--- a/workflow/run_tomo.py	Wed Mar 22 12:56:22 2023 +0000
+++ b/workflow/run_tomo.py	Wed Mar 22 16:46:26 2023 +0000
@@ -15,7 +15,7 @@
 
 from multiprocessing import cpu_count
 from nexusformat.nexus import *
-from os import mkdir
+from os import mkdir, environ
 from os import path as os_path
 try:
     from skimage.transform import iradon
@@ -99,7 +99,7 @@
             self.num_core = num_core
 
     def __enter__(self):
-        self.num_core_org = ne.set_num_threads(self.num_core)
+        self.num_core_org = ne.set_num_threads(min(self.num_core, ne.MAX_THREADS))
 
     def __exit__(self, exc_type, exc_value, traceback):
         ne.set_num_threads(self.num_core_org)
@@ -773,7 +773,7 @@
 
         # Take median
         if tdf_stack.ndim == 2:
-            tdf = tdf_stack
+            tdf = tdf_stack.astype('float64')
         elif tdf_stack.ndim == 3:
             tdf = np.median(tdf_stack, axis=0)
             del tdf_stack
@@ -841,7 +841,7 @@
            We don’t typically account for them but potentially could.
         """
         if tbf_stack.ndim == 2:
-            tbf = tbf_stack
+            tbf = tbf_stack.astype('float64')
         elif tbf_stack.ndim == 3:
             tbf = np.median(tbf_stack, axis=0)
             del tbf_stack
@@ -856,7 +856,7 @@
 
         # Set any non-positive values to one
         # (avoid negative bright field values for spikes in dark field)
-        tbf[tbf < 1] = 1
+        tbf[tbf < 1.0] = 1.0
 
         # Plot bright field
         if self.galaxy_flag:
@@ -1069,23 +1069,29 @@
         """
         # Get full bright field
         tbf = np.asarray(reduced_data.data.bright_field)
-        tbf_shape = tbf.shape
+        img_shape = tbf.shape
 
         # Get image bounds
-        img_x_bounds = tuple(reduced_data.get('img_x_bounds', (0, tbf_shape[0])))
-        img_y_bounds = tuple(reduced_data.get('img_y_bounds', (0, tbf_shape[1])))
+        img_x_bounds = tuple(reduced_data.get('img_x_bounds', (0, img_shape[0])))
+        img_y_bounds = tuple(reduced_data.get('img_y_bounds', (0, img_shape[1])))
+        if img_x_bounds == (0, img_shape[0]) and img_y_bounds == (0, img_shape[1]):
+            resize_flag = False
+        else:
+            resize_flag = True
 
         # Get resized dark field
-#        if 'dark_field' in data:
-#            tbf = np.asarray(reduced_data.data.dark_field[
-#                    img_x_bounds[0]:img_x_bounds[1],img_y_bounds[0]:img_y_bounds[1]])
-#        else:
-#            logger.warning('Dark field unavailable')
-#            tdf = None
-        tdf = None
+        if 'dark_field' in reduced_data.data:
+            if resize_flag:
+                tdf = np.asarray(reduced_data.data.dark_field[
+                        img_x_bounds[0]:img_x_bounds[1],img_y_bounds[0]:img_y_bounds[1]])
+            else:
+                tdf = np.asarray(reduced_data.data.dark_field)
+        else:
+            logger.warning('Dark field unavailable')
+            tdf = None
 
         # Resize bright field
-        if img_x_bounds != (0, tbf.shape[0]) or img_y_bounds != (0, tbf.shape[1]):
+        if resize_flag:
             tbf = tbf[img_x_bounds[0]:img_x_bounds[1],img_y_bounds[0]:img_y_bounds[1]]
 
         # Get the tomography images
@@ -1145,13 +1151,15 @@
         else:
             path = self.output_folder
         for i, tomo_stack in enumerate(tomo_stacks):
-            # Resize the tomography images
-            # Right now the range is the same for each set in the image stack.
-            if img_x_bounds != (0, tbf.shape[0]) or img_y_bounds != (0, tbf.shape[1]):
+            # Resize the tomography images as needed
+            # Right now the range is the same for each set in the image stack
+            if resize_flag:
                 t0 = time()
                 tomo_stack = tomo_stack[:,img_x_bounds[0]:img_x_bounds[1],
                         img_y_bounds[0]:img_y_bounds[1]].astype('float64')
                 logger.debug(f'Resizing tomography images took {time()-t0:.2f} seconds')
+            else:
+                tomo_stack = tomo_stack.astype('float64')
 
             # Subtract dark field
             if tdf is not None: