myokit 1.35.0__py3-none-any.whl → 1.35.2__py3-none-any.whl

myokit/gui/datalog_viewer.py

@@ -14,6 +14,7 @@ from myokit.gui import QtWidgets, QtGui, QtCore, Qt
 
 import myokit
 import myokit.gui
+import myokit.gui.progress
 import myokit.formats.axon
 import myokit.formats.wcp
 
@@ -79,16 +80,18 @@ LICENSE = myokit.LICENSE_HTML
 FILTER_ABF = 'ABF files (*.abf *.pro)'
 FILTER_ATF = 'ATF files (*.atf)'
 FILTER_CSV = 'CSV files (*.csv)'
-FILTER_MAT = 'MAT files (*.mat)'
-FILTER_TXT = 'TXT files (*.txt)'
+FILTER_MAT = 'Matlab files (*.mat)'
+FILTER_DAT = 'PatchMaster files (*.dat)'
+FILTER_TXT = 'Text files (*.txt)'
 FILTER_WCP = 'WCP files (*.wcp)'
 FILTER_ZIP = 'Zipped DataLog files (*.zip)'
 FILTER_ANY = 'All files (*.*)'
-FILTER_ALL = 'Data files (*.abf *.csv *.mat *.pro *.txt *.wcp *.zip)'
+FILTER_ALL = 'Data files (*.abf *.csv *.dat *.mat *.pro *.txt *.wcp *.zip)'
 FILTER_LIST = ';;'.join([
     FILTER_ALL,
     FILTER_ABF,
     FILTER_CSV,
+    FILTER_DAT,
     FILTER_MAT,
     FILTER_TXT,
     FILTER_WCP,
@@ -141,6 +144,7 @@ class DataLogViewer(myokit.gui.MyokitApplication):
             '.abf': self.load_abf_file,
             '.atf': self.load_atf_file,
             '.csv': self.load_datalog,
+            '.dat': self.load_dat_file,
             '.pro': self.load_abf_file,
             '.txt': self.load_txt_file,
             '.wcp': self.load_wcp_file,
@@ -184,6 +188,18 @@ class DataLogViewer(myokit.gui.MyokitApplication):
         gc.collect()
         del tab
 
+    def action_first_var(self):
+        """ Select the first variable in the current file. """
+        tab = self._tabs.currentWidget()
+        if tab:
+            tab.first()
+
+    def action_last_var(self):
+        """ Select the last variable in the current file. """
+        tab = self._tabs.currentWidget()
+        if tab:
+            tab.last()
+
     def action_license(self):
         """
         Displays this program's licensing information.
@@ -295,6 +311,8 @@ class DataLogViewer(myokit.gui.MyokitApplication):
         self._tool_prev_file.triggered.connect(self.action_prev_file)
         self._tool_prev_file.setEnabled(False)
         self._menu_view.addAction(self._tool_prev_file)
+        # View > ----
+        self._menu_view.addSeparator()
         # View > Next variable
         self._tool_next_var = QtGui.QAction('Next variable', self)
         self._tool_next_var.setShortcut('PgDown')
@@ -309,6 +327,20 @@ class DataLogViewer(myokit.gui.MyokitApplication):
         self._tool_prev_var.triggered.connect(self.action_prev_var)
         self._tool_prev_var.setEnabled(False)
         self._menu_view.addAction(self._tool_prev_var)
+        # View > First variable
+        self._tool_first_var = QtGui.QAction('First variable', self)
+        self._tool_first_var.setShortcut('Home')
+        self._tool_first_var.setStatusTip('Show the first variable')
+        self._tool_first_var.triggered.connect(self.action_first_var)
+        self._tool_first_var.setEnabled(False)
+        self._menu_view.addAction(self._tool_first_var)
+        # View > Last var
+        self._tool_last_var = QtGui.QAction('Last variable', self)
+        self._tool_last_var.setShortcut('End')
+        self._tool_last_var.setStatusTip('Show the last variable')
+        self._tool_last_var.triggered.connect(self.action_last_var)
+        self._tool_last_var.setEnabled(False)
+        self._menu_view.addAction(self._tool_last_var)
         # Help menu
         self._menu_help = self._menu.addMenu('&Help')
         # Help > About
@@ -382,9 +414,7 @@ class DataLogViewer(myokit.gui.MyokitApplication):
         action(filename)
 
     def load_abf_file(self, filename):
-        """
-        Loads an abf file.
-        """
+        """ Loads an ABF file. """
         try:
             abf = myokit.formats.axon.AbfFile(filename)
         except Exception:
@@ -395,9 +425,7 @@ class DataLogViewer(myokit.gui.MyokitApplication):
         self._tabs.addTab(AbfTab(self, abf), os.path.basename(filename))
 
     def load_atf_file(self, filename):
-        """
-        Loads an ATF file.
-        """
+        """ Loads an ATF file. """
         try:
             atf = myokit.formats.axon.AtfFile(filename)
         except Exception:
@@ -407,10 +435,47 @@ class DataLogViewer(myokit.gui.MyokitApplication):
         self._path = os.path.dirname(filename)
         self._tabs.addTab(AtfTab(self, atf), os.path.basename(filename))
 
+    def load_dat_file(self, filename):
+        """ Loads a PatchMaster dat file. """
+
+        pbar = myokit.gui.progress.ProgressBar(
+            self, 'Loading groups and series')
+        pbar.show()
+        reporter = pbar.reporter()
+        reporter.enter()
+
+        flag = QtCore.QEventLoop.ProcessEventsFlag.ExcludeUserInputEvents
+        QtWidgets.QApplication.processEvents(flag)
+
+        try:
+            with myokit.formats.heka.PatchMasterFile(filename) as f:
+                n = sum([len(list(g.complete_series())) for g in f])
+                i = 0
+                stop = False
+                for group in f:
+                    for series in group.complete_series():
+                        self._tabs.addTab(
+                            PatchMasterTab(self, series),
+                            f'{group.label()} {series.label()}')
+                        i += 1
+                        if not reporter.update(i / n):
+                            stop = True
+                            break
+                        QtWidgets.QApplication.processEvents(flag)
+                    if stop:
+                        break
+                self._path = os.path.dirname(filename)
+        except Exception:
+            e = traceback.format_exc()
+            QtWidgets.QMessageBox.critical(self, TITLE, e)
+            return
+        finally:
+            reporter.exit()
+            pbar.close()
+            pbar.deleteLater()
+
     def load_datalog(self, filename):
-        """
-        Loads a DataLog from csv or zip file.
-        """
+        """ Loads a DataLog from csv or zip file. """
         try:
             if filename[-4:].lower() == '.csv':
                 log = myokit.DataLog.load_csv(filename)
@@ -443,9 +508,7 @@ class DataLogViewer(myokit.gui.MyokitApplication):
         self._tabs.addTab(MatTab(self, mat, name), name)
 
     def load_txt_file(self, filename):
-        """
-        Loads a csv file.
-        """
+        """ Loads a text file. """
         try:
             data = np.loadtxt(filename)
         except Exception:
@@ -457,9 +520,7 @@ class DataLogViewer(myokit.gui.MyokitApplication):
         self._tabs.addTab(TxtTab(self, data, name), name)
 
     def load_wcp_file(self, filename):
-        """
-        Loads a wcp file.
-        """
+        """ Loads a WinWCP file. """
         try:
             wcp = myokit.formats.wcp.WcpFile(filename)
         except Exception:
@@ -506,21 +567,30 @@ class DataLogViewer(myokit.gui.MyokitApplication):
         if index >= 0:
             tab = self._tabs.widget(index)
             if tab.count() > 1:
-                self._tool_prev_var.setEnabled(True)
+                self._tool_first_var.setEnabled(True)
+                self._tool_last_var.setEnabled(True)
                 self._tool_next_var.setEnabled(True)
+                self._tool_prev_var.setEnabled(True)
                 return
+        self._tool_first_var.setEnabled(False)
+        self._tool_last_var.setEnabled(False)
         self._tool_prev_var.setEnabled(False)
         self._tool_next_var.setEnabled(False)
 
 
 class TabWidget(QtWidgets.QTabWidget):
-    """
-    Tab widget that can move up and down when asked.
-    """
+    """ Generic tab widget with first/last next/previous methods. """
+
+    def first(self):
+        """ Select the first widget. """
+        self.setCurrentIndex(0)
+
+    def last(self):
+        """ Select the last widget. """
+        self.setCurrentIndex(self.count() - 1)
+
     def next(self):
-        """
-        Select the next widget.
-        """
+        """ Select the next widget. """
         n = self.count()
         if n < 2:
             return
@@ -528,9 +598,7 @@ class TabWidget(QtWidgets.QTabWidget):
         self.setCurrentIndex(0 if i >= n else i)
 
     def previous(self):
-        """
-        Select the previous widget.
-        """
+        """ Select the previous widget. """
         n = self.count()
         if n < 2:
             return
@@ -538,121 +606,144 @@ class TabWidget(QtWidgets.QTabWidget):
         self.setCurrentIndex(n - 1 if i < 0 else i)
 
 
-class AbfTab(TabWidget):
-    """
-    A widget displaying an ABF file.
-    """
-    def __init__(self, parent, abf):
+class GraphTabWidget(TabWidget):
+    """ Tab widget to graph a data source. """
+
+    def __init__(self, parent):
         super().__init__(parent)
+
         self.setTabsClosable(False)
         self.setTabPosition(self.TabPosition.East)
-        self._abf = abf
+
         self._figures = []
         self._axes = []
-        for i in range(self._abf.data_channels()):
-            tab, name = self.create_graph_tab(i)
-            self.addTab(tab, name)
-        for i in range(self._abf.protocol_channels()):
-            tab, name = self.create_protocol_tab(i)
-            self.addTab(tab, name)
-        self.addTab(self.create_info_tab(), 'Info')
-        del self._abf
 
-    def create_graph_tab(self, channel):
-        """
-        Creates a widget displaying the main data.
-        """
+    def deleteLater(self):
+        """ Deletes this tab (later). """
+        for figure in self._figures:
+            figure.clear()
+        for axes in self._axes:
+            axes.cla()
+        del self._figures, self._axes
+        gc.collect()
+        super().deleteLater()
+
+
+class SweepSourceTab(GraphTabWidget):
+    """ A tab widget for sources implementing the SweepSource interface. """
+
+    def __init__(self, parent, source):
+        super().__init__(parent)
+
+        # Add A/D
+        for i in range(source.channel_count()):
+            self._add_graph_tab(source, i)
+
+        # Add D/A
+        for i in range(source.da_count()):
+            self._add_graph_tab(source, i, True)
+
+        # Add meta data
+        self._add_meta_tab(source)
+
+    def _add_graph_tab(self, source, index, da=False):
+        """ Adds a tab for a graph. """
+
+        # Create widget
         widget = QtWidgets.QWidget(self)
+
         # Create figure
         figure = matplotlib.figure.Figure()
-        figure.suptitle(self._abf.filename())
         canvas = backend.FigureCanvasQTAgg(figure)
         canvas.setParent(widget)
-        axes = figure.add_subplot(1, 1, 1)
         toolbar = backend.NavigationToolbar2QT(canvas, widget)
-        # Draw lines
-        name = 'AD(' + str(channel) + ')'   # Default if no data is present
-        times = None
-        for i, sweep in enumerate(self._abf):
-            if times is None:
-                name = 'AD' + str(sweep[channel].number()) + ': ' \
-                    + sweep[channel].name()
-                times = sweep[channel].times()
-            axes.plot(times, sweep[channel].values())
+
+        # Draw signal
+        join_sweeps = not source.equal_length_sweeps()
+        if da:
+            name = source.da_names(index)
+            units = source.da_units(index)
+            times, values = source.da(index, join_sweeps)
+        else:
+            name = source.channel_names(index)
+            units = source.channel_units(index)
+            times, values = source.channel(index, join_sweeps)
+
+        axes = figure.add_subplot(1, 1, 1)
+        axes.set_xlabel(f'Time {source.time_unit()}')
+        axes.set_ylabel(f'{name} {units}')
+        if join_sweeps:
+            axes.plot(times, values)
+        else:
+            for v in values:
+                axes.plot(times[0], v)
+
+        # Store for later deletion
+        self._figures.append(figure)
+        self._axes.append(axes)
+
         # Create a layout
         vbox = QtWidgets.QVBoxLayout()
         vbox.addWidget(canvas)
         vbox.addWidget(toolbar)
         widget.setLayout(vbox)
-        self._figures.append(figure)
-        self._axes.append(axes)
-        return widget, name
 
-    def create_protocol_tab(self, channel):
-        """
-        Creates a widget displaying a stored D/A signal.
-        """
+        # Add tab
+        self.addTab(widget, name)
+
+    '''
+    def debug_tab(self, channel_index, da=True):
+        """ Add a tab graphing data using the DataLog method. """
         widget = QtWidgets.QWidget(self)
+
+        # Create widget
+        widget = QtWidgets.QWidget(self)
+
         # Create figure
         figure = matplotlib.figure.Figure()
         figure.suptitle(self._abf.filename())
         canvas = backend.FigureCanvasQTAgg(figure)
         canvas.setParent(widget)
-        axes = figure.add_subplot(1, 1, 1)
         toolbar = backend.NavigationToolbar2QT(canvas, widget)
+
         # Draw lines
-        name = 'DA(' + str(channel) + ')'   # Default if no data is present
-        times = None
-        for i, sweep in enumerate(self._abf.protocol()):
-            if times is None:
-                name = 'DA' + str(sweep[channel].number()) + ': ' \
-                    + sweep[channel].name()
-                times = sweep[channel].times()
-            axes.plot(times, sweep[channel].values())
+        p = self._abf.da_protocol(channel_index, tu='s', vu='V')
+        times, _ = self._abf.da(channel_index)
+        for t in times:
+            d = p.log_for_interval(t[0], t[-1], for_drawing=True).npview()
+            axes.plot(d['time'] - t[0], d['pace'])
+
         # Create a layout
         vbox = QtWidgets.QVBoxLayout()
         vbox.addWidget(canvas)
         vbox.addWidget(toolbar)
         widget.setLayout(vbox)
-        self._figures.append(figure)
-        self._axes.append(axes)
-        return widget, name
 
-    def create_info_tab(self):
-        """
-        Creates a tab displaying information about the file.
-        """
-        widget = QtWidgets.QTextEdit(self)
-        widget.setText(self._abf.info(show_header=True))
-        widget.setReadOnly(True)
-        return widget
+        # Add tab
+        self.addTab(widget, name)
+'''
 
-    def deleteLater(self):
-        """
-        Deletes this tab (later).
-        """
-        for figure in self._figures:
-            figure.clear()
-        for axes in self._axes:
-            axes.cla()
-        del self._figures, self._axes
-        gc.collect()
-        super().deleteLater()
+    def _add_meta_tab(self, source):
 
+        meta = source.meta_str(True)
+        if meta:
+            widget = QtWidgets.QTextEdit(self)
+            widget.setText(meta)
+            widget.setReadOnly(True)
+            self.addTab(widget, 'info')
 
-class AtfTab(TabWidget):
-    """
-    A widget displaying an AGF file.
-    """
+
+class AbfTab(SweepSourceTab):
+    """ A widget displaying an ABF file. """
+    pass
+
+
+class AtfTab(GraphTabWidget):
+    """ A widget displaying an ATF file. """
     def __init__(self, parent, atf):
         super().__init__(parent)
         self._atf = atf
 
-        self.setTabsClosable(False)
-        self.setTabPosition(self.TabPosition.East)
-
-        self._figures = []
-        self._axes = []
         keys = list(self._atf.keys())
         if len(keys) > 1:
             time = keys[0]  # Time is always first (and regularly sampled)
@@ -690,28 +781,14 @@ class AtfTab(TabWidget):
         return widget
 
     def create_info_tab(self):
-        """
-        Creates a tab displaying information about the file.
-        """
+        """ Creates a tab displaying information about the file. """
         widget = QtWidgets.QTextEdit(self)
         widget.setText(self._atf.info())
         widget.setReadOnly(True)
         return widget
 
-    def deleteLater(self):
-        """
-        Deletes this tab (later).
-        """
-        for figure in self._figures:
-            figure.clear()
-        for axes in self._axes:
-            axes.cla()
-        del self._figures, self._axes
-        gc.collect()
-        super().deleteLater()
-
 
-class CsvTab(TabWidget):
+class CsvTab(GraphTabWidget):
     """
     A widget displaying a CSV file.
 
@@ -719,12 +796,9 @@ class CsvTab(TabWidget):
     """
     def __init__(self, parent, log, filename):
         super().__init__(parent)
-        self.setTabsClosable(False)
-        self.setTabPosition(self.TabPosition.East)
+
         self._log = log.npview()
         self._filename = filename
-        self._figures = []
-        self._axes = []
 
         # Check time key was found
         time = log.time_key()
@@ -767,9 +841,7 @@ class CsvTab(TabWidget):
             self.addTab(self.create_graph_tab(k, groups.get(k)), k)
 
     def create_graph_tab(self, key, indices=None):
-        """
-        Creates a widget displaying the data stored under ``key``.
-        """
+        """ Creates a widget displaying the data stored under ``key``. """
         widget = QtWidgets.QWidget(self)
 
         # Create figure
@@ -797,30 +869,13 @@ class CsvTab(TabWidget):
         self._axes.append(axes)
         return widget
 
-    def deleteLater(self):
-        """
-        Deletes this tab (later).
-        """
-        for figure in self._figures:
-            figure.clear()
-        for axes in self._axes:
-            axes.cla()
-        del self._figures, self._axes
-        gc.collect()
-        super().deleteLater()
-
 
-class MatTab(TabWidget):
-    """
-    A widget displaying a MAT file.
-    """
+class MatTab(GraphTabWidget):
+    """ A widget displaying a .mat file. """
     def __init__(self, parent, mat, filename):
         super().__init__(parent)
-        self.setTabsClosable(False)
-        self.setTabPosition(self.TabPosition.East)
-        self._figures = []
+
         self._filename = filename
-        self._axes = []
 
         # Find usable data
         for key in mat.keys():
@@ -885,30 +940,19 @@ class MatTab(TabWidget):
         self._axes.append(axes)
         return widget
 
-    def deleteLater(self):
-        """
-        Deletes this tab (later).
-        """
-        for figure in self._figures:
-            figure.clear()
-        for axes in self._axes:
-            axes.cla()
-        del self._figures, self._axes
-        gc.collect()
-        super().deleteLater()
 
+class PatchMasterTab(SweepSourceTab):
+    """ A widget displaying a PatchMaster series. """
+    pass
+
+
+class TxtTab(GraphTabWidget):
+    """ A widget displaying a .txt file (with lots of heuristics!). """
 
-class TxtTab(TabWidget):
-    """
-    A widget displaying a TXT file (with lots of heuristics!).
-    """
     def __init__(self, parent, data, filename):
         super().__init__(parent)
-        self.setTabsClosable(False)
-        self.setTabPosition(self.TabPosition.East)
-        self._figures = []
+
         self._filename = filename
-        self._axes = []
 
         # Find usable data
         if np.prod(data.shape) == np.max(data.shape):
@@ -967,70 +1011,7 @@ class TxtTab(TabWidget):
         self._axes.append(axes)
         return widget
 
-    def deleteLater(self):
-        """
-        Deletes this tab (later).
-        """
-        for figure in self._figures:
-            figure.clear()
-        for axes in self._axes:
-            axes.cla()
-        del self._figures, self._axes
-        gc.collect()
-        super().deleteLater()
-
-
-class WcpTab(TabWidget):
-    """
-    A widget displaying a WCP file.
-    """
-    def __init__(self, parent, wcp):
-        super().__init__(parent)
-        self.setTabsClosable(False)
-        self.setTabPosition(self.TabPosition.East)
-        self._wcp = wcp
-        self._figures = []
-        self._axes = []
-        for i in range(self._wcp.records()):
-            self.addTab(self.create_graph_tab(i), 'Record ' + str(i))
-        del self._wcp
-
-    def create_graph_tab(self, record):
-        """
-        Creates a widget displaying the data in record i
-        """
-        widget = QtWidgets.QWidget(self)
-        # Create figure
-        figure = matplotlib.figure.Figure()
-        figure.suptitle(self._wcp.filename())
-        canvas = backend.FigureCanvasQTAgg(figure)
-        canvas.setParent(widget)
-        axes = figure.add_subplot(1, 1, 1)
-        toolbar = backend.NavigationToolbar2QT(canvas, widget)
-        # Draw lines
-        for i in range(self._wcp.channels()):
-            axes.plot(
-                np.array(self._wcp.times(), copy=True),
-                np.array(self._wcp.values(record, i), copy=True),
-            )
-        # Create a layout
-        vbox = QtWidgets.QVBoxLayout()
-        vbox.addWidget(canvas)
-        vbox.addWidget(toolbar)
-        widget.setLayout(vbox)
-        self._figures.append(figure)
-        self._axes.append(axes)
-        return widget
 
-    def deleteLater(self):
-        """
-        Deletes this tab (later).
-        """
-        for figure in self._figures:
-            figure.clear()
-        for axes in self._axes:
-            axes.cla()
-        del self._figures, self._axes
-        gc.collect()
-        super().deleteLater()
+class WcpTab(SweepSourceTab):
+    pass
 

myokit/tests/ansic_event_based_pacing.py

@@ -22,7 +22,7 @@ class AnsicEventBasedPacing(myokit.CModule):
     """
     _index = 0
 
-    def __init__(self, protocol):
+    def __init__(self, protocol, initial_time=0):
         super().__init__()
 
         # Unique id
@@ -42,8 +42,8 @@ class AnsicEventBasedPacing(myokit.CModule):
         self._sys = self._compile(module_name, fname, args, libs, libd, incd)
 
         # Initialize
-        self._sys.init(protocol.clone())
-        self.advance(0)
+        self._sys.init(protocol.clone(), initial_time)
+        self.advance(initial_time)
 
     def __del__(self):
         # Free the memory used by the pacing system