KTH-microCT-openCT-conversion

Repository to convert microCT raw output bin-data to openCT format, including correction for dark current, geometry misalignment, phase lag, and light field.

Requirements

The script rely on several python modules, paritculatrly

os
glob
dicom

The dicom module can be most easily installed by easy_install pydicom. Note that the conversion here intends to generate DICOM-CT-PD-format, instead of standard DICOM. For this, the default _dicom_dict.py dictionary in pydicom has to be replaced by the _dicom_dict.py file given in this repository. Generally, this file (to be replaced) can be found in /path/to/lib/python2.7/site-packages/pydicom-0.9.8-py2.7.egg/dicom/.

For the reconstruction, the python library odl is also used.

Files

functions/calibration.py

Utility file for calibrating microCT data, including

RemoveDeadPixel
GeometryCalibration
DarkFieldCalibration
LightFieldCalibration
LogCalibration
PhaseLagCalibration

Note that for GeometryCalibration, pUP and pLEFT corresponds to calibration measurements in the form of dx and -dz, respectively (see thesis by L. di Sopra).

functions/conversion.py

Utility for conversion of microCT data. Header information is hard coded and has to be adjusted to the settings of the microCT (e.g. NumberOfFramesInRotation, DistanceSourceToDetector, etc. all in lines 172-226).

example/DarkCurrentConversion.py

Conversion of acquired dark current images into dicom-format (Dark_Field.dcm). Needs input in the form of the directory where the DC images are located, and a template dicom file (given by default in this directory).

example/LightFieldConversion.py

Conversion of acquired light field images into dicom-format (Light_Field.dcm). Needs input in the form of the directory where the LF images are located, the converted dark current image, and a template dicom file (given by default in this directory).

example/ConvertOneBin.py

Example conversion of one bin-file into openCT-dicom format. NOTE: This does not include correction from DC, LF, etc.

example/ConvertMultipleBins.py

Example conversion of multiple bin-files into openCT-dicom format. NOTE: This does not include correction from DC, LF, etc.

example/ConvertAndCalibrateBins.py

Conversion of microCT bin-files to openCT-dicom. This includes geometry alignment, DC correction, and phase lag. Requires input directories, template file, and dark current dicom.

example/FBP_reconstruction.py

Simple example of coarse FBP reconstruction of generated dcm-data using odl.

Usage

1. Make sure you have the correct _dicom_dict.py in the pydicom-directory.
2. Run DarkCurrentCorrection.py to generate Dark_Field.dcm
3. Run LightFieldCorrection.py to generate Light_Field.dcm
4. Run ConvertAndCalibrateBins.py to convert and calibrate raw bin data
5. Reconstruct using e.g. FBP_reconstruction.py