Read and analyse CCD FLI images

Requirements

GIT version control system ≥ 1.7

Python Distribute for installing the python scripts

Numpy for calculations

h5py storing and reading the images

skimage for the pitch.py script.

TOMCAT's gridrec only for the tomographic reconstruction

Report Bugs & Request Features

please report any bug or feature request using the issues webpage.

Download

:::bash
git clone https://bitbucket.org/Enucatl/readimages.git

or

:::bash
git clone [email protected]:Enucatl/readimages.git

Install

:::bash
python setup.py develop

if you do not have root permissions, you can still install it by appending the --user flag.

Programmes

Use the -h flag to get help.

View CCDFLI raw files

read a single file

• ccdfli_viewer.py

Make HDF5 file

reads all images in a folder and convert them from RAW to HDF5. This file is then used in all the other scripts.

• make_hdf5.py

X-ray flux analysis

• intensity_scan.py: plot the integral in the image as a function of the image number.

Analyse stacks

The easiest way to reconstruct a 2D image out of 1D lines is to stack the lines together. More tools are then provided to analyse the stack:

• projection_stack.py: make the stacked image.
• export_stack.py: save the stacked image in a different format (default: png).

Alignment tools

• pitch.py: rotation about the y axis.

Differential phase contrast

The differential phase contrast images can be calculated from phase stepping scans:

• dpc_radiography.py: reconstruct the absorption, differential phase, and visibility reduction images.
• phase_drift.py: show the drift of the phase values during a scan.
• visibility_map.py: draw a graph with the visibility as a function of the pixel in the detector.
• dpc_scan.py: reconstruct the scan taken with the dpc scan SPEC macro

Tomographic reconstruction

Reconstruct a dataset with gridrec.

• ct_reconstruction.py: reconstruct a dataset with gridrec.