added example streamlit papaya

.gitattributes

@@ -33,3 +33,4 @@ saved_model/**/* filter=lfs diff=lfs merge=lfs -text
 *.zip filter=lfs diff=lfs merge=lfs -text
 *.zst filter=lfs diff=lfs merge=lfs -text
 *tfevents* filter=lfs diff=lfs merge=lfs -text
+*.nii.gz filter=lfs diff=lfs merge=lfs -text

.gitignore

@@ -0,0 +1,2 @@
+__pycache__
+static/tmp

.streamlit/config.toml

@@ -0,0 +1,2 @@
+[server]
+enableStaticServing = true

NOTES.md

@@ -0,0 +1,14 @@
+
+```
+python3.8 -m venv  /mnt/scratch/venv/streamlit
+source /mnt/scratch/venv/streamlit/bin/activate
+
+pip install -r requirements.txt
+```
+
+'''
+alternatives
+https://github.com/amine0110/medical-visualization-with-streamlit/tree/main
+https://neurosnippets.com/posts/diesitcom
+
+'''

app.py

@@ -0,0 +1,59 @@
+
+import os
+import streamlit as st
+
+papaya_script = """
+<style>
+:root {
+  background-color: black;
+}
+</style>
+<script src="https://cdn.jsdelivr.net/npm/papaya-viewer@1.0.1455/release/current/standard/papaya.min.js"></script>
+<link href="https://cdn.jsdelivr.net/npm/papaya-viewer@1.0.1455/release/current/standard/papaya.min.css" rel="stylesheet">
+<script type="text/javascript">
+    var params = [];
+    params["luts"] = [{"name": "Custom", "data":[[0, 0, 0, 0], [0.5, 0, 0, 0], [1, 1, 0, 0]]}];
+    params["images"] = ["{{IMAGE_FULLPATH}}","{{MASK_FULLPATH}}"];
+    params["{{MASK_BASENAME}}"] = {"min": 0, "max": 1, "lut": "Custom", "alpha":0.5};
+</script>
+<div class="papaya" data-params="params"></div>
+"""
+
+
+def handle_input(myimage,mymask,papaya_script):
+    mydict = {}
+    os.makedirs('static/tmp/',exist_ok=True)
+    image_path = 'static/tmp/image.nii.gz'
+    mask_path = 'static/tmp/mask.nii.gz'
+    for file_path,uploaded_file in [(image_path,myimage),(mask_path,mymask)]:
+        bytes_data = uploaded_file.getvalue()
+        with open(file_path,'wb') as f:
+            f.write(bytes_data)
+
+    image_path = './app/static/tmp/image.nii.gz'
+    mask_path = './app/static/tmp/mask.nii.gz'
+    papaya_script = papaya_script.replace("{{IMAGE_FULLPATH}}",image_path)
+    papaya_script = papaya_script.replace("{{MASK_FULLPATH}}",mask_path)
+    papaya_script = papaya_script.replace("{{MASK_BASENAME}}","mask.nii.gz")
+
+    st.components.v1.html(papaya_script,height=600,width=800)
+
+def main():
+    
+    st.subheader("papaya-image-viewer")
+    myimage = st.file_uploader(
+        "Upload your image nifti file", accept_multiple_files=False)
+    mymask = st.file_uploader(
+        "Upload your mask nifti file here and click on 'Render'", accept_multiple_files=False)
+    if st.button("Render"):
+        with st.spinner("Processing"):
+            handle_input(myimage,mymask,papaya_script)
+
+
+if __name__ == '__main__':
+    main()
+
+
+# papaya_script = papaya_script.replace("{{IMAGE_FULLPATH}}","./app/static/promis12-test-Case00.nii.gz")
+# papaya_script = papaya_script.replace("{{MASK_FULLPATH}}","./app/static/promis12-test-Case00-mask.nii.gz")
+# papaya_script = papaya_script.replace("{{MASK_BASENAME}}","promis12-test-Case00-mask.nii.gz")

requirements.txt

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+streamlit>=1.19.0

static/promis12-test-Case00-mask.nii.gz

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+version https://git-lfs.github.com/spec/v1
+oid sha256:14b159df22eb0b404a7a8851315a0269b37ad9bff1517577d681abb3514fc742
+size 7774

static/promis12-test-Case00.nii.gz

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:813dda4c7e60436017707cf7d371c311a1401750681e338fe29dac6bb087185c
+size 2832200