Ericspod Eidolon Versions Save

I have finally ported to Python 3 and PyQt5. This shouldn't be a major change from the user's perspective and script files should all work still if they don't use print.

Other changes:

• Numerous bug fixes
• Glyph and other point representations can be rendered per-element now
• A Deformation object can now be created through Create menu to apply manual non-rigid deformation to meshes, this is an alpha feature right now
• Extra tests scripts added
• The Concurrency module now allows @concurrent to be applied to functions which are not imported at starttime, that is those not defined in modules or built-in plugins. This allows concurrent functions to be defined script files, plugins imported later, and in the console. This relies on the decorated function to have a __code__ member.
• Fixes to various plugins
• VTKPlugin can now use Pandas if present to read data into matrices more efficiently
• TextFigure has been added as a way of rendering camera-facing text on screen
• setup.py files cleaned up
• Installation and building information updated to strongly recommend the use of Anaconda/Miniconda to setup the Python environment

This release has these files for fully-contained distributables:

• Eidolon_All_0.5.0.zip -- contains the code and libraries for all platforms but does not have Python included

NOTE: There are a number of issues with PyInstaller I'm still working out so no self-contained application packages yet. Follow the instructions for installation to setup Anaconda/Miniconda or some other Python distro to run Eidolon from the above package.

This version fixes a number of bugs and adds a few minor features:

• A few new unit tests and changes to how unit tests are run
• Python 3 compatibility changes
• A few new routines in ImageAlgorithms relating to motion and masks
• Changes to how ImagePlugin.getImageObjectArray() and processImageNp() function, this is in their respective docstrings
• Fixes to UI classes to handle Qt5/Python3 API differences
• A menu item under "Help" has been added to check the most recent version on Github
• Fixes for mouse wheel handling
• Added key controls in 2D and 3D views
• CardiacMotionPlugin has an analysis section for measuring mask volumes over time
• DicomPlugin can load Dicoms from a zip file
• A number of tweaks to NiftiPlugin to match other changes and fixes
• Removed the UI .py files from src/ui, the .ui files are now read directly (is running from source) or a resource file is made (running from app package)

Eidolon should now work with Python 3 but it will require a recompile of libraries. Some of the requisite libraries may have problems with Python 3, the porting is a work in progress. Eventually Eidolon will use Python 3 by default and the libraries will be compiled in the repo for that version.

This release has 4 files for fully-contained distributables:

• Eidolon_All_0.4.1.zip -- contains the code and libraries for all platforms but does not have Python included
• Eidolon_OSX64_0.4.1.dmg -- OSX .app application containing the Python interpreter and libraries, no Python install needed
• Eidolon_Win64_0.4.1.zip -- Win7/8/10 application containing the Python interpreter and libraries, no Python install needed
• Eidolon_Linux64_0.4.1.zip -- (NOT WORKING: use Eidolon_all_0.4.1.zip or checkout) Linux application containing the Python interpreter and libraries, no Python install needed. This is for Linux versions with glibc 2.19 and up (ie. Ubuntu 14.04). It has only been tested on Ubuntu 14.04 and 16.04 (plus a cursory test on Mint 18) so this is a somewhat experimental package.

This new version adds a few small things and fixes a lot of bigger things. Things changed or added:

• More unit tests and integration with pytest instead of nose
• The segmentation dialog box now has an option to crop a chosen image by the extents of the segmentation
• Fix Cython generated code to make it compatible with Python distributions compiled with and without the --with-fpectl flag (ie. between Anaconda and system Python)
• Image cropping based on motion now works a lot better and is based on using FFT transforms to calculate where movement is found in a cine image
• Figures and other renderer objects have been made more thread-safe so that they can be filled with data and cleaned asynchronously
• F11 toggles full screen mode
• On-going code cleanup
• Other bug fixes

This release has 4 files for fully-contained distributables:

• Eidolon_All_0.4.0.zip -- contains the code and libraries for all platforms but does not have Python included
• Eidolon_OSX64_0.4.0.dmg -- OSX .app application containing the Python interpreter and libraries, no Python install needed
• Eidolon_Win64_0.4.0.zip -- Win7/8/10 application containing the Python interpreter and libraries, no Python install needed
• Eidolon_Linux64_0.4.0.zip -- Linux application containing the Python interpreter and libraries, no Python install needed. This is for Linux versions with glibc 2.19 and up (ie. Ubuntu 14.04). It has only been tested on Ubuntu 14.04 and 16.04 (plus a cursor test on Mint 18) so this is a somewhat experimental package.

Various fixes including how Dicom files are exported, how CHeart file times was done, some code cleanup, and adding experimental X4DF file format (ignore this for now).

One important change with the LV segmentation feature is that the AHA region assignment begins on the plane where the RV anterior attachment point is. If there are segmentations above this plane (ie. towards the valves) the geometry in this area will be assigned to a non-AHA region. This allows part of the geometry to be ignored when performing region-based calculations like strain, thickness, displacement, etc.

This release has 4 files for fully-contained distributables:

• Eidolon_All_0.3.3.zip -- contains the code and libraries for all platforms but does not have Python included
• Eidolon_OSX64_0.3.3.dmg -- OSX .app application containing the Python interpreter and libraries, no Python install needed
• Eidolon_Win64_0.3.3.zip -- Win7/8/10 application containing the Python interpreter and libraries, no Python install needed
• Eidolon_Linux64_0.3.3.zip -- Linux application containing the Python interpreter and libraries, no Python install needed. This is for Linux versions with glibc 2.19 and up (ie. Ubuntu 14.04). It has only been tested on Ubuntu 14.04 and 16.04 so this is a somewhat experimental package.

Various fixes have been made for this release.

This release has 4 files for fully-contained distributables:

• Eidolon_All_0.3.2.zip -- contains the code and libraries for all platforms but does not have Python included
• Eidolon_OSX64_0.3.2.dmg -- OSX .app application containing the Python interpreter and libraries, no Python install needed
• Eidolon_Win64_0.3.2.zip -- Win7/8/10 application containing the Python interpreter and libraries, no Python install needed
• Eidolon_Linux64_0.3.2.zip -- Linux application containing the Python interpreter and libraries, no Python install needed. This is for Linux versions with glibc 2.19 and up (ie. Ubuntu 14.04). It has only been tested on Ubuntu 14.04 and 16.04 so this is a somewhat experimental package.

Various fixes have been made for this release. A few UI elements have been changed as well especially in the CardiacMotionPlugin.

This release has 4 files for fully-contained distributables:

• Eidolon_All_0.3.1.zip -- contains the code and libraries for all platforms but does not have Python included
• Eidolon_OSX64_0.3.1.dmg -- OSX .app application containing the Python interpreter and libraries, no Python install needed
• Eidolon_Win64_0.3.1.zip -- Win7/8/10 application containing the Python interpreter and libraries, no Python install needed
• Eidolon_Linux64_0.3.1.zip -- Linux application containing the Python interpreter and libraries, no Python install needed. This is for Linux versions with glibc 2.19 and up (ie. Ubuntu 14.04). It has only been tested on Ubuntu 14.04 and 16.04 so this is a somewhat experimental package.

Additions:

• MIRTK used for applying transformations, motion tracking with non-rigid registration, image align and rigid registration still with IRTK
• History file for console
• Added motion tracking to measurements. This plugin is still a work in progress but the goal is to have a generic way of measuring properties in images, for now it's just displacement, area, circumference, length.

Bug fixes:

• Deleting TextFigure objects no longer deletes the "BaseWhite" material used as the internal default
• Fixed how config files are read to prioritize values in the .eidolon directory
• Setting path related variables correctly in IRTKPluginMixin

This release has 4 files for fully-contained distributables:

• Eidolon_All_0.3.0.zip -- contains the code and libraries for all platforms but does not have Python included
• Eidolon_OSX64_0.3.0.dmg -- OSX .app application containing the Python interpreter and libraries, no Python install needed
• Eidolon_Win64_0.3.0.zip -- Win7/8/10 application containing the Python interpreter and libraries, no Python install needed
• Eidolon_Linux64_0.3.0.zip -- Linux application containing the Python interpreter and libraries, no Python install needed. This is for Linux versions with glibc 2.19 and up (ie. Ubuntu 14.04). It has only been tested on Ubuntu 14.04 and 16.04 so this is a somewhat experimental package.

A few bug fixes including rigid registration dialog, motion tracking in the context of the strain calculations,and some UI cleanup.

This release has 3 files for fully-contained distributables:

This release has 3 files for fully-contained distributables:

• Eidolon_All_0.2.2.zip -- contains the code and libraries for all platforms but does not have Python included
• Eidolon_OSX64_0.2.2.dmg -- OSX .app application containing the Python interpreter and libraries, no Python install needed
• Eidolon_Win64_0.2.2.zip -- Win7/8/10 application containing the Python interpreter and libraries, no Python install needed

This includes a few bug fixes in the UI and allowing transparent screenshots with supported image formats such as png. As usual this release includes application packages for Windows and OSX plus the all inclusive zip file which doesn't have the Python interpreter.

This new release doesn't add anything significant but fixes a number of issues:

• Radial, circumferential, and longitudinal directions on meshes are calculated correctly
• Strain is calculated properly now
• Track directories will now get a track.ini file which contains a lot more info about the tracked image, enough that the original image doesn't need to be referenced any more when using the track info, so the "source" boxes will get removed from the UI soon. Older tracking directories without this file will cause the project to ask the user to identify which image was tracked to produce that data.
• Cython fixes to get the newer versions to work, through some quirk some ambiguities with *Matrix add/sub/div/mul were working when they shouldn't have
• Deadlock bug with AlgorithmProcess.sync() fixed, this was causes tasks to hang forever in some cases
• Reorganizing code into packages in the correct Pythonic way
• ImageAlignPlugin now called CardiacMotionPlugin
• Numerous minor fixes

This release has 3 files for fully-contained distributables:

• Eidolon_All_0.2.0.zip -- contains the code and libraries for all platforms but does not have Python included
• Eidolon_OSX64_0.2.0.dmg -- OSX .app application containing the Python interpreter and libraries, no Python install needed
• Eidolon_Win64_0.2.0.zip -- Win7/8/10 application containing the Python interpreter and libraries, no Python install needed