siibra 0.4a91__tar.gz → 0.4a93__tar.gz

{siibra-0.4a91/siibra.egg-info → siibra-0.4a93}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: siibra
-Version: 0.4a91
+Version: 0.4a93
 Summary: siibra - Software interfaces for interacting with brain atlases
 Home-page: https://github.com/FZJ-INM1-BDA/siibra-python
 Author: Big Data Analytics Group, Forschungszentrum Juelich, Institute of Neuroscience and Medicine (INM-1)

siibra-0.4a93/siibra/VERSION

@@ -0,0 +1 @@
+0.4a93

{siibra-0.4a91 → siibra-0.4a93}/siibra/configuration/factory.py

@@ -26,7 +26,7 @@ from ..features.image import sections, volume_of_interest
 from ..core import atlas, parcellation, space, region
 from ..locations import point, pointset
 from ..retrieval import datasets, repositories
-from ..volumes import gifti, volume, nifti, neuroglancer, sparsemap, parcellationmap
+from ..volumes import gifti, volume, nifti, neuroglancer, freesurfer, sparsemap, parcellationmap
 
 from os import path
 import json
@@ -253,7 +253,9 @@ class Factory:
             nifti.NiftiProvider,
             nifti.ZipContainedNiftiProvider,
             gifti.GiftiMesh,
-            gifti.GiftiSurfaceLabeling
+            gifti.GiftiSurfaceLabeling,
+            freesurfer.FreesurferAnnot,
+            freesurfer.ZippedFreesurferAnnot,
         ]
 
         for srctype, provider_spec in spec.get("providers", {}).items():

{siibra-0.4a91 → siibra-0.4a93}/siibra/retrieval/requests.py

@@ -30,7 +30,7 @@ import json
 from zipfile import ZipFile
 import requests
 import os
-from nibabel import Nifti1Image, GiftiImage, streamlines
+from nibabel import Nifti1Image, GiftiImage, streamlines, freesurfer
 from skimage import io as skimage_io
 import gzip
 from io import BytesIO
@@ -54,6 +54,34 @@ if TYPE_CHECKING:
 
 USER_AGENT_HEADER = {"User-Agent": f"siibra-python/{__version__}"}
 
+
+def read_as_bytesio(function: Callable, suffix: str, bytesio: BytesIO):
+    """
+    Helper method to provide BytesIO to methods that only takes file path and
+    cannot handle BytesIO normally (e.g., `nibabel.freesurfer.read_annot()`).
+
+    Writes the bytes to a temporary file on cache and reads with the
+    original function.
+
+    Parameters
+    ----------
+    function : Callable
+    suffix : str
+        Must match the suffix expected by the function provided.
+    bytesio : BytesIO
+
+    Returns
+    -------
+    Return type of the provided function.
+    """
+    tempfile = CACHE.build_filename(f"temp_{suffix}") + suffix
+    with open(tempfile, "wb") as bf:
+        bf.write(bytesio.getbuffer())
+    result = function(tempfile)
+    os.remove(tempfile)
+    return result
+
+
 DECODERS = {
     ".nii": lambda b: Nifti1Image.from_bytes(b),
     ".gii": lambda b: GiftiImage.from_bytes(b),
@@ -65,6 +93,7 @@ DECODERS = {
     ".zip": lambda b: ZipFile(BytesIO(b)),
     ".png": lambda b: skimage_io.imread(BytesIO(b)),
     ".npy": lambda b: np.load(BytesIO(b)),
+    ".annot": lambda b: read_as_bytesio(freesurfer.read_annot, '.annot', BytesIO(b)),
 }
 
 

{siibra-0.4a91 → siibra-0.4a93}/siibra/volumes/__init__.py

@@ -18,6 +18,7 @@ from .parcellationmap import Map
 from .neuroglancer import NeuroglancerProvider, NeuroglancerMesh
 from .nifti import NiftiProvider
 from .gifti import GiftiSurfaceLabeling, GiftiMesh
+from .freesurfer import FreesurferAnnot, ZippedFreesurferAnnot
 
 
 def warm_cache():

siibra-0.4a93/siibra/volumes/freesurfer.py

@@ -0,0 +1,123 @@
+# Copyright 2018-2025
+# 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 typing import Union, Dict, TYPE_CHECKING
+
+import numpy as np
+
+from . import volume
+from ..retrieval.requests import HttpRequest, ZipfileRequest
+
+if TYPE_CHECKING:
+    from ..locations import boundingbox as _boundingbox
+
+
+class FreesurferAnnot(volume.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 background as -1 while siibra uses 0
+            vertex_labels.append(frag_labels)
+
+        return {"labels": np.hstack(vertex_labels)}
+
+    @property
+    def boundingbox(self) -> '_boundingbox.BoundingBox':
+        raise NotImplementedError(
+            f"Bounding box access to {self.__class__.__name__} objects not yet implemented."
+        )
+
+    @property
+    def fragments(self):
+        return [k for k in self._loaders if k is not None]
+
+    @property
+    def _url(self) -> Union[str, Dict[str, str]]:
+        return self._init_url
+
+
+class ZippedFreesurferAnnot(volume.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 background as -1 while siibra uses 0
+            vertex_labels.append(frag_labels)
+
+        return {"labels": np.hstack(vertex_labels)}
+
+    @property
+    def boundingbox(self) -> '_boundingbox.BoundingBox':
+        raise NotImplementedError(
+            f"Bounding box access to {self.__class__.__name__} objects not yet implemented."
+        )
+
+    @property
+    def fragments(self):
+        return [k for k in self._loaders if k is not None]
+
+    @property
+    def _url(self) -> Union[str, Dict[str, str]]:
+        return self._init_url

{siibra-0.4a91 → siibra-0.4a93}/siibra/volumes/volume.py

@@ -49,7 +49,9 @@ class Volume:
         "neuroglancer/precompmesh",
         "neuroglancer/precompmesh/surface",
         "gii-mesh",
-        "gii-label"
+        "gii-label",
+        "freesurfer-annot",
+        "zip/freesurfer-annot",
     ]
 
     SUPPORTED_FORMATS = IMAGE_FORMATS + MESH_FORMATS
@@ -218,7 +220,7 @@ class Volume:
         # try the selected format only
         for try_count in range(6):
             try:
-                if selected_format == "gii-label":
+                if selected_format in ["gii-label", "freesurfer-annot", "zip/freesurfer-annot"]:
                     tpl = self.space.get_template(variant=kwargs.get('variant'))
                     mesh = tpl.fetch(**kwargs)
                     labels = self._providers[selected_format].fetch(**kwargs)

{siibra-0.4a91 → siibra-0.4a93/siibra.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: siibra
-Version: 0.4a91
+Version: 0.4a93
 Summary: siibra - Software interfaces for interacting with brain atlases
 Home-page: https://github.com/FZJ-INM1-BDA/siibra-python
 Author: Big Data Analytics Group, Forschungszentrum Juelich, Institute of Neuroscience and Medicine (INM-1)

{siibra-0.4a91 → siibra-0.4a93}/siibra.egg-info/SOURCES.txt

@@ -70,6 +70,7 @@ siibra/vocabularies/gene_names.json
 siibra/vocabularies/receptor_symbols.json
 siibra/vocabularies/region_aliases.json
 siibra/volumes/__init__.py
+siibra/volumes/freesurfer.py
 siibra/volumes/gifti.py
 siibra/volumes/neuroglancer.py
 siibra/volumes/nifti.py

siibra-0.4a91/siibra/VERSION

@@ -1 +0,0 @@
-0.4a91