bluecellulab 2.6.46__py3-none-any.whl → 2.6.47__py3-none-any.whl

bluecellulab/tools.py

@@ -268,7 +268,8 @@ def detect_spike_step(
     inj_stop: float,
     step_level: float,
     section: str = "soma[0]",
-    segx: float = 0.5
+    segx: float = 0.5,
+    step_thresh: float = -20.
 ) -> bool:
     """Detect if there is a spike at a certain step level."""
     with IsolatedProcess() as runner:
@@ -284,7 +285,8 @@ def detect_spike_step(
                 inj_stop,
                 step_level,
                 section,
-                segx
+                segx,
+                step_thresh
             ],
         )
     return spike_detected
@@ -300,7 +302,8 @@ def detect_spike_step_subprocess(
     inj_stop: float,
     step_level: float,
     section: str = "soma[0]",
-    segx: float = 0.5
+    segx: float = 0.5,
+    step_thresh: float = -20.
 ) -> bool:
     """Detect if there is a spike at a certain step level."""
     cell = bluecellulab.Cell(
@@ -321,19 +324,19 @@ def detect_spike_step_subprocess(
     time = cell.get_time()
     voltage = cell.get_voltage_recording(section=neuron_section, segx=segx)
     voltage_step = voltage[np.where((time > inj_start) & (time < inj_stop))]
-    spike_detected = detect_spike(voltage_step)
+    spike_detected = detect_spike(voltage_step, step_thresh)
 
     cell.delete()
 
     return spike_detected
 
 
-def detect_spike(voltage: np.ndarray) -> bool:
+def detect_spike(voltage: np.ndarray, step_thresh: float = -20.) -> bool:
     """Detect if there is a spike in the voltage trace."""
     if len(voltage) == 0:
         return False
     else:
-        return bool(np.max(voltage) > -20)  # bool not np.bool_
+        return bool(np.max(voltage) > step_thresh)  # bool not np.bool_
 
 
 def search_threshold_current(
@@ -348,7 +351,8 @@ def search_threshold_current(
     max_current: float,
     current_precision: float = 0.01,
     section: str = "soma[0]",
-    segx: float = 0.5
+    segx: float = 0.5,
+    step_thresh: float = -20.
 ):
     """Search current necessary to reach threshold."""
     if abs(max_current - min_current) < current_precision:
@@ -359,7 +363,7 @@ def search_threshold_current(
     spike_detected = detect_spike_step(
         template_name, morphology_path, template_format, emodel_properties,
         hyp_level, inj_start, inj_stop, med_current,
-        section=section, segx=segx
+        section=section, segx=segx, step_thresh=step_thresh
     )
     logger.info("Spike threshold detection at: %f nA" % med_current)
 
@@ -369,14 +373,16 @@ def search_threshold_current(
                                         hyp_level, inj_start, inj_stop,
                                         min_current, med_current,
                                         current_precision,
-                                        section=section, segx=segx)
+                                        section=section, segx=segx,
+                                        step_thresh=step_thresh)
     else:
         return search_threshold_current(template_name, morphology_path,
                                         template_format, emodel_properties,
                                         hyp_level, inj_start, inj_stop,
                                         med_current, max_current,
                                         current_precision,
-                                        section=section, segx=segx)
+                                        section=section, segx=segx,
+                                        step_thresh=step_thresh)
 
 
 def check_empty_topology() -> bool:
@@ -435,7 +441,8 @@ def calculate_rheobase(cell: Cell,
                        threshold_search_stim_start: float = 300.0,
                        threshold_search_stim_stop: float = 1000.0,
                        section: str = "soma[0]",
-                       segx: float = 0.5) -> float:
+                       segx: float = 0.5,
+                       step_thresh: float = -20.) -> float:
     """Calculate the rheobase by first computing the upper bound threshold
     current.
 
@@ -474,7 +481,8 @@ def calculate_rheobase(cell: Cell,
         max_current=upperbound_threshold_current,
         current_precision=0.005,
         section=section,
-        segx=segx
+        segx=segx,
+        step_thresh=threshold_voltage
     )
 
     return rheobase

{bluecellulab-2.6.46.dist-info → bluecellulab-2.6.47.dist-info}/METADATA

@@ -1,6 +1,6 @@
-Metadata-Version: 2.2
+Metadata-Version: 2.4
 Name: bluecellulab
-Version: 2.6.46
+Version: 2.6.47
 Summary: Biologically detailed neural network simulations and analysis.
 Author: Blue Brain Project, EPFL
 License: Apache2.0
@@ -27,6 +27,7 @@ Requires-Dist: pydantic<3.0.0,>=2.5.2
 Requires-Dist: typing-extensions>=4.8.0
 Requires-Dist: networkx>=3.1
 Requires-Dist: h5py>=3.8.0
+Dynamic: license-file
 
 |banner|
 

{bluecellulab-2.6.46.dist-info → bluecellulab-2.6.47.dist-info}/RECORD

@@ -10,7 +10,7 @@ bluecellulab/plotwindow.py,sha256=ePU-EegZ1Sqk0SoYYiQ6k24ZO4s3Hgfpx10uePiJ5xM,27
 bluecellulab/psection.py,sha256=FSOwRNuOTyB469BM-jPEf9l1J59FamXmzrQgBI6cnP4,6174
 bluecellulab/psegment.py,sha256=PTgoGLqM4oFIdF_8QHFQCU59j-8TQmtq6PakiGUQhIo,3138
 bluecellulab/rngsettings.py,sha256=2Ykb4Ylk3XTs58x1UIxjg8XJqjSpnCgKRZ8avXCDpxk,4237
-bluecellulab/tools.py,sha256=pljNpD7dXvnKlgKoyc3YdGH3uDvhukWPHH7ausROwVM,17604
+bluecellulab/tools.py,sha256=yy2_XBANaCQEqBeCIRiQfWJUidth9_igldVOSuSp5l4,18018
 bluecellulab/type_aliases.py,sha256=DvgjERv2Ztdw_sW63JrZTQGpJ0x5uMTFB5hcBHDb0WA,441
 bluecellulab/utils.py,sha256=SbOOkzw1YGjCKV3qOw0zpabNEy7V9BRtgMLsQJiFRq4,1526
 bluecellulab/verbosity.py,sha256=T0IgX7DrRo19faxrT4Xzb27gqxzoILQ8FzYKxvUeaPM,1342
@@ -65,9 +65,9 @@ bluecellulab/stimulus/stimulus.py,sha256=a_hKJUtZmIgjiFjbJf6RzUPokELqn0IHCgIWGw5
 bluecellulab/synapse/__init__.py,sha256=RW8XoAMXOvK7OG1nHl_q8jSEKLj9ZN4oWf2nY9HAwuk,192
 bluecellulab/synapse/synapse_factory.py,sha256=NHwRMYMrnRVm_sHmyKTJ1bdoNmWZNU4UPOGu7FCi-PE,6987
 bluecellulab/synapse/synapse_types.py,sha256=zs_yBvGTH4QrbQF3nEViidyq1WM_ZcTSFdjUxB3khW0,16871
-bluecellulab-2.6.46.dist-info/AUTHORS.txt,sha256=EDs3H-2HXBojbma10psixk3C2rFiOCTIREi2ZAbXYNQ,179
-bluecellulab-2.6.46.dist-info/LICENSE,sha256=dAMAR2Sud4Nead1wGFleKiwTZfkTNZbzmuGfcTKb3kg,11335
-bluecellulab-2.6.46.dist-info/METADATA,sha256=K_c4bi64niRS0b4hN6OuhhTO9ax-u6hlzCLz_CAZjQ0,8214
-bluecellulab-2.6.46.dist-info/WHEEL,sha256=52BFRY2Up02UkjOa29eZOS2VxUrpPORXg1pkohGGUS8,91
-bluecellulab-2.6.46.dist-info/top_level.txt,sha256=VSyEP8w9l3pXdRkyP_goeMwiNA8KWwitfAqUkveJkdQ,13
-bluecellulab-2.6.46.dist-info/RECORD,,
+bluecellulab-2.6.47.dist-info/licenses/AUTHORS.txt,sha256=EDs3H-2HXBojbma10psixk3C2rFiOCTIREi2ZAbXYNQ,179
+bluecellulab-2.6.47.dist-info/licenses/LICENSE,sha256=dAMAR2Sud4Nead1wGFleKiwTZfkTNZbzmuGfcTKb3kg,11335
+bluecellulab-2.6.47.dist-info/METADATA,sha256=rydGOCvn6Y2v-KNPtssf3Au4IxaW2B_mo5nT5hf1QXA,8236
+bluecellulab-2.6.47.dist-info/WHEEL,sha256=0CuiUZ_p9E4cD6NyLD6UG80LBXYyiSYZOKDm5lp32xk,91
+bluecellulab-2.6.47.dist-info/top_level.txt,sha256=VSyEP8w9l3pXdRkyP_goeMwiNA8KWwitfAqUkveJkdQ,13
+bluecellulab-2.6.47.dist-info/RECORD,,

{bluecellulab-2.6.46.dist-info → bluecellulab-2.6.47.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: setuptools (76.0.0)
+Generator: setuptools (80.3.1)
 Root-Is-Purelib: true
 Tag: py3-none-any