Merge pull request #188 from rolfverberg/main

fix: fixed memory issues in tiff writer for large data sets

Author: rolfverberg

CHAP/common/processor.py

@@ -873,6 +873,11 @@ def process(
         if not save_figures and not interactive:
             return
 
+        # Third party modules
+        from nexusformat.nexus import nxsetconfig
+
+        nxsetconfig(memory=100000)
+
         # Load the default data
         try:
             nxdata = self.get_data(data).get_default()
@@ -1008,6 +1013,7 @@ def process(
                        column_coords[-1], column_coords[0]),
             'vrange': vrange,
         }
+        self.logger.debug(f'figure configuration:\n{self._figconfig}')
 
         if len(axis_coords) == 1:
             # Create a figure for a single image slice
@@ -1056,8 +1062,9 @@ def process(
                         self.logger.warning(
                             'Ignoring inconsistent file extension')
                     fileformat = 'tif'
-                    image_data = ((data*255.0 - vrange[0])/ 
-                                  (vrange[1] - vrange[0])).astype(np.uint8)
+                    data = 255.0*((data - vrange[0])/ 
+                                  (vrange[1] - vrange[0]))
+                    image_data = data.astype(np.uint8)
 
         if save_figures:
             return {'image_data': image_data, 'fileformat': fileformat}

CHAP/common/writer.py

@@ -49,11 +49,15 @@ def write_image(data, filename, logger, force_overwrite=False):
         if image_data.ndim == 2:
             # Third party modules
             from imageio import imwrite
+
+            imwrite(filename, image_data)
         elif image_data.ndim == 3:
             # Third party modules
-            from imageio import mimwrite as imwrite
+#            from imageio import mimwrite as imwrite
+            from tifffile import imwrite
 
-        imwrite(filename, image_data)
+            kwargs = {'bigtiff': True}
+            imwrite(filename, image_data, **kwargs)
     elif isinstance(image_data, animation.FuncAnimation):
         image_data.save(filename)
     else: