siibra 1.0.1a0__py3-none-any.whl → 1.0.1a1__py3-none-any.whl

siibra/retrieval/requests.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");
@@ -94,8 +94,8 @@ DECODERS = {
 def find_suitiable_decoder(url: str) -> Callable:
     """
     By supplying a url or a filename, obtain a suitable decoder function
-    for siibra to digest based on predifined DECODERS. An extra layer of
-    gzip decompresser automatically added for gzipped files.
+    for siibra to digest based on predefined DECODERS. An extra layer of
+    gzip decompressor automatically added for gzipped files.
 
     Parameters
     ----------
@@ -193,7 +193,7 @@ class HttpRequest:
         """
         Populates the file cache with the data from http if required.
         noop if 1/ data is already cached and 2/ refresh flag not set
-        The caller should load the cachefile after _retrieve successfuly executes
+        The caller should load the cachefile after _retrieve successfully executes
         """
         if self.cached and not self.refresh:
             return
@@ -457,9 +457,9 @@ class EbrainsRequest(HttpRequest):
 
             if resp.status_code == 200:
                 json_resp = resp.json()
-                logger.debug("Device flow sucessful:", json_resp)
+                logger.debug("Device flow successful:", json_resp)
                 cls._KG_API_TOKEN = json_resp.get("access_token")
-                print("ebrains token successfuly set.")
+                print("ebrains token successfully set.")
                 break
 
             if resp.status_code == 400:

siibra/vocabularies/__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");

siibra/volumes/__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");

siibra/volumes/parcellationmap.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");
@@ -503,7 +503,7 @@ class Map(concept.AtlasConcept, configuration_folder="maps"):
         taking the voxelwise maximum across the mapped volumes and fragments,
         and re-labelling regions sequentially.
 
-        Paramaters
+        Parameters
         ----------
         **kwargs: Takes the fetch arguments of its space's template.
 
@@ -690,7 +690,7 @@ class Map(concept.AtlasConcept, configuration_folder="maps"):
             name=f"Custom colorization of {self}"
         )
 
-    def get_colormap(self, region_specs: Iterable = None):
+    def get_colormap(self, region_specs: Iterable = None, *, allow_random_colors: bool = False):
         """
         Generate a matplotlib colormap from known rgb values of label indices.
 
@@ -698,13 +698,23 @@ class Map(concept.AtlasConcept, configuration_folder="maps"):
         ----------
         region_specs: iterable(regions), optional
             Optional parameter to only color the desired regions.
+        allow_random_colors: bool , optional
 
         Returns
         -------
         ListedColormap
         """
-        from matplotlib.colors import ListedColormap
-        import numpy as np
+        try:
+            from matplotlib.colors import ListedColormap
+        except ImportError as e:
+            logger.error(
+                "matplotlib not available. Please install matplotlib to create a matplotlib colormap."
+            )
+            raise e
+        if allow_random_colors:
+            seed = len(self.regions)
+            np.random.seed(seed)
+            logger.info(f"Random colors are allowed for regions without preconfgirued colors. Random seee: {seed}.")
 
         colors = {}
         if region_specs is not None:
@@ -725,14 +735,25 @@ class Map(concept.AtlasConcept, configuration_folder="maps"):
                     region = self.get_region(index=index)
                     if region.rgb is not None:
                         colors[index.label] = region.rgb
+                    elif allow_random_colors:
+                        random_clr = [np.random.randint(0, 255) for r in range(3)]
+                        while random_clr in list(colors.values()):
+                            random_clr = [np.random.randint(0, 255) for r in range(3)]
+                        colors[index.label] = random_clr
+
+        if len(colors) == 0:
+            raise exceptions.NoPredifinedColormapException(
+                f"There is no predefined/preconfigured colormap for '{self}'."
+                "Set `allow_random_colors=True` to a colormap with random values"
+            )
 
-        pallette = np.array(
+        palette = np.array(
             [
                 list(colors[i]) + [1] if i in colors else [0, 0, 0, 0]
                 for i in range(max(colors.keys()) + 1)
             ]
         ) / [255, 255, 255, 1]
-        return ListedColormap(pallette)
+        return ListedColormap(palette)
 
     def sample_locations(self, regionspec, numpoints: int):
         """ Sample 3D locations inside a given region.
@@ -750,7 +771,7 @@ class Map(concept.AtlasConcept, configuration_folder="maps"):
         Returns
         -------
         PointCloud
-            Sample points in physcial coordinates corresponding to this
+            Sample points in physical coordinates corresponding to this
             parcellationmap
         """
         index = self.get_index(regionspec)
@@ -923,7 +944,7 @@ class Map(concept.AtlasConcept, configuration_folder="maps"):
         if len(assignments) == 0:
             return pd.DataFrame(columns=columns)
         # determine the unique set of observed indices in order to do region lookups
-        # only once for each map index occuring in the point list
+        # only once for each map index occurring in the point list
         labelled = self.is_labelled  # avoid calling this in a loop
         observed_indices = {  # unique set of observed map indices. NOTE: len(observed_indices) << len(assignments)
             (
@@ -1032,7 +1053,7 @@ class Map(concept.AtlasConcept, configuration_folder="maps"):
                         assignments.append(
                             MapAssignment(
                                 input_structure=pointindex,
-                                centroid=tuple(np.array(position).round(2)),
+                                centroid=tuple(position),
                                 volume=vol,
                                 fragment=frag,
                                 map_value=value

siibra/volumes/providers/__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");

siibra/volumes/providers/freesurfer.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");
@@ -54,7 +54,7 @@ class FreesurferAnnot(_provider.VolumeProvider, srctype="freesurfer-annot"):
                 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
+                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)}
@@ -98,7 +98,7 @@ class ZippedFreesurferAnnot(_provider.VolumeProvider, srctype="zip/freesurfer-an
                 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
+                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)}

siibra/volumes/providers/gifti.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");

siibra/volumes/providers/neuroglancer.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");
@@ -52,7 +52,7 @@ def shift_ng_transfrom(
     Parameters
     ----------
     transform_nm: np.ndarray
-        Transform array created for dispalying an image correctly from
+        Transform array created for displaying an image correctly from
         neuroglancer precomputed format in neuroglancer viewer.
     max_resolution_nm: np.ndarray
         The voxel resolution of the highest level of resolution.
@@ -174,7 +174,7 @@ class NeuroglancerProvider(_provider.VolumeProvider, srctype="neuroglancer/preco
         Parameters
         ----------
         fetch_kwargs:
-            key word arguments that are used for fetchin volumes,
+            key word arguments that are used for fetching volumes,
             such as voi or resolution_mm.
         """
         bbox = None
@@ -422,7 +422,7 @@ class NeuroglancerScale:
         return self.res_nm / 1e6
 
     def resolves(self, resolution_mm):
-        """Test wether the resolution of this scale is sufficient to provide the given resolution."""
+        """Test whether the resolution of this scale is sufficient to provide the given resolution."""
         return all(r / 1e6 <= resolution_mm for r in self.res_nm)
 
     def __lt__(self, other):
@@ -594,7 +594,7 @@ class NeuroglancerMesh(_provider.VolumeProvider, srctype="neuroglancer/precompme
         elif isinstance(resource, dict):
             self._meshes = {n: self._fragmentinfo(u) for n, u in resource.items()}
         else:
-            raise ValueError(f"Resource specificaton not understood for {self.__class__.__name__}: {resource}")
+            raise ValueError(f"Resource specification not understood for {self.__class__.__name__}: {resource}")
 
     @property
     def _url(self) -> Union[str, Dict[str, str]]:
@@ -635,7 +635,7 @@ class NeuroglancerMesh(_provider.VolumeProvider, srctype="neuroglancer/precompme
                 result[name] = (f"{spec['url']}/{mesh_key}/{fragment_names[0]}", transform)
             else:
                 # only one mesh was configures, so we might still
-                # see muliple fragments under the mesh url
+                # see multiple fragments under the mesh url
                 for fragment_name in fragment_names:
                     result[fragment_name] = (f"{spec['url']}/{mesh_key}/{fragment_name}", transform)
 

siibra/volumes/providers/nifti.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");

siibra/volumes/providers/provider.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");

siibra/volumes/sparsemap.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");

siibra/volumes/volume.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");
@@ -191,7 +191,7 @@ class Volume(structure.BrainStructure):
             ----
             To use it, clip must be True.
         fetch_kwargs:
-            key word arguments that are used for fetchin volumes,
+            key word arguments that are used for fetching volumes,
             such as voi or resolution_mm. Currently, only possible for
             Neuroglancer volumes except for `format`.
 
@@ -206,7 +206,7 @@ class Volume(structure.BrainStructure):
         if not self.provides_image:
             raise NotImplementedError("Bounding box calculation of meshes is not implemented yet.")
 
-        if clip:  # clippin requires fetching the image
+        if clip:  # clipping requires fetching the image
             img = self.fetch(**fetch_kwargs)
             assert isinstance(img, Nifti1Image)
             return boundingbox.from_array(
@@ -214,7 +214,7 @@ class Volume(structure.BrainStructure):
                 background=background,
             ).transform(img.affine, space=self.space)
 
-        # if clipping is not required, providers migth have methods of creating
+        # if clipping is not required, providers might have methods of creating
         # bounding boxes without fetching the image
         fmt = fetch_kwargs.get("format")
         if (fmt is not None) and (fmt not in self.formats):
@@ -365,7 +365,7 @@ class Volume(structure.BrainStructure):
         this map.
 
 
-        Paramaters
+        Parameters
         ----------
         points: PointCloud
         keep_labels: bool
@@ -407,7 +407,7 @@ class Volume(structure.BrainStructure):
             return self.get_boundingbox(clip=True, background=0.0, **fetch_kwargs).intersection(other)
         elif isinstance(other, Volume):
             if self.space != other.space:
-                raise NotImplementedError("Cannot intersect volumes from different spaces. Try comparing their boudning boxes.")
+                raise NotImplementedError("Cannot intersect volumes from different spaces. Try comparing their bounding boxes.")
             format = fetch_kwargs.pop('format', 'image')
             v1 = self.fetch(format=format, **fetch_kwargs)
             v2 = other.fetch(format=format, **fetch_kwargs)
@@ -461,7 +461,7 @@ class Volume(structure.BrainStructure):
             format = 'neuroglancer/precomputed'
 
         if format is None:
-            # preseve fetch order in SUPPORTED_FORMATS
+            # preserve fetch order in SUPPORTED_FORMATS
             possible_formats = [f for f in self.SUPPORTED_FORMATS if f in self.formats]
         elif format in self._FORMAT_LOOKUP:  # allow use of aliases
             possible_formats = [f for f in self._FORMAT_LOOKUP[format] if f in self.formats]
@@ -519,7 +519,7 @@ class Volume(structure.BrainStructure):
                     break
                 else:
                     break
-            # udpate the cache if fetch is successful
+            # update the cache if fetch is successful
             if result is not None:
                 self._FETCH_CACHE[fetch_hash] = result
                 while len(self._FETCH_CACHE) >= self._FETCH_CACHE_MAX_ENTRIES:
@@ -539,7 +539,7 @@ class Volume(structure.BrainStructure):
         """
         img = self.fetch(**fetch_kwargs)
         assert isinstance(img, Nifti1Image), NotImplementedError(
-            f"Connected components for type {type(img)} is not yet implemeneted."
+            f"Connected components for type {type(img)} is not yet implemented."
         )
         for label, component in connected_components(np.asanyarray(img.dataobj)):
             yield (
@@ -569,7 +569,7 @@ class Volume(structure.BrainStructure):
     def draw_samples(self, N: int, sample_size: int = 100, e: float = 1, sigma_mm=None, invert=False, **kwargs):
         """
         Draw samples from the volume, by interpreting its values as an
-        unnormalized empirical probability distribtution.
+        unnormalized empirical probability distributions.
         Any keyword arguments are passed over to fetch()
         """
         if not self.provides_image:
@@ -814,7 +814,7 @@ def from_pointcloud(
     sigmas = np.array(points.sigma_mm)[selection]
     bandwidth = np.mean(sigmas)
     if len(np.unique(sigmas)) > 1:
-        logger.warning(f"KDE of pointcloud uses average bandwith {bandwidth} instead of the points' individual sigmas.")
+        logger.warning(f"KDE of pointcloud uses average bandwidth {bandwidth} instead of the points' individual sigmas.")
 
     filtered_arr = filters.gaussian(voxelcount_img, bandwidth)
     if normalize:
@@ -841,7 +841,7 @@ def merge(volumes: List[Volume], labels: List[int] = [], **fetch_kwargs) -> Volu
     ----------
     volumes : List[Volume]
     labels : List[int], optional
-        Supply new labels to replace exisiting values per volume.
+        Supply new labels to replace existing values per volume.
 
     Returns
     -------

{siibra-1.0.1a0.dist-info → siibra-1.0.1a1.dist-info}/METADATA

@@ -1,6 +1,6 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.2
 Name: siibra
-Version: 1.0.1a0
+Version: 1.0.1a1
 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)
@@ -27,6 +27,15 @@ Requires-Dist: nilearn
 Requires-Dist: typing-extensions; python_version < "3.8"
 Requires-Dist: filelock
 Requires-Dist: ebrains-drive>=0.6.0
+Dynamic: author
+Dynamic: author-email
+Dynamic: classifier
+Dynamic: description
+Dynamic: description-content-type
+Dynamic: home-page
+Dynamic: requires-dist
+Dynamic: requires-python
+Dynamic: summary
 
 |License| |PyPI version| |doi| |Python versions| |Documentation Status|
 
@@ -34,7 +43,7 @@ Requires-Dist: ebrains-drive>=0.6.0
 siibra - Software interface for interacting with brain atlases
 ==============================================================
 
-Copyright 2020-2024, Forschungszentrum Jülich GmbH
+Copyright 2018-2024, Forschungszentrum Jülich GmbH
 
 *Authors: Big Data Analytics Group, Institute of Neuroscience and
 Medicine (INM-1), Forschungszentrum Jülich GmbH*

siibra-1.0.1a1.dist-info/RECORD

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