Merge pull request #181 from mehta-lab/error-mismatched-bkg-and-img

Always load background and warn if background and image sizes are mismatched

recOrder/io/utils.py

@@ -59,9 +59,9 @@ def load_bg(bg_path, height, width, ROI=None):
  Parameters
  ----------
  bg_path : (str) path to the folder containing background images
- height : (int) height of image in pixels
- width : (int) width of image in pixels
- ROI : (tuple) ROI of the background images to use, if None, full FOV will be used
+ height : (int) height of image in pixels # Remove for 1.0.0
+ width : (int) width of image in pixels # Remove for 1.0.0
+ ROI : (tuple) ROI of the background images to use, if None, full FOV will be used # Remove for 1.0.0
 
  Returns
  -------
@@ -70,8 +70,8 @@ def load_bg(bg_path, height, width, ROI=None):
 
  bg_paths = glob.glob(os.path.join(bg_path, '*.tif'))
  bg_paths.sort()
- bg_data = np.zeros([len(bg_paths), height, width])
-
+
+ # Backwards compatibility warning
  if ROI is not None and ROI != (0, 0, width, height): # TODO: Remove for 1.0.0
  warning_msg = """
  Earlier versions of recOrder (0.1.2 and earlier) would have averaged over the background ROI. 
@@ -80,11 +80,22 @@ def load_bg(bg_path, height, width, ROI=None):
  """
  logging.warning(warning_msg)
 
- for i in range(len(bg_paths)):
- img = tiff.imread(bg_paths[i])
- bg_data[i, :, :] = img
+ # Load background images 
+ bg_img_list = []
+ for bg_path in bg_paths:
+ bg_img_list.append(tiff.imread(bg_path))
+ bg_img_arr = np.array(bg_img_list) # CYX
+
+ # Warn if shapes do not match
+ # TODO: 1.0.0 move these validation check to waveorder's Polscope_bg_correction
+ if bg_img_arr.shape[1:] != (height, width):
+ warning_msg = """
+ The background image has a different X/Y size than the acquired image. 
+ You can expect a downstream error or an incorrect background correction. 
+ """
+ logging.warning(warning_msg)
 
- return bg_data
+ return bg_img_arr # CYX
 
 
 def create_grid_from_coordinates(xy_coords, rows, columns):