Merge pull request #464 from flatironinstitute/dev

Dev
flatironinstitute · Feb 20, 2019 · 3c70e6b · 3c70e6b
2 parents 4f89df7 + 77cce24
commit 3c70e6b
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Showing 4 changed files with 8 additions and 8 deletions.
diff --git a/caiman/base/movies.py b/caiman/base/movies.py
@@ -254,8 +254,8 @@ def extract_shifts(self, max_shift_w=5, max_shift_h=5, template=None, method='op
         min_val = np.percentile(self, 1)
         if min_val < - 0.1:
             logging.debug("min_val in extract_shifts: " + str(min_val))
-            warnings.warn(
-                '** Pixel averages are too negative. Removing 1 percentile. **')
+            logging.warning(
+                'Movie average is negative. Removing 1st percentile.')
             self = self - min_val
         else:
             min_val = 0
@@ -273,8 +273,7 @@ def extract_shifts(self, max_shift_w=5, max_shift_h=5, template=None, method='op
             template = np.median(self, axis=0)
         else:
             if np.percentile(template, 8) < - 0.1:
-                warnings.warn(
-                    'Pixel averages are too negative for template. Removing 1 percentile.')
+                logging.warning('Movie average is negative. Removing 1st percentile.')
                 template = template - np.percentile(template, 1)
 
         template = template[ms_h:h_i - ms_h,

diff --git a/caiman/motion_correction.py b/caiman/motion_correction.py
@@ -2551,7 +2551,7 @@ def motion_correction_piecewise(fname, splits, strides, overlaps, add_to_movie=0
     if num_splits is not None:
         idxs = np.array(idxs)[np.random.randint(0, len(idxs), num_splits)]
         save_movie = False
-        logging.warning('**** MOVIE NOT SAVED BECAUSE num_splits is not None ****')
+        #logging.warning('**** MOVIE NOT SAVED BECAUSE num_splits is not None ****')
 
     if save_movie:
         if base_name is None:
@@ -2561,6 +2561,7 @@ def motion_correction_piecewise(fname, splits, strides, overlaps, add_to_movie=0
         fname_tot = os.path.join(os.path.split(fname)[0], fname_tot)
         np.memmap(fname_tot, mode='w+', dtype=np.float32,
                   shape=prepare_shape(shape_mov), order=order)
+        logging.info('Saving file as {}'.format(fname_tot))
     else:
         fname_tot = None
 

diff --git a/demos/general/demo_pipeline.py b/demos/general/demo_pipeline.py
@@ -158,7 +158,7 @@ def main():
 # %%  parameters for source extraction and deconvolution
     p = 1                    # order of the autoregressive system
     gnb = 2                  # number of global background components
-    merge_thresh = 0.8       # merging threshold, max correlation allowed
+    merge_thr = 0.85         # merging threshold, max correlation allowed
     rf = 15
     # half-size of the patches in pixels. e.g., if rf=25, patches are 50x50
     stride_cnmf = 6          # amount of overlap between the patches in pixels
@@ -179,7 +179,7 @@ def main():
                  'stride': stride_cnmf,
                  'method_init': method_init,
                  'rolling_sum': True,
-                 'merge_thr': merge_thresh,
+                 'merge_thr': merge_thr,
                  'n_processes': n_processes,
                  'only_init': True,
                  'ssub': ssub,

diff --git a/demos/notebooks/demo_pipeline.ipynb b/demos/notebooks/demo_pipeline.ipynb
@@ -146,7 +146,7 @@
     "# parameters for source extraction and deconvolution\n",
     "p = 1                       # order of the autoregressive system\n",
     "gnb = 2                     # number of global background components\n",
-    "merge_thr = 0.8             # merging threshold, max correlation allowed\n",
+    "merge_thr = 0.85            # merging threshold, max correlation allowed\n",
     "rf = 15                     # half-size of the patches in pixels. e.g., if rf=25, patches are 50x50\n",
     "stride_cnmf = 6             # amount of overlap between the patches in pixels\n",
     "K = 4                       # number of components per patch\n",