

siibra/features/image/sections.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");

siibra/features/image/volume_of_interest.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");

siibra/features/tabular/__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");

siibra/features/tabular/bigbrain_intensity_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");

siibra/features/tabular/cell_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");
@@ -70,7 +70,8 @@ class CellDensityProfile(
         url: str,
         anchor: _anchor.AnatomicalAnchor,
         datasets: list = [],
-        id: str = None
+        id: str = None,
+        prerelease: bool = False,
     ):
         """
         Generate a cell density profile from a URL to a cloud folder
@@ -83,7 +84,8 @@ class CellDensityProfile(
             unit="cells / 0.1mm3",
             anchor=anchor,
             datasets=datasets,
-            id=id
+            id=id,
+            prerelease=prerelease,
         )
         self._step = 0.01
         self._url = url

siibra/features/tabular/cortical_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");
@@ -57,7 +57,8 @@ class CorticalProfile(tabular.Tabular, Compoundable):
         unit: str = None,
         boundary_positions: Dict[Tuple[int, int], float] = None,
         datasets: list = [],
-        id: str = None
+        id: str = None,
+        prerelease: bool = False,
     ):
         """Initialize profile.
 
@@ -98,7 +99,8 @@ class CorticalProfile(tabular.Tabular, Compoundable):
             anchor=anchor,
             data=None,  # lazy loader below
             datasets=datasets,
-            id=id
+            id=id,
+            prerelease=prerelease,
         )
 
     def _check_sanity(self):

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");

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");

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");
@@ -56,7 +56,8 @@ class LayerwiseCellDensity(
         layerfiles: list,
         anchor: _anchor.AnatomicalAnchor,
         datasets: list = [],
-        id: str = None
+        id: str = None,
+        prerelease: bool = False,
     ):
         tabular.Tabular.__init__(
             self,
@@ -65,7 +66,8 @@ class LayerwiseCellDensity(
             anchor=anchor,
             datasets=datasets,
             data=None,  # lazy loading below
-            id=id
+            id=id,
+            prerelease=prerelease,
         )
         self.unit = "# detected cells/0.1mm3"
         self._filepairs = list(zip(segmentfiles, layerfiles))

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");
@@ -43,7 +43,8 @@ class ReceptorDensityFingerprint(
         tsvfile: str,
         anchor: _anchor.AnatomicalAnchor,
         datasets: list = [],
-        id: str = None
+        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.
@@ -55,7 +56,8 @@ class ReceptorDensityFingerprint(
             anchor=anchor,
             data=None,  # lazy loading below
             datasets=datasets,
-            id=id
+            id=id,
+            prerelease=prerelease,
         )
         self._loader = requests.HttpRequest(tsvfile)
 

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");
@@ -42,7 +42,8 @@ class ReceptorDensityProfile(
         tsvfile: str,
         anchor: _anchor.AnatomicalAnchor,
         datasets: list = [],
-        id: str = None
+        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.
@@ -53,7 +54,8 @@ class ReceptorDensityProfile(
             modality="Receptor density",
             anchor=anchor,
             datasets=datasets,
-            id=id
+            id=id,
+            prerelease=prerelease
         )
         self.receptor = receptor
         self._data_cached = None

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");
@@ -49,7 +49,8 @@ class RegionalTimeseriesActivity(tabular.Tabular, Compoundable):
         description: str = "",
         datasets: list = [],
         subject: str = "average",
-        id: str = None
+        id: str = None,
+        prerelease: bool = False,
     ):
         """
         """
@@ -60,7 +61,8 @@ class RegionalTimeseriesActivity(tabular.Tabular, Compoundable):
             anchor=anchor,
             datasets=datasets,
             data=None,  # lazy loading below
-            id=id
+            id=id,
+            prerelease=prerelease,
         )
         self.cohort = cohort.upper()
         if isinstance(connector, str) and connector:

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");
@@ -45,7 +45,8 @@ class Tabular(feature.Feature):
         anchor: _anchor.AnatomicalAnchor,
         data: pd.DataFrame,  # sample x feature dimension
         datasets: list = [],
-        id: str = None
+        id: str = None,
+        prerelease: bool = False,
     ):
         feature.Feature.__init__(
             self,
@@ -53,7 +54,8 @@ class Tabular(feature.Feature):
             description=description,
             anchor=anchor,
             datasets=datasets,
-            id=id
+            id=id,
+            prerelease=prerelease
         )
         self._data_cached = data
 

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");

siibra/livequeries/allen.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");
@@ -19,7 +19,7 @@ from .query import LiveQuery
 from ..core import space as _space, structure
 from ..features import anchor as _anchor
 from ..features.tabular.gene_expression import GeneExpressions
-from ..commons import logger, Species, MapType
+from ..commons import logger, Species
 from ..locations import point, pointset
 from ..retrieval import HttpRequest
 from ..vocabularies import GENE_NAMES
@@ -101,9 +101,6 @@ class AllenBrainAtlasQuery(LiveQuery, args=['gene'], FeatureType=GeneExpressions
         """
         LiveQuery.__init__(self, **kwargs)
         gene = kwargs.get('gene')
-        self.maptype = kwargs.get("maptype", None)
-        if isinstance(self.maptype, str):
-            self.maptype = MapType[self.maptype.upper()]
 
         def parse_gene(spec):
             if isinstance(spec, str):
@@ -137,6 +134,9 @@ class AllenBrainAtlasQuery(LiveQuery, args=['gene'], FeatureType=GeneExpressions
                 measurements.append(measurement)
                 coordinates.append(pt)
 
+        if len(points_inside) == 0:
+            raise StopIteration
+
         # 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.
@@ -292,7 +292,10 @@ class AllenBrainAtlasQuery(LiveQuery, args=['gene'], FeatureType=GeneExpressions
         url = AllenBrainAtlasQuery._QUERY["microarray"].format(
             probe_ids=",".join([str(id) for id in probe_ids]), donor_id=donor_id
         )
-        response = HttpRequest(url, json.loads).get()
+        try:
+            response = HttpRequest(url, json.loads).get()
+        except json.JSONDecodeError as e:
+            raise RuntimeError(f"Allen institute site produced an empty response - please try again later.\n{e}")
         if not response["success"]:
             raise Exception(
                 "Invalid response when retrieving microarray data: {}".format(url)

siibra/livequeries/bigbrain.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");

siibra/livequeries/ebrains.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");

siibra/livequeries/query.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");

siibra/locations/__init__.py

@@ -1,4 +1,4 @@
-# Copyright 2018-2023
+# Copyright 2018-2024
 # Institute of Neuroscience and Medicine (INM-1), Forschungszentrum Jülich GmbH
 
 # Licensed under the Apache License, Version 2.0 (the "License");

siibra/locations/boundingbox.py

@@ -1,4 +1,4 @@
-# Copyright 2018-2023
+# 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 +19,7 @@ from . import point, pointset, location
 from ..commons import logger
 from ..exceptions import SpaceWarpingFailedError
 
+from itertools import product
 import hashlib
 import numpy as np
 from typing import TYPE_CHECKING, Union
@@ -75,6 +76,7 @@ class BoundingBox(location.Location):
             s1, s2 = sigma_mm
         else:
             raise ValueError(f"Cannot interpret sigma_mm parameter value {sigma_mm} for bounding box")
+        self.sigma_mm = [s1, s2]
         self.minpoint = point.Point([min(xyz1[i], xyz2[i]) for i in range(3)], space, sigma_mm=s1)
         self.maxpoint = point.Point([max(xyz1[i], xyz2[i]) for i in range(3)], space, sigma_mm=s2)
         if minsize is not None:
@@ -82,6 +84,9 @@ class BoundingBox(location.Location):
                 if self.shape[d] < minsize:
                     self.maxpoint[d] = self.minpoint[d] + minsize
 
+        if self.volume == 0:
+            logger.warning("Created BoundedBox's have zero volume.")
+
     @property
     def id(self) -> str:
         return hashlib.md5(str(self).encode("utf-8")).hexdigest()
@@ -110,12 +115,12 @@ class BoundingBox(location.Location):
     def __str__(self):
         if self.space is None:
             return (
-                f"Bounding box from ({','.join(f'{v:.2f}' for v in self.minpoint)}) mm "
-                f"to ({','.join(f'{v:.2f}' for v in self.maxpoint)}) mm"
+                f"Bounding box from ({','.join(f'{v:.2f}' for v in self.minpoint)})mm "
+                f"to ({','.join(f'{v:.2f}' for v in self.maxpoint)})mm"
             )
         else:
             return (
-                f"Bounding box from ({','.join(f'{v:.2f}' for v in self.minpoint)}) mm "
+                f"Bounding box from ({','.join(f'{v:.2f}' for v in self.minpoint)})mm "
                 f"to ({','.join(f'{v:.2f}' for v in self.maxpoint)})mm in {self.space.name} space"
             )
 
@@ -183,12 +188,18 @@ class BoundingBox(location.Location):
                 result_minpt.append(A[dim])
                 result_maxpt.append(B[dim])
 
+        if result_minpt == result_maxpt:
+            return result_minpt
+
         bbox = BoundingBox(
             point1=point.Point(result_minpt, self.space),
             point2=point.Point(result_maxpt, self.space),
             space=self.space,
         )
-        return bbox if bbox.volume > 0 else None
+
+        if bbox.volume == 0 and sum(cmin == cmax for cmin, cmax in zip(result_minpt, result_maxpt)) == 2:
+            return None
+        return bbox
 
     def _intersect_mask(self, mask: 'Nifti1Image', threshold=0):
         """Intersect this bounding box with an image mask. Returns None if they do not intersect.
@@ -245,6 +256,35 @@ class BoundingBox(location.Location):
             sigma_mm=[self.minpoint.sigma, self.maxpoint.sigma]
         )
 
+    @property
+    def corners(self):
+        """
+        Returns all 8 corners of the box as a pointset.
+
+        Note
+        ----
+        x0, y0, z0 = self.minpoint
+        x1, y1, z1 = self.maxpoint
+        all_corners = [
+            (x0, y0, z0),
+            (x1, y0, z0),
+            (x0, y1, z0),
+            (x1, y1, z0),
+            (x0, y0, z1),
+            (x1, y0, z1),
+            (x0, y1, z1),
+            (x1, y1, z1)
+        ]
+
+        TODO: deal with sigma. Currently, returns the mean of min and max point.
+        """
+        xs, ys, zs = zip(self.minpoint, self.maxpoint)
+        return pointset.PointSet(
+            coordinates=[[x, y, z] for x, y, z in product(xs, ys, zs)],
+            space=self.space,
+            sigma_mm=np.mean([self.minpoint.sigma, self.maxpoint.sigma])
+        )
+
     def warp(self, space):
         """Returns a new bounding box obtained by warping the
         min- and maxpoint of this one into the new target space.
@@ -257,13 +297,10 @@ class BoundingBox(location.Location):
             return self
         else:
             try:
-                return self.__class__(
-                    point1=self.minpoint.warp(spaceobj),
-                    point2=self.maxpoint.warp(spaceobj),
-                    space=spaceobj,
-                )
-            except ValueError:
+                warped_corners = self.corners.warp(spaceobj)
+            except SpaceWarpingFailedError:
                 raise SpaceWarpingFailedError(f"Warping {str(self)} to {spaceobj.name} not successful.")
+            return warped_corners.boundingbox
 
     def transform(self, affine: np.ndarray, space=None):
         """Returns a new bounding box obtained by transforming the
@@ -282,12 +319,9 @@ class BoundingBox(location.Location):
         """
         from ..core.space import Space
         spaceobj = Space.get_instance(space)
-        return self.__class__(
-            point1=self.minpoint.transform(affine, spaceobj),
-            point2=self.maxpoint.transform(affine, spaceobj),
-            space=space,
-            sigma_mm=[self.minpoint.sigma, self.maxpoint.sigma]  # TODO: error propagation
-        )
+        result = self.corners.transform(affine, spaceobj).boundingbox
+        result.sigma_mm = [self.minpoint.sigma, self.maxpoint.sigma]  # TODO: error propagation
+        return result
 
     def shift(self, offset):
         return self.__class__(

siibra/locations/location.py

@@ -1,4 +1,4 @@
-# Copyright 2018-2023
+# Copyright 2018-2024
 # Institute of Neuroscience and Medicine (INM-1), Forschungszentrum Jülich GmbH
 
 # Licensed under the Apache License, Version 2.0 (the "License");
@@ -21,6 +21,10 @@ from ..core.structure import BrainStructure
 import numpy as np
 from abc import abstractmethod
 
+from typing import TYPE_CHECKING, Union, Dict
+if TYPE_CHECKING:
+    from siibra.core.space import Space
+
 
 class Location(BrainStructure):
     """
@@ -42,15 +46,19 @@ class Location(BrainStructure):
     _MASK_MEMO = {}  # cache region masks for Location._assign_region()
     _ASSIGNMENT_CACHE = {}  # caches assignment results, see Region.assign()
 
-    def __init__(self, space):
-        self._space_spec = space
+    def __init__(self, spacespec: Union[str, Dict[str, str], "Space"]):
+        self._space_spec = spacespec
         self._space_cached = None
 
     @property
     def space(self):
         if self._space_cached is None:
             from ..core.space import Space
-            self._space_cached = Space.get_instance(self._space_spec)
+            if isinstance(self._space_spec, dict):
+                spec = self._space_spec.get("@id") or self._space_spec.get("name")
+                self._space_cached = Space.get_instance(spec)
+            else:
+                self._space_cached = Space.get_instance(self._space_spec)
         return self._space_cached
 
     @abstractmethod

siibra/locations/point.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");
@@ -18,6 +18,7 @@ from . import location, boundingbox, pointset
 
 from ..commons import logger
 from ..retrieval.requests import HttpRequest
+from ..exceptions import SpaceWarpingFailedError, NoneCoordinateSuppliedError
 
 from urllib.parse import quote
 import re
@@ -55,10 +56,14 @@ class Point(location.Location):
             if len(digits) == 3:
                 return tuple(float(d) for d in digits)
         elif isinstance(spec, (tuple, list)) and len(spec) in [3, 4]:
+            if any(v is None for v in spec):
+                raise NoneCoordinateSuppliedError("Cannot parse cooridantes containing None values.")
             if len(spec) == 4:
                 assert spec[3] == 1
             return tuple(float(v.item()) if isinstance(v, np.ndarray) else float(v) for v in spec[:3])
         elif isinstance(spec, np.ndarray) and spec.size == 3:
+            if any(np.isnan(v) for v in spec):
+                raise NoneCoordinateSuppliedError("Cannot parse cooridantes containing NaN values.")
             return tuple(float(v.item()) if isinstance(v, np.ndarray) else float(v) for v in spec[:3])
         elif isinstance(spec, Point):
             return spec.coordinate
@@ -125,7 +130,7 @@ class Point(location.Location):
         if spaceobj == self.space:
             return self
         if any(_ not in location.Location.SPACEWARP_IDS for _ in [self.space.id, spaceobj.id]):
-            raise ValueError(
+            raise SpaceWarpingFailedError(
                 f"Cannot convert coordinates between {self.space.id} and {spaceobj.id}"
             )
         url = "{server}/transform-point?source_space={src}&target_space={tgt}&x={x}&y={y}&z={z}".format(
@@ -137,9 +142,9 @@ class Point(location.Location):
             z=self.coordinate[2],
         )
         response = HttpRequest(url, lambda b: json.loads(b.decode())).get()
-        if any(map(np.isnan, response['target_point'])):
-            logger.debug(f'Warping {str(self)} to {spaceobj.name} resulted in NaN')
-            return None
+        if np.any(np.isnan(response['target_point'])):
+            raise SpaceWarpingFailedError(f'Warping {str(self)} to {spaceobj.name} resulted in NaN')
+
         return self.__class__(
             coordinatespec=tuple(response["target_point"]),
             space=spaceobj.id,