add copy file github action

.github/workflows/copy_file.yml

@@ -0,0 +1,26 @@
+name: copy_file
+
+on: workflow_dispatch
+#  push:
+#    branches:
+#      - master
+
+jobs:
+  copy-file:
+    runs-on: ubuntu-latest
+    steps:
+    - name: Checkout
+      uses: actions/checkout@v2
+
+    - name: Pushes file
+      uses: dmnemec/copy_file_to_another_repo_action@main
+      env:
+        API_TOKEN_GITHUB: ${{ secrets.API_TOKEN_GITHUB }}
+      with:
+        source_file: './documentation/data/website.yml'
+        destination_repo: 'GSTT-CSC/gstt-csc.github.io'
+        destination_folder: '_projects'
+        #email and username of the user associated with the token
+        user_email: ''
+        user_name: ''
+        commit_message: ''

.github/workflows/render_and_push.yml

@@ -0,0 +1,61 @@
+# make sure main_image_path in website.yml is correct
+name: render_and_push
+
+# left as manual for testing, to be changed to on push
+on: workflow_dispatch
+#  push:
+#    branches:
+#      - main
+
+jobs:
+  update-and-copy-md:
+    runs-on: ubuntu-latest
+    steps:
+    - name: Checkout
+      uses: actions/checkout@v2
+    - name: render md and graphs
+      # set up environment, render website_modelcard.md with yml data in data directory, and plot demographics data
+      # NOTE to fix - currently fails if demo_graphs dir already exists in repo AND has files in
+      run: |
+        python -m venv testenv
+        . testenv/bin/activate
+        pip install --upgrade pip
+        pip install rdm
+        pip install matplotlib
+        pip install pillow
+        cd ./documentation
+        make ./release/website_modelcard.md
+        mkdir ../md-to-send
+        mv ./release/website_modelcard.md ../md-to-send/${GITHUB_REPOSITORY#*/}_modelcard.md
+        mkdir demo_graphs
+        python plotyml.py
+    - name: Pushes md
+      uses: SpinyOwl/publish-artifact-to-git@1.0.1
+      with:
+        # need to create a personal access token with read/write access to website repo, and save it to secrets. access tokens expire after 60 days.
+        # a user based naming convention for secrets may be necessary, to ensure each user calls their own access token (if multiple access tokens saved to a repo's secrets)
+        github_pat: '${{ secrets.MODEL_CARD_DEMO }}'
+        repository: GSTT-CSC/gstt-csc.github.io
+        # sending to branch for testing, to be changed to main/master
+        branch: 228_add_modelcard_layout
+        # source folder path needs to match the md-to-send directory created in render md and graphs step above
+        source_folder: ./md-to-send
+        # set target folder in website repo for modelcard md file
+        target_folder: _projects
+        no_delete: true
+    - name: Pushes graphs
+      uses: SpinyOwl/publish-artifact-to-git@1.0.1
+      with:
+        github_pat: '${{ secrets.MODEL_CARD_DEMO }}'
+        repository: GSTT-CSC/gstt-csc.github.io
+        # sending to branch for testing, to be changed to main/master
+        branch: 228_add_modelcard_layout
+        # source folder path needs to match the demo_graphs directory created in render md and graphs step above
+        source_folder: ./documentation/demo_graphs
+        target_folder: assets/img/projects
+        no_delete: true
+
+# works but get this Warning: The `set-output` command is deprecated and will be disabled soon...
+# Please upgrade to using Environment Files...
+# For more information see: https://github.blog/changelog/2022-10-11-github-actions-deprecating-save-state-and-set-output-commands/
+# link says command disable is postponed because of high use

documentation/data/device.yml

@@ -6,6 +6,18 @@ name: "DEVICE"
 # Shorthand Name for device, (max 5 characters)
 name_sh: "DEV"
 
+statement_of_purpose: PURPOSE
+
+summary: SUMMARY
+
+modality: MODALITY
+
+pathology: PATHOLOGY
+
+rationale: RATIONALE
+
+patient_pathway: PATHWAY
+
 # The current release number for the device
 version: "v0.1.0"
 
@@ -22,9 +34,25 @@ safety_class: B
 # "III" -
 mhra_class: "IIb"
 
-# link ot the website page
+# link to the website page
 csc_website_url:
 
 #the GitHub URL
 github_url:
 
+#path to logo
+logo:
+
+# Name of or department that approved the project
+Project_approver:
+
+#
+Approval_date:
+
+#is project service development (bool)
+Service_Dev:
+
+#expected completion date
+exp_comp_date:
+
+

documentation/data/documents.yml

@@ -0,0 +1,42 @@
+- document: proposal
+  version:
+- document: software_req_spec
+  version:
+- document: hazard_log
+  version:
+- document: software_design_spec
+  version:
+- document: design_plan
+  version:
+- document: verif_and_validation_plan
+  version:
+- document: user_acceptance_criteria
+  version:
+- document: support_agreement
+  version:
+- document: post_deployment_surveillance_plan
+  version:
+- document: clinical_safety_case_report
+  version:
+- document: clinical_risk_management_plan
+  version:
+- document: cyber_security
+  version:
+- document: revision_level_history
+  version:
+- document: risk_management_report
+  version:
+- document: software_description
+  version:
+- document: software_development_and_maintenance_rec
+  version:
+- document: software_plan
+  version:
+- document: software_release_activity_record
+  version:
+- document: test_record
+  version:
+- document: unresolved_anomalies
+  version:
+- document: data_description
+  version:

documentation/data/model.yml

@@ -0,0 +1,12 @@
+model_architecture: "model"
+
+MLFlow artefacts:
+# will this path be in project or website repo or elsewhere?
+- image: path/to/performance_image1.png
+  description: "text description"
+- image: image2.png
+  description: "text description"
+
+model_version: "v2.0"
+date:
+pytorch_version:

documentation/data/roles.yml

@@ -0,0 +1,14 @@
+- role: clinical lead
+  people:
+- role: Clinical Safety Officer
+  people:
+- role: csc_development_lead
+  people:
+- role: csc_ml_lead
+  people:
+- role: stakeholder
+  people:
+- role: hod_for_deployment
+  people:
+- role: staff_training_lead
+  people:

documentation/data/training_data.yml

@@ -1,10 +1,51 @@
-xnat_project_name:
+xnat_project_name: NAME
 
-dataset_version:
+dataset_version: VERSION
 
-preprocess_description:
+preprocess_description: DESCRIPTION
+
+train_dataset_summary: DATASET SUMMARY
+train_data_excl: Exclusion Criteria
+train_dataset_size: SIZE
+train_input: Images
 
 train_dataset:
+- total:
+    subgroups:
+    - gender:
+        Female: 10
+        Male: 10
+    - ethnicity:
+        Not Stated:
+        Asian:
+        Black:
+        Latin American:
+        Mixed:
+        White:
+    - Age:
+        0-15:
+        16-20:
+        21-25:
+        26-30:
+        31-35:
+        36-40:
+        41-45:
+        46-50:
+        51-55:
+        56-60:
+        61-65:
+        66-70:
+        71-75:
+        76-80:
+        81-85:
+        86-90:
+        91+:
+- positive:
+    subgroups:
+- postive_female_mixed:
+    subgroups:
+    - age:
+
 
 test_dataset:
 

documentation/data/website.yml

@@ -0,0 +1,13 @@
+project_title: PROJECT TITLE
+status: Developing
+
+# image path in website repo
+main_image_path: /assets/img/projects/IMAGE_TITLE.jpg
+
+# logo path in website repo
+logo: path/to/logo
+
+errors: ERRORS
+goals: GOALS
+success_criteria: CRITERIA
+

documentation/documents/website_modelcard.md

@@ -0,0 +1,35 @@
+---
+layout: modelcard
+title: {{website.project_title}}
+devicename: {{device.name}}
+status: {{website.status}}
+image: {{website.main_image_path}}
+sex_graph: /assets/img/projects/{{device.name}}_sex_graph.png
+ethn_graph: /assets/img/projects/{{device.name}}_ethn_graph.png
+age_graph: /assets/img/projects/{{device.name}}_age_graph.png
+summary: {{device.summary}}
+modality: {{device.modality}}
+model: {{model.model_architecture}}
+pathology: {{device.pathology}}
+rationale: {{device.rationale}}
+patient-pathway: {{device.patient_pathway}}
+training-data: {{training_data.train_dataset_summary}}
+train_data_excl: {{training_data.train_data_excl}}
+train_input: {{training_data.train_input}}
+train_size: {{training_data.train_dataset_size}}
+errors: {{website.errors}}
+goals: {{website.goals}}
+success-criteria: {{website.success_criteria}}
+
+alternatives: <a href="http://www.gleamer.ai/">Gleamer</a>, which specialise in trauma x-rays, has been considered for this purpose but was decided not suitable to solve this particular clinical problem. The decision was made to train an in-house algorithm instead.
+
+
+
+
+---
+
+**Project Plan**
+<br> 1. Meeting of all persons involved to determine AI specifications. <br><br> 2.	Setting technical and system requirements for AI model. <br> 3. Dataset curation (retrospective). <br><br> 4.	Model training<br><br>5.	Model testing <br><br>6.	Implementation <br><br>7. Audit
+<br>
+<br>
+<b>References</b>:<br>

documentation/documents/website_project.md

@@ -0,0 +1,30 @@
+---
+layout: project_page
+title: {{website.project_title}}
+status: {{website.status}}
+image: {{website.main_image_path}}
+summary: {{device.summary}}
+modality: {{device.modality}}
+pathology: {{device.pathology}}
+rationale: {{device.rationale}}
+patient-pathway: {{device.patient_pathway}}
+training-data: {{training_data.train_dataset.summary}}
+errors: {{website.errors}}
+goals: {{website.goals}}
+success-criteria: {{website.success_criteria}}
+
+csc-lead: <a href="/team_member/Dika.html">Dika</a>
+alternatives: <a href="http://www.gleamer.ai/">Gleamer</a>, which specialise in trauma x-rays, has been considered for this purpose but was decided not suitable to solve this particular clinical problem. The decision was made to train an in-house algorithm instead
+
+---
+MRI imaging is superior in identification of occult carpal fracture, but is not always accessible. Imaging from X-rays can give suboptimal views, and the presentation of arthritis can make small fractures difficult to see. An AI tool to aide clinical diagnosis of occult carpal fractures using x-rays would increase diagnostic sensitivity in areas and situations where MRI is not available. 
+A computer aided diagnosis tool which would automatically run when either a scaphoid fracture is suspected or if a patient is referred for a hand/wrist x-ray from A&E would increase sensitivity and confidence of diagnosis. Carpal fractures can be difficult to identify and patients with high clinical suspicion are put in a splint and referred to the fracture clinic even if a fracture isn’t seen on the x-ray by the clinician. Subtle lucency of an un-displaced fracture and the significance of a small bone fragment is currently easily missed. A successful tool would therefore increase diagnostic confidence and accuracy and reduce repeated x-rays and needless fracture clinic referrals
+<br>
+<br>
+<b>Clinical lead</b>: {% for r in roles %}{% if r.role == "clinical lead" %}{{r.people | join('<br>, ')}}{% endif %}{% endfor %} <br>
+<br>
+**Project Plan** <br>
+<strike>1.	Meeting of all persons involved to determine AI specifications. <br><br> 2.	Setting technical and system requirements for AI model. </strike> <br> 3. Dataset curation (retrospective). <br><br> 4.	Model training<br><br>5.	Model testing <br><br>6.	Implementation <br><br>7. Audit
+<br>
+<br>
+<b>References</b>:<br> <a href="https://online.boneandjoint.org.uk/doi/full/10.1302/0301-620X.101B8.BJJ-2018-1590.R1"> TOHETI trial results </a>