diff --git a/README.md b/README.md index a454a2c2a96b9180490bb8e6ff159d2e95d73f2a..ca913ad304be60d46aaff73ae7acf4665c2174c0 100644 --- a/README.md +++ b/README.md @@ -1,13 +1,9 @@ AmpScan ======= -AmpScan is a Python package that provides matrix manipulation tools specifically for -the design of prosthetic sockets. It provides functions for handling common design workflows -such as importing, aligning and registering meshes. AmpScan relies heavily on [NumPy](http://www.numpy.org/) -and [SciPy](https://www.scipy.org/) to perform mathematical operations with vizualisation handled by -[PyQt](https://riverbankcomputing.com/software/pyqt/intro) and [VTK](https://www.vtk.org/). The package is -still under development by researchers at the University of Southampton. For full documentation, -visit the [AmpScan website](https://ampscan.readthedocs.io/en/latest/). +AmpScan is an open-source Python package for analysis and visualisation of digitised surface scan data, specifically for applications within Prosthetics and Orthotics. These industries are increasingly using surface scanners as part of clinical practice to capture the patient's individual geometry to design personalised devices. AmpScan gives researchers within this field access to powerful tools to analyse the collected scans to help inform clinical practice towards improved patient-outcomes. This package has been designed to be accessible for researchers with only a limited knowledge of Python. Therefore, analysis procedures can all be accessed using the lightweight Graphical User Interface. + +AmpScan relies heavily on [NumPy](http://www.numpy.org/) and [SciPy](https://www.scipy.org/) to perform mathematical operations with visualisation handled by [PyQt](https://riverbankcomputing.com/software/pyqt/intro) and [VTK](https://www.vtk.org/). The package is still under development by researchers at the University of Southampton. For full documentation, visit the [AmpScan website](https://ampscan.readthedocs.io/en/latest/). Installing with Conda (Recommended) ----------------------------------- diff --git a/joss/paper.md b/joss/paper.md index 28b59d7e63195304562ba2aa8fd147f6d120dba1..40f266a1258fe5d14f19cad3c14c5b3513eba469 100644 --- a/joss/paper.md +++ b/joss/paper.md @@ -5,7 +5,7 @@ bibliography: paper.bib --- # Summary -The increasing accessability of digitised surface scanners are incresingly used. In particular, these devices are being used with prosthetics and orthotics clinics where they are used to capture the patients individual geometry. These scans are imported into computer-aided design packages in order to generate patient-specific medical devices. Despite this, the analysis performed on these scans is limited. +The increasing accessibility of digitised surface scanners are increasingly used. In particular, these devices are being used with prosthetics and orthotics clinics where they are used to capture the patients individual geometry. These scans are imported into computer-aided design packages in order to generate patient-specific medical devices. Despite this, the analysis performed on these scans is limited. In a previously published paper [@Dickinson:2016], a method was detailed for comparing between pairs of surface scans using alignment, registration and visualisation. In this paper, this method was used for evaluation of the accuracy and inter- and intra-reliability of the scanners. Further studies have also demonstrated using this package for comparing the consistency of casting techniques [Dickinson: ], statistical shape modelling across the population [@Worsley: ISPO World] and quantifying rectifications between the residual limb and the prosthetic socket [@Steer: AOPA]. @@ -15,11 +15,10 @@ Further, several researchers have indicated an interest in using these scanners The AmpScan package has been designed with clinical researchers in mind, with an appreciation that they may not have an extensive knowledge of code. To this aim, this software has been developed in Python and leverages the commonly used libraries of NumPy, SciPy, matplotlib, vtk and pyqt. As such full functionality of the software can be utlisied without requiring additional installs such as CMake. The core analysis of the package can be carried out with, additionally, a simple GUI has been supplied to allow the user to access the core functionality of AmpScan without scripting. -In general, the core process for analysis of the scans involves: -1) Import of the baseline STL file as an AmpObject -2) Import of the target STL file as an AmpObject +The core functionality of AmpScan is summarised below with a more detailed description available in the online [documentation](https://ampscan.readthedocs.io/en/latest/): +- The [AmpObject](https://ampscan.readthedocs.io/en/latest/source/AmpScan.html#AmpScan.core.AmpObject), this is the key object of the package and holds the key data and methods. The key data held within the AmpObject is the mesh data including arrays of the vertices, faces, normals and field values. Additionally, the vtk actor for visualisation is also stored. The [core](https://ampscan.readthedocs.io/en/latest/source/core.html) methods of the AmpObject include imports for .stl files, saving .stl files, rotation and translation. Additional methods are added via mixins for [analysis](https://ampscan.readthedocs.io/en/latest/source/analyse.html), [smoothing](https://ampscan.readthedocs.io/en/latest/source/smooth.html), [trimming](https://ampscan.readthedocs.io/en/latest/source/trim.html) and [visualisation](https://ampscan.readthedocs.io/en/latest/source/ampVis.html). -Other packages perform the specific tasks of AmpScan more comprehensively such as [mayavi](https://docs.enthought.com/mayavi/mayavi/index.html) for scientfic data visualisation, [open3d](http://www.open3d.org/docs/getting_started.html) for alignment and registration techniques. We encourage researchers who have developed their own alignment and registration algorithms in python, further the package does not contain any mesh fixing tools that may be required from messy scans. Until such methods are implemented, the authors recommend [meshlab](http://www.meshlab.net/) which also contains methods for alignment and visualisation. +Other packages perform the specific tasks of AmpScan more comprehensively such as [mayavi](https://docs.enthought.com/mayavi/mayavi/index.html) for scientific data visualisation, [open3d](http://www.open3d.org/docs/getting_started.html) for alignment and registration techniques. We encourage researchers who have developed their own alignment and registration algorithms in python, further the package does not contain any mesh fixing tools that may be required from messy scans. Until such methods are implemented, the authors recommend [meshlab](http://www.meshlab.net/) which also contains methods for alignment and visualisation.