Changeset 707

Timestamp:

02/12/10 11:29:45 (2 years ago)

Author:

apdavison

Message:

Some documentation updates

Location:

trunk/doc

Files:

• fileformats.txt (added)
• highlevelapi.txt (modified) (3 diffs)
• lowlevelapi.txt (modified) (5 diffs)
• testdocs.py (modified) (1 diff)

trunk/doc/highlevelapi.txt

@@ -258 +258 @@
 Again, there is a performance penalty for this, so if you wish each node to write its own file, add ``gather=False`` to the argument list.
 
-It is possible to save data in various different formats. The default (if you pass a filename) is a text file, but you can also save in various binary formats. To save in HDF5 format, for example::
+It is possible to save data in various different formats. The default (if you pass a filename) is a text file, but you can also save in various binary formats. To save in HDF5 format (this requires the PyTables package to be installed), for example::
 
     >>> h5file = recording.files.HDF5ArrayFile("spikefile.h5", "w")
@@ -393 +393 @@
 The second example connects each neuron to all its neighbours within a range of 3 units (distance is in µm if positions have been specified, in array coordinate distance otherwise). Note that boolean values ``True`` and ``False`` are automatically converted to numerical values ``1.0`` and ``0.0``.
 
-The calculation of distance may be controlled by specifying a `Space` object.
+The calculation of distance may be controlled by specifying a ``Space`` object.
 
 By default, the 3D distance between cell positions is used, but the ``axes`` argument may be used to change this, e.g.::
@@ -516 +516 @@
     >>> prj1_1.randomizeDelays(delay_distr)
 
-## NOTE: Need to add information about getting/setting individual weights and delays
+It is also possible to access the attributes of individual connections using the
+``connections`` attribute of a projection::
+
+    >>> for c in prj1_1.connections[:5]:
+    ...   c.weight *= 2
+    
+In general, though, this is less efficient than using list- or array-based access.
 
 Accessing weights and delays

trunk/doc/lowlevelapi.txt

@@ -25 +25 @@
     >>> setup()
     
-``setup()`` takes various optional arguments: setting the simulation timestep (there is currently no support in the API for variable timestep methods although native simulator code can be used to select this option where the simulator supports it), setting the minimum and maximum synaptic delays, and turning debugging output on and off, e.g.::
-
-    >>> setup(timestep=0.1, min_delay=0.1, max_delay=0.5, debug=False)
-    
-Debugging information is written to a log file in the working directory.
+``setup()`` takes various optional arguments: setting the simulation timestep (there is currently no support in the API for variable timestep methods although native simulator code can be used to select this option where the simulator supports it) and setting the minimum and maximum synaptic delays, e.g.::
+
+    >>> setup(timestep=0.1, min_delay=0.1, max_delay=0.5)
+    
+In previous versions, ``setup()`` took a ``debug`` argument for configuring logging. To allow more flexibility, configuration of logging must now be done separately. There is a convenience function in the ``pyNN.utility`` module to simplify this::
+
+    >>> from pyNN.utility import init_logging
+    >>> init_logging("logfile", debug=True)
+    
+or you can configure the Python ``logging`` module directly.
 
 Creating neurons
@@ -81 +86 @@
     >>> create(IF_curr_alpha, cellparams={'tau_m': 'bar'})
     Traceback (most recent call last):
-      File "/usr/lib/python/site-packages/pyNN/nest1.py", line 228, in create
+      File "<stdin>", line 1, in ?
+        create(IF_curr_alpha, cellparams={'tau_m': 'bar'})
+      File "/usr/lib/python/site-packages/pyNN/common.py", line 655, in create
+        all_cells, mask_local, first_id, last_id = simulator.create_cells(cellclass, cellparams, n)
+      File "/usr/lib/python/site-packages/pyNN/neuron/simulator.py", line 287, in create_cells
         celltype = cellclass(cellparams)
-      File "/usr/lib/python/site-packages/pyNN/nest1.py", line 68, in __init__
-        common.IF_curr_alpha.__init__(self,parameters) # checks supplied parameters and adds default
-      File "/usr/lib/python/site-packages/pyNN/common.py", line 113, in __init__
-        self.parameters = self.checkParameters(parameters, with_defaults=True)
-      File "/usr/lib/python/site-packages/pyNN/common.py", line 90, in checkParameters
-        raise InvalidParameterValueError, (type(supplied_parameters[k]), type(default_parameters[k]))
-    InvalidParameterValueError: (<type 'str'>, <type 'float'>)
-
+      File "/usr/lib/python/site-packages/pyNN/neuron/cells.py", line 442, in __init__
+        cells.IF_curr_alpha.__init__(self, parameters) # checks supplied parameters and adds default
+      File "/usr/lib/python/site-packages/pyNN/common.py", line 460, in __init__
+        self.parameters = self.__class__.checkParameters(parameters, with_defaults=True)
+      File "/usr/lib/python/site-packages/pyNN/common.py", line 494, in checkParameters
+        raise InvalidParameterValueError(err_msg)
+    InvalidParameterValueError: For tau_m in IF_curr_alpha, expected <type 'float'>, got <type 'str'> (bar)
     
 If you wish to do something with the cell after creating it: record from it, change a parameter, connect it to another cell, you should assign the return value of the function to a variable, e.g.::
@@ -180 +188 @@
     
 Positions must always be in 3D, and may be given as integers or floating-point values, and as tuples or as numpy arrays.
-No specific scale of units is assumed, although many parts of PyNN do assume a Euclidean coordinate system.
+No specific coordinate system or scale of units is assumed, although many parts of PyNN do assume a Euclidean coordinate system.
 
 Injecting current
@@ -235 +243 @@
 In this case, use the ``compatible_output=False`` argument to the ``end()`` function.
 
-Considerable enhancements to file formats are planned for future releases of PyNN, including recording to binary (HDF5) rather than text files, support for variable time-step recording, and user-specified output formats.
+For recording to binary (e.g. HDF5) rather than text files, see the chapter on file formats.
 
 Running a simulation
@@ -244 +252 @@
     >>> run(1000.0)
     
+
+Repeating a simulation
+======================
+
+If you wish to reset network time to zero to run a new simulation with the same
+network (with different parameter values, perhaps), use the ``reset()`` function.
+Note that this does not change the network structure, nor the choice of which
+neurons to record (from previous ``record()`` calls).
+
+    
 Finishing up
 ============

trunk/doc/testdocs.py

@@ -10 +10 @@
 
 optionflags = doctest.IGNORE_EXCEPTION_DETAIL+doctest.NORMALIZE_WHITESPACE
+#optionflags = doctest.NORMALIZE_WHITESPACE
 
 class MyOutputChecker(doctest.OutputChecker):