Merge pull request #740 from int-brain-lab/iblrigv8dev

8.25.0
int-brain-lab · Nov 15, 2024 · 51f0ef2 · 51f0ef2
2 parents 6671d7b + 5ad937d
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -1,6 +1,12 @@
 Changelog
 =========
 
+8.25.0
+------
+* feature: fiber photometry loader
+* feature: dataframe converter for Bpod session data 
+* removed: remaining tkinter dialogs
+
 8.24.7
 ------
 * fix: debiasing not working in trainingCW

diff --git a/devices/neurophotometrics/FP3002_digital_inputs.bonsai b/devices/neurophotometrics/FP3002_digital_inputs.bonsai
@@ -0,0 +1,140 @@
+<?xml version="1.0" encoding="utf-8"?>
+<WorkflowBuilder Version="2.8.2"
+                 xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+                 xmlns:p1="clr-namespace:Neurophotometrics.V2;assembly=Neurophotometrics"
+                 xmlns:io="clr-namespace:Bonsai.IO;assembly=Bonsai.System"
+                 xmlns="https://bonsai-rx.org/2018/workflow">
+  <Workflow>
+    <Nodes>
+      <Expression xsi:type="ExternalizedMapping">
+        <Property Name="PortName" DisplayName="PortName" />
+      </Expression>
+      <Expression xsi:type="Combinator">
+        <Combinator xsi:type="p1:FP3002">
+          <p1:AcquisitionMode>StartPhotometry</p1:AcquisitionMode>
+          <p1:PortName>COM4</p1:PortName>
+          <p1:Regions>
+            <p1:PhotometryRegion>
+              <p1:Index>0</p1:Index>
+              <p1:Channel>Green</p1:Channel>
+              <p1:Rectangle>
+                <p1:Location>
+                  <p1:X>824</p1:X>
+                  <p1:Y>492</p1:Y>
+                </p1:Location>
+                <p1:Size>
+                  <p1:Width>166</p1:Width>
+                  <p1:Height>180</p1:Height>
+                </p1:Size>
+                <p1:X>824</p1:X>
+                <p1:Y>492</p1:Y>
+                <p1:Width>166</p1:Width>
+                <p1:Height>180</p1:Height>
+              </p1:Rectangle>
+              <p1:Name>G0</p1:Name>
+            </p1:PhotometryRegion>
+            <p1:PhotometryRegion>
+              <p1:Index>1</p1:Index>
+              <p1:Channel>Green</p1:Channel>
+              <p1:Rectangle>
+                <p1:Location>
+                  <p1:X>703</p1:X>
+                  <p1:Y>353</p1:Y>
+                </p1:Location>
+                <p1:Size>
+                  <p1:Width>154</p1:Width>
+                  <p1:Height>180</p1:Height>
+                </p1:Size>
+                <p1:X>703</p1:X>
+                <p1:Y>353</p1:Y>
+                <p1:Width>154</p1:Width>
+                <p1:Height>180</p1:Height>
+              </p1:Rectangle>
+              <p1:Name>G1</p1:Name>
+            </p1:PhotometryRegion>
+            <p1:PhotometryRegion>
+              <p1:Index>2</p1:Index>
+              <p1:Channel>Green</p1:Channel>
+              <p1:Rectangle>
+                <p1:Location>
+                  <p1:X>943</p1:X>
+                  <p1:Y>134</p1:Y>
+                </p1:Location>
+                <p1:Size>
+                  <p1:Width>180</p1:Width>
+                  <p1:Height>176</p1:Height>
+                </p1:Size>
+                <p1:X>943</p1:X>
+                <p1:Y>134</p1:Y>
+                <p1:Width>180</p1:Width>
+                <p1:Height>176</p1:Height>
+              </p1:Rectangle>
+              <p1:Name>G2</p1:Name>
+            </p1:PhotometryRegion>
+            <p1:PhotometryRegion>
+              <p1:Index>3</p1:Index>
+              <p1:Channel>Green</p1:Channel>
+              <p1:Rectangle>
+                <p1:Location>
+                  <p1:X>767</p1:X>
+                  <p1:Y>180</p1:Y>
+                </p1:Location>
+                <p1:Size>
+                  <p1:Width>176</p1:Width>
+                  <p1:Height>182</p1:Height>
+                </p1:Size>
+                <p1:X>767</p1:X>
+                <p1:Y>180</p1:Y>
+                <p1:Width>176</p1:Width>
+                <p1:Height>182</p1:Height>
+              </p1:Rectangle>
+              <p1:Name>G3</p1:Name>
+            </p1:PhotometryRegion>
+          </p1:Regions>
+        </Combinator>
+      </Expression>
+      <Expression xsi:type="Combinator">
+        <Combinator xsi:type="p1:PhotometryData" />
+      </Expression>
+      <Expression xsi:type="ExternalizedMapping">
+        <Property Name="FileName" DisplayName="FileNamePhotometry" />
+      </Expression>
+      <Expression xsi:type="Combinator">
+        <Combinator xsi:type="p1:PhotometryWriter">
+          <p1:IncludeRegions>false</p1:IncludeRegions>
+          <p1:IncludePlots>false</p1:IncludePlots>
+          <p1:IncludeVideo>false</p1:IncludeVideo>
+          <p1:FileName>D:\iblrigv8_data\neurophotometrics\2024-10-10\T142948\raw_photometry.csv</p1:FileName>
+          <p1:Suffix>None</p1:Suffix>
+        </Combinator>
+      </Expression>
+      <Expression xsi:type="Combinator">
+        <Combinator xsi:type="p1:DigitalIOs">
+          <p1:Input0>true</p1:Input0>
+          <p1:Input1>true</p1:Input1>
+          <p1:Output0>false</p1:Output0>
+          <p1:Output1>false</p1:Output1>
+        </Combinator>
+      </Expression>
+      <Expression xsi:type="ExternalizedMapping">
+        <Property Name="FileName" DisplayName="FileNameDigitalInput" />
+      </Expression>
+      <Expression xsi:type="io:CsvWriter">
+        <io:FileName>D:\iblrigv8_data\neurophotometrics\2024-10-10\T142948\digital_inputs.csv</io:FileName>
+        <io:Append>false</io:Append>
+        <io:Overwrite>false</io:Overwrite>
+        <io:Suffix>None</io:Suffix>
+        <io:IncludeHeader>false</io:IncludeHeader>
+      </Expression>
+    </Nodes>
+    <Edges>
+      <Edge From="0" To="1" Label="Source1" />
+      <Edge From="1" To="2" Label="Source1" />
+      <Edge From="1" To="5" Label="Source1" />
+      <Edge From="2" To="4" Label="Source1" />
+      <Edge From="3" To="4" Label="Source2" />
+      <Edge From="5" To="7" Label="Source1" />
+      <Edge From="6" To="7" Label="Source2" />
+    </Edges>
+  </Workflow>
+</WorkflowBuilder>
diff --git a/devices/neurophotometrics/FP3002_digital_inputs.bonsai.layout b/devices/neurophotometrics/FP3002_digital_inputs.bonsai.layout
@@ -0,0 +1,101 @@
+<?xml version="1.0" encoding="utf-8"?>
+<VisualizerLayout xmlns:xsd="http://www.w3.org/2001/XMLSchema"
+                  xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+                 >
+  <DialogSettings>
+    <Visible>false</Visible>
+    <Location>
+      <X>0</X>
+      <Y>0</Y>
+    </Location>
+    <Size>
+      <Width>0</Width>
+      <Height>0</Height>
+    </Size>
+    <WindowState>Normal</WindowState>
+  </DialogSettings>
+  <DialogSettings>
+    <Visible>false</Visible>
+    <Location>
+      <X>0</X>
+      <Y>0</Y>
+    </Location>
+    <Size>
+      <Width>0</Width>
+      <Height>0</Height>
+    </Size>
+    <WindowState>Normal</WindowState>
+  </DialogSettings>
+  <DialogSettings>
+    <Visible>false</Visible>
+    <Location>
+      <X>0</X>
+      <Y>0</Y>
+    </Location>
+    <Size>
+      <Width>0</Width>
+      <Height>0</Height>
+    </Size>
+    <WindowState>Normal</WindowState>
+  </DialogSettings>
+  <DialogSettings>
+    <Visible>false</Visible>
+    <Location>
+      <X>0</X>
+      <Y>0</Y>
+    </Location>
+    <Size>
+      <Width>0</Width>
+      <Height>0</Height>
+    </Size>
+    <WindowState>Normal</WindowState>
+  </DialogSettings>
+  <DialogSettings>
+    <Visible>false</Visible>
+    <Location>
+      <X>0</X>
+      <Y>0</Y>
+    </Location>
+    <Size>
+      <Width>0</Width>
+      <Height>0</Height>
+    </Size>
+    <WindowState>Normal</WindowState>
+  </DialogSettings>
+  <DialogSettings>
+    <Visible>false</Visible>
+    <Location>
+      <X>0</X>
+      <Y>0</Y>
+    </Location>
+    <Size>
+      <Width>0</Width>
+      <Height>0</Height>
+    </Size>
+    <WindowState>Normal</WindowState>
+  </DialogSettings>
+  <DialogSettings>
+    <Visible>false</Visible>
+    <Location>
+      <X>0</X>
+      <Y>0</Y>
+    </Location>
+    <Size>
+      <Width>0</Width>
+      <Height>0</Height>
+    </Size>
+    <WindowState>Normal</WindowState>
+  </DialogSettings>
+  <DialogSettings>
+    <Visible>false</Visible>
+    <Location>
+      <X>0</X>
+      <Y>0</Y>
+    </Location>
+    <Size>
+      <Width>0</Width>
+      <Height>0</Height>
+    </Size>
+    <WindowState>Normal</WindowState>
+  </DialogSettings>
+</VisualizerLayout>
diff --git a/devices/neurophotometrics/_neurophotometrics_fpData.channels.csv b/devices/neurophotometrics/_neurophotometrics_fpData.channels.csv
@@ -0,0 +1,13 @@
+Condition,No LED ON,L415,L470,L560
+No additional signal,0,1,2,4
+Output 1 signal HIGH,8,9,10,12
+Output 0 signal HIGH,16,17,18,20
+Stimulation ON,32,33,34,36
+GPIO Line 2 HIGH,64,65,66,68
+GPIO Line 3 HIGH,128,129,130,132
+Input 1 HIGH,256,257,258,260
+Input 0 HIGH,512,513,514,516
+Output 0 signal HIGH + Stimulation,48,49,50,52
+Output 0 signal HIGH + Input 0 signal HIGH,528,529,530,532
+Input 0 signal HIGH + Stimulation,544,545,546,548
+Output 0 HIGH + Input 0 HIGH + Stimulation,560,561,562,564
diff --git a/docs/source/usage_neurophotometrics.rst b/docs/source/usage_neurophotometrics.rst
@@ -0,0 +1,68 @@
+Neurophotometrics recording with iblrigv8
+=========================================
+
+This document describes how to use the iblrigv8 software to record Photometry using Neurophotometrics FP3002 system.
+
+Setup
+-----
+
+- iblrigv8 is installed according to the instructions
+- `settings/iblrig_settings.yaml` file is configured with the local folder and remote folder for the data transfer.
+- `settings/hardware_settings.yaml` file is configured with the neurophotometrics device
+
+   .. code:: yaml
+      RIG_NAME: photometry
+      MAIN_SYNC: False
+      device_neurophotometrics:
+         DEVICE_MODEL: NP3002
+         BONSAI_EXECUTABLE: C:\Users\IBLuser\AppData\Local\Bonsai\Bonsai.exe
+         BONSAI_WORKFLOW: devices\neurophotometrics\FP3002.bonsai
+         COM_NEUROPHOTOMETRY: COM3
+
+
+Starting a photometry recording
+--------------------------------
+
+- Start the Bonsai workflow by running the following command in powershell:
+.. code:: powershell
+
+   cd C:\iblrigv8\
+   venv\scripts\Activate.ps1
+   start_neurophotometrics
+- in Bonsai click on the FP3002 node and load the desired photometry settings file
+- start the task
+
+The photometry recording will start and the photometry data will be saved in the data local folder with the following stucture:
+- {local_data_folder}\neurophotometrics\yyyy-mm-dd\THHMMSS
+Where yyyy-mm-dd is the date of the recording and HHMMSS is the time of the recording.
+
+
+
+Starting a photometry session
+--------------------------------
+
+- Start the Bonsai workflow by running the following command in powershell:
+.. code:: powershell
+
+   cd C:\iblrigv8\
+   venv\scripts\Activate.ps1
+   start_photometry_session --subject=Mickey --roi G0 G1 --location NBM SI
+
+
+
+Copy command
+------------
+
+Usage
+~~~~~
+
+To initiate the data transfer from the local server to the remote server, open a terminal and type.
+
+.. code:: powershell
+
+   C:\iblrigv8\venv\scripts\Activate.ps1
+   transfer_data --tag photometry
+
+The transfer local and remote directories are set in the
+``iblrig/settings/iblrig_settings.py`` file.
+
diff --git a/iblrig/__init__.py b/iblrig/__init__.py
@@ -6,7 +6,7 @@
 # 5) git tag the release in accordance to the version number below (after merge!)
 # >>> git tag 8.15.6
 # >>> git push origin --tags
-__version__ = '8.24.7'
+__version__ = '8.25.0'
 
 
 from iblrig.version_management import get_detailed_version_string

diff --git a/iblrig/base_choice_world.py b/iblrig/base_choice_world.py
@@ -16,7 +16,6 @@
 from pydantic import NonNegativeFloat, NonNegativeInt
 
 import iblrig.base_tasks
-import iblrig.graphic
 from iblrig import choiceworld, misc
 from iblrig.hardware import SOFTCODE
 from iblrig.pydantic_definitions import TrialDataModel