bluecellulab 2.5.9__py3-none-any.whl → 2.5.10__py3-none-any.whl

bluecellulab/cell/core.py

@@ -142,7 +142,8 @@ class Cell(InjectableMixin, PlottableMixin):
                             dt=self.record_dt)
 
         self.delayed_weights = queue.PriorityQueue()  # type: ignore
-        self.psections, self.secname_to_psection = init_psections(public_hoc_cell(self.cell))
+        self.psections: dict[int, PSection] = {}
+        self.secname_to_psection: dict[str, PSection] = {}
 
         # Keep track of when a cell is made passive by make_passive()
         # Used to know when re_init_rng() can be executed
@@ -155,6 +156,11 @@ class Cell(InjectableMixin, PlottableMixin):
         # as the object exists
         self.persistent: list[HocObjectType] = []
 
+    def _init_psections(self) -> None:
+        """Initialize the psections of the cell."""
+        if not self.psections:
+            self.psections, self.secname_to_psection = init_psections(public_hoc_cell(self.cell))
+
     def _extract_sections(self, sections) -> SectionMapping:
         res: SectionMapping = {}
         for section in sections:
@@ -198,6 +204,7 @@ class Cell(InjectableMixin, PlottableMixin):
 
     def get_psection(self, section_id: int | str) -> PSection:
         """Return a python section with the specified section id."""
+        self._init_psections()
         if isinstance(section_id, int):
             return self.psections[section_id]
         elif isinstance(section_id, str):

bluecellulab/cell/plotting.py

@@ -60,6 +60,7 @@ class PlottableMixin:
             scale_bar_size=10.0,
             fig_title=None):
         """Show a dendrogram of the cell."""
+        self._init_psections()
         cell_dendrogram = bluecellulab.Dendrogram(
             self.psections,
             variable=variable,

bluecellulab/psection.py

@@ -13,6 +13,7 @@
 # limitations under the License.
 """Represents a python version of NEURON Section (for drawing)."""
 from __future__ import annotations
+import re
 import neuron
 
 import bluecellulab
@@ -75,21 +76,6 @@ class PSection:
         self.pchildren: list[PSection] = []
         self.isec = isec
 
-        if 'apic' in self.name:
-            self.section_type = 'apical'
-        elif 'dend' in self.name:
-            self.section_type = 'basal'
-        elif 'soma' in self.name:
-            self.section_type = 'somatic'
-        elif 'axon' in self.name:
-            self.section_type = 'axonal'
-        elif 'myelin' in self.name:
-            self.section_type = 'myelin'
-        else:
-            raise Exception(
-                "PSection: Section of unknown type: %s" %
-                self.name)
-
         self.psegments: list[PSegment] = []
         self.maxsegdiam = 0.0
         for hsegment in hsection:
@@ -101,6 +87,15 @@ class PSection:
         self.xSpacing = 1.0
         self.ySpacing = 5.0
 
+    @property
+    def section_type(self) -> str:
+        """Return the type of the section."""
+        # From Cell[0].soma[0] -> soma
+        matches = re.findall(r'\.([^.\[\]]+)\[', self.name)
+        if matches:
+            return matches[-1]  # Return the last match
+        return 'unknown'  # Return 'unknown' if no matches are found
+
     @property
     def is_leaf(self) -> bool:
         """Return true if section is a leaf in the morphological structure."""

bluecellulab/psegment.py

@@ -17,7 +17,7 @@ import neuron
 
 from bluecellulab.neuron_interpreter import eval_neuron
 
-type_colormap = {'apical': 'm', 'basal': 'r', 'somatic': 'k', 'axonal': 'b', 'myelin': 'g'}
+type_colormap = {'apic': 'm', 'dend': 'r', 'soma': 'k', 'axon': 'b', 'myelin': 'g', 'unknown': 'c'}
 
 
 class PSegment:

{bluecellulab-2.5.9.dist-info → bluecellulab-2.5.10.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: bluecellulab
-Version: 2.5.9
+Version: 2.5.10
 Summary: Biologically detailed neural network simulations and analysis.
 Author: Blue Brain Project, EPFL
 License: Apache2.0

{bluecellulab-2.5.9.dist-info → bluecellulab-2.5.10.dist-info}/RECORD

@@ -7,8 +7,8 @@ bluecellulab/graph.py,sha256=ODiQy4xjRVxtNITXeXpYnqHas0wR7gZ_aXuDAF7jMq4,3419
 bluecellulab/importer.py,sha256=zwVi1Nx2f8xzFfzxzYoXa7gfi7DQapqkRJII5sBbRyY,2900
 bluecellulab/neuron_interpreter.py,sha256=hXig_u3T6JmEHbkV8ZblEZtX0kY80ate4VpRtANNFrM,2185
 bluecellulab/plotwindow.py,sha256=UVHzml-BB83m5Qr-YGkjR9kB-vSW8mM0Owh2j95yIaU,2721
-bluecellulab/psection.py,sha256=EgAS8IS9DcYv2xOkNISgfg_CfRc0nDfRFjvgQhyi9eY,6328
-bluecellulab/psegment.py,sha256=rBryDYHC_uDK9itfXXrFZ0DL9F6WgRICL0j5EHN56QM,3125
+bluecellulab/psection.py,sha256=SYI2mGUIp8UiuMkyp9ITChHVLbJ0fDsEmen1pAbgNJQ,6174
+bluecellulab/psegment.py,sha256=02DkvazPGjnwjfjn1K8CZqdcVWnUhYpgrjqjoHNz6jM,3133
 bluecellulab/rngsettings.py,sha256=Dlt34dc4AoWyxCCzUK3Jlui90VCK20xHg6gD_OJzPIw,4237
 bluecellulab/tools.py,sha256=JrAfMVozfucwcyGklweMvEM7uGnTnWIDmk4eqI-43Es,11169
 bluecellulab/type_aliases.py,sha256=DvgjERv2Ztdw_sW63JrZTQGpJ0x5uMTFB5hcBHDb0WA,441
@@ -18,9 +18,9 @@ bluecellulab/analysis/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3h
 bluecellulab/analysis/inject_sequence.py,sha256=jfEESRAUKAWgjceNWfx3Rwe1gDNWhxwZL4PfnJZCzrg,4930
 bluecellulab/cell/__init__.py,sha256=Sbc0QOsJ8E7tSwf3q7fsXuE_SevBN6ZmoCVyyU5zfII,208
 bluecellulab/cell/cell_dict.py,sha256=PVmZsjhZ9jp3HC-8QmdFqp-crAcVMSVeLWujcOPLlpo,1346
-bluecellulab/cell/core.py,sha256=uxAWAZ6NpODJ3O77p0JWL6AVey3lOyetU3SVZxP4a9Q,31201
+bluecellulab/cell/core.py,sha256=MtrVQAxT82dc9uQuWZyTQfc6Oczrnc_y_9hcyBqUT7w,31467
 bluecellulab/cell/injector.py,sha256=XC49VSHw78xCHzLJKO_-unnnVZAZXsYg5qbmZPx01AA,18091
-bluecellulab/cell/plotting.py,sha256=_hZs5oYG4vmJBVf05cJ2O_cVazi5Eap8OkL9BtIwjW8,4001
+bluecellulab/cell/plotting.py,sha256=hW5KAmaSonJ1tgR6xRrnfVe33I5mBsBUrKJQwGvAbUc,4032
 bluecellulab/cell/random.py,sha256=FDby9BN4eJT27COwHP59bhDE2v-c6rdOKNFj3cYZTVY,1773
 bluecellulab/cell/recording.py,sha256=dekJspPb_5yrS6WR3aXtvZ6KWwMNbyhe5aIOVtNDHpY,342
 bluecellulab/cell/section_distance.py,sha256=J8-oqgCHzRaJkpfjPUR6NFtXDhwbrXad9nDaTCKNkTU,3908
@@ -61,9 +61,9 @@ bluecellulab/stimulus/factory.py,sha256=AOby3Sp2g8BJsRccz3afazfCyysyWIgLtcliWlye
 bluecellulab/synapse/__init__.py,sha256=RW8XoAMXOvK7OG1nHl_q8jSEKLj9ZN4oWf2nY9HAwuk,192
 bluecellulab/synapse/synapse_factory.py,sha256=YkvxbdGF-u-vxYdbRNTlX-9AtSC_3t_FQRFhybwzgrk,6805
 bluecellulab/synapse/synapse_types.py,sha256=4gne-hve2vq1Lau-LAVPsfLjffVYqAYBW3kCfC7_600,16871
-bluecellulab-2.5.9.dist-info/AUTHORS.txt,sha256=EDs3H-2HXBojbma10psixk3C2rFiOCTIREi2ZAbXYNQ,179
-bluecellulab-2.5.9.dist-info/LICENSE,sha256=xOouu1gC1GGklDxkITlaVl60I9Ab860O-nZsFbWydvU,11749
-bluecellulab-2.5.9.dist-info/METADATA,sha256=zDUbQYoAFBVjKO3yIkbYZvBC0sUA_8nO3TbECj-qFM4,7025
-bluecellulab-2.5.9.dist-info/WHEEL,sha256=GJ7t_kWBFywbagK5eo9IoUwLW6oyOeTKmQ-9iHFVNxQ,92
-bluecellulab-2.5.9.dist-info/top_level.txt,sha256=VSyEP8w9l3pXdRkyP_goeMwiNA8KWwitfAqUkveJkdQ,13
-bluecellulab-2.5.9.dist-info/RECORD,,
+bluecellulab-2.5.10.dist-info/AUTHORS.txt,sha256=EDs3H-2HXBojbma10psixk3C2rFiOCTIREi2ZAbXYNQ,179
+bluecellulab-2.5.10.dist-info/LICENSE,sha256=xOouu1gC1GGklDxkITlaVl60I9Ab860O-nZsFbWydvU,11749
+bluecellulab-2.5.10.dist-info/METADATA,sha256=MEgGgaV3rXDUcTU5EntzGyw3GinZSWicJnC0cQuPrXo,7026
+bluecellulab-2.5.10.dist-info/WHEEL,sha256=GJ7t_kWBFywbagK5eo9IoUwLW6oyOeTKmQ-9iHFVNxQ,92
+bluecellulab-2.5.10.dist-info/top_level.txt,sha256=VSyEP8w9l3pXdRkyP_goeMwiNA8KWwitfAqUkveJkdQ,13
+bluecellulab-2.5.10.dist-info/RECORD,,