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Implemented flag review features and updated layout. Existing flags now can be visualized on table by clicking load_flags button and enable visualization checkbox. Flags on table can be visualized on the figure subplots by clicking on cells. Flagging qc/qa workflow will be implemented through new components, checklist and buttons under the table.

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florez_j
2024-11-18 07:46:28 +01:00
parent 371657b8e1
commit 0535eca9c7
1 changed files with 222 additions and 63 deletions
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285
data_flagging_app.py
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@ -32,6 +32,69 @@ import threading
import webbrowser
from time import sleep
EnableVisCheckbox = dbc.Col(dbc.Row([dbc.Col(dcc.Checklist(
id='enable-flag-checkbox',
options=[{'label': html.Span('Enable Flag Visualization', style={'font-size': 15, 'padding-left': 10}), 'value': True}],
value=[],
inline=True),width=6),
dbc.Col(dbc.Button("Load Flags", id='load-flags-button', color='primary'),width=4)],
justify="center", align="center"),
width=12)
FlagVisTable = html.Div(dash_table.DataTable(data=[],
columns=[{"name": i, "id": i} for i in ['id','startdate','enddate','flag_description','parent_ch_pos','parent_channel']],
id='tbl',
style_header={'textAlign': 'center'},
fixed_rows={'headers': True}, # Fixed table headers
style_table={'height': '1000px'}, # Make table scrollable
style_cell={'textAlign': 'left', 'padding': '10px'}, # Cell styling
),
style={
'background-color': '#f0f0f0', # Background color for the table
#'height': '1000px', # Match the table's height
'padding': '5px', # Optional padding around the table
'border': '1px solid #ccc', # Optional border around the background
} )
ReviewOpsPannel = dbc.Col([
# Row 1
dbc.Row([html.Div("Flagging Status", style={'font-size': 20})]),
# Row 2
dbc.Row([
#dbc.Col(html.Div("Review Status"), width=6),
dcc.Checklist(
id='flag-review-status-checklist',
options=[
{'label': [html.Span("Verify Flags", style={'font-size': 15, 'padding-left': 2})], 'value': 'will review'},
{'label': [html.Span("Ready to Record Flags", style={'font-size': 15, 'padding-left': 2})], 'value': 'will transfer'},
{'label': [html.Span("Finalize Flagging", style={'font-size': 15, 'padding-left': 2})], 'value': 'will apply'}
],
value=[],
#inline=True,
style={
"display": "flex", # Flexbox for left alignment
"flexDirection": "column", # Arrange the items vertically
"alignItems": "flex-start" # Align the items to the left
}
),
]),
# Row 3
dbc.Row([
#dbc.Col(dbc.Button("Load Flags", id='button-1', color='primary'),width=4),
dbc.Col(dbc.Button("Record Flags", id='button-2', color='primary'),width=4),
dbc.Col(dbc.Button("Apply Flags", id='button-3', color='primary'),width=4)],
justify="center", align="center"),
# Row 4
#dbc.Row([
# dbc.Col(html.Div("Apply Flags"), width=6),
# dbc.Col(dbc.Button("Button 2", id='button-2', color='secondary'), width=6),
#]),
],width=12)
# Initialize Dash app with Bootstrap theme
app = dash.Dash(__name__, external_stylesheets=[dbc.themes.BOOTSTRAP])
@ -91,58 +154,11 @@ app.layout = dbc.Container([
#'modeBarButtonsToRemove': ['zoom', 'pan']}),], width=12)
dbc.Col([
html.Div([
dash_table.DataTable(data=[],
columns=[{"name": i, "id": i} for i in ['id','startdate','enddate','flag_description']],
id='tbl',
style_header={'textAlign': 'center'},
fixed_rows={'headers': True}, # Fixed table headers
style_table={'height': '1000px'}, # Make table scrollable
style_cell={'textAlign': 'left', 'padding': '10px'}, # Cell styling
),
dbc.Container([
# Row 1
dbc.Row([
dbc.Col(html.Div("Visualize Flags"), width=6),
dbc.Col(dcc.RadioItems(
id='yes-no-radio',
options=[
{'label': 'Yes', 'value': 'Yes'},
{'label': 'No', 'value': 'No'}
],
value='Yes',
inline=True
), width=6),
]),
# Row 2
dbc.Row([
dbc.Col(html.Div("Review Status"), width=6),
dbc.Col(dcc.RadioItems(
id='pass-nopass-radio',
options=[
{'label': 'Pass', 'value': 'Pass'},
{'label': 'NoPass', 'value': 'NoPass'}
],
value='Pass',
inline=True
), width=6),
]),
# Row 3
dbc.Row([
dbc.Col(html.Div("Transfer Flags"), width=6),
dbc.Col(dbc.Button("Button 1", id='button-1', color='primary'), width=6),
]),
# Row 4
dbc.Row([
dbc.Col(html.Div("Apply Flags"), width=6),
dbc.Col(dbc.Button("Button 2", id='button-2', color='secondary'), width=6),
]),
], fluid=True)
],
style={'height': '1000px','overflowY': 'auto'}), # Set a fixed height for the div
EnableVisCheckbox,
FlagVisTable,
ReviewOpsPannel,
],
style={'height': '1000px','overflowY': 'auto'}), # Set a fixed height for the div
],
width=4,
@ -182,11 +198,12 @@ def load_data(filename, contents):
df = DataOps.dataset_metadata_df
# TODO: allow selection of instrument folder
instfolder = df['parent_instrument'].unique()[0]
fig = data_flagging_utils.create_loaded_file_figure(path_to_file, instfolder)
fig, channel_names = data_flagging_utils.create_loaded_file_figure(path_to_file, instfolder)
data['data_loaded_flag'] = True
data['path_to_uploaded_file'] = path_to_file
data['instfolder'] = instfolder
data['channel_names'] = channel_names
DataOps.unload_file_obj()
@ -309,6 +326,8 @@ def clear_flag_mode_title(relayoutData, fig, data):
else:
return dash.no_update, dash.no_update, dash.no_update
def extract_number(s):
return int(s[1:])-1 if s[1:].isdigit() else 0
@callback(Output('tbl', 'data'),
Input('commit-flag-button','n_clicks'),
@ -325,8 +344,10 @@ def commit_flag(n_clicks,flag_value,selected_Data, data):
return []
# TODO: modify the name path/to/name to reflect the directory provenance
instfolder = data['instfolder']
flagfolderpath = os.path.join(os.path.splitext(data['path_to_uploaded_file'])[0],f'{instfolder}_flags')
instFolder = data['instfolder']
filePath = data['path_to_uploaded_file']
flagfolderpath = os.path.join(os.path.splitext(data['path_to_uploaded_file'])[0],f'{instFolder}_flags')
if not os.path.isdir(flagfolderpath):
os.makedirs(flagfolderpath)
@ -342,13 +363,15 @@ def commit_flag(n_clicks,flag_value,selected_Data, data):
display_flag_registry = True
if not display_flag_registry:
data = []
tableData = []
else:
data = []
for pathtofile in dirlist_sorted_by_creation:
if '.json' in pathtofile:
with open(pathtofile,'r') as f:
data.append(json.load(f))
tableData = data_flagging_utils.load_flags(filePath, instFolder)
#tableData = []
#for pathtofile in dirlist_sorted_by_creation:
# if '.json' in pathtofile:
# with open(pathtofile,'r') as f:
# tableData.append(json.load(f))
number_of_existing_flags = len(dirlist_sorted_by_creation)
flagid = number_of_existing_flags+1
@ -361,12 +384,19 @@ def commit_flag(n_clicks,flag_value,selected_Data, data):
#return f'You have entered: \n{value}'
channel_names = data.get('channel_names', [])
for key, value in selected_Data['range'].items():
if 'x' in key:
new_row = {'id':flagid,'startdate':value[0],'enddate':value[1],'flag_code': flag_value}
new_row.update(data_flagging_utils.flags_dict.get(flag_value,{}))
data.append(new_row)
if channel_names:
channel_pos = extract_number(key)
parent_channel, parent_dataset = tuple(channel_names[channel_pos].split(','))
new_row.update({'parent_ch_pos': str(channel_pos), 'parent_channel':parent_channel, 'parent_dataset': parent_dataset})
tableData.append(new_row)
#data = [{'startdate':value[0],'enddate':value[1],'value':90}]
if not os.path.exists(flag_filename):
with open(flag_filename,'w') as flagsfile:
@ -378,7 +408,136 @@ def commit_flag(n_clicks,flag_value,selected_Data, data):
#json.dump({'row'+str(len(data)): new_row}, flagsfile)
#data = [json_flagsobject[key] for key in json_flagsobject.keys()]
return data
return tableData
#@callback(Output('memory-output','data',allow_duplicate=True),
# [Input('enable-flag-checkbox', 'value'), State('memory-output','data')],
# prevent_initial_call=True)
#[Input('tbl','active_cell'), Input('enable-flag-checkbox', 'value') State('timeseries-plot', 'figure'), State('tbl','data')],)
#def enable_flag_visualization(value, memory):
# if isinstance(memory,dict):
# memory.update({'vis_enabled' : value})
# return memory
# return dash.no_update
@callback(Output('timeseries-plot', 'figure',allow_duplicate=True),
[Input('enable-flag-checkbox', 'value'), State('timeseries-plot', 'figure')],
prevent_initial_call = True)
def clear_flags_from_figure(value, figure):
vis_enabled = value[0] if value and isinstance(value, list) else False
if not vis_enabled and figure:
shapes = figure.get('layout', {}).get('shapes', [])
if shapes: # If there are shapes in the figure, clear them
new_figure = figure.copy() # Create a copy to avoid mutation
new_figure['layout']['shapes'] = []
return new_figure
return dash.no_update
@callback(Output('timeseries-plot', 'figure',allow_duplicate=True),
[Input('tbl','active_cell'),
State('enable-flag-checkbox', 'value'), State('timeseries-plot', 'figure'), State('tbl','data')],
prevent_initial_call = True)
def visualize_flag_on_figure(active_cell, value, figure, data):
if value:
vis_enabled = value[0]
else:
vis_enabled = False
if active_cell and vis_enabled:
row = active_cell['row']
startdate = data[row]['startdate']
enddate = data[row]['enddate']
parent_ch_pos = data[row].get('parent_ch_pos',None)
if parent_ch_pos != None:
# Ensure that startdate and enddate are parsed correctly
#startdate = pd.to_datetime(startdate)
#enddate = pd.to_datetime(enddate)
# Determine y-axis range directly from layout
yaxis_key = f"yaxis{int(parent_ch_pos) + 1}" if int(parent_ch_pos) > 0 else "yaxis"
xaxis_key = f"xaxis{int(parent_ch_pos) + 1}" if int(parent_ch_pos) > 0 else "xaxis"
#y_min = figure['layout'].get(yaxis_key, {}).get('range', [0, 1])[0]
#y_max = figure['layout'].get(yaxis_key, {}).get('range', [0, 1])[1]
# Add a vertical region to the specified subplot
figure['layout']['shapes'] = figure['layout'].get('shapes', []) + [
dict(
type="rect",
xref=xaxis_key.replace('axis', ''),
yref=yaxis_key.replace('axis', ''),
x0=startdate,
x1=enddate,
y0=figure['layout'][yaxis_key]['range'][0],
y1=figure['layout'][yaxis_key]['range'][1],
line=dict(color="rgba(50, 171, 96, 1)", width=2),
fillcolor="rgba(50, 171, 96, 0.3)",
)
]
return figure
return dash.no_update
@callback(Output('tbl', 'data',allow_duplicate=True),
[Input('load-flags-button','n_clicks'),State('enable-flag-checkbox', 'value'),State('memory-output', 'data')],
prevent_initial_call = True)
def visualize_flags_on_table(n_clicks,value,memoryData):
instFolder = memoryData.get('instfolder', '')
filePath = memoryData.get('path_to_uploaded_file', '')
#flagfolderpath = os.path.join(os.path.splitext(memoryData['path_to_uploaded_file'])[0],f'{instfolder}_flags')
if not filePath:
return dash.no_update
#flagfolderpath = os.path.join(os.path.splitext(memoryData['path_to_uploaded_file'])[0],f'{instfolder}_flags')
## Return no table update if there is no flags folder
#if not os.path.exists(flagfolderpath):
# return dash.no_update
#files = [os.path.join(flagfolderpath, f) for f in os.listdir(flagfolderpath)]
vis_enabled = value[0] if value and isinstance(value, list) else False
if n_clicks > 0 and vis_enabled: # and len(files) > 0:
tableData = data_flagging_utils.load_flags(filePath, instFolder)
if not tableData:
return dash.no_update
else:
return tableData
# # Sort files by creation time
# dirlist_sorted_by_creation = sorted(files, key=os.path.getctime)
# tableData = []
# for pathtofile in dirlist_sorted_by_creation:
# if '.json' in pathtofile:
# try:
# with open(pathtofile,'r') as f:
# tableData.append(json.load(f))
# except (json.JSONDecodeError, FileNotFoundError) as e:
# print(e)
# continue # Skip invalid or missing files
# return tableData
return dash.no_update
def open_browser():
"""Wait for the server to start, then open the browser."""