bluecellulab 2.5.8__tar.gz → 2.5.10__tar.gz

{bluecellulab-2.5.8 → bluecellulab-2.5.10}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: bluecellulab
-Version: 2.5.8
+Version: 2.5.10
 Summary: Biologically detailed neural network simulations and analysis.
 Author: Blue Brain Project, EPFL
 License: Apache2.0

{bluecellulab-2.5.8 → bluecellulab-2.5.10}/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-2.5.8 → bluecellulab-2.5.10}/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-2.5.8 → bluecellulab-2.5.10}/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-2.5.8 → bluecellulab-2.5.10}/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-2.5.8 → bluecellulab-2.5.10}/bluecellulab/tools.py

@@ -290,8 +290,7 @@ def detect_spike_step_subprocess(
 
     time = cell.get_time()
     voltage = cell.get_soma_voltage()
-    time_step = time[np.where((time > inj_start) & (time < inj_stop))]
-    voltage_step = voltage[np.where((time_step > inj_start) & (time_step < inj_stop))]
+    voltage_step = voltage[np.where((time > inj_start) & (time < inj_stop))]
     spike_detected = detect_spike(voltage_step)
 
     cell.delete()

{bluecellulab-2.5.8 → bluecellulab-2.5.10}/bluecellulab.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: bluecellulab
-Version: 2.5.8
+Version: 2.5.10
 Summary: Biologically detailed neural network simulations and analysis.
 Author: Blue Brain Project, EPFL
 License: Apache2.0

{bluecellulab-2.5.8 → bluecellulab-2.5.10}/tests/test_psection.py

@@ -79,3 +79,12 @@ class TestPSection:
         assert len(self.psections) > 0
         assert len(self.secname_to_psection) > 0
         assert len(self.psections) == len(self.secname_to_psection)
+
+    def test_section_type(self):
+        """Test section type property."""
+        soma_section = self.psections[0]
+        assert soma_section.section_type == "soma"
+        leaf_section = self.psections[245]
+        assert leaf_section.section_type == "apic"
+        leaf_section.name = "a pattern that does not match"
+        assert leaf_section.section_type == "unknown"