Merge branch 'patch-upgrade-scm' of gitlab.pasteur.fr:aaristov/nd2shrink into patch-upgrade-scm

src/droplet_growth/poisson.py

@@ -25,5 +25,5 @@ def fit(numbers:np.ndarray, max_value=None, xlabel='Initial number of cells',
                 print(f'Save histogram {save_fig_path}')
             except Exception as e:
                 print('saving histogram failed', e.args)
-        # plt.show()
+        plt.close()
     return l

src/droplet_growth/register.py

@@ -44,7 +44,6 @@ def align_stack(data_or_path, template16, mask2, plot=False, path_to_save=None,
         print(path, stack.shape)
     else:
         assert data_or_path.ndim == 3 and data_or_path.shape[0] == 2
-        assert path_to_save is not None, "Please provide the path to save the data"
         stack = data_or_path
 
     print(f'Aligned stack will be saved to {path_to_save}')
@@ -55,7 +54,7 @@ def align_stack(data_or_path, template16, mask2, plot=False, path_to_save=None,
     stack_mask_scale = binnings[2] // binnings[0]
     
     f_bf = bf[::stack_temp_scale, ::stack_temp_scale]
-
+    f_bf_sm = ndi.gaussian_filter(f_bf, 2)
     # f_bf = filter_by_fft(
     #     bf[::stack_temp_scale, ::stack_temp_scale], 
     #     sigma=40,
@@ -63,7 +62,7 @@ def align_stack(data_or_path, template16, mask2, plot=False, path_to_save=None,
     #     fix_vertical_stripes=True,
     #     highpass=True
     # )
-    tvec8 = get_transform(f_bf, template16, plot=plot)
+    tvec8 = get_transform(f_bf_sm, template16, plot=plot)
     plt.show()
     tvec = scale_tvec(tvec8, mask_temp_scale)
     print(tvec)
@@ -89,7 +88,8 @@ def align_stack(data_or_path, template16, mask2, plot=False, path_to_save=None,
 
     aligned_stack = np.stack((aligned_bf, aligned_tritc, mask2)).astype('uint16')
 
-    imwrite(path_to_save, aligned_stack, imagej=True, metadata=META_ALIGNED)
+    if path_to_save is not None:
+        imwrite(path_to_save, aligned_stack, imagej=True, metadata=META_ALIGNED)
     print(f'Saved aligned stack {path_to_save}')
     return aligned_stack, tvec