siibra 1.0.1a5__py3-none-any.whl → 1.0.1a8__py3-none-any.whl

siibra/VERSION

@@ -1 +1 @@
-1.0.1-alpha.5
+1.0.1-alpha.8

siibra/features/tabular/layerwise_cell_density.py

@@ -84,17 +84,20 @@ class LayerwiseCellDensity(
             )
             fields = cellfile.split("/")
             for layer in layer_volumes.index:
-                data.append({
-                    'layer': layer,
-                    'layername': layers["Name"].loc[layer],
-                    'counts': counts.loc[layer],
-                    'area_mu2': layers["Area(micron**2)"].loc[layer],
-                    'volume': layer_volumes.loc[layer],
-                    'density': counts.loc[layer] / layer_volumes.loc[layer],
-                    'regionspec': fields[-5],
-                    'section': int(fields[-3]),
-                    'patch': int(fields[-2]),
-                })
+                try:
+                    data.append({
+                        'layer': layer,
+                        'layername': layers["Name"].loc[layer],
+                        'counts': counts.loc[layer],
+                        'area_mu2': layers["Area(micron**2)"].loc[layer],
+                        'volume': layer_volumes.loc[layer],
+                        'density': counts.loc[layer] / layer_volumes.loc[layer],
+                        'regionspec': fields[-5],
+                        'section': int(fields[-3]),
+                        'patch': int(fields[-2]),
+                    })
+                except KeyError:
+                    continue
         return pd.DataFrame(data)
 
     @property

siibra/locations/location.py

@@ -31,7 +31,8 @@ class Location(BrainStructure):
     """
 
     # backend for transforming coordinates between spaces
-    SPACEWARP_SERVER = "https://hbp-spatial-backend.apps.hbp.eu/v1"
+    # for detail, see https://github.com/HumanBrainProject/hbp-spatial-backend
+    SPACEWARP_SERVER = "https://siibra-spatial-backend.apps.ebrains.eu/v1"
 
     # lookup of space identifiers to be used by SPACEWARP_SERVER
     SPACEWARP_IDS = {

siibra/volumes/parcellationmap.py

@@ -370,10 +370,9 @@ class Map(concept.AtlasConcept, configuration_folder="maps"):
         if kwargs_fragment is not None:
             if (mapindex.fragment is not None) and (kwargs_fragment != mapindex.fragment):
                 raise exceptions.ConflictingArgumentException(
-                    "Conflicting specifications for fetching volume fragment: "
-                    f"{mapindex.fragment} / {kwargs_fragment}"
+                    f"Conflicting specifications for fetching volume fragment{f' for region {region}'}: "
+                    f"supplied: {kwargs_fragment}, preconfigured: {mapindex.fragment}"
                 )
-            mapindex.fragment = kwargs_fragment
 
         if mapindex.volume is None:
             mapindex.volume = 0
@@ -387,7 +386,7 @@ class Map(concept.AtlasConcept, configuration_folder="maps"):
         return _volume.FilteredVolume(
             parent_volume=self.volumes[mapindex.volume],
             label=mapindex.label,
-            fragment=mapindex.fragment,
+            fragment=kwargs_fragment or mapindex.fragment,
         )
 
     def fetch(

{siibra-1.0.1a5.dist-info → siibra-1.0.1a8.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: siibra
-Version: 1.0.1a5
+Version: 1.0.1a8
 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-1.0.1a5.dist-info → siibra-1.0.1a8.dist-info}/RECORD

@@ -1,4 +1,4 @@
-siibra/VERSION,sha256=ipm-gM9pHLEb5l5Cx8ZcZ8wKJBYKiaWH87grIEoJ_OM,14
+siibra/VERSION,sha256=dmqTQ9qMHhodkJqBTHpXdWezVzO2JGnokqQCVhTeAZM,14
 siibra/__init__.py,sha256=1uWhsE93KG4N9wiWoMdEokUXxfoRcyznXDktjAGhpEI,4496
 siibra/commons.py,sha256=KmbRdX6pfKTgIgbYufxhkE9YiLQ35GObbw6VyFdRm_w,28016
 siibra/exceptions.py,sha256=6MlXOadwXcCsceOE4lmy4fLJyAaBCCVvJF6BZlMYjU8,1371
@@ -37,7 +37,7 @@ siibra/features/tabular/cell_density_profile.py,sha256=ScpjD9W-w-lLxdG6q42Zfyqe8
 siibra/features/tabular/cortical_profile.py,sha256=x0TqZh8FzcVx13EwPtbt8kBYfF1dREWWuf9BhpWzj7o,12542
 siibra/features/tabular/gene_expression.py,sha256=8gJuUrL13oIySOPgiy5j46a5Udae_cJ1_QfrUHA72CI,10309
 siibra/features/tabular/layerwise_bigbrain_intensities.py,sha256=iFCNG641yCSuIXFTY30xgRQqLERDHMqJrAy3SdKkAJ4,2118
-siibra/features/tabular/layerwise_cell_density.py,sha256=MYFiUfDfx6XQj8dezV5-3eKWBg0VOn0T3a1utELE2PM,6513
+siibra/features/tabular/layerwise_cell_density.py,sha256=nMgREMddxff-nW43wnLGfaYTDaapiSu2z2vyHfaUm0M,6640
 siibra/features/tabular/receptor_density_fingerprint.py,sha256=CvFJv940whxzavhEQWnTjueDEq0ZoiuYVpqUpR8t-Ec,8065
 siibra/features/tabular/receptor_density_profile.py,sha256=VW2Ry8ifQLfmiBDKqIdvaN7K1YzMENGU92Lnm4wA8P0,3724
 siibra/features/tabular/regional_timeseries_activity.py,sha256=wuno4oI1I-dyxRr8-tLFj42iaD6dYZiPigCqVMhrG50,10027
@@ -50,7 +50,7 @@ siibra/livequeries/query.py,sha256=P_uUVFxv4KyOPQXh2WnDQxuaSSBK_dXPKEr8I0-4xSQ,1
 siibra/locations/__init__.py,sha256=yTJVMdv-pICm_gUYLQ09lDKSkZBfgUihM6LNv07e_yk,3546
 siibra/locations/boundingbox.py,sha256=ACRittMABMZwLPzGnv5Z5E6cIHJfCFWv851s5Bg87WQ,16442
 siibra/locations/experimental.py,sha256=kd9yroLKpnY-N6hoMVgtHK4pVdgeGqhpad4GyxYy6LU,14484
-siibra/locations/location.py,sha256=tb__0td1c7_3BKJFqqEqwspO5m8BZ8ZlyYwvtVBq8SY,4706
+siibra/locations/location.py,sha256=ay2UoyQZdnzdCMAwpK-evnnzx4DCVEhbQRz55EzerfI,4792
 siibra/locations/point.py,sha256=cL2hqbejec24ZoXpbBQQXtHZ-H7KcyxnbITzSBjkXTs,12675
 siibra/locations/pointcloud.py,sha256=AxtR43xG4i1hUXNmal4F_g5WKQo_A1ZtW4l4jsf3p6o,14108
 siibra/retrieval/__init__.py,sha256=E-UA8rDQZFGkHmAcmit6siONo7G2mH_Y0xgLlR1RfvY,1062
@@ -64,7 +64,7 @@ siibra/vocabularies/gene_names.json,sha256=i-gnh753GyZtQfX_dWibNYr_d5ccDPHooOwsd
 siibra/vocabularies/receptor_symbols.json,sha256=F6DZIArPCBmJV_lWGV-zDpBBH_GOJOZm67LBE4qzMa4,5722
 siibra/vocabularies/region_aliases.json,sha256=T2w1wRlxPNTsPppXn0bzC70tNsb8mOjLsoHuxDSYm2w,8563
 siibra/volumes/__init__.py,sha256=9eiVjgGTqq9BiFJaLVLABtTrhIcE2k3Cn51yC4EKplg,936
-siibra/volumes/parcellationmap.py,sha256=z5wWxK_kcFpS_ROpc9ny4aCbM7P9qc3DRDxrOKGp2Hk,51409
+siibra/volumes/parcellationmap.py,sha256=M1ZGEWZ0owDcP5O9yrsZr8HloQa1knZzbI9g-v4rcYo,51430
 siibra/volumes/sparsemap.py,sha256=Yv07LIlt5yigw-ubWFq89hHnsivT7dymYCsCTe7Wu9I,17167
 siibra/volumes/volume.py,sha256=wLmtqoXBDoPvE3WBO_Hc8uny3cdE9mB0KgdCq0LOTa0,32408
 siibra/volumes/providers/__init__.py,sha256=AHZCjutCqO4mnHxyykVjqxlz85jDqFWcSjsa4ciwc1A,934
@@ -73,8 +73,8 @@ siibra/volumes/providers/gifti.py,sha256=JGuixlSJTVjbDU_M5oMDCV8BAwIzuczhnI-qZ7L
 siibra/volumes/providers/neuroglancer.py,sha256=b3TiJ6yrx_akLFKgHRKZyHculzzRIqbZ7U3TMQHy6-k,28618
 siibra/volumes/providers/nifti.py,sha256=aAzkmeDZaXRZ-dkAeEb2cSywNn9WzIz0z7yFtN6iNpU,10135
 siibra/volumes/providers/provider.py,sha256=Vn02au_LKynO5SIfqLyjqzxCf7JD9Wm4i7yEFcTX0WU,3585
-siibra-1.0.1a5.dist-info/licenses/LICENSE,sha256=xx0jnfkXJvxRnG63LTGOxlggYnIysveWIZ6H3PNdCrQ,11357
-siibra-1.0.1a5.dist-info/METADATA,sha256=CO_Qej2SZ4h9saebuTGGPQLhPZOI4PQE4xSEHKVqKl4,9301
-siibra-1.0.1a5.dist-info/WHEEL,sha256=0CuiUZ_p9E4cD6NyLD6UG80LBXYyiSYZOKDm5lp32xk,91
-siibra-1.0.1a5.dist-info/top_level.txt,sha256=NF0OSGLL0li2qyC7MaU0iBB5Y9S09_euPpvisD0-8Hg,7
-siibra-1.0.1a5.dist-info/RECORD,,
+siibra-1.0.1a8.dist-info/licenses/LICENSE,sha256=xx0jnfkXJvxRnG63LTGOxlggYnIysveWIZ6H3PNdCrQ,11357
+siibra-1.0.1a8.dist-info/METADATA,sha256=Gn0sAsS0D8fMfA0Zvlw8VScF18At_CnN_wJU2lc6h6c,9301
+siibra-1.0.1a8.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+siibra-1.0.1a8.dist-info/top_level.txt,sha256=NF0OSGLL0li2qyC7MaU0iBB5Y9S09_euPpvisD0-8Hg,7
+siibra-1.0.1a8.dist-info/RECORD,,

{siibra-1.0.1a5.dist-info → siibra-1.0.1a8.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: setuptools (80.3.1)
+Generator: setuptools (80.9.0)
 Root-Is-Purelib: true
 Tag: py3-none-any