Merge branch 'master' of gitlab.esrf.fr:tomotools/nabu

nabu/__init__.py

-__version__ = "2021.2.1-rc1"
+__version__ = "2021.2.1-rc3"
 __nabu_modules__ = [
     "app",
     "cuda",

nabu/estimation/cor.py

@@ -273,8 +273,8 @@ class CenterOfRotationSlidingWindow(CenterOfRotation):
 
         # number of pixels where the window will "slide".
         n = img_shape[-1] - window_width
-        diffs_mean = np.empty((n,), dtype=img_1.dtype)
-        diffs_std = np.empty((n,), dtype=img_1.dtype)
+        diffs_mean = np.zeros((n,), dtype=img_1.dtype)
+        diffs_std = np.zeros((n,), dtype=img_1.dtype)
 
         for ii in progress_bar(range(n), verbose=self.verbose):
             win_1_start, win_1_end = ii, ii + window_width
@@ -484,8 +484,8 @@ class CenterOfRotationGrowingWindow(CenterOfRotation):
                 + "Found the following configuration instead => Side: %s, #1: %d, #2: %d" % (side, n1, n2)
             )
 
-        diffs_mean = np.empty((n1,), dtype=img_1.dtype)
-        diffs_std = np.empty((n1,), dtype=img_1.dtype)
+        diffs_mean = np.zeros((n1,), dtype=img_1.dtype)
+        diffs_std = np.zeros((n1,), dtype=img_1.dtype)
 
         for ii in progress_bar(range(n1), verbose=self.verbose):
             win_1 = window_bounds(win_1_mid_start + ii)

nabu/estimation/translation.py

@@ -154,7 +154,7 @@ class DetectorTranslationAlongBeam(AlignmentBase):
         cc_vs = np.fft.fftfreq(img_shape[-2], 1 / img_shape[-2])
         cc_hs = np.fft.fftfreq(img_shape[-1], 1 / img_shape[-1])
 
-        shifts_vh = np.empty((num_imgs, 2))
+        shifts_vh = np.zeros((num_imgs, 2))
         for ii, cc in enumerate(ccs):
             (f_vals, fv, fh) = self.extract_peak_region_2d(cc, peak_radius=peak_fit_radius, cc_vs=cc_vs, cc_hs=cc_hs)
             shifts_vh[ii + 1, :] = self.refine_max_position_2d(f_vals, fv, fh)

nabu/io/utils.py

@@ -46,6 +46,9 @@ def get_compacted_dataslices(urls, subsampling=None):
     def merge_slices(slice1, slice2):
         return slice(slice1.start, slice2.stop)
 
+    if len(urls) == 0:
+        return urls
+
     sorted_files_indices = sorted(urls.keys())
     idx0 = sorted_files_indices[0]
     first_url = urls[idx0]