bluecellulab 2.6.57__py3-none-any.whl → 2.6.58__py3-none-any.whl

bluecellulab/analysis/analysis.py

@@ -350,7 +350,6 @@ class BPAP:
         validated = True
         notes = ""
         popt_dend, popt_apic = self.fit(soma_amp, dend_amps, dend_dist, apic_amps, apic_dist)
-        logging.warning(popt_dend)
         if dend_amps is not None:
             plt.cla()
             plt.plot([0], soma_amp, '.')

bluecellulab/validation/validation.py

@@ -25,6 +25,7 @@ from bluecellulab.analysis.analysis import compute_plot_iv_curve
 from bluecellulab.analysis.inject_sequence import run_multirecordings_stimulus
 from bluecellulab.analysis.inject_sequence import run_stimulus
 from bluecellulab.cell.core import Cell
+from bluecellulab.simulation.neuron_globals import NeuronGlobals
 from bluecellulab.stimulus.factory import IDRestTimings
 from bluecellulab.stimulus.factory import StimulusFactory
 from bluecellulab.tools import calculate_input_resistance
@@ -33,15 +34,17 @@ from bluecellulab.tools import calculate_rheobase
 logger = logging.getLogger(__name__)
 
 
-def plot_trace(recording, out_dir, fname, title):
+def plot_trace(recording, out_dir, fname, title, plot_current=True):
     """Plot a trace with inout current given a recording."""
     outpath = out_dir / fname
     fig, ax1 = plt.subplots(figsize=(10, 6))
     plt.plot(recording.time, recording.voltage, color="black")
-    current_axis = ax1.twinx()
-    current_axis.plot(recording.time, recording.current, color="gray", alpha=0.6)
-    current_axis.set_ylabel("Stimulus Current [nA]")
-    fig.suptitle(title)
+    if plot_current:
+        current_axis = ax1.twinx()
+        current_axis.plot(recording.time, recording.current, color="gray", alpha=0.6)
+        current_axis.set_ylabel("Stimulus Current [nA]")
+    if title:
+        fig.suptitle(title)
     ax1.set_xlabel("Time [ms]")
     ax1.set_ylabel("Voltage [mV]")
     fig.tight_layout()
@@ -410,8 +413,42 @@ def fi_test(template_params, rheobase, out_dir, spike_threshold_voltage=-30.):
     }
 
 
+def thumbnail_test(template_params, rheobase, out_dir):
+    """Thumbnail test: creating a thumbnail."""
+    stim_factory = StimulusFactory(dt=1.0)
+    step_stimulus = stim_factory.idrest(threshold_current=rheobase, threshold_percentage=130)
+    recording = run_stimulus(
+        template_params,
+        step_stimulus,
+        "soma[0]",
+        0.5,
+        add_hypamp=True,
+    )
+
+    # plotting
+    outpath = plot_trace(
+        recording,
+        out_dir,
+        fname="thumbnail.pdf",
+        title="",
+        plot_current=False
+    )
+
+    return {
+        "name": "thumbnail",
+        "passed": True,
+        "validation_details": "",
+        "figures": [outpath],
+    }
+
+
 def run_validations(
-    cell, cell_name, spike_threshold_voltage=-30, output_dir="./memodel_validation_figures"
+    cell,
+    cell_name,
+    spike_threshold_voltage=-30,
+    v_init=-80.0,
+    celsius=34.0,
+    output_dir="./memodel_validation_figures"
 ):
     """Run all the validations on the cell.
 
@@ -419,11 +456,18 @@ def run_validations(
         cell (Cell): The cell to validate.
         cell_name (str): The name of the cell, used in the output directory.
         spike_threshold_voltage (float): The voltage threshold for spike detection.
+        v_init: Initial membrane potential. Default is -80.0 mV.
+        celsius: Temperature in Celsius. Default is 34.0.
         output_dir (str): The directory to save the validation figures.
     """
     out_dir = pathlib.Path(output_dir) / cell_name
     out_dir.mkdir(parents=True, exist_ok=True)
 
+    # 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
     if cell.threshold:
@@ -473,6 +517,9 @@ def run_validations(
     # Validation 9: FI Test
     fi_test_result = fi_test(cell.template_params, rheobase, out_dir, spike_threshold_voltage)
 
+    # Validation 10: Thumbnail Test
+    thumbnail_result = thumbnail_test(cell.template_params, rheobase, out_dir)
+
     return {
         "memodel_properties": {
             "holding_current": holding_current,
@@ -487,4 +534,5 @@ def run_validations(
         "rin_test": rin_result,
         "iv_test": iv_test_result,
         "fi_test": fi_test_result,
+        "thumbnail_test": thumbnail_result,
     }

{bluecellulab-2.6.57.dist-info → bluecellulab-2.6.58.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: bluecellulab
-Version: 2.6.57
+Version: 2.6.58
 Summary: Biologically detailed neural network simulations and analysis.
 Author: Blue Brain Project, EPFL
 License: Apache2.0

{bluecellulab-2.6.57.dist-info → bluecellulab-2.6.58.dist-info}/RECORD

@@ -15,7 +15,7 @@ bluecellulab/type_aliases.py,sha256=DvgjERv2Ztdw_sW63JrZTQGpJ0x5uMTFB5hcBHDb0WA,
 bluecellulab/utils.py,sha256=0NhwlzyLnSi8kziSfDsQf7pokO4qDkMJVAO33kSX4O0,2227
 bluecellulab/verbosity.py,sha256=T0IgX7DrRo19faxrT4Xzb27gqxzoILQ8FzYKxvUeaPM,1342
 bluecellulab/analysis/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-bluecellulab/analysis/analysis.py,sha256=rZdM7AjjCLFoW7x0d_R6oQPLAasz_R6UxSVgcKTUJW0,21646
+bluecellulab/analysis/analysis.py,sha256=O2nKHdVqVuL8SP_Q-FjyaRyHJdJCf0315bNrCTVies4,21611
 bluecellulab/analysis/inject_sequence.py,sha256=bpi_C1oz_G5cZv_CvvZG8SnGYaKIlDsIFHdkOAkDm-E,12666
 bluecellulab/analysis/plotting.py,sha256=PqRoaZz33ULMw8A9YnZXXrxcUd84M_dwlYMTFhG7YT4,3999
 bluecellulab/analysis/utils.py,sha256=eMirP557D11BuedgSqjripDxOq1haIldNbnYNetV1bg,121
@@ -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=00g16X9ngQeVxKpec4SpXb8oTJ3qzfTfifEP5D8AWVE,17149
-bluecellulab-2.6.57.dist-info/licenses/AUTHORS.txt,sha256=EDs3H-2HXBojbma10psixk3C2rFiOCTIREi2ZAbXYNQ,179
-bluecellulab-2.6.57.dist-info/licenses/LICENSE,sha256=dAMAR2Sud4Nead1wGFleKiwTZfkTNZbzmuGfcTKb3kg,11335
-bluecellulab-2.6.57.dist-info/METADATA,sha256=xzTnRYLR2MSR8x0mNnKVnhqOol-zmA2hNJcHkxBvovg,8259
-bluecellulab-2.6.57.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
-bluecellulab-2.6.57.dist-info/top_level.txt,sha256=VSyEP8w9l3pXdRkyP_goeMwiNA8KWwitfAqUkveJkdQ,13
-bluecellulab-2.6.57.dist-info/RECORD,,
+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,,