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Update the standardization to work with incoherent probes and move over the synthesis

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This commit is contained in:
Abe Levitan
2019-04-24 22:01:09 -04:00
parent 374683fe35
commit 9a35d44689
3 changed files with 144 additions and 62 deletions
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CDTools/scripts/synthesize.py
+11 -47
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@@ -11,52 +11,6 @@ from CDTools.tools import image_processing as ip
from CDTools.tools.analysis import *
def synthesize_reconstructions(probes, objects, use_probe=False, obj_slice=None):
if obj_slice is None:
obj_slice = np.s_[(objects[0].shape[0]//8)*3:(objects[0].shape[0]//8)*5,
(objects[0].shape[1]//8)*3:(objects[0].shape[1]//8)*5]
probes = [cmath.complex_to_torch(probe).to(t.float32) for probe in probes]
objects = [cmath.complex_to_torch(obj).to(t.float32) for obj in objects]
synth_probe, synth_obj = standardize(probes[0], objects[0])
obj_stack = [cmath.torch_to_complex(synth_obj)]
for i, (probe, obj) in enumerate(zip(probes[1:],objects[1:])):
probe, obj = standardize(probe, obj)
probe = probe[0]
print(i)
#plt.imshow(np.angle(cmath.torch_to_complex(obj[obj_slice])))
#plt.show()
if use_probe:
shift = ip.find_shift(synth_probe,probe, resolution=50)
else:
shift = ip.find_shift(synth_obj[obj_slice],obj[obj_slice], resolution=50)
obj = ip.sinc_subpixel_shift(obj,np.array(shift))
probe = ip.sinc_subpixel_shift(probe,tuple(shift))
#obj = t.roll(obj,tuple(int(s) for s in shift),dims=(0,1))
#probe = t.roll(probe,tuple(int(s) for s in shift),dims=(0,1))
synth_probe += probe
synth_obj += obj
obj_stack.append(cmath.torch_to_complex(obj))
# If there only was one image
try:
i
except:
i = -1
synth_probe = cmath.torch_to_complex(synth_probe)
synth_obj = cmath.torch_to_complex(synth_obj)
return synth_probe/(i+2), synth_obj/(i+2), obj_stack
def calc_prtf(synth_obj, objects, basis, obj_slice=None):
@@ -114,16 +68,26 @@ if __name__ == '__main__':
freqs, prtf = calc_prtf(synth_obj, aligned_objs, dataset['basis'])
print(np.linalg.norm(dataset['basis'],axis=0))
plotting.plot_phase(dataset['probe'][0][0],basis=1e6*dataset['basis'])
plotting.plot_amplitude(dataset['probe'][0][0],basis=1e6*dataset['basis'])
plotting.plot_colorized(dataset['probe'][0][0],basis=1e6*dataset['basis'])
plotting.plot_phase(synth_probe[1],basis=1e6*dataset['basis'])
plotting.plot_amplitude(synth_probe[1],basis=1e6*dataset['basis'])
plotting.plot_colorized(synth_probe[1],basis=1e6*dataset['basis'])
plotting.plot_amplitude(synth_obj,basis=1e6*dataset['basis'])
plotting.plot_colorized(synth_obj,basis=1e6*dataset['basis'])
plotting.plot_phase(synth_obj,basis=1e6*dataset['basis'])
plt.figure()
plt.show()
exit()
real_translations = dataset['basis'].dot(dataset['translation'][0].transpose())
real_translations -= np.min(real_translations,axis=1)[:,None]
plt.plot(real_translations[0]*1e6,real_translations[1]*1e6,'k.')