Example parameter files

Example for reconstruction of series

This is basically the example from the _sec-tutorial, but without defocus adjustment:

{
    // Path of hologram files (using printf format, integer argument). Required.
    "object_names" : "holo_%03d.dm3",

    // Index of first hologram.
    "object_first" : 1,

    // Index of last hologram. Required.
    "object_last" : 20,

    // Same (name, first index, last index) for "empty" holograms.
    "empty_names" : "empty_%03d.dm3",
    "empty_first" : 1,
    "empty_last" : 20,

    // Sampling (nm/px) of object holograms.
    // Defaults to value in data files.
    //"sampling" : 0.00519824,

    // Voltage in kV. Default to value recorded in data files.
    //"voltage": 300,

    // Size (in px) used for reconstruction of "empty" holograms. Required.
    "empty_size" : 512,

    // Size (in px) used for reconstruction of "object" holograms Required.
    "object_size" : 384,

    // X, Y Position of sideband in FFT pixels (origin is in center). Required.
    "sideband_pos" : [1136, 1304],

    // Reconstruction region in pixels (L, T, R, B). Defaults to full region.
    "roi" : [128, 128, 1920, 1920],

    // Region for raw alignment in pixels (L, T, R, B). Defaults to roi.
    //"align_roi" : [256, 256, 1536, 1536],

    // Disable raw alignment. Raw alignment is enabled by default.
    //"enable_raw_alignment" : false,

    // Output file name (will be HDF5 file). Required.
    "output_name" : "holo.hdf5",

    // Mask type (see FilterFunction for details). Defaults to "EDGE"
    // "filter_func" : "EDGE",
    "filter_func" : ["BUTTERWORTH", 14],

    // cut off frequency in 1/nm (q_max). Required.
    "cut_off" : 14.5,

    // Parameterization for MTF
    "mtf" : [["CONSTANT", -2.25536738e-02],
             ["LORENTZIAN", 1.02543658e-05, 1.15367655e-04],
             ["LORENTZIAN", 2.49224357e-02, 5.35262063e-02],
             ["GAUSSIAN", 4.60461599e-01, 4.36842560e+02]],

    // Correct phase by empty phase only (true), or full complex reconstruction (false).
    // Defaults to false.
    "only_phase": false,
}

Only reconstruct empty hologram

This will reconstruct only the empty hologram. This can be used in for instance in subsequent reconstructions (see other examples):

{
    // Leave "object_names" unset

    // Usual empty hologram input
    "empty_names" : "empty.%d.dm3",
    "empty_first" : 1,
    "empty_last" : 10,

    // Size (in px) used for reconstruction of "empty" holograms. Required.
    "empty_size" : 1536,

    // X, Y Position of side band in FFT pixels (origin is in center). Required.
    "sideband_pos" : [1011, 1091],

    // Output file name (will be HDF5 file). Empty hologram will be in dataset "empty"
    "output_name" : "my_empty_reco.hdf5",

    // Mask type (see FilterFunction for details). Defaults to "EDGE"
    "filter_func" : ["BUTTERWORTH", 14],

    // Reconstruction cutoff in 1/nm
    "cut_off" : 3.0,

    // Parameterization for MTF
    // "mtf" : ...
}

Use pre-reconstructed empty hologram for normalization

This example uses a prereconstructed empty hologram for normalization (also see Normalization):

{
    // Object holograms (as usual). Here series of DM3 files
    "object_names" : "hologram.%d.dm3",     // Filename format
    "object_first" : 1,                     // Index of first
    "object_last" : 5,                      // Index of last (inclusive)

    // Use pre-reconstructed empty hologram for normalization, here dataset from HDF5 file.
    "empty_override" : "somefile.hdf5?dataset=empty",

    // Reconstruction parameters
    "object_size" : 1536,                   // Reconstruction size in px
    "sideband_pos" : [1011, 1091],          // X, Y Position of side band in FFT pixels (origin is in center).
    "cut_off" : 3.0,                        // Reconstruction cut off in 1/nm
    "filter_func" : ["BUTTERWORTH", 14],    // Mask type

    // Optional reconstruction region (L, T, R, B). Defaults to full region.
    //"roi" : [166, 388, 1701, 1923],

    // Output file name (will be HDF5 file). Required.
    "output_name" : "my_reco.hdf5",

    // Parameterization for MTF
    //"mtf" : ...
}

Use predetermined camera distortions for normalization

This example creates an synthetic empty hologram for normalization. The synthetic empty hologram is creacted from predetermined camera distortions (also see Normalization):

{
    // Object holograms (as usual). Here series of DM3 files
    "object_names" : "hologram.%d.dm3",     // Filename format
    "object_first" : 1,                     // Index of first
    "object_last" : 5,                      // Index of last (inclusive)

    // Enable synthetic empty holograms
    "synthesize_empty": true,

    // Two datasets, same size as holograms, with displacements in px for each pixel
    // First in X direction, Second in Y direction
    "camera_distortions": ["camera.hdf5?dataset=dx", "camera.hdf5?dataset=dy"],

    // Reconstruction parameters (as usual)
    "object_size" : 1536,                   // Reconstruction size in px
    "sideband_pos" : [1011, 1091],          // X, Y Position of side band in FFT pixels (origin is in center).
    "cut_off" : 3.0,                        // Reconstruction cut off in 1/nm
    "filter_func" : ["BUTTERWORTH", 14],    // Mask type

    // Optional reconstruction region (L, T, R, B). Defaults to full region.
    //"roi" : [166, 388, 1701, 1923],

    // Output file name (will be HDF5 file). Required.
    "output_name" : "my_reco.hdf5",

    // Parameterization for MTF
    //"mtf" : ...
}

Only reconstruct single hologram (no averaging)

This example reconstructs a single (object) hologram, and normalizes with a single empty hologram:

{
    // Output file name (will be HDF5 file). Required.
    "output_name" : "output.hdf5",

    // List with just a single filename
    "object_names" : ["my_hologram.dm3"],

    // Empty hologram (list with single filename)
    "object_names" : ["empty.dm3"],

    // Reconstruction parameters
    "object_size" : 512,
    "sideband_pos" : [749, 1019],
    "filter_func" : ["BUTTERWORTH", 14],
    "cut_off" : 1.0
}