Added multi_selector to shifted_correlation.

mdevaluate/coordinates.py

@@ -162,7 +162,8 @@ class CoordinateFrame(np.ndarray):
         if self.mode != "nojump":
             if self.mode is not None:
                 logger.warn(
-                    "Combining Nojump with other Coordinate modes is not supported and may cause unexpected results."
+                    "Combining Nojump with other Coordinate modes is not supported and "
+                    "may cause unexpected results."
                 )
             frame = nojump(self)
             frame.mode = "nojump"

mdevaluate/correlation.py

@@ -99,12 +99,13 @@ def shifted_correlation(
     function,
     frames,
     selector=None,
+    multi_selector=None,
     segments=10,
     skip=0.1,
     window=0.5,
     average=True,
     points=100,
-    nodes=8,
+    nodes=1,
 ):
     """
     Calculate the time series for a correlation function.
@@ -118,7 +119,13 @@ def shifted_correlation(
         selector (opt.):
                     A function that returns the indices depending on
                     the staring frame for which particles the
-                    correlation should be calculated
+                    correlation should be calculated.
+                    Can not be used with multi_selector.
+        multi_selector (opt.):
+                    A function that returns multiple lists of indices depending on
+                    the staring frame for which particles the
+                    correlation should be calculated.
+                    Can not be used with selector.
         segments (int, opt.):
                     The number of segments the time window will be
                     shifted
@@ -150,14 +157,9 @@ def shifted_correlation(
         >>> time, data = shifted_correlation(msd, coords)
     """
 
-    def get_correlation(start_frame, idx, selector=None):
+    def get_correlation(frames, start_frame, index, shifted_idx):
-        shifted_idx = idx + start_frame
-        if selector:
-            index = selector(frames[start_frame])
-        else:
-            index = np.arange(len(frames[start_frame]))
         if len(index) == 0:
-            return np.zeros(len(idx))
+            correlation = np.zeros(len(shifted_idx))
         else:
             start = frames[start_frame][index]
             correlation = np.array(
@@ -165,6 +167,32 @@ def shifted_correlation(
             )
         return correlation
 
+    def apply_selector(start_frame, frames, idx, selector=None, multi_selector=None):
+        shifted_idx = idx + start_frame
+        if selector is None and multi_selector is None:
+            index = np.arange(len(frames[start_frame]))
+            return get_correlation(frames, start_frame, index, shifted_idx)
+
+        elif selector is not None and multi_selector is not None:
+            raise ValueError(
+                "selector and multi_selector can not be used at the same time"
+            )
+
+        elif selector is not None:
+            index = selector(frames[start_frame])
+            return get_correlation(frames, start_frame, index, shifted_idx)
+
+        elif multi_selector is not None:
+            indices = multi_selector(frames[start_frame])
+            correlation = []
+            for index in indices:
+                correlation.append(
+                    get_correlation(
+                        frames, start_frame, index, shifted_idx
+                    )
+                )
+            return correlation
+
     if 1 - skip < window:
         window = 1 - skip
 
@@ -175,7 +203,7 @@ def shifted_correlation(
             num=segments,
             endpoint=False,
             dtype=int,
-        )
+            )
     )
 
     num_frames = int(len(frames) * window)
@@ -186,7 +214,9 @@ def shifted_correlation(
     if nodes == 1:
         result = np.array(
             [
-                get_correlation(start_frame, idx=idx, selector=selector)
+                apply_selector(start_frame, frames=frames, idx=idx,
+                               selector=selector,
+                               multi_selector=multi_selector)
                 for start_frame in start_frames
             ]
         )
@@ -198,7 +228,11 @@ def shifted_correlation(
         try:
             result = np.array(
                 pool.map(
-                    partial(get_correlation, idx=idx, selector=selector), start_frames
+                    partial(apply_selector,
+                            frames=frames,
+                            idx=idx,
+                            selector=selector,
+                            multi_selector=multi_selector), start_frames
                 )
             )
         finally: