Sync with upstream (#8)

* Create initial documentation

* Added tests for functions in Particle Analysis

Added testing functions for the following functions:

-ParticleAnalysis()
-store_image()
-store_maps()
-store_spectrum()
-get_composition()

* Added files for travis

Added travis yml file and requirements file for travis builds.

* Added test for particle list loading

* Update requirements.txt

Changed hyperspy dependency.

* Update requirements.txt

Updated PyQt5 requirements

* Update requirements.txt

* Syntax corrections

Corrected import syntax

* Revert "Syntax corrections"

This reverts commit 600e2bf.

* Updated import syntax

* Update .travis.yml

Added installation in virtual env

* Changed path to parameters file

* Updated the example notebook

* Improve Find Zone-axis procedure and bug fixes

Update find_zoneaxis and particleanalysis in order to more reliably find zone axes from noisy data.

Bug fixed in reading old segmentation parameters.

* Add kernel size for local thresholding

Added option to change the kernel size for local thresholding (was previously set to default 21 pixels).

* Changed max limits in SegUI

Changed the max values for the spin boxes in SegUI. They should now scale with the image size rather than being fixed to 99.

* Added Local Otsu

Added Local Otsu to thresholding options.

* Added (Local + Global) Otsu Threshold

Added Threshold Option that combines the result of the Local and Global Otsu Thresholds.

* Fixed uint8 bug

Fixed bug that would incorrectly scale integer images. Now converts to float before scaling.

* Update find_zoneaxis.py

* Updated requirements for uploading to PyPI

* Update README.md

* Update setup.py

Include check for PyQT5 import to avoid clash with pyqt package in conda.

* Update setup.py

* Updates for building a wheel

Updated file requirements in setup.py nad MANIFEST.in for correctly building.

* Update setup.py

Bug fix

* Update setup.py

* Add radial profile

Added function to plot a radial profile of signals from a particle.

Also added the option of defining the number of bins in the histogram plotters.

* Create requirements.txt

* Update to radial profile plotting

* Fix list issue and add radius marker.

- Finally fixed the issue to do with adding particles to previously created particle lists.
- Added a radius marker to the radial profiles.

* Update Particle Analysis to include zone axis determination

* Set theme jekyll-theme-architect

* Added tests for functions in Particle Analysis

Added testing functions for the following functions:

-ParticleAnalysis()
-store_image()
-store_maps()
-store_spectrum()
-get_composition()

* Added files for travis

Added travis yml file and requirements file for travis builds.

* Added test for particle list loading

* Update requirements.txt

Changed hyperspy dependency.

* Update requirements.txt

Updated PyQt5 requirements

* Update requirements.txt

* Syntax corrections

Corrected import syntax

* Revert "Syntax corrections"

This reverts commit 600e2bf.

* Updated import syntax

* Update .travis.yml

Added installation in virtual env

* Changed path to parameters file

* Updated the example notebook

* Improve Find Zone-axis procedure and bug fixes

Update find_zoneaxis and particleanalysis in order to more reliably find zone axes from noisy data.

Bug fixed in reading old segmentation parameters.

* Add kernel size for local thresholding

Added option to change the kernel size for local thresholding (was previously set to default 21 pixels).

* Changed max limits in SegUI

Changed the max values for the spin boxes in SegUI. They should now scale with the image size rather than being fixed to 99.

* Added Local Otsu

Added Local Otsu to thresholding options.

* Added (Local + Global) Otsu Threshold

Added Threshold Option that combines the result of the Local and Global Otsu Thresholds.

* Fixed uint8 bug

Fixed bug that would incorrectly scale integer images. Now converts to float before scaling.

* Update find_zoneaxis.py

* Updated requirements for uploading to PyPI

* Update README.md

* Update setup.py

Include check for PyQT5 import to avoid clash with pyqt package in conda.

* Update setup.py

* Updates for building a wheel

Updated file requirements in setup.py nad MANIFEST.in for correctly building.

* Update setup.py

Bug fix

* Update setup.py

* Add radial profile

Added function to plot a radial profile of signals from a particle.

Also added the option of defining the number of bins in the histogram plotters.

* Create requirements.txt

* Update to radial profile plotting

* Fix list issue and add radius marker.

- Finally fixed the issue to do with adding particles to previously created particle lists.
- Added a radius marker to the radial profiles.

* Update Particle Analysis to include zone axis determination

* Set theme jekyll-theme-architect

* Add initial documentation source files

* Update .travis.yml

* Update .travis.yml

* Update .travis.yml

* Update .travis.yml

* Update .travis.yml

* Update README.md

* Revamped particle properties and added new properties

Revamped particle properties so that properties are held as a dictionary rather than as separate class members.

Added eccentricity, major and minor axes and equivalent circular diameter to properties.

Added new plot function to particle list that plots a histogram of any particle property.

* Minor corrections

Updated diameter equation and modified property names.

* Fix tests

* Update .travis.yml

* Update doc strings

* Documentation Update

Updated documentation to include page on segmentation.

* Add particle intensity

Added total particle intensity measure.

* Add Particle Analysis Documentation

Author: TomSlater