Add FLASHIda Support

.github/workflows/build-windows-executable-app.yaml

@@ -313,6 +313,7 @@ jobs:
         cp -r src streamlit_exe
         cp -r content streamlit_exe
         cp -r assets streamlit_exe
+        cp -r scripts streamlit_exe
         cp -r static streamlit_exe
         cp -r example-data streamlit_exe
         cp openms-bin/*.dll streamlit_exe

app.py

@@ -35,5 +35,14 @@
         ],
     }
 
+    with open('settings.json', 'r') as f:
+        settings = json.load(f)
+    if settings['enable_flashida']:
+        pages["🧠 FLASHIda"] = ([
+            st.Page(Path("content", "FLASHIda", "FLASHIdaWorkflow.py"), title="Workflow", icon="⚙️"),
+            st.Page(Path("content", "FLASHIda", "FLASHIdaSimulatorWorkflow.py"), title="Simulator", icon="⚙️"),
+            st.Page(Path("content", "FLASHIda", "FLASHIdaViewer.py"), title="Viewer", icon="👀"),
+        ])
+
     pg = st.navigation(pages, expanded=True)
     pg.run()

content/FLASHIda/FLASHIdaSimulatorWorkflow.py

@@ -0,0 +1,21 @@
+import streamlit as st
+
+from src.Workflow import IdaSimulatorWorkflow
+from src.common.common import page_setup
+
+
+params = page_setup()
+
+wf = IdaSimulatorWorkflow()
+
+st.title('FLASHIda - Intelligent Data Acquisition')
+
+t = st.tabs(["📁 **File Upload**", "⚙️ **Configure**", "🚀 **Run**"])
+with t[0]:
+    wf.show_file_upload_section()
+
+with t[1]:
+    wf.show_parameter_section()
+
+with t[2]:
+    wf.show_execution_section()

content/FLASHIda/FLASHIdaViewer.py

@@ -0,0 +1,126 @@
+import streamlit as st
+
+from pathlib import Path
+
+from src.common.common import page_setup, save_params
+from src.workflow.FileManager import FileManager
+from src.render.render import render_grid
+
+DEFAULT_LAYOUT = [['ms1_deconv_heat_map']]
+
+def select_experiment():
+    st.session_state.selected_experiment0_ida = st.session_state.selected_experiment_dropdown_ida
+    print(st.session_state.selected_experiment0_ida)
+    if len(layout) > 1:
+        for exp_index in range(1, len(layout)):
+            if st.session_state[f'selected_experiment_dropdown_{exp_index}_ida'] is None:
+                continue
+            st.session_state[f"selected_experiment{exp_index}_ida"] = st.session_state[f'selected_experiment_dropdown_{exp_index}_ida']
+
+def validate_selected_index(file_manager, selected_experiment):
+    results = file_manager.get_results_list(['simulation_dfs'])
+    if selected_experiment in st.session_state:
+        if st.session_state[selected_experiment] in results:
+            return name_to_index[st.session_state[selected_experiment]]
+        else:
+            del st.session_state[selected_experiment]
+    return None
+
+# page initialization
+params = page_setup()
+
+# Get available results
+file_manager = FileManager(
+    st.session_state["workspace"],
+    Path(st.session_state['workspace'], 'flashidasimulator', 'cache')
+)
+
+results = file_manager.get_results_list(['simulation_dfs'])
+
+if file_manager.result_exists('layout', 'layout'):
+    layout = file_manager.get_results('layout', 'layout')['layout']
+    side_by_side = layout['side_by_side']
+    layout = layout['layout']
+
+else:
+    layout = [DEFAULT_LAYOUT]
+    side_by_side = False
+
+### if no input file is given, show blank page
+if len(results) == 0:
+    st.error('No results to show yet. Please run a workflow first!')
+    st.stop()
+
+# Map names to index
+name_to_index = {n : i for i, n in enumerate(results)}
+
+if len(layout) == 2 and side_by_side:
+    c1, c2 = st.columns(2)
+    with c1:
+        st.selectbox(
+            "choose experiment", results, 
+            key="selected_experiment_dropdown_ida", 
+            index=validate_selected_index(file_manager, 'selected_experiment0_ida'),
+            on_change=select_experiment
+        )
+        if 'selected_experiment0_ida' in st.session_state:
+            render_grid(
+                st.session_state.selected_experiment0_ida, layout[0], file_manager, 
+                'flashidasimulator', "selected_experiment0_ida", 'flash_viewer_grid_0_ida'
+            )
+    with c2:
+        st.selectbox(
+            "choose experiment", results, 
+            key=f'selected_experiment_dropdown_1_ida',
+            index=validate_selected_index(file_manager, 'selected_experiment1_ida'),
+            on_change=select_experiment
+        )
+        if f"selected_experiment1_ida" in st.session_state:
+            with st.spinner('Loading component...'):
+                render_grid(
+                     st.session_state["selected_experiment1_ida"], layout[1], 
+                     file_manager, 'flashidasimulator', 'selected_experiment1_ida', 
+                     'flash_viewer_grid_1_ida'
+                )
+
+else:
+    ### for only single experiment on one view
+    st.selectbox(
+        "choose experiment", results, 
+        key="selected_experiment_dropdown_ida", 
+        index=validate_selected_index(file_manager, 'selected_experiment0_ida'),
+        on_change=select_experiment
+    )
+
+
+    if 'selected_experiment0_ida' in st.session_state:
+        print('Lets go!')
+        render_grid(
+            st.session_state.selected_experiment0_ida, layout[0], file_manager, 
+            'flashidasimulator', 'selected_experiment0_ida'
+        )
+
+    ### for multiple experiments on one view
+    if len(layout) > 1:
+
+        for exp_index, exp_layout in enumerate(layout):
+            if exp_index == 0: continue  # skip the first experiment
+
+            st.divider()  # horizontal line
+
+            st.selectbox(
+                "choose experiment", results, 
+                key=f'selected_experiment_dropdown_{exp_index}_ida',
+                index=validate_selected_index(file_manager, f'selected_experiment{exp_index}_ida'),
+                on_change=select_experiment
+            )
+            # if #experiment input files are less than #layouts, all the pre-selection will be the first experiment
+            if f"selected_experiment{exp_index}_ida" in st.session_state:
+                render_grid(
+                     st.session_state["selected_experiment%d_ida" % exp_index], 
+                     layout[exp_index], file_manager, 'flashidasimulator', 
+                     "selected_experiment%d_ida" % exp_index, 
+                     'flash_viewer_grid_%d_ida' % exp_index
+                )
+
+save_params(params)

content/FLASHIda/FLASHIdaWorkflow.py

@@ -0,0 +1,20 @@
+import streamlit as st
+
+from src.Workflow import IdaWorkflow
+from src.common.common import page_setup
+
+
+params = page_setup()
+
+wf = IdaWorkflow()
+
+st.title('FLASHIda - Intelligent Data Acquisition')
+
+t = st.tabs(["⚙️ **Configure**", "🚀 **Run**"])
+
+
+with t[0]:
+    wf.show_parameter_section()
+
+with t[1]:
+    wf.show_execution_section()

scripts/flashida/write_method.py

@@ -0,0 +1,107 @@
+import json
+import sys
+
+import xml.etree.ElementTree as ET
+
+############################
+# default paramter values #
+###########################
+#
+# Mandatory keys for each parameter
+# key: a unique identifier
+# value: the default value
+#
+# Optional keys for each parameter
+# name: the name of the parameter
+# hide: don't show the parameter in the parameter section (e.g. for input/output files)
+# options: a list of valid options for the parameter
+# min: the minimum value for the parameter (int and float)
+# max: the maximum value for the parameter (int and float)
+# step_size: the step size for the parameter (int and float)
+# help: a description of the parameter
+# widget_type: the type of widget to use for the parameter (default: auto)
+# advanced: whether or not the parameter is advanced (default: False)
+
+DEFAULTS = [
+    {"key": "in", "value": [], "help": "Input files for Python Script.", "hide": True},
+    {'key': 'TopN', 'name': 'TopN', 'value': 3},
+    {'key': 'Duration', 'name': 'Duration', 'value': 67},
+    'MS1',
+    {'key': 'Analyzer', 'name': 'Analyzer', 'value': 'Orbitrap'},
+    {'key': 'FirstMass', 'name': 'FirstMass', 'value': 400},
+    {'key': 'LastMass', 'name': 'LastMass', 'value': 2000},
+    {'key': 'OrbitrapResolution', 'name': 'OrbitrapResolution', 'value': 120000},
+    {'key': 'AGCTarget', 'name': 'AGCTarget', 'value': 800000},
+    {'key': 'MaxIT', 'name': 'MaxIT', 'value': 50},
+    {'key': 'Microscans', 'name': 'Microscans', 'value': 1},
+    {'key': 'DataType', 'name': 'DataType', 'value': 'Centroid'},
+    {'key': 'RFLens', 'name': 'RFLens', 'value': 30},
+    {'key': 'SourceCID', 'name': 'SourceCID', 'value': 0},
+    'MS2',
+    {'key': 'Analyzer', 'name': 'Analyzer', 'value': 'Orbitrap'},
+    {'key': 'FirstMass', 'name': 'FirstMass', 'value': 200},
+    {'key': 'OrbitrapResolution', 'name': 'OrbitrapResolution', 'value': 60000},
+    {'key': 'AGCTarget', 'name': 'AGCTarget', 'value': 500000},
+    {'key': 'MaxIT', 'name': 'MaxIT', 'value': 118},
+    {'key': 'Microscans', 'name': 'Microscans', 'value': 1},
+    {'key': 'DataType', 'name': 'DataType', 'value': 'Centroid'},
+    {'key': 'Activation', 'name': 'Activation', 'value': 'HCD'},
+    {'key': 'CollisionEnergy', 'name': 'CollisionEnergy', 'value': 29},
+    'IDA',
+    {'key': 'MaxMs2CountPerMs1', 'name': 'MaxMs2CountPerMs1','value': 4},
+    {'key': 'QScoreThreshold', 'name': 'QScoreThreshold', 'value': 0.2},
+    {'key': 'TQScoreThreshold', 'name': 'TQScoreThreshold', 'value': 0.99},
+    {'key': 'MinCharge', 'name': 'MinCharge', 'value': 4},
+    {'key': 'MaxCharge', 'name': 'MaxCharge', 'value': 50},
+    {'key': 'MinMass', 'name': 'MinMass', 'value': 500},
+    {'key': 'MaxMass', 'name': 'MaxMass', 'value': 50000},
+    {'key': 'Tolerances', 'name': 'Tolerances', 'value': [10.0, 10.0]},
+    {'key': 'TargetLogs', 'name': 'TargetLogs', 'value': [r'C:\Users\KyowonJeong\Desktop\FLASHIdaTmp\test1.log']},
+    {'key': 'RTWindow', 'name': 'RTWindow', 'value': 180},
+    {'key': 'TargetMode', 'name': 'TargetMode', 'value': 0},
+    {'key': 'UseFAIMS', 'name': 'UseFAIMS', 'value': False},
+    {'key': 'UseCVQScore', 'name': 'UseCVQScore', 'value': False},
+    {'key': 'CycleTime', 'name': 'CycleTime', 'value': 180},
+    {'key': 'CVValues', 'name': 'CVValues', 'value': [-10.0, -30.0, -40.0, -50.0, -60.0]},
+]
+
+def get_params():
+    if len(sys.argv) > 1:
+        with open(sys.argv[1], "r") as f:
+            return json.load(f)
+    else:
+        return {}
+
+if __name__ == "__main__":
+    params = get_params()
+
+    input_xml = params.pop('input_xml')
+
+    # Create method.xml
+    root = ET.Element("MethodParameters")
+    subsections = {}
+    for key, value in params.items():
+        if ':' in key:
+            section, param = key.split(':')
+            if section not in subsections:
+                subsections[section] = ET.SubElement(root, section)
+            section = subsections[section]
+            tag = ET.SubElement(section, param)
+        else:
+            tag = ET.SubElement(root, key)
+        # Handle list inputs
+        if key in ['IDA:Tolerances', 'IDA:CVValues']:
+            for item in value.split('\n'):
+                element = ET.SubElement(tag, 'double')
+                element.text = item.strip()
+        elif key in ['IDA:TargetLogs']:
+            for item in value.split('\n'):
+                element = ET.SubElement(tag, 'string')
+                element.text = item.strip().replace('\\\\', '\\')
+        elif isinstance(value, bool):
+            tag.text = str(value).lower()
+        else:
+            tag.text = str(value)
+    tree = ET.ElementTree(root)
+    ET.indent(tree, space="  ")
+    tree.write(input_xml, encoding="utf-8", xml_declaration=True)

settings.json

@@ -14,6 +14,7 @@
         }
     },
     "online_deployment": false,
+    "enable_flashida": true,
     "enable_workspaces": true,
     "test": true,
     "workspaces_dir": ".."