remove trotter_sign -- correct is negative

py4DSTEM/process/phase/direct_ptychography.py

@@ -1461,7 +1461,6 @@ def _reconstruct_single_frequency(
  probe_conj,
  aperture,
  probe_kwargs,
- trotter_sign,
  phase_compensation: bool = True,
  virtual_detector_masks: Sequence[np.ndarray] = None,
  xp=np,
@@ -1513,35 +1512,19 @@ def _reconstruct_single_frequency(
  gamma_ind = gamma_abs > threshold
  normalization = gamma_abs[gamma_ind]
 
- if trotter_sign == "+":
- numerator = -G[gamma_ind].conj() * gamma[gamma_ind]
- elif trotter_sign == "-":
- numerator = G[gamma_ind] * gamma[gamma_ind].conj()
- else:
- raise ValueError()
-
- return (numerator / normalization).sum()
+ return (G[gamma_ind] * gamma[gamma_ind].conj() / normalization).sum()
 
  else:
  aperture_plus = aperture_plus > threshold
  aperture_minus = aperture_minus > threshold
 
- if trotter_sign == "+":
- aperture_solo = xp.logical_and(
- xp.logical_and(aperture, aperture_plus), ~aperture_minus
- )
- return G[aperture_solo].sum().conj()
- elif trotter_sign == "-":
- aperture_solo = xp.logical_and(
- xp.logical_and(aperture, aperture_minus), ~aperture_plus
- )
- return G[aperture_solo].sum()
- else:
- raise ValueError()
+ aperture_solo = xp.logical_and(
+ xp.logical_and(aperture, aperture_minus), ~aperture_plus
+ )
+ return G[aperture_solo].sum()
 
  def reconstruct(
  self,
- trotter_sign="-",
  phase_compensation=True,
  num_jobs=None,
  threads_per_job=None,
@@ -1557,8 +1540,6 @@ def reconstruct(
 
  Parameters
  --------
- trotter_sign: str, optional
- Sign of single-side trotter to use. One of '+','-'.
  phase_compensation: bool, optional
  If True, the measured phase is compensated using a complex virtual detector. Recommnended.
  num_jobs: int, optional
@@ -1630,7 +1611,6 @@ def reconstruct(
  probe_conj,
  aperture,
  probe_kwargs,
- trotter_sign=trotter_sign,
  phase_compensation=phase_compensation,
  virtual_detector_masks=virtual_detector_masks,
  xp=xp,
@@ -1666,7 +1646,6 @@ def wrapper_function(**kwargs):
  probe_conj=probe_conj,
  aperture=aperture,
  probe_kwargs=probe_kwargs,
- trotter_sign=trotter_sign,
  phase_compensation=phase_compensation,
  virtual_detector_masks=virtual_detector_masks,
  xp=xp,
@@ -1707,7 +1686,6 @@ def _reconstruct_single_frequency(
  probe_conj,
  probe_normalization,
  probe_kwargs,
- trotter_sign,
  virtual_detector_masks: Sequence[np.ndarray] = None,
  xp=np,
  ):
@@ -1748,18 +1726,10 @@ def _reconstruct_single_frequency(
  d = probe_normalization[gamma_ind]
  normalization = d * xp.sqrt(xp.sum(normalization**2 / d))
 
- if trotter_sign == "+":
- numerator = -G[gamma_ind].conj() * gamma[gamma_ind]
- elif trotter_sign == "-":
- numerator = G[gamma_ind] * gamma[gamma_ind].conj()
- else:
- raise ValueError()
-
- return (numerator / normalization).sum()
+ return (G[gamma_ind] * gamma[gamma_ind].conj() / normalization).sum()
 
  def reconstruct(
  self,
- trotter_sign="-",
  num_jobs=None,
  threads_per_job=None,
  virtual_detector_masks: Sequence[np.ndarray] = None,
@@ -1774,8 +1744,6 @@ def reconstruct(
 
  Parameters
  --------
- trotter_sign: str, optional
- Sign of single-side trotter to use. One of '+','-'.
  num_jobs: int, optional
  Number of processes to use. Default is None, which spawns as many processes as CPUs on
  the system.
@@ -1849,7 +1817,6 @@ def reconstruct(
  probe_conj,
  probe_normalization,
  probe_kwargs,
- trotter_sign=trotter_sign,
  virtual_detector_masks=virtual_detector_masks,
  xp=xp,
  )
@@ -1884,7 +1851,6 @@ def wrapper_function(**kwargs):
  probe_conj=probe_conj,
  probe_normalization=probe_normalization,
  probe_kwargs=probe_kwargs,
- trotter_sign=trotter_sign,
  virtual_detector_masks=virtual_detector_masks,
  xp=xp,
  )
@@ -1923,43 +1889,32 @@ def _reconstruct_single_frequency(
  probe,
  epsilon,
  probe_kwargs,
- trotter_sign,
  xp=np,
  ):
  """ """
 
  array_G = xp.asarray(intensities_FFT)
  array_H = xp.fft.ifft2(array_G)
 
- if trotter_sign == "+":
- Kx_Qx = Kx + Qx
- Ky_Qy = Ky + Qy
- elif trotter_sign == "-":
- Kx_Qx = Kx - Qx
- Ky_Qy = Ky - Qy
- else:
- raise ValueError()
+ Kx_Qx = Kx - Qx
+ Ky_Qy = Ky - Qy
 
  probe_shifted = ComplexProbe(
  **probe_kwargs,
  force_spatial_frequencies=(Kx_Qx, Ky_Qy),
  )._evaluate_ctf()
 
- if trotter_sign == "+":
- wdd_probe = xp.fft.ifft2(probe * probe_shifted.conj())
- else:
- wdd_probe = xp.fft.ifft2(probe.conj() * probe_shifted)
+ wdd_probe = xp.fft.ifft2(probe.conj() * probe_shifted)
  wdd_probe_conj = wdd_probe.conj()
 
  array_D = wdd_probe_conj * array_H / (wdd_probe * wdd_probe_conj + epsilon)
  array_D_FFT = xp.fft.fft2(array_D)
 
- return array_D_FFT[0, 0].conj() if trotter_sign == "+" else array_D_FFT[0, 0]
+ return array_D_FFT[0, 0]
 
  def reconstruct(
  self,
  relative_wiener_epsilon,
- trotter_sign="-",
  num_jobs=None,
  threads_per_job=None,
  virtual_detector_masks: Sequence[np.ndarray] = None,
@@ -1974,8 +1929,6 @@ def reconstruct(
 
  Parameters
  --------
- trotter_sign: str, optional
- Sign of single-side trotter to use. One of '+','-'.
  worker_pool: WorkerPool
  If not None, reconstruction is dispatched to mpire WorkerPool instance.
  virtual_detector_masks: np.ndarray
@@ -2042,7 +1995,6 @@ def reconstruct(
  self._fourier_probe,
  epsilon,
  probe_kwargs,
- trotter_sign=trotter_sign,
  xp=xp,
  )
  else:
@@ -2075,7 +2027,6 @@ def wrapper_function(**kwargs):
  probe=self._fourier_probe,
  epsilon=epsilon,
  probe_kwargs=probe_kwargs,
- trotter_sign=trotter_sign,
  xp=xp,
  )