.. role:: raw-latex(raw)
   :format: latex
..

Installation
============

Download and install Anaconda or Miniconda (Python 3.x version)
http://docs.continuum.io/anaconda/install

Installation on Windows
------------

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   <details>

The Windows installation process differs more widely from installation
on Linux or MacOSX and has different issues you may run into.

Process
-------

-  Increase the maximum size of your pagefile to 64G or more
   (http://www.tomshardware.com/faq/id-2864547/manage-virtual-memory-pagefile-windows.html
   ) - The Windows memmap interface is sensitive to the maximum setting
   and leaving it at the default can cause errors when processing larger
   datasets

   -  Download and install Anaconda (Python 3.x)
      http://docs.continuum.io/anaconda/install. Allow the installer to
      modify your PATH variable
   -  Use Conda to install git (With “conda install git”) - use of
      another commandline git is acceptable, but may lead to issues
      depending on default settings
   -  Install Microsoft Build Tools for Visual Studio 2017
      https://www.visualstudio.com/downloads/#build-tools-for-visual-studio-2017.
      Check the “Build Tools” box, and in the detailed view on the right
      check the “C/C++ CLI Tools” component too. The specifics of this
      occasionally change as Microsoft changes its products and website;
      you may need to go off-script.

Use the following menu item to launch a anaconda-enabled command prompt:
start>programs>anaconda3>anaconda prompt From that prompt. issue the
following commands (if you wish to use the dev branch, you may switch
branches after the clone):

.. code:: bash

     git clone https://github.com/flatironinstitute/CaImAn
     cd CaImAn
     conda env create -f environment.yml -n caiman
     conda install -n caiman vs2017_win-64

At this point you will want to remove a startup script that visual
studio made for your conda environment that can cause conda to crash
while entering the caiman environment. Use the Windows find-file utility
(under the Start Menu) to look for vs2015_compiler_vars.bat and/or
vs2015_compiler_vars.bat under your home directory. At least one copy
should show up. Delete the version that has
conda:raw-latex:`\envs`:raw-latex:`\caiman `as part of its location. You
may also want to do a search for keras_activate.bat under your home
directory, find the one in conda:raw-latex:`\envs`:raw-latex:`\caiman`,
and edit it so KERAS_BACKEND is set to tensorflow rather than theano.
You may then continue the installation.

.. code:: bash

     activate caiman
     pip install . (OR pip install -e . if you want to develop code)
     copy caimanmanager.py ..
     conda install numba
     cd ..

Setting up a data directory with caimanmanager
----------------------------------------------

Now that you have stepped out of the caiman source directory, you are
ready to make a data directory with code samples and datasets. You will
not use the source tree directory any more.

::

     caimanmanager.py install

or ``python caimanmanager.py install --inplace`` if you used “pip
install -e .”

This will place that directory under your home directory in a directory
called caiman_data. If you have, some of the demos or datafiles may have
changed since your last install, to follow API changes. You can check to
see if they have by doing ``caimanmanager.py check``. If they have not,
you may keep using them. If they have, we recommend moving your old
caiman data directory out of the way (or just remove them if you have no
precious data) and doing a new data install as per above.

If you prefer to manage this information somewhere else, the
``CAIMAN_DATA`` environment variable can be set to customise it. The
caimanmanager tool and other libraries will respect that.

Setting up environment variables
--------------------------------

To make the package work *efficiently* and eliminate “crosstalk” between
different processes, run these commands before launching Python:

.. code:: bash

     set MKL_NUM_THREADS=1
     set OPENBLAS_NUM_THREADS=1
     set KERAS_BACKEND=tensorflow

The commands should be run every time you enter the caiman conda
environment. We recommend you save these values inside your environment
so you do not have to repeat this process every time. You can do this by
following the instructions
`here <https://conda.io/projects/conda/en/latest/user-guide/tasks/manage-environments.html#saving-environment-variables>`__.

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Installation on MacOS and Linux
-------------

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   <details>

.. code:: bash

     git clone https://github.com/flatironinstitute/CaImAn
     cd CaImAn/
     conda env create -f environment.yml -n caiman
     source activate caiman
     pip install .

If you want to develop code then replace the last command with
``pip install -e .`` If any of these steps gives you errors do not
proceed to the following step without resolving it

known issues
~~~~~~~~~~~~

If you recently upgraded to OSX Mojave you may need to perform the
following steps before your first install:

::

     xcode-select --install
     open /Library/Developer/CommandLineTools/Packages/

and install the package file you will find in the folder that pops up

.. _setting-up-environment-variables-1:

Setting up environment variables
--------------------------------

To make the package work *efficiently* and eliminate “crosstalk” between
different processes, run these commands before launching Python (this is
for Linux and OSX):

.. code:: bash

     export MKL_NUM_THREADS=1
     export OPENBLAS_NUM_THREADS=1
     export KERAS_BACKEND=tensorflow

The commands should be run every time before launching python. It is
recommended that you save these values inside your environment so you
don’t have to repeat this process every time. You can do this by
following the instructions
`here <https://conda.io/projects/conda/en/latest/user-guide/tasks/manage-environments.html#saving-environment-variables>`__.

Setting up caimanmanager
------------------------

Once CaImAn is installed, you may want to get a working directory with
code samples and datasets; pip installed a caimanmanager.py command that
manages this. If you have not installed Caiman before, you can do
``caimanmanager.py install`` or
``python caimanmanager.py install --inplace`` if you used “pip install
-e .”

This will place that directory under your home directory in a directory
called caiman_data. If you have, some of the demos or datafiles may have
changed since your last install, to follow API changes. You can check to
see if they have by doing ``caimanmanager.py check``. If they have not,
you may keep using them. If they have, we recommend moving your old
caiman data directory out of the way (or just remove them if you have no
precious data) and doing a new data install as per above.

If you prefer to manage this information somewhere else, the
``CAIMAN_DATA`` environment variable can be set to customise it. The
caimanmanager tool and other libraries will respect that.

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Upgrading
=========

If you already have CaImAn installed with the pip installer (May 2018 or
later), but want to upgrade, please follow the procedure below. If you
reinstall CaImAn frequently, you can try skip deleting and recreating
your Conda environment. In this case you can do only steps 1, 5, and 7
below to update the code. However, if the environment file has changed
since your last update this may lead to you not the latest version.

From the conda environment you used to install CaImAn: 

1. ``pip uninstall caiman`` 

2. remove or rename your ~/caiman_data directory 

3. Remove your conda environment: ``conda env remove -n NAME_OF_YOUR_ENVIRONMENT``

4. Close and reopen your shell (to clear out the old conda environment) 

5. Do a ``git pull`` from inside your CaImAn folder. 

6. Recreate and reenter your conda environment as you did in the installation instructions 

7. Do a ``pip install .`` inside that code checkout

8. Run ``caimanmanager.py install`` to reinstall the data directory (use ``--inplace`` if you used the ``pip install -e .`` during your initial installation).

-  If you used the ``pip install -e .`` option when installing, then you
   can try updating by simply doing a ``git pull``. Again, this might
   not lead to the latest version of the code if the environment
   variables have changed.

-  The same applies if you want to modify some internal function of
   CaImAn. If you used the ``pip install -e .`` option then you can
   directly modify it (that’s why it’s called developer mode). If you
   used the ``pip install .`` option then you will need to
   ``pip uninstall caiman`` followed by ``pip install .`` for your
   changes to take effect. Depending on the functions you’re changing so
   you might be able to skip this step.

Installing additional packages
==============================

CaImAn uses the conda-forge conda channel for installing its required
packages. If you want to install new packages into your conda
environment for CaImAn, it is important that you not mix conda-forge and
the defaults channel; we recommend only using conda-forge. To ensure
you’re not mixing channels, perform the install (inside your
environment) as follows:

::

   conda install -c conda-forge --override-channels NEW_PACKAGE_NAME
  
You will notice that any packages installed this way will mention, in
their listing, that they’re from conda-forge, with none of them having a
blank origin. If you fail to do this, differences between how packages
are built in conda-forge versus the default conda channels may mean that
some packages (e.g. OpenCV) stop working despite showing as installed.
