Merge pull request #1363 from proektlab/summary-images-3d

Fix removeBL for 3D movies

.gitignore

@@ -52,7 +52,7 @@ __pycache__/
 
 # C extensions
 *.so
-*.c
+caiman/source_extraction/cnmf/oasis.cpp
 
 #movie tif
 *.tif

caiman/base/movies.py

@@ -550,17 +550,17 @@ def removeBL(self, windowSize:int=100, quantilMin:int=8, in_place:bool=False, re
             self -= caiman.movie(cv2.resize(res,pixs.shape[::-1]),fr=self.fr).to3DFromPixelxTime(self.shape) 
             return self
 
-    def to2DPixelxTime(self, order='F'):
+    def to2DPixelxTime(self, order='F') -> 'movie':
         """
-        Transform 3D movie into 2D
+        Transform 3D or 4D movie into 2D (pixels x time)
         """
-        return self.transpose([2,1,0]).reshape((-1,self.shape[0]),order=order)  
+        return self.T.reshape((-1,self.shape[0]),order=order)
 
-    def to3DFromPixelxTime(self, shape, order='F'):
+    def to3DFromPixelxTime(self, shape, order='F') -> 'movie':
         """
-            Transform 2D movie into 3D
+        Transform 2D movie (pixels x time) into 3D or 4D
         """
-        return to_3D(self,shape[::-1],order=order).transpose([2,1,0])
+        return to_3D(self,shape[::-1],order=order).T
 
     def computeDFF(self, secsWindow: int = 5, quantilMin: int = 8, method: str = 'only_baseline', in_place: bool = False,
                    order: str = 'F') -> tuple[Any, Any]:

caiman/tests/test_movies.py

@@ -2,18 +2,37 @@
 import numpy as np
 import numpy.testing as npt
 import os
-from caiman.base.movies import load, load_iter
+from caiman.base import movies
 from caiman.paths import caiman_datadir
 
 
 def test_load_iter():
     fname = os.path.join(caiman_datadir(), 'example_movies', 'demoMovie.tif')
     for subindices in (None, slice(100, None, 2)):
-        m = load_iter(fname, subindices=subindices)
+        m = movies.load_iter(fname, subindices=subindices)
         S = 0
         while True:
             try:
                 S += np.sum(next(m))
             except StopIteration:
                 break
-        npt.assert_allclose(S, load(fname, subindices=subindices).sum(), rtol=1e-6)
+        npt.assert_allclose(S, movies.load(fname, subindices=subindices).sum(), rtol=1e-6)
+
+
+def test_to2D_to3D():
+    def reference_to2D(mov, order: str):
+        return mov.T.reshape((-1, mov.shape[0]), order=order)
+
+    # set up small test movies
+    rng = np.random.default_rng()
+    T, y, x, z = 10, 6, 4, 2
+    movie_3D = movies.movie(rng.random((T, y, x)))
+    movie_4D = movies.movie(rng.random((T, y, x, z)))
+
+    for movie in (movie_3D, movie_4D):
+        for order in ('F', 'C'):
+            shape = movie.shape
+            movie_flat = movie.to2DPixelxTime(order=order)
+            npt.assert_array_equal(movie_flat, reference_to2D(movie, order))
+            movie_from_flat = movie_flat.to3DFromPixelxTime(shape, order)
+            npt.assert_array_equal(movie_from_flat, movie)