bmtool 0.6.4__py3-none-any.whl → 0.6.5.1__py3-none-any.whl

bmtool/SLURM.py

@@ -208,7 +208,7 @@ class SimulationBlock:
         # Conditional account linegit
         account_line = f"#SBATCH --account={self.account}\n" if self.account else ""
         env_var_component_path = f"export COMPONENT_PATH={self.component_path}" if self.component_path else ""
-        
+        mem_per_cpu = int(int(self.mem)/int(self.ntasks))
 
         # Write the batch script to the file
         with open(batch_script_path, 'w') as script_file:
@@ -220,7 +220,7 @@ class SimulationBlock:
 #SBATCH --partition={self.partition}
 #SBATCH --nodes={self.nodes}
 #SBATCH --ntasks={self.ntasks}
-#SBATCH --mem={self.mem}
+#SBATCH --mem-per-cpu={mem_per_cpu}G
 {account_line}
 
 # Additional user-defined commands

bmtool/connectors.py

@@ -1082,7 +1082,7 @@ class ReciprocalConnector(AbstractConnector):
 
 class UnidirectionConnector(AbstractConnector):
     """
-    Object for buiilding unidirectional connections in bmtk network model with
+    Object for building unidirectional connections in bmtk network model with
     given probability within a single population (or between two populations).
 
     Parameters:

bmtool/synapses.py

@@ -178,6 +178,11 @@ class SynapseTuner:
         """
         self._set_up_cell()
         self._set_up_synapse()
+        
+        # user slider values if the sliders are set up
+        if hasattr(self, 'dynamic_sliders'):
+            syn_props = {var: slider.value for var, slider in self.dynamic_sliders.items()}
+            self._set_syn_prop(**syn_props)
 
         # Set up the stimulus
         self.nstim = h.NetStim()
@@ -204,10 +209,17 @@ class SynapseTuner:
         self.nstim.number = 1
         self.nstim2.start = h.tstop
         h.run()
+        
+        current = np.array(self.rec_vectors[self.current_name])
+        syn_prop = self._get_syn_prop(short=True)
+        current = (current - syn_prop['baseline']) * 1000  # Convert to pA
+        current_integral = np.trapz(current, dx=h.dt)  # pA·ms
+        
         self._plot_model([self.general_settings['tstart'] - 5, self.general_settings['tstart'] + self.general_settings['tdur']])
         syn_props = self._get_syn_prop(rise_interval=self.general_settings['rise_interval'])     
         for prop in syn_props.items():
             print(prop)
+        print(f'Current Integral in pA: {current_integral:.2f}')
 
 
     def _find_first(self, x):
@@ -436,27 +448,25 @@ class SynapseTuner:
         return amp
 
 
-    def _find_max_amp(self, amp, normalize_by_trial=True):
+    def _find_max_amp(self, amp):
         """
-        Determines the maximum amplitude from the response data.
+        Determines the maximum amplitude from the response data and returns the max in pA
 
         Parameters:
         -----------
         amp : array-like
             Array containing the amplitudes of synaptic responses.
-        normalize_by_trial : bool, optional
-            If True, normalize the maximum amplitude within each trial. Default is True.
         
         Returns:
         --------
         max_amp : float
             The maximum or minimum amplitude based on the sign of the response.
         """
-        max_amp = amp.max(axis=1 if normalize_by_trial else None)
-        min_amp = amp.min(axis=1 if normalize_by_trial else None)
+        max_amp = max(amp)
+        min_amp = min(amp)
         if(abs(min_amp) > max_amp):
-            return min_amp
-        return max_amp
+            return min_amp * 1000 # scale unit
+        return max_amp * 1000 # scale unit
 
 
     def _calc_ppr_induction_recovery(self,amp, normalize_by_trial=True,print_math=True):
@@ -589,17 +599,19 @@ class SynapseTuner:
         duration0 = 300
         vlamp_status = self.vclamp
 
-        w_run = widgets.Button(description='Run', icon='history', button_style='primary')
+        w_run = widgets.Button(description='Run Train', icon='history', button_style='primary')
+        w_single = widgets.Button(description='Single Event', icon='check', button_style='success')
         w_vclamp = widgets.ToggleButton(value=vlamp_status, description='Voltage Clamp', icon='fast-backward', button_style='warning')
         w_input_mode = widgets.ToggleButton(value=False, description='Continuous input', icon='eject', button_style='info')
         w_input_freq = widgets.SelectionSlider(options=freqs, value=freq0, description='Input Freq')
 
+
         # Sliders for delay and duration
         self.w_delay = widgets.SelectionSlider(options=delays, value=delay0, description='Delay')
         self.w_duration = widgets.SelectionSlider(options=durations, value=duration0, description='Duration')
 
         # Generate sliders dynamically based on valid numeric entries in self.slider_vars
-        dynamic_sliders = {}
+        self.dynamic_sliders = {}
         print("Setting up slider! The sliders ranges are set by their init value so try changing that if you dont like the slider range!")
         for key, value in self.slider_vars.items():
             if isinstance(value, (int, float)):  # Only create sliders for numeric values
@@ -609,18 +621,25 @@ class SynapseTuner:
                         slider = widgets.FloatSlider(value=value, min=0, max=1000, step=1, description=key)
                     else:
                         slider = widgets.FloatSlider(value=value, min=0, max=value*20, step=value/5, description=key)
-                    dynamic_sliders[key] = slider
+                    self.dynamic_sliders[key] = slider
                 else:
                     print(f"skipping slider for {key} due to not being a synaptic variable")
 
+        def run_single_event(*args):
+            clear_output()
+            display(ui)
+            self.vclamp = w_vclamp.value
+            # Update synaptic properties based on slider values
+            self.ispk=None
+            self.SingleEvent()
+
         # Function to update UI based on input mode
         def update_ui(*args):
             clear_output()
             display(ui)
             self.vclamp = w_vclamp.value
             self.input_mode = w_input_mode.value
-            # Update synaptic properties based on slider values
-            syn_props = {var: slider.value for var, slider in dynamic_sliders.items()}
+            syn_props = {var: slider.value for var, slider in self.dynamic_sliders.items()}
             self._set_syn_prop(**syn_props)
             if self.input_mode == False:
                 self._simulate_model(w_input_freq.value, self.w_delay.value, w_vclamp.value)
@@ -629,9 +648,6 @@ class SynapseTuner:
             amp = self._response_amplitude()
             self._plot_model([self.general_settings['tstart'] - self.nstim.interval / 3, self.tstop])
             _ = self._calc_ppr_induction_recovery(amp)
-            # print('Single trial ' + ('PSC' if self.vclamp else 'PSP'))
-            # print(f'Induction: {induction_single:.2f}; Recovery: {recovery:.2f}')
-            #print(f'Rest Amp: {amp[0]:.2f}; Maximum Amp: {maxamp:.2f}')
 
         # Function to switch between delay and duration sliders
         def switch_slider(*args):
@@ -648,23 +664,23 @@ class SynapseTuner:
         # Hide the duration slider initially until the user selects it
         self.w_duration.layout.display = 'none'  # Hide duration slider
 
+        w_single.on_click(run_single_event)
         w_run.on_click(update_ui)
 
         # Add the dynamic sliders to the UI
-        slider_widgets = [slider for slider in dynamic_sliders.values()]
+        slider_widgets = [slider for slider in self.dynamic_sliders.values()]
 
-        # Divide sliders into two columns
-        half = len(slider_widgets) // 2
-        col1 = VBox(slider_widgets[:half])  # First half of sliders
-        col2 = VBox(slider_widgets[half:])  # Second half of sliders
+        button_row = HBox([w_run, w_single, w_vclamp, w_input_mode])
+        slider_row = HBox([w_input_freq, self.w_delay, self.w_duration])
         
-        # Create a two-column layout with HBox
+        half = len(slider_widgets) // 2
+        col1 = VBox(slider_widgets[:half])
+        col2 = VBox(slider_widgets[half:])
         slider_columns = HBox([col1, col2])
 
-        ui = VBox([HBox([w_run, w_vclamp, w_input_mode]), HBox([w_input_freq, self.w_delay, self.w_duration]), slider_columns])
+        ui = VBox([button_row, slider_row, slider_columns])
 
         display(ui)
-        # run model with default parameters 
         update_ui()
 
 class GapJunctionTuner:
@@ -817,11 +833,12 @@ class SynapseOptimizer:
         self.tuner._simulate_model(50, 250) # 50 Hz with 250ms Delay
         amp = self.tuner._response_amplitude()
         ppr, induction, recovery = self.tuner._calc_ppr_induction_recovery(amp, print_math=False)
+        amp = self.tuner._find_max_amp(amp)
         return {
             'induction': float(induction),  # Ensure these are scalar values
             'ppr': float(ppr),
             'recovery': float(recovery),
-            'amplitudes': amp
+            'max_amplitude': float(amp)
         }
         
     def _default_cost_function(self, metrics: Dict[str, float], target_metrics: Dict[str, float]) -> float:

{bmtool-0.6.4.dist-info → bmtool-0.6.5.1.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: bmtool
-Version: 0.6.4
+Version: 0.6.5.1
 Summary: BMTool
 Home-page: https://github.com/cyneuro/bmtool
 Download-URL: 

{bmtool-0.6.4.dist-info → bmtool-0.6.5.1.dist-info}/RECORD

@@ -1,13 +1,13 @@
-bmtool/SLURM.py,sha256=4KvtrPofaHv5iairetgrlXdhAdowJfg_aeTx9W59JDM,16618
+bmtool/SLURM.py,sha256=KNt6X0vMuUvVr94OKleq3MAhOuuiCkHWEzzCwZbH-38,16679
 bmtool/__init__.py,sha256=ZStTNkAJHJxG7Pwiy5UgCzC4KlhMS5pUNPtUJZVwL_Y,136
 bmtool/__main__.py,sha256=TmFkmDxjZ6250nYD4cgGhn-tbJeEm0u-EMz2ajAN9vE,650
 bmtool/bmplot.py,sha256=Im-Jrv8TK3CmTtksFzHrVogAve0l9ZwRrCW4q2MFRiA,53966
-bmtool/connectors.py,sha256=2vVUsqYMaCuWZ-4C5eUzqwsFItFM9vm0ytZdRQdWgoc,72243
+bmtool/connectors.py,sha256=hWkUUcJ4tmas8NDOFPPjQT-TgTlPcpjuZsYyAW2WkPA,72242
 bmtool/graphs.py,sha256=K8BiughRUeXFVvAgo8UzrwpSClIVg7UfmIcvtEsEsk0,6020
 bmtool/manage.py,sha256=_lCU0qBQZ4jSxjzAJUd09JEetb--cud7KZgxQFbLGSY,657
 bmtool/plot_commands.py,sha256=Tqujyf0c0u8olhiHOMwgUSJXIIE1hgjv6otb25G9cA0,12298
 bmtool/singlecell.py,sha256=MQiLucsI6OBIjtcJra3Z9PTFQOE-Zn5ST-R9SmFvrbQ,27049
-bmtool/synapses.py,sha256=FPpNZavsTe-ZuKgO6NUOeFP6mfnEn2KISYuEqdF503w,47984
+bmtool/synapses.py,sha256=jQFOpi9hzzBEijDQ7dsWfcxW-DtxN9v0UWxCqDSlcTs,48466
 bmtool/debug/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 bmtool/debug/commands.py,sha256=AwtcR7BUUheM0NxvU1Nu234zCdpobhJv5noX8x5K2vY,583
 bmtool/debug/debug.py,sha256=xqnkzLiH3s-tS26Y5lZZL62qR2evJdi46Gud-HzxEN4,207
@@ -16,9 +16,9 @@ bmtool/util/commands.py,sha256=zJF-fiLk0b8LyzHDfvewUyS7iumOxVnj33IkJDzux4M,64396
 bmtool/util/util.py,sha256=00vOAwTVIifCqouBoFoT0lBashl4fCalrk8fhg_Uq4c,56654
 bmtool/util/neuron/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 bmtool/util/neuron/celltuner.py,sha256=xSRpRN6DhPFz4q5buq_W8UmsD7BbUrkzYBEbKVloYss,87194
-bmtool-0.6.4.dist-info/LICENSE,sha256=qrXg2jj6kz5d0EnN11hllcQt2fcWVNumx0xNbV05nyM,1068
-bmtool-0.6.4.dist-info/METADATA,sha256=USR9YbT2CPKOw_bz3ZspPCBrI10NkDsLV9imF8-ND54,20224
-bmtool-0.6.4.dist-info/WHEEL,sha256=In9FTNxeP60KnTkGw7wk6mJPYd_dQSjEZmXdBdMCI-8,91
-bmtool-0.6.4.dist-info/entry_points.txt,sha256=0-BHZ6nUnh0twWw9SXNTiRmKjDnb1VO2DfG_-oprhAc,45
-bmtool-0.6.4.dist-info/top_level.txt,sha256=gpd2Sj-L9tWbuJEd5E8C8S8XkNm5yUE76klUYcM-eWM,7
-bmtool-0.6.4.dist-info/RECORD,,
+bmtool-0.6.5.1.dist-info/LICENSE,sha256=qrXg2jj6kz5d0EnN11hllcQt2fcWVNumx0xNbV05nyM,1068
+bmtool-0.6.5.1.dist-info/METADATA,sha256=mCHLJ27JL7d17fe5atQTwQGkVfzVQ6MhqHlhgbm8yh4,20226
+bmtool-0.6.5.1.dist-info/WHEEL,sha256=In9FTNxeP60KnTkGw7wk6mJPYd_dQSjEZmXdBdMCI-8,91
+bmtool-0.6.5.1.dist-info/entry_points.txt,sha256=0-BHZ6nUnh0twWw9SXNTiRmKjDnb1VO2DfG_-oprhAc,45
+bmtool-0.6.5.1.dist-info/top_level.txt,sha256=gpd2Sj-L9tWbuJEd5E8C8S8XkNm5yUE76klUYcM-eWM,7
+bmtool-0.6.5.1.dist-info/RECORD,,