brainglobe / brainglobe/brainrender

Actor subclasses [Enhancement]

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enhancement
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Description

I was planning to overhaul the documentation for the `Actor` subclasses. However, this turned out to be more complex than anticipated, so that I have now run out of the time that I am able to contribute for the moment. Below hence three items:

1. A text dump of the documentation that I have already written.
2. Some general suggestions on how I would structure the documentation.
3. Comments on the actor subclasses code.

I hope some of these will be useful.

# A actors.md draft

Objects in 3D renderings are computationally represented as sets of 3D coordinates that form dense meshes, which delineate the surface of the object. Standard neurobiological data formats, however, typically do not specify the surface of their objects directly. For example, an SWC file specifies the morphology of a neuron as a graph of segments, with each segment being represented as a truncated cone with a start point, a diameter at the start point, an end point, and a diameter at the endpoint. So while this specification clearly implies a surface, it does not contain any explicit surface information. Actors in `brainrender` are classes that implement this transformation, i.e. they map user-provided numerical data to [`vedo Mesh`](https://vedo.embl.es/) objects, which can then be rendered.

Available actors are:

* `Point(pos, name, radius, color, alpha, res)`: render a (anterior-posterior, dorsal-vental, medial-lateral) point coordinate as a sphere with a specified name, radius, color, opacity, and resolution. The name is a string used as a handle, when modifying the scene. A color can be a valid matplotlib or VTK color specification, which includes the [standard named web colors](https://en.wikipedia.org/wiki/Web_colors) derived from the [CSS Color Module Level 3 standard](https://www.w3.org/TR/css-color-3/), hex codes, and RGB tuples. The opacity `alpha` is a float between 0 and 1. The integer resolution determines the density of the created mesh. Higher densities result in smoother surfaces (but are computationally more resource intensive).

``` python
from brainrender import Scene
from brainrender.actors import Point

s = Scene()
s.add(Point((1000, 2000, 3000), radius=100, color="blue", alpha=0.33, res=20))
s.add(Point((4000, 5000, 6000), radius=200, color="#ff0000", alpha=0.66, res=10))
s.add(Point((7000, 8000, 9000), radius=400, color=(0, 255, 0), alpha=1., res=5))
s.render()
```

* `Points(data, name, colors, alpha, radius, res)`: convenience class to render multiple `Point` actors at once. The `data` argument is either an (N, 3) numpy array or a filepath. `radius` and `colors` (plural!) are single floats and valid color specifications, respectively, or lists thereof matching the length of the coordinate array. Due to limitations in upstream packages, however, `radius` and `colors` cannot both be sequences. Other parameter specifications are as for `Point`

``` python
import numpy as np
from brainrender import Scene
from brainrender.actors import Points

s = Scene()

# supported: single radius, single color
s.add(Points(np.array([[1000, 2000, 3000], [4000, 5000, 6000]]), radius=100, colors="blue"))

# supported: multiple radii, single color
s.add(Points(np.array([[1000, 2000, 3000], [4000, 5000, 6000]]), radius=[50, 100], colors="blue", alpha=1))

# supported: multiple colors, single radius
s.add(Points(np.array([[1000, 2000, 3000], [4000, 5000, 6000]]), radius=100, colors=[blue", "red"], alpha=1))

# not supported: multiple radii, multiple colors
# s.add(Points(np.array([[1000, 2000, 3000], [4000, 5000, 6000]]), radius=[50, 100], colors=["blue", "red"], alpha=1))

# supported: import coordinates from .npy file
s.add(Points("/path/to/coordinates.npy", radius=100, color="blue"))

s.render()
```

* `Line(coordinates, color, alpha, linewidth, name)`: render an (N, 3) numpy array of (anterior-posterior, dorsal-vental, medial-lateral) point coordinates as a line. `linewidth` is a float; other parameter specifications are as for `Point`.

```python
import numpy as np
from brainrender import Scene
from brainrender.actors import Line

s = Scene()
s.add(Line(np.array([[1000, 2000, 3000], [4000, 5000, 6000]]), linewidth=10))
s.render()
```

* `Volume(griddata, voxel_size, cmap, min_quantile, min_value, name, as_surface)`: render volumetric data (e.g. gene expression) from a numpy array or from a .npy file.

* `Neuron(data, color, alpha, neurite_radius, soma_radius, name)`: render neuron morphology data from a `MorphoNeuron` object (e.g. instantiated with `morphapi`) or from a .swc file.

* `Streamlines`

* `Cylinder`

* `Ruler`

# General comments on the documentation

The documentation currently is a weird in-between of a reference and a tutorial, which makes it unhelpful to both audiences, experienced developers and first-time users. Its structure strongly mirrors the structure of the code. However, while it compiles an inventory of available classes and methods, it lacks sufficient detail to be a useful reference. The style is colloquial but it contains no examples and the order in which material is covered doesn't mirror a typical workflow, so it's not a particular useful tutorial either.

To address this tension, I would split the documentation in two: a reference, preferably compiled from overhauled doc-strings, and a guided tour with many, simple examples that covers the topics in the order in which a first time user needs to know about them. For the latter, I would suggest the following structure:

```
0. Installation

1. Instantiating a `Scene` with a reference atlas

1.1 Basic invocation
1.2 Available atlases
1.3 Highlighting brain regions

2. Adding experimental data

2.1 Registering data to the reference atlas
2.2 Adding actors to a scene
2.3 Available actors
2.4 Manipulating actors

3. Rendering & exporting

3.1 Basic invocation
3.2 Cameras
3.3 Export to PNG or HTML
3.4 Animations

4. Known issues

4.1 Notebooks
4.2 IPython

```

# Code comments

## General comments

Actor arguments are in dire need of standardisation:

- argument order varies widely between actors
- most variables have proper names but some don't (`res`, `s`)
- some actors have a `res` parameter even though probably most could/should
- there are subtle naming differences and inconsistencies:

`Point` has the `color` argument, but `Points` has `colors` even though `colors` can be a single color specification. Both have the argument `radius`, which, however, can also be a sequence in `Points` (albeit an undocumented feature)!

## Actor-specific

### `Neuron`

IIRC, the SWC file standard supports neurite segment start and end thicknesses and soma diameters. As far as I can tell, the implementation, however, does not appear to expect/use that information. If that assessment is mistaken, `neurite_radius` and `soma_radius` should probably be called something else (`default_neurite_radius`, etc?).

### `Volume`

The `min_quantile`/`min_value` argument pair is very difficult to communicate. I would either have a single `threshold` argument (and let the user compute percentiles). Or, I would follow `vedo` and have `vmin`/`vmax` arguments, which would pair better with `cmap` and additionally lean on people's familiarity with matplotlib.

### `Streamlines`

There is no documentation anywhere on what the basic streamlines data structure entails. Even the `examples/streamlines.py` file downloads data from the ABA. This makes it quite difficult to document the class.

### `ruler` & `ruler_from_surface`

Why are these functions when all other actors are classes?

Also, I would remove the `unit` and `unit_scale` arguments and hardcode "micrometers" as `unit`. Currently, coordinates are implicitly in micrometers, but the default `unit` is the empty string, and the `unit_scale` is 1, neither of which communicates this to the user. I would remove the arguments as everything about them is confusing and near-impossible to communicate.

### `Cylinder`

Currently, cylinders are hard-coded to be vertical (unless I am missing something). Making the second argument another 3d coordinate (instead of `Scene.root`) would make this class a lot more flexible and easier to explain.

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