User documentation for CTAS Package

As it was mentioned on the main page, the package has advanced command line interface with the main executable called ctas. It is used as the interface to all tools from the package with the following syntax:
@ ctas <tool>

Here is the list of all tools in the package:
tool description
ff Flat field correction.
ct CT reconstruction of one sinogram.
ct-abs All-in-one absorption-based CT reconstruction.
ct-dei All-in-one DEI-based CT reconstruction.
ct-edei All-in-one EDEI-based CT reconstruction.
ct-ipc All-in-one IPC-based CT reconstruction.
ct-line Prototype of the reconstruct-as-acquired approach.
dei DEI contrast processing.
edei EDEI contrast processing.
ipc IPC contrast processing.
f2i Converts float-point image to the integer one.
rc2fd Converts the rocking curve of the analyzer to the function used in the EDEI.
sino Prepares sinogram from the stack of files.
sino-abs Forms absorption-based sinogram(s) using describing file.
sino-dei Forms DEI-based sinogram(s) using describing file.
sino-edei Forms EDEI-based sinogram(s) using describing file.
sino-ipc Forms IPC-based sinogram(s) using describing file.
ts Tomosynthesis reconstruction.
list Lists all existing commands.
help Prints brief help message including the list of all tools with short description of each.
usage Outputs brief usage message

Notes on input/output file formats

The programs from the ctas package use several file formats for the input/otput operations. Basically they are recorded or reconstructed images and text data files which may include strings, numbers, etc. Each file format is described in the manual page of each tool which makes use of it. The package does not use any structured information on it's input and therefore usage of complicated formats (xml, etc.) sounds to be redundant.

Many of the tools included into the package read the images as the input data, process them and output other images. The input images can be of any type supported by the ImageMagick library (see this page for the list). Note that the ImageMagick MUST be compiled with NO HDRI support (details here) because the HDRI support in the ImageMagick is very experimental and writing HDRI images is not reliable for the current moment. Moreover the HDRI support mixes up the write procedure for integer images. I use LibTIFF for writing 32-bit float point images in TIFF format (what may change in future versions if the ImageMagick stabilizes the HDRI support). The data processing in most of the algorithms is performed in the float numbers space and saving the results as an integer value causes the loss of the accuracy. Therefore the results, by default, are always saved as the 32-bit float point TIFF file (regardless of the file extension ot the output file). However, quite a few of the image viewers/editors can work correctly with the HDRI images (I can advice ImageJ). Therefore all the tools which have image output can understand option
short option long option description
-i --int output image in the 16-bit integer format
which forces the output image to be saved in the integer numbers. In this case the format of the image is defined by the extension of the output file (defaulting to TIFF if the extension does not correspond to any output format). The color depth of the image is 16-bit if the format supports it and 8-bit otherwise. The values of the black and white are respectively defined by the minimum and maximum values of the array to be exported to the image. All output images are greyscale, while the input images can be colorful (the value of each pixel is taken into account). The alpha channel (transparency) of the input images is always ignored.

Another disadvantage the ImageMagick is it's low efficiency. The library was developed to support as many formats as possible, providing unified interface to all formats, but the other side of this approach is quite low speed of the I/O operations. It may turn to the strong problem when using lage stacks of the high-resolution images. For example preparing the sinogram of 644 images with the resolution 4008(w) x 2671(h) pixels took approximately 15 minutes on the high-end MacPro workstation (2x QuadCore Xeons + 16Gb DDR2 memory + 15k RPM HDD) under Linux OS. Therefore, when possible I make use of LibTiff and FreeImage projects.

Terminology and abbreviations used in the documentation

term description
CT Computed Tomography.
TS Tomosynthesis.
RC Rocking curve. In most cases refers to the RC of the analyzing crystall in the DEI/EDEI experimental setup.
FD Function derived from the RC used for the EDEI data processing (see function $ F^{-1} $ defined in eq.(3) in [3]).
DEI Diffraction Enhanced Imaging. A method in the X-ray imaging which can separate the apparent absorption and refraction components of the analyzer-based contrast.
EDEI Extended Diffraction Enhanced Imaging: nonlinear extension of the Diffraction Enhanced Imaging.
ROI Region of interest.
CLI Command line interface.
DC Dark current of the detector.
IPC Inline Phase Contrast.
MBA Modified Bronnikov Algorithm.
BAC Bronnikov Aided Correction.
... ... to add more ...