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

siibra/volumes/providers/__init__.py

@@ -0,0 +1,20 @@
+# Copyright 2018-2024
+# Institute of Neuroscience and Medicine (INM-1), Forschungszentrum Jülich GmbH
+
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+
+#     http://www.apache.org/licenses/LICENSE-2.0
+
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+"""Subpackage handling the digestion of different volume and mesh types"""
+
+from .neuroglancer import NeuroglancerProvider, NeuroglancerMesh
+from .nifti import NiftiProvider
+from .gifti import GiftiSurfaceLabeling, GiftiMesh
+from .freesurfer import ZippedFreesurferAnnot, FreesurferAnnot

siibra/volumes/providers/freesurfer.py

@@ -0,0 +1,113 @@
+# Copyright 2018-2024
+# Institute of Neuroscience and Medicine (INM-1), Forschungszentrum Jülich GmbH
+
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+
+#     http://www.apache.org/licenses/LICENSE-2.0
+
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+"""Handles reading and preparing gii files."""
+
+from . import provider as _provider
+
+from ...retrieval.requests import HttpRequest, ZipfileRequest
+
+import numpy as np
+from typing import Union, Dict, TYPE_CHECKING
+
+if TYPE_CHECKING:
+    from ...locations import boundingbox as _boundingbox
+
+
+class FreesurferAnnot(_provider.VolumeProvider, srctype="freesurfer-annot"):
+    def __init__(self, url: Union[str, dict]):
+        self._init_url = url
+        if isinstance(url, str):  # single mesh labelling
+            self._loaders = {None: HttpRequest(url)}
+        elif isinstance(url, dict):   # named label fragments
+            self._loaders = {lbl: HttpRequest(u) for lbl, u in url.items()}
+        else:
+            raise NotImplementedError(f"Urls for {self.__class__.__name__} are expected to be of type str.")
+
+    def fetch(self, fragment: str = None, label: int = None, **kwargs):
+        """Returns a 1D numpy array of label indices."""
+        vertex_labels = []
+        if fragment is None:
+            matched_frags = list(self._loaders.keys())
+        else:
+            matched_frags = [frg for frg in self._loaders.keys() if fragment.lower() in frg.lower()]
+            if len(matched_frags) != 1:
+                raise ValueError(
+                    f"Requested fragment '{fragment}' could not be matched uniquely "
+                    f"to [{', '.join(self._loaders)}]"
+                )
+        for frag in matched_frags:
+            frag_labels, *_ = self._loaders[frag].data
+            if label is not None:  # create the mask
+                selected_label = frag_labels == label
+                frag_labels[selected_label] = 1
+                frag_labels[~selected_label] = 0
+            else:
+                frag_labels[frag_labels == -1] = 0  # annot files store backgorund as -1 while siibra uses 0
+            vertex_labels.append(frag_labels)
+
+        return {"labels": np.hstack(vertex_labels)}
+
+    def get_boundingbox(self, clip=False, background=0.0) -> '_boundingbox.BoundingBox':
+        raise NotImplementedError(
+            f"Bounding box access to {self.__class__.__name__} objects not yet implemented."
+        )
+
+    @property
+    def _url(self) -> Union[str, Dict[str, str]]:
+        return self._init_url
+
+
+class ZippedFreesurferAnnot(_provider.VolumeProvider, srctype="zip/freesurfer-annot"):
+    def __init__(self, url: Union[str, dict]):
+        self._init_url = url
+        if isinstance(url, str):  # single mesh labelling
+            self._loaders = {None: ZipfileRequest(*url.split(" "))}
+        elif isinstance(url, dict):   # named label fragments
+            self._loaders = {lbl: ZipfileRequest(*u.split(" ")) for lbl, u in url.items()}
+        else:
+            raise NotImplementedError(f"Urls for {self.__class__.__name__} are expected to be of type str.")
+
+    def fetch(self, fragment: str = None, label: int = None, **kwargs):
+        """Returns a 1D numpy array of label indices."""
+        vertex_labels = []
+        if fragment is None:
+            matched_frags = list(self._loaders.keys())
+        else:
+            matched_frags = [frg for frg in self._loaders.keys() if fragment.lower() in frg.lower()]
+            if len(matched_frags) != 1:
+                raise ValueError(
+                    f"Requested fragment '{fragment}' could not be matched uniquely "
+                    f"to [{', '.join(self._loaders)}]"
+                )
+        for frag in matched_frags:
+            frag_labels, *_ = self._loaders[frag].data
+            if label is not None:  # create the mask
+                selected_label = frag_labels == label
+                frag_labels[selected_label] = 1
+                frag_labels[~selected_label] = 0
+            else:
+                frag_labels[frag_labels == -1] = 0  # annot files store backgorund as -1 while siibra uses 0
+            vertex_labels.append(frag_labels)
+
+        return {"labels": np.hstack(vertex_labels)}
+
+    def get_boundingbox(self, clip=False, background=0.0) -> '_boundingbox.BoundingBox':
+        raise NotImplementedError(
+            f"Bounding box access to {self.__class__.__name__} objects not yet implemented."
+        )
+
+    @property
+    def _url(self) -> Union[str, Dict[str, str]]:
+        return self._init_url

siibra/volumes/{gifti.py → providers/gifti.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");
@@ -14,17 +14,17 @@
 # limitations under the License.
 """Handles reading and preparing gii files."""
 
-from . import volume
+from . import provider as _provider
 
-from ..retrieval import requests
-from ..commons import logger, merge_meshes
-from ..locations import boundingbox as _boundingbox
+from ...retrieval import requests
+from ...commons import logger, merge_meshes
+from ...locations import boundingbox as _boundingbox
 
 import numpy as np
 from typing import Union, Dict
 
 
-class GiftiMesh(volume.VolumeProvider, srctype="gii-mesh"):
+class GiftiMesh(_provider.VolumeProvider, srctype="gii-mesh"):
     """
     One or more surface mesh fragments in Gifti format.
     """
@@ -44,8 +44,10 @@ class GiftiMesh(volume.VolumeProvider, srctype="gii-mesh"):
     def _url(self) -> Union[str, Dict[str, str]]:
         return self._init_url
 
-    @property
-    def boundingbox(self) -> _boundingbox.BoundingBox:
+    def get_boundingbox(self, clip=False, background=0.0, **fetch_kwargs) -> '_boundingbox.BoundingBox':
+        """
+        Bounding box calculation is not yet implemented for meshes.
+        """
         raise NotImplementedError(
             f"Bounding box access to {self.__class__.__name__} objects not yet implemented."
         )
@@ -118,7 +120,7 @@ class GiftiMesh(volume.VolumeProvider, srctype="gii-mesh"):
         return (self.fetch(v) for v in self.variants)
 
 
-class GiftiSurfaceLabeling(volume.VolumeProvider, srctype="gii-label"):
+class GiftiSurfaceLabeling(_provider.VolumeProvider, srctype="gii-label"):
     """
     A mesh labeling, specified by a gifti file.
     """
@@ -132,21 +134,30 @@ class GiftiSurfaceLabeling(volume.VolumeProvider, srctype="gii-label"):
         else:
             raise NotImplementedError(f"Urls for {self.__class__.__name__} are expected to be of type str or dict.")
 
-    def fetch(self, fragment: str = None, **kwargs):
+    def fetch(self, fragment: str = None, label: int = None, **kwargs):
         """Returns a 1D numpy array of label indices."""
         labels = []
-        for fragment_name, loader in self._loaders.items():
-            if fragment is not None and fragment.lower() not in fragment_name.lower():
-                continue
-            assert len(loader.data.darrays) == 1
-            labels.append(loader.data.darrays[0].data)
+        if fragment is None:
+            matched_frags = list(self._loaders.keys())
+        else:
+            matched_frags = [frg for frg in self._loaders.keys() if fragment.lower() in frg.lower()]
+            if len(matched_frags) != 1:
+                raise ValueError(
+                    f"Requested fragment '{fragment}' could not be matched uniquely "
+                    f"to [{', '.join(self._loaders)}]"
+                )
+        for frag in matched_frags:
+            assert len(self._loaders[frag].data.darrays) == 1
+            if label is not None:
+                labels.append((self._loaders[frag].data.darrays[0].data == label).astype('uint8'))
+            else:
+                labels.append(self._loaders[frag].data.darrays[0].data)
 
         return {"labels": np.hstack(labels)}
 
-    @property
-    def boundingbox(self) -> _boundingbox.BoundingBox:
+    def get_boundingbox(self, clip=False, background=0.0) -> '_boundingbox.BoundingBox':
         raise NotImplementedError(
-            f"Bounding boxes of {self.__class__.__name__} objects not defined."
+            f"Bounding box access to {self.__class__.__name__} objects not yet implemented."
         )
 
     @property