Installing

Manual install (recommended)

To manually install RetinotopicMapping you can download the package here.

Then open the command line, move to the directory that the package was installed in and run the setup.py file like follows:

cd <package_path>
conda env create -f environment.yml     # this will take a while
activate retinotopic_mapping            # Windows
source activate retinotopic_mapping     # Mac or Linux
python setup.py install

PIP install

An even simpler way to install the package is with pip. To do so type the following in the command line:

pip install retinotopic_mapping

This will install all the dependencies (takes long time and not always work). If you want to install the package without dependencies, run:

pip install retinotopic_mapping --no-deps

Dependencies

1. pytest, version 3.3.0 or later
2. numpy, version 1.13.1 or later
3. scipy, version 0.17.1 or later
4. matplotlib, version 1.5.1 or later
5. h5py, version 2.7.1 or later
6. pillow, version 5.0.0 or later
7. psychopy, version 1.85.2 or later
8. pyglet, version 1.2.4
9. OpenCV [a]
10. scikit-image, version 0.12.3 or later [b]
11. tifffile, version >=0.7.0 [c]
12. PIL, version 4.3.0 or later
13. PyDAQmx, version 1.3.2 or later [d]
14. configobj, version 5.0.6 or later
15. sphinx, version 1.6.3 or later (just for documentation)
16. numpydoc, version 0.7.0 (just for documentation)

[a]	This can be 1) OpenCV-Python 3.1.0 or later (pip version) or 2) opencv 2.4.11 (conda cloud version from menpo channel) or 3) opencv3 3.2.0 (conda cloud version from menpo channel)

[b]	On windows systems, conda install scikit-image is recommended. pip install scikit-image will sometimes fail. Due to the skimage.external.tifffile module. This solution usually fix the problem.

[c]	Same as b.

[d]	Requires National Instruments DAQmx driver.

Operating Systems Supported

• Windows
• Linux
• Mac

Making sure PyDAQmx works

The PyDAQmx module allows users to integrate National Instruments data-acquisition hardware into their experimental setup (see their documentation for more information).

To get PyDAQmx to function correctly there are a couple of important points to mention:

• The NIDAQmx driver must first be installed
• Once NIDAQmx driver is installed it is not guaranteed that the module will work, so it is important to know how to troubleshoot this issue. The main issue is tracking down where two files are on your computer, a filepath ending with DAQMX.h and another path ending with nicaiu.dll. The PyDAQmx module tries to find these files for you, but if it cannot, the user needs to manually find and enter the path within the DAQmxConfig.py file. See this page for a more thorough explanation).

Note

This is the most likely issue to come up in debugging. Chances are if you are having a related issue it either has something to do with not supplying a correct path or making improper import statements somewhere in your script.