Templates

The templates here are routines to analyze the X-ray tomographic data. It is exemplified by the case of data acquired at ID16A beamline of ESRF, but it can easily adapted to datas from any other beamline.

They consists basically into an step of load the projections data, the main step to be adapted for different beamlines, the implementation of processing step and, finally the saving step. For ID16A data, you should not need to adapt the code.

Tomographic Reconstruction

The tomographic reconstruction of high resolution data is divided in several steps:

  • Processing of the projections, for example, the phase-retrieval for phase contrast imaging, the fluorescence fitting for XRF-tomographic dataset and other.

  • Restoration of the projections in case of phase wrapping or linear phase ramp for phase-contrast imaging, and the normalization of the XRF datasets.

  • Alignment of the stack of projections.

  • Finally, the tomographic reconstruction.

The templates here will then guide you through the steps above. After each step, the files are saved and can be used for the next step. All the files, except Tiff conversion, are saved in HDF5 format. For the analysis, it is important to have the latest version of Python packages. For people working with data from ID16A and with access to beamline computing resources, this can be obtained by using the ID16A Python environment, which is activated by typing py3venv_on on the Linux prompt.

The python scripts can be run from shell, from ipython or from Jupyter notebook. This dependes on the user`s preference. For illustration purposes only, the description below supposes you will launch the scripts from shell.

Loading of the projections

Edit load_projections.py with proper parameters and run

python load_projections.py

The instructions of what to do appear on the screen. It loads either .tif or .edf files. The next step consists of the vertical registration of the projections.

Linear Phase ramp removal

Edit remove_phase_ramp.py with proper parameters and run

python remove_phase_ramp.py

This open a GUI interface with buttons to allow to proceed with the phase ramp removal.

Phase unwrapping

Edit phase_unwrapping.py with proper parameters and run

python phase_unwrapping.py

The instructions of what to do appear on the screen.

Vertical alignment

Edit vertical_alignment.py with proper parameters and run

python vertical_alignment.py

The instructions of what to do appear on the screen.

Derivatives of the Projection

Edit projections_derivatives.py with proper parameters and run

python projections_derivatives.py

The instructions of what to do appear on the screen.

Sinogram inspection

Edit sinogram_inspection.py with proper parameters and run

python sinogram_inspection.py

The instructions of what to do appear on the screen.

Horizontal alignment

Edit horizontal_alignment.py with proper parameters and run

python horizontal_alignment.py

The instructions of what to do appear on the screen.

Tomographic reconstruction

Edit tomographic_reconstruction.py with proper parameters and run

python tomographic_reconstruction.py

The instructions of what to do appear on the screen.

Tiff 8 or 16 bits conversion

This step is only necessary for people who want to have the tomographic slices as tiff rather than as HDF5.

Edit tiff_conversion.py with proper parameters and run

python tiff_conversion.py

The instructions of what to do appear on the screen.