# Usage and data model

## Usage
Scikit-rt can be used in scripts, to be run from the command line
or to be executed on a batch system; and can be used in
[Jupyter](https://jupyter.org/) notebooks, where interactive features
are enabled for image viewing.  The Scikit-rt installation includes both
[Jupyter Notebook](https://jupyter-notebook.readthedocs.io/en/latest/)
 and [JupyterLab](https://github.com/jupyterlab/jupyterlab).

Scikit-rt is able to load [DICOM](https://www.dicomstandard.org/current)
 data (images, RTDOSE, RTSTRUCT, RTPLAN) and
[NIfTI](https://nifti.nimh.nih.gov/) data (images, dose images,
regions of interest (ROIs) represented as masks), and to convert between them.

## Data model

The different types of radiotherapy data are represented in scikit-rt by
different classes:

- [Image](https://scikit-rt.github.io/scikit-rt/skrt.image.html#skrt.image.Image);
- [Dose](https://scikit-rt.github.io/scikit-rt/skrt.dose.html#skrt.dose.Dose);  
- [ROI](https://scikit-rt.github.io/scikit-rt/skrt.structures.html#skrt.structures.ROI) (region of interest);
- [StructureSet](https://scikit-rt.github.io/scikit-rt/skrt.structures.html#skrt.structures.StructureSet);
- [Plan](https://scikit-rt.github.io/scikit-rt/skrt.dose.html#skrt.dose.Plan).

There are associations between class instances:

- a StructureSet is composed of ROIs, and relates to a specific Image;
- a Plan has constraints relating to a StructureSet;
- a Dose is calculated on the basis of a Plan and the material densities
  represented by an Image.

Data relating to an indidual patient are typically grouped into one or
more studies.  This is represented by the classes:
- [Patient](https://scikit-rt.github.io/scikit-rt/skrt.patient.html#skrt.patient.Patient);
- [Study](https://scikit-rt.github.io/scikit-rt/skrt.patient.html#skrt.patient.Study).

A class diagram for the data model is shown below.

<img src="_static/scikit-rt_data_model.png" alt="Scikit-rt data model" style="width:80%">

## Data loading

The constructors of the classes `Image`, `Dose`, `ROI`, `StructureSet`,
`Plan` each take a boolean parameter `load`.

- If `load` is set to `True` (the default), values of object attributes
  are loaded when the object is created.

- If `load` is set to `False`, values of object attributes are loaded
  by the first call to an object method that accesses an attribute,
  or may be loaded explicitly using the object's `load()` method.

The `Patient` and `Study` create data objects with `load` set to
`False`.  Attributes of these objects should usually be accessed using
their getter methods, rather than directly, as these will ensure
that attribute values have been loaded.  This strategy of loading
data as needed avoids the memory and time costs of loading data
that might not be used.