Usage

Examples

Command Line Interface

tomocupy includes a commad-line-interface (CLI). The simplest way to set a reconstruction parameter is to directly pass it as an option to the tomocupy command. Some options also accept an argument, while others simple enable certain behavior. Parameters given directly via the command line will override those given via a parameter file or global configuration file.

To list all the options supported by the tomocupy CLI, after installing tomocupy, type:

(tomocupy)$ tomocupy -h
(tomocupy)$ tomocupy recon -h
(tomocupy)$ tomocupy recon_steps -h

Below are different reconstruction examples

Try center

(tomocupy)$ tomocupy recon --file-name data/test_data.h5 --nsino-per-chunk 4 --reconstruction-type try --center-search-width 100

Full volume

(tomocupy)$ tomocupy recon --file-name data/test_data.h5 --nsino-per-chunk 4 --rotation-axis 700 --reconstruction-type full

Double FOV

(tomocupy)$ (tomocupy)$ tomocupy recon --file-name data/test_data.h5 --nsino-per-chunk 4 --rotation-axis 700 --reconstruction-type full --file-type double_fov

Full volume rec with phase retrieval

(tomocupy)$ tomocupy recon_steps --file-name data/test_data.h5 --nsino-per-chunk 4 --rotation-axis 700 --reconstruction-type full --energy 20 --pixel-size 1.75 --propagation-distance 100 --retrieve-phase-alpha 0.001 --retrieve-phase-method paganin --reconstruction-type full

Laminographic try

(tomocupy)$ tomocupy recon_steps --file-name data/test_data.h5 --nsino-per-chunk 8 --nproj-per-chunk 8 --reconstruction-type try --center-search-width 100 --lamino-angle 20

Laminographic try angle

(tomocupy)$ tomocupy recon_steps --file-name data/test_data.h5 --nsino-per-chunk 8 --nproj-per-chunk 8 --rotation-axis 700 --reconstruction-type try_lamino --lamino-search-width 2 --lamino-angle 20

Laminographic full rec

(tomocupy)$ tomocupy recon_steps --file-name data/test_data.h5 --nsino-per-chunk 8 --nproj-per-chunk 8--reconstruction-type full --rotation-axis 700 --lamino-angle 20

Reconstruct APS data

This section contains the readrec_aps script.

Download file: readrec_aps.py

import sys
import pathlib
import dxchange
import tomocupy

from tomocupy.dataio import reader
from tomocupy.dataio import writer
from tomocupy.global_vars import args

def read_aps(fname):

    _, meta_dict = dxchange.read_hdf_meta(fname)

    params_dict = {}
    for section in tomocupy.config.RECON_STEPS_PARAMS:
        for key, value in tomocupy.config.SECTIONS[section].items():
            key = key.replace('-', '_')
            params_dict[key] = value['default']

    # create a parameter object identical to the one passed using the CLI
    global args
    args.__dict__.update(params_dict)
    
    # set only the parameters that are different from the default
    args.reconstruction_type          = 'try'
    args.file_name                    = fname
    args.rotation_axis_auto           = 'auto'
    args.out_path_name                = '/data/tmpfdc/' 
    args.clear_folder                 = True
    args.fbp_filter                   = 'shepp' 
    args.retrieve_phase_method        = None 
    args.remove_stripe_method         = 'vo'
    args.pixel_size                   = meta_dict['measurement_instrument_detection_system_objective_resolution'][0] * 1e-4
    args.propagation_distance         = meta_dict['measurement_instrument_detector_motor_stack_setup_z'][0]
    args.energy                       = meta_dict['measurement_instrument_monochromator_energy'][0]
    args.retrieve_phase_alpha         = 0.0008

def main():

    if len(sys.argv) == 1:
        print ('ERROR: Must provide an hdf file name')
        print ('Example:')
        print ('        python readrec_aps.py /data/aps_dataset.h5')
        sys.exit(1)
    else:
        file_name = sys.argv[1]
        p = pathlib.Path(file_name)
        if p.is_file():
            read_aps(file_name)
            
            cl_reader = reader.Reader()
            cl_writer = writer.Writer()

            clrotthandle = tomocupy.FindCenter(cl_reader)
            args.rotation_axis = clrotthandle.find_center()*2**args.binning
            print(f'set rotaion  axis {args.rotation_axis}')

            clpthandle = tomocupy.GPURec(cl_reader, cl_writer)
            clpthandle.recon_all()

            print('Done!')


        else:
            print('ERROR: %s does not exist' % p)
            sys.exit(1)


if __name__ == "__main__":
   main()