Event Annotator for Biosignals

biosppy/__init__.py

@@ -5,7 +5,7 @@
 
 A toolbox for biosignal processing written in Python.
 
-:copyright: (c) 2015-2021 by Instituto de Telecomunicacoes
+:copyright: (c) 2015-2023 by Instituto de Telecomunicacoes
 :license: BSD 3-clause, see LICENSE for more details.
 """
 

biosppy/__version__.py

@@ -5,7 +5,7 @@
 
 Version tracker.
 
-:copyright: (c) 2015-2021 by Instituto de Telecomunicacoes
+:copyright: (c) 2015-2023 by Instituto de Telecomunicacoes
 :license: BSD 3-clause, see LICENSE for more details.
 """
 

biosppy/biometrics.py

@@ -10,7 +10,7 @@
 * identify: determine the identity of collected biometric dataset;
 * authenticate: verify the identity of collected biometric dataset.
 
-:copyright: (c) 2015-2018 by Instituto de Telecomunicacoes
+:copyright: (c) 2015-2023 by Instituto de Telecomunicacoes
 :license: BSD 3-clause, see LICENSE for more details.
 """
 

biosppy/clustering.py

@@ -6,7 +6,7 @@
 This module provides various unsupervised machine learning (clustering)
 algorithms.
 
-:copyright: (c) 2015-2018 by Instituto de Telecomunicacoes
+:copyright: (c) 2015-2023 by Instituto de Telecomunicacoes
 :license: BSD 3-clause, see LICENSE for more details.
 """
 

biosppy/inter_plotting/__init__.py

@@ -5,9 +5,10 @@
 
 This package provides methods to interactively display plots for the
 following physiological signals (biosignals):
+    * Acceleration (ACC)
     * Electrocardiogram (ECG)
 
-:copyright: (c) 2015-2021 by Instituto de Telecomunicacoes
+:copyright: (c) 2015-2023 by Instituto de Telecomunicacoes
 :license: BSD 3-clause, see LICENSE for more details.
 """
 

biosppy/inter_plotting/acc.py

@@ -5,7 +5,7 @@
 
 This module provides an interactive display option for the ACC plot.
 
-:copyright: (c) 2015-2018 by Instituto de Telecomunicacoes
+:copyright: (c) 2015-2023 by Instituto de Telecomunicacoes
 :license: BSD 3-clause, see LICENSE for more details.
 
 """

biosppy/inter_plotting/config.py

@@ -0,0 +1,190 @@
+# -*- coding: utf-8 -*-
+"""
+biosppy.inter_plotting.ecg
+-------------------
+
+This module provides configuration functions and variables for the Biosignal Annotator.
+
+:copyright: (c) 2015-2023 by Instituto de Telecomunicacoes
+:license: BSD 3-clause, see LICENSE for more details.
+
+"""
+
+from matplotlib.backend_bases import MouseButton
+import matplotlib.colors as mcolors
+from ..signals import eda
+from ..signals import ecg
+from ..signals import abp
+from ..signals import emg
+from ..signals import pcg
+from ..signals import ppg
+
+
+def UI_intention(event, var_edit_plots=None, var_toggle_Ctrl=None, var_zoomed_in=None, window_in_border=None,
+                 closest_event=False):
+    """Returns the user intention and action given an event.
+
+    Parameters
+    ----------
+    var_edit_plots : None
+        Enables (if set to 1) or disables (if set to 0) annotation editing.
+    var_toggle_Ctrl : None
+        Stores whether currently zoomed-in (if set to 1) or zoomed-out (if set to 0) in amplitude.
+    var_zoomed_in : None
+        Stores whether currently zoomed-in (if true) or zoomed-out (if false) in time.
+    window_in_border: None
+        Stores whether the current zoomed-in window is in the borders of the time range (x-scale).
+    closest_event : None
+        Stores whether closest event is within defined range (if true) or not (false).
+
+    Returns
+    -------
+    return_dict : dict
+        The returned dictionary with keys 'triggered_intention' and 'triggered_action'.
+
+    """
+
+    triggered_intention = None
+    triggered_action = None
+
+    if hasattr(event, 'inaxes'):
+
+        if event.inaxes is not None and not event.dblclick:  # and var_edit_plots.get() == 1
+
+            if event.button == MouseButton.RIGHT:
+                triggered_intention = "rmv_annotation"
+
+                if var_edit_plots is not None:
+
+                    if var_edit_plots.get() == 1 and closest_event:
+                        triggered_action = "rmv_annotation"
+
+                    elif var_edit_plots.get() == 1 and not closest_event:
+                        triggered_action = "rmv_annotation_not_close"
+
+                # else the action remain None
+
+            elif event.button == MouseButton.LEFT:
+                triggered_intention = "add_annotation"
+
+                if var_edit_plots is not None:
+
+                    if var_edit_plots.get() == 1:
+                        triggered_action = "add_annotation"
+
+    elif hasattr(event, 'keysym'):
+
+        # Moving to the Right (right arrow)
+        if event.keysym == 'Right':
+            triggered_intention = "move_right"
+
+            if window_in_border is not None:
+                if not window_in_border:
+                    triggered_action = "move_right"
+
+                # else, window doesn't move to the right (stays the same)
+
+        # Moving to the left (left arrow)
+        elif event.keysym == 'Left':
+            triggered_intention = "move_left"
+
+            if window_in_border is not None:
+                if not window_in_border:
+                    triggered_action = "move_left"
+                # else, window doesn't move to the left (stays the same)
+
+        # Zooming out to original xlims or to previous zoomed in lims
+        elif event.keysym == 'Shift_L':
+            triggered_intention = "adjust_in_time"
+
+            if var_zoomed_in is not None:
+                # if the window was not zoomed in, it should zoom in
+                if not var_zoomed_in:
+                    triggered_action = "zooming_in"
+
+                # else, it should zoom out
+                else:
+                    triggered_action = "zooming_out"
+
+        # if Left Control is pressed
+        elif event.keysym == 'Control_L':
+
+            triggered_intention = "adjust_in_amplitude"
+
+            if var_toggle_Ctrl is not None:
+
+                # if the window was not zoomed in, it should zoom in
+                if var_toggle_Ctrl.get() == 0:
+                    triggered_action = "zooming_in"
+
+                # else, it should zoom out
+                else:
+                    triggered_action = "zooming_out"
+
+        elif event.keysym == 'Escape':
+            triggered_intention = "quit_ui"
+
+    return_dict = {'triggered_intention': triggered_intention, 'triggered_action': triggered_action}
+    return return_dict
+
+# possible intentions and actions
+UI_intentions_actions = {
+
+    "adjust_in_amplitude": {None: "Error", "zooming_in": "Amplitude Zoom-in", "zooming_out": "Amplitude Zoom-out"},
+
+    "adjust_in_time": {None: "Error", "zooming_in": "Time zoom-in", "zooming_out": "Time zoom-out"},
+
+    "move_right": {None: "Cannot move further to the right (signal ends there).", "move_right": "Moving right"},
+    "move_left": {None: "Cannot move further to the left (signal ends there).", "move_left": "Moving left"},
+
+    "add_annotation": {None: "Click on \'Edit Annotations\' checkbox", "add_annotation": "Adding Annotation"},
+    "rmv_annotation": {None: "Click on \'Edit Annotations\' checkbox", "rmv_annotation": "Removing Annotation",
+                       "rmv_annotation_not_close": "Click closer to the annotation."},
+
+}
+
+# listed BioSPPy default filtering methods and main feature extraction methods.
+list_functions = {'EDA': {
+    'Basic SCR Extractor - Onsets': {'preprocess': eda.preprocess_eda, 'function': eda.basic_scr,
+                                     'template_key': 'onsets'},
+    'Basic SCR Extractor - Peaks': {'preprocess': eda.preprocess_eda, 'function': eda.basic_scr,
+                                    'template_key': 'onsets'},
+    'KBK SCR Extractor - Onsets': {'preprocess': eda.preprocess_eda, 'function': eda.kbk_scr,
+                                   'template_key': 'peaks'},
+    'KBK SCR Extractor - Peaks': {'preprocess': eda.preprocess_eda, 'function': eda.kbk_scr,
+                                  'template_key': 'peaks'}},
+    'ECG': {'R-peak Hamilton Segmenter': {'preprocess': ecg.preprocess_ecg,
+                                          'function': ecg.hamilton_segmenter, 'template_key': 'rpeaks'},
+            'R-peak SSF Segmenter': {'preprocess': ecg.preprocess_ecg, 'function': ecg.ssf_segmenter,
+                                     'template_key': 'rpeaks'},
+            'R-peak Christov Segmenter': {'preprocess': ecg.preprocess_ecg,
+                                          'function': ecg.christov_segmenter, 'template_key': 'rpeaks'},
+            'R-peak Engzee Segmenter': {'preprocess': ecg.preprocess_ecg,
+                                        'function': ecg.engzee_segmenter, 'template_key': 'rpeaks'},
+            'R-peak Gamboa Segmenter': {'preprocess': ecg.preprocess_ecg,
+                                        'function': ecg.gamboa_segmenter, 'template_key': 'rpeaks'},
+            'R-peak ASI Segmenter': {'preprocess': ecg.preprocess_ecg, 'function': ecg.ASI_segmenter,
+                                     'template_key': 'rpeaks'}},
+    'ABP': {'Onset Extractor': {'preprocess': abp.preprocess_abp, 'function': abp.find_onsets_zong2003,
+                                'template_key': 'onsets'}},
+    'EMG': {'Basic Onset Finder': {'preprocess': emg.preprocess_emg, 'function': emg.find_onsets,
+                                   'template_key': 'onsets'}},
+
+    # 'Hodges Onset Finder': {'preprocess': emg.preprocess_emg,'function': emg.hodges_bui_onset_detector, 'template_key': 'onsets'},
+    #     'Bonato Onset Finder': {'preprocess': emg.preprocess_emg,'function': emg.bonato_onset_detector, 'template_key': 'onsets'},
+    #     'Lidierth Onset Finder': {'preprocess': emg.preprocess_emg,'function': emg.lidierth_onset_detector, 'template_key': 'onsets'},
+    #     'Abbink Onset Finder': {'preprocess': emg.preprocess_emg,'function': emg.abbink_onset_detector, 'template_key': 'onsets'},
+    #     'Solnik Onset Finder': {'preprocess': emg.preprocess_emg,'function': emg.solnik_onset_detector, 'template_key': 'onsets'},
+    #     'Silva Onset Finder': {'preprocess': emg.preprocess_emg,'function': emg.silva_onset_detector, 'template_key': 'onsets'},
+    #     'londral_onset_detector': {'preprocess': emg.preprocess_emg,'function': emg.londral_onset_detector, 'template_key': 'onsets'}},
+
+    'PCG': {
+        'Basic Peak Finger': {'preprocess': None, 'function': pcg.find_peaks, 'template_key': 'peaks'}},
+    'PPG': {'Elgendi Onset Finder': {'preprocess': ppg.preprocess_ppg,
+                                     'function': ppg.find_onsets_elgendi2013, 'template_key': 'onsets'},
+            'Kavsaoglu Onset Finder': {'preprocess': ppg.preprocess_ppg,
+                                       'function': ppg.find_onsets_kavsaoglu2016,
+                                       'template_key': 'onsets'}}
+}
+
+plot_colors = list(mcolors.TABLEAU_COLORS.values())

biosppy/inter_plotting/ecg.py

@@ -5,7 +5,7 @@
 
 This module provides an interactive display option for the ECG plot.
 
-:copyright: (c) 2015-2018 by Instituto de Telecomunicacoes
+:copyright: (c) 2015-2023 by Instituto de Telecomunicacoes
 :license: BSD 3-clause, see LICENSE for more details.
 
 """