siibra 1.0a14__py3-none-any.whl → 1.0.1a0__py3-none-any.whl

siibra/VERSION

@@ -1 +1 @@
-1.0a14
+1.0.1-alpha.0

siibra/__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");
@@ -39,7 +39,7 @@ from . import configuration
 from . import experimental
 from .configuration import factory
 from . import features, livequeries
-from siibra.locations import Point, PointSet
+from siibra.locations import Point, PointCloud
 
 import os as _os
 logger.info(f"Version: {__version__}")
@@ -51,7 +51,7 @@ logger.info(
 # forward access to some functions
 set_ebrains_token = _EbrainsRequest.set_token
 fetch_ebrains_token = _EbrainsRequest.fetch_token
-find_regions = _parcellation.Parcellation.find_regions
+find_regions = _parcellation.find_regions
 from_json = factory.Factory.from_json
 
 
@@ -107,6 +107,14 @@ def set_feasible_download_size(maxsize_gbyte):
 
 
 def set_cache_size(maxsize_gbyte: int):
+    """
+    siibra runs maintainance on its local cache to keep it under a predetermined
+    size of 2 gigabytes. This method changes the cache size.
+
+    Parameters
+    ----------
+    maxsize_gbyte : int
+    """
     assert maxsize_gbyte >= 0
     cache.SIZE_GIB = maxsize_gbyte
     logger.info(f"Set cache size to {maxsize_gbyte} GiB.")
@@ -142,7 +150,7 @@ def __dir__():
         "get_template",
         "MapType",
         "Point",
-        "PointSet",
+        "PointCloud",
         "QUIET",
         "VERBOSE",
         "fetch_ebrains_token",
@@ -150,5 +158,7 @@ def __dir__():
         "vocabularies",
         "__version__",
         "cache",
-        "warm_cache"
+        "warm_cache",
+        "set_cache_size",
+        "from_json",
     ]

siibra/commons.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");
@@ -35,6 +35,7 @@ except ImportError:
     # support python 3.7
     from typing_extensions import TypedDict
 
+logging.addLevelName(21, "INFO_WO_PROGRESS_BARS")
 logger = logging.getLogger(__name__.split(os.path.extsep)[0])
 ch = logging.StreamHandler()
 formatter = logging.Formatter("[{name}:{levelname}] {message}", style="{")
@@ -297,7 +298,7 @@ def siibra_tqdm(iterable: Iterable[T] = None, *args, **kwargs):
     return tqdm(
         iterable,
         *args,
-        disable=kwargs.pop("disable", False) or (logger.level > 20),
+        disable=kwargs.pop("disable", False) or (logger.level > logging.INFO),
         **kwargs
     )
 
@@ -365,9 +366,6 @@ class MapType(Enum):
     STATISTICAL = 2
 
 
-SIIBRA_DEFAULT_MAPTYPE = MapType.LABELLED
-SIIBRA_DEFAULT_MAP_THRESHOLD = 0.0
-
 REMOVE_FROM_NAME = [
     "hemisphere",
     " -",
@@ -585,49 +583,6 @@ def connected_components(
     )
 
 
-class PolyLine:
-    """Simple polyline representation which allows equidistant sampling.."""
-
-    def __init__(self, pts):
-        self.pts = pts
-        self.lengths = [
-            np.sqrt(np.sum((pts[i, :] - pts[i - 1, :]) ** 2))
-            for i in range(1, pts.shape[0])
-        ]
-
-    def length(self):
-        return sum(self.lengths)
-
-    def sample(self, d):
-
-        # if d is interable, we assume a list of sample positions
-        try:
-            iter(d)
-        except TypeError:
-            positions = [d]
-        else:
-            positions = d
-
-        samples = []
-        for s_ in positions:
-            s = min(max(s_, 0), 1)
-            target_distance = s * self.length()
-            current_distance = 0
-            for i, length in enumerate(self.lengths):
-                current_distance += length
-                if current_distance >= target_distance:
-                    p1 = self.pts[i, :]
-                    p2 = self.pts[i + 1, :]
-                    r = (target_distance - current_distance + length) / length
-                    samples.append(p1 + (p2 - p1) * r)
-                    break
-
-        if len(samples) == 1:
-            return samples[0]
-        else:
-            return np.array(samples)
-
-
 def unify_stringlist(L: list):
     """Adds asterisks to strings that appear multiple times, so the resulting
     list has only unique strings but still the same length, order, and meaning.

siibra/configuration/__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/configuration/configuration.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");