Ge dev

.dockerignore

@@ -2,8 +2,14 @@
 .git
 test
 test_data
-output_folder
+output_folder/**
+!output_folder/NiChart_sMRI_Demo1
+!output_folder/NiChart_sMRI_Demo2
 **/*.nii.gz
 build
 **/build
 src/NiChart_Website
+
+# Ignore hidden files and directories
+.*
+

.gitignore

@@ -181,3 +181,4 @@ test/test_output
 
 ## make sure no data go to the repo
 ##*.nii.gz
+

Dockerfile

@@ -46,16 +46,17 @@ RUN grep -v -E '^(torch)' /tmp/requirements.txt > /tmp/requirements2.txt
 USER root
 RUN apt-get update && apt-get install -y python3-tk git
 USER $MAMBA_USER
-RUN pip install --verbose -r /tmp/requirements2.txt && pip uninstall -y torch && pip install --verbose torch==2.3.1 --index-url https://download.pytorch.org/whl/cu${CUDA_VERSION}
+RUN pip install --verbose -r /tmp/requirements2.txt
 RUN mkdir ~/dummyinput && mkdir ~/dummyoutput
 RUN git clone https://github.com/CBICA/PredCRD.git && cd PredCRD && pip install -e .
 RUN git clone https://github.com/CBICA/DLWMLS.git && cd DLWMLS && pip install -e . && DLWMLS -i ~/dummyinput -o ~/dummyoutput
+RUN pip uninstall -y torch && pip install --verbose torch==2.3.1 --index-url https://download.pytorch.org/whl/cu${CUDA_VERSION}
 ## Cache DLMUSE and DLICV models with an empty job so no download is needed later
 RUN DLMUSE -i ~/dummyinput -o ~/dummyoutput && DLICV -i ~/dummyinput -o ~/dummyoutput
 USER root
 COPY . /app/
-RUN useradd -s /bin/bash streamlit && mkdir /app/output_folder && \
-    chmod a+w /app/output_folder && chmod a-rw / && chmod a-w /app && touch /app/src/viewer/pipeline.log && \
+RUN useradd -s /bin/bash streamlit && \
+    chmod -R a+rw /app/output_folder && chmod a-rw / && chmod a-w /app && touch /app/src/viewer/pipeline.log && \
     chmod a+rw /app/src/viewer/pipeline.log
 USER streamlit
 WORKDIR /app/src/viewer/

cloud-config.json

@@ -0,0 +1,5 @@
+{
+    "lambda_urls": {
+        "update_stats": "https://gpzw2o0kxd.execute-api.us-east-1.amazonaws.com/default/cbica-nichart-updatestats"
+    }
+}

docs2/api.rst

@@ -0,0 +1,22 @@
+Developers - API
+===========================
+
+Submodules
+----------
+            df_muse = pd.DataFrame(
+                columns=['MRID', '702', '701', '600', '601', '...'],
+                data=[
+                    ['Subj1', '...', '...', '...', '...', '...'],
+                    ['Subj2', '...', '...', '...', '...', '...'],
+                    ['Subj3', '...', '...', '...', '...', '...'],
+                    ['...', '...', '...', '...', '...', '...']
+                ]
+            )
+            st.markdown(
+                """
+                ### DLMUSE File:
+                The DLMUSE CSV file contains volumes of ROIs (Regions of Interest) segmented by the DLMUSE algorithm. This file is generated as output when DLMUSE is applied to a set of images.
+                """
+            )
+            st.write('Example MUSE data file:')
+            st.dataframe(df_muse)

src/viewer/pages/home.py

@@ -3,7 +3,7 @@
 import utils.utils_session as utilss
 import utils.utils_st as utilst
 from streamlit_extras.stylable_container import stylable_container
-import webbrowser
+from streamlitextras.webutils import stxs_javascript
 
 # Page config should be called for each page
 utilss.config_page()
@@ -94,14 +94,14 @@ def set_pipeline() -> None:
         """
     )
 
-#st.markdown("""
-#<style>
-    #.st-bb {
-        #background-color: #4CAF50; /* Green */
-        #color: white;
-    #}
-#</style>
-#""", unsafe_allow_html=True)
+# st.markdown("""
+# <style>
+# .st-bb {
+# background-color: #4CAF50; /* Green */
+# color: white;
+# }
+# </style>
+# """, unsafe_allow_html=True)
 
 with st.container(border=True):
 
@@ -111,35 +111,43 @@ def set_pipeline() -> None:
     )
 
     with stylable_container(
-        key="my_button_container", 
+        key="my_button_container",
         css_styles="""
             button {
                 background-color: #FF7944;
                 color: white;
                 border-radius: 20px;
             }
-            """
+            """,
     ):
         if st.button(
-            '📝 NiChart User Experience',
+            "📝 NiChart User Experience",
         ):
-            webbrowser.open_new_tab('https://forms.office.com/r/mM1kx1XsgS')
+            # This code only works locally, not on a container or server.
+            # webbrowser.open_new_tab('https://forms.office.com/r/mM1kx1XsgS')
+            stxs_javascript(
+                """window.open('https://forms.office.com/r/mM1kx1XsgS', '_blank').focus()"""
+            )
 
         if st.button(
-            '📝 Shaping the Future of NiChart',
+            "📝 Shaping the Future of NiChart",
         ):
-            webbrowser.open_new_tab('https://forms.office.com/r/acwgn2WCc4')
-
-    ### Bg color on link_button was not supported in styllable container
-    #st.link_button(
-        #'📝 NiChart User Experience',
-        #'https://forms.office.com/r/mM1kx1XsgS',
-    #)
-
-    #st.link_button(
-        #'📝 Shaping the Future of NiChart',
-        #'https://forms.office.com/r/acwgn2WCc4',
-    #)
+            # This code only works locally, not on a container or server.
+            # webbrowser.open_new_tab('https://forms.office.com/r/acwgn2WCc4')
+            stxs_javascript(
+                """window.open('https://forms.office.com/r/acwgn2WCc4', '_blank').focus()"""
+            )
+
+    # Bg color on link_button was not supported in styllable container
+    # st.link_button(
+    # '📝 NiChart User Experience',
+    # 'https://forms.office.com/r/mM1kx1XsgS',
+    # )
+
+    # st.link_button(
+    # '📝 Shaping the Future of NiChart',
+    # 'https://forms.office.com/r/acwgn2WCc4',
+    # )
 
 # FIXME: For DEBUG
 utilst.add_debug_panel()

src/viewer/pages/pipeline_dlwmls.py

@@ -1,7 +1,8 @@
+import os
+
 import streamlit as st
 import utils.utils_menu as utilmenu
 import utils.utils_session as utilss
-import os
 
 # Page config should be called for each page
 utilss.config_page()