siibra 0.4a86__py3-none-any.whl → 0.4a88__py3-none-any.whl

siibra/VERSION

@@ -1 +1 @@
-0.4a86
+0.4a88

siibra/commons.py

@@ -698,6 +698,7 @@ class Species(Enum):
     MACACA_MULATTA = 5
     MACACA_FUSCATA = 6
     CHLOROCEBUS_AETHIOPS_SABAEUS = 7
+    CALLITHRIX_JACCHUS = 8
 
     UNSPECIFIED_SPECIES = 999
 

siibra/configuration/factory.py

@@ -460,6 +460,10 @@ class Factory:
             return volume_of_interest.LSFMVolumeOfInterest(
                 modality="Light Sheet Fluorescence Microscopy", **kwargs
             )
+        elif modality == "morphometry":
+            return volume_of_interest.MorphometryVolumeOfInterest(
+                modality="Morphometry", **kwargs
+            )
         else:
             raise ValueError(f"No method for building image section feature type {modality}.")
 

siibra/features/anchor.py

@@ -146,24 +146,21 @@ class AnatomicalAnchor:
         """
         if concept not in self._assignments:
             matches: List[AnatomicalAssignment] = []
-            if isinstance(concept, Space):
-                if self.space == concept:
-                    matches.append(
-                        AnatomicalAssignment(self.space, concept, AssignmentQualification.EXACT)
-                    )
-            elif isinstance(concept, Region):
-                if concept.species in self.species:
-                    if any(_.matches(self._regionspec) for _ in concept) \
-                            or self.has_region_aliases:  # dramatic speedup, since decoding _regionspec is expensive
-                        for r in self.regions:
-                            matches.append(AnatomicalAnchor.match_regions(r, concept))
-                    if len(concept.root.find(self._regionspec)) == 0:
-                        # We perform the (quite expensive) location-to-region test
-                        # only if this anchor's regionspec is not known to the
-                        # parcellation of the query region. Otherwise we can rely
-                        # on the region-to-region test.
-                        if self.location is not None:
-                            matches.append(AnatomicalAnchor.match_location_to_region(self.location, concept))
+            if isinstance(concept, Space) and self.space == concept:
+                matches.append(
+                    AnatomicalAssignment(self.space, concept, AssignmentQualification.EXACT)
+                )
+            elif isinstance(concept, Region) and concept.species in self.species:
+                hierarchy_search = concept.root.find(self._regionspec)
+                if len(hierarchy_search) > 0 or self.has_region_aliases:  # dramatic speedup, since decoding _regionspec is expensive
+                    for r in self.regions:
+                        matches.append(AnatomicalAnchor.match_regions(r, concept))
+                if len(hierarchy_search) == 0 and self.location is not None:
+                    # We perform the (quite expensive) location-to-region test
+                    # only if this anchor's regionspec is not known to the
+                    # parcellation of the query region. Otherwise we can rely
+                    # on the region-to-region test.
+                    matches.append(AnatomicalAnchor.match_location_to_region(self.location, concept))
             elif isinstance(concept, Location):
                 if self.location is not None:
                     matches.append(AnatomicalAnchor.match_locations(self.location, concept))

siibra/features/image/__init__.py

@@ -21,7 +21,8 @@ from .volume_of_interest import (
     MRIVolumeOfInterest,
     XPCTVolumeOfInterest,
     LSFMVolumeOfInterest,
-    DTIVolumeOfInterest
+    DTIVolumeOfInterest,
+    MorphometryVolumeOfInterest
     # SegmentedVolumeOfInterest
 )
 from .sections import CellbodyStainedSection

siibra/features/image/volume_of_interest.py

@@ -79,6 +79,14 @@ class LSFMVolumeOfInterest(
     def __init__(self, modality, **kwargs):
         image.Image.__init__(self, **kwargs, modality=modality)
 
+class MorphometryVolumeOfInterest(
+    image.Image,
+    configuration_folder="features/images/vois/morphometry",
+    category="macrostructural"
+):
+    def __init__(self, modality, **kwargs):
+        image.Image.__init__(self, **kwargs, modality=modality)
+
 # class SegmentedVolumeOfInterest(
 #     image.Image,
 #     configuration_folder="features/images/vois/segmentation",

{siibra-0.4a86.dist-info → siibra-0.4a88.dist-info}/METADATA

@@ -1,6 +1,6 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.4
 Name: siibra
-Version: 0.4a86
+Version: 0.4a88
 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)
@@ -25,6 +25,16 @@ 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: license-file
+Dynamic: requires-dist
+Dynamic: requires-python
+Dynamic: summary
 
 |License| |PyPI version| |doi| |Python versions| |Documentation Status|
 

{siibra-0.4a86.dist-info → siibra-0.4a88.dist-info}/RECORD

@@ -1,9 +1,9 @@
-siibra/VERSION,sha256=kzqfd3af8_hjOX7jAHdp_vlcXbPCyzBwJa_k6MVj4Ow,7
+siibra/VERSION,sha256=qY8OsFdKoScwOjQMSZKCgqDP2JATV_eRVzVbFMJYt5U,7
 siibra/__init__.py,sha256=qBxxMRyl9RojNt0twQr2LDk1Nyk5eNsPHFxxoIwnpx4,4540
-siibra/commons.py,sha256=PImsqrZBp2Mn_9ZEJOxEOd4i-w_HPMv4sUcHCtN9cPw,25868
+siibra/commons.py,sha256=y0yLQw1wWn8N9EgQGW2B0aAuo3FM_5zthMcEcvuvmH8,25895
 siibra/configuration/__init__.py,sha256=-_Kuf0TfMEdFXiSCTAdcHUL_krA8-cxhJypSNNay53Q,752
 siibra/configuration/configuration.py,sha256=x06QsaqGQbce1d9TuFCCYEgMWJBlLbkt8B3zTfYz5RE,6887
-siibra/configuration/factory.py,sha256=fpeyl3BbeDsjBdtqd9gNdQ_gEFuZQ1qUmDXYA5rB8Wg,20901
+siibra/configuration/factory.py,sha256=olRMm__Q2DeQX5CoBFkmfBdgXlWhZ3Wsy-oKG7s9BuQ,21071
 siibra/core/__init__.py,sha256=z22elfoi5_TscUb17-pBoGyfT_q9PQpvgOgSLEJe2WE,916
 siibra/core/atlas.py,sha256=YwhVWAIT0XGfzKjSuQUNpljdIE4VP4crNQ3VNfTrgKg,7868
 siibra/core/concept.py,sha256=rKR7FO1HaFdy076Dy0y9Bjcdu_tcYUHbxLYNZxH7XTY,9595
@@ -15,7 +15,7 @@ siibra/explorer/__init__.py,sha256=_9gCCp7P8AniGlztulrRyleIOEKcNZlBFVurtnI8GBM,4
 siibra/explorer/url.py,sha256=mUAFN7OHfLELfdqqJmSdAkmXJjKCv6Qh5RHtyxNQjfo,5868
 siibra/explorer/util.py,sha256=Z2ruicDL3S_qcxhHHW0GF1q5-r963tJpzgtQmAn8YSM,1424
 siibra/features/__init__.py,sha256=Y5q2M7HoToTcfAdO50jmnPGZybJOi5GyEcbxQRscJjo,1518
-siibra/features/anchor.py,sha256=1w9VuSEWC3oapph8GtbsW26kvMcE7_9ik7281oRMjlE,14245
+siibra/features/anchor.py,sha256=6XQC8kViFyxd6Xcwp4lMJi2XLoZVNpWevczU5lnhfgk,14135
 siibra/features/feature.py,sha256=YdIBmyJYFlJby6oIXxK1zFV6FJVr3_eygDynCLCe7vk,20478
 siibra/features/connectivity/__init__.py,sha256=ybKN9OfmabSeTx1I6WSrULu5dT6raefty8QB2XaiUrE,1077
 siibra/features/connectivity/functional_connectivity.py,sha256=AkRYufi4r3CeV50FLaI6kjKraQ4t9G58iPn521HRRGk,1407
@@ -25,10 +25,10 @@ siibra/features/connectivity/streamline_lengths.py,sha256=0a09Dag-eRvs1KgHSU47I3
 siibra/features/connectivity/tracing_connectivity.py,sha256=pyTMTLvkJL3ftk56s0AbT8dHexV4EyuTJ2yX27kLGfc,1083
 siibra/features/dataset/__init__.py,sha256=5h_wstfa3h35emL1qoKOtcFOiIjKZX9oIy-GwsChEyc,748
 siibra/features/dataset/ebrains.py,sha256=wdb1-4ovHE1duw2a9NSU0PYgqnlt8-f4pLsGwfTa8xw,2542
-siibra/features/image/__init__.py,sha256=UIECVLwKYKeuCPNa4WcjcLDuNr_3JxCyiOQSjBRf36U,1013
+siibra/features/image/__init__.py,sha256=V83hLmG0M0OYG60M2wYpUm9_H1kKTjadyDgnV25fBZc,1046
 siibra/features/image/image.py,sha256=1K4u6X6q2CV8avguE56LQQSe5ziahnLr8QFIdvMmFKE,3348
 siibra/features/image/sections.py,sha256=d4TQSs6nIKQ5vgi89htERfWOMgnvOA9k4LhaXBMWNbE,961
-siibra/features/image/volume_of_interest.py,sha256=DIv9GNOptfungLddA_CfrrCfY8p36rbWCT9xkE6K66w,2654
+siibra/features/image/volume_of_interest.py,sha256=6-Gu0Nw2tcNQC7RRnl7dMWP83BZeSwebLrooo5JLCnE,2910
 siibra/features/tabular/__init__.py,sha256=3DBwa8JtGd-npeOyyw6kJzcveKXadbqSATyJtTnY3-w,1176
 siibra/features/tabular/bigbrain_intensity_profile.py,sha256=-dXzznb6r1BhMjE8jOeugbZ3MjXo0AJkTtOw25SehYs,2238
 siibra/features/tabular/cell_density_profile.py,sha256=QICybWoFvyzyH0sVA79Q8WUEmXZLyIdge6arfOLkV78,9209
@@ -67,8 +67,8 @@ siibra/volumes/nifti.py,sha256=nGSCedjpsiy43XIiHQ2SRy9rPRK8Ci9QDq4AHKclCck,9030
 siibra/volumes/parcellationmap.py,sha256=phoMzNLI3Ig9rWvuD_c1yBm3ejLxAJGXtTHMXqw-ivc,44243
 siibra/volumes/sparsemap.py,sha256=j41ozLSgKri68-KDsqo46gEs4lT4aYsf2yMF4l-ruCo,21752
 siibra/volumes/volume.py,sha256=h_KrdDkpeoENnOrE7BlTZNXaZQGTrJXHX0eSyArxF-4,11667
-siibra-0.4a86.dist-info/LICENSE,sha256=xx0jnfkXJvxRnG63LTGOxlggYnIysveWIZ6H3PNdCrQ,11357
-siibra-0.4a86.dist-info/METADATA,sha256=qUNg7MNR_r_sL6BvtRddSiqRicW6hyvoY0Yw808w-_o,8328
-siibra-0.4a86.dist-info/WHEEL,sha256=PZUExdf71Ui_so67QXpySuHtCi3-J3wvF4ORK6k_S8U,91
-siibra-0.4a86.dist-info/top_level.txt,sha256=NF0OSGLL0li2qyC7MaU0iBB5Y9S09_euPpvisD0-8Hg,7
-siibra-0.4a86.dist-info/RECORD,,
+siibra-0.4a88.dist-info/licenses/LICENSE,sha256=xx0jnfkXJvxRnG63LTGOxlggYnIysveWIZ6H3PNdCrQ,11357
+siibra-0.4a88.dist-info/METADATA,sha256=Q09Y1v799aCg8izE1g9Ay0JeTKiIRBkfEHCb3Fntje0,8547
+siibra-0.4a88.dist-info/WHEEL,sha256=ooBFpIzZCPdw3uqIQsOo4qqbA4ZRPxHnOH7peeONza0,91
+siibra-0.4a88.dist-info/top_level.txt,sha256=NF0OSGLL0li2qyC7MaU0iBB5Y9S09_euPpvisD0-8Hg,7
+siibra-0.4a88.dist-info/RECORD,,

{siibra-0.4a86.dist-info → siibra-0.4a88.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: setuptools (75.6.0)
+Generator: setuptools (80.0.1)
 Root-Is-Purelib: true
 Tag: py3-none-any