old_contents: #!/usr/bin/env python
  # -*- coding: utf-8 -*-
  # labview.py
  """
  Thin wrapper so that labview can perform phase retrieval.
  
  Copyright (c) 2018, David Hoffman
  """
  
  from pyOTF.phaseretrieval import retrieve_phase
  from pyOTF.utils import prep_data_for_PR
  
  
  def labview(data, wl, na, ni, res, zres, max_iters=200, pupil_tol=1e-8, mse_tol=1e-8, phase_only=False):
      """Generate a PSF object
  
      Parameters
      ----------
      data : ndarray (3 dim)
          The experimentally measured PSF of a subdiffractive source
      wl : numeric
          Emission wavelength of the simulation
      na : numeric
          Numerical aperature of the simulation
      ni : numeric
          index of refraction for the media
      res : numeric
          x/y resolution of the simulation, must have same units as wl
      zres : numeric
          z resolution of simuation, must have same units a wl
      max_iters : int
          The maximum number of iterations to run, default is 200
      pupil_tol : float
          the tolerance in percent change in change in pupil, default is 1e-8
      mse_tol : float
          the tolerance in percent change for the mean squared error between
          data and simulated data, default is 1e-8
      phase_only : bool
          True means only the phase of the back pupil is retrieved while the
          amplitude is not.
      """
  
      params = dict(wl=wl, na=na, ni=ni, res=res, zres=zres)
  
      data_prepped = prep_data_for_PR(data)
  
      pr_result = retrieve_phase(data_prepped, params, max_iters, pupil_tol, mse_tol, phase_only)
  
      return pr_result.phase
  
  
  if __name__ == "__main__":
      # phase retrieve a pupil
      import os
      import time
      import logging
      from skimage.external import tifffile as tif
      from matplotlib import pyplot as plt
  
      logging.basicConfig()
      logging.getLogger().setLevel(logging.INFO)
      # read in data from fixtures
      data = tif.imread(os.path.split(__file__)[0] + "/fixtures/psf_wl520nm_z300nm_x130nm_na0.85_n1.0.tif")
      # set up model params
      params = dict(
          wl=520,
          na=0.85,
          ni=1.0,
          res=130,
          zres=300
      )
      # retrieve the phase
      pr_start = time.time()
      print("Starting phase retrieval with data of size {}".format(data.shape))
      phase = labview(data, **params, pupil_tol=1e-6)
      print("It took {} seconds to retrieve the pupil function".format(
          time.time() - pr_start))
      # plot
      max_val = abs(phase).max()
      plt.matshow(phase, cmap="seismic", vmin=-max_val, vmax=max_val)
      plt.colorbar()
      # show
      plt.show()
  
new_contents: #!/usr/bin/env python
  # -*- coding: utf-8 -*-
  # labview.py
  """
  Thin wrapper so that labview can perform phase retrieval.
  
  Copyright (c) 2018, David Hoffman
  """
  
  from pyOTF.phaseretrieval import retrieve_phase
  from pyOTF.utils import prep_data_for_PR
  
  
  def labview(data, wl, na, ni, res, zres, max_iters=200, pupil_tol=1e-8, mse_tol=1e-8, phase_only=False):
      """Generate a PSF object
  
      Parameters
      ----------
      data : ndarray (3 dim)
          The experimentally measured PSF of a subdiffractive source
      wl : numeric
          Emission wavelength of the simulation
      na : numeric
          Numerical aperature of the simulation
      ni : numeric
          index of refraction for the media
      res : numeric
          x/y resolution of the simulation, must have same units as wl
      zres : numeric
          z resolution of simuation, must have same units a wl
      max_iters : int
          The maximum number of iterations to run, default is 200
      pupil_tol : float
          the tolerance in percent change in change in pupil, default is 1e-8
      mse_tol : float
          the tolerance in percent change for the mean squared error between
          data and simulated data, default is 1e-8
      phase_only : bool
          True means only the phase of the back pupil is retrieved while the
          amplitude is not.
      """
  
      params = dict(wl=wl, na=na, ni=ni, res=res, zres=zres)
  
      data_prepped = prep_data_for_PR(data)
  
      pr_result = retrieve_phase(data_prepped, params, max_iters, pupil_tol, mse_tol, phase_only)
  
      return pr_result.phase
  
  
  if __name__ == "__main__":
      # phase retrieve a pupil
      import os
      import time
      import logging
      from skimage.external import tifffile as tif
      from matplotlib import pyplot as plt
  
      logging.basicConfig()
      logging.getLogger().setLevel(logging.INFO)
      # read in data from fixtures
      data = tif.imread(os.path.split(__file__)[0] + "/fixtures/psf_wl520nm_z300nm_x130nm_na0.85_n1.0.tif")
      # set up model params
      params = dict(
          wl=520,
          na=0.85,
          ni=1.0,
          res=130,
          zres=300
      )
      # retrieve the phase
      pr_start = time.time()
      print("Starting phase retrieval with data of size {}".format(data.shape))
      phase = labview(data[6:-5], **params, pupil_tol=1e-6)
      print("It took {} seconds to retrieve the pupil function".format(
          time.time() - pr_start))
      # plot
      max_val = abs(phase).max()
      plt.matshow(phase, cmap="seismic", vmin=-max_val, vmax=max_val)
      plt.colorbar()
      # show
      plt.show()
  
subject: Update labview.py