Photometry copier

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>

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>

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

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.
+

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

iblrig/base_tasks.py

@@ -28,7 +28,6 @@
 from pythonosc import udp_client
 
 import ibllib.io.session_params as ses_params
-import iblrig.graphic as graph
 import iblrig.path_helper
 import pybpodapi
 from ibllib.oneibl.registration import IBLRegistrationClient
@@ -39,7 +38,7 @@
 from iblrig.hifi import HiFi
 from iblrig.path_helper import load_pydantic_yaml
 from iblrig.pydantic_definitions import HardwareSettings, RigSettings, TrialDataModel
-from iblrig.tools import call_bonsai
+from iblrig.tools import call_bonsai, get_number
 from iblrig.transfer_experiments import BehaviorCopier, VideoCopier
 from iblrig.valve import Valve
 from iblutil.io.net.base import ExpMessage
@@ -617,10 +616,10 @@ def run(self):
         self.create_session()
         # When not running the first chained protocol, we can skip the weighing dialog
         first_protocol = int(self.paths.SESSION_RAW_DATA_FOLDER.name.split('_')[-1]) == 0
+
+        # get subject weight
         if self.session_info.SUBJECT_WEIGHT is None and self.interactive and first_protocol:
-            self.session_info.SUBJECT_WEIGHT = graph.numinput(
-                'Subject weighing (gr)', f'{self.session_info.SUBJECT_NAME} weight (gr):', nullable=False
-            )
+            self.session_info.SUBJECT_WEIGHT = get_number('Subject weight (g): ', float, lambda x: x > 0)
 
         def sigint_handler(*args, **kwargs):
             # create a signal handler for a graceful exit: create a stop flag in the session folder
@@ -637,10 +636,11 @@ def sigint_handler(*args, **kwargs):
         log.critical('Graceful exit')
         log.info(f'Session {self.paths.SESSION_RAW_DATA_FOLDER}')
         self.session_info.SESSION_END_TIME = datetime.datetime.now().isoformat()
+
+        # get poop count
         if self.interactive and not self.wizard:
-            self.session_info.POOP_COUNT = graph.numinput(
-                'Poop count', f'{self.session_info.SUBJECT_NAME} droppings count:', nullable=True, askint=True
-            )
+            self.session_info.POOP_COUNT = get_number('Droppings count: ', int, lambda x: x >= 0)
+
         self.save_task_parameters_to_json_file()
         self.register_to_alyx()
         self._execute_mixins_shared_function('stop_mixin')