Fix some issues

.github/workflows/black.yml

@@ -0,0 +1,11 @@
+name: Lint
+
+on: [push, pull_request]
+
+jobs:
+  lint:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+      - uses: actions/setup-python@v2
+      - uses: psf/black@stable

.gitignore

@@ -213,4 +213,7 @@ $RECYCLE.BIN/
 # Windows shortcuts
 *.lnk
 
-# End of https://www.gitignore.io/api/macos,linux,python,windows,jupyternotebook,visualstudiocode
+# End of https://www.gitignore.io/api/macos,linux,python,windows,jupyternotebook,visualstudiocode
+
+.idea
+.vscode

jointly/__init__.py

@@ -1,4 +1,4 @@
 from .abstract_extractor import *
-from .segment_selector import *
 from .shake_extractor import *
+from .segment_selector import *
 from .synchronizer import *

jointly/abstract_extractor.py

@@ -2,7 +2,6 @@
 
 
 class AbstractExtractor(metaclass=abc.ABCMeta):
-
     def __init__(self):
         self.segments = {}
 
@@ -12,7 +11,7 @@ def get_segments(self, signals):
         return dictionary with start and end timestamps for each signal.
 
         Format of dictionary:
-        >>> { 
+        >>> {
         >>>     'column_name': {
         >>>         'first': {
         >>>             'start': timestamp,
@@ -25,21 +24,21 @@ def get_segments(self, signals):
         >>>     },
         >>>     ...
         >>> }
-        
+
         """
 
     def _init_segments(self, columns):
         self.segments = {}
         for column_name in columns:
             self.segments[column_name] = {
-                'first': {},
-                'second': {},
+                "first": {},
+                "second": {},
             }
 
     def _set_first_segment(self, column_name, start, end):
-        self.segments[column_name]['first']['start'] = start
-        self.segments[column_name]['first']['end'] = end
+        self.segments[column_name]["first"]["start"] = start
+        self.segments[column_name]["first"]["end"] = end
 
     def _set_second_segment(self, column_name, start, end):
-        self.segments[column_name]['second']['start'] = start
-        self.segments[column_name]['second']['end'] = end
+        self.segments[column_name]["second"]["start"] = start
+        self.segments[column_name]["second"]["end"] = end

jointly/helpers.py

@@ -6,6 +6,7 @@
 
 ### Signal processing
 
+
 def normalize(x):
     """Normalizes signal to interval [-1, 1] with mean 0."""
     xn = x - np.mean(x)
@@ -17,32 +18,39 @@ def get_equidistant_signals(signals, frequency):
     """Returns copy of dataframe with signals
     sampled equidistantly at the specified frequency.
     """
-    freq = '{}us'.format(int(1e6 / frequency))
-    df = pd.DataFrame(index=pd.date_range(start=pd.to_datetime(signals.index.min(), unit='s'),
-                                        end=pd.to_datetime(signals.index.max(), unit='s'),
-                                        freq=freq))
-    df = df.join(signals.copy(), how='outer')
-    df = df.interpolate(method='time', limit_area='inside').asfreq(freq)
+    freq = "{}N".format(int(1e9 / frequency))
+    df = pd.DataFrame(
+        {
+            name: signals[name].dropna().resample(freq).nearest()
+            for name in signals.columns
+        },
+        index=pd.date_range(
+            start=pd.to_datetime(signals.index.min(), unit="s"),
+            end=pd.to_datetime(signals.index.max(), unit="s"),
+            freq=freq,
+        ),
+    )
     return df
 
 
 ### Plotting
 
+
 def plot_signals(df, cols=None, title=None, tags=None):
-    cmap = matplotlib.cm.get_cmap('tab10')
+    cmap = matplotlib.cm.get_cmap("tab10")
     fig, ax = pyplot.subplots(figsize=(15, 6))
     if cols is None:
         cols = df.columns
     if title is not None:
         ax.set_title(title)
     if tags is not None:
         for tag in tags:
-            timestamp = pd.to_datetime(tag, unit='s')
+            timestamp = pd.to_datetime(tag, unit="s")
             if timestamp > df.index.min() and timestamp < df.index.max():
-                ax.axvline(timestamp, color='grey')
+                ax.axvline(timestamp, color="grey")
     for index, col in enumerate(cols):
         ax.plot(df.index, df[col], color=cmap(index), label=col)
-        ax.set_xlabel('Time')
+        ax.set_xlabel("Time")
     fig.tight_layout()
     pyplot.legend()
     pyplot.show()
@@ -58,25 +66,34 @@ def plot_segments(dataframe, segments, together=True, seperate=True):
         nrows = len(segment_names)
         fig, axes = pyplot.subplots(nrows, ncols, figsize=(15, 4 * nrows))
         for index, segment_name in enumerate(segment_names):
-            axes[index].set_title('{} segment'.format(segment_name))
-            signals_with_segment = list(filter(lambda x: segment_name in segments[x], signal_names))
-            start = np.amin([segments[x][segment_name]['start'] for x in signals_with_segment])
-            end = np.amax([segments[x][segment_name]['end'] for x in signals_with_segment])
+            axes[index].set_title("{} segment".format(segment_name))
+            signals_with_segment = list(
+                filter(lambda x: segment_name in segments[x], signal_names)
+            )
+            start = np.amin(
+                [segments[x][segment_name]["start"] for x in signals_with_segment]
+            )
+            end = np.amax(
+                [segments[x][segment_name]["end"] for x in signals_with_segment]
+            )
             dataframe[start:end].plot(ax=axes[index])
         fig.tight_layout()
 
     if seperate is True:
         # plot signals seperately
         ncols = len(segment_names)
         nrows = len(segments.keys())
-        cmap = matplotlib.cm.get_cmap('tab10')
+        cmap = matplotlib.cm.get_cmap("tab10")
         fig, axes = pyplot.subplots(nrows, ncols, figsize=(15, 4 * nrows))
         for index, signal_name in enumerate(segments.keys()):
             for index_seg, segment_name in enumerate(segment_names):
                 if segment_name not in segments[signal_name]:
                     continue
-                axes[index, index_seg].set_title('{} segment of {}'.format(segment_name, signal_name))
+                axes[index, index_seg].set_title(
+                    "{} segment of {}".format(segment_name, signal_name)
+                )
                 segment = segments[signal_name][segment_name]
-                dataframe[signal_name][segment['start']:segment['end']] \
-                    .plot(ax=axes[index, index_seg], color=cmap(index))
+                dataframe[signal_name][segment["start"] : segment["end"]].plot(
+                    ax=axes[index, index_seg], color=cmap(index)
+                )
         fig.tight_layout()

jointly/log.py

@@ -2,5 +2,5 @@
 
 FORMAT = "[%(lineno)3s - %(funcName)20s() ] %(message)s"
 logging.basicConfig(format=FORMAT)
-logger = logging.getLogger('jointly')
+logger = logging.getLogger("jointly")
 logger.setLevel(logging.CRITICAL)

jointly/segment_selector.py

@@ -10,9 +10,10 @@ def __init__(self, signals, segments=None):
         if segments is None:
             self.segments = {
                 signal: {
-                    'first': {},
-                    'second': {},
-                } for signal in signals.columns
+                    "first": {},
+                    "second": {},
+                }
+                for signal in signals.columns
             }
         self._display_plots()
 
@@ -23,13 +24,13 @@ def _display_plots(self):
 
         for index, name in enumerate(self.signals.columns):
             axes[index].set_title(name)
-            axes[index].plot(self.signals[name].interpolate(method='time').values)
+            axes[index].plot(self.signals[name].interpolate(method="time").values)
         fig.tight_layout()
 
-        bp_id = fig.canvas.mpl_connect('button_press_event', self._on_click)
+        bp_id = fig.canvas.mpl_connect("button_press_event", self._on_click)
 
     def _display_segments(self):
-        print('Do')
+        print("Do")
 
     def _on_click(self, event):
         # if not event.dblclick:
@@ -40,8 +41,8 @@ def _on_click(self, event):
         title = event.inaxes.title.get_text()
         index = int(event.xdata)
 
-        for segment in ['first', 'second']:
-            for time in ['start', 'end']:
+        for segment in ["first", "second"]:
+            for time in ["start", "end"]:
                 if time not in self.segments[title][segment]:
                     self.segments[title][segment][time] = self.signals.index[index]
                     break