image_to_hdf

The image_to_hdf function converts image data into a hdf representation suitable for 3D analysis.

Some analyses may require the extraction of voxel data contained within an hdf file and conversion to an internal Python type. One extension of this application is the direct conversion of an image stack into a HDF, which may be utilized for instance analysis.

The image_to_hdf functionality is provided as a command line interface. A HDF file can be produced from a folder of images.

Contents of image_to_hdf.yml:

cli_entry_points:
- image_to_hdf

semantic_images_dir: tests/data/letter_f
semantic_images_type: .tif
semantic_imagestack_name: letter_f_test

voxel_size:
  dx: 1.0
  dy: 1.0
  dz: 1.0
origin:
  x0: 0.0 # (float), real space units of the origin in x
  y0: 0.0 # (float), real space units of the origin in y
  z0: 0.0 # (float), real space units of the origin in z
pixel_units: "voxel"

out_dir: recon3d/data/temp
h5_filename: letter_f_test

image_to_hdf image_to_hdf.yml produces:

Success: database created from file: image_to_hdf.yml
key, value, type
---, -----, ----
cli_entry_points, ['image_to_hdf'], <class 'list'>
semantic_images_dir, tests/data/letter_f, <class 'str'>
semantic_images_type, .tif, <class 'str'>
semantic_imagestack_name, letter_f_test, <class 'str'>
voxel_size, {'dx': 1.0, 'dy': 1.0, 'dz': 1.0}, <class 'dict'>
origin, {'x0': 0.0, 'y0': 0.0, 'z0': 0.0}, <class 'dict'>
pixel_units, voxel, <class 'str'>
out_dir, recon3d/data/temp, <class 'str'>
h5_filename, letter_f_test, <class 'str'>
Processing specification file: image_to_hdf.yml
Success: database created from file: image_to_hdf.yml
key, value, type
---, -----, ----
cli_entry_points, ['image_to_hdf'], <class 'list'>
semantic_images_dir, tests/data/letter_f, <class 'str'>
semantic_images_type, .tif, <class 'str'>
semantic_imagestack_name, letter_f_test, <class 'str'>
voxel_size, {'dx': 1.0, 'dy': 1.0, 'dz': 1.0}, <class 'dict'>
origin, {'x0': 0.0, 'y0': 0.0, 'z0': 0.0}, <class 'dict'>
pixel_units, voxel, <class 'str'>
out_dir, recon3d/data/temp, <class 'str'>
h5_filename, letter_f_test, <class 'str'>