add save/load functionality.

ripplemapper/classes.py

@@ -193,5 +193,5 @@ def _load(self, file: str):
  """Load the image series from a file."""
  with gzip.open(file, 'rb') as f:
  image_files = pickle.load(f)
-
- self.images = [RippleImage(image_file) for image_file in image_files]
+ base_path = Path(file).parent
+ self.images = [RippleImage(str(base_path / image_file.split("/")[-1])) for image_file in image_files] # TODO Path ojets should be accepted by RippleImage, etc.

ripplemapper/visualisation.py

@@ -25,7 +25,24 @@ def plot_image(ripple_image, include_contours: bool=True, *args, **kwargs):
  include_contours : bool, optional
  whether to include all the RippleContours on the plot, by default True
  """
- plt.imshow(ripple_image.image, cmap='gray')
+ if ripple_image.image is None:
+ if ripple_image.contours is None:
+ raise ValueError("RippleImage object must have an image or contours to plot.")
+ warnings.warn(f"Image not loaded for image: {ripple_image.source_file} plotting contours only.")
+ x_max = y_max = 150
+ x_min = y_min = np.Inf
+ for contour in ripple_image.contours:
+ x_max = max(x_max, np.max(contour.values[1]))
+ x_min = min(x_min, np.min(contour.values[1]))
+ y_max = max(y_max, np.max(contour.values[0]))
+ y_min = min(y_min, np.min(contour.values[0]))
+ x_min, x_max, y_min, y_max = int(np.floor(x_min)), int(np.ceil(x_max)), int(np.floor(y_min)), int(np.ceil(y_max))
+ plt.imshow(np.zeros((y_max, x_max)), cmap='gray')
+ plt.xlim(x_min, x_max)
+ plt.ylim(y_min, y_max)
+ plt.gca().invert_yaxis()
+ else:
+ plt.imshow(ripple_image.image, cmap='gray')
  if include_contours:
  if len(ripple_image.contours) == 0:
  warnings.warn(f"No contours found for image: {ripple_image.source_file} but you selected include_contours=True.")