def __init__(self, name: str, *, start: float = None, end: float = None):
from gui import PALMS
from logic.databases.DatabaseHandler import Database
track = Database.get().tracks[Database.get().main_track_label]
super().__init__((start, end))
self.setBounds([start, end])
self.track = track
self.start = start
self.end = end
self.mid = self.start + (self.end - self.start) / 2
self.name = name
self.label = pg.TextItem(name)
self.label.setFont(
QFont("", PALMS.config['epoch_labels_font_size'], QFont.Bold))
self.label.setAnchor((0.5, 1))
# self.label.setColor(QColor('k'))
try:
label_y = EpochModeConfig.get().label_to_ypos[name]
except:
label_y = self.track.get_yrange_between(self.start, self.end)[0]
self.label.setPos(self.mid, label_y)
# self.sigRegionChangeFinished.connect(self.region_moved)
EpochWindow._instance = weakref.ref(self)()
qInfo('Window at [{:0.2f}; {:0.2f}] '.format(self.start, self.end))
def from_click(cls, name: str, *, click_x: float):
"""construct SinglePartition from single point: calculate its start/end considering other partitions"""
from logic.databases.DatabaseHandler import Database
from gui import PALMS
track = Database.get().tracks[Database.get().main_track_label]
initial_span = (track.maxX - track.minX) * 0.01
initial_span = PALMS.config['initial_partition_span_sec'] # NB: set initial span of just created partition
left_bound, right_bound = Partitions.calculate_boundaries(click_x, click_x)
left_bound = left_bound if left_bound is not None else track.minX
right_bound = right_bound if right_bound is not None else track.maxX
start = max([max([click_x - initial_span / 2, track.minX]), left_bound])
end = min([min([click_x + initial_span / 2, track.maxX]), right_bound])
return cls(name, start=start, end=end)
def zoomChanged(self):
try: # this is to avoid redrawing if it is already zoomed out to max
newRange = self.main_window.selectedView.renderer.vb.targetRange(
)[0]
viewRange = self.main_window.selectedView.renderer.vb.viewRange(
)[0]
# newRange = self.main_vb.viewRange()[0]
if newRange[-1] >= Database.get().get_longest_track_duration(
) and newRange[0] <= 0: # TODO what if offset not 0
if self.FLAG_full_zoom_out:
return
else:
self.FLAG_full_zoom_out = True
else:
self.FLAG_full_zoom_out = False
except:
pass
if self.main_vb.geometry():
try:
pixel_width = self.main_vb.viewPixelSize()[0]
self.main_vb.setLimits(xMin=-pixel_width)
for vb in self.vbs.values():
vb.setLimits(xMin=-pixel_width)
self.redraw_fiducials()
if self.display_panel is not None and len(
self.display_panel.panel.views) > 0:
self.setYRange()
EpochModeConfig.get().redraw_epochs()
except Exception as e:
Dialog().warningMessage(
'Exception occured\r\n'
'Using more than one frame may have caused this!\r\n' +
str(e))
def from_csv(cls, csv):
from gui import PALMS
settings_init = pd.read_csv(csv)
db = Database.get()
fiducials = []
for _, row_data in settings_init.iterrows():
assert all([k in row_data for k in PALMS.config['annotationConfig_columns']])
# NB: recover aConf.pinned_to changes from json
# it is not needed as one can rewrite annotation config from AnnotationConfigDialog Save button
# see also AnnotationConfigDialog where applied data is saved
# try:
# tmp_singleFiducialConfig = SingleFiducialConfig(row_data)
# pinned_to_prev_state = PALMS.config['pinned_to_last_state'][tmp_singleFiducialConfig.name]
# pinned_to_prev_state = pinned_to_prev_state.split()
# if pinned_to_prev_state[0] in PALMS.config['pinned_to_options'] and \
# pinned_to_prev_state[1] in db.tracks_to_plot_initially:
# row_data['pinned_to'] = " ".join(pinned_to_prev_state)
# qInfo('Annotation Config updated with config.json data')
# except Exception as e:
# pass
fiducials.append(SingleFiducialConfig(row_data))
aConf = AnnotationConfig.get()
aConf.reset_fiducials_config(fiducials)
try: # NB: nice to do it here, but Viewer object might still not be created
from gui.viewer import Viewer
Viewer.get().annotationConfig.aConf_to_table(aConf)
Viewer.get().annotationConfig.reset_pinned_to_options_to_existing_views()
except:
pass
return aConf
def move_left():
EpochWindow.hide()
from logic.databases.DatabaseHandler import Database
from gui.viewer import Viewer
from gui.plot_area import PlotArea
track = Database.get().tracks[Database.get().main_track_label]
success = EpochModeConfig.CURRENT_WINDOW_IDX.decrease()
if success:
st, en, label = EpochModeConfig.get().get_window_data(
EpochModeConfig.CURRENT_WINDOW_IDX.get())
EpochWindow(label, start=st, end=en)
while EpochWindow.is_out_of_scope():
Viewer.get().shiftLeft()
EpochWindow.show()
PlotArea.get_main_view().renderer.plot_area.setFocus()
def select_main_view(self):
try:
all_views = [
v.track.label for v in self.main_window.selectedPanel.views
]
self.selectRow(all_views.index(Database.get().main_track_label)
) # select the main signal again
except:
pass
def __init__(self, name: str, *, start: float = None, end: float = None):
"""
constructor when start/end are given explicitly. when created from mouse click (single point) see self.from_click
"""
from gui import PALMS
from logic.databases.DatabaseHandler import Database
track = Database.get().tracks[Database.get().main_track_label]
left_bound, right_bound = Partitions.calculate_boundaries(start, end)
left_bound = left_bound if left_bound is not None else track.minX
right_bound = right_bound if right_bound is not None else track.maxX
start = max([max([start, track.minX]), left_bound])
end = min([min([end, track.maxX]), right_bound])
super().__init__((start, end))
self.setBounds([left_bound, right_bound])
self.track = track
self.start = start
self.end = end
self.mid = self.start + (self.end - self.start) / 2
self.name = name
self.label = pg.TextItem(name)
self.label.setFont(QFont("", PALMS.config['partition_labels_font_size'], QFont.Bold))
# self.label.setColor(QColor('k'))
self.label.setAnchor((0.5, 1))
self.label.setPos(self.mid, self.track.get_yrange_between(self.start, self.end)[0])
Partitions.add(self)
Partitions.update_all_bounds(self)
# # update config with new partition name
# from gui.viewer import PALMS
# PALMS.config['default_partition_labels'] = list(
# unique_everseen(PALMS.config['default_partition_labels'] + Partitions.unique_labels()))
self.sigRegionChangeFinished.connect(self.region_moved)
qInfo('Region {} [{:0.2f}; {:0.2f}] created'.format(self.name, self.start, self.end))
def toggleAllViewsExceptMain(self):
# TODO: make a method to get all views over all panels
from logic.databases.DatabaseHandler import Database
all_views = [v for v in self.main_window.selectedPanel.views]
if self.ALL_VIEWS_HIDDEN:
for v in all_views:
v.show = True
self.showView(v)
self.ALL_VIEWS_HIDDEN = False
else:
for v in all_views:
if not v.track.label is Database.get().main_track_label:
v.show = False
self.hideView(v)
self.ALL_VIEWS_HIDDEN = True
self.display_panel.view_table.update_showCheckbox_state()
def get_main_view():
from gui.viewer import Viewer
from logic.databases.DatabaseHandler import Database
main_track_label = Database.get().main_track_label
if Viewer.get() is None:
return None
for frame in Viewer.get().frames:
all_views = [v for v in frame.displayPanel.panel.views]
all_views_labels = [v.track.label for v in all_views]
main_track_idx = all_views_labels.index(
main_track_label
) if main_track_label in all_views_labels else None
if main_track_idx is not None:
break
if main_track_idx is None: # in case main view is not created yet
return None
main_view = all_views[main_track_idx]
return main_view
def split_pinned_to(self):
try:
from gui.viewer import PALMS
if self.pinned_to in PALMS.config['pinned_to_options']:
self.pinned_to = self.pinned_to + ' ' + Database.get().main_track_label
pinned_to_split = self.pinned_to.split()
# TODO: make it more generic and foolproof, now it is assumed that pinned_to consists of two words: peak\valley + track_label
assert_text = '{} pinned_to setting must consist of two words:\r\n' \
'"peak" or "valley" + track_label from the database;\r\n' \
'Current pinned_to value is {}\r\n' \
'Check your AnnotationConfig file {} and run the tool again'.format(self.name, self.pinned_to,
Database.get().annotation_config_file.stem)
assert len(pinned_to_split) == 2, assert_text
assert pinned_to_split[0] in PALMS.config['pinned_to_options'], assert_text
self.pinned_to_location = pinned_to_split[0]
self.pinned_to_track_label = pinned_to_split[1]
except Exception as e:
from utils.utils_gui import Dialog
Dialog().warningMessage('Error in split_pinned_to():\r\n' + str(e))
raise ValueError
def create_RRinterval_track(self):
db = Database.get()
to_HR = db.RR_interval_as_HR
track_fs = db.tracks[db.main_track_label].fs
track_ts = db.tracks[db.main_track_label].ts
closest_int_fs = int(min([np.ceil(1 / min(np.diff(self.x))), track_fs]))
fs = track_fs # maximum zooming is defined by the lowest sampling freq of all tracks
rr_ts = np.arange(track_ts[0], track_ts[-1], 1 / fs)
new_ts_idx = np.arange(bisect.bisect_right(rr_ts, self.x[1]), bisect.bisect_left(rr_ts, self.x[-1]))
rr = np.zeros_like(rr_ts)
from gui.tracking import Wave
if to_HR:
rr[new_ts_idx] = np.interp(rr_ts[new_ts_idx], self.x[1:], 60 / np.diff(self.x))
rr_int_wave = Wave(rr, fs, rr_ts, offset=0, label='HR(' + self.name + ')', unit='BPM')
rr_int_wave.type = 'HR'
else:
rr[new_ts_idx] = np.interp(rr_ts[new_ts_idx], self.x[1:], np.diff(self.x))
rr_int_wave = Wave(rr, fs, rr_ts, offset=0, label='RR(' + self.name + ')', unit='sec')
rr_int_wave.type = 'RR'
return rr_int_wave
def __init__(self,
*,
winLen=10,
labels: List[str] = None,
keys: List[str] = None,
default_label=None,
description: List[str] = None):
if labels is None:
labels = ['low', 'good']
if keys is None:
keys = list(np.arange(len(labels)).astype(str))
if description is None:
description = labels
if default_label is not None:
if isinstance(default_label, str):
if default_label not in labels:
default_label = labels[0]
qInfo(
'Given default_label is not in given labels. Changed to {} '
.format(default_label))
elif isinstance(default_label, int):
if default_label <= len(labels):
default_label = labels[default_label]
else:
default_label = labels[0]
qInfo(
'Given default_label is not in given labels. Changed to {} '
.format(default_label))
else:
default_label = EpochModeConfig.NONE_LABEL
from logic.databases.DatabaseHandler import Database
track = Database.get().tracks[Database.get().main_track_label]
self.window_data = pd.DataFrame(columns={'start', 'end', 'label'})
self.visuals = []
self.label_to_ypos = {}
self.labels_to_keys = {}
self.keys_to_labels = {}
self.labels_to_color = {}
self.toggle_fiducials = True
self.window_overlap = 0 # sec
self.window_length = winLen # sec
self.labels = labels
self.default_label = default_label
self.keys = keys
self.description = description
all_starts = np.arange(track.time[0], track.time[-1],
self.window_length)
all_ends = all_starts + self.window_length
if all_ends[-1] > track.time[-1]:
all_ends[-1] = track.time[-1]
self.window_data['start'] = all_starts
self.window_data['end'] = all_ends
self.window_data['is_modified'] = 0
self.window_data['label'] = self.default_label
self.test_epoch_config()
# colors to be assigned to different labels, colors do not mean anything and can be counterintuitive as Good=Red, Bad=Green
colors = cycle(['r', 'g', 'b', 'c', 'm', 'y', 'w'])
for l, k in zip(self.labels, self.keys):
self.labels_to_keys[l] = k
self.keys_to_labels[k] = l
self.labels_to_color[l] = next(colors)
st, en, label = self.get_window_data(
EpochModeConfig.CURRENT_WINDOW_IDX.get())
EpochWindow(label, start=st, end=en)
self.redraw_epochs()
EpochModeConfig._instance = weakref.ref(self)()
def viewPopup(self, point):
if isinstance(self.sender(), QtWidgets.QHeaderView):
row = self.sender().logicalIndexAt(point)
elif isinstance(self.sender(), QtWidgets.QLabel):
row = self.rowFromWidget(self.sender())
else:
logging.error(f'do not know how to handle getting index of ',
f'{self.sender()} object')
self.main_window.application.viewer.status(
f'do not know how to handle getting index of ',
f'{self.sender()} object')
raise TypeError
view = self.panel.views[row]
menu = QtWidgets.QMenu(self.verticalHeader())
menu.clear()
move_menu = menu.addMenu('&Move View')
link_menu = menu.addMenu("&Link Track")
copy_menu = menu.addMenu("Copy View")
derive_menu = menu.addMenu("Add derived tracks")
linkAction = QtWidgets.QAction('Create Link in this Panel', self)
linkAction.triggered.connect(
partial(self.display_panel.linkTrack, view,
self.main_window.model.panels.index(self.panel)))
link_menu.addAction(linkAction)
link_menu.addSeparator()
link_menu.setEnabled(False)
copyAction = QtWidgets.QAction("Duplicate View in this Panel", self)
copyAction.triggered.connect(
partial(self.display_panel.copyView, view,
self.main_window.model.panels.index(self.panel)))
copy_menu.addAction(copyAction)
copy_menu.addSeparator()
copy_menu.setEnabled(False)
addDerivativeAction = QtWidgets.QAction('1st derivative', self)
addDerivativeAction.triggered.connect(
partial(self.display_panel.addDerivative, view,
self.main_window.model.panels.index(self.panel), 1))
# TODO: derivative filters GUI
derive_menu.addAction(addDerivativeAction)
addDerivativeAction = QtWidgets.QAction('2nd derivative', self)
addDerivativeAction.triggered.connect(
partial(self.display_panel.addDerivative, view,
self.main_window.model.panels.index(self.panel), 2))
derive_menu.addAction(addDerivativeAction)
menu.addSeparator()
try:
addRRintervalMenu = menu.addMenu('RR-intevals')
from logic.operation_mode.annotation import AnnotationConfig
RRintervalMenu_actions = []
for f in AnnotationConfig.all_fiducials():
f_idx = AnnotationConfig.get().find_idx_by_name(f)
if AnnotationConfig.get(
).fiducials[f_idx].annotation.x.size > 2:
action = QtWidgets.QAction(f,
self,
checkable=False,
enabled=True)
action.triggered.connect(
partial(
self.main_window.application.add_view_from_track,
AnnotationConfig.get().fiducials[f_idx].annotation.
create_RRinterval_track(),
self.main_window.model.panels.index(self.panel)))
RRintervalMenu_actions.append(action)
addRRintervalMenu.addAction(action)
except Exception as e:
Dialog().warningMessage('Creating RR interval plot failed\r\n'
'The error was:\r\n' + str(e))
# TODO: load another track
# TODO: move existing view
db = Database.get()
add_menu = menu.addMenu("Add tracks from DB")
add_menu.setEnabled(False)
if db is not None and db.ntracks() > 0:
add_menu.setEnabled(True)
for label, track in db.tracks.items():
plot_signal_action = QtWidgets.QAction(label, self)
plot_signal_action.triggered.connect(
partial(self.main_window.application.add_view_from_track,
track,
self.main_window.model.panels.index(self.panel)))
add_menu.addAction(plot_signal_action)
if label not in self.allViewsTrackLabels():
plot_signal_action.setEnabled(True)
else:
plot_signal_action.setEnabled(False)
menu.addSeparator()
process_action = QtWidgets.QAction('Processor Config', self)
process_action.triggered.connect(
partial(self.main_window.application.viewer.processorConfig.show,
self.selectedView()))
menu.addAction(process_action)
process_action.setEnabled(False)
menu.addSeparator()
invertAction = QtWidgets.QAction('&Invert Track', self)
invertAction.triggered.connect(self.main_window.invertView)
invertAction.setEnabled(False)
menu.addAction(invertAction)
menu.addSeparator()
deleteAction = QtWidgets.QAction('&Delete Track', self)
deleteAction.triggered.connect(self.main_window.guiDelView)
menu.addAction(deleteAction)
for index, panel in enumerate(self.main_window.model.panels):
if panel is self.panel:
continue
linkAction = QtWidgets.QAction(f'Link to Panel {index + 1}', self)
linkAction.triggered.connect(
partial(self.display_panel.linkTrack, view, index))
link_menu.addAction(linkAction)
moveAction = QtWidgets.QAction(f'Move To Panel {index + 1}', self)
moveAction.triggered.connect(
partial(self.display_panel.moveView, view, index))
move_menu.addAction(moveAction)
copyAction = QtWidgets.QAction(f'Copy to Panel {index + 1}', self)
copyAction.triggered.connect(
partial(self.display_panel.copyView, view, index))
copy_menu.addAction(copyAction)
moveAction = QtWidgets.QAction(f'Move to New Panel', self)
moveAction.triggered.connect(
partial(self.display_panel.moveView, view, -1))
linkAction = QtWidgets.QAction(f'Link to New Panel', self)
linkAction.triggered.connect(
partial(self.display_panel.linkTrack, view, -1))
copyAction = QtWidgets.QAction(f'Copy to New Panel', self)
copyAction.triggered.connect(
partial(self.display_panel.copyView, view, -1))
move_menu.addSeparator()
link_menu.addSeparator()
copy_menu.addSeparator()
move_menu.addAction(moveAction)
link_menu.addAction(linkAction)
copy_menu.addAction(copyAction)
menu.popup(QtGui.QCursor.pos())
def is_main_view_in_current_panel(self):
from logic.databases.DatabaseHandler import Database
main_track_label = Database.get().main_track_label
return main_track_label in [
s.track.label for s in self.display_panel.panel.views
]
def mousePressEvent(self, event: QtGui.QMouseEvent):
"""
The following only has effect if the main track is selected in the track table view on the right
Annotation mode:
**LeftMouseButton** places a new fiducial. By default it is the first fiducial as set in the annotationConfig,
unless before that a keyboard button was pressed corresponding to another fiducial or "sticky fiducial" mode is on.
**RightMouseButton** removes the nearest fiducial (default), unless "sticky fiducial" mode is on. Keyboard has no effect
Partition mode:
**CTRL + LeftMouseButton** creates a new partition which takes 2% of the whole track duration or less to avoid overlapping
partiotions;
**CTRL + RightMouseButton** removes partition under the click
**SHIFT + LeftMouseButton** to drag partition borders or move the partition. Repositioning is possible within the limits of
neighboring partition. Moving the partition fully inside another one or reducing its size to 1 sample deletes the partition.
#NOTE: creating partition of desired size directly by click and drag might not be that convenient and harder to implement
Epoch mode:
# NB: when adding\removing mouse click operations also adapt self.mouseReleaseEvent() and self.mouseMoveEvent()
"""
def which_fiducial_to_add(last_keypress_event_key):
from gui.viewer import Viewer
# first check if 'sticky' fiducial option is enabled for one of the fiducials
sticky_fiducial = [
item.isChecked() for item in
Viewer.get().annotation_menu.sticky_fiducial_menu.actions()
]
if any(sticky_fiducial):
idx = np.argwhere(sticky_fiducial)[0]
return AnnotationConfig.get().find_idx_by_name(
Viewer.get().annotation_menu.sticky_fiducial_menu.actions(
)[idx[0]].text())
# if 'sticky' fiducial option is off, check what key was pressed the last
default_fiducial_idx = 0 # default: first fiducial
if last_keypress_event_key is not None:
qInfo('Last pressed: ' + str(last_keypress_event_key[1]))
for fiducial_idx, f in enumerate(
AnnotationConfig.get().fiducials):
if f.key.lower() == last_keypress_event_key[1].lower():
return fiducial_idx
return default_fiducial_idx
else:
return default_fiducial_idx
def which_fiducial_to_delete(click_x):
from gui.viewer import Viewer
# first check if 'sticky' fiducial option is enabled for one of the fiducials
sticky_fiducial = [
item.isChecked() for item in
Viewer.get().annotation_menu.sticky_fiducial_menu.actions()
]
if any(sticky_fiducial):
idx = np.argwhere(sticky_fiducial)[0]
return AnnotationConfig.get().find_idx_by_name(
Viewer.get().annotation_menu.sticky_fiducial_menu.actions(
)[idx[0]].text())
dist = np.inf
fiducial_name, fiducial_idx = None, None
for f_idx, f in enumerate(AnnotationConfig.get().fiducials):
if f.annotation.x.size > 0:
closest_idx, _, _ = find_closest(f.annotation.x,
np.array([click_x]))
dist_new = abs(click_x - f.annotation.x[closest_idx])
if dist_new < dist:
dist = dist_new
fiducial_name, fiducial_idx = f.name, f_idx
if not dist == np.inf:
return fiducial_idx
try:
from gui.viewer import Viewer
Viewer.get().selectFrame(self.display_panel.parent(
)) # first select the frame where the click was made
if Mode.is_epoch_mode():
EpochModeConfig.get().process_mouseclick(event)
return
vb = self.vbs[self.selected_view()]
click_x = vb.mapSceneToView(event.pos()).x()
if self.selected_view().track.label is Database.get(
).main_track_label: # TODO: do this check properly and uniformly everywhere
if Mode.is_annotation_mode():
if AnnotationConfig.get().is_valid():
if event.button(
) == QtCore.Qt.LeftButton: # Left click to mark
fiducial_idx = which_fiducial_to_add(
self.last_keypress_event_key)
AnnotationConfig.get().fiducials[
fiducial_idx].annotation.signal_annotate.emit(
click_x)
elif event.button(
) == pg.QtCore.Qt.RightButton: # right click to delete
fiducial_idx = which_fiducial_to_delete(click_x)
if fiducial_idx is not None:
AnnotationConfig.get().fiducials[
fiducial_idx].annotation.signal_delete_annotation.emit(
click_x)
else:
qInfo('No annotation found to be deleted')
self.last_keypress_event_key = None # need to press extra key every time to annotate secondary fiducial
elif Mode.is_partition_mode():
if event.button() == QtCore.Qt.LeftButton:
if event.modifiers() == QtCore.Qt.ControlModifier:
self.create_new_partition(event)
else:
super().mousePressEvent(event)
qInfo(
'CTRL+Left: create region; SHIFT+Left: move region'
) # event.accept()
elif event.button() == QtCore.Qt.RightButton:
if event.modifiers() == QtCore.Qt.ControlModifier:
p = Partitions.find_partition_by_point(click_x)
if p is not None:
p.region_deleted() # event.accept()
elif event.modifiers() == QtCore.Qt.ShiftModifier:
p = Partitions.find_partition_by_point(click_x)
if p is not None:
self.partition_context_menu(event)
else:
qInfo(
'No partition found...CTRL+Right: delete region; SHIFT+Right: region context menu'
)
else:
super().mousePressEvent(event)
qInfo(
'CTRL+Right: delete region; SHIFT+Right: region context menu'
)
else:
super().mousePressEvent(event)
elif Mode.mode == Modes.browse:
super().mousePressEvent(event)
else:
if not self.is_main_view_in_current_panel(
): # click on a panel, without the main track
Dialog().warningMessage(
'Selected display panel does not contain the main track ({}).\r\n'
.format(Database.get().main_track_label) +
'Try clicking on another display panel')
else: # click on a correct panel, but the main track is not selected
Dialog().warningMessage(
'Selected signal is not the main one.\r\n'
'Click on the '
'{}'
' track in the control area on the right.'.format(
Database.get().main_track_label))
return
except Exception as e:
Dialog().warningMessage('Mouse click processing failed\r\n'
'What unusual did you do?\r\n' + str(e))
return