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Commit e62d5981 authored by Andi Gerken's avatar Andi Gerken
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Minor documentation updates

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This module defines the command line interface.
All commands have a ``--help`` option to get more info about them in the command line.
## Print
```bash
robofish-io-print example.hdf5
```
Checking out the content of files.
<small>
```
usage: robofish-io-print [-h] [--output_format {shape,full}] path
This function can be used to print hdf5 files from the command line
positional arguments:
path The path to a hdf5 file
optional arguments:
-h, --help show this help message and exit
--output_format {shape,full}
Choose how datasets are printed, either the shapes or the full content is printed
```
</small>
## Evaluate
```bash
robofish-io-evaluate *analysis_type* example.hdf5
```
Show some property of a file.
<small>
```
usage: robofish-io-evaluate [-h] [--names NAMES [NAMES ...]] [--save_path SAVE_PATH]
{speed,turn,orientation,relative_orientation,distance_to_wall,tank_positions,trajectories,evaluate_positionVec,follow_iid} paths [paths ...]
This function can be called from the commandline to evaluate files.
Different evaluation methods can be called, which generate graphs from the given files.
With the first argument 'analysis_type', the type of analysis is chosen.
positional arguments:
{speed,turn,orientation,relative_orientation,distance_to_wall,tank_positions,trajectories,evaluate_positionVec,follow_iid}
The type of analysis.
speed - Evaluate the speed of the entities as histogram.
turn - Evaluate the turn angles of the entities as histogram.
orientation - Evaluate the orientations of the entities on a 2d grid.
relative_orientation - Evaluate the relative orientations of the entities as a histogram.
distance_to_wall - Evaluate the distances of the entities to the walls as a histogram.
tank_positions - Evaluate the positions of the entities as a heatmap.
trajectories - Evaluate the trajectories of the entities.
evaluate_positionVec - Evaluate the vectors pointing from the focal fish to the conspecifics as heatmap.
follow_iid - Evaluate the follow metric in respect to the inter individual distance (iid).
paths The paths to files or folders. Multiple paths can be given to compare experiments.
optional arguments:
-h, --help show this help message and exit
--names NAMES [NAMES ...]
Names, that should be used in the graphs instead of the pahts.
--save_path SAVE_PATH
Filename for saving resulting graphics.
```
</small>
## Trackviewer
```bash
robofish-trackviewer example.hdf5
```
The trackviewer is from a different repository. It was included in the install instructions.
<small>
```
usage: robofish-trackviewer [-h] [--draw-labels] [--draw-view-vectors] [--far-plane FAR_PLANE] [--view-of-agents field of perception number of bins] [--view-of-walls field of perception number of bins]
[--view-of-walls-matches]
[trackset_file]
View RoboFish tracks in a GUI.
positional arguments:
trackset_file Path to HDF5 file containing the tracks to view
optional arguments:
-h, --help show this help message and exit
--draw-labels Whether to draw labels inside the agents' outlines
--draw-view-vectors Whether to draw view vectors to the right of / below the trackfile
--far-plane FAR_PLANE
Maximum distance an agent can see
--view-of-agents field of perception number of bins
--view-of-walls field of perception number of bins
--view-of-walls-matches
```
</small>
\ No newline at end of file
...@@ -153,6 +153,7 @@ If you find bugs or get stuck somewhere, please text `Andi` on Mattermost or by ...@@ -153,6 +153,7 @@ If you find bugs or get stuck somewhere, please text `Andi` on Mattermost or by
In the [Track Format Specification](https://git.imp.fu-berlin.de/bioroboticslab/robofish/track_format/uploads/f76d86e7a629ca38f472b8f23234dbb4/RoboFish_Track_Format_-_1.0.pdf) and in this package there are more possibilities, we don't describe explicitly here. If you want to use any of the following features, please ask Andi: In the [Track Format Specification](https://git.imp.fu-berlin.de/bioroboticslab/robofish/track_format/uploads/f76d86e7a629ca38f472b8f23234dbb4/RoboFish_Track_Format_-_1.0.pdf) and in this package there are more possibilities, we don't describe explicitly here. If you want to use any of the following features, please ask Andi:
Built in robofish.io and not described: Built in robofish.io and not described:
- Multiple sampling frequencies - Multiple sampling frequencies
- Timestamps per timestep - Timestamps per timestep
- Calendar points - Calendar points
...@@ -160,6 +161,7 @@ Built in robofish.io and not described: ...@@ -160,6 +161,7 @@ Built in robofish.io and not described:
- Obstacles - Obstacles
Planned in Track Format but not implemented: Planned in Track Format but not implemented:
- 3D Tracks - 3D Tracks
......
# -*- coding: utf-8 -*- # -*- coding: utf-8 -*-
"""
.. include:: ../../../docs/app.md
"""
# ----------------------------------------------------------- # -----------------------------------------------------------
# Functions available to be used in the commandline to show and validate hdf5
# according to the Robofish track format (1.0 Draft 7). The standard is
# available at https://git.imp.fu-berlin.de/bioroboticslab/robofish/track_format
#
# Dec 2020 Andreas Gerken, Berlin, Germany # Dec 2020 Andreas Gerken, Berlin, Germany
# Released under GNU 3.0 License # Released under GNU 3.0 License
# email andi.gerken@gmail.com # email andi.gerken@gmail.com
......
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