The tutorial chapter has been updated to explain the new iterators in…

… Table,

Group and File, multidimensional columns in tables and the new row deletion
capability.


git-svn-id: http://www.pytables.org/svn/pytables/trunk@151 1b98710c-d8ec-0310-ae81-f5f2bcd8cb94

examples/array1.py

@@ -1,4 +1,5 @@
-from Numeric import *
+from numarray import *
+from numarray import strings
 from tables import *
 
 # Open a new empty HDF5 file
@@ -7,17 +8,17 @@
 root = fileh.root
 
 # Create an array
-a = array(['1', '2', '4'], "c")
+a = strings.array(['1', '2', '4'])
 # Save it on the HDF5 file
 hdfarray = fileh.createArray(root, 'array_c', a, "Character array")
 
 # Create other
-a = array([-1, 2, 4], "1")
+a = array([-1, 2, 4], Int8)
 # Save it on the HDF5 file
 hdfarray = fileh.createArray(root, 'array_1', a, "Signed byte array")
 
 # This is amusing, just create another one ;-)
-a = array([-1, 2, 4], "b")
+a = array([-1, 2, 4], UInt8)
 # Save it on the HDF5 file
 hdfarray = fileh.createArray(root, 'array_b', a, "Unsigned byte array")
 

examples/array2.py

@@ -1,4 +1,4 @@
-from Numeric import *
+from numarray import *
 from tables import *
 
 # Open a new empty HDF5 file

examples/array3.py

@@ -1,4 +1,5 @@
-from Numeric import *
+from numarray import *
+from numarray import strings
 from tables import *
 
 # Open a new empty HDF5 file
@@ -8,10 +9,10 @@
 
 # Create a large array
 #a = reshape(array(range(2**16), "s"), (2,) * 16)
-a = ones((2,) * 8, "c")
+a = ones((2,) * 8, Int8)
 print "About to write array a"
 print "  with shape: ==>", a.shape
-print "  and typecode ==> %c" % a.typecode()
+print "  and type: ==> %s" % a.type()
 
 # Save it on the HDF5 file
 hdfarray = fileh.createArray(root, 'carray', a, "Large array")

examples/array4.py

@@ -1,4 +1,4 @@
-from Numeric import *
+from numarray import *
 from tables import *
 
 basedim = 4
@@ -8,15 +8,14 @@
 # Get the root group
 group = fileh.root
 # Set the type codes to test
-#typecodes = ["c", 'b', '1', 's', 'w', 'i', 'u', 'l', 'f', 'd']
-# Reduce the set of typecodes because numarray miss some
-typecodes = ['c', 'b', '1', 's', 'i', 'l', 'f', 'd']
+#typecodes = ['c', 'b', '1', 's', 'i', 'l', 'f', 'd']
+typecodes = [Int8, UInt8, Int16, Int, Float32, Float]
 i = 1
 for typecode in typecodes:
     # Create an array of typecode, with incrementally bigger ranges
     a = ones((basedim,) * i, typecode)
     # Save it on the HDF5 file
-    dsetname = 'array_' + typecode
+    dsetname = 'array_' + str(typecode)
     hdfarray = fileh.createArray(group, dsetname, a, "Large array")
     print "Created dataset:", hdfarray
     # Create a new group
@@ -33,17 +32,21 @@
 # Get the root group
 group = fileh.root
 # Get the metadata on the previosly saved arrays
-for i in range(1,len(typecodes)):
+for i in range(1,len(typecodes)+1):
     # Create an array for later comparison
     a = ones((basedim,) * (i), typecodes[i-1])
     # Get the dset object hangin from group
-    dset = getattr(group, 'array_' + typecodes[i-1])
+    dset = getattr(group, 'array_' + str(typecodes[i-1]))
     print "Info from dataset:", repr(dset)
     # Read the actual data in array
     b = dset.read()
-    print "Array b read from file. Shape: ==>", b.shape,
-    print ". Typecode ==> %c" % b.typecode()
-    assert a == b
+    print "Array b read from file. Shape ==>", b.shape,
+    print ". Type ==> %s" % b.type()
+    # Test if the original and read arrays are equal
+    if allclose(a, b):
+        print "Good: Read array is equal to the original"
+    else:
+        print "Error: Read array and the original differs!"
     # Iterate over the next group
     group = getattr(group, 'group' + str(i))
 

examples/table-tree.py

@@ -81,7 +81,7 @@ class Particle(IsDescription):
                    "Pressure column", atomictype=0)
 print "gcolumns.pressure type ==> ", gcolumns.pressure.type
 
-# Do the same with TDCcount
+# Do the same with TDCcount, but with a numarray object
 TDC = [ p['TDCcount'] for p in table.iterrows() ]
 print "TDC ==>", TDC
 print "TDC shape ==>", array(TDC).shape

examples/tutorial1-1.py

@@ -7,7 +7,7 @@
 
 
 import sys
-from Numeric import *
+from numarray import *
 from tables import *
 
 
@@ -58,7 +58,6 @@ class Particle(IsDescription):
     particle['grid_j'] = 10 - i
     particle['pressure'] = float(i*i)
     particle['energy'] = float(particle['pressure'] ** 4)
-    #particle['energy'] = 4
     particle['idnumber'] = i * (2 ** 34)
     # Insert a new particle record
     particle.append()
@@ -72,26 +71,26 @@ class Particle(IsDescription):
 # Read actual data from table. We are interested in collecting pressure values
 # on entries where TDCcount field is greater than 3 and pressure less than 50
 pressure = [ x['pressure'] for x in table
-             if x['TDCcount'] > 3 and x['pressure'] < 50 ]
+             if x['TDCcount']>3 and 20<=x['pressure']<50 ]
 print "Last record read:"
 print x
 print "Field pressure elements satisfying the cuts ==>", pressure
 
 # Read also the names with the same cuts
 names = [ x['name'] for x in table
-          if x['TDCcount'] > 3 and x['pressure'] < 50 ]
+          if x['TDCcount'] > 3 and 20 <= x['pressure'] < 50 ]
 
 print
 print	'-**-**-**-**-**-**- array object creation  -**-**-**-**-**-**-**-'
 
 print "Creating a new group called '/columns' to hold new arrays"
 gcolumns = h5file.createGroup(h5file.root, "columns", "Pressure and Name")
 
-print "Creating a Numeric array called 'pressure' under '/columns' group"
+print "Creating an array called 'pressure' under '/columns' group"
 h5file.createArray(gcolumns, 'pressure', array(pressure), 
                    "Pressure column selection")
 
-print "Creating another Numeric array called 'name' under '/columns' group"
+print "Creating another array called 'name' under '/columns' group"
 h5file.createArray('/columns', 'name', names, "Name column selection")
 
 # Close the file

examples/tutorial1-2.py

@@ -7,7 +7,7 @@
 
 
 import sys
-from Numeric import *
+from numarray import *
 from tables import *
 
 # Filename to work with
@@ -36,28 +36,33 @@
     print node
 print
 
-# List all the Leafs (using File iterator) on tree
-print "Leafs in file:"
-for node in h5file(classname="Leaf"):
-    print node
-print
-
 # Now, only list all the groups on tree
 print "Groups in file:"
 for group in h5file(classname="Group"):
     print group
 print
 
-# List only the arrays (using Group iterator) hanging from /
-print "Arrays in /:"
-for array in h5file.root(classname="Array", recursive=1):
+# List only the arrays hanging from /
+print "Arrays in file (I):"
+for group in h5file.walkGroups("/"):
+    for array in h5file.listNodes(group, classname = 'Array'):
+        print array
+
+# This do the same result
+print "Arrays in file (II):"
+for array in h5file("/", "Array"):
     print array
 print
+# And finally, list only leafs on /detector group (there should be one!)
+print "Leafs in group '/detector' (I):"
+for leaf in h5file.listNodes("/detector", 'Leaf'):
+    print leaf
+
+# Other way using iterators and natural naming
+print "Leafs in group '/detector' (II):"
+for leaf in h5file.root.detector('Leaf'):
+    print leaf
 
-# And finally, list only tables on /detector group (there should be one!)
-print "Tables in group '/detector':"
-for table in h5file.listNodes("/detector", 'Leaf'):
-    print table
 
 
 print
@@ -123,7 +128,7 @@
 print "Number of rows in table:", table.nrows
 print "Table variable names with their type and shape:"
 for name in table.colnames:
-    print "  ", name, ':=', table.coltypes[name], table.colshapes[name]
+    print name, ':= %s, %s' % (table.coltypes[name], table.colshapes[name])
 print    
 
 # Get the object in "/columns pressure"
@@ -140,7 +145,7 @@
 # Read the 'name' Array actual data
 nameArray = h5file.root.columns.name.read()
 
-# Check the kind of object we have created (they should be Numeric arrays)
+# Check the kind of object we have created (they should be numarray arrays)
 print "pressureArray is an object of type:", type(pressureArray)
 print "nameArray is an object of type:", type(nameArray)
 print
@@ -186,11 +191,23 @@
 # Flush this table
 table.flush()
 
+# Print the data using the table iterator:
+for r in table:
+    print "%-16s | %11.1f | %11.4g | %6d | %6d | %8d |" % \
+          (r['name'], r['pressure'], r['energy'], r['grid_i'], r['grid_j'], 
+           r['TDCcount'])
+
+print
+print "Total number of entries in resulting table:", table.nrows
+
+print
+print	'-**-**-**-**- remove records from a table -**-**-**-**-**-'
+
 # Delete some rows on the Table (yes, rows can be removed!)
 table.removeRows(5,10)
 
 # Print some table columns, for comparison with array data
-print "Some columns on enlarged table:"
+print "Some columns in final table:"
 print
 # Print the headers
 print "%-16s | %11s | %11s | %6s | %6s | %8s |" % \
@@ -206,7 +223,7 @@
            r['TDCcount'])
 
 print
-print "Total number of entries after appending new rows:", table.nrows
+print "Total number of entries in final table:", table.nrows
 
 # Close the file
 h5file.close()

examples/tutorial2.py

@@ -5,15 +5,16 @@
 
 """
 
+from numarray import *
 from tables import *
 
 # Describe a particle record
 class Particle(IsDescription):
     name        = StringCol(length=16) # 16-character String
     lati        = IntCol()             # integer
     longi       = IntCol()             # integer
-    pressure    = Float32Col()         # float  (single-precision)
-    temperature = FloatCol()           # double (double-precision)
+    pressure    = Float32Col(shape=(2,3)) # array of floats (single-precision)
+    temperature = FloatCol(shape=(2,3))   # array of doubles (double-precision)
 
 # Another way to describe the columns of a table
 Event = {
@@ -48,8 +49,8 @@ class Particle(IsDescription):
         particle['name'] = 'Particle: %6d' % (i)
         particle['lati'] = i 
         particle['longi'] = 10 - i
-        particle['pressure'] = float(i*i)
-        particle['temperature'] = float(i**2)
+        particle['pressure'] = array(i*arange(2*3), shape=(2,3))
+        particle['temperature'] = array((i**2)*arange(2*3, shape=(2,3)))
         # This injects the Record values
         particle.append()      
 
@@ -67,15 +68,12 @@ class Particle(IsDescription):
     for i in xrange(257):
         # First, assign the values to the Event record
         event['name']  = 'Event: %6d' % (i)
-        # Range checks no longer works on 0.4. Hope that
-        # next version of numarray can support that!
-        #event['TDCcount'] = i            # Wrong range.
         event['TDCcount'] = i % (1<<8)   # Correct range
         ########### Detectable errors start here. Play with them!
-        #event['xcoord'] = float(i**2)   # Correct spelling
-        event['xcoor'] = float(i**2)     # Wrong spelling
-        #event['ADCcount'] = i * 2        # Correct type
-        event['ADCcount'] = "s"          # Wrong type
+        event['xcoord'] = float(i**2)   # Correct spelling
+        #event['xcoor'] = float(i**2)     # Wrong spelling
+        event['ADCcount'] = i * 2        # Correct type
+        #event['ADCcount'] = "s"          # Wrong type
         ########### End of errors
         event['ycoord'] = float(i)**4
         # This injects the Record values

tables/AttributeSet.py

@@ -5,7 +5,7 @@
 #       Author:  Francesc Alted - falted@openlc.org
 #
 #       $Source: /home/ivan/_/programari/pytables/svn/cvs/pytables/pytables/tables/AttributeSet.py,v $
-#       $Id: AttributeSet.py,v 1.12 2003/07/16 20:17:56 falted Exp $
+#       $Id: AttributeSet.py,v 1.13 2003/07/27 20:40:16 falted Exp $
 #
 ########################################################################
 
@@ -31,7 +31,7 @@
 
 """
 
-__version__ = "$Revision: 1.12 $"
+__version__ = "$Revision: 1.13 $"
 
 import warnings, types, cPickle
 import hdf5Extension
@@ -298,7 +298,7 @@ def __str__(self):
         classname = self.__class__.__name__
         # The attrribute names
         attrnumber = len(self._v_attrnames)
-        return "%s (%s): %s attributes" % (pathname, classname, attrnumber)
+        return "%s (%s), %s attributes" % (pathname, classname, attrnumber)
 
     def __repr__(self):
         """A detailed string representation for this object."""
@@ -307,6 +307,6 @@ def __repr__(self):
                 for attr in self._v_attrnames ]
         attrlist = '[%s]' % (',\n    '.join(rep))
 
-        return "%s\n   %s" % \
+        return "%s:\n   %s" % \
                (str(self), attrlist)
 

tables/File.py

@@ -4,7 +4,7 @@
 #       Author:  Francesc Alted - falted@openlc.org
 #
 #       $Source: /home/ivan/_/programari/pytables/svn/cvs/pytables/pytables/tables/File.py,v $
-#       $Id: File.py,v 1.47 2003/07/26 18:42:53 falted Exp $
+#       $Id: File.py,v 1.48 2003/07/27 20:40:16 falted Exp $
 #
 ########################################################################
 
@@ -31,7 +31,7 @@
 
 """
 
-__version__ = "$Revision: 1.47 $"
+__version__ = "$Revision: 1.48 $"
 format_version = "1.1"                     # File format version we write
 compatible_formats = []                    # Old format versions we can read
 
@@ -620,6 +620,11 @@ def _iterTree(self, where="/", classname=""):
         if classname == "Group":
             for group in self.walkGroups(where):
                 yield group
+        elif classname in [None, ""]:
+            yield self.getNode(where, "")
+            for group in self.walkGroups(where):
+                for leaf in self.listNodes(group, ""):
+                    yield leaf
         else:
             for group in self.walkGroups(where):
                 for leaf in self.listNodes(group, classname):