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Merge pull request #740 from int-brain-lab/iblrigv8dev
8.25.0
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‎CHANGELOG.md

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Changelog
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=========
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8.25.0
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------
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* feature: fiber photometry loader
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* feature: dataframe converter for Bpod session data
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* removed: remaining tkinter dialogs
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8.24.7
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------
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* fix: debiasing not working in trainingCW

‎devices/neurophotometrics/FP3002_digital_inputs.bonsai

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<?xml version="1.0" encoding="utf-8"?>
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<WorkflowBuilder Version="2.8.2"
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xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
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xmlns:p1="clr-namespace:Neurophotometrics.V2;assembly=Neurophotometrics"
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xmlns:io="clr-namespace:Bonsai.IO;assembly=Bonsai.System"
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xmlns="https://bonsai-rx.org/2018/workflow">
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<p1:Name>G1</p1:Name>
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<p1:Name>G2</p1:Name>
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</p1:Rectangle>
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<p1:Name>G3</p1:Name>
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<Combinator xsi:type="p1:PhotometryData" />
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<Property Name="FileName" DisplayName="FileNamePhotometry" />
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</Expression>
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<Expression xsi:type="Combinator">
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<Combinator xsi:type="p1:PhotometryWriter">
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<p1:IncludeRegions>false</p1:IncludeRegions>
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<p1:IncludePlots>false</p1:IncludePlots>
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<p1:IncludeVideo>false</p1:IncludeVideo>
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<p1:FileName>D:\iblrigv8_data\neurophotometrics\2024-10-10\T142948\raw_photometry.csv</p1:FileName>
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<p1:Suffix>None</p1:Suffix>
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</Combinator>
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</Expression>
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<Expression xsi:type="Combinator">
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<Combinator xsi:type="p1:DigitalIOs">
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<p1:Input0>true</p1:Input0>
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<p1:Input1>true</p1:Input1>
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<p1:Output0>false</p1:Output0>
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<p1:Output1>false</p1:Output1>
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</Combinator>
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</Expression>
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<Expression xsi:type="ExternalizedMapping">
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<Property Name="FileName" DisplayName="FileNameDigitalInput" />
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</Expression>
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<io:FileName>D:\iblrigv8_data\neurophotometrics\2024-10-10\T142948\digital_inputs.csv</io:FileName>
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<io:Append>false</io:Append>
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<io:Overwrite>false</io:Overwrite>
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<io:Suffix>None</io:Suffix>
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<io:IncludeHeader>false</io:IncludeHeader>
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</Edges>
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</Workflow>
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</WorkflowBuilder>

‎devices/neurophotometrics/FP3002_digital_inputs.bonsai.layout

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‎devices/neurophotometrics/_neurophotometrics_fpData.channels.csv

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Condition,No LED ON,L415,L470,L560
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No additional signal,0,1,2,4
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Output 1 signal HIGH,8,9,10,12
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Output 0 signal HIGH,16,17,18,20
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Stimulation ON,32,33,34,36
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GPIO Line 2 HIGH,64,65,66,68
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GPIO Line 3 HIGH,128,129,130,132
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Input 1 HIGH,256,257,258,260
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Input 0 HIGH,512,513,514,516
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Output 0 signal HIGH + Stimulation,48,49,50,52
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Output 0 signal HIGH + Input 0 signal HIGH,528,529,530,532
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Input 0 signal HIGH + Stimulation,544,545,546,548
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Output 0 HIGH + Input 0 HIGH + Stimulation,560,561,562,564

‎docs/source/usage_neurophotometrics.rst

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Neurophotometrics recording with iblrigv8
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=========================================
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This document describes how to use the iblrigv8 software to record Photometry using Neurophotometrics FP3002 system.
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Setup
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-----
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- iblrigv8 is installed according to the instructions
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- `settings/iblrig_settings.yaml` file is configured with the local folder and remote folder for the data transfer.
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- `settings/hardware_settings.yaml` file is configured with the neurophotometrics device
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.. code:: yaml
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RIG_NAME: photometry
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MAIN_SYNC: False
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device_neurophotometrics:
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DEVICE_MODEL: NP3002
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BONSAI_EXECUTABLE: C:\Users\IBLuser\AppData\Local\Bonsai\Bonsai.exe
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BONSAI_WORKFLOW: devices\neurophotometrics\FP3002.bonsai
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COM_NEUROPHOTOMETRY: COM3
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Starting a photometry recording
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--------------------------------
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- Start the Bonsai workflow by running the following command in powershell:
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.. code:: powershell
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cd C:\iblrigv8\
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venv\scripts\Activate.ps1
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start_neurophotometrics
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- in Bonsai click on the FP3002 node and load the desired photometry settings file
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- start the task
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The photometry recording will start and the photometry data will be saved in the data local folder with the following stucture:
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- {local_data_folder}\neurophotometrics\yyyy-mm-dd\THHMMSS
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Where yyyy-mm-dd is the date of the recording and HHMMSS is the time of the recording.
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Starting a photometry session
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--------------------------------
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- Start the Bonsai workflow by running the following command in powershell:
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.. code:: powershell
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cd C:\iblrigv8\
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venv\scripts\Activate.ps1
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start_photometry_session --subject=Mickey --roi G0 G1 --location NBM SI
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Copy command
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------------
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Usage
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~~~~~
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To initiate the data transfer from the local server to the remote server, open a terminal and type.
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.. code:: powershell
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C:\iblrigv8\venv\scripts\Activate.ps1
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transfer_data --tag photometry
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The transfer local and remote directories are set in the
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``iblrig/settings/iblrig_settings.py`` file.
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‎iblrig/__init__.py

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# 5) git tag the release in accordance to the version number below (after merge!)
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# >>> git tag 8.15.6
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# >>> git push origin --tags
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__version__ = '8.24.7'
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__version__ = '8.25.0'
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from iblrig.version_management import get_detailed_version_string

‎iblrig/base_choice_world.py

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from pydantic import NonNegativeFloat, NonNegativeInt
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import iblrig.base_tasks
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import iblrig.graphic
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from iblrig import choiceworld, misc
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from iblrig.hardware import SOFTCODE
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from iblrig.pydantic_definitions import TrialDataModel

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