Shifts for subparticles are reverted

OPIC-Oxford · Mar 12, 2019 · afc1d4b · afc1d4b
1 parent 805553b
commit afc1d4b
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Showing 2 changed files with 8 additions and 6 deletions.
diff --git a/lib/localrec/localized_reconstruction.py b/lib/localrec/localized_reconstruction.py
@@ -127,7 +127,7 @@ def angles_to_degrees(particle):
 def create_subparticles(particle, symmetry_matrices, subparticle_vector_list,
                         part_image_size, randomize, output,
                         unique, subparticles_total, align_subparticles,
-                        subtract_masked_map, do_create_star, filters):
+                        subtract_masked_map, do_create_star, filters, ang_pix):
     """ Obtain all subparticles from a given particle and set
     the properties of each such subparticle. """
 
@@ -189,17 +189,18 @@ def create_subparticles(particle, symmetry_matrices, subparticle_vector_list,
 
             # modify the subparticle defocus paramaters by its z location
             if hasattr(particle, 'rlnDefocusU'):
-                subpart.rlnDefocusU = particle.rlnDefocusU + z
-                subpart.rlnDefocusV = particle.rlnDefocusV + z
+                z_ang = ang_pix * z
+                subpart.rlnDefocusU = particle.rlnDefocusU + z_ang
+                subpart.rlnDefocusV = particle.rlnDefocusV + z_ang
 
             # save the subparticle coordinates (integer part) relative to the
             # user given image size and as a small shift in the origin (decimal part)
             x_d, x_i = math.modf(x)
             y_d, y_i = math.modf(y)
             subpart.rlnCoordinateX = int(part_image_size / 2) - x_i
             subpart.rlnCoordinateY = int(part_image_size / 2) - y_i
-            subpart.rlnOriginX = -x_d
-            subpart.rlnOriginY = -y_d
+            subpart.rlnOriginX = x_d
+            subpart.rlnOriginY = y_d
 
             overlaps = (unique >= 0 and
                         not filter_unique(subparticles, subpart, unique))

diff --git a/relion_localized_reconstruction.py b/relion_localized_reconstruction.py
@@ -224,7 +224,8 @@ def main(self):
                                                        args.align_subparticles,
                                                        args.masked_map,
                                                        True,
-                                                       filters)
+                                                       filters,
+                                                       args.angpix)
 
                 mdOut.addData(subparticles)
                 mdOutSub.addData(subtracted)