Edit

Author: gurayerus

src/NiChart_Viewer/src/pages/view_plot_data.py

@@ -11,6 +11,24 @@
 from streamlit_plotly_events import plotly_events
 from utils_trace import *
 from st_pages import hide_pages
+import os
+import tkinter as tk
+from tkinter import filedialog
+
+
+def browse_file_folder(is_file, init_dir):
+    root = tk.Tk()
+    # root.withdraw()  # Hide the main window
+    if is_file == True:
+        out_path = filedialog.askopenfilenames(initialdir = init_dir, multiple=0)
+    else:
+        out_path = filedialog.askdirectory(initialdir = init_dir)
+
+    print('aaaaaa')
+    print(out_path[0:5])
+    input()
+
+    return out_path
 
 #hide_pages(["Image Processing", "Data Analytics"])
 
@@ -202,80 +220,91 @@ def filter_dataframe(df: pd.DataFrame, pid) -> pd.DataFrame:
 # # Config page
 # st.set_page_config(page_title="DataFrame Demo", page_icon="📊", layout='wide')
 
-# FIXME: Input data is hardcoded here for now
-fname = "../examples/test_input3/ROIS_tmp2.csv"
-df = pd.read_csv(fname)
+dir_root = os.path.dirname(os.path.dirname(os.path.dirname(os.getcwd())))
 
 # Page controls in side bar
 with st.sidebar:
-
     with st.container(border=True):
 
-        # Slider to set number of plots in a row
-        st.session_state.plot_per_raw = st.slider('Plots per raw',1, 5, 3, key='a_per_page')
+        # Input file name (user can enter either using the file browser or type  full path)
+        default_spare_name = ''
+        fname_spare = st.sidebar.button("Select input file", on_click = browse_file_folder, key = 'fname_spare_btn', args=[True, dir_root])
+        if fname_spare == False:
+            fname_spare = default_spare_name
+        spare_csv = st.sidebar.text_input("Enter the name of the ROI csv file:", value = fname_spare,
+                                        label_visibility="collapsed")
 
-    with st.container(border=True):
+if os.path.exists(spare_csv):
+    df = pd.read_csv(spare_csv)
+
+    with st.sidebar:
+        with st.container(border=True):
+
+            # Slider to set number of plots in a row
+            st.session_state.plot_per_raw = st.slider('Plots per raw',1, 5, 3, key='a_per_page')
+
+        with st.container(border=True):
+
+            st.write('Plot Settings')
+
+            # Tabs for parameters
+            ptabs = st.tabs([":lock:", ":large_orange_circle:", ":large_yellow_circle:",
+                            ":large_green_circle:"])
 
-        st.write('Plot Settings')
-
-        # Tabs for parameters
-        ptabs = st.tabs([":lock:", ":large_orange_circle:", ":large_yellow_circle:",
-                        ":large_green_circle:"])
-
-        # Tab 0: to set plotting parameters
-        with ptabs[1]:
-            # Default values for plot params
-            st.session_state.default_hue_var = 'Sex'
-
-            def_ind_x = 0
-            if st.session_state.default_x_var in df.columns:
-                def_ind_x = df.columns.get_loc(st.session_state.default_x_var)
-
-            def_ind_y = 0
-            if st.session_state.default_y_var in df.columns:
-                def_ind_y = df.columns.get_loc(st.session_state.default_y_var)
-
-            def_ind_hue = 0
-            if st.session_state.default_hue_var in df.columns:
-                def_ind_hue = df.columns.get_loc(st.session_state.default_hue_var)
-
-            st.session_state.default_x_var = st.selectbox("Default X Var", df.columns, key=f"x_var_init",
-                                                        index = def_ind_x)
-            st.session_state.default_y_var = st.selectbox("Default Y Var", df.columns, key=f"y_var_init",
-                                                        index = def_ind_y)
-            st.session_state.default_hue_var = st.selectbox("Default Hue Var", df.columns, key=f"hue_var_init",
-                                                            index = def_ind_hue)
-            trend_index = st.session_state.trend_types.index(st.session_state.default_trend_type)
-            st.session_state.default_trend_type = st.selectbox("Default Trend Line", st.session_state.trend_types,
-                                                            key=f"trend_type_init", index = trend_index)
-
-    # Button to add a new plot
-    if st.button("Add plot"):
+            # Tab 0: to set plotting parameters
+            with ptabs[1]:
+                # Default values for plot params
+                st.session_state.default_hue_var = 'Sex'
+
+                def_ind_x = 0
+                if st.session_state.default_x_var in df.columns:
+                    def_ind_x = df.columns.get_loc(st.session_state.default_x_var)
+
+                def_ind_y = 0
+                if st.session_state.default_y_var in df.columns:
+                    def_ind_y = df.columns.get_loc(st.session_state.default_y_var)
+
+                def_ind_hue = 0
+                if st.session_state.default_hue_var in df.columns:
+                    def_ind_hue = df.columns.get_loc(st.session_state.default_hue_var)
+
+                st.session_state.default_x_var = st.selectbox("Default X Var", df.columns, key=f"x_var_init",
+                                                            index = def_ind_x)
+                st.session_state.default_y_var = st.selectbox("Default Y Var", df.columns, key=f"y_var_init",
+                                                            index = def_ind_y)
+                st.session_state.default_hue_var = st.selectbox("Default Hue Var", df.columns, key=f"hue_var_init",
+                                                                index = def_ind_hue)
+                trend_index = st.session_state.trend_types.index(st.session_state.default_trend_type)
+                st.session_state.default_trend_type = st.selectbox("Default Trend Line", st.session_state.trend_types,
+                                                                key=f"trend_type_init", index = trend_index)
+
+        # Button to add a new plot
+        if st.button("Add plot"):
+            add_plot()
+
+    # Add a single plot (initial page includes one plot)
+    if st.session_state.plots.shape[0] == 0:
         add_plot()
 
-# Add a single plot (initial page includes one plot)
-if st.session_state.plots.shape[0] == 0:
-    add_plot()
-
-# Read plot ids
-df_p = st.session_state.plots
-p_index = df_p.PID.tolist()
-plot_per_raw = st.session_state.plot_per_raw
-
-# Render plots
-#  - iterates over plots;
-#  - for every "plot_per_raw" plots, creates a new columns block, resets column index, and displays the plot
-for i in range(0, len(p_index)):
-    column_no = i % plot_per_raw
-    if column_no == 0:
-        blocks = st.columns(plot_per_raw)
-    with blocks[column_no]:
-        display_plot(p_index[i])
-
-
-# FIXME: this is for debugging for now; will be removed
-# with st.expander('Saved DataFrames'):
-with st.container():
-    st.session_state.plots
+    # Read plot ids
+    df_p = st.session_state.plots
+    p_index = df_p.PID.tolist()
+    plot_per_raw = st.session_state.plot_per_raw
+
+    # Render plots
+    #  - iterates over plots;
+    #  - for every "plot_per_raw" plots, creates a new columns block, resets column index, and displays the plot
+    for i in range(0, len(p_index)):
+        column_no = i % plot_per_raw
+        if column_no == 0:
+            blocks = st.columns(plot_per_raw)
+        with blocks[column_no]:
+            display_plot(p_index[i])
+
+
+    # FIXME: this is for debugging for now; will be removed
+    # with st.expander('Saved DataFrames'):
+    with st.container():
+        st.session_state.plots
 
 

src/NiChart_Viewer/src/pages/workflow_sMRI.py

@@ -9,17 +9,28 @@
 import plotly.express as px
 from math import ceil
 import os
+from tempfile import NamedTemporaryFile
 
-def dir_selector(folder_path='.'):
-    dirnames = [d for d in os.listdir(folder_path) if os.path.isdir(os.path.join(folder_path, d))]
-    selected_folder = st.sidebar.selectbox('Select a folder', dirnames)
-    if selected_folder is None:
-        return None
-    return os.path.join(folder_path, selected_folder)
+import tkinter as tk
+from tkinter import filedialog
 
-st.write('Select folder')
-dirname = dir_selector()
+def browse_file_folder(is_file, init_dir):
+    root = tk.Tk()
+    root.withdraw()  # Hide the main window
+    if is_file == True:
+        out_path = filedialog.askopenfilename(initialdir = init_dir)
+    else:
+        out_path = filedialog.askdirectory(initialdir = init_dir)
 
+    print('bb')
+    print(out_path)
+
+    root.destroy()
+
+    print('aaa')
+    print(out_path)
+
+    return out_path
 
 st.markdown(
         """
@@ -35,32 +46,69 @@ def dir_selector(folder_path='.'):
 
 with st.container(border=True):
 
-    # Input text boxes
+    # Get path to root folder
+    dir_root = os.path.dirname(os.path.dirname(os.path.dirname(os.getcwd())))
+
+    # Default file names
     # FIXME: The init values for the input fields are set here to run tests quickly
-    #        they will be removed or replaced in the future
-    dset_name = st.text_input("Give a name to your dataset", value = 'Study1')
+    #        - they will be replaced in the future with values used to link I/O
+    #          between modules (i.e if DLMUSE pipeline was run, it's out file will be set as input'
+    default_study_name = 'Study1'
+    default_roi_name = f'{dir_root}/test/test_input/test2_rois/Study1/Study1_DLMUSE.csv'
+    default_demog_name = f'{dir_root}/test/test_input/test2_rois/Study1/Study1_Demog.csv'
+    default_out_name = f'{dir_root}/test/test_output/test2_rois/Study1'
+
+    # Dset name: We use this to name all output for a study
+    dset_name = st.text_input("Give a name to your dataset", value = default_study_name)
 
-    # input_rois = st.text_input("Enter the input rois file name:", key = 'input_rois')
-    # upload_rois = st.file_uploader("Upload the file:", key = 'upload_rois')
+    # Roi file name (user can enter either using the file browser or type  full path)
+    tmpcol = st.columns((1,8))
+    fname_rois = default_roi_name
+    with tmpcol[0]:
+        if st.button("Select ROI file"):
+            fname_rois = browse_file_folder(True, dir_root)
+    with tmpcol[1]:
+        input_rois = st.text_input("Enter the name of the ROI csv file:", value = fname_rois,
+                                   label_visibility="collapsed")
 
-    input_rois = st.text_input("path to DLMUSE csv file", value = '/home/gurayerus/GitHub/CBICA/NiChart_Project/test/test_input/test2_rois/Study1/Study1_DLMUSE.csv')
-    input_demog = st.text_input("path to demographic csv file", value = '/home/gurayerus/GitHub/CBICA/NiChart_Project/test/test_input/test2_rois/Study1/Study1_Demog.csv')
-    dir_output = st.text_input("path to output folder", value = '/home/gurayerus/GitHub/CBICA/NiChart_Project/test/test_output/test2_rois')
+    # Demog file name (user can enter either using the file browser or type  full path)
+    tmpcol = st.columns((1,8))
+    fname_demog = default_demog_name
+    with tmpcol[0]:
+        if st.button("Select demog file"):
+            fname_demog = browse_file_folder(True, dir_root)
+    with tmpcol[1]:
+        input_demog = st.text_input("Enter the name of the demog csv file:", value = fname_demog,
+                                   label_visibility="collapsed")
+
+    # Out folder name (user can enter either using the file browser or type  full path)
+    tmpcol = st.columns((1,8))
+    dname_out = default_out_name
+    with tmpcol[0]:
+        if st.button("Select output folder"):
+            dname_out = browse_file_folder(False, dir_root)
+    with tmpcol[1]:
+        dir_output = st.text_input("Enter the name of the output folder:", value = dname_out,
+                                   label_visibility="collapsed")
+
+    flag_files = 1
 
     # Check input files
     if not os.path.exists(input_rois):
         st.warning("Path to input DLMUSE csv doesn't exist")
-    if not os.path.exists(input_rois):
+        flag_files = 0
+
+    if not os.path.exists(input_demog):
         st.warning("Path to input demographic csv doesn't exist")
-    if not os.path.exists(dir_output):
-        st.warning("Path to output folder doesn't exist")
+        flag_files = 0
 
     run_dir='../../workflow/workflows/w_sMRI'
 
     # Run workflow
-    if st.button("Run w_sMRI"):
-        st.write("Pipeline is running, please wait!")
-        os.system(f"cd {run_dir}")
-        cmd = f"python3 {run_dir}/call_snakefile.py --run_dir {run_dir} --dset_name {dset_name} --input_rois {input_rois} --input_demog {input_demog} --dir_output {dir_output}"
-        os.system(cmd)
-        st.write("Run completed!")
+    if flag_files == 1:
+        if st.button("Run w_sMRI"):
+            st.write("Pipeline is running, please wait!")
+            os.system(f"cd {run_dir}")
+            cmd = f"python3 {run_dir}/call_snakefile.py --run_dir {run_dir} --dset_name {dset_name} --input_rois {input_rois} --input_demog {input_demog} --dir_output {dir_output}"
+            os.system(cmd)
+            st.write("Run completed!")