Merge branch 'ag-dev' into 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"
+    }
+}

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()
@@ -123,12 +123,16 @@ def set_pipeline() -> None:
         if st.button(
             '📝 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',
         ):
-            webbrowser.open_new_tab('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(

src/viewer/pages/prep_sMRI_dicomtonifti.py

@@ -8,6 +8,7 @@
 import utils.utils_nifti as utilni
 import utils.utils_session as utilss
 import utils.utils_st as utilst
+import utils.utils_cloud as utilcloud
 from stqdm import stqdm
 
 # Page config should be called for each page
@@ -242,6 +243,9 @@ def panel_extract() -> None:
             )
             if num_nifti == 0:
                 st.warning(':material/thumb_down: The extraction process did not produce any Nifti images!')
+            else:
+              if st.session_state.has_cloud_session:
+                utilcloud.update_stats_db(st.session_state.cloud_user_id, "NIFTIfromDICOM", num_nifti)
 
         df_files = utilio.get_file_names(
             st.session_state.paths[st.session_state.sel_mod], ".nii.gz"

src/viewer/pages/process_sMRI_DLMUSE.py

@@ -10,6 +10,7 @@
 import utils.utils_rois as utilroi
 import utils.utils_session as utilss
 import utils.utils_st as utilst
+import utils.utils_cloud as utilcloud
 from stqdm import stqdm
 
 # Page config should be called for each page
@@ -174,6 +175,9 @@ def panel_dlmuse() -> None:
 
             with st.spinner("Wait for it..."):
                 fcount = utilio.get_file_count(st.session_state.paths["T1"])
+                if st.session_state.has_cloud_session:
+                    utilcloud.update_stats_db(st.session_state.cloud_user_id, "DLMUSE", fcount)
+
                 progress_bar = stqdm(total=9, desc="Current step", position=0)
                 progress_bar.set_description("Starting...")
 

src/viewer/pages/process_sMRI_DLWMLS.py

@@ -7,6 +7,7 @@
 import utils.utils_nifti as utilni
 import utils.utils_session as utilss
 import utils.utils_st as utilst
+import utils.utils_cloud as utilcloud
 from stqdm import stqdm
 
 # Page config should be called for each page
@@ -164,6 +165,10 @@ def panel_dlwmls() -> None:
                 os.makedirs(st.session_state.paths["dlwmls"])
 
             with st.spinner("Wait for it..."):
+                fcount = utilio.get_file_count(st.session_state.paths["FL"])
+                if st.session_state.has_cloud_session:
+                    utilcloud.update_stats_db(st.session_state.cloud_user_id, "DLWMLS", fcount)
+
                 dlwmls_cmd = f"DLWMLS -i {st.session_state.paths['FL']} -o {st.session_state.paths['dlwmls']} -d {device}"
                 st.info(f"Running: {dlwmls_cmd}", icon=":material/manufacturing:")
 

src/viewer/pages/workflow_sMRI_MLScores.py

@@ -7,6 +7,7 @@
 import utils.utils_menu as utilmenu
 import utils.utils_session as utilss
 import utils.utils_st as utilst
+import utils.utils_cloud as utilcloud
 
 run_dir = os.path.join(st.session_state.paths["root"], "src", "workflows", "w_sMRI")
 sys.path.append(run_dir)
@@ -284,6 +285,9 @@ def panel_run() -> None:
 
             with st.spinner("Wait for it..."):
                 st.info("Running: mlscores_workflow ", icon=":material/manufacturing:")
+                fcount = df_tmp.shape[0]
+                if st.session_state.has_cloud_session:
+                    utilcloud.update_stats_db(st.session_state.cloud_user_id, "MLScores", fcount)
 
                 try:
                     if flag_harmonize:

src/viewer/utils/utils_cloud.py

@@ -0,0 +1,47 @@
+import requests
+import json
+import os
+
+def load_cloud_config(config_file: str):
+    """
+    Load Lambda URLs from a local JSON file.
+    """
+    try:
+        with open(config_file, "r") as f:
+            config = json.load(f)
+            return config
+    except FileNotFoundError:
+        raise FileNotFoundError(f"Configuration file '{config_file}' not found.")
+    except json.JSONDecodeError:
+        raise ValueError(f"Error parsing the configuration file '{config_file}'.")
+
+def update_stats_db(user_id, job_type, count):
+    current_dir = os.path.dirname(os.path.abspath(__file__))
+
+    # Traverse up to the top-level directory (assuming 'config.json' is in the repo root)
+    repo_root = os.path.abspath(os.path.join(current_dir, "..", "..", ".." ))  
+    print(f"repo root: {repo_root}")
+
+    # Construct the full path to the config file
+    config_file = os.path.join(repo_root, "cloud-config.json")
+    cloud_config = load_cloud_config(config_file)
+
+    lambda_urls = cloud_config.get("lambda_urls", None)
+    if lambda_urls is None:
+        print("Lambda URL not provided in cloud config!")
+
+    update_stats_url = lambda_urls["update_stats"]
+
+    payload = {
+        "user_id": user_id,
+        "job_type": job_type,
+        "count": count
+    }
+    headers = {"Content-Type": "application/json"}
+
+    try:
+        response = requests.post(update_stats_url, json=payload, headers=headers)
+        #response.raise_for_status()
+        print("Success:", response.json())
+    except requests.exceptions.RequestException as e:
+        print("Error:", e)

src/viewer/utils/utils_session.py

@@ -6,6 +6,7 @@
 import utils.utils_rois as utilroi
 import utils.utils_io as utilio
 from PIL import Image
+import shutil
 
 from streamlit.web.server.websocket_headers import _get_websocket_headers
 import jwt
@@ -212,6 +213,19 @@ def init_session_state() -> None:
 
         if not os.path.exists(st.session_state.paths["dir_out"]):
             os.makedirs(st.session_state.paths["dir_out"])
+
+        # Copy demo folders into user folders as needed
+        if st.session_state.has_cloud_session:
+            ## Copy demo dirs to user folder (TODO: make this less hardcoded)
+            demo_dir_paths = [os.path.join(st.session_state.paths["root"], "output_folder", "NiChart_sMRI_Demo1" ),
+                              os.path.join(st.session_state.paths["root"], "output_folder", "NiChart_sMRI_Demo2" )
+                            ]
+            for demo in demo_dir_paths:
+                demo_name = os.path.basename(demo)
+                destination_path = os.path.join(st.session_state.paths["dir_out"], demo_name)
+                if os.path.exists(destination_path):
+                    shutil.rmtree(destination_path)
+                shutil.copytree(demo, destination_path, dirs_exist_ok=True)
 
         ############
         # FIXME : set init folder to test folder outside repo