Changeset 400 for trunk

Timestamp:

06/15/09 23:30:10 (3 years ago)

Author:

pierre

Message:

Add dependencies, but mainly optionnal. A particular package, TableIO, speeds up the loading time of big text data files. Could be useful. For the moment, it's only added in io.py as an option, and not even suggested in the dependency, but why not. The other stuffs is the creation of a tisean wrapper. TISEAN is a well-known and famoust toolbox for non linear analysis. Maybe a lot of those functions could be used for SpikeList analysis, and it should be considered, at least for testing purpose, and even better for a real use. TISEAN must be installed, nothing is really done yet for integration, this is just a proposal

Location:

trunk

Files:

• setup.py (modified) (1 diff)
• src/__init__.py (modified) (1 diff)
• src/io.py (modified) (1 diff)
• src/tisean (added)
• src/tisean/__init__.py (added)
• src/tisean/tisean.py (added)

trunk/setup.py

@@ -9 +9 @@
     packages = ['NeuroTools',
                 'NeuroTools.utilities',
+                'NeuroTools.tisean',
                 'NeuroTools.spike2',
                 'NeuroTools.signals',

trunk/src/__init__.py

@@ -35 +35 @@
 """
 
-__all__ = ['analysis', 'parameters', 'plotting', 'signals', 'stgen', 'io', 'datastore', 'utilities', 'spike2', 'random', 'optimize']
+__all__ = ['analysis', 'parameters', 'plotting', 'signals', 'stgen', 'io', 'datastore', 'utilities', 'spike2', 'random', 'optimize', 'tisean']
 __version__ = "0.1.0 (Asynchronous Astrocyte)"
 

trunk/src/io.py

@@ -158 +158 @@
         Load data from a text file and returns an array of the data
         """
-        myfile = open(self.filename, "r", DEFAULT_BUFFER_SIZE)
-        contents = myfile.readlines()
-        myfile.close()
-        data = []
-        for line in contents:
-            if (line[0] != skipchar):
-                line = line.strip().split(sepchar)
-                id   = [int(float(line[-1]))]
-                id.extend(map(float, line[0:-1]))
-                data.append(id)
-        logging.debug("Loaded %d lines of data from %s" % (len(data), self))
-        return numpy.array(data, numpy.float32)
-    
+        try:
+            import TableIO
+            data = TableIO.readTableAsArray(self.filename, skipchar)
+        except ImportError:
+            myfile = open(self.filename, "r", DEFAULT_BUFFER_SIZE)
+            contents = myfile.readlines()
+            myfile.close()
+            data = []
+            for line in contents:
+                if (line[0] != skipchar):
+                    line = line.strip().split(sepchar)
+                    id   = [int(float(line[-1]))]
+                    id.extend(map(float, line[0:-1]))
+                    data.append(id)
+            logging.debug("Loaded %d lines of data from %s" % (len(data), self))
+            data = numpy.array(data, numpy.float32)
+        return data
+
     #def get_data(self, sepchar = "\t", skipchar = "#"):
         #return numpy.loadtxt(self.filename, dtype=numpy.float32)