bluecellulab 2.6.58__py3-none-any.whl → 2.6.60__py3-none-any.whl

bluecellulab/tools.py

@@ -26,6 +26,7 @@ import bluecellulab
 from bluecellulab.cell import Cell
 from bluecellulab.circuit.circuit_access import EmodelProperties
 from bluecellulab.exceptions import UnsteadyCellError
+from bluecellulab.simulation.neuron_globals import NeuronGlobals
 from bluecellulab.simulation.parallel import IsolatedProcess
 from bluecellulab.utils import CaptureOutput
 from bluecellulab.type_aliases import NeuronSection
@@ -590,3 +591,37 @@ def resolve_source_nodes(source, source_type, cells, population):
             node_ids = [node_id for (pop, node_id) in cells.keys() if pop == population]
         compartment_nodes = None
     return node_ids, compartment_nodes
+
+
+def compute_memodel_properties(
+    cell,
+    spike_threshold_voltage=-30,
+    v_init=-80.0,
+    celsius=34.0,
+):
+    """Compute the threshold current and the input resistance of the cell.
+
+    Args:
+        cell (Cell): The cell model to compute properties for.
+        spike_threshold_voltage (float, optional): Voltage threshold for spike detection. Default is -30 mV.
+        v_init (float, optional): Initial membrane potential. Default is -80 mV.
+        celsius (float, optional): Temperature in Celsius. Default is 34.0 C.
+    """
+    # set initial voltage and temperature
+    neuron_globals = NeuronGlobals.get_instance()
+    neuron_globals.temperature = celsius
+    neuron_globals.v_init = v_init
+
+    # get me-model properties
+    holding_current = cell.hypamp if cell.hypamp else 0.0
+    rheobase = calculate_rheobase(
+        cell=cell, section="soma[0]", segx=0.5, threshold_voltage=spike_threshold_voltage
+    )
+    rin = calculate_input_resistance(
+        template_path=cell.template_params.template_filepath,
+        morphology_path=cell.template_params.morph_filepath,
+        template_format=cell.template_params.template_format,
+        emodel_properties=cell.template_params.emodel_properties,
+    )
+
+    return {"holding_current": holding_current, "rheobase": rheobase, "rin": rin}

bluecellulab/validation/validation.py

@@ -429,7 +429,7 @@ def thumbnail_test(template_params, rheobase, out_dir):
     outpath = plot_trace(
         recording,
         out_dir,
-        fname="thumbnail.pdf",
+        fname="thumbnail.png",
         title="",
         plot_current=False
     )

{bluecellulab-2.6.58.dist-info → bluecellulab-2.6.60.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: bluecellulab
-Version: 2.6.58
+Version: 2.6.60
 Summary: Biologically detailed neural network simulations and analysis.
 Author: Blue Brain Project, EPFL
 License: Apache2.0

{bluecellulab-2.6.58.dist-info → bluecellulab-2.6.60.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=Cc-Pv_7ban1EA9aqj8mfnjq-187llqj5WVzuQdesqhc,20395
+bluecellulab/tools.py,sha256=Wj3zEalJuyMzp0btoyWHXsCRpxyg6lNEuJfvmudlQmc,21767
 bluecellulab/type_aliases.py,sha256=DvgjERv2Ztdw_sW63JrZTQGpJ0x5uMTFB5hcBHDb0WA,441
 bluecellulab/utils.py,sha256=0NhwlzyLnSi8kziSfDsQf7pokO4qDkMJVAO33kSX4O0,2227
 bluecellulab/verbosity.py,sha256=T0IgX7DrRo19faxrT4Xzb27gqxzoILQ8FzYKxvUeaPM,1342
@@ -67,10 +67,10 @@ 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/validation/validation.py,sha256=X8Pwj2oCPiMjBdMMWj2SwRSbnyZcUjqFo3PGT-6lWho,18465
-bluecellulab-2.6.58.dist-info/licenses/AUTHORS.txt,sha256=EDs3H-2HXBojbma10psixk3C2rFiOCTIREi2ZAbXYNQ,179
-bluecellulab-2.6.58.dist-info/licenses/LICENSE,sha256=dAMAR2Sud4Nead1wGFleKiwTZfkTNZbzmuGfcTKb3kg,11335
-bluecellulab-2.6.58.dist-info/METADATA,sha256=OzN36WwPMe2uppSyBP5xvseDBhpFjou8kce_gnut0mc,8259
-bluecellulab-2.6.58.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
-bluecellulab-2.6.58.dist-info/top_level.txt,sha256=VSyEP8w9l3pXdRkyP_goeMwiNA8KWwitfAqUkveJkdQ,13
-bluecellulab-2.6.58.dist-info/RECORD,,
+bluecellulab/validation/validation.py,sha256=vLaOAyCO1qwwQ5Ud9X9NDX3iSsh_2S5tUA9xRmoDHiA,18465
+bluecellulab-2.6.60.dist-info/licenses/AUTHORS.txt,sha256=EDs3H-2HXBojbma10psixk3C2rFiOCTIREi2ZAbXYNQ,179
+bluecellulab-2.6.60.dist-info/licenses/LICENSE,sha256=dAMAR2Sud4Nead1wGFleKiwTZfkTNZbzmuGfcTKb3kg,11335
+bluecellulab-2.6.60.dist-info/METADATA,sha256=kLm4ryHnVcbAotV6m-03Mp3ZCxRQrPtA5j2Ot0YvE6Y,8259
+bluecellulab-2.6.60.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+bluecellulab-2.6.60.dist-info/top_level.txt,sha256=VSyEP8w9l3pXdRkyP_goeMwiNA8KWwitfAqUkveJkdQ,13
+bluecellulab-2.6.60.dist-info/RECORD,,