Add python data loading script for neuropixels 1.0e headstage workflow

workflows/hardware/np1e/bno055.bonsai

@@ -9,15 +9,16 @@
       <Expression xsi:type="Combinator">
         <Combinator xsi:type="onix1:PolledBno055Data">
           <onix1:DeviceName>NeuropixelsV1eHeadstage/PolledBno055</onix1:DeviceName>
+          <onix1:PolledRegisters>All</onix1:PolledRegisters>
         </Combinator>
       </Expression>
       <Expression xsi:type="io:CsvWriter">
         <io:FileName>bno055_.csv</io:FileName>
         <io:Append>false</io:Append>
         <io:Overwrite>false</io:Overwrite>
-        <io:Suffix>Timestamp</io:Suffix>
+        <io:Suffix>FileCount</io:Suffix>
         <io:IncludeHeader>false</io:IncludeHeader>
-        <io:Selector>it</io:Selector>
+        <io:Selector>Clock,EulerAngle,Quaternion,Acceleration,Gravity,Temperature</io:Selector>
       </Expression>
       <Expression xsi:type="MemberSelector">
         <Selector>Quaternion</Selector>

workflows/hardware/np1e/load-np1e.py

@@ -0,0 +1,110 @@
+import numpy as np
+import matplotlib.pyplot as plt
+
+# Load data from neuropixels board tutorial workflow
+suffix = '4'; # Change to match file names' suffix
+np_ap_gain = 1000 # Change to the AP band gain used
+np_lfp_gain = 50 # Change to the lfp band gain used
+
+plt.close('all')
+
+#%% Metadata
+dt = {'names': ('time', 'acq_clk_hz', 'block_read_sz', 'block_write_sz'),
+      'formats': ('datetime64[us]', 'u4', 'u4', 'u4')}
+meta = np.genfromtxt('start-time_' + suffix + '.csv', delimiter=',', dtype=dt, skip_header=1)
+print(f"Recording was started at {meta['time']} GMT")
+
+#%% Hardware FIFO buffer use
+dt = {'names': ('clock', 'bytes', 'percent'),
+      'formats': ('u8', 'u4', 'f8')}
+memory_use = np.genfromtxt('memory-use_' + suffix + '.csv', delimiter=',', dtype=dt)
+
+plt.figure()
+plt.plot(memory_use['clock'] / meta['acq_clk_hz'], memory_use['percent'])
+plt.xlabel("time (sec)")
+plt.ylabel("FIFO used (%)")
+
+
+#%% Neuropixels 1.0
+start_t = 9.0 # when to start plotting data (seconds)
+dur = 1.0 # duration of data to plot
+plot_channel_offset_uV = 100 # Vertical offset between each channel in the time series
+
+npx = {}
+npx['spike_time'] = np.fromfile('np1-clock_' + suffix + '.raw', dtype=np.uint64) / meta['acq_clk_hz']
+npx['spike'] = np.reshape(np.fromfile('np1-spike_' + suffix + '.raw', dtype=np.uint16), (-1, 384))
+
+npx['lfp_time'] = npx['spike_time'][::12] # 12 spike samples per lfp sample
+npx['lfp'] = np.reshape(np.fromfile('np1-lfp_' + suffix + '.raw', dtype=np.uint16), (-1, 384))
+
+# Make arrays for plotting
+b = np.bitwise_and(npx['spike_time'] >= start_t, npx['spike_time'] < start_t + dur)
+spike_time = npx['spike_time'][b]
+spike_wave = npx['spike'][b, :].astype(np.double)
+b = np.bitwise_and(npx['lfp_time'] >= start_t, npx['lfp_time'] < start_t + dur)
+lfp_time = npx['lfp_time'][b]
+lfp_wave = npx['lfp'][b, :].astype(np.double)
+
+# Convert to uV and offset each channel by some plot_channel_offset_uV 
+ap_uV_per_lsb = 1e6 * 1.2 / 1024 / np_ap_gain
+lfp_uV_per_lsb = 1e6 * 1.2 / 1024 / np_lfp_gain
+spike_wave = (spike_wave - 512) * ap_uV_per_lsb + np.arange(spike_wave.shape[1])[None, :] * plot_channel_offset_uV
+lfp_wave =  (lfp_wave - 512) * lfp_uV_per_lsb + np.arange(lfp_wave.shape[1])[None, :] * plot_channel_offset_uV
+
+plt.figure()
+plt.subplot(121)
+plt.plot(spike_time, spike_wave, 'k', linewidth=0.25)
+plt.tick_params(axis='y', which='both', left=False, right=False, labelleft=False) 
+plt.xlabel("time (sec)")
+plt.ylabel("channel")
+plt.title('Spike Band')
+
+plt.subplot(122)
+plt.plot(lfp_time, lfp_wave, 'k', linewidth=0.25)
+plt.tick_params(axis='y', which='both', left=False, right=False, labelleft=False) 
+plt.xlabel("time (sec)")
+plt.ylabel("channel")
+plt.title('LFP Band')
+
+#%% Bno055
+dt = {'names': ('clock', 'euler', 'quat', 'is_quat_id', 'accel', 'grav', 'temp'),
+      'formats': ('u8', '(1,3)f8', '(1,4)f8', '?', '(1,3)f8', '(1,3)f8', 'f8')}
+bno055 = np.genfromtxt('bno055_' + suffix + '.csv', delimiter=',', dtype=dt)
+
+bno055_time = bno055['clock'] / meta['acq_clk_hz']
+
+plt.figure()
+plt.subplot(231)
+plt.plot(bno055_time, bno055['euler'].squeeze())
+plt.xlabel("time (sec)")
+plt.ylabel("angle (deg.)")
+plt.ylim(-185, 365)
+plt.legend(['yaw', 'pitch', 'roll'])
+plt.title('Euler')
+
+plt.subplot(232)
+plt.plot(bno055_time, bno055['quat'].squeeze())
+plt.xlabel("time (sec)")
+plt.ylim(-1.1, 1.1)
+plt.legend(['X', 'Y', 'Z', 'W'])
+plt.title('Quaternion')
+
+plt.subplot(233)
+plt.plot(bno055_time, bno055['accel'].squeeze())
+plt.xlabel("time (sec)")
+plt.ylabel("accel. (m/s^2)")
+plt.legend(['X', 'Y', 'Z'])
+plt.title('Lin. Accel.')
+
+plt.subplot(234)
+plt.plot(bno055_time, bno055['grav'].squeeze())
+plt.xlabel("time (sec)")
+plt.ylabel("accel. (m/s^2)")
+plt.legend(['X', 'Y', 'Z'])
+plt.title('Gravity Vec.')
+
+plt.subplot(235)
+plt.plot(bno055_time, bno055['temp'].squeeze())
+plt.xlabel("time (sec)")
+plt.ylabel("temp. (deg. C)")
+plt.title('Headstage Temp.')

workflows/hardware/np1e/memory-monitor.bonsai

@@ -0,0 +1,31 @@
+<?xml version="1.0" encoding="utf-8"?>
+<WorkflowBuilder Version="2.8.5"
+                 xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+                 xmlns:onix1="clr-namespace:OpenEphys.Onix1;assembly=OpenEphys.Onix1"
+                 xmlns:io="clr-namespace:Bonsai.IO;assembly=Bonsai.System"
+                 xmlns="https://bonsai-rx.org/2018/workflow">
+  <Workflow>
+    <Nodes>
+      <Expression xsi:type="Combinator">
+        <Combinator xsi:type="onix1:MemoryMonitorData">
+          <onix1:DeviceName>BreakoutBoard/MemoryMonitor</onix1:DeviceName>
+        </Combinator>
+      </Expression>
+      <Expression xsi:type="io:CsvWriter">
+        <io:FileName>memory-use_.csv</io:FileName>
+        <io:Append>false</io:Append>
+        <io:Overwrite>false</io:Overwrite>
+        <io:Suffix>FileCount</io:Suffix>
+        <io:IncludeHeader>false</io:IncludeHeader>
+        <io:Selector>Clock,BytesUsed,PercentUsed</io:Selector>
+      </Expression>
+      <Expression xsi:type="MemberSelector">
+        <Selector>PercentUsed</Selector>
+      </Expression>
+    </Nodes>
+    <Edges>
+      <Edge From="0" To="1" Label="Source1" />
+      <Edge From="1" To="2" Label="Source1" />
+    </Edges>
+  </Workflow>
+</WorkflowBuilder>

workflows/hardware/np1e/np1.bonsai

@@ -18,7 +18,7 @@
       <Expression xsi:type="Combinator">
         <Combinator xsi:type="dsp:MatrixWriter">
           <dsp:Path>np1-clock_.raw</dsp:Path>
-          <dsp:Suffix>Timestamp</dsp:Suffix>
+          <dsp:Suffix>FileCount</dsp:Suffix>
           <dsp:Overwrite>false</dsp:Overwrite>
           <dsp:Layout>ColumnMajor</dsp:Layout>
         </Combinator>
@@ -29,7 +29,7 @@
       <Expression xsi:type="Combinator">
         <Combinator xsi:type="dsp:MatrixWriter">
           <dsp:Path>np1-spike_.raw</dsp:Path>
-          <dsp:Suffix>Timestamp</dsp:Suffix>
+          <dsp:Suffix>FileCount</dsp:Suffix>
           <dsp:Overwrite>false</dsp:Overwrite>
           <dsp:Layout>ColumnMajor</dsp:Layout>
         </Combinator>
@@ -40,7 +40,7 @@
       <Expression xsi:type="Combinator">
         <Combinator xsi:type="dsp:MatrixWriter">
           <dsp:Path>np1-lfp_.raw</dsp:Path>
-          <dsp:Suffix>Timestamp</dsp:Suffix>
+          <dsp:Suffix>FileCount</dsp:Suffix>
           <dsp:Overwrite>false</dsp:Overwrite>
           <dsp:Layout>ColumnMajor</dsp:Layout>
         </Combinator>

workflows/hardware/np1e/port-status.bonsai

@@ -19,9 +19,9 @@
         <io:FileName>port-status_.csv</io:FileName>
         <io:Append>false</io:Append>
         <io:Overwrite>false</io:Overwrite>
-        <io:Suffix>Timestamp</io:Suffix>
+        <io:Suffix>FileCount</io:Suffix>
         <io:IncludeHeader>false</io:IncludeHeader>
-        <io:Selector>Timestamp,Value.Clock,Value.StatusCode,Value.SerdesLocked,Value.SerdesPass</io:Selector>
+        <io:Selector>Timestamp,Value.Clock,Value.StatusCode</io:Selector>
       </Expression>
     </Nodes>
     <Edges>