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Model incoherent background #341

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Model incoherent background #341

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31 changes: 31 additions & 0 deletions ptypy/core/manager.py
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Original file line number Diff line number Diff line change
Expand Up @@ -923,6 +923,14 @@ class _Full(object):
choices = ['achromatic', 'linear', 'irregular']
userlevel = 2

[coherence.add_background_mode]
default = False
help = Adding additional probe and object modes to model incoherent background
doc = If True, an additional probe mode will be created and linked to an additional empty object mode (ones).
This can help to deal with a background due to parasitic scattering.
type = bool
userlevel = 2

[resolution]
default = None
help = Will force the reconstruction to adapt to the given resolution, this might lead to cropping/padding in diffraction space which could reduce performance.
Expand Down Expand Up @@ -954,6 +962,11 @@ def _create_pods(self):
object_id = 'S' + self.label
probe_id = 'S' + self.label

# Additional probe/object modes to model incoherent background
if self.p.coherence.add_background_mode:
self.p.coherence.num_probe_modes += 1
self.p.coherence.num_object_modes += 1

# Loop through diffraction patterns
for i in range(len(self.new_diff_views)):
dv, mv = self.new_diff_views.pop(0), self.new_mask_views.pop(0)
Expand Down Expand Up @@ -1006,6 +1019,16 @@ def _create_pods(self):
# layermap access
exit_index = index * 10000 + pm * 100 + om

# Break link between background probe mode and valid object modes
# Breal link between backgrpund object mode and valid probe modes
if self.p.coherence.add_background_mode:
bgmode_probe = self.p.coherence.num_probe_modes - 1
bgmode_object = self.p.coherence.num_object_modes - 1
if (pm == bgmode_probe) and (om != bgmode_object):
continue
if (pm != bgmode_probe) and (om == bgmode_object):
continue

# Create views
# Please note that mostly references are passed,
# i.e. the views do mostly not own the accessrule
Expand Down Expand Up @@ -1046,11 +1069,19 @@ def _create_pods(self):
views=views,
geometry=geometry) # , meta=meta)

# Force background pods to be empty (this has no effect in accelerated/serialized engines)
if self.p.coherence.add_background_mode:
bgmode_probe = self.p.coherence.num_probe_modes - 1
bgmode_object = self.p.coherence.num_object_modes - 1
if (pm == bgmode_probe) and (om == bgmode_object):
pod.is_empty = True

new_pods.append(pod)

pod.probe_weight = 1.0
pod.object_weight = 1.0


return new_pods, new_probe_ids, new_object_ids

def _initialize_geo(self, common):
Expand Down
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