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Added manual entry of demog data in ml scores
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@gurayerus
gurayerus committed Dec 13, 2024
1 parent e909408 commit 8adfcae
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Showing 2 changed files with 113 additions and 56 deletions.
166 changes: 111 additions & 55 deletions src/viewer/pages/workflow_sMRI_MLScores.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -30,8 +30,10 @@
# Update status of checkboxes
if '_check_ml_wdir' in st.session_state:
st.session_state.checkbox['ml_wdir'] = st.session_state._check_ml_wdir
if '_check_ml_in' in st.session_state:
st.session_state.checkbox['ml_in'] = st.session_state._check_ml_in
if '_check_ml_inrois' in st.session_state:
st.session_state.checkbox['ml_inrois'] = st.session_state._check_ml_inrois
if '_check_ml_indemog' in st.session_state:
st.session_state.checkbox['ml_indemog'] = st.session_state._check_ml_indemog
if '_check_ml_run' in st.session_state:
st.session_state.checkbox['ml_run'] = st.session_state._check_ml_run
if '_check_ml_download' in st.session_state:
Expand Down Expand Up @@ -61,19 +63,19 @@ def panel_wdir() -> None:

utilst.util_workingdir_get_help()

def panel_indata() -> None:
def panel_inrois() -> None:
"""
Panel for uploading input files
Panel for uploading input rois
"""
msg = st.session_state.app_config[st.session_state.app_type]["msg_infile"]
icon = st.session_state.icon_thumb[st.session_state.flags["csv_dlmuse+demog"]]
show_panel_indata = st.checkbox(
f":material/upload: {msg} Data {icon}",
icon = st.session_state.icon_thumb[st.session_state.flags["csv_dlmuse"]]
st.checkbox(
f":material/upload: {msg} ROIs {icon}",
disabled=not st.session_state.flags["dir_out"],
key='_check_ml_in',
value=st.session_state.checkbox['ml_in']
key='_check_ml_inrois',
value=st.session_state.checkbox['ml_inrois']
)
if not st.session_state._check_ml_in:
if not st.session_state._check_ml_inrois:
return

with st.container(border=True):
Expand All @@ -85,20 +87,6 @@ def panel_indata() -> None:
False,
"visible",
)
if os.path.exists(st.session_state.paths["csv_dlmuse"]):
p_dlmuse = st.session_state.paths["csv_dlmuse"]
st.success(f"Data is ready ({p_dlmuse})", icon=":material/thumb_up:")

utilst.util_upload_file(
st.session_state.paths["csv_demog"],
"Demographics csv",
"uploaded_demog_file",
False,
"visible",
)
if os.path.exists(st.session_state.paths["csv_demog"]):
p_demog = st.session_state.paths["csv_dlmuse"]
st.success(f"Data is ready ({p_demog})", icon=":material/thumb_up:")

else: # st.session_state.app_type == 'desktop'
utilst.util_select_file(
Expand All @@ -107,38 +95,19 @@ def panel_indata() -> None:
st.session_state.paths["csv_dlmuse"],
st.session_state.paths["file_search_dir"],
)
if os.path.exists(st.session_state.paths["csv_dlmuse"]):
p_dlmuse = st.session_state.paths["csv_dlmuse"]
st.success(f"Data is ready ({p_dlmuse})", icon=":material/thumb_up:")

utilst.util_select_file(
"selected_demog_file",
"Demographics csv",
st.session_state.paths["csv_demog"],
st.session_state.paths["file_search_dir"],
)
if os.path.exists(st.session_state.paths["csv_demog"]):
p_demog = st.session_state.paths["csv_demog"]
st.success(f"Data is ready ({p_demog})", icon=":material/thumb_up:")

# Check the input data
if st.button('Verify input data'):
[f_check, m_check] = w_mlscores.check_input(
st.session_state.paths["csv_dlmuse"],
st.session_state.paths["csv_demog"],
)
if f_check == 0:
st.session_state.flags["csv_dlmuse+demog"] = True
st.success(m_check, icon=":material/thumb_up:")
st.session_state.flags["csv_mlscores"] = True
else:
st.session_state.flags["csv_dlmuse+demog"] = False
st.error(m_check, icon=":material/thumb_down:")
st.session_state.flags["csv_mlscores"] = False
if os.path.exists(st.session_state.paths["csv_dlmuse"]):
p_dlmuse = st.session_state.paths["csv_dlmuse"]
st.session_state.flags["csv_dlmuse"] = True
st.success(f"Data is ready ({p_dlmuse})", icon=":material/thumb_up:")

df_rois = pd.read_csv(st.session_state.paths["csv_dlmuse"])
with st.expander('Show ROIs', expanded=False):
st.dataframe(df_rois)

# Check the input data
@st.dialog("Input data requirements") # type:ignore
def help_input_data():
def help_inrois_data():
df_muse = pd.DataFrame(
columns=['MRID', '702', '701', '600', '601', '...'],
data=[
Expand All @@ -157,6 +126,92 @@ def help_input_data():
st.write('Example MUSE data file:')
st.dataframe(df_muse)

col1, col2 = st.columns([0.5, 0.1])
with col2:
if st.button('Get help 🤔', key='key_btn_help_mlinrois', use_container_width=True):
help_inrois_data()

def panel_indemog() -> None:
"""
Panel for uploading demographics
"""
msg = st.session_state.app_config[st.session_state.app_type]["msg_infile"]
icon = st.session_state.icon_thumb[st.session_state.flags["csv_demog"]]


st.checkbox(
f":material/upload: {msg} Demographics {icon}",
disabled=not st.session_state.flags["csv_dlmuse"],
key='_check_ml_indemog',
value=st.session_state.checkbox['ml_indemog']
)
if not st.session_state._check_ml_indemog:
return

with st.container(border=True):
flag_manual = st.checkbox(
'Enter data manually',
False
)
if flag_manual:
st.info('Please enter values for your sample')
df_rois = pd.read_csv(st.session_state.paths["csv_dlmuse"])
df_tmp = pd.DataFrame({'MRID': df_rois['MRID'], 'Age': None, 'Sex': None})
df_user = st.data_editor(df_tmp)

if st.button('Save data'):
if not os.path.exists(os.path.dirname(st.session_state.paths["csv_demog"])):
os.makedirs(os.path.dirname(st.session_state.paths["csv_demog"]))

df_user.to_csv(st.session_state.paths["csv_demog"], index=False)
st.success(f"Data saved to {st.session_state.paths['csv_demog']}")

else:
if st.session_state.app_type == "cloud":
utilst.util_upload_file(
st.session_state.paths["csv_demog"],
"Demographics csv",
"uploaded_demog_file",
False,
"visible",
)

else: # st.session_state.app_type == 'desktop'
utilst.util_select_file(
"selected_demog_file",
"Demographics csv",
st.session_state.paths["csv_demog"],
st.session_state.paths["file_search_dir"],
)

if os.path.exists(st.session_state.paths["csv_demog"]):
p_demog = st.session_state.paths["csv_demog"]
st.session_state.flags["csv_demog"] = True
st.success(f"Data is ready ({p_demog})", icon=":material/thumb_up:")

df_demog = pd.read_csv(st.session_state.paths["csv_demog"])
with st.expander('Show demographics data', expanded=False):
st.dataframe(df_demog)

# Check the input data
if os.path.exists(st.session_state.paths["csv_demog"]):
if st.button('Verify input data'):
[f_check, m_check] = w_mlscores.check_input(
st.session_state.paths["csv_dlmuse"],
st.session_state.paths["csv_demog"],
)
if f_check == 0:
st.session_state.flags["csv_dlmuse+demog"] = True
st.success(m_check, icon=":material/thumb_up:")
st.session_state.flags["csv_mlscores"] = True
else:
st.session_state.flags["csv_dlmuse+demog"] = False
st.error(m_check, icon=":material/thumb_down:")
st.session_state.flags["csv_mlscores"] = False

# Help
@st.dialog("Input data requirements") # type:ignore
def help_indemog_data():
df_demog = pd.DataFrame(
columns=['MRID', 'Age', 'Sex'],
data=[
Expand All @@ -182,8 +237,8 @@ def help_input_data():

col1, col2 = st.columns([0.5, 0.1])
with col2:
if st.button('Get help 🤔', key='key_btn_help_mlinput', use_container_width=True):
help_input_data()
if st.button('Get help 🤔', key='key_btn_help_mlindemog', use_container_width=True):
help_indemog_data()


def panel_run() -> None:
Expand Down Expand Up @@ -302,7 +357,8 @@ def panel_download() -> None:

st.divider()
panel_wdir()
panel_indata()
panel_inrois()
panel_indemog()
panel_run()
if st.session_state.app_type == "cloud":
panel_download()
Expand Down
3 changes: 2 additions & 1 deletion src/viewer/utils/utils_session.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -111,7 +111,8 @@ def init_session_state() -> None:
"dlmuse_view": False,
"dlmuse_download": False,
"ml_wdir": False,
"ml_in": False,
"ml_inrois": False,
"ml_indemog": False,
"ml_run": False,
"ml_download": False,
"view_wdir": False,
Expand Down

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