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Commit 6d5041cb authored by David Tadres's avatar David Tadres
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assign head and tail even if there's more than 2 endpoints by checking 1)...

assign head and tail even if there's more than 2 endpoints by checking 1) which endpoint is closest to the previous tail and 2) which endpoint is farthest away from that point.
parent 537409f0
## 1.4.16
### 21st of October, 2020
1. Updated install instructions to work with MacIOS to fix #41.
2. Removed install instructions from README.MD - everything is on
readthedocs now.
## 1.4.15
### 10th of October, 2020
......
......@@ -74,7 +74,7 @@ Install PiVR on a PC
conda install -y natsort
conda install -y -c conda-forge scikit-image
conda install -y scikit-image
conda install -c conda-forge opencv
......
__author__ = 'David Tadres'
__project__ = 'PiVR'
__version__ = '1.4.15'
__date__ = '10th of October, 2020'
__version__ = '1.4.16'
__date__ = '21st of October, 2020'
#####################################################
# This seems to be necessary in order to run on MacOS
......
# PiVR - virtual reality for small animals
PiVR is a virtual reality system for small animals.
PiVR is a virtual reality system for small animals. It is described
in detail in our recent publication: https://doi.org/10.1371/journal.pbio.3000712
This wepage (and this Readme) is intended to mainly be the home of the software.
Scientific American has written an article describing our work:
https://www.scientificamerican.com/article/fruit-flies-plug-into-the-matrix/
For examples what the system has been used for, how it might be useful for you and how to build your own tracking
system please head over to PiVR.org
For examples what the system has been used for, how it might be useful
for you and how to build your own tracking system please head over
to https://PiVR.org
## Getting Started
This Readme will only show you how to install the software on your PC.
### Prerequisites
1) Install either Miniconda (https://conda.io/miniconda.html) or Anaconda (https://www.anaconda.com/download/).
2) Install Git (https://git-scm.com/downloads) (already installed on many Linux distributions!)
### Installing
### Windows (only Win10, 64bit tested):
*Note: If you are having trouble, do the manual install (see below)!*
1) Open the git bash command prompt
2) Navigate to the folder you want to put all the source files (~130Mbyte)
```
for example type (without the <>) <cd C:\Users\UserA\Documents>
```
3) Clone the repository by typing:
```
git clone https://gitlab.com/louislab/PiVR
```
4) After it finished downloading, open the Anaconda terminal as **Administrator**
5) Navigate to the "Installation_update" folder of the repository you just cloned:
```
for example type (without the <>): <cd C:\Users\UserA\Documents\PiVR\PiVR\Installation_update>
```
6) Create the virtual environment needed to run the software by typing
```
conda create --name PiVR_environment --file PiVR_Win64.txt
```
7) Once done, activate the virtual environment by typing:
```
activate PiVR_environment
```
You know you successfully activated the virtual enviroment if it says '(PiVR)' at the beginnig of the line in the
terminal.
8) Navigate to the PiVR folder
```
for example type (without the <>): <cd C:\Users\UserA\Documents\PiVR\PiVR\>
```
9) Start the program by typing:
```
python start_GUI.py
```
10) If everything works as expected this will lead to the GUI (graphical user interface) to pop up.
### Linux (only Ubuntu, 64bit tested)
*Note: If you are having trouble, do the manual install (see below)!*
1) Open terminal
2) Navigate to the folder you want to put all the source files (~130Mbyte)
```
for example type (without the <>) <cd /home/UserA>
```
3) Clone the repository by typing:
```
git clone https://gitlab.com/louislab/PiVR
```
4) Navigate to the "Installation_update" folder of the repository you just cloned:
```
for example type (without the <>): <cd /home/UserA/PiVR/PiVR/Installation_update>
```
5) Create the virtual environment needed to run the software by typing
```
conda create --name PiVR_environment --file PiVR_Linux64.txt
```
If this does not work, try the following:
```
conda create --name PiVR_environment --file PiVR_Linux64_2.txt
```
6) Once done, activate the virtual environment by typing:
```
source activate PiVR_environment
```
You know you successfully activated the virtual enviroment if it says '(PiVR)' at the beginnig of the line in the
terminal.
8) Navigate to the PiVR folder
```
for example type (without the <>): <cd /home/UserA/PiVR/PiVR/>
```
9) Start the program by typing:
```
python start_GUI.py
```
10) If everything works as expected this will lead to the GUI (graphical user interface) to pop up.
### Manual Install (Any system)
1. open Terminal(Mac/Linux) or Command Prompt (Windows)
2. create an empty conda environment
`conda create --name PiVR_environment`
3. activate the environment you've just created:
Linux/Mac:
`source activate PiVR_environment`
Windows:
`activate PiVR_environment`
4. install python:
`conda install -y python=3.7`
5. Install the other packages by copying each line of code into your
Terminal/Command Prompt
`conda install -y matplotlib`
`conda install -y pandas`
`conda install -y scipy`
`conda install -y natsort`
`conda install -y -c conda-forge scikit-image`
`conda install -c conda-forge opencv`
Windows/Linux:
`conda install -c conda-forge imageio-ffmpeg`
MacOS:
`conda install -c conda-forge ffmpeg`
6. In the terminal, change directory to a place where you want to
install the PiVR software.
```
for example type (without the <>) <cd C:\Users\UserA\Documents>
```
7. Download the PiVR software by typing:
```
git clone https://gitlab.com/louislab/PiVR
```
8. Check if installation was successful by navigating to the folder
you've installed PiVR to, e.g.
`for example type (without the <>): <cd /home/UserA/PiVR/PiVR>`
9. Now just type the following:
`python start_GUI.py`
A window should pop up, letting you use the 'offline' features of
the PiVR software.
10. If there's an error, please report it as a **Issue** at:
https://gitlab.com/louislab/pivr/issues
The more information you include into the Issue the better other
people will be able to help you. At the very least make sure to
include:
a) Operating System
b) Is the OS 64 or 32 bit?
c) Where exactly you got stuck
d) What the error says
A screenshot of the Terminal/Command Prompt will also greatly help
in resolving your issue.
\ No newline at end of file
You will also find installation instructions there.
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