path to save

droplet_growth/register.py

@@ -25,7 +25,7 @@ META_ALIGNED = {'ImageJ': '1.53c',
  'LUTs': [grey, green, blue]
  }
 
-def align_stack(data_or_path, template16, mask2, plot=False, path=None, binnings=(1,16,2), suffix='.aligned.tif'):
+def align_stack(data_or_path, template16, mask2, plot=False, path_to_save=None, binnings=(1,16,2), suffix='.aligned.tif'):
     '''
     stack should contain two channels: bright field and fluorescence.
     BF will be binned 8 times and registered with template8 (aligned BF).
@@ -44,9 +44,11 @@ def align_stack(data_or_path, template16, mask2, plot=False, path=None, binnings
         print(path, stack.shape)
     else:
         assert data_or_path.ndim == 3 and data_or_path.shape[0] == 2
-        assert path is not None
+        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}')
+
     bf, tritc = stack[:2]
     stack_temp_scale = binnings[1] // binnings[0]
     mask_temp_scale = binnings[1] // binnings[2]
@@ -64,7 +66,7 @@ def align_stack(data_or_path, template16, mask2, plot=False, path=None, binnings
     tvec8 = get_transform(f_bf, template16, plot=plot)
     plt.show()
     tvec = scale_tvec(tvec8, mask_temp_scale)
-    print(path, tvec)
+    print(tvec)
     try:
         aligned_tritc = unpad(transform(tritc[::stack_mask_scale, ::stack_mask_scale], tvec), mask2.shape)
         aligned_bf = unpad(transform(bf[::stack_mask_scale, ::stack_mask_scale], tvec), mask2.shape)
@@ -87,12 +89,12 @@ def align_stack(data_or_path, template16, mask2, plot=False, path=None, binnings
 
     aligned_stack = np.stack((aligned_bf, aligned_tritc, mask2)).astype('uint16')
 
-    imwrite((p:="".join((*path.split('.')[:-1] , suffix))), aligned_stack, imagej=True, metadata=META_ALIGNED)
-    print(f'Saved aligned stack {p}')
-    return aligned_stack
+    imwrite(path_to_save, aligned_stack, imagej=True, metadata=META_ALIGNED)
+    print(f'Saved aligned stack {path_to_save}')
+    return aligned_stack, tvec
 
 
-def align_stack_nd(stack, template16, mask2, path=None, plot=False, binnings=(1,16,2), suffix='.aligned.tif')  -> (np.ndarray, dict):
+def align_stack_nd(stack, template16, mask2, path=None, plot=False, binnings=(1,16,2), suffix='.aligned.tif'):
     '''
     stack should contain two channels: bright field and fluorescence.
     BF will be binned 8 times and registered with template8 (aligned BF).