Note
Python provides native support for manipulating files. Use that whenever possible to ensure your code is understandable by the greatest number of people.
- Syntax:
fobj = h.File()fobj = h.File("filename")- Description:
This class allows you to open several files at once, whereas the top level functions, :func:`ropen` and :func:`wopen` , allow you to deal only with one file at a time.
The functionality of :func:`xopen` is not implemented in this class so use
h.xopen(fobj.getname())
to execute a sequence of interpreter commands in a file.
Example:
from neuron import h f1 = h.File() //state that f1, f2, and f3 are pointers to the File class f2 = h.File() f3 = h.File() f1.ropen("file1") //open file1 for reading f2.wopen("file2") //open file2 for writing f3.aopen("file3") //open file3 for appending to the end of the fileopens file1, file2, and file3 for reading, writing, and appending (respectively).
Warning
The mswindows/dos version must deal with the difference between binary and text mode files. The difference is transparent to the user except for one limitation. If you mix text and binary data and you write text first to the file, then you need to do a File.seek(0) to explicitly switch to binary mode just after opening the file and prior to the first File.printf. An error message will occur if you read/write text to a file in text mode and then try to read/write a binary vector. This issue does not arise with the unix version.
.. seealso::
:ref:`printf_doc`, :func:`ropen`, :func:`xopen`, :func:`wopen`
.. method:: File.ropen
Syntax:
``.ropen()``
``.ropen("name")``
Description:
Open the file for reading. If the argument is
not present it opens (for reading) the last specified file.
.. method:: File.wopen
Syntax:
``.wopen()``
``.wopen("name")``
Description:
Open the file for writing. If the argument is
not present it opens the last specified file.
.. method:: File.aopen
Syntax:
``.aopen()``
``.aopen("name")``
Description:
Open the file for appending to the end of the file. If the argument is
not present it opens the last specified file.
.. method:: File.xopen
Syntax:
``.xopen()``
``.xopen("name")``
Description:
Open the file and execute it. (**not implemented**)
Note: if instead of a "*name*", the number 0,1,or 2 is specified then
the stdin, stdout, or stderr is opened. (**not implemented**)
.. method:: File.close
Syntax:
``.close()``
Description:
Flush and close the file. This occurs automatically
whenever opening another file or destroying the object.
.. method:: File.mktemp
Syntax:
``success = f.mktemp()``
Description:
Sets the name to a temporary filename in the /tmp directory (or other
writable path for mswin and mac). Success returns 1.
Example of creating a temporary file:
.. code-block::
python
f = h.File()
if f.mktemp() != 1:
raise Exception('Unable to create temporary file')
# create a tempoary file, get its name
temp_file_name = f.getname()
# do stuff, possibly using regular Python File IO instead
# dispose of the temporary file
f.unlink()
.. method:: File.unlink
Syntax:
``success = f.unlink()``
Description:
Remove the file specified by the current name. A return value of
1 means the file was removed (or at least it's link count was reduced by
one and the filename no longer exists).
.. method:: File.printf
Syntax:
``.printf("format", args, ...)``
Description:
As in standard C \ ``printf`` and the normal
NEURON :func:`printf` .
.. method:: File.scanvar
Syntax:
``.scanvar()``
Description:
Reads the next number as in the function ``fscan()`` and
returns its value.
Note: in order that .eof will return
true after the last number, the last digit of that number
should either be the last character in the file or
be followed by a newline which is the last character in the file.
.. method:: File.scanstr
Syntax:
``.scanstr(strptr)``
Description:
Read the next string (delimited by whitespace) into
\ ``strptr`` (must be a pointer to a NEURON string *not* a Python string).
Returns the length of a string (if failure then returns
-1 and the string pointed to by ``strptr`` is unchanged).
.. method:: File.gets
Syntax:
``.gets(_ref_str)``
Description:
Read up to and including end of line. Returns length of string.
If at the end of file, returns -1 and does not change the argument.
``_ref_str`` is a reference to a NEURON string (e.g. one created via
``_ref_str = h.ref('')``); it is not a Python string.
.. method:: File.getname
Syntax:
``name = fobj.getname()``
``name = fobj.getname(strptr)``
Description:
Return the name of the last specified file as a string.
For backward compatibility, if the arg is present (must a pointer to a NEURON string) also copy it to that.
.. method:: File.dir
Syntax:
``dirname = file.dir()``
Description:
Return the pathname of the last directory moved to in the chooser.
If the :meth:`File.chooser` has not been created, return the empty string.
.. method:: File.eof
Syntax:
``fobj.eof()``
Description:
Return true if at end of ropen'd file.
.. method:: File.flush
Syntax:
``fobj.flush()``
Description:
Flush pending output to the file.
.. method:: File.isopen
Syntax:
``fobj.isopen()``
Description:
Return true if a file is open.
.. method:: File.chooser
Syntax:
``.chooser()``
``.chooser("w,r,a,x,d or nothing")``
``.chooser("w,r,a,x,d or nothing", "Banner", "filter", "accept", "cancel", "path")``
Description:
File chooser interface for writing , reading, appending, or
just specifying a directory or filename without opening. The banner is
optional. The filter, eg. \ ``"*.dat"`` specifies the files shown
in the browser part of the chooser.
The "path" arg specifies the file or directory to use when the
browser first pops up.
The form with args sets the style of the chooser but
does not pop it up. With no args, the browser pops up and can
be called several times. Each time starting where it left
off previously.
The "d" style is used for selecting a directory (in
contrast to a file).
With the "d" style, three buttons are placed beneath the
browser area with :guilabel:`Open` centered beneath the :guilabel:`Show`, :guilabel:`Cancel` button pair.
The :guilabel:`Open` button must be pressed for the
dialog to return the name of the directory. The :guilabel:`Show` button merely
selects the highlighted browser entry and shows the relevant directory
contents. A returned directory
string always has a final "/".
The "*x*" style is unimplemented. Use
.. code-block::
none
f.chooser("", "Execute a hoc file", "*.hoc", "Execute")
if f.chooser():
h.xopen(f.getname())
Example:
.. code-block::
python
from neuron import h, gui
f = h.File()
f.chooser('', 'Example file browser', '*', 'Type file name', 'Cancel')
while f.chooser():
print(f.getname())
.. image:: ../../images/filechooser.png
:align: center
The following comes courtesy of Zach Mainen, zach@helmholtz.sdsc.edu:
.. method:: File.vwrite
Syntax:
``.vwrite(_ref_x)``
``.vwrite(n, _ref_x)``
Description:
Write binary doubles to a file from an array or variable
using \ ``fwrite()``. The form with two arguments specifies the
number of elements to write and the address from which to
begin writing. With one argument, *n* is assumed to be 1.
Must be careful that *x*\ [] has at least *n*
elements after its passed address.
i.e. If ``x = h.Vector(10)`` and ``f`` is an instance of a :class:`File`
opened for writing, then one might call ``f.vwrite(5, x._ref_x[0]`` to write
the first five values to a file.)
.. method:: File.vread
Syntax:
``.vread(_ref_x)``
``.vread(n, _ref_x)``
Description:
Read binary doubles from a file into a pre-existing :class:`Vector`
or variable using \ ``fread()``.
.. seealso::
:func:`vwrite`
.. method:: File.seek
Syntax:
``.seek()``
``.seek(offset)``
``.seek(offset,origin)``
Description:
Set the file position. Any subsequent file access will access
data beginning at the new position. Without arguments, goes to
the beginning of file. Offset is in characters and is measured
from the beginning of the file unless origin is 1 (measures from
the current position) or 2 (from the end of the file). Returns
0 if successful, non-zero on error. Used with :meth:`tell`.
.. method:: File.tell
Syntax:
``.tell()``
Description:
Return the current file position or -1 on error. Used with :meth:`seek`.