bluecellulab 2.6.52__tar.gz → 2.6.54__tar.gz

{bluecellulab-2.6.52 → bluecellulab-2.6.54}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: bluecellulab
-Version: 2.6.52
+Version: 2.6.54
 Summary: Biologically detailed neural network simulations and analysis.
 Author: Blue Brain Project, EPFL
 License: Apache2.0

{bluecellulab-2.6.52 → bluecellulab-2.6.54}/bluecellulab/analysis/analysis.py

@@ -4,11 +4,9 @@ try:
 except ImportError:
     efel = None
 from itertools import islice
-from itertools import repeat
 import logging
 from matplotlib.collections import LineCollection
 import matplotlib.pyplot as plt
-from multiprocessing import Pool
 import neuron
 import numpy as np
 import pathlib
@@ -97,20 +95,15 @@ def compute_plot_iv_curve(cell,
         for amp in list_amp
     ]
 
-    with Pool(len(steps)) as p:
-        recordings = p.starmap(
-            run_stimulus,
-            zip(
-                repeat(cell.template_params),
-                steps,
-                repeat(injecting_section),
-                repeat(injecting_segment),
-                repeat(True),  # cvode
-                repeat(True),  # add_hypamp
-                repeat(recording_section),
-                repeat(recording_segment),
-            )
-        )
+    recordings = []
+    for step in steps:
+        recording = run_stimulus(cell.template_params,
+                                 step,
+                                 section=injecting_section,
+                                 segment=injecting_segment,
+                                 recording_section=recording_section,
+                                 recording_segment=recording_segment)
+        recordings.append(recording)
 
     steady_states = []
     # compute steady state response
@@ -208,24 +201,19 @@ def compute_plot_fi_curve(cell,
         for amp in list_amp
     ]
 
-    with Pool(len(steps)) as p:
-        recordings = p.starmap(
-            run_stimulus,
-            zip(
-                repeat(cell.template_params),
-                steps,
-                repeat(injecting_section),
-                repeat(injecting_segment),
-                repeat(True),  # cvode
-                repeat(True),  # add_hypamp
-                repeat(recording_section),
-                repeat(recording_segment),
-                repeat(True),  # enable_spike_detection
-                repeat(threshold_voltage),  # threshold_spike_detection
-            )
-        )
+    spikes = []
+    for step in steps:
+        recording = run_stimulus(cell.template_params,
+                                 step,
+                                 section=injecting_section,
+                                 segment=injecting_segment,
+                                 recording_section=recording_section,
+                                 recording_segment=recording_segment,
+                                 enable_spike_detection=True,
+                                 threshold_spike_detection=threshold_voltage)
+        spikes.append(recording.spike)
 
-    spike_count = [len(recording.spike) for recording in recordings]
+    spike_count = [len(spike) for spike in spikes]
 
     plot_fi_curve(list_amp,
                   spike_count,
@@ -248,7 +236,7 @@ class BPAP:
         self.cell = cell
         self.dt = 0.025
         self.stim_start = 1000
-        self.stim_duration = 3
+        self.stim_duration = 5
         self.basal_cmap = sns.color_palette("crest", as_cmap=True)
         self.apical_cmap = sns.color_palette("YlOrBr_r", as_cmap=True)
 
@@ -301,7 +289,11 @@ class BPAP:
             for rec in recs.values()
         ]
         features_results = efel.get_feature_values(traces, [efel_feature_name])
-        amps = [feat_res[efel_feature_name][0] for feat_res in features_results]
+        amps = [
+            feat_res[efel_feature_name][0]
+            for feat_res in features_results
+            if feat_res[efel_feature_name] is not None
+        ]
 
         return amps
 
@@ -320,7 +312,7 @@ class BPAP:
 
     def get_amplitudes_and_distances(self):
         soma_rec, dend_rec, apic_rec = self.get_recordings()
-        soma_amp = self.amplitudes({"soma": soma_rec})[0]
+        soma_amp = self.amplitudes({"soma": soma_rec})
         dend_amps = None
         dend_dist = None
         apic_amps = None
@@ -334,20 +326,21 @@ class BPAP:
 
         return soma_amp, dend_amps, dend_dist, apic_amps, apic_dist
 
-    def fit(self, soma_amp, dend_amps, dend_dist, apic_amps, apic_dist):
+    @staticmethod
+    def fit(soma_amp, dend_amps, dend_dist, apic_amps, apic_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
+            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
+            amps = soma_amp + apic_amps  # add soma amplitude
             popt_apic, _ = curve_fit(exp_decay, dist, amps)
 
         return popt_dend, popt_apic
@@ -357,10 +350,18 @@ 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, '.')
+            plt.plot(dend_dist, dend_amps, '.')
+            x = np.linspace(0, max(dend_dist), 100)
+            plt.plot(x, exp_decay(x, *popt_dend), color='darkgreen', linestyle='--', label='Basal Dendritic Fit')
+            plt.savefig("bad_dendritic_fit.png")
         if popt_dend is None:
             logger.debug("No dendritic recordings found.")
             notes += "No dendritic recordings found.\n"
-        elif popt_dend[1] <= 0:
+        elif popt_dend[1] <= 0 or popt_dend[0] <= 0:
             logger.debug("Dendritic fit is not decaying.")
             validated = False
             notes += "Dendritic fit is not decaying.\n"
@@ -369,7 +370,7 @@ class BPAP:
         if popt_apic is None:
             logger.debug("No apical recordings found.")
             notes += "No apical recordings found.\n"
-        elif popt_apic[1] <= 0:
+        elif popt_apic[1] <= 0 or popt_apic[0] <= 0:
             logger.debug("Apical fit is not decaying.")
             validated = False
             notes += "Apical fit is not decaying.\n"
@@ -395,7 +396,7 @@ class BPAP:
 
         outpath = pathlib.Path(output_dir) / output_fname
         fig, ax1 = plt.subplots(figsize=(10, 6))
-        ax1.scatter([0], [soma_amp], marker="^", color='black', label='Soma')
+        ax1.scatter([0], soma_amp, marker="^", color='black', label='Soma')
         if dend_amps and dend_dist:
             ax1.scatter(
                 dend_dist,

{bluecellulab-2.6.52 → bluecellulab-2.6.54}/bluecellulab/validation/validation.py

@@ -438,68 +438,38 @@ def run_validations(
     )
 
     logger.debug("Running validations...")
-    from bluecellulab.utils import NestedPool
-    with NestedPool(processes=8) as pool:
-        # Validation 1: Spiking Test
-        spiking_test_result_future = pool.apply_async(
-            spiking_test,
-            (cell.template_params, rheobase, out_dir, spike_threshold_voltage)
-        )
-
-        # Validation 2: Depolarization Block Test
-        depolarization_block_result_future = pool.apply_async(
-            depolarization_block_test,
-            (cell.template_params, rheobase, out_dir)
-        )
+    # Validation 1: Spiking Test
+    spiking_test_result = spiking_test(
+        cell.template_params, rheobase, out_dir, spike_threshold_voltage
+    )
 
-        # Validation 3: Backpropagating AP Test
-        bpap_result_future = pool.apply_async(
-            bpap_test,
-            (cell.template_params, rheobase, out_dir)
-        )
+    # Validation 2: Depolarization Block Test
+    depolarization_block_result = depolarization_block_test(
+        cell.template_params, rheobase, out_dir
+    )
 
-        # Validation 4: Postsynaptic Potential Test
-        # We have to wait for ProbAMPANMDA_EMS to be present in entitycore to implement this test
+    # Validation 3: Backpropagating AP Test
+    bpap_result = bpap_test(cell.template_params, rheobase, out_dir)
 
-        # Validation 5: AIS Spiking Test
-        ais_spiking_test_result_future = pool.apply_async(
-            ais_spiking_test,
-            (cell.template_params, rheobase, out_dir, spike_threshold_voltage)
-        )
+    # Validation 4: Postsynaptic Potential Test
+    # We have to wait for ProbAMPANMDA_EMS to be present in entitycore to implement this test
 
-        # Validation 6: Hyperpolarization Test
-        hyperpolarization_result_future = pool.apply_async(
-            hyperpolarization_test,
-            (cell.template_params, rheobase, out_dir)
-        )
+    # Validation 5: AIS Spiking Test
+    ais_spiking_test_result = ais_spiking_test(
+        cell.template_params, rheobase, out_dir, spike_threshold_voltage
+    )
 
-        # Validation 7: Rin Test
-        rin_result_future = pool.apply_async(
-            rin_test,
-            (rin,)
-        )
+    # Validation 6: Hyperpolarization Test
+    hyperpolarization_result = hyperpolarization_test(cell.template_params, rheobase, out_dir)
 
-        # # Validation 8: IV Test
-        iv_test_result_future = pool.apply_async(
-            iv_test,
-            (cell.template_params, rheobase, out_dir, spike_threshold_voltage)
-        )
+    # Validation 7: Rin Test
+    rin_result = rin_test(rin)
 
-        # # Validation 9: FI Test
-        fi_test_result_future = pool.apply_async(
-            fi_test,
-            (cell.template_params, rheobase, out_dir, spike_threshold_voltage)
-        )
+    # Validation 8: IV Test
+    iv_test_result = iv_test(cell.template_params, rheobase, out_dir, spike_threshold_voltage)
 
-        # Wait for all validations to complete
-        spiking_test_result = spiking_test_result_future.get()
-        depolarization_block_result = depolarization_block_result_future.get()
-        bpap_result = bpap_result_future.get()
-        ais_spiking_test_result = ais_spiking_test_result_future.get()
-        hyperpolarization_result = hyperpolarization_result_future.get()
-        rin_result = rin_result_future.get()
-        iv_test_result = iv_test_result_future.get()
-        fi_test_result = fi_test_result_future.get()
+    # Validation 9: FI Test
+    fi_test_result = fi_test(cell.template_params, rheobase, out_dir, spike_threshold_voltage)
 
     return {
         "memodel_properties": {

{bluecellulab-2.6.52 → bluecellulab-2.6.54}/bluecellulab.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: bluecellulab
-Version: 2.6.52
+Version: 2.6.54
 Summary: Biologically detailed neural network simulations and analysis.
 Author: Blue Brain Project, EPFL
 License: Apache2.0

{bluecellulab-2.6.52 → bluecellulab-2.6.54}/tox.ini

@@ -15,6 +15,7 @@ deps =
     pytest-timeout>=2.1.0
     pytest-xdist>=3.3.1  # multiprocessing
     pytest-forked>=1.6.0  # isolation
+    efel
 download = true
 allowlist_externals =
     make