fixing resizing bug, issue flatironinstitute#651

GrimmSnark · Oct 9, 2019 · ef5228e · ef5228e
1 parent 52b69d2
commit ef5228e
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Showing 3 changed files with 25 additions and 8 deletions.
diff --git a/caiman/base/movies.py b/caiman/base/movies.py
@@ -923,7 +923,25 @@ def extract_traces_from_masks(self, masks:np.ndarray) -> trace:
         return traces
 
     def resize(self, fx=1, fy=1, fz=1, interpolation=cv2.INTER_AREA):
-        # todo: todocument
+        """
+        Resizing caiman movie into a new one. Note that the temporal
+        dimension is controlled by fz and fx, fy, fz correspond to
+        magnification factors. For example to downsample in time by
+        a factor of 2, you need to set fz = 0.5.
+
+        Args:
+            fx (float):
+                Magnification factor along x-dimension
+
+            fy (float):
+                Magnification factor along y-dimension
+
+            fz (float):
+                Magnification factor along temporal dimension
+
+        Returns:
+            self (caiman movie)
+        """
         T, d1, d2 = self.shape
         d = d1 * d2
         elm = d * T

diff --git a/caiman/source_extraction/cnmf/initialization.py b/caiman/source_extraction/cnmf/initialization.py
@@ -79,8 +79,8 @@ def downscale(Y, ds, opencv=False):
             Y = Y[..., None]
             ds = tuple(ds) + (1,)
         else:
-            Y_ds = movie(Y).resize(fx=1. / ds[0], fy=1. / ds[1], fz=1. / ds[2],
-                                   interpolation=cv2.INTER_AREA)
+            Y_ds = movie(Y.transpose(2, 0, 1)).resize(fx=1. / ds[0], fy=1. / ds[1], fz=1. / ds[2],
+                                                      interpolation=cv2.INTER_AREA).transpose(1, 2, 0)
         logging.info('Downscaling using OpenCV')
     else:
         if d > 3:
@@ -298,15 +298,15 @@ def initialize_components(Y, K=30, gSig=[5, 5], gSiz=None, ssub=1, tsub=1, nIter
     if ssub != 1 or tsub != 1:
 
         if method == 'corr_pnr':
-            logging.info("Spatial downsampling 1-photon")
+            logging.info("Spatial/Temporal downsampling 1-photon")
             # this icrements the performance against ground truth and solves border problems
             Y_ds = downscale(Y, tuple([ssub] * len(d) + [tsub]), opencv=False)
         else:
-            logging.info("Spatial downsampling 2-photon")
+            logging.info("Spatial/Temporal downsampling 2-photon")
             # this icrements the performance against ground truth and solves border problems
             Y_ds = downscale(Y, tuple([ssub] * len(d) + [tsub]), opencv=True)
 #            mean_val = np.mean(Y)
-#            Y_ds = downscale_local_mean(Y, tuple([ssub] * len(d) + [tsub]), cval=mean_val) # this gives better results against ground truth for 2-photon datasets
+#            Y_ds = downscale_local_mean(Y, tuple([ssub] * len(d) + [tsub]), cval=mean_val)
     else:
         Y_ds = Y
 
@@ -416,7 +416,6 @@ def initialize_components(Y, K=30, gSig=[5, 5], gSiz=None, ssub=1, tsub=1, nIter
 
     if Ain.size > 0:
         Cin = resize(Cin, [K, T])
-
         center = np.asarray(
             [center_of_mass(a.reshape(d, order='F')) for a in Ain.T])
     else:

diff --git a/docs/source/Handling_Movies.rst b/docs/source/Handling_Movies.rst
@@ -121,7 +121,7 @@ the opencv library. Below an example putting it all together:
    movies_chained = cm.concatenate([movie1, movie2] , axis = 1).resize(1,1,.5).play(magnification=2, fr=50)
 
 This command will concatenate `movie1` and `movie2` along axis `x`, then it will
-downsample the resulting movie along the axis y by a factor of 2, and finally it
+downsample the resulting movie along the temporal axis by a factor of 2, and finally it
 will play the resulting movie magnified by a factor of 2.
 
 Noe that unlike `cm.concatenate`, for `movie.resize` the axis ordering is