trialized and localization notebooks

README.md

@@ -9,6 +9,7 @@ A complete electrophysiology workflow can be built using the DataJoint Elements.
 + [element-animal](https://github.com/datajoint/element-animal)
 + [element-session](https://github.com/datajoint/element-session)
 + [element-array-ephys](https://github.com/datajoint/element-array-ephys)
++ Optionally, [element-event](https://github.com/datajoint/element-event)
 
 This repository provides demonstrations for:
 1. Set up a workflow using DataJoint Elements (see
@@ -17,11 +18,12 @@ This repository provides demonstrations for:
 convention, and directory lookup methods (see
 [workflow_array_ephys/paths.py](workflow_array_ephys/paths.py)).
 3. Ingestion of clustering results.
+4. Ingestion of experimental condition information and downstream [PSTH analysis](https://www.sciencedirect.com/topics/neuroscience/peristimulus-time-histogram).
 
 ## Workflow architecture
 
-The electrophysiology workflow presented here uses components from 4 DataJoint 
-Elements (`element-lab`, `element-animal`, `element-session`,
+The electrophysiology workflow presented here uses components from 5 DataJoint 
+Elements (`element-lab`, `element-animal`, `element-session`, `element-event`,
 `element-array-ephys`) assembled together to form a fully functional workflow.
 
 ### element-lab
@@ -34,9 +36,17 @@ https://github.com/datajoint/element-lab/raw/main/images/lab_diagram.svg)
 ![element-animal](
 https://github.com/datajoint/element-animal/raw/main/images/subject_diagram.svg)
 
-### assembled with element-array-ephys
+### Assembled with element-array-ephys
 
-![element-array-ephys](images/attached_array_ephys_element.svg)
+![attached-element-array-ephys](images/attached_array_ephys_element.svg)
+
+### Assembled with element-event and workflow analysis
+
+![attached-trial-analysis](./images/attached_trial_analysis.svg)
+
+## Assembled with element-electrode-localization
+
+![attached-electrode-localization](./images/attached_electrode_localization.svg)
 
 ## Installation instructions
 
@@ -45,7 +55,8 @@ https://github.com/datajoint/element-animal/raw/main/images/subject_diagram.svg)
 
 ## Interacting with the DataJoint workflow
 
-+ Please refer to the following workflow-specific 
- [Jupyter notebooks](/notebooks) for an in-depth explanation of how to run the 
- workflow ([03-process.ipynb](notebooks/03-process.ipynb)) and explore the data 
- ([05-explore.ipynb](notebooks/05-explore.ipynb)).
+Please refer to the following workflow-specific 
+ [Jupyter notebooks](/notebooks) for an in-depth explanation of how to ...
++ run the workflow ([03-process.ipynb](notebooks/03-process.ipynb)) 
++ explore the data ([05-explore.ipynb](notebooks/05-explore.ipynb))
++ visualize trial-based analyses ([07-downstream-analysis.ipynb](notebooks/07-downstream-analysis.ipynb))

docker/Dockerfile.dev

@@ -17,6 +17,7 @@ COPY --chown=anaconda:anaconda ./element-lab /main/element-lab
 COPY --chown=anaconda:anaconda ./element-animal /main/element-animal
 COPY --chown=anaconda:anaconda ./element-session /main/element-session
 COPY --chown=anaconda:anaconda ./element-trial /main/element-trial
+COPY --chown=anaconda:anaconda ./element-electrode-localization /main/element-electrode-localization
 COPY --chown=anaconda:anaconda ./element-array-ephys /main/element-array-ephys
 COPY --chown=anaconda:anaconda ./workflow-array-ephys /main/workflow-array-ephys
 
@@ -25,6 +26,7 @@ RUN pip install -e /main/element-lab
 RUN pip install -e /main/element-animal
 RUN pip install -e /main/element-session
 RUN pip install -e /main/element-trial
+RUN pip install -e /main/element-electrode-localization
 RUN pip install -e /main/element-array-ephys
 RUN pip install -e /main/workflow-array-ephys
 RUN pip install -r /main/workflow-array-ephys/requirements_test.txt

docker/Dockerfile.test

@@ -15,27 +15,34 @@ WORKDIR /main/workflow-array-ephys
 # RUN pip install git+https://github.com/<user>element-lab.git
 # RUN pip install git+https://github.com/<user>/element-animal.git
 # RUN pip install git+https://github.com/<user>/element-session.git
+# RUN pip install git+https://github.com/<user>/element-trial.git
+# RUN pip install git+https://github.com/<user>/element-electrode-localization.git
 # RUN pip install git+https://github.com/<user>/element-array-ephys.git
 # RUN git clone https://github.com/<user>/workflow-array-ephys.git /main/workflow-array-ephys
 
 # Option 3 - Install user's local fork of element and workflow
-RUN mkdir /main/element-lab \
-          /main/element-animal \
-          /main/element-session \
-          /main/element-array-ephys \
-          /main/workflow-array-ephys
+RUN mkdir -p /main/element-lab \
+             /main/element-animal \
+             /main/element-session \
+             /main/element-trial \
+             /main/element-array-ephys \
+             /main/workflow-array-ephys
 
 COPY --chown=anaconda:anaconda ./element-lab /main/element-lab
 COPY --chown=anaconda:anaconda ./element-animal /main/element-animal
 COPY --chown=anaconda:anaconda ./element-session /main/element-session
+COPY --chown=anaconda:anaconda ./element-trial /main/element-trial
+COPY --chown=anaconda:anaconda ./element-electrode-localization /main/element-electrode-localization
 COPY --chown=anaconda:anaconda ./element-array-ephys /main/element-array-ephys
 COPY --chown=anaconda:anaconda ./workflow-array-ephys /main/workflow-array-ephys
 
 RUN pip install -e /main/element-lab
 RUN pip install -e /main/element-animal
 RUN pip install -e /main/element-session
+RUN pip install -e /main/element-trial
+RUN pip install -e /main/element-electrode-localization
 RUN pip install -e /main/element-array-ephys
-RUN rm -f /main/workflow-array-ephys/dj_local_conf.json
+# RUN rm -f /main/workflow-array-ephys/dj_local_conf.json
 
 # Install the workflow
 RUN pip install /main/workflow-array-ephys

docker/docker-compose-dev.yaml

@@ -6,18 +6,20 @@ x-net: &net
   networks:
       - main
 services:
-  array-ephys-dev-db:
+  db:
     <<: *net
     image: datajoint/mysql:5.7
+    container_name: workflow-array-ephys-dev-db
     environment:
       - MYSQL_ROOT_PASSWORD=simple
-  array-ephys-dev-workflow:
+  workflow:
     <<: *net
     build:
       context: ../../
       dockerfile: ./workflow-array-ephys/docker/Dockerfile.dev
     env_file: .env
-    image: workflow_array_ephys_dev:0.1.0a4
+    image: workflow-array-ephys-dev:0.1.0a4
+    container_name: workflow-array-ephys-dev
     environment:
       - EPHYS_ROOT_DATA_DIR=/main/test_data/workflow_ephys_data1/,/main/test_data/workflow_ephys_data2/
     volumes:
@@ -27,6 +29,7 @@ services:
       - ../../element-animal:/main/element-animal
       - ../../element-session:/main/element-session
       - ../../element-trial:/main/element-trial
+      - ../../element-electrode-localization:/main/element-electrode-localization
       - ../../element-array-ephys:/main/element-array-ephys
       - ..:/main/workflow-array-ephys
     depends_on:

docker/docker-compose-test.yaml

@@ -9,22 +9,25 @@ x-net: &net
   networks:
       - main
 services:
-  array-ephys-test-db:
+  db:
     <<: *net
     image: datajoint/mysql:5.7
+    container_name: workflow-array-ephys-test-db
     environment:
       - MYSQL_ROOT_PASSWORD=simple
-  array-ephys-test-workflow:
+  workflow:
     <<: *net
     build:
       context: ../../
       dockerfile: ./workflow-array-ephys/docker/Dockerfile.test
     env_file: .env
-    image: workflow_array_ephys_test:0.1.0a4
+    image: workflow-array-ephys-test:0.1.0a4
+    container_name: workflow-array-ephys-test
     environment:
       - DJ_HOST=db
       - DJ_USER=root
       - DJ_PASS=simple
+      - EPHYS_MODE=no-curation
       - EPHYS_ROOT_DATA_DIR=/main/test_data/workflow_ephys_data1/,/main/test_data/workflow_ephys_data2/
       - DATABASE_PREFIX=test_
     command:
@@ -40,11 +43,12 @@ services:
       - ../../element-lab:/main/element-lab
       - ../../element-animal:/main/element-animal
       - ../../element-session:/main/element-session
+      - ../../element-electrode-localization:/main/element-electrode-localization
       - ../../element-trial:/main/element-trial
       - ../../element-array-ephys:/main/element-array-ephys
       - ..:/main/workflow-array-ephys
     depends_on:
-      array-ephys-test-db:
+      db:
         condition: service_healthy
 networks:
   main: