tifffile.imsave to imwrite

track_analyzer/plotting.py

@@ -95,7 +95,7 @@ def stack_max_proj(image_fn, z_dim, t_dim=None):
             new_im[i] = np.max(im[i], axis=0)
     fn, file_ext = osp.splitext(image_fn)
     out_fn = fn + '_maxproj.tif'
-    tifff.imsave(out_fn, new_im)
+    tifff.imwrite(out_fn, new_im)
 
 
 def plot_cmap(plot_dir, label, cmap, vmin, vmax, plot_config=None, suffix=''):
@@ -1028,7 +1028,7 @@ def plot_all_traj(data_dir, df, image={'image_fn': None, 't_dim': None, 'z_dim':
 
         if save_as_stack:
             stack = np.array(stack)
-            tifff.imsave(osp.join(plot_dir,'traj.tiff'), stack)
+            tifff.imwrite(osp.join(plot_dir,'traj.tiff'), stack)
 
 
 def plot_all_scalar_fields(data_dir, df, data, field, image={'image_fn': None, 't_dim': None, 'z_dim': None},
@@ -1080,7 +1080,7 @@ def plot_all_scalar_fields(data_dir, df, data, field, image={'image_fn': None, '
 
     if save_as_stack:
         stack = np.array(stack)
-        tifff.imsave(osp.join(plot_dir, field +'.tiff'), stack)
+        tifff.imwrite(osp.join(plot_dir, field +'.tiff'), stack)
 
 
 
@@ -1136,7 +1136,7 @@ def plot_all_vector_fields(data_dir, df, data, field, plot_on_field=None, dim=3,
 
     if save_as_stack:
         stack = np.array(stack)
-        tifff.imsave(osp.join(plot_dir,'vector_' + field +'.tiff'), stack)
+        tifff.imwrite(osp.join(plot_dir,'vector_' + field +'.tiff'), stack)
 
 def plot_all_Voronoi(data_dir, df, data, show_local_area=True, df_mean = None,
                      image={'image_fn': None, 't_dim': None, 'z_dim': None},
@@ -1208,7 +1208,7 @@ def plot_all_Voronoi(data_dir, df, data, show_local_area=True, df_mean = None,
 
     if save_as_stack:
         stack = np.array(stack)
-        tifff.imsave(osp.join(plot_dir,'voronoi.tiff'), stack)
+        tifff.imwrite(osp.join(plot_dir,'voronoi.tiff'), stack)
 
 
 def plot_all_MSD(data_dir, df=None, df_out=None, fit_model="biased_diff", msd_all=None, refresh=False, hue=None,