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Ge dev #46

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merged 6 commits into from
Dec 10, 2024
Merged

Ge dev #46

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ae19723
Edit visibility of frames on each page
gurayerus Dec 9, 2024
843e479
Add reset when plot data or working dir changes
Dec 10, 2024
7734291
Edit variable selection panel
gurayerus Dec 10, 2024
b1ed7c3
Edit variable selection panel
gurayerus Dec 10, 2024
d646bec
Fix typo
gurayerus Dec 10, 2024
3c8c71f
Fix bug
gurayerus Dec 10, 2024
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94 changes: 61 additions & 33 deletions src/viewer/pages/plot_sMRI_vars_study.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -33,15 +33,28 @@
"""
)

# Update status of checkboxes
if '_check_view_wdir' in st.session_state:
st.session_state.checkbox['view_wdir'] = st.session_state._check_view_wdir
if '_check_view_in' in st.session_state:
st.session_state.checkbox['view_in'] = st.session_state._check_view_in
if '_check_view_select' in st.session_state:
st.session_state.checkbox['view_select'] = st.session_state._check_view_select
if '_check_view_plot' in st.session_state:
st.session_state.checkbox['view_plot'] = st.session_state._check_view_plot


def panel_wdir() -> None:
"""
Panel for selecting the working dir
"""
icon = st.session_state.icon_thumb[st.session_state.flags["dir_out"]]
show_panel_wdir = st.checkbox(
f":material/folder_shared: Working Directory {icon}", value=False
f":material/folder_shared: Working Directory {icon}",
key='_check_view_wdir',
value=st.session_state.checkbox['view_wdir']
)
if not show_panel_wdir:
if not st.session_state._check_view_wdir:
return

with st.container(border=True):
Expand All @@ -66,11 +79,20 @@ def panel_incsv() -> None:
show_panel_incsv = st.checkbox(
f":material/upload: {msg} Data {icon}",
disabled=not st.session_state.flags["dir_out"],
value=False,
key='_check_view_in',
value=st.session_state.checkbox['view_in']
)
if not show_panel_incsv:
if not st.session_state._check_view_in:
return

# Read data if working dir changed
if st.session_state.plot_var["df_data"].shape[0] == 0:
st.session_state.plot_var["df_data"] = utildf.read_dataframe(
st.session_state.paths["csv_plot"]
)
utilss.reset_plots()
st.session_state.is_updated["csv_plot"] = False

with st.container(border=True):
if st.session_state.app_type == "cloud":
st.session_state.is_updated["csv_plot"] = utilst.util_upload_file(
Expand All @@ -88,8 +110,6 @@ def panel_incsv() -> None:
st.session_state.paths["file_search_dir"],
)

print(f'aaaa {st.session_state.is_updated["csv_plot"]}')

if os.path.exists(st.session_state.paths["csv_plot"]):
p_plot = st.session_state.paths["csv_plot"]
st.success(f"Data is ready ({p_plot})", icon=":material/thumb_up:")
Expand All @@ -102,6 +122,7 @@ def panel_incsv() -> None:
st.session_state.plot_var["df_data"] = utildf.read_dataframe(
st.session_state.paths["csv_plot"]
)
utilss.reset_plots()
st.session_state.is_updated["csv_plot"] = False

# Show input data
Expand Down Expand Up @@ -182,9 +203,10 @@ def panel_select() -> None:
show_panel_select = st.checkbox(
":material/playlist_add: Select Variables (optional)",
disabled=not st.session_state.flags["csv_plot"],
value=False,
key='_check_view_select',
value=st.session_state.checkbox['view_select']
)
if not show_panel_select:
if not st.session_state._check_view_select:
return

with st.container(border=True):
Expand All @@ -209,35 +231,35 @@ def panel_select() -> None:
)

if sel_cat is None:
sel_vars = []
sel_vars_cat = []
else:
sel_vars = dict_categories[sel_cat]
sel_vars = [x for x in sel_vars if x in df.columns]
sel_vars_cat = dict_categories[sel_cat]
sel_vars_cat = [x for x in sel_vars_cat if x in df.columns]

with cols_tmp[1]:
sel_vars = st.multiselect(
sel_vars_cat = st.multiselect(
"Select variables from this category",
sel_vars,
sel_vars,
sel_vars_cat,
sel_vars_cat,
help="The list shows variables that are present in the data file! If the list is empty, it means that none of the variables in this category are present in the data file.",
)

with cols_tmp[2]:
if st.button("Add selected variables"):
sel_vars_uniq = [
v for v in sel_vars if v not in st.session_state.plot_sel_vars
sel_vars_cat_uniq = [
v for v in sel_vars_cat if v not in st.session_state.plot_sel_vars
]
st.session_state.plot_sel_vars += sel_vars_uniq
st.session_state.plot_sel_vars += sel_vars_cat_uniq

sel_vars_all = st.multiselect(
sel_vars_final = st.multiselect(
"Select final variables to keep",
st.session_state.plot_sel_vars,
st.session_state.plot_sel_vars,
)

# Select the ones in current dataframe
sel_vars_all = [x for x in sel_vars_all if x in df.columns]
st.session_state.plot_sel_vars = sel_vars_all
sel_vars_final = [x for x in sel_vars_final if x in df.columns]
st.session_state.plot_sel_vars = sel_vars_final

if st.button("Select variables"):
if "MRID" not in st.session_state.plot_sel_vars:
Expand All @@ -247,14 +269,15 @@ def panel_select() -> None:
sel_vars = st.session_state.plot_sel_vars
st.success(f"Selected variables: {sel_vars}")

# Add centile vars
vars_cent = []
for tmp_var in sel_vars:
if tmp_var + '_centiles' in df.columns:
vars_cent.append(tmp_var + '_centiles')
sel_vars = sel_vars + vars_cent
st.session_state.plot_sel_vars = sel_vars

df = df[st.session_state.plot_sel_vars]
c_var=tmp_var + '_centiles'
if c_var in df.columns and c_var not in sel_vars:
vars_cent.append(c_var)
sel_vars_wcent = sel_vars + vars_cent
df = df[sel_vars_wcent]
st.session_state.plot_var["df_data"] = df

with st.expander('Show selected data', expanded=False):
Expand All @@ -267,8 +290,10 @@ def panel_select() -> None:
st.session_state.plot_var["df_data"] = utildf.read_dataframe(
st.session_state.paths["csv_plot"]
)
utilss.reset_plots()
st.session_state.is_updated["csv_plot"] = False
st.session_state.plot_sel_vars = []
st.rerun()

s_title="Variable Selection"
s_text="""
Expand Down Expand Up @@ -376,7 +401,6 @@ def show_plots(df: pd.DataFrame, btn_plots: bool) -> None:
"""
Display plots
"""

# Add a plot (a first plot is added by default; others at button click)
if st.session_state.plots.shape[0] == 0 or btn_plots:
# Select xvar and yvar, if not set yet
Expand Down Expand Up @@ -442,17 +466,21 @@ def panel_plot() -> None:
show_panel_plots = st.checkbox(
":material/bid_landscape: Plot Data",
disabled=not st.session_state.flags["csv_plot"],
key='_check_view_plot',
value=st.session_state.checkbox['view_plot']
)

if not show_panel_plots:
if not st.session_state._check_view_plot:
return

# Read dataframe
if st.session_state.plot_var["df_data"].shape[0] == 0:
st.session_state.plot_var["df_data"] = utildf.read_dataframe(
st.session_state.paths["csv_plot"]
)
# if st.session_state.plot_var["df_data"].shape[0] == 0:
# st.session_state.plot_var["df_data"] = utildf.read_dataframe(
# st.session_state.paths["csv_plot"]
# )
df = st.session_state.plot_var["df_data"]
if df.shape[0] == 0:
st.warning('Dataframe has 0 rows!')
return

# Add sidebar parameters
with st.sidebar:
Expand Down
61 changes: 40 additions & 21 deletions src/viewer/pages/prep_sMRI_dicomtonifti.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -19,21 +19,36 @@

st.write("# Dicom to Nifti Conversion")

# Update status of checkboxes
if '_check_dicoms_wdir' in st.session_state:
st.session_state.checkbox['dicoms_wdir'] = st.session_state._check_dicoms_wdir
if '_check_dicoms_in' in st.session_state:
st.session_state.checkbox['dicoms_in'] = st.session_state._check_dicoms_in
if '_check_dicoms_series' in st.session_state:
st.session_state.checkbox['dicoms_series'] = st.session_state._check_dicoms_series
if '_check_dicoms_run' in st.session_state:
st.session_state.checkbox['dicoms_run'] = st.session_state._check_dicoms_run
if '_check_dicoms_view' in st.session_state:
st.session_state.checkbox['dicoms_view'] = st.session_state._check_dicoms_view
if '_check_dicoms_download' in st.session_state:
st.session_state.checkbox['dicoms_download'] = st.session_state._check_dicoms_download


def progress(p: int, i: int, decoded: Any) -> None:
with result_holder.container():
st.progress(p, f"Progress: Token position={i}")


def panel_wdir() -> None:
"""
Panel for selecting the working dir
"""
icon = st.session_state.icon_thumb[st.session_state.flags["dir_out"]]
show_panel_wdir = st.checkbox(
f":material/folder_shared: Working Directory {icon}", value=False
st.checkbox(
f":material/folder_shared: Working Directory {icon}",
key='_check_dicoms_wdir',
value=st.session_state.checkbox['dicoms_wdir']
)
if not show_panel_wdir:
if not st.session_state._check_dicoms_wdir:
return

with st.container(border=True):
Expand All @@ -53,12 +68,13 @@ def panel_indicoms() -> None:
"""
msg = st.session_state.app_config[st.session_state.app_type]["msg_infile"]
icon = st.session_state.icon_thumb[st.session_state.flags["dir_dicom"]]
show_panel_indicoms = st.checkbox(
st.checkbox(
f":material/upload: {msg} Dicoms {icon}",
disabled=not st.session_state.flags["dir_out"],
value=False,
key='_check_dicoms_in',
value=st.session_state.checkbox['dicoms_in']
)
if not show_panel_indicoms:
if not st.session_state._check_dicoms_in:
return

with st.container(border=True):
Expand Down Expand Up @@ -113,12 +129,13 @@ def panel_detect() -> None:
Panel for detecting dicom series
"""
icon = st.session_state.icon_thumb[st.session_state.flags["dicom_series"]]
show_panel_detect = st.checkbox(
st.checkbox(
f":material/manage_search: Detect Dicom Series {icon}",
disabled=not st.session_state.flags["dir_dicom"],
value=False,
key='_check_dicoms_series',
value=st.session_state.checkbox['dicoms_series']
)
if not show_panel_detect:
if not st.session_state._check_dicoms_series:
return

with st.container(border=True):
Expand Down Expand Up @@ -163,12 +180,13 @@ def panel_extract() -> None:
Panel for extracting dicoms
"""
icon = st.session_state.icon_thumb[st.session_state.flags["dir_nifti"]]
show_panel_extract = st.checkbox(
st.checkbox(
f":material/auto_awesome_motion: Extract Scans {icon}",
disabled=not st.session_state.flags["dicom_series"],
value=False,
key='_check_dicoms_run',
value=st.session_state.checkbox['dicoms_run']
)
if not show_panel_extract:
if not st.session_state._check_dicoms_run:
return

with st.container(border=True):
Expand Down Expand Up @@ -243,13 +261,13 @@ def panel_view() -> None:
"""
Panel for viewing extracted nifti images
"""

show_panel_view = st.checkbox(
st.checkbox(
":material/visibility: View Scans",
disabled=not st.session_state.flags["dir_nifti"],
value=False,
key='_check_dicoms_view',
value=st.session_state.checkbox['dicoms_view']
)
if not show_panel_view:
if not st.session_state._check_dicoms_view:
return

with st.container(border=True):
Expand Down Expand Up @@ -329,14 +347,15 @@ def panel_view() -> None:

def panel_download() -> None:
"""
Panel for viewing extracted nifti images
Panel for downloading extracted nifti images
"""
show_panel_view = st.checkbox(
st.checkbox(
":material/download: Download Scans",
disabled=not st.session_state.flags["dir_nifti"],
value=False,
key='_check_dicoms_download',
value=st.session_state.checkbox['dicoms_download']
)
if not show_panel_view:
if not st.session_state._check_dicoms_download:
return

with st.container(border=True):
Expand Down
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