diff --git a/eit_dash/app.py b/eit_dash/app.py index 7aa5acc..26d5407 100644 --- a/eit_dash/app.py +++ b/eit_dash/app.py @@ -1,9 +1,16 @@ import dash_bootstrap_components as dbc from dash import Dash +from .utils import data_singleton + +# this is a shared object to use the data through different pages +# it is initialized here, and imported by the callbacks pages when needed +data_object = data_singleton.get_singleton() FONT_AWESOME = "https://use.fontawesome.com/releases/v5.13.0/css/all.css" external_stylesheets = [dbc.themes.BOOTSTRAP, FONT_AWESOME] -app = Dash(__name__, - use_pages=True, - external_stylesheets=external_stylesheets, - suppress_callback_exceptions=True) +app = Dash( + __name__, + use_pages=True, + external_stylesheets=external_stylesheets, + suppress_callback_exceptions=True, +) diff --git a/eit_dash/callbacks/load_callbacks.py b/eit_dash/callbacks/load_callbacks.py index d2300e4..6642989 100644 --- a/eit_dash/callbacks/load_callbacks.py +++ b/eit_dash/callbacks/load_callbacks.py @@ -1,67 +1,259 @@ +import os +from pathlib import Path + import dash_bootstrap_components as dbc -from dash import Input, Output, State, callback, ctx, html +from dash import Input, Output, State, callback, ctx, html, ALL +from dash.exceptions import PreventUpdate import eit_dash.definitions.element_ids as ids +from eit_dash.app import data_object from eit_dash.definitions.option_lists import InputFiletypes +from eit_dash.utils.common import create_slider_figure, get_signal_options +from eitprocessing.eit_data import EITData +from eitprocessing.sequence import Sequence + +import plotly.graph_objects as go + +file_data: Sequence | None = None + +def create_info_card(dataset: Sequence, file_type: int, dataset_name: str) -> dbc.Card: + """ + Create the card with the information on the loaded dataset + to be displayed in the Results section + Args: + dataset: Sequence object containing the selected dataset + file_type: index of the selected type of selected + """ + info_data = { + "Name": dataset.eit_data.path.name, + "n_frames": dataset.eit_data.nframes, + "start_time": dataset.eit_data.time[0], + "end_time": dataset.eit_data.time[-1], + "vendor": dataset.eit_data.vendor, + "path": str(dataset.eit_data.path), + } + + card_list = [ + html.H4(dataset_name, className="card-title"), + html.H6(InputFiletypes(file_type).name, className="card-subtitle"), + ] + card_list += [ + dbc.Row(f"{data}: {value}", style={"margin-left": 10}) + for data, value in info_data.items() + ] + + card = dbc.Card(dbc.CardBody(card_list), id="card-1") + + return card + + +# managing the file selection. Confirm button clicked @callback( - [Output(ids.CHOOSE_DATA_POPUP, 'is_open'), Output(ids.NFILES_PLACEHOLDER, 'children')], - [Input(ids.ADD_DATA_BUTTON, 'n_clicks'), Input(ids.SELECT_FILES_BUTTON, 'n_clicks')], - prevent_initial_call=True + Output(ids.CHOOSE_DATA_POPUP, "is_open"), + Output(ids.NFILES_PLACEHOLDER, "children"), + Output(ids.ALERT_LOAD, "is_open"), + Input(ids.SELECT_FILES_BUTTON, "n_clicks"), + Input(ids.SELECT_CONFIRM_BUTTON, "n_clicks"), + State(ids.STORED_CWD, "data"), + State(ids.INPUT_TYPE_SELECTOR, "value"), + prevent_initial_call=True, ) -def open_modal(add_data_click, select_files_click): # pylint: disable=unused-argument - flag = False +# load the information selected from the file (e.g., signals, time span) +def load_selected_data( + select_file, confirm_select, file_path, file_type # pylint: disable=unused-argument +): + open_modal = True + data = None + show_alert = False + read_data_flag = False trigger = ctx.triggered_id + + # when the button for selecting the file has been clicked if trigger == ids.SELECT_FILES_BUTTON: - flag = True + # if a file has been loaded already, the data should not be cancelled, + # unless a new file is loaded. if `data` is None, the selection is cancelled + data = file_path if file_data else None - return True, flag + # if the callback has not been triggered by the select files button, + # get the information on the selected file and try to read it + if trigger == ids.SELECT_CONFIRM_BUTTON: + path = Path(file_path) + extension = path.suffix if not path.name.startswith(".") else path.name + + int_type = int(file_type) + + # check if the file extension is compatible with the file type selected + if (int_type == InputFiletypes.Draeger.value and extension == ".bin") or ( + int_type == InputFiletypes.Timpel.value + and extension == ".txt" + or (int_type == InputFiletypes.Sentec.value and extension == ".zri") + ): + read_data_flag = True + + # if the type check is ok, then close the file selector and read the data + if read_data_flag: + data = file_path + open_modal = False + + # if it's not ok, then show an alert + else: + show_alert = True + + return open_modal, data, show_alert @callback( - Output(ids.DATA_SELECTOR_OPTIONS, 'hidden'), - Input(ids.NFILES_PLACEHOLDER, 'children'), + Output(ids.DATA_SELECTOR_OPTIONS, "hidden"), + Output(ids.CHECKBOX_SIGNALS, "options"), + Output(ids.FILE_LENGTH_SLIDER, "figure"), + Input(ids.NFILES_PLACEHOLDER, "children"), + Input(ids.LOAD_CANCEL_BUTTON, "n_clicks"), + State(ids.INPUT_TYPE_SELECTOR, "value"), prevent_initial_call=True, ) -def load_file(flag): - if flag: - return False - return True +# read the file selected in the file selector +def open_data_selector(data, cancel_load, file_type): # pylint: disable=unused-argument + global file_data + + trigger = ctx.triggered_id + + # cancelled selection. Reset the data and turn of the data selector + if trigger == ids.LOAD_CANCEL_BUTTON: + data = None + file_data = None + + if not data: + # this is needed, because a figure object must be returned for the graph, evn if empty + figure = go.Figure() + return True, [], figure + + path = Path(data) + eit_data, continuous_data, sparse_data = EITData.from_path( + path, + vendor=InputFiletypes(int(file_type)).name.lower(), + return_non_eit_data=True, + ) + + file_data = Sequence( + eit_data=eit_data, continuous_data=continuous_data, sparse_data=sparse_data + ) + + options = get_signal_options(file_data) + + figure = create_slider_figure(file_data) + + return False, options, figure + @callback( - Output(ids.DATASET_CONTAINER, 'children'), - Input(ids.LOAD_CONFIRM_BUTTON, 'n_clicks'), - State(ids.DATASET_CONTAINER, 'children'), - State(ids.INPUT_TYPE_SELECTOR, 'value'), + Output(ids.DATASET_CONTAINER, "children"), + Input(ids.LOAD_CONFIRM_BUTTON, "n_clicks"), + State(ids.NFILES_PLACEHOLDER, "children"), + State(ids.DATASET_CONTAINER, "children"), + State(ids.INPUT_TYPE_SELECTOR, "value"), + State(ids.FILE_LENGTH_SLIDER, "relayoutData"), + State(ids.CHECKBOX_SIGNALS, "value"), prevent_initial_call=True, ) -def show_info(confirm_click, container_state, filetype): - #TODO read data from file - #TODO read secondary input parameters from input selection - - dummy_data = { - 'N_signals': 3, - 'duration': 12, - 'n_frames': 234, - 'filename': 'file.bin', - 'etc': 'etc', - } +def show_info( + btn_click, + loaded_data, # pylint: disable=unused-argument, disable=too-many-arguments + container_state, + filetype, + slidebar_stat, + selected_signals, +): + if file_data: + if slidebar_stat is not None and "xaxis.range" in slidebar_stat: + start_sample = slidebar_stat["xaxis.range"][0] + stop_sample = slidebar_stat["xaxis.range"][1] + else: + start_sample = file_data.eit_data.time[0] + stop_sample = file_data.eit_data.time[-1] - card_list = [ - html.H4(f'Dataset {confirm_click}', className="card-title"), - html.H6(InputFiletypes(int(filetype)).name, className="card-subtitle"), - ] - card_list += [dbc.Row(f'{data}: {value}', style={'margin-left': 10}) for data, value in dummy_data.items()] - - card = dbc.Card( - dbc.CardBody(card_list), - id=f'card-{confirm_click}' - ) - if container_state: - container_state += [card] - else: - container_state = [card] + dataset_name = f"Dataset {data_object.get_list_length()}" + + # TODO: adapt this to also continuous data + cut_data = Sequence( + label=dataset_name, + eit_data=file_data.eit_data.select_by_time(start_sample, stop_sample), + continuous_data=file_data.continuous_data, + ) + + # save the selected data in the singleton + data_object.add_sequence(cut_data) + + # create the info summary card + card = create_info_card(cut_data, int(filetype), dataset_name) + + # add the card to the current results + if container_state: + container_state += [card] + else: + container_state = [card] return container_state + + +# file browser +@callback( + Output(ids.CWD, "children"), + Input(ids.STORED_CWD, "data"), + Input(ids.PARENT_DIR, "n_clicks"), + Input(ids.CWD, "children"), + prevent_initial_call=True, +) +def get_parent_directory( + stored_cwd, n_clicks, currentdir +): # pylint: disable=unused-argument + triggered_id = ctx.triggered_id + if triggered_id == ids.STORED_CWD: + return stored_cwd + parent = Path(currentdir).parent.as_posix() + return parent + + +@callback(Output(ids.CWD_FILES, "children"), Input(ids.CWD, "children")) +def list_cwd_files(cwd): + path = Path(cwd) + + cwd_files = [] + if path.is_dir(): + files = sorted(os.listdir(path), key=str.lower) + for i, file in enumerate(files): + filepath = Path(file) + + full_path = os.path.join(cwd, filepath.as_posix()) + + is_dir = Path(full_path).is_dir() + link = html.A( + [ + html.Span( + file, + id={"type": "listed_file", "index": i}, + title=full_path, + style={"fontWeight": "bold"} if is_dir else {}, + ) + ], + href="#", + ) + prepend = "" if not is_dir else "📂" + cwd_files.append(prepend) + cwd_files.append(link) + cwd_files.append(html.Br()) + return cwd_files + + +@callback( + Output(ids.STORED_CWD, "data"), + Input({"type": "listed_file", "index": ALL}, "n_clicks"), + State({"type": "listed_file", "index": ALL}, "title"), +) +def store_clicked_file(n_clicks, title): + if not n_clicks or set(n_clicks) == {None}: + raise PreventUpdate + index = ctx.triggered_id["index"] + return title[index] diff --git a/eit_dash/definitions/element_ids.py b/eit_dash/definitions/element_ids.py index ef104a5..fca23f1 100644 --- a/eit_dash/definitions/element_ids.py +++ b/eit_dash/definitions/element_ids.py @@ -1,15 +1,22 @@ # load page ADD_DATA_BUTTON = 'add-data-button' +ALERT_LOAD = 'alert-load' +CHECKBOX_SIGNALS = 'checkbox-signals' CHOOSE_DATA_POPUP = 'choose-data-popup' +CWD = 'cwd' +CWD_FILES = 'cwd-files' INPUT_TYPE_SELECTOR = 'input-type-selector' SELECT_FILES_BUTTON = 'select-files-button' METADATA = 'metadata' -CHECKBOX = 'checkbox' FILE_LENGTH_SLIDER = 'file-length-slider' DATA_SELECTOR_OPTIONS = 'data-selector-options' NFILES_PLACEHOLDER = 'nfiles-placeholder' DATASET_CONTAINER = 'dataset-container' LOAD_CONFIRM_BUTTON = 'load-confirm-button' +LOAD_CANCEL_BUTTON = 'load-cancel-button' +PARENT_DIR = 'parent-dir' +STORED_CWD = 'stored-cwd' +SELECT_CONFIRM_BUTTON = 'select-confirm-button' # preprocessing page CONFIRM_RESAMPLING_BUTTON = 'confirm-resampling-button' diff --git a/eit_dash/definitions/layout_styles.py b/eit_dash/definitions/layout_styles.py index 1175126..65e8301 100644 --- a/eit_dash/definitions/layout_styles.py +++ b/eit_dash/definitions/layout_styles.py @@ -1,4 +1,8 @@ -CARD_FOOTER = {'textAlign': 'right'} -COLUMN_TITLE = {'textAlign': 'center'} -LOAD_RESULTS = {'textAlign': 'center'} -SUMMARY_ELEMENT = {'textAlign': 'center'} +BUTTONS_ROW = {"textAlign": "center", "margin-top": "30px"} +CARD_FOOTER = {"textAlign": "right"} +CHECKBOX_INPUT = {"margin-right": "10px"} +COLUMN_TITLE = {"textAlign": "center"} +FILE_BROWSER = {"height": 500, "overflow": "scroll"} +LOAD_RESULTS = {"textAlign": "center"} +SUMMARY_ELEMENT = {"textAlign": "center"} +SECTION_TITLE = {"margin-top": "50px"} diff --git a/eit_dash/definitions/option_lists.py b/eit_dash/definitions/option_lists.py index f1a9cf3..2c95523 100644 --- a/eit_dash/definitions/option_lists.py +++ b/eit_dash/definitions/option_lists.py @@ -10,10 +10,12 @@ class InputFiletypes(Enum): class SignalSelections(Enum): - airway_pressure = 0 - flow = 1 - esophageal_pressure = 2 - ignored = 3 + raw = 0 + airway_pressure = 1 + flow = 2 + esophageal_pressure = 3 + volume = 4 + CO2 = 5 class PeriodsSelectMethods(Enum): diff --git a/eit_dash/pages/load.py b/eit_dash/pages/load.py index 46bf24c..ace80b5 100644 --- a/eit_dash/pages/load.py +++ b/eit_dash/pages/load.py @@ -1,101 +1,163 @@ +import os + import dash_bootstrap_components as dbc from dash import dcc, html, register_page import eit_dash.definitions.element_ids as ids import eit_dash.definitions.layout_styles as styles -from eit_dash.definitions.option_lists import InputFiletypes, SignalSelections - -register_page(__name__, path='/load') - -summary = dbc.Col([ - html.H2('Summary', style=styles.COLUMN_TITLE) - ]) - - -actions = dbc.Col([ - html.H2('Load datasets', style=styles.COLUMN_TITLE), - dbc.Row(dbc.Button('Add dataset', id=ids.ADD_DATA_BUTTON)), -]) +from eit_dash.definitions.option_lists import InputFiletypes +register_page(__name__, path="/load") -results = dbc.Col([ - html.H2('Results', style=styles.COLUMN_TITLE), - html.Div(id=ids.DATASET_CONTAINER, style=styles.LOAD_RESULTS) -]) +summary = dbc.Col([html.H2("Summary", style=styles.COLUMN_TITLE)]) +results = dbc.Col( + [ + html.H2("Results", style=styles.COLUMN_TITLE), + html.Div(id=ids.DATASET_CONTAINER, style=styles.LOAD_RESULTS), + ] +) -input_type_selector = html.Div([ - dbc.Select( - id =ids.INPUT_TYPE_SELECTOR, - options = [{'label': filetype.name, "value": filetype.value} for filetype in InputFiletypes], - value = str(InputFiletypes.Sentec.value), - ), - html.P(), - dbc.Row(dbc.Button('Select files', id=ids.SELECT_FILES_BUTTON)), - dbc.Row(dbc.Label(id=ids.METADATA)), -]) +input_type_selector = html.Div( + [ + dbc.Select( + id=ids.INPUT_TYPE_SELECTOR, + options=[ + {"label": filetype.name, "value": filetype.value} + for filetype in InputFiletypes + ], + value=str(InputFiletypes.Sentec.value), + ), + html.P(), + dbc.Row(dbc.Button("Select files", id=ids.SELECT_FILES_BUTTON)), + dbc.Row(dbc.Label(id=ids.METADATA)), + ] +) max_slider_length = 100 -add_data_selector = html.Div( - id=ids.DATA_SELECTOR_OPTIONS, - hidden = True, - children = [ +add_data_selector = dcc.Loading( + html.Div( + id=ids.DATA_SELECTOR_OPTIONS, + hidden=True, + children=[ + html.P(), + html.H5("Signal selections", style=styles.SECTION_TITLE), + dbc.Row( + dcc.Checklist(id=ids.CHECKBOX_SIGNALS, inputStyle=styles.CHECKBOX_INPUT) + ), + html.H5("Pre selection", style=styles.SECTION_TITLE), + dcc.Graph(id=ids.FILE_LENGTH_SLIDER), + html.Div(), + dbc.Row( + [ + dbc.Col( + [ + dbc.Button( + "Confirm", + id=ids.LOAD_CONFIRM_BUTTON, + className="ms-auto", + color="success", + n_clicks=0, + ) + ] + ), + dbc.Col( + [ + dbc.Button( + "Cancel", + id=ids.LOAD_CANCEL_BUTTON, + className="ms-auto", + color="danger", + n_clicks=0, + ) + ] + ), + ], + style=styles.BUTTONS_ROW, + ), + ], + ) +) + +actions = dbc.Col( + [ + html.H2("Load datasets", style=styles.COLUMN_TITLE), html.P(), - html.H5('Signal selections'), - dbc.Row(dbc.Checklist(id=ids.CHECKBOX, - options = [{'label': signal.name, "value": signal.value} for signal in SignalSelections], - # value = [signal.value for signal in SignalSelections], - )), + input_type_selector, html.P(), - html.H5('Pre selection'), - dcc.RangeSlider(0,max_slider_length,1, - value = [10,50], - id = ids.FILE_LENGTH_SLIDER, - marks = {n: str(n) for n in range(0, max_slider_length, max_slider_length//10)}, - tooltip = {"placement": "bottom", "always_visible": True}, - allowCross = False, - ), - ], + add_data_selector, + ] ) +placeholder_nfiles = html.Div( + hidden=True, + id=ids.NFILES_PLACEHOLDER, + children=0, +) -modal_dialog = html.Div( +file_browser = html.Div( [ - dbc.Modal( + dbc.Row( [ - dbc.ModalHeader(dbc.ModalTitle("Close"), close_button=True), - dbc.ModalBody([input_type_selector, add_data_selector]), - dbc.ModalFooter( - dbc.Button( - "Confirm", - id=ids.LOAD_CONFIRM_BUTTON, - className="ms-auto", - n_clicks=0, - ) + dcc.Store(id=ids.STORED_CWD, data=os.getcwd()), + html.H5( + html.B(html.A("⬆️ Parent directory", href="#", id=ids.PARENT_DIR)) ), - ], - id=ids.CHOOSE_DATA_POPUP, - centered=True, - is_open=False, - backdrop=False, - scrollable=True - ), + html.H3([html.Code(os.getcwd(), id=ids.CWD)]), + html.Br(), + html.Br(), + html.Div(id=ids.CWD_FILES, style=styles.FILE_BROWSER), + ] + ) ] ) - -placeholder_nfiles = html.Div( - hidden=True, - id = ids.NFILES_PLACEHOLDER, - children=0, +alert_load = dbc.Alert( + "The selected file cannot be loaded", + id=ids.ALERT_LOAD, + color="primary", + dismissable=True, + is_open=False, + duration=3000, ) +modal_dialog = html.Div( + [ + dcc.Loading( + [ + dbc.Modal( + [ + dbc.ModalHeader( + dbc.ModalTitle("Select a file"), close_button=True + ), + dbc.ModalBody([alert_load, file_browser]), + dbc.ModalFooter( + dbc.Button( + "Confirm", + id=ids.SELECT_CONFIRM_BUTTON, + className="ms-auto", + n_clicks=0, + ) + ), + ], + id=ids.CHOOSE_DATA_POPUP, + centered=True, + is_open=False, + backdrop=False, + scrollable=True, + ) + ] + ) + ] +) -layout = dbc.Row([ - html.H1('LOAD DATA', style=styles.COLUMN_TITLE), - summary, - actions, - results, - modal_dialog, - placeholder_nfiles -]) +layout = dbc.Row( + [ + html.H1("LOAD DATA", style=styles.COLUMN_TITLE), + summary, + actions, + results, + placeholder_nfiles, + modal_dialog, + ] +) diff --git a/eit_dash/utils/__init__.py b/eit_dash/utils/__init__.py new file mode 100644 index 0000000..e69de29 diff --git a/eit_dash/utils/common.py b/eit_dash/utils/common.py new file mode 100644 index 0000000..083636d --- /dev/null +++ b/eit_dash/utils/common.py @@ -0,0 +1,120 @@ +from eit_dash.definitions.option_lists import SignalSelections +from eitprocessing.sequence import Sequence +from typing import List, Dict + +import plotly.graph_objects as go + + +def create_slider_figure( + dataset: Sequence, + eit_variants: List[str] = ["raw"], + continuous_data: List[str] = [], +) -> go.Figure: + """ + Create the figure for the selection of range. + + Args: + dataset: Sequence object containing the selected dataset + eit_variants: list of the eit variants to be plotted + continuous_data: list of the continuous data signals to be plotted + """ + traces = [] + + for eit_variant in eit_variants: + # TODO: This is a patch! Needs to be changed + if eit_variant == "raw": + try: + impedance = dataset.eit_data.variants[eit_variant].global_impedance + except KeyError: + impedance = dataset.eit_data.variants[None].global_impedance + traces.append( + { + "x": dataset.eit_data.time, + "y": impedance, + "type": "scatter", + "mode": "lines", + "name": "a_level", + } + ) + + for cont_signal in continuous_data: + traces.append( + { + "x": dataset.continuous_data[cont_signal].time, + "y": dataset.continuous_data[cont_signal].variants["raw"].values, + "type": "scatter", + "mode": "lines", + "name": "a_level", + } + ) + + figure = go.Figure( + data=traces, + layout=go.Layout( + xaxis={"rangeslider": {"visible": True}}, + margin={"t": 0, "l": 0, "b": 0, "r": 0}, + ), + ) + for event in dataset.eit_data.events: + annotation = dict(text=f"{event.text}", textangle=-90) + figure.add_vline( + x=event.time, + line_width=3, + line_dash="dash", + line_color="green", + annotation=annotation, + ) + + return figure + + +def get_signal_options( + dataset: Sequence, show_eit: bool = False +) -> List[Dict[str, int | str]]: + """ + Get the options for signal selection to be shown in the signal selection section. + + Args: + dataset: Sequence object containing the selected dataset + show_eit: include eit data in the option if True. Default false + Returns: + A list of label - value options for populating the options list + """ + options = [] + if show_eit: + # iterate over eit data + for variant in dataset.eit_data.variants: + # TODO: the None check is just a temporary fix. + # The select_by_index should be adjusted instead. + + if variant == "raw" or variant is None: + label = SignalSelections.raw.name + value = SignalSelections.raw.value + else: + label = variant + value = max(len(SignalSelections), len(options) + 1) + options.append({"label": label, "value": value}) + + if dataset.continuous_data: + for cont in dataset.continuous_data: + # if cont == "airway pressure": + # label = SignalSelections.airway_pressure.name + # value = SignalSelections.airway_pressure.value + # elif cont == "flow": + # label = SignalSelections.flow.name + # value = SignalSelections.flow.value + # elif cont == "esophageal pressure": + # label = SignalSelections.esophageal_pressure.name + # value = SignalSelections.esophageal_pressure.value + # elif cont == "volume": + # label = SignalSelections.volume.name + # value = SignalSelections.volume.value + # elif cont == "CO2": + # label = SignalSelections.CO2.name + # value = SignalSelections.CO2.value + # else: + # label = cont + # value = max(len(SignalSelections), len(options) + 1) + options.append({"label": cont, "value": len(options)}) + + return options diff --git a/eit_dash/utils/data_singleton.py b/eit_dash/utils/data_singleton.py new file mode 100644 index 0000000..0a25cce --- /dev/null +++ b/eit_dash/utils/data_singleton.py @@ -0,0 +1,39 @@ +from threading import Lock +from typing import List +from eitprocessing.sequence import Sequence + +_singleton = None +_lock = Lock() + + +def get_singleton(): + with _lock: + global _singleton + + if _singleton is None: + _singleton = LoadedData() + + return _singleton + + +class LoadedData: + def __init__(self): + self._data: List[Sequence] = [] + + def add_sequence(self, new_sequence: Sequence): + self._data.append(new_sequence) + + def clear_data(self): + self._data.clear() + + def get_all_sequences(self): + return self._data + + def get_list_length(self): + return len(self._data) + + def get_sequence_at(self, index: int): + if index > (length := self.get_list_length()): + raise ValueError(f"Index higher than list length {length}") + + return self._data[index] diff --git a/poetry.lock b/poetry.lock index 06626e3..940686d 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,1958 +1,2561 @@ -# This file is automatically @generated by Poetry 1.5.1 and should not be changed by hand. - 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