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INSTALLATION.md

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Some help on the installation of required packages

There is a number of software dependences require installation. I suggest creating a conda environment where all packages can be conveniently installed. Some information how to star with conda can be found here and on conda management here.

Get all required scripts and presentations from the dedicated ITT9 PAGE

Installing conda and creating an environment

  1. Download and install Anaconda:selecting Python 3.7 option

  2. Create own conda environment called itt with: conda create -n itt numpy=1.13 python=3.6

  3. In a terminal (In Windows type Anaconda Prompt to initialise a terminal) activate the environment: source activate itt or activate itt for Windows

  4. Now you're ready to install software into your itt environment, do:

    conda install -c astra-toolbox astra-toolbox
conda install pillow=4.1.1
conda install scikit-learn
conda install scikit-image	
conda install matplotlib
conda install -c anaconda h5py	
conda install spyder
conda install -c nexpy nexusformat
conda install ipywidgets
conda install -c pyviz holoviews bokeh
conda install hyperspy -c conda-forge

  5. Install TomoPhantom software for tomographic data modelling:

    conda install -c dkazanc tomophantom

  6. Install TomoRec package for reconstruction, normalisation routines:

    conda install -c dkazanc tomorec

  7. Install CCPi Regularisation toolkit which might be helpful to run some denoising routines for Objects tracking and Dynamic imaging challenges.

  8. Download hyperspy and hyperspy_gui_ipywidgets repositories from https://github.com/pquinn-dls This a modified version of hyperspy used at Diamond

    conda install ccpi-regulariser -c ccpi -c conda-forge - for Linux or

    conda install -c dkazanc ccpi-regulariser - for Windows

Other useful conda commands

  • the list of environments: conda info --envs
  • delete created itt environment: conda remove --name itt --all