Data Formats and File Layout

pyPhase can handle hdm5, tiff and edf files.

Tiff and Edf directory layout

Projects using tiff or edf data must be organized as follows:

  • A directory/folder name_ (project's name followed by and underscore symbol) in the project's root. The the phase retrieval's resulting files are output to this location.

  • The directory name_ shall contain a parammeter file, named phase_parameter.yml.

  • Directories name_1_, name_2_, ..., name_N_, containing the projection images for each distance N.

  • Each of the directories name_N_ contains M tiff (or edf) files named name_N_000M.tif (name_N_000M.edf respectively).

  • Each directories name_1_, name_2_, ..., name_N_ shall also contain dark and reference image files necessary for flat-field correction.

Note: Make sure that to use the same name when you instantiate DataSet objects.

Data Layout Example

Bellow is an example of a directory structure, for a project named holosim, with data for 3 distances, with 2 projections (each).

HoloSim
│
└───holosim_
│       phase_parameters.yml
│       [output files]
│       
└───holosim_1_
│       refHST0000.edf
│           
│       holosim_1_0000.edf
│       holosim_1_0001.edf
│
└───holosim_2_
│       holosim_2_0000.edf
│       holosim_2_0001.edf
│
└───holosim_3_
        holosim_3_0000.edf
        holosim_3_0001.edf

Parameter File

A parameter file, named pyphase_parameter.yml can be to the your_project_path/name_ directory. If the file does not exist, pyPhase will try to find the parameters in the projects .info and '.xmlfiles. Thepyphase_parameter.yml` file has the following parameters (the values are shown as an example):

axis_position: 256.5
distances: [0, 0.18, 0.38, 0.918]
dss: 145
energy: 24
nD: 4
nbprojections: 1200
distance_number: [1, 2, 3, 4]
nx: 512
ny: 512
pixel_size: 7.5
reference_interval: 300
reference_plane: 1
scan_range: 360

This file can be edited to change the any of the parameters. May be particularly useful when choosing the number of distances to use.

Dark and Reference Images

Each directory name_1_, name_2_, ..., name_N_ shall contain

  • a dark.tif (or dark.edf) containing a dark frame
  • Files refHST0000.tif (or refHST0000.edf) containing the reference (flat-field) images, one per

for flat field correction. The numbering of the re