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Move the standardizing tool over to analysis and write a test for it

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This commit is contained in:
Abe Levitan
2019-04-24 19:23:51 -04:00
parent 75b257f816
commit 374683fe35
4 changed files with 155 additions and 60 deletions
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CDTools/scripts/synthesize.py
+9 -54
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@@ -8,66 +8,23 @@ from scipy import fftpack
from CDTools.tools import cmath, plotting
from CDTools.tools import image_processing as ip
from CDTools.tools.analysis import *
def standardize(probe, obj, obj_slice=None):
# First, we normalize the probe intensity to a fixed value.
# Should this be the maximum or the integrated intensity? I think
# probably the integrated intensity. We set the average per-[ixel
# intensity in the probe to be one
normalization = np.sqrt(np.sum(np.abs(probe)**2) / len(probe.ravel()))
probe = cmath.complex_to_torch(probe / normalization)
obj = cmath.complex_to_torch(obj * normalization)
# Default slice of the object to use for alignment, etc.
if obj_slice is None:
obj_slice = np.s_[(obj.shape[0]//8)*3:(obj.shape[0]//8)*5,
(obj.shape[1]//8)*3:(obj.shape[1]//8)*5]
# Now we get rid of the probe's phase ramp
# Currently disabled
#center_freq = ip.centroid_sq(cmath.fftshift(t.fft(probe,2)),comp=True)
#center_freq -= (t.tensor(probe.shape[:-1]) // 2).to(t.float32)
#center_freq /= t.tensor(probe.shape[:-1]).to(t.float32)
#Is, Js = np.mgrid[:probe.shape[0],:probe.shape[1]]
#probe_phase_ramp = cmath.expi(2*np.pi *
# (center_freq[0] * t.tensor(Is).to(t.float32) +
# center_freq[1] * t.tensor(Js).to(t.float32)))
#probe = cmath.cmult(probe, cmath.cconj(probe_phase_ramp))
#Is, Js = np.mgrid[:obj.shape[0],:obj.shape[1]]
#obj_phase_ramp = cmath.expi(2*np.pi *
# (center_freq[0] * t.tensor(Is).to(t.float32) +
# center_freq[1] * t.tensor(Js).to(t.float32)))
#obj = cmath.cmult(obj, obj_phase_ramp)
# Then, we set them to consistent absolute phases
probe_angle = cmath.cphase(t.sum(probe,dim=(0,1)))
obj_angle = cmath.cphase(t.sum(obj[obj_slice],dim=(0,1)))
probe = cmath.cmult(probe, cmath.expi(-probe_angle))
obj = cmath.cmult(obj, cmath.expi(-obj_angle))
return probe, obj
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])))
@@ -154,19 +111,17 @@ if __name__ == '__main__':
synth_probe, synth_obj, aligned_objs = synthesize_reconstructions(
dataset['probe'], dataset['obj'], args.use_probe)
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_amplitude(synth_obj[400:750,450:850],basis=1e6*dataset['basis'])
#plotting.plot_colorized(synth_obj[400:750,450:850],basis=1e6*dataset['basis'])
#plotting.plot_phase(synth_obj[400:750,450:850],basis=1e6*dataset['basis'])
plotting.plot_amplitude(synth_obj[::-1,::-1][450:900,325:775],basis=1e6*dataset['basis'])
plotting.plot_phase(synth_obj[::-1,::-1][450:900,325:775],basis=1e6*dataset['basis'])
plotting.plot_colorized(synth_obj[::-1,::-1][450:900,325:775],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()
real_translations = dataset['basis'].dot(dataset['translation'][0].transpose())