toon 0.15.9
Tools for neuroscience experiments
License: MIT
Keywords: psychophysics neuroscience input experiment

# toon

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[![image](https://img.shields.io/pypi/l/toon.svg)](https://raw.githubusercontent.com/aforren1/toon/master/LICENSE.txt)
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## Description

Additional tools for neuroscience experiments, including:

- A framework for polling input devices on a separate process.
- A framework for keyframe-based animation.
- High-resolution clocks.

Everything should work on Windows/Mac/Linux.

## Install

Current release:

`pip install toon`

Development version:

`pip install -i https://test.pypi.org/simple/ toon --pre`

Or for the latest commit (requires compilation):

`pip install git+https://github.com/aforren1/toon`

See the [demos/](https://github.com/aforren1/toon/tree/master/demos) folder for usage examples (note: some require additional packages).

## Overview

### Input

`toon` provides a framework for polling from input devices, including common peripherals like mice and keyboards, with the flexibility to handle less-common devices like eyetrackers, motion trackers, and custom devices (see `toon/input/` for examples). The goal is to make it easier to use a wide variety of devices, including those with sampling rates >1kHz, with minimal performance impact on the main process.

We use the built-in `multiprocessing` module to control a separate process that hosts the device, and, in concert with `numpy`, to move data to the main process via shared memory. It seems that under typical conditions, we can expect single `read()` operations to take less than 500 microseconds (and more often < 100 us). See [demos/bench_plot.py](https://github.com/aforren1/toon/blob/master/demos/bench_plot.py) for an example of measuring user-side read performance.

Typical use looks like this:

```python
from toon.input import MpDevice
from mymouse import Mouse
from timeit import default_timer

device = MpDevice(Mouse())

with device:
    t1 = default_timer() + 10
    while default_timer() < t1:
        res = device.read()
        # alternatively, unpack immediately
        # time, data = device.read()
        if res:
            time, data = res # unpack (or access via res.time, res.data)
            # N-D array of data (0th dim is time)
            print(data)
            # 1D array of times
            print(time)
```

Creating a custom device is relatively straightforward, though there are a few boxes to check.

```python
from ctypes import c_double

class MyDevice(BaseDevice):
    # optional: give a hint for the buffer size (we'll allocate 1 sec worth of this)
    sampling_frequency = 500

    # this can either be introduced at the class level, or during __init__
    shape = (3, 3)
    # ctype can be a python type, numpy dtype, or ctype
    # including ctypes.Structures
    ctype = c_double

    # optional. Do not start device communication here, wait until `enter`
    def __init__(self):
        pass

    ## Use `enter` and `exit`, rather than `__enter__` and `__exit__`
    # optional: configure the device, start communicating
    def enter(self):
        pass

    # optional: clean up resources, close device
    def exit(self):
        pass

    # required
    def read(self):
        # See demos/ for examples of sharing a time source between the processes
        time = self.clock()
        # store new data with a timestamp
        data = get_data()
        return time, data
```

This device can then be passed to a `toon.input.MpDevice`, which preallocates the shared memory and handles other details.

A few things to be aware of for data returned by `MpDevice`:

- If there's no data for a given `read`, `None` is returned.
- The returned data is a _copy_ of the local copy of the data. If you don't need copies, set `use_views=True` when instantiating the `MpDevice`.
- If receiving batches of data when reading from the device, you can return a list of (time, data) tuples.
- You can optionally use `device.start()`/`device.stop()` instead of a context manager.
- You can check for remote errors at any point using `device.check_error()`, though this automatically happens after entering the context manager and when reading.
- In addition to python types/dtypes/ctypes, devices can return `ctypes.Structure`s (see input tests or the [example_devices](https://github.com/aforren1/toon/tree/master/example_devices) folder for examples).

### Animation

This is still a work in progress, though I think it has some utility as-is. It's a port of the animation component in the [Magnum](https://magnum.graphics/) framework, though lacking some of the features (e.g. Track extrapolation, proper handling of time scaling).

Example:

```python
from math import sin, pi

from time import sleep
from timeit import default_timer
import matplotlib.pyplot as plt
from toon.anim import Track, Player
# see toon/anim/easing.py for all available easings
from toon.anim.easing import LINEAR, ELASTIC_IN

class Circle(object):
    x = 0
    y = 0

circle = Circle()
# list of (time, value)
keyframes = [(0.2, -0.5), (0.5, 0), (3, 0.5)]
x_track = Track(keyframes, easing=LINEAR)

# we can reuse keyframes
y_track = Track(keyframes, easing=ELASTIC_IN)

player = Player(repeats=3)

# directly modify an attribute
player.add(x_track, 'x', obj=circle)

def y_cb(val, obj):
    obj.y = val

# modify via callback
player.add(y_track, y_cb, obj=circle)

t0 = default_timer()
player.start(t0)
vals = []
times = []
while player.is_playing:
    t = default_timer()
    player.advance(t)
    times.append(t)
    vals.append([circle.x, circle.y])
    # sleep(1/60)

plt.plot(times, vals)
plt.show()
```

Other notes:

- Non-numeric attributes, like color strings, can also be modified in this framework (easing is ignored).
- Multiple objects can be modified simultaneously by feeding a list of objects into `player.add()`.

### Utilities

The `util` module includes high-resolution clocks/timers via `QueryPerformanceCounter/Frequency` on Windows, `mach_absolute_time` on MacOS, and `clock_gettime(CLOCK_MONOTONIC)` on Linux. The class is called `MonoClock`, and an instantiation called `mono_clock` is created upon import. Usage:

```python
from toon.util import mono_clock, MonoClock

clk = mono_clock # re-use pre-instantiated clock
clk2 = MonoClock(relative=False) # time relative to whenever the system's clock started

t0 = clk.get_time()
```

Another utility currently included is a `priority` function, which tries to improve the determinism of the calling script. This is derived from Psychtoolbox's `Priority` (doc [here](http://psychtoolbox.org/docs/Priority)). General usage is:

```python
from toon.util import priority

if not priority(1):
    raise RuntimeError('Failed to raise priority.')

# ...do stuff...

priority(0)
```

The input should be a 0 (no priority/cancel), 1 (higher priority), or 2 (realtime). If the requested level is rejected, the function will return `False`. The exact implementational details depend on the host operating system. All implementations disable garbage collection.

#### Windows

- Uses `SetPriorityClass` and `SetThreadPriority`/`AvSetMmMaxThreadCharacteristics`.
- `level = 2` only seems to work if running Python as administrator.

#### MacOS

- Only disables/enables garbage collection; I don't have a Mac to test on.

#### Linux

- Sets the scheduler policy and parameters `sched_setscheduler`.
- If `level == 2`, locks the calling process's virtual address space into RAM via `mlockall`.
- Any `level > 0` seems to fail unless the user is either superuser, or has the right capability. I've used setcap: `sudo setcap cap_sys_nice=eip <path to python>` (disable by passing `sudo setcap cap_sys_nice= <path>`). For memory locking, I've used Psychtoolbox's [99-psychtoolboxlimits.conf](https://github.com/Psychtoolbox-3/Psychtoolbox-3/blob/master/Psychtoolbox/PsychBasic/99-psychtoolboxlimits.conf) and added myself to the psychtoolbox group.

Your mileage may vary on whether these _actually_ improve latency/determinism. When in doubt, measure! Read the warnings [here](http://psychtoolbox.org/docs/Priority).

Notes about checking whether parts are working:

#### Windows

- In the task manager under details, right-clicking on python and mousing over "Set priority" will show the current priority level. I haven't figured out how to verify the Avrt threading parts are working.

#### Linux

- Check `mlockall` with `cat /proc/{python pid}/status | grep VmLck`
- Check priority with `top -c -p $(pgrep -d',' -f python)`