tomopy-gui is UI for tomopy an open-source Python package for tomographic data processing and image reconstruction.
tomopy-gui is derived from tofu.
This repository contains a customized version of tofu's data processing scripts to be used with the tomopy framework.
First, you must have Conda <http://continuum.io/downloads>_ installed.
Next, install TomoPy and all its dependencies into a new Conda environment
called tomopy by running::
$ conda create --name tomopy --channel conda-forge tomopy
Use this TomoPy installation by activating this environment::
$ conda activate tomopy
then::
$ conda clone https://github.com/tomography/tomopy-gui.git
$ cd tomopy-gui
$ python setup.py install
.. warning:: If your python installation is in a location different from #!/usr/bin/env python please edit the first line of the bin/ufot file to match yours.
Install the following packages:
- conda install -c dgursoy tomopy
- conda install pyqt=4
To do a tomographic reconstruction:
$ ufot rec --last-file $PATH_TO_DATA_EXCHANGE_FILE
from the command line. To get correct results, you may need to append
options such as --center/-c to set the rotation axis position.
$ ufot tomo --center=1024.0 --last-file /local/data.h5
You can get a help for all options by running
$ ufot rec -h
You can also load reconstruction parameters from a configuration file called
ufot.conf. You can create a template with
$ ufot init
Besides scripted reconstructions, one can also run a standalone GUI for both reconstruction and quick assessment of the reconstructed data via
$ ufot gui
