sleap-anipose 0.1.8
SLEAP to Anipose triangulation pipeline for 3D multi-animal pose tracking.
License: BSD 3-Clause License
Keywords: sleap, pose tracking, pose estimation, behavior

# sleap-anipose

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SLEAP to Anipose triangulation pipeline for 3D multi-animal pose tracking.

## Installation
```
pip install sleap-anipose
```

If you are using conda 
```
conda create -n sleap-anipose python=3.8
conda activate sleap-anipose
pip install sleap-anipose
```

### Development
For development, use the following syntax to install in editable mode:
```
conda env create -f environment.yml
```
This will create a conda environment called `sleap-anipose`.

To run tests, first activate the environment:
```
conda activate sleap-anipose
```
Then run `pytest` with:
```
pytest tests
```
To start fresh, just delete the environment:
```
conda env remove -n sleap-anipose
```

## Usage

**From the command line**

1. Activate the conda environment (assuming you installed via conda).
```
conda activate sleap-anipose
```

2. Generate a calibration board matching the details of the board presented before the cameras. 

```
slap-draw_board --board_name my/path/board.jpg --board_x 8 --board_y 11 --square_length 24.0 --marker_length 18.75 --marker_bits 4 --dict_size 1000 --img_width 1440 --img_height 1440 --save my/path/board.toml
```

The draw_board function saves both an image of the board design and a board parameters file. 

The requried `board_name` parameter specifies the path to save the board to, and the file extension can end in any open-cv suitable image format such as `.jpg` and `.png`. 

The required `board_x` and `board_y` arguments specify the number of squares along the width and height of the board respectively. The `square_length` and `marker_length` arguments specify the length of the checkerboard square edges and marker square edges respectively. They can be in any units so long as they are the same. 

The required `marker_bits` and `dict_size` arguments are related to the aruco markers themselves and detail the number of bits used to make each marker and the size of the dictionary that the markers are sampled from. The `image_width` and `image_height` arguments specify the number of pixels along the image width and height respectively. 

Lastly, the `save` argument is an optional input that specifies the path to save a board parameters file to, and it must end in `.toml`. The board parameter file compiles the `board_x`, `board_y`, `square_length`, `marker_length`, `marker_bits`, `dict_size` arguments into a `.toml` file that is then used during the calibration procedure. **This file is mandatory to run calibration**. It is important to note that if the optional `save` parameter is not given, the `.toml` parameter file will not be saved using the `draw_board` function.

If a user already has a board design and only needs to generate the parameters file, the user can take advantage of the write_board function, which takes in the same types of arguments that draw_board does. 

```
slap-write_board --board_name my/path/board.toml --board_x 8 --board_y 11 --square_length 24.0 --marker_length 18.75 --marker_bits 4 --dict_size 1000
```

3. Calibrate your camera setup by displaying the calibration board to all cameras. Make sure to do this before running any experiments. See [`CALIBRATION_GUIDE.md`](docs/CALIBRATION_GUIDE.md) for more information.

4. Track your data using SLEAP. Make sure that animal tracks are matching across multiple views. See [`SLEAP_GUIDE.md`](docs/SLEAP_GUIDE.md) for more information.

5. Set up your data according to [`FOLDER_STRUCTURE.md`](docs/FOLDER_STRUCTURE.md).

6. Generate the calibration for your cameras:
```
slap-calibrate --session my/path --board my/path/board.toml --excluded_views side --excluded_views top --calib_fname my/path/calibration.toml --metadata_fname my/path/calibration_metadata.h5 --histogram_path my/path/reprojection_histogram.png --reproj_path my/path
```

The required `session` argument is a path pointing to the session folder to calibrate. This folder should contain the calibration videos and / or images within its view subfolders. 

The required `board` argument points to the calibration board parameters file that was created with either the draw_board or write_board function. 

The required `calib_fname` argument specifies the path to save the calibration results to and it must end in `.toml`. 

The optional multiple input `excluded_views` argument specifies camera views that are to be excluded from calibration. These arguments are the names for the cameras to be excluded from calibration, not the paths pointing to the view subfolders. To specify more than 1 view, the parameter must be called multiple times as shown above. 

The `metadata_fname` argument specifies the path to save the calibration metadata and it must end in .h5. This file contains some useful information about the board detections that were used for calibration, and more importantly, these board detections can later be used to assess the quality of calibration. **It is important to note that this file will not save unless the user inputs a path to save it to.**

The `histogram_path` argument points to the path to save the histogram of reprojection errors to. Lastly, the `reproj_path` argument points to the session to save the images contrasting calibration board corner detections against reprojected corner positions. **It is important to note that neither of these files will save unless the user inputs a path to save them to.**

8. Generate the triangulated 3D points based on your tracking and calibration:

```
slap-triangulate --p2d my/path --calib my/path/calibration.toml --fname my/path/points3d.h5 --frames 1000 2000 --excluded_views side --excluded_view top --disp_progress True \
--constraints 0 1 --constraints 2 3 --weak_constraints 4 5 --scale_smooth 3 --scale_length 4 --scale_length_weak 1 --reproj_error_threshold 10 --reproj_loss l2 --n_deriv_smooth 2
```

The required `p2d` argument points to the session containing the tracked and proofread files to be used for triangulation. 

The required `calib` argument is a path pointing to the .toml file containing the results of calibration.

The required `fname` argument is the path to save the triangulated points to and it muse end in .h5.

The optional `frames` argument is a tuple covering the range of frames to triangulate (inclusive lower end, exclusive upper end).

The multi-input optional `excluded_views` argument specifies the camera views to exclude in the triangulation process. The only restriction on this feature is that the views used for triangulation must a subset of the views found in the calibration file.  

The optional `disp_progress` argument is a flag that determines whether or not to display the progress of the triangulation procedure (default False). 

Aniposelib has the capability to optimize for spatiotemporal consistency along with accuracy in its optimization process. The user can take full advantage of this feature using the additional keyword arguments shown in the triangulation function. The optional `constraints` and `constraints_weak` arguments detail which edges in the animal skeleton have a fixed length. Whereas the `constraints` argument corresponds to rigid limbs such as arm length in human beings, the `constraints_weak` argument corresponds to more flexible limbs such as the tarsus length in flies. Both are K x 2 arrays, with K being the number of constraints. In the example shown above, `--constraints 0 1 --constraints 2 3` denotes two different rigid limbs, one between nodes 0 and 1, and the other between nodes 2 and 3. The same logic extends to the `constraints_weak` argument, where there is a weak constraint between nodes 4 and 5.

The optional `scale_smooth` argument denotes the weight of temporal smoothing in the optimization procedure, and it is set to 4 by default.

The optional `scale_length` and `scale_length_weak` arguments denote the weight of their respective constraints in the optimization loss function. They are 2 and 0.5 respectively by default.

The triangulation algorithm rejects points that have a reprojection error above the threshold (points are roughly triangulated and reprojection errors are calculated before the final triangulation step is performed), which is denoted by the optional `reproj_error_threshold` argument. This argument is set to 15.0 by default.

The user can change the loss function with the optional `reproj_loss` argument, which is 'soft_l1 by default. See [the scipy least squares documentation](scipy.optimize.least_squares) for more information regarding the loss function options.

Lastly, the optional `n_deriv_smooth` argument details the order of derivative to smooth for in the temporal filtering process, and it is 1 by default. To learn more, refer to the [aniposelib documentation](https://github.com/lambdaloop/aniposelib/tree/master/aniposelib).


**As a script**

```python
import sleap_anipose as slap

slap.draw_board(board_name = 'my/path/board.jpg', 
                board_x = 8, 
                board_y = 11, 
                square_length = 24.0, 
                marker_length = 18.75, 
                marker_bits = 4, 
                dict_size = 1000, 
                img_width = 1440, 
                img_height = 1440, 
                save = 'my/path/board.toml')

cgroup, metadata = slap.calibrate(session = "my/path", 
                                board = "my/path/board.toml", 
                                excluded_views = ('side', 'top'),
                                calib_fname = "my/path/calibration.toml", 
                                metadata_fname = "my/path/calibration.metadata.h5", 
                                histogram_path = "my/path/reprojection_histogram.png", 
                                reproj_path = "my/path")


points3d = slap.triangulate(p2d = 'my/path', 
                            calib = 'my/path/calibration.toml', 
                            frames = (1000, 2000), 
                            excluded_views = ('side', 'top'),
                            fname = 'my/path/points3d.h5', 
                            disp_progress=True, 
                            constraints = [[0,1], [2,3]], 
                            constraints_weak = [[4,5]],
                            scale_smooth = 3, 
                            scale_length = 4, 
                            scale_length_weak = 1, 
                            reproj_error_threshold = 10, 
                            reproj_loss = 'l2', 
                            n_deriv_smooth = 2)
```

*It is important to note that while saving is automatic from the command line, it is optional when running the commands in a script or notebook.*
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received notice of violation of this License (for any work) from that
copyright holder, and you cure the violation prior to 30 days after
your receipt of the notice.

  Termination of your rights under this section does not terminate the
licenses of parties who have received copies or rights from you under
this License.  If your rights have been terminated and not permanently
reinstated, you do not qualify to receive new licenses for the same
material under section 10.

  9. Acceptance Not Required for Having Copies.

  You are not required to accept this License in order to receive or
run a copy of the Program.  Ancillary propagation of a covered work
occurring solely as a consequence of using peer-to-peer transmission
to receive a copy likewise does not require acceptance.  However,
nothing other than this License grants you permission to propagate or
modify any covered work.  These actions infringe copyright if you do
not accept this License.  Therefore, by modifying or propagating a
covered work, you indicate your acceptance of this License to do so.

  10. Automatic Licensing of Downstream Recipients.

  Each time you convey a covered work, the recipient automatically
receives a license from the original licensors, to run, modify and
propagate that work, subject to this License.  You are not responsible
for enforcing compliance by third parties with this License.

  An "entity transaction" is a transaction transferring control of an
organization, or substantially all assets of one, or subdividing an
organization, or merging organizations.  If propagation of a covered
work results from an entity transaction, each party to that
transaction who receives a copy of the work also receives whatever
licenses to the work the party's predecessor in interest had or could
give under the previous paragraph, plus a right to possession of the
Corresponding Source of the work from the predecessor in interest, if
the predecessor has it or can get it with reasonable efforts.

  You may not impose any further restrictions on the exercise of the
rights granted or affirmed under this License.  For example, you may
not impose a license fee, royalty, or other charge for exercise of
rights granted under this License, and you may not initiate litigation
(including a cross-claim or counterclaim in a lawsuit) alleging that
any patent claim is infringed by making, using, selling, offering for
sale, or importing the Program or any portion of it.

  11. Patents.

  A "contributor" is a copyright holder who authorizes use under this
License of the Program or a work on which the Program is based.  The
work thus licensed is called the contributor's "contributor version".

  A contributor's "essential patent claims" are all patent claims
owned or controlled by the contributor, whether already acquired or
hereafter acquired, that would be infringed by some manner, permitted
by this License, of making, using, or selling its contributor version,
but do not include claims that would be infringed only as a
consequence of further modification of the contributor version.  For
purposes of this definition, "control" includes the right to grant
patent sublicenses in a manner consistent with the requirements of
this License.

  Each contributor grants you a non-exclusive, worldwide, royalty-free
patent license under the contributor's essential patent claims, to
make, use, sell, offer for sale, import and otherwise run, modify and
propagate the contents of its contributor version.

  In the following three paragraphs, a "patent license" is any express
agreement or commitment, however denominated, not to enforce a patent
(such as an express permission to practice a patent or covenant not to
sue for patent infringement).  To "grant" such a patent license to a
party means to make such an agreement or commitment not to enforce a
patent against the party.

  If you convey a covered work, knowingly relying on a patent license,
and the Corresponding Source of the work is not available for anyone
to copy, free of charge and under the terms of this License, through a
publicly available network server or other readily accessible means,
then you must either (1) cause the Corresponding Source to be so
available, or (2) arrange to deprive yourself of the benefit of the
patent license for this particular work, or (3) arrange, in a manner
consistent with the requirements of this License, to extend the patent
license to downstream recipients.  "Knowingly relying" means you have
actual knowledge that, but for the patent license, your conveying the
covered work in a country, or your recipient's use of the covered work
in a country, would infringe one or more identifiable patents in that
country that you have reason to believe are valid.

  If, pursuant to or in connection with a single transaction or
arrangement, you convey, or propagate by procuring conveyance of, a
covered work, and grant a patent license to some of the parties
receiving the covered work authorizing them to use, propagate, modify
or convey a specific copy of the covered work, then the patent license
you grant is automatically extended to all recipients of the covered
work and works based on it.

  A patent license is "discriminatory" if it does not include within
the scope of its coverage, prohibits the exercise of, or is
conditioned on the non-exercise of one or more of the rights that are
specifically granted under this License.  You may not convey a covered
work if you are a party to an arrangement with a third party that is
in the business of distributing software, under which you make payment
to the third party based on the extent of your activity of conveying
the work, and under which the third party grants, to any of the
parties who would receive the covered work from you, a discriminatory
patent license (a) in connection with copies of the covered work
conveyed by you (or copies made from those copies), or (b) primarily
for and in connection with specific products or compilations that
contain the covered work, unless you entered into that arrangement,
or that patent license was granted, prior to 28 March 2007.

  Nothing in this License shall be construed as excluding or limiting
any implied license or other defenses to infringement that may
otherwise be available to you under applicable patent law.

  12. No Surrender of Others' Freedom.

  If conditions are imposed on you (whether by court order, agreement or
otherwise) that contradict the conditions of this License, they do not
excuse you from the conditions of this License.  If you cannot convey a
covered work so as to satisfy simultaneously your obligations under this
License and any other pertinent obligations, then as a consequence you may
not convey it at all.  For example, if you agree to terms that obligate you
to collect a royalty for further conveying from those to whom you convey
the Program, the only way you could satisfy both those terms and this
License would be to refrain entirely from conveying the Program.

  13. Use with the GNU Affero General Public License.

  Notwithstanding any other provision of this License, you have
permission to link or combine any covered work with a work licensed
under version 3 of the GNU Affero General Public License into a single
combined work, and to convey the resulting work.  The terms of this
License will continue to apply to the part which is the covered work,
but the special requirements of the GNU Affero General Public License,
section 13, concerning interaction through a network will apply to the
combination as such.

  14. Revised Versions of this License.

  The Free Software Foundation may publish revised and/or new versions of
the GNU General Public License from time to time.  Such new versions will
be similar in spirit to the present version, but may differ in detail to
address new problems or concerns.

  Each version is given a distinguishing version number.  If the
Program specifies that a certain numbered version of the GNU General
Public License "or any later version" applies to it, you have the
option of following the terms and conditions either of that numbered
version or of any later version published by the Free Software
Foundation.  If the Program does not specify a version number of the
GNU General Public License, you may choose any version ever published
by the Free Software Foundation.

  If the Program specifies that a proxy can decide which future
versions of the GNU General Public License can be used, that proxy's
public statement of acceptance of a version permanently authorizes you
to choose that version for the Program.

  Later license versions may give you additional or different
permissions.  However, no additional obligations are imposed on any
author or copyright holder as a result of your choosing to follow a
later version.

  15. Disclaimer of Warranty.

  THERE IS NO WARRANTY FOR THE PROGRAM, TO THE EXTENT PERMITTED BY
APPLICABLE LAW.  EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT
HOLDERS AND/OR OTHER PARTIES PROVIDE THE PROGRAM "AS IS" WITHOUT WARRANTY
OF ANY KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING, BUT NOT LIMITED TO,
THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
PURPOSE.  THE ENTIRE RISK AS TO THE QUALITY AND PERFORMANCE OF THE PROGRAM
IS WITH YOU.  SHOULD THE PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF
ALL NECESSARY SERVICING, REPAIR OR CORRECTION.

  16. Limitation of Liability.

  IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING
WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MODIFIES AND/OR CONVEYS
THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY
GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE
USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED TO LOSS OF
DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD
PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER PROGRAMS),
EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF
SUCH DAMAGES.

  17. Interpretation of Sections 15 and 16.

  If the disclaimer of warranty and limitation of liability provided
above cannot be given local legal effect according to their terms,
reviewing courts shall apply local law that most closely approximates
an absolute waiver of all civil liability in connection with the
Program, unless a warranty or assumption of liability accompanies a
copy of the Program in return for a fee.

                     END OF TERMS AND CONDITIONS

            How to Apply These Terms to Your New Programs

  If you develop a new program, and you want it to be of the greatest
possible use to the public, the best way to achieve this is to make it
free software which everyone can redistribute and change under these terms.

  To do so, attach the following notices to the program.  It is safest
to attach them to the start of each source file to most effectively
state the exclusion of warranty; and each file should have at least
the "copyright" line and a pointer to where the full notice is found.

    <one line to give the program's name and a brief idea of what it does.>
    Copyright (C) <year>  <name of author>

    This program is free software: you can redistribute it and/or modify
    it under the terms of the GNU General Public License as published by
    the Free Software Foundation, either version 3 of the License, or
    (at your option) any later version.

    This program is distributed in the hope that it will be useful,
    but WITHOUT ANY WARRANTY; without even the implied warranty of
    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
    GNU General Public License for more details.

    You should have received a copy of the GNU General Public License
    along with this program.  If not, see <https://www.gnu.org/licenses/>.

Also add information on how to contact you by electronic and paper mail.

  If the program does terminal interaction, make it output a short
notice like this when it starts in an interactive mode:

    <program>  Copyright (C) <year>  <name of author>
    This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'.
    This is free software, and you are welcome to redistribute it
    under certain conditions; type `show c' for details.

The hypothetical commands `show w' and `show c' should show the appropriate
parts of the General Public License.  Of course, your program's commands
might be different; for a GUI interface, you would use an "about box".

  You should also get your employer (if you work as a programmer) or school,
if any, to sign a "copyright disclaimer" for the program, if necessary.
For more information on this, and how to apply and follow the GNU GPL, see
<https://www.gnu.org/licenses/>.

  The GNU General Public License does not permit incorporating your program
into proprietary programs.  If your program is a subroutine library, you
may consider it more useful to permit linking proprietary applications with
the library.  If this is what you want to do, use the GNU Lesser General
Public License instead of this License.  But first, please read
<https://www.gnu.org/licenses/why-not-lgpl.html>.