bluecellulab 2.6.63__py3-none-any.whl → 2.6.65__py3-none-any.whl

bluecellulab/analysis/analysis.py

@@ -351,29 +351,32 @@ class BPAP:
         return soma_amp, dend_amps, dend_dist, apic_amps, apic_dist
 
     @staticmethod
-    def fit(soma_amp, dend_amps, dend_dist, apic_amps, apic_dist):
+    def fit(soma_amp, branch_amps, branch_dist):
         """Fit the amplitudes vs distances to an exponential decay function."""
         from scipy.optimize import curve_fit
 
-        popt_dend = None
-        if dend_amps and dend_dist:
-            dist = [0] + dend_dist  # add soma distance
-            amps = soma_amp + dend_amps  # add soma amplitude
-            popt_dend, _ = curve_fit(exp_decay, dist, amps)
-
-        popt_apic = None
-        if apic_amps and apic_dist:
-            dist = [0] + apic_dist  # add soma distance
-            amps = soma_amp + apic_amps  # add soma amplitude
-            popt_apic, _ = curve_fit(exp_decay, dist, amps)
-
-        return popt_dend, popt_apic
+        if not branch_amps or not branch_dist or len(branch_amps) != len(branch_dist):
+            return None, False
+        try:
+            dist = [0] + branch_dist
+            amps = soma_amp + branch_amps
+            popt, _ = curve_fit(exp_decay, dist, amps)
+            return popt, False
+        except RuntimeError:
+            return None, True
 
     def validate(self, soma_amp, dend_amps, dend_dist, apic_amps, apic_dist):
         """Check that the exponential fit is decaying."""
         validated = True
         notes = ""
-        popt_dend, popt_apic = self.fit(soma_amp, dend_amps, dend_dist, apic_amps, apic_dist)
+        popt_dend, dend_fit_error = self.fit(soma_amp, dend_amps, dend_dist)
+        popt_apic, apic_fit_error = self.fit(soma_amp, apic_amps, apic_dist)
+        if dend_fit_error or apic_fit_error:
+            logger.debug("Fitting error occurred.")
+            validated = False
+            notes += "Validation failed: Fitting error occurred.\n"
+            return validated, notes
+
         if dend_amps is not None:
             plt.cla()
             plt.plot([0], soma_amp, '.')
@@ -415,7 +418,8 @@ class BPAP:
         output_fname="bpap.pdf",
     ):
         """Plot the results of the BPAP analysis."""
-        popt_dend, popt_apic = self.fit(soma_amp, dend_amps, dend_dist, apic_amps, apic_dist)
+        popt_dend, _ = self.fit(soma_amp, dend_amps, dend_dist)
+        popt_apic, _ = self.fit(soma_amp, apic_amps, apic_dist)
 
         outpath = pathlib.Path(output_dir) / output_fname
         fig, ax1 = plt.subplots(figsize=(10, 6))

bluecellulab/tools.py

@@ -40,7 +40,7 @@ def calculate_input_resistance(
     morphology_path: str | Path,
     template_format: str,
     emodel_properties: EmodelProperties | None,
-    current_delta: float = 0.01,
+    current_delta: float = -0.02,
     section: str = "soma[0]",
     segx: float = 0.5
 ) -> float:

bluecellulab/validation/validation.py

@@ -83,7 +83,7 @@ def plot_traces(recordings, out_dir, fname, title, labels=None, xlim=None):
     return outpath
 
 
-def spiking_test(template_params, rheobase, out_dir, spike_threshold_voltage=-30.):
+def spiking_test(template_params, rheobase, out_dir, spike_threshold_voltage=-20.):
     """Spiking test: cell should spike."""
     stim_factory = StimulusFactory(dt=1.0)
     step_stimulus = stim_factory.idrest(threshold_current=rheobase, threshold_percentage=200)
@@ -194,7 +194,7 @@ def bpap_test(template_params, rheobase, out_dir="./"):
     }
 
 
-def ais_spiking_test(template_params, rheobase, out_dir, spike_threshold_voltage=-30.):
+def ais_spiking_test(template_params, rheobase, out_dir, spike_threshold_voltage=-20.):
     """AIS spiking test: axon should spike before soma."""
     name = "Simulatable Neuron AIS Spiking Validation"
     # Check that the cell has an axon
@@ -337,7 +337,7 @@ def rin_test(rin):
     }
 
 
-def iv_test(template_params, rheobase, out_dir, spike_threshold_voltage=-30., n_processes=None):
+def iv_test(template_params, rheobase, out_dir, spike_threshold_voltage=-20., n_processes=None):
     """IV curve should have a positive slope."""
     name = "Simulatable Neuron IV Curve Validation"
     amps, steady_states = compute_plot_iv_curve(
@@ -377,7 +377,7 @@ def iv_test(template_params, rheobase, out_dir, spike_threshold_voltage=-30., n_
     }
 
 
-def fi_test(template_params, rheobase, out_dir, spike_threshold_voltage=-30., n_processes=None):
+def fi_test(template_params, rheobase, out_dir, spike_threshold_voltage=-20., n_processes=None):
     """FI curve should have a positive slope."""
     name = "Simulatable Neuron FI Curve Validation"
     amps, spike_counts = compute_plot_fi_curve(
@@ -449,7 +449,7 @@ def thumbnail_test(template_params, rheobase, out_dir):
 def run_validations(
     cell,
     cell_name,
-    spike_threshold_voltage=-30,
+    spike_threshold_voltage=-20,
     v_init=-80.0,
     celsius=34.0,
     output_dir="./memodel_validation_figures",
@@ -489,6 +489,7 @@ def run_validations(
         morphology_path=cell.template_params.morph_filepath,
         template_format=cell.template_params.template_format,
         emodel_properties=cell.template_params.emodel_properties,
+        current_delta=-0.2 * rheobase,
     )
 
     logger.debug("Running validations...")

{bluecellulab-2.6.63.dist-info → bluecellulab-2.6.65.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: bluecellulab
-Version: 2.6.63
+Version: 2.6.65
 Summary: Biologically detailed neural network simulations and analysis.
 Author: Blue Brain Project, EPFL
 License: Apache2.0

{bluecellulab-2.6.63.dist-info → bluecellulab-2.6.65.dist-info}/RECORD

@@ -10,12 +10,12 @@ 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=Wj3zEalJuyMzp0btoyWHXsCRpxyg6lNEuJfvmudlQmc,21767
+bluecellulab/tools.py,sha256=EGrX1RQyaEIFEN9pvcw1oxBP_vONgcx7U7a2N_11Z_g,21768
 bluecellulab/type_aliases.py,sha256=DvgjERv2Ztdw_sW63JrZTQGpJ0x5uMTFB5hcBHDb0WA,441
 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=W5MBCJthuuA7fFEJRZExONjTEWOhgDbtmTq23Cv7fbc,22449
+bluecellulab/analysis/analysis.py,sha256=_ggribmdjerotj8u3qJYUojP7Y2IfKpGLZRBzFX8vdE,22596
 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
@@ -74,10 +74,10 @@ 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=csy1xKOOWdlo3NYHdknePPxb7KBRTjoUV-81ZmWo2CM,20041
-bluecellulab-2.6.63.dist-info/licenses/AUTHORS.txt,sha256=EDs3H-2HXBojbma10psixk3C2rFiOCTIREi2ZAbXYNQ,179
-bluecellulab-2.6.63.dist-info/licenses/LICENSE,sha256=dAMAR2Sud4Nead1wGFleKiwTZfkTNZbzmuGfcTKb3kg,11335
-bluecellulab-2.6.63.dist-info/METADATA,sha256=J9j4rWRv1plUDoTz99tw1JxhVUNpJq4f1jk6qbLM5p4,8259
-bluecellulab-2.6.63.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
-bluecellulab-2.6.63.dist-info/top_level.txt,sha256=VSyEP8w9l3pXdRkyP_goeMwiNA8KWwitfAqUkveJkdQ,13
-bluecellulab-2.6.63.dist-info/RECORD,,
+bluecellulab/validation/validation.py,sha256=n1KgQo41vFM7DZcVY3Yx8WOIfVE0ke0s7S-EeDDM6mQ,20080
+bluecellulab-2.6.65.dist-info/licenses/AUTHORS.txt,sha256=EDs3H-2HXBojbma10psixk3C2rFiOCTIREi2ZAbXYNQ,179
+bluecellulab-2.6.65.dist-info/licenses/LICENSE,sha256=dAMAR2Sud4Nead1wGFleKiwTZfkTNZbzmuGfcTKb3kg,11335
+bluecellulab-2.6.65.dist-info/METADATA,sha256=7j3p6Wktfp4qD8zwGsVHN6YzOk_AL-uJ4so5Fmfgh0g,8259
+bluecellulab-2.6.65.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+bluecellulab-2.6.65.dist-info/top_level.txt,sha256=VSyEP8w9l3pXdRkyP_goeMwiNA8KWwitfAqUkveJkdQ,13
+bluecellulab-2.6.65.dist-info/RECORD,,