def _load_annotation_table(self, *args, filename=None):
"""Load annotations."""
# Get file name :
if filename is None:
filename = dialog_load(
self, "Import annotations", '',
"CSV file (*.csv);;Text file (*.txt);;"
"All files (*.*)")
# Clean annotations :
self._AnnotateTable.setRowCount(0)
start, end, annot = annotations_to_array(filename)
# Fill table :
self._AnnotateTable.setRowCount(len(start))
# File the table :
for k, (s, e, a) in enumerate(zip(start, end, annot)):
# Starting index :
self._AnnotateTable.setItem(k, 0,
QtWidgets.QTableWidgetItem(str(s)))
# Ending index :
self._AnnotateTable.setItem(k, 1,
QtWidgets.QTableWidgetItem(str(e)))
# Text :
self._AnnotateTable.setItem(k, 2,
QtWidgets.QTableWidgetItem(str(a)))
# Set the current tab to the annotation tab :
self.QuickSettings.setCurrentIndex(5)
# Set markers :
middle = (start.astype(np.float32) + end.astype(np.float32)) / 2
self._annot_mark = middle
self._fcn_slider_move()
def _load_annotation_table(self, *args, filename=None):
"""Load annotations."""
# Get file name :
if filename is None:
filename = dialog_load(self, "Import annotations", '',
"CSV file (*.csv);;Text file (*.txt);;"
"All files (*.*)")
# Clean annotations :
self._AnnotateTable.setRowCount(0)
start, end, annot = annotations_to_array(filename)
# Fill table :
self._AnnotateTable.setRowCount(len(start))
# File the table :
for k, (s, e, a) in enumerate(zip(start, end, annot)):
# Starting index :
self._AnnotateTable.setItem(
k, 0, QtWidgets.QTableWidgetItem(str(s)))
# Ending index :
self._AnnotateTable.setItem(
k, 1, QtWidgets.QTableWidgetItem(str(e)))
# Text :
self._AnnotateTable.setItem(
k, 2, QtWidgets.QTableWidgetItem(str(a)))
# Set the current tab to the annotation tab :
self.QuickSettings.setCurrentIndex(5)
# Set markers :
middle = (start.astype(np.float32) + end.astype(np.float32)) / 2
self._annot_mark = middle
self._fcn_slider_move()
def _load_detect_select(self, *args, filename=None):
"""Load a specific detection."""
# Get file name :
if filename is None:
filename = dialog_load(
self, "Import table", '',
"CSV file (*.csv);;Text file (*.txt);;"
"All files (*.*)")
if filename:
# Get channel / method from file name :
(chan, meth) = filename.split('_')[-1].split('.')[0].split('-')
# Load the file :
(st, end) = np.genfromtxt(filename,
delimiter=',',
encoding='utf-8')[3::, 0:2].T
# Sort by starting index :
idxsort = np.argsort(st)
st, end = st[idxsort], end[idxsort]
# Concatenate (starting, ending) index :
index = np.c_[st, end]
# Convert into index :
index = np.round(index * self._sf).astype(int)
# Set index :
self._detect[(chan, meth)]['index'] = index
# Plot update :
self._fcn_slider_move()
self._loc_line_report()
self._check_detect_menu()
def _load_detect_select(self, *args, filename=None):
"""Load a specific detection."""
# Get file name :
if filename is None:
filename = dialog_load(self, "Import table", '',
"CSV file (*.csv);;Text file (*.txt);;"
"All files (*.*)")
if filename:
# Get channel / method from file name :
(chan, meth) = filename.split('_')[-1].split('.')[0].split('-')
# Load the file :
(st, end) = np.genfromtxt(filename, delimiter=',',
encoding='utf-8')[3::, 0:2].T
# Sort by starting index :
idxsort = np.argsort(st)
st, end = st[idxsort], end[idxsort]
# Concatenate (starting, ending) index :
index = np.c_[st, end]
# Convert into index :
index = np.round(index * self._sf).astype(int)
# Set index :
self._detect[(chan, meth)]['index'] = index
# Plot update :
self._fcn_slider_move()
self._loc_line_report()
self._check_detect_menu()
def _load_detect_all(self, *args, filename=None):
"""Load all detections."""
# Dialog window for detection file :
if filename is None:
filename = dialog_load(self, "Import detections", '',
"NumPy (*.npy);;All files (*.*)")
self._detect.dict = np.ndarray.tolist(np.load(filename))
# Made canvas visbles :
for k in self._detect:
if self._detect[k]['index'].size:
# Get channel number :
idx = self._channels.index(k[0])
self._canvas_set_visible(idx, True)
self._chan.visible[idx] = True
# Plot update :
self._fcn_slider_move()
self._loc_line_report()
self._check_detect_menu()
def _load_detect_all(self, *args, filename=None):
"""Load all detections."""
# Dialog window for detection file :
if filename is None:
filename = dialog_load(self, "Import detections", '',
"NumPy (*.npy);;All files (*.*)")
self._detect.dict = np.ndarray.tolist(np.load(filename))
# Made canvas visbles :
for k in self._detect:
if self._detect[k]['index'].size:
# Get channel number :
idx = self._channels.index(k[0])
self._canvas_set_visible(idx, True)
self._chan.visible[idx] = True
# Plot update :
self._fcn_slider_move()
self._loc_line_report()
self._check_detect_menu()
def _fcn_load_annotations(self, *args, filename=None):
"""Load annotations."""
# Get file name :
if filename is None:
filename = dialog_load(self, "Import annotations", '',
"CSV file (*.csv);;Text file (*.txt);;"
"All files (*.*)")
# Clean annotations :
self._annot_table.setRowCount(0)
# Load the file :
if isinstance(filename, str): # 'file.txt'
# Get starting/ending/annotation :
time, amp, signal, text = np.genfromtxt(filename, delimiter='_',
dtype=str).T
coords = np.c_[time, amp].astype(float)
# Fill table :
self._signal.clean_annotations()
self._annot_table.setRowCount(0)
# File the table :
for k in range(len(signal)):
self._annotate_event(signal[k], coords[k, :], text=text[k])
def _load_hypno(self, *args, filename=None):
"""Load a hypnogram."""
# Define default filename for the hypnogram :
if not isinstance(self._file, str):
hyp_file = 'hypno'
else:
hyp_file = os.path.basename(self._file) + '_hypno'
# Get filename :
if filename is None:
filename = dialog_load(self, 'Load hypnogram File', hyp_file,
"Text file (*.txt);;CSV file (*.csv);;"
"Elan file (*.hyp);;Excel file (*.xlsx);;"
"All files (*.*)")
if filename:
# Load the hypnogram :
self._hypno, _ = read_hypno(filename, time=self._time)
self._hypno = oversample_hypno(self._hypno, self._N)[::self._dsf]
self._hyp.set_data(self._sf, self._hypno, self._time)
# Update info table :
self._fcn_info_update()
# Update scoring table :
self._fcn_hypno_to_score()
self._fcn_score_to_hypno()
def _fcn_load_annotations(self, *args, filename=None):
"""Load annotations."""
# Get file name :
if filename is None:
filename = dialog_load(
self, "Import annotations", '',
"CSV file (*.csv);;Text file (*.txt);;"
"All files (*.*)")
# Clean annotations :
self._annot_table.setRowCount(0)
# Load the file :
if isinstance(filename, str): # 'file.txt'
# Get starting/ending/annotation :
time, amp, signal, text = np.genfromtxt(filename,
delimiter='_',
dtype=str).T
coords = np.c_[time, amp].astype(float)
# Fill table :
self._signal.clean_annotations()
self._annot_table.setRowCount(0)
# File the table :
for k in range(len(signal)):
self._annotate_event(signal[k], coords[k, :], text=text[k])
def _load_hypno(self, *args, filename=None):
"""Load a hypnogram."""
# Define default filename for the hypnogram :
if not isinstance(self._file, str):
hyp_file = 'hypno'
else:
hyp_file = os.path.basename(self._file) + '_hypno'
# Get filename :
if filename is None:
filename = dialog_load(
self, 'Load hypnogram File', hyp_file,
"Text file (*.txt);;CSV file (*.csv);;"
"Elan file (*.hyp);;Excel file (*.xlsx);;"
"All files (*.*)")
if filename:
# Load the hypnogram :
self._hypno, _ = read_hypno(filename, time=self._time)
self._hypno = oversample_hypno(self._hypno, self._N)[::self._dsf]
self._hyp.set_data(self._sf, self._hypno, self._time)
# Update info table :
self._fcn_info_update()
# Update scoring table :
self._fcn_hypno_to_score()
self._fcn_score_to_hypno()
def _load_config(self, *args, filename=None):
"""Load a config file (.json) containing several display parameters."""
import json
if not filename:
filename = dialog_load(
self, 'Load config File', 'config',
"JSON file (*.json);;Text files (*.txt);;"
"All files (*.*)")
if filename:
with open(filename) as f:
# Load the configuration file :
config = json.load(f)
def _try(string, self=self, config=config):
"""Execute the string.
This function insure backward compatibility for loading the
configuration file.
"""
try:
exec(string)
except:
pass
# Channels
for i, k in enumerate(self._chanChecks):
self._chanChecks[i].setChecked(
config['Channel_Visible'][i])
self._ymaxSpin[i].setValue(config['Channel_Amplitude'][i])
# Amplitudes :
# _try("self._PanAllAmpMin.setValue(config['AllAmpMin'])")
# _try("self._PanAllAmpMax.setValue(config['AllAmpMax'])")
_try("self._PanAmpSym.setChecked(config['SymAmp'])")
_try("self._PanAmpAuto.setChecked(config['AutoAmp'])")
# Spectrogram
_try("self.menuDispSpec.setChecked(config['Spec_Visible'])")
_try("self._PanSpecMethod.setCurrentIndex("
"config['Spec_Method'])")
_try("self._PanSpecNfft.setValue(config['Spec_Length'])")
_try("self._PanSpecStep.setValue(config['Spec_Overlap'])")
_try("self._PanSpecCmap.setCurrentIndex(config['Spec_Cmap'])")
_try("self._PanSpecCmapInv.setChecked(config['Spec_CmapInv'])")
_try("self._PanSpecChan.setCurrentIndex(config['Spec_Chan'])")
_try("self._PanSpecFstart.setValue(config['Spec_Fstart'])")
_try("self._PanSpecFend.setValue(config['Spec_Fend'])")
_try("self._PanSpecCon.setValue(config['Spec_Con'])")
_try("self._PanSpecInterp.setCurrentIndex("
"config['Spec_Interp'])")
# Hypnogram/time axis/navigation/topo/indic/zoom :
_try("self.menuDispHypno.setChecked(config['Hyp_Visible'])")
_try("self.menuDispTimeax.setChecked(config['Time_Visible'])")
_try("self.menuDispTopo.setChecked(config['Topo_Visible'])")
_try("self.menuDispNavbar.setChecked(config['Nav_Visible'])")
_try("self.menuDispIndic.setChecked(config['Indic_Visible'])")
_try("self._PanHypnoLw.setValue(config['Hyp_Lw'])")
_try("self._PanHypnoColor.setChecked(config['Hyp_Color'])")
# Navigation bar properties :
_try("self._SlVal.setValue(config['Slider'])")
_try("self._SigSlStep.setValue(config['Step'])")
_try("self._SigWin.setValue(config['Display_Window'])")
_try("self._ScorWin.setValue(config['Scoring_Window'])")
_try("self._SlGoto.setValue(config['Goto'])")
_try("self._slMagnify.setChecked(config['Magnify'])")
_try("self._slAbsTime.setChecked(config['AbsTime'])")
_try("self._slGrid.setChecked(config['Grid'])")
_try("self._ScorWinVisible.setChecked("
"config['Display_Scoring_Window'])")
_try("self._slRules.setCurrentIndex(config['Unit'])")
# Update display
self._fcn_chan_viz()
self._fcn_chan_amplitude()
self._fcn_spec_set_data()
self._disptog_spec()
self._disptog_hyp()
self._disptog_timeax()
self._disptog_topo()
self._disptog_indic()
self._disptog_zoom()
self._fcn_grid_toggle()
self._fcn_scorwin_indicator_toggle()
self._fcn_update_amp_info()
self._fcn_chan_auto_amp()
self._fcn_chan_sym_amp()
self._fcn_set_hypno_lw()
self._fcn_set_hypno_color()
def _fcn_load_config(self, _, filename=None):
"""Load the configuration."""
if not filename:
filename = dialog_load(self, 'Load config File', 'config',
"Text file (*.txt);;All files (*.*)")
if filename:
config = load_config_json(filename)
def _try(string, self=self, config=config):
"""Execute the string.
This function insure backward compatibility for loading the
configuration file.
"""
try:
exec(string)
except:
warn("Cannot execute for loading the config : " + string)
# ----------------- VISIBLE OBJECTS -----------------
# Settings :
_try("self.menuDispQuickSettings.setChecked("
"config['SettingViz'])")
_try("self._fcn_menu_disp_set()")
# Engram :
_try("self.menuDispEngram.setChecked(config['EngramViz'])")
_try("self._fcn_menu_disp_engram()")
# Sources
_try("self.menuDispSources.setChecked(config['SourcesViz'])")
_try("self._fcn_menu_disp_sources()")
# Connect :
_try("self.menuDispConnect.setChecked(config['ConnectViz'])")
_try("self._fcn_menu_disp_connect()")
# ROI :
_try("self.menuDispROI.setChecked(config['ROIViz'])")
_try("self._fcn_menu_disp_roi()")
# Cbar :
_try("self.menuDispCbar.setChecked(config['CbarViz'])")
_try("self._fcn_menu_disp_cbar()")
# ----------------- CAMERA -----------------
_try("self.view.wc.camera.set_state(config['CamState'])")
_try("self.cbqt.cbviz._wc.camera.rect=config['CamCbState']")
# ----------------- BRAIN -----------------
# Surroundings :
_try("self._engram_translucent.setChecked(config['EngramTransp'])")
_try("self._engramPickHemi.setCurrentIndex(config["
"'EngramHemi'])")
_try("self._engramTemplate.setCurrentIndex(config["
"'EngramTemplate'])")
_try("self._engram_control()")
_try("self._light_reflection()")
# ROIs :
_try("self._roiTransp.setChecked(config['RoiTransp'])")
_try("self._roiDiv.setCurrentIndex(config['RoiAnat'])")
_try("self._roiSmooth.setValue(config['RoiSmooth'])")
_try("self._roiToAdd.clear()")
_try("self._fcn_build_roi_list()")
_try("self._fcn_set_selected_rois(config['RoiStruct'])")
_try("self._fcn_update_list()")
# Cross-sections :
_try("self._csSagit.setValue(config['CsSagit'])")
_try("self._csCoron.setValue(config['CsCoron'])")
_try("self._csAxial.setValue(config['CsAxial'])")
_try("self._csDiv.setCurrentIndex(config['CsDiv'])")
_try("self._csCmap.setCurrentIndex(config['CsCmap'])")
_try("self._csTransp.setChecked(config['CsTransp'])")
_try("self._csSplit.setChecked(config['CsSplit'])")
_try("self.grpSec.setChecked(config['CsGrp'])")
_try("self._fcn_crossec_change()")
_try("self._fcn_crossec_split()")
# Volume :
_try("self._volDiv.setCurrentIndex(config['VolDiv'])")
_try("self._volRendering.setCurrentIndex(config['VolRendering'])")
_try("self._volCmap.setCurrentIndex(config['VolCmap'])")
_try("self._volIsoTh.setValue(config['VolTh'])")
_try("self.grpVol.setChecked(config['VolGrp'])")
_try("self._fcn_vol_change()")
# ----------------- SOURCES -----------------
# Sources object :
_try("self._sourcesPickdisp.setCurrentIndex(config["
"'SourcesDisp'])")
_try("self._fcn_sources_display()")
_try("self.s_Symbol.setCurrentIndex(config['SourcesSym'])")
_try("self.s_EdgeColor.setText(str(config['SourcesEcol']))")
_try("self.s_EdgeWidth.setValue(config['SourcesEw'])")
_try("self._fcn_sources_look()")
_try("self.s_radiusMin.setValue(config['SourcesRm'])")
_try("self.s_radiusMax.setValue(config['SourcesRM'])")
_try("self.s_Scaling.setChecked(config['SourcesScale'])")
_try("self._fcn_sources_radius()")
# Source's text :
_try("self.grpText.setChecked(config['StextShow'])")
_try("self.q_stextsize.setValue(config['StextSz'])")
_try("self.q_stextcolor.setText(str(config['StextCol']))")
_try("self.x_text.setValue(config['StextXYZ'][0])")
_try("self.y_text.setValue(config['StextXYZ'][1])")
_try("self.z_text.setValue(config['StextXYZ'][2])")
# Source's projection settings :
_try("self._uitRadius.setValue(config['SprojRad'])")
_try("self._uitPickProj.setCurrentIndex(config['SprojType'])")
_try("self._uitProjectOn.setCurrentIndex(config['SprojOn'])")
_try("self._uitContribute.setChecked(config['SprojCon'])")
# Source's time-series :
_try("self._tsWidth.setValue(config['StsWidth'])")
_try("self._tsAmp.setValue(config['StsAmp'])")
_try("self._tsLw.setValue(config['StsLw'])")
_try("self._tsDx.setValue(config['StsDxyz'][0])")
_try("self._tsDy.setValue(config['StsDxyz'][1])")
_try("self._tsDz.setValue(config['StsDxyz'][2])")
_try("self._tsColor.setText(str(config['StsColor']))")
_try("self._fcn_ts_update()")
# ----------------- CONNECTIVITY -----------------
_try("self.uiConnect_colorby.setCurrentIndex(config["
"'ConnectCby'])")
_try("self._connectStaDynTransp.setCurrentIndex(config["
"'ConnectAlp'])")
_try("self.uiConnect_dynMin.setValue(config['ConnectMin'])")
_try("self.uiConnect_dynMax.setValue(config['ConnectMax'])")
_try("self._densityRadius.setValue(config['ConnectRad'])")
_try("self.uiConnect_lw.setValue(config['ConnectLw'])")
_try("self._conBlEnable.setChecked(config['ConnectBun'])")
_try("self._conBlRadius.setValue(config['ConnectBunRad'])")
_try("self._conBlDxyz.setValue(config['ConnectBunDxyz'])")
# ----------------- GUI SETTINGS -----------------
# Background color :
rgb = config['BcgColor']
_try("self.bgd_red.setValue(" + str(rgb[0]) + ")")
_try("self.bgd_green.setValue(" + str(rgb[1]) + ")")
_try("self.bgd_blue.setValue(" + str(rgb[2]) + ")")
_try("self._fcn_bgd_color()")
# Tab :
_try("self.QuickSettings.setCurrentIndex(config[" "'CurrentTab'])")
# ----------------- CBAR -----------------
# Cbar visual :
_try("self.cbqt.cbobjs.from_dict(config['Cbar'])")
_try("self.cbqt._disconnect()")
_try("self.cbqt._initialize()")
_try("self.cbqt._connect()")
_try("self.cbqt.link('Projection', self._fcn_link_proj, "
"self._fcn_minmax_proj)")
_try("self.cbqt.link('Connectivity', self._fcn_link_connect, "
"self._fcn_minmax_connect)")
def _load_config(self, *args, filename=None):
"""Load a config file (.json) containing several display parameters."""
import json
if not filename:
filename = dialog_load(self, 'Load config File', 'config',
"JSON file (*.json);;Text files (*.txt);;"
"All files (*.*)")
if filename:
with open(filename) as f:
# Load the configuration file :
config = json.load(f)
def _try(string, self=self, config=config):
"""Execute the string.
This function insure backward compatibility for loading the
configuration file.
"""
try:
exec(string)
except:
pass
# Channels
for i, k in enumerate(self._chanChecks):
self._chanChecks[i].setChecked(
config['Channel_Visible'][i])
self._ymaxSpin[i].setValue(config['Channel_Amplitude'][i])
# Amplitudes :
# _try("self._PanAllAmpMin.setValue(config['AllAmpMin'])")
# _try("self._PanAllAmpMax.setValue(config['AllAmpMax'])")
_try("self._PanAmpSym.setChecked(config['SymAmp'])")
_try("self._PanAmpAuto.setChecked(config['AutoAmp'])")
# Spectrogram
_try("self.menuDispSpec.setChecked(config['Spec_Visible'])")
_try("self._PanSpecMethod.setCurrentIndex("
"config['Spec_Method'])")
_try("self._PanSpecNfft.setValue(config['Spec_Length'])")
_try("self._PanSpecStep.setValue(config['Spec_Overlap'])")
_try("self._PanSpecCmap.setCurrentIndex(config['Spec_Cmap'])")
_try("self._PanSpecCmapInv.setChecked(config['Spec_CmapInv'])")
_try("self._PanSpecChan.setCurrentIndex(config['Spec_Chan'])")
_try("self._PanSpecFstart.setValue(config['Spec_Fstart'])")
_try("self._PanSpecFend.setValue(config['Spec_Fend'])")
_try("self._PanSpecCon.setValue(config['Spec_Con'])")
_try("self._PanSpecInterp.setCurrentIndex("
"config['Spec_Interp'])")
# Hypnogram/time axis/navigation/topo/indic/zoom :
_try("self.menuDispHypno.setChecked(config['Hyp_Visible'])")
_try("self.menuDispTimeax.setChecked(config['Time_Visible'])")
_try("self.menuDispTopo.setChecked(config['Topo_Visible'])")
_try("self.menuDispNavbar.setChecked(config['Nav_Visible'])")
_try("self.menuDispIndic.setChecked(config['Indic_Visible'])")
_try("self._PanHypnoLw.setValue(config['Hyp_Lw'])")
_try("self._PanHypnoColor.setChecked(config['Hyp_Color'])")
# Navigation bar properties :
_try("self._SlVal.setValue(config['Slider'])")
_try("self._SigSlStep.setValue(config['Step'])")
_try("self._SigWin.setValue(config['Window'])")
_try("self._SlGoto.setValue(config['Goto'])")
_try("self._slMagnify.setChecked(config['Magnify'])")
_try("self._slAbsTime.setChecked(config['AbsTime'])")
_try("self._slGrid.setChecked(config['Grid'])")
_try("self._slRules.setCurrentIndex(config['Unit'])")
# Update display
self._fcn_chan_viz()
self._fcn_chan_amplitude()
self._fcn_spec_set_data()
self._disptog_spec()
self._disptog_hyp()
self._disptog_timeax()
self._disptog_topo()
self._disptog_indic()
self._disptog_zoom()
self._fcn_grid_toggle()
self._fcn_update_amp_info()
self._fcn_chan_auto_amp()
self._fcn_chan_sym_amp()
self._fcn_set_hypno_lw()
self._fcn_set_hypno_color()