def main_InteractivelySetParameters():
#######################################################################################################################
############################################### User Parameters ######################################################
#######################################################################################################################
# GENFIRE's reconstruction parameters can be edited here by the user and run interactively, any inputs provided
# by either the command line or the GUI will override these momentarily
print ("starting main_InteractivelySetParameters")
filename_projections = 'projections.mrc' #filename of projections, which should be size NxNxN_projections where N_projections is the number of projections
filename_angles = 'angles.txt' #angles can be either a 1xN_projections array containing a single tilt series, or 3xN_projections array containing 3 Euler angles for each projections in the form [phi;theta;psi]
filename_support = '' #NxNxN binary array specifying a region of 1's in which the reconstruction can exist
filename_initialObject = None #initial object to use in reconstruction; set to None to provide no initial guess
filename_results = 'GENFIRE_rec.mrc' #filename to save results
resolutionExtensionSuppressionState = 2 # 1) Turn on resolution extension/suppression, 2) No resolution extension/suppression, 3) Just resolution extension
numIterations = 100 #number of iterations to run in iterative reconstruction
oversamplingRatio = 3 #input projections will be padded internally to match this oversampling ratio. If you prepad your projections, set this to 1
interpolationCutoffDistance = 0.7 #radius of spherical interpolation kernel (in pixels) within which to include measured datapoints
doYouWantToDisplayFigure = True
displayFigure = genfire.reconstruct.DisplayFigure()
displayFigure.DisplayFigureON = doYouWantToDisplayFigure
calculateRFree = True
if filename_support is None:
useDefaultSupport = True
else:
useDefaultSupport = False
reconstruction_parameters = ReconstructionParameters()
reconstruction_parameters.projections = filename_projections
reconstruction_parameters.eulerAngles = filename_angles
reconstruction_parameters.support = filename_support
reconstruction_parameters.interpolationCutoffDistance = interpolationCutoffDistance
reconstruction_parameters.numIterations = numIterations
reconstruction_parameters.oversamplingRatio = oversamplingRatio
reconstruction_parameters.displayFigure = displayFigure
reconstruction_parameters.calculateRfree = calculateRFree
reconstruction_parameters.resolutionExtensionSuppressionState = resolutionExtensionSuppressionState
reconstruction_parameters.useDefaultSupport = useDefaultSupport
if os.path.isfile(filename_results): # If a valid initial object was provided, use it
reconstruction_parameters.initialObject = filename_results
main(reconstruction_parameters)
filename_results
except NameError as e:
filename_results='GENFIRE_rec.mrc'
#end
try:
interpolationCutoffDistance = float(interpolationCutoffDistance)
except NameError as e:
interpolationCutoffDistance = 0.7
#end
reconstruction_parameters = ReconstructionParameters()
reconstruction_parameters.projections = filename_projections
reconstruction_parameters.eulerAngles = filename_angles
reconstruction_parameters.support = filename_support
reconstruction_parameters.interpolationCutoffDistance = interpolationCutoffDistance
reconstruction_parameters.numIterations = numIterations
reconstruction_parameters.oversamplingRatio = oversamplingRatio
reconstruction_parameters.displayFigure = displayFigure
reconstruction_parameters.calculateRfree = calculateRFree
reconstruction_parameters.resolutionExtensionSuppressionState = resolutionExtensionSuppressionState
reconstruction_parameters.methodState = methodState
reconstruction_parameters.useDefaultSupport = useDefaultSupport
if os.path.isfile(filename_results): # If a valid initial object was provided, use it
reconstruction_parameters.initialObject = filename_results
try:
main(reconstruction_parameters)
except (NameError, IOError):
main(reconstruction_parameters)
#end