Installing

Installing in Windows

WinPython HyperSpy installer

Currently, the easiest way to install Atomap is by using the WinPython HyperSpy installer. Firstly download and install the WinPython HyperSpy bundle: HyperSpy-1.3 for Windows 64-bits.

After installing the bundle, there should be a folder in the start menu called “HyperSpy WinPython Bundle”, and this folder should contain the “WinPython prompt”. Start the “WinPython prompt”. This will open a terminal window called “WinPython prompt”, in this window type and run:

pip install atomap

To check everything is working correctly, go to the “HyperSpy WinPython Bundle” and start “Jupyter QtConsole”. This will open a new window. In this window, run:

%matplotlib qt4
import hyperspy.api as hs
import atomap.api as am

If this works, continue with the Finding the atom lattice. If you get some kind of error, please report it as a New issue on the Atomap GitLab.

Alternative Windows installation

If you already have HyperSpy running in an Anaconda Python environment Anaconda environment, Atomap can be installed from the Anaconda prompt (Start menu - Anaconda3), this will open a command line prompt. In this prompt run:

$ pip install atomap

Installing in Linux

The recommended way to install Atomap is using PIP, which is a package manager for python. It is recommended to first install the precompiled dependencies using the system package manager.

HyperSpy is also included as Atomap relies heavily on the modelling and visualization functionality in HyperSpy.

Ubuntu 17.10

$ sudo apt-get install ipython3 python3-pip python3-numpy python3-scipy python3-matplotlib python3-sklearn python3-skimage python3-h5py python3-dask python3-traits python3-tqdm python3-pint python3-dask python3-pyqt4 python3-lxml
$ sudo apt-get install python3-sympy --no-install-recommends
$ pip3 install --upgrade pip
$ pip3 install --user atomap

Ubuntu 16.04

Due to the old version of matplotlib in the repository, the system matplotlib has to be removed. This is due to conflicts between the newer 2.x version in PIP and the older 1.5.x version in the repository.

In addition, due to a recent bug with HyperSpy and matplotlib 2.1.x, matplotlib 2.0.2 has to be installed.

$ sudo apt-get install python3-pip python3-numpy python3-scipy python3-h5py ipython3 python3-natsort python3-sklearn python3-dill python3-ipython-genutils python3-pyqt4
$ sudo apt-get install python3-sympy --no-install-recommends
$ sudo apt-get remove python3-matplotlib
$ pip3 install --user --upgrade pip
$ pip3 install --user matplotlib==2.0.2
$ pip3 install --user atomap

Starting Atomap

To check that everything is working, open a terminal and run ipython3 --matplotlib qt4. In the ipython terminal run:

import hyperspy.api as hs
import atomap.api as am

If this works, continue with the Finding the atom lattice. If you get some kind of error, please report it as a New issue on the Atomap GitLab. Note, having the system and pip version of matplotlib installed at the same might cause an error with matplotlib not finding matplotlib.external. The easiest way of fixing this is by removing the system version of matplotlib.

Development version

Grab the development version using the version control system git:

$ git clone https://gitlab.com/atomap/atomap.git

Then install it using pip:

$ cd atomap
$ pip3 install -e .