Metadata-Version: 2.1
Name: quantiphyse
Version: 0.9.3.post2
Summary: Quantiphyse is a data viewer and analysis platform for volumetric medical imaging data
Home-page: https://quantiphyse.readthedocs.io/
Author: Martin Craig
Author-email: martin.craig@eng.ox.ac.uk
License: License granted by University of Oxford for use by academics carrying out research and not for use by consumers or commercial businesses. See LICENSE file for more details
Description: # Quantiphyse
        
        Viewer and data processing for 3D/4D medical imaging data
        
        ## Overview
        
        Quantiphyse provides tools for modelling and analysis of 3D/4D volumetric data, principally MRI data. 
        
        Core features:
        - Loading/Saving 3D/4D NIFTI files
        - Analysis tools including single/multiple voxel analysis and data comparison
        - Generic processing including smoothing, resampling, clustering
        
        Features available via plugins
        - Registration, motion correction
        - Modelling tools for DCE, ASL, DSC and CEST MRI
        - Integration of selected FSL tools
        
        See: [http://quantiphyse.readthedocs.org/en/latest/](http://quantiphyse.readthedocs.org/en/latest/) for full documentation.
        
        ## License
        
        Quantiphyse is available free under an academic (non-commercial) license. See the `LICENSE` file for
        full details, and contact [OUI](https://process.innovation.ox.ac.uk/software) if interested in 
        commercial licensing.
        
        ## Installation
        
        See https://quantiphyse.readthedocs.io/en/latest/basics/install.html for current installation
        instructions
        
        ### Running from source code (for developers)
        
        Running from source is recommended only if your are interested in developing the software further.
        
        1. Install the dependencies:
        
        The list of Python dependencies is in `requirements.txt`
        
        For example:
        
            pip install -r requirements.txt
        
        2. Build extensions
        
        `python setup.py build_ext --inplace`
        
        3. Run from source directory
        
        `python qp.py`
        
        ### Packaging
        
        The scripts packaging/build.py is used to build a frozen distribution package in the form of a compressed archive (`tar.gz` or `.zip`) 
        and a platform-dependent package (`deb`, `msi` or `dpg`). It should run autonomously, however you may need to input the sudo password 
        on Linux in order to build a `deb` package. 
        
        The `--snapshot` option removes the version number from package filenames so you can provided them for download without having to change the link URLs.
        
        The `--maxi` option builds a package which includes selected plugins, assuming these are downloaded
        
        ## To Do list
        
        ### Issue tracker
        
        Current issues can be viewed on the GitHub issue tracker (https://github.com/ibme-qubic/quantiphyse/issues)
        
        ### Roadmap
        
        #### v0.6 (Released June 2018)
        
         - ASL tools first version (preprocess, model fit, calibration, multiphase)
         - Improved viewer (full resolution, aligned)
        
        #### v0.8 (Target Mar 2019)
        
         - Integration of selected FSL tools (FLIRT, FAST, BET, FSL_ANAT?)      DONE
         - Improved registration support (apply transform)                      DONE
         - Improved ASL tools based on oxasl (inc. ENABLE, VEASL, DEBLUR)       DONE
         - Fabber T1                                                            DONE
         - Fabber DCE                                                           DONE
         - DSC widget                                                           DONE
         - Improvements to ROI builder - working 'paint' tool                   DONE
         - Motion simulation                                                    DONE
         - Add noise                                                            DONE
        
        #### v1.0 (Target June 2019)
        
         - Stable interface for QpWidget, QpData, Process
         - Python 3                                                             DONE needs testing
         - Support PySide and PySide2 - ideally the latter by default           pyside2 branch needs testing
         - Improved manual data alignment tools                                 PART DONE
         - Otherwise no firm plans yet - selection from 'Vague plans' below
        
        ### Migration to PySide2
        
         - The current implementation uses PySide which is based on Qt4
         - Update to PySide2 when released which uses Qt5
         - Will provide support for HiDPI screens and proper scaling in OSx
         - PyQtgraph is currently the stumbling block as release version does not support Pyside2
         - Current git version has PySide2 modifications but not yet tested
         - Consider move to VisPy if this does not come to fruition
        
        #### Vague Plans for Future
        
         - Refactoring of view classes
           - This is a mess at the moment. Need all view options to be stored as metadata
             and cleaner separation between the ImageView widget and the individual OrthoView
             widgets.
        
         - MoCo/Registration
           - Bartek's MC method
        
         - 3D view
           - Probably not that useful but fun and may be easy(?) with vispy. Reliant on good refactoring of ImageView
           - Application to surfaces (Tom K?)
        
         - Add Jola's texture analysis which sounds cool, whatever it is
        
         - PK modelling validation
           - QIBA in progress
           - QIN
        
         - Simplify/rewrite generic Fabber interface
        
         - Improve memory usage by swapping out data which are not being displayed?
        
         - All widgets which process within ROI should work with the subimage within the bounding box of the
           ROI, not the whole image. 
            - Supervoxels does this already with great performance improvement.
        
         - Support other file formats using NIBABEL.
           - DICOM conversion included where DCMSTACK is available
        
         - Add semiquantitative measures
           - Area under the curve
           - Enhancing fraction
        
         - Simulation tools
           - Fabber test data
           - 'Simulated brain'
        
Platform: UNKNOWN
Classifier: Development Status :: 3 - Alpha
Classifier: Intended Audience :: Science/Research
Classifier: Programming Language :: Python :: 2.7
Classifier: Programming Language :: Python :: 3
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: License :: Free for non-commercial use
Description-Content-Type: text/markdown
