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Changes for Brian 1 users
=========================
.. contents::
:local:
:depth: 1
.. note::
If you need to run existing Brian 1 simulations, have a look at
:doc:`brian1_to_2/container`.
In most cases, Brian 2 works in a very similar way to Brian 1 but there are
some important differences to be aware of. The major distinction is that
in Brian 2 you need to be more explicit about the definition of your
simulation in order to avoid inadvertent errors. In some cases, you will now
get a warning in other even an error -- often the error/warning message
describes a way to resolve the issue.
Specific examples how to convert code from Brian 1 can be found in the document
:doc:`brian1_to_2/index`.
Physical units
--------------
The unit system now extends to arrays, e.g. ``np.arange(5) * mV`` will retain
the units of volts and not discard them as Brian 1 did. Brian 2 is therefore
also more strict in checking the units. For example, if the state variable
``v`` uses the unit of volt, the statement ``G.v = np.rand(len(G)) / 1000.``
will now raise an error. For consistency, units are returned everywhere, e.g.
in monitors. If ``mon`` records a state variable v, ``mon.t`` will return a
time in seconds and ``mon.v`` the stored values of ``v`` in units of volts.
If you need a pure numpy array without units for further processing, there
are several options: if it is a state variable or a recorded variable in a
monitor, appending an underscore will refer to the variable values without
units, e.g. ``mon.t_`` returns pure floating point values. Alternatively, you
can remove units by diving by the unit (e.g. ``mon.t / second``) or by
explicitly converting it (``np.asarray(mon.t)``).
Here's an overview showing a few expressions and their respective values in
Brian 1 and Brian 2:
================================ ================================ =================================
Expression Brian 1 Brian 2
================================ ================================ =================================
1 * mV 1.0 * mvolt 1.0 * mvolt
np.array(1) * mV 0.001 1.0 * mvolt
np.array([1]) * mV array([ 0.001]) array([1.]) * mvolt
np.mean(np.arange(5) * mV) 0.002 2.0 * mvolt
np.arange(2) * mV array([ 0. , 0.001]) array([ 0., 1.]) * mvolt
(np.arange(2) * mV) >= 1 * mV array([False, True], dtype=bool) array([False, True], dtype=bool)
(np.arange(2) * mV)[0] >= 1 * mV False False
(np.arange(2) * mV)[1] >= 1 * mV DimensionMismatchError True
================================ ================================ =================================
Unported packages
-----------------
The following packages have not (yet) been ported to Brian 2. If your simulation
critically depends on them, you should consider staying with Brian 1 for now.
* ``brian.tools``
* ``brian.library.modelfitting``
* ``brian.library.electrophysiology``
Replacement packages
--------------------
The following packages that were included in Brian 1 have now been split into separate
packages.
* ``brian.hears`` has been updated to
`brian2hears <https://brian2hears.readthedocs.io/>`_. Note that there is a
legacy package ``brian2.hears`` included in ``brian2``, but this is now deprecated and
will be removed in a future release. For now, see :ref:`brian_hears` for details.
Removed classes/functions and their replacements
------------------------------------------------
In Brian 2, we have tried to keep the number of classes/functions to a minimum, but make
each of them flexible enough to encompass a large number of use cases. A lot of the classes
and functions that existed in Brian 1 have therefore been removed.
The following table lists (most of) the classes that existed in Brian 1 but do no longer
exist in Brian 2. You can consult it when you get a ``NameError`` while converting an
existing script from Brian 1. The third column links to a document with further explanation
and the second column gives either:
1. the equivalent class in Brian 2 (e.g. `StateMonitor` can record multiple variables now
and therefore replaces ``MultiStateMonitor``);
2. the name of a Brian 2 class in square brackets (e.g. [`Synapses`] for ``STDP``), this
means that the class can be used as a replacement but needs some additional
code (e.g. explicitly specified STDP equations). The "More details" document should
help you in making the necessary changes;
3. "string expression", if the functionality of a previously existing class can
be expressed using the general string expression framework (e.g.
`threshold=VariableThreshold('Vt', 'V')` can be replaced by
`threshold='V > Vt'`);
4. a link to the relevant github issue if no equivalent class/function does exist so far
in Brian 2;
5. a remark such as "obsolete" if the particular class/function is no longer needed.
=============================== ================================= ================================================================
Brian 1 Brian 2 More details
=============================== ================================= ================================================================
``AdEx`` [`Equations`] :doc:`brian1_to_2/library`
``aEIF`` [`Equations`] :doc:`brian1_to_2/library`
``AERSpikeMonitor`` :issue:`298` :doc:`brian1_to_2/monitors`
``alpha_conductance`` [`Equations`] :doc:`brian1_to_2/library`
``alpha_current`` [`Equations`] :doc:`brian1_to_2/library`
``alpha_synapse`` [`Equations`] :doc:`brian1_to_2/library`
``AutoCorrelogram`` [`SpikeMonitor`] :doc:`brian1_to_2/monitors`
``biexpr_conductance`` [`Equations`] :doc:`brian1_to_2/library`
``biexpr_current`` [`Equations`] :doc:`brian1_to_2/library`
``biexpr_synapse`` [`Equations`] :doc:`brian1_to_2/library`
``Brette_Gerstner`` [`Equations`] :doc:`brian1_to_2/library`
``CoincidenceCounter`` [`SpikeMonitor`] :doc:`brian1_to_2/monitors`
``CoincidenceMatrixCounter`` [`SpikeMonitor`] :doc:`brian1_to_2/monitors`
``Compartments`` :issue:`443` :doc:`brian1_to_2/multicompartmental`
``Connection`` `Synapses` :doc:`brian1_to_2/synapses`
``Current`` :issue:`443` :doc:`brian1_to_2/multicompartmental`
``CustomRefractoriness`` [string expression] :doc:`brian1_to_2/neurongroup`
``DefaultClock`` `Clock` :doc:`brian1_to_2/networks_and_clocks`
``EmpiricalThreshold`` string expression :doc:`brian1_to_2/neurongroup`
``EventClock`` `Clock` :doc:`brian1_to_2/networks_and_clocks`
``exp_conductance`` [`Equations`] :doc:`brian1_to_2/library`
``exp_current`` [`Equations`] :doc:`brian1_to_2/library`
``exp_IF`` [`Equations`] :doc:`brian1_to_2/library`
``exp_synapse`` [`Equations`] :doc:`brian1_to_2/library`
``FileSpikeMonitor`` :issue:`298` :doc:`brian1_to_2/monitors`
``FloatClock`` `Clock` :doc:`brian1_to_2/networks_and_clocks`
``FunReset`` [string expression] :doc:`brian1_to_2/neurongroup`
``FunThreshold`` [string expression] :doc:`brian1_to_2/neurongroup`
``hist_plot`` no equivalent --
``HomogeneousPoissonThreshold`` string expression :doc:`brian1_to_2/neurongroup`
``IdentityConnection`` `Synapses` :doc:`brian1_to_2/synapses`
``IonicCurrent`` :issue:`443` :doc:`brian1_to_2/multicompartmental`
``ISIHistogramMonitor`` [`SpikeMonitor`] :doc:`brian1_to_2/monitors`
``Izhikevich`` [`Equations`] :doc:`brian1_to_2/library`
``K_current_HH`` [`Equations`] :doc:`brian1_to_2/library`
``leak_current`` [`Equations`] :doc:`brian1_to_2/library`
``leaky_IF`` [`Equations`] :doc:`brian1_to_2/library`
``MembraneEquation`` :issue:`443` :doc:`brian1_to_2/multicompartmental`
``MultiStateMonitor`` `StateMonitor` :doc:`brian1_to_2/monitors`
``Na_current_HH`` [`Equations`] :doc:`brian1_to_2/library`
``NaiveClock`` `Clock` :doc:`brian1_to_2/networks_and_clocks`
``NoReset`` obsolete :doc:`brian1_to_2/neurongroup`
``NoThreshold`` obsolete :doc:`brian1_to_2/neurongroup`
``OfflinePoissonGroup`` [`SpikeGeneratorGroup`] :doc:`brian1_to_2/inputs`
``OrnsteinUhlenbeck`` [`Equations`] :doc:`brian1_to_2/library`
``perfect_IF`` [`Equations`] :doc:`brian1_to_2/library`
``PoissonThreshold`` string expression :doc:`brian1_to_2/neurongroup`
``PopulationSpikeCounter`` `SpikeMonitor` :doc:`brian1_to_2/monitors`
``PulsePacket`` [`SpikeGeneratorGroup`] :doc:`brian1_to_2/inputs`
``quadratic_IF`` [`Equations`] :doc:`brian1_to_2/library`
``raster_plot`` ``plot_raster`` (``brian2tools``) `brian2tools documentation <http://brian2tools.readthedocs.io>`_
``RecentStateMonitor`` no direct equivalent :doc:`brian1_to_2/monitors`
``Refractoriness`` string expression :doc:`brian1_to_2/neurongroup`
``RegularClock`` `Clock` :doc:`brian1_to_2/networks_and_clocks`
``Reset`` string expression :doc:`brian1_to_2/neurongroup`
``SimpleCustomRefractoriness`` [string expression] :doc:`brian1_to_2/neurongroup`
``SimpleFunThreshold`` [string expression] :doc:`brian1_to_2/neurongroup`
``SpikeCounter`` `SpikeMonitor` :doc:`brian1_to_2/monitors`
``StateHistogramMonitor`` [`StateMonitor`] :doc:`brian1_to_2/monitors`
``StateSpikeMonitor`` `SpikeMonitor` :doc:`brian1_to_2/monitors`
``STDP`` [`Synapses`] :doc:`brian1_to_2/synapses`
``STP`` [`Synapses`] :doc:`brian1_to_2/synapses`
``StringReset`` string expression :doc:`brian1_to_2/neurongroup`
``StringThreshold`` string expression :doc:`brian1_to_2/neurongroup`
``Threshold`` string expression :doc:`brian1_to_2/neurongroup`
``VanRossumMetric`` [`SpikeMonitor`] :doc:`brian1_to_2/monitors`
``VariableReset`` string expression :doc:`brian1_to_2/neurongroup`
``VariableThreshold`` string expression :doc:`brian1_to_2/neurongroup`
=============================== ================================= ================================================================
List of detailed instructions
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
.. toctree::
:maxdepth: 2
brian1_to_2/index
|
