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 _save_as_csv(self, *, filename: str, save_idx: bool):
from logic.operation_mode.annotation import AnnotationConfig
aConf = AnnotationConfig.get()
fullpath = pathlib.Path(self.output_folder, 'annotation_' + filename).as_posix()
aConf.to_csv(fullpath, save_idx=save_idx)
fullpath = pathlib.Path(self.output_folder, 'partition_' + filename).as_posix()
Partitions.to_csv(fullpath)
fullpath = pathlib.Path(self.output_folder, 'epoch_' + filename).as_posix()
EpochModeConfig.to_csv(fullpath)
qInfo('{} saved'.format(fullpath))
def keyPressEvent(self, event):
"""
#TODO: what else can be parametrized with keypresses?
"""
if Mode.is_epoch_mode():
# print((event.key(), event.text()))
from logic.operation_mode.epoch_mode import EpochModeConfig
EpochModeConfig.get().process_keypress(event.text())
else:
# save last pressed button to later decide which fiducial is to be marked
self.last_keypress_event_key = (event.key(), event.text())
qInfo('Key pressed: {}'.format(event.text()))
event.accept()
def load(self, fullpath):
try:
hf = self._get_matfile_object(fullpath)
assert all(s in hf.keys() for s in ['annotations', 'partitions']), r'h5 must have {} groups'.format(
['annotations', 'partitions'])
assert all([s in hf['partitions'] for s in ['label', 'start', 'end']]), r'h5.partitions must have {} groups'.format(
['label', 'start', 'end'])
labels = hf['partitions/label']
labels = [n.decode('ascii', 'ignore') for n in labels]
start = np.array(hf['partitions/start'])
end = np.array(hf['partitions/end'])
assert len(labels) == start.size & start.size == end.size, 'Every partition should have label, start and end'
Partitions.add_all(labels, start, end)
from logic.operation_mode.annotation import AnnotationConfig
assert all([s in AnnotationConfig.all_fiducials() for s in hf['annotations']]), 'All h5.annotations must be in {} groups'.format(
AnnotationConfig.all_fiducials())
for f_name in hf['annotations'].keys():
self._set_annotation_from_time(f_name, np.array(hf['annotations/' + f_name + '/ts']))
from gui.viewer import Viewer
try: # when loaded during initialization
Viewer.get().selectedDisplayPanel.plot_area.redraw_fiducials() # to update and show loaded data
except:
pass
try: # can be removed after thorough testing
if 'epoch' in hf.keys():
assert all(
[f in hf['epoch'] for f in
['start', 'end', 'is_modified', 'label', 'all_labels', 'keys',
'default_label']]), 'Loaded file contains incorrect epoch mode data'
labels = [n.decode('ascii', 'ignore') for n in hf['epoch/label']]
epoch_data = pd.DataFrame(
{'start': hf['epoch/start'], 'end': hf['epoch/end'], 'is_modified': hf['epoch/is_modified'], 'label': labels})
keys = [n.decode('ascii', 'ignore') for n in hf['epoch/keys']]
all_labels = [n.decode('ascii', 'ignore') for n in hf['epoch/all_labels']]
description = [n.decode('ascii', 'ignore') for n in hf['epoch/description']]
default_label = hf['epoch/default_label'][0]
NONE_LABEL = hf['epoch/NONE_LABEL'][0]
EpochModeConfig.load_from_hdf5(epoch_data, keys, all_labels, default_label, NONE_LABEL, description=description)
except Exception as e:
Dialog().warningMessage('Epoch mode data cannot be loaded\r\n' +
'The error was:\r\n' + str(e))
except Exception as e:
Dialog().warningMessage('Loading existing annotations failed\r\n' +
'The error was:\r\n' + str(e))
def redraw_fiducials(self):
if self.selected_view() is None:
return
main_view = PlotArea.get_main_view()
if main_view is None:
return
main_track = main_view.renderer.track
vb = main_view.renderer.vb
for item in vb.temporary_items:
vb.removeItem(item)
vb.temporary_items.clear()
x_min, x_max = self.main_vb.viewRange()[0]
if Mode.mode in [
Modes.annotation, Modes.browse, Modes.partition, Modes.epoch
]: # NB: change to disable drawing annotations in other modes
if Mode.mode == Modes.epoch and EpochModeConfig.get(
).toggle_fiducials == False:
return # if EpochMode and Fiducials are switched off
if hasattr(main_track, 'aConf'):
aConf = AnnotationConfig.get()
for a in aConf:
points_x, points_y = a.annotation.find_annotation_between_two_ts(
x_min, x_max)
if points_x.size > 0 and points_y.size > 0:
loadedFiducials = pg.PlotDataItem(
points_x,
points_y,
symbol=a.symbol,
symbolSize=a.symbol_size,
pen=None,
symbolPen=a.symbol_pen,
name=a.name)
vb.addItem(loadedFiducials)
vb.temporary_items.append(loadedFiducials)
def save(self, **kwargs):
# TODO: popup warning when rewriting existing files
try:
from gui.viewer import Viewer
filename = kwargs.get('filename', self.fullpath.stem)
try:
filename = self.outputfile_prefix + filename
except Exception as e:
qInfo('Output file prefix could not be added')
fullpath = pathlib.Path(self.output_folder, filename + '.h5')
OVERWRITE = kwargs.get('OVERWRITE', Viewer.get().settings_menu.save_overwrite_action.isChecked())
if fullpath.is_file(): # don't overwrite files
if not OVERWRITE:
path, filename = os.path.split(fullpath)
filename = os.path.splitext(filename)[0]
newfilename = filename + '_' + strftime("%Y_%m_%d_%H_%M_%S", gmtime()) + fullpath.suffix
fullpath = pathlib.Path(path, newfilename)
qInfo('Existing file found. Not overwriting')
else:
qInfo('Existing file OVERWRITTEN!')
from logic.operation_mode.annotation import AnnotationConfig
aConf = AnnotationConfig.get()
hf = h5py.File(fullpath, 'w')
group_annotations = hf.create_group('annotations')
for f_idx, f in enumerate(aConf.fiducials):
group_annotations.create_group(f.name)
group_annotations.create_dataset(f.name + '/ts', data=f.annotation.x)
group_annotations.create_dataset(f.name + '/idx', data=f.annotation.idx)
group_annotations.create_dataset(f.name + '/amp', data=f.annotation.y)
group_partitions = hf.create_group('partitions')
asciiList = [n.encode("ascii", "ignore") for n in Partitions.all_labels()]
group_partitions.create_dataset('label', data=asciiList)
group_partitions.create_dataset('start', data=Partitions.all_startpoints())
group_partitions.create_dataset('end', data=Partitions.all_endpoints())
group_epoch = hf.create_group('epoch')
group_epoch.create_dataset('start', data=EpochModeConfig.get().window_data['start'].values)
group_epoch.create_dataset('end', data=EpochModeConfig.get().window_data['end'].values)
group_epoch.create_dataset('is_modified', data=EpochModeConfig.get().window_data['is_modified'].values)
asciiList = [n.encode("ascii", "ignore") for n in EpochModeConfig.get().window_data['label'].values]
group_epoch.create_dataset('label', data=asciiList)
asciiList = [n.encode("ascii", "ignore") for n in EpochModeConfig.get().keys]
group_epoch.create_dataset('keys', data=asciiList)
asciiList = [n.encode("ascii", "ignore") for n in EpochModeConfig.get().labels]
group_epoch.create_dataset('all_labels', data=asciiList)
asciiList = [n.encode("ascii", "ignore") for n in EpochModeConfig.get().description]
group_epoch.create_dataset('description', data=asciiList)
dt = h5py.special_dtype(vlen=str)
group_epoch.create_dataset('default_label', (1,), dtype=dt)
group_epoch['default_label'][:] = EpochModeConfig.get().default_label
group_epoch.create_dataset('NONE_LABEL', (1,), dtype=dt)
group_epoch['NONE_LABEL'][:] = EpochModeConfig.get().NONE_LABEL
group_meta = hf.create_group('meta')
dt = h5py.special_dtype(vlen=str)
group_meta.create_dataset('timestamp', (1,), dtype=dt)
group_meta['timestamp'][:] = strftime("%Y_%m_%d_%H_%M_%S", gmtime())
group_meta.create_dataset('filename', (1,), dtype=dt)
group_meta['filename'][:] = self.fullpath.stem
group_meta.create_dataset('filepath', (1,), dtype=dt)
group_meta['filepath'][:] = self.fullpath.parent.as_posix()
group_meta.create_dataset('main_track_label', (1,), dtype=dt)
group_meta['main_track_label'][:] = self.main_track_label
if Viewer.get().settings_menu.save_tracks_action.isChecked():
group_tracks = hf.create_group('tracks')
for label, track in Database.get().tracks.items():
group_tracks.create_dataset(label + '/ts', data=track.ts)
group_tracks.create_dataset(label + '/amp', data=track.value)
group_tracks.create_dataset(label + '/offset', data=track.offset)
group_tracks.create_dataset(label + '/fs', data=track.fs)
hf.close()
qInfo('{} saved'.format(fullpath.as_posix()))
except Exception as e:
try:
hf.close()
except:
pass
self._save_as_csv(filename=self.fullpath.stem, save_idx=False)
Dialog().warningMessage('Default save crashed\r\n' +
e.__repr__() +
'\r\nSaved using deprecated method, as CSV files.')
def set_epochMode_config(self):
from logic.operation_mode.epoch_mode import EpochModeConfig
if not self.epoch_config_file is None:
EpochModeConfig.initialize_epoch_mode_settings_from_csv(csv=self.epoch_config_file.as_posix())
else:
EpochModeConfig()
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