Using Session Files for Saving and Retrieving Windows
Saving the windows of an interface for later re-use is an essential
operation. The position, size, and contents of all the windows you have
constructed often represent a great deal of labor that you don't want to
do over again. Losing a CellBuild or a MulRunFitter window can be a
This article explains how to save windows, how to save them in groups
in separate files in order to keep separate the ideas of specification,
control, graphing, optimization, etc., and how to recover as much work as
possible in the event that a saved window generates an error when
it is read from a file.
What is a session?
A "session" is the set of all of NEURON's graphical windows,
including hidden windows.
How (and when) to save all windows to a ses file, and how to retrieve them
The simplest way to save NEURON's graphical
windows is to save all of them at
once with NEURONMainMenu / File / save session.
This creates a session file which
NEURON can use to recreate the windows that were saved.
Session files, which are
generally given the suffix ".ses"
to distinguish them from user-written hoc files,
are discussed below in more detail.
It's an excellent practice to save the entire
session whenever a crash
would cause distress because of the loss of
all work since the previous save,
so save early and save often.
Be sure to verify that the new session file
can be retrieved (NEURONMainMenu / File / load session)
before you overwrite an earlier session file that works!
It is most useful to retrieve such a session file
right after launching NEURON, when no other windows are
present on the screen.
It is especially useful if one of the windows is a
CellBuild or NetGUI, because most windows depend on the
existence of information
declared by them.
Conflicts can arise if there are multiple CellBuild or
NetGui windows that could interfere with one another,
especially if they create sections with the same names.
How (and why) to save selected windows
The main problem with saving all windows in a single session file is
that it mixes specification, control, parameter, and graphing windows.
Experience has shown that it is best to segregate these categories
in order to have more conceptual control over a modeling project.
This allows you to easily start a simulation by retrieving the desired
variant of a CellBuilder window, separately retrieving
one of several possible stimulus
protocols and parameter sets, and lastly retrieving groups of graph windows.
If your custom interface is simple,
the Print & File Window Manager (PFWM)
offers an easy way to save a few windows
This tool is discussed elsewhere--see the FAQ list entry
"Q: How do I print a hard copy of a NEURON window?" under the heading
"Using NEURON--general questions".
Select the windows you want to save, just as if you were going to
After you have chosen the windows to be saved,
click on the Session button instead of the Print button,
and scroll down to the item "Save selected".
A more powerful tool for managing windows is the Window Group Manager.
The Window Group Manager
The NEURONMainMenu / Window / GroupManager enables the separate creation
of such session files with only a little more effort than the bulk
NEURONMainMenu / File/ save session. With the "NewGroup" and "ChangeName"
buttons one can define several named groups, e.g. "Cell", "Stimulus",
"Control", and "Voltage Graphs".
The names of window groups appear in the left panel of the
window group manager.
If you click on one of these names,
the titles of the windows that belong to it will appear
in the center panel.
Clicking on one of these titles removes it from the group,
and the title will now appear in the right panel,
which lists the ungrouped windows.
To add a window to the group, just click on the
window title in the right panel.
You can move a window from one
window group to another by following this sequence :
- Select the group it is currently in.
- Select its window title. (Makes it ungrouped)
- Select the group you want it to be in.
- Select its window title in the ungrouped list.
To save any window group to its own session file,
click on the SaveGroup button.
The Window Group Manager is a dialog box and so must be closed before
other windows will accept further input.
It may be opened at any time via the NEURONMainMenu / Window / GroupManager
menu item and groups re-saved, new windows added to existing groups, etc.
What's in a ses file
A session file is actually just a sequence of hoc instructions
for reconstructing the windows that have been saved to it.
In a session file, the
instructions for each window are identified by comments.
It is often
a simple matter to use a text editor to modify those instructions,
e.g. change the value of a parameter,
or remove all the instructions for a
window if it is preventing the file from being loaded.
Below we discuss how the latter can happen.
There are circumstances in which a
window in the current session may not easily be made to start again when
NEURON is exited and relaunched.
What can go wrong, and how to fix it
The most common cause of errors during retrieval of a session file
is that one or more variables used by a window have not yet been defined.
Thus, retrieving a point process manager window
before the prerequisite cable section has been created will result
in a hoc error. Retrieving a Graph of SEClamp.i will not succeed
if SEClamp does not exist. In most cases, loading the prerequisite
sessions first will fix the error.
To make sure that session files are loaded in the proper sequence,
it can be helpful to create a file called init.hoc that contains
a series of load_file statements, e.g.
Errors due to mismatched object IDs are easy
to correct by editing the session file. Mismatched object IDs
can occur from particular sequences of creation and destruction
of windows by the user. For example, suppose you
If you now exit and re-launch NEURON and retrieve the session,
the old IClamp will be re-created as IClamp, and the
creation of the Graph window will fail due to the invalid variable
name it is attempting to define. The fix is just to edit the
session file and change the IClamp.i string to IClamp.i
- Start a PointProcessManager and
create the first instance of an IClamp. This will be IClamp
- Start another PointProcessManager and
create a second instance of an IClamp. This will be IClamp
- Close the first PointProcessManager. That destroys IClamp.
- Start a graph and plot IClamp.i
- Save the session.
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