.. _config_disp:

===========
config_disp
===========
| The "config_disp" file defines parameters needed to run postprocessing that will allow visualization of the reconstructed image. By configuring parameters in the config_disp file user can obtain various images viewable with Paraview.
| By default user will get the visualized image as amplitudes and phases (or real and imagnary if configured complex_mode = "ReIm"), support, and optionally unwrapped phases. User can add interpolation to the processing by configuring interpolation_mode. This option will create vts file containing interpolated image. Another optional return is reciprocal space visualization, i.e. phasing data and inverse fourier transfer. User can request it by setting write_recip = True. To view resolution in direct and reciprocal space user can set determine_resolution_type. This will produce vts file containing resolution.

Parameters
==========
- results_dir

| Optional, defaults to <experiment_dir>/results_phasing. A directory that has a tree, or leaf with reconstruction results. The results will be used as input to the visualization processing. There could be several results in the given directory tree, and all will be processed in parallel.

::

    results_dir = "/path/to/results_phasing"

- rampups

| Optional, upsize when running ramp removal, default is 1. Expect long processing time for greater numbers.

::

    rampups = 2

- unwrap

| Defaults to False. If True the vts file will contain unwrapped phase in addition to phase and amplitude.

::

    unwrap = False

- make_twin

| A switch to whether visualize twin image.

::

    make_twin = False

- complex_mode

| This mode determines arrays that will be saved in the direct space images file. If mode is "AmpPhase" the "imAmp" and "imPh" arrays will be saved that hold image amplitudes and image phases. if mode is "ReIm" the "imRe" and "imImag" arrays will be saved that hold real values and imaginary values. Defaults to "AmpPhase".

::

    complex_mode = "AmpPhase"

- crop_type

| Optional, Defines how crop is determined. Supported values: "fraction' and "tight". If defined as fraction, the defined fraction of each dimension is cropped around maximum value. The "tight" defines crop being determined by imcrop_margin and imcrop_thresh parameters applied to the image. The extend subarray will be derived from image array by finding points greater than threshold multiplied by maximum value. A margin will be added to each side of the extend array.

::

    crop_type = "tight"
    crop_type = "fraction"

- crop_fraction

| Required parameter when crop_type is configured "fraction". Defines size of the cropped array relative to the full image array. The full array is cropped around maximum value.

::

    crop_fraction = [.5, .5, .5]

- crop_margin

| Required parameter when crop_type is configured "tight". The margin will be added to each side of the extend array.

::

    crop_margin = 10

- crop_thresh

| Required parameter when crop_type is configured "tight". The threshold will determine the extend of the array.

::

    crop_thresh = 0.5

- interpolation_mode

| If present the reconstructed object will be interpolated. The parameter defines how the image is interpolated. Supported values: "AmpPhase" and "ReIm". If defined as "AmpPhase" the image amplitudes and image phases are interpolated. If defined as "ReIm" the image real values and imaginary are interpolated, and then the interpolated image amplitudes and image phases are calculated.

::

    interpolation_mode = "AmpPhase"

- interpolation_resolution

| Required parameter for interpolation. Supported values: "min_deconv_res", int value, float value, list. If set to "min_deconv_res" the resolution will be determined by including the deconvolution resolution. If defined as integer value the resolution will be set to this value in each dimension. If defined as list, the list will define resolution in corresponding dimension. If set to "min_deconv_res" the resolution capability must be configured by setting the "determine_resolution_type" parameter.

::

    interpolation_resolution = "min_deconv_res"

- determine_resolution_type

| If present, the resolution in direct and reciprocal spaces will be found. Supported value: "deconv".

::

    determine_resolution_type = "deconv"

- resolution_deconv_contrast

| A fraction less than 0, required when "determine_resolution_type" is set to "deconv".

::

    resolution_deconv_contrast = 0.25

- write_recip

| If True the reciprocal_space.vts file will be saved with arrays of phasing data and inverse fourier of that data.

::

    write_recip = True

- Bragg_displacement

| If configured the vts file with image will also include displacement array. Currently supporting a float value and "Q", where the Q vector from the diffractometer is used for the projection of the derivative of displacement field.

::

    Bragg_displacement = "Q"
    Bragg_displacement = 2.33  #nm

- compute strain

| If True the vts file with image will also include strain. For this to work the Bragg_displacement parameter has to be configured.

::

    compute strain = True