add .gitignore

git-svn-id: https://bucket.mit.edu/svn/nilm/nilmdb@11380 ddd99763-3ecb-0310-9145-efcb8ce7c51f

nilmdb/bxintersect.pyx

@@ -1,26 +1,7 @@
 # cython: profile=False
-# This is from bx-python 554:07aca5a9f6fc (BSD licensed), modified to
+# This is based on bxintersect in bx-python 554:07aca5a9f6fc (BSD licensed);
-# store interval ranges as doubles rather than 32-bit integers.
+# modified to store interval ranges as doubles rather than 32-bit integers,
-
+# use fully closed intervals, support deletion, etc.
-"""
-Data structure for performing intersect queries on a set of intervals which
-preserves all information about the intervals (unlike bitset projection methods).
-
-:Authors: James Taylor (james@jamestaylor.org),
-          Ian Schenk (ian.schenck@gmail.com),
-          Brent Pedersen (bpederse@gmail.com)
-"""
-
-# Historical note:
-#    This module original contained an implementation based on sorted endpoints
-#    and a binary search, using an idea from Scott Schwartz and Piotr Berman.
-#    Later an interval tree implementation was implemented by Ian for Galaxy's
-#    join tool (see `bx.intervals.operations.quicksect.py`). This was then
-#    converted to Cython by Brent, who also added support for
-#    upstream/downstream/neighbor queries. This was modified by James to
-#    handle half-open intervals strictly, to maintain sort order, and to
-#    implement the same interface as the original Intersecter.
-
 #cython: cdivision=True
 
 import operator
@@ -72,7 +53,7 @@ cdef class IntervalNode:
     cdef public object interval
     cdef public double start, end
     cdef double minend, maxend, minstart
-    cdef public IntervalNode cleft, cright, croot
+    cdef IntervalNode cleft, cright, croot
 
     property left_node:
         def __get__(self):
@@ -194,76 +175,6 @@ cdef class IntervalNode:
             self.cright._intersect( start, end, results )
 
 
-    cdef void _seek_left(IntervalNode self, double position, list results, int n, double max_dist):
-        # we know we can bail in these 2 cases.
-        if self.maxend + max_dist < position:
-            return
-        if self.minstart > position:
-            return
-
-        # the ordering of these 3 blocks makes it so the results are
-        # ordered nearest to farest from the query position
-        if self.cright is not EmptyNode:
-            self.cright._seek_left(position, results, n, max_dist)
-
-        if -1 < position - self.end < max_dist:
-            results.append(self.interval)
-
-        # TODO: can these conditionals be more stringent?
-        if self.cleft is not EmptyNode:
-                self.cleft._seek_left(position, results, n, max_dist)
-
-
-
-    cdef void _seek_right(IntervalNode self, double position, list results, int n, double max_dist):
-        # we know we can bail in these 2 cases.
-        if self.maxend < position: return
-        if self.minstart - max_dist > position: return
-
-        #print "SEEK_RIGHT:",self, self.cleft, self.maxend, self.minstart, position
-
-        # the ordering of these 3 blocks makes it so the results are
-        # ordered nearest to farest from the query position
-        if self.cleft is not EmptyNode:
-                self.cleft._seek_right(position, results, n, max_dist)
-
-        if -1 < self.start - position < max_dist:
-            results.append(self.interval)
-
-        if self.cright is not EmptyNode:
-                self.cright._seek_right(position, results, n, max_dist)
-
-
-    cpdef left(self, position, int n=1, double max_dist=2500):
-        """
-        find n features with a start > than `position`
-        f: a Interval object (or anything with an `end` attribute)
-        n: the number of features to return
-        max_dist: the maximum distance to look before giving up.
-        """
-        cdef list results = []
-        # use start - 1 becuase .left() assumes strictly left-of
-        self._seek_left( position - 1, results, n, max_dist )
-        if len(results) == n: return results
-        r = results
-        r.sort(key=operator.attrgetter('end'), reverse=True)
-        return r[:n]
-
-    cpdef right(self, position, int n=1, double max_dist=2500):
-        """
-        find n features with a end < than position
-        f: a Interval object (or anything with a `start` attribute)
-        n: the number of features to return
-        max_dist: the maximum distance to look before giving up.
-        """
-        cdef list results = []
-        # use end + 1 becuase .right() assumes strictly right-of
-        self._seek_right(position + 1, results, n, max_dist)
-        if len(results) == n: return results
-        r = results
-        r.sort(key=operator.attrgetter('start'))
-        return r[:n]
-
     def traverse(self):
         if self.cleft is not EmptyNode:
             for node in self.cleft.traverse():
@@ -390,15 +301,9 @@ cdef class IntervalTree:
     def __cinit__( self ):
         root = None
 
-    # Helper for plots
-    def emptynode( self ):
-        return EmptyNode
-
-    def rootnode( self ):
-        return self.root
-
     # ---- Position based interfaces -----------------------------------------
 
+    ## KEEP
     def insert( self, double start, double end, object value=None ):
         """
         Insert the interval [start,end) associated with value `value`.
@@ -408,8 +313,14 @@ cdef class IntervalTree:
         else:
             self.root = self.root.insert( start, end, value )
 
-    add = insert
+    def delete( self, double start, double end, object value=None ):
-
+        """
+        Delete the interval [start,end) associated with value `value`.
+        """
+        if self.root is None:
+            self.root = IntervalNode( start, end, value )
+        else:
+            self.root = self.root.insert( start, end, value )
 
     def find( self, start, end ):
         """
@@ -419,26 +330,9 @@ cdef class IntervalTree:
             return []
         return self.root.find( start, end )
 
-    def before( self, position, num_intervals=1, max_dist=2500 ):
-        """
-        Find `num_intervals` intervals that lie before `position` and are no
-        further than `max_dist` positions away
-        """
-        if self.root is None:
-            return []
-        return self.root.left( position, num_intervals, max_dist )
-
-    def after( self, position, num_intervals=1, max_dist=2500 ):
-        """
-        Find `num_intervals` intervals that lie after `position` and are no
-        further than `max_dist` positions away
-        """
-        if self.root is None:
-            return []
-        return self.root.right( position, num_intervals, max_dist )
-
     # ---- Interval-like object based interfaces -----------------------------
 
+    ## KEEP
     def insert_interval( self, interval ):
         """
         Insert an "interval" like object (one with at least start and end
@@ -446,50 +340,6 @@ cdef class IntervalTree:
         """
         self.insert( interval.start, interval.end, interval )
 
-    add_interval = insert_interval
-
-    def before_interval( self, interval, num_intervals=1, max_dist=2500 ):
-        """
-        Find `num_intervals` intervals that lie completely before `interval`
-        and are no further than `max_dist` positions away
-        """
-        if self.root is None:
-            return []
-        return self.root.left( interval.start, num_intervals, max_dist )
-
-    def after_interval( self, interval, num_intervals=1, max_dist=2500 ):
-        """
-        Find `num_intervals` intervals that lie completely after `interval` and
-        are no further than `max_dist` positions away
-        """
-        if self.root is None:
-            return []
-        return self.root.right( interval.end, num_intervals, max_dist )
-
-    def upstream_of_interval( self, interval, num_intervals=1, max_dist=2500 ):
-        """
-        Find `num_intervals` intervals that lie completely upstream of
-        `interval` and are no further than `max_dist` positions away
-        """
-        if self.root is None:
-            return []
-        if interval.strand == -1 or interval.strand == "-":
-            return self.root.right( interval.end, num_intervals, max_dist )
-        else:
-            return self.root.left( interval.start, num_intervals, max_dist )
-
-    def downstream_of_interval( self, interval, num_intervals=1, max_dist=2500 ):
-        """
-        Find `num_intervals` intervals that lie completely downstream of
-        `interval` and are no further than `max_dist` positions away
-        """
-        if self.root is None:
-            return []
-        if interval.strand == -1 or interval.strand == "-":
-            return self.root.left( interval.start, num_intervals, max_dist )
-        else:
-            return self.root.right( interval.end, num_intervals, max_dist )
-
     def traverse(self):
         """
         iterator that traverses the tree

nilmdb/interval.py

@@ -8,20 +8,25 @@ Intervals are closed, ie. they include timestamps [start, end]
 # First implementation kept a sorted list of intervals and used
 # biesct() to optimize some operations, but this was too slow.
 
-# This version is based on the quicksect implementation from python-bx,
+# Second version was based on the quicksect implementation from
-# modified slightly to handle floating point intervals.
+# python-bx, modified slightly to handle floating point intervals.
+# This didn't support deletion.
+
+# Third version is more similar to the first version, using a rb-tree
+# instead of a simple sorted list to maintain O(log n) operations.
+
+# Fourth version is an optimized rb-tree that stores interval starts
+# and ends directly in the tree, like bxinterval did.
+
+# Fifth version is back to modified bxintersect...
 
-import pyximport
-pyximport.install()
 import bxintersect
 
-import bisect
-
 class IntervalError(Exception):
     """Error due to interval overlap, etc"""
     pass
 
-class Interval(bxintersect.Interval):
+class Interval(object):
     """Represents an interval of time."""
 
     def __init__(self, start, end):
@@ -30,7 +35,8 @@ class Interval(bxintersect.Interval):
         """
         if start > end:
             raise IntervalError("start %s must precede end %s" % (start, end))
-        bxintersect.Interval.__init__(self, start, end)
+        self.start = float(start)
+        self.end = float(end)
 
     def __repr__(self):
         s = repr(self.start) + ", " + repr(self.end)
@@ -39,6 +45,20 @@ class Interval(bxintersect.Interval):
     def __str__(self):
         return "[" + str(self.start) + " -> " + str(self.end) + "]"
 
+    def __cmp__(self, other):
+        """Compare two intervals.  If non-equal, order by start then end"""
+        if not isinstance(other, Interval):
+            raise TypeError("bad type")
+        if self.start == other.start:
+            if self.end < other.end:
+                return -1
+            if self.end > other.end:
+                return 1
+            return 0
+        if self.start < other.start:
+            return -1
+        return 1
+
     def intersects(self, other):
         """Return True if two Interval objects intersect"""
         if (self.end <= other.start or self.start >= other.end):
@@ -66,6 +86,7 @@ class DBInterval(Interval):
         end = 150
         db_end = 200, db_endpos = 20000
     """
+
     def __init__(self, start, end,
                  db_start, db_end,
                  db_startpos, db_endpos):
@@ -109,12 +130,14 @@ class IntervalSet(object):
         """
         'source' is an Interval or IntervalSet to add.
         """
-        self.tree = bxintersect.IntervalTree()
+        self.tree = bxinterval.IntervalTree()
         if source is not None:
             self += source
 
     def __iter__(self):
-        return self.tree.traverse()
+        for node in self.tree:
+            if node.obj:
+                yield node.obj
 
     def __len__(self):
         return sum(1 for x in self)
@@ -195,6 +218,17 @@ class IntervalSet(object):
                 self.__iadd__(x)
         return self
 
+    def __isub__(self, other):
+        """Inplace subtract -- modifies self
+
+        Removes an interval from the set.  Must exist exactly
+        as provided -- cannot remove a subset of an existing interval."""
+        i = self.tree.find(other.start, other.end)
+        if i is None:
+            raise IntervalError("interval " + str(other) + " not in tree")
+        self.tree.delete(i)
+        return self
+
     def __add__(self, other):
         """Add -- returns a new object"""
         new = IntervalSet(self)
@@ -211,11 +245,12 @@ class IntervalSet(object):
         out = IntervalSet()
 
         if not isinstance(other, IntervalSet):
-            other = [ other ]
+            for i in self.intersection(other):
-
+                out.tree.insert(rbtree.RBNode(i))
-        for x in other:
+        else:
-            for i in self.intersection(x):
+            for x in other:
-                out.tree.insert_interval(i)
+                for i in self.intersection(x):
+                    out.tree.insert(rbtree.RBNode(i))
 
         return out
 
@@ -229,13 +264,30 @@ class IntervalSet(object):
         Output intervals are built as subsets of the intervals in the
         first argument (self).
         """
-        for i in self.tree.find(interval.start, interval.end):
+        if not isinstance(interval, Interval):
-            if i.start > interval.start and i.end < interval.end:
+            raise TypeError("bad type")
-                yield i
+        for n in self.tree.intersect(interval.start, interval.end):
-            else:
+            i = n.obj
-                yield i.subset(max(i.start, interval.start),
+            if i:
-                               min(i.end, interval.end))
+                if i.start >= interval.start and i.end <= interval.end:
+                    yield i
+                elif i.start > interval.end:
+                    break
+                else:
+                    subset = i.subset(max(i.start, interval.start),
+                                      min(i.end, interval.end))
+                    yield subset
 
     def intersects(self, other):
+        ### PROBABLY WRONG
         """Return True if this IntervalSet intersects another interval"""
-        return len(self.tree.find(other.start, other.end)) > 0
+        node = self.tree.find_left(other.start, other.end)
+        if node is None:
+            return False
+        for n in self.tree.inorder(node):
+            if n.obj:
+                if n.obj.intersects(other):
+                    return True
+                if n.obj > other:
+                    break
+        return False

nilmdb/rbtree.py

@@ -0,0 +1,392 @@
+"""Red-black tree, where keys are stored as start/end timestamps."""
+
+import sys
+
+class RBNode(object):
+    """One node of the Red/Black tree.  obj points to any object,
+    'start' and 'end' are timestamps that represent the key."""
+    def __init__(self, obj = None, start = None, end = None):
+        """If given an object but no start/end times, get the
+        start/end times from the object.
+
+        If given start/end times, obj can be anything, including None."""
+        self.obj = obj
+        if start is None:
+            start = obj.start
+        if end is None:
+            end = obj.end
+        self.start = start
+        self.end = end
+        self.red = False
+        self.left = None
+        self.right = None
+
+    def __str__(self):
+        if self.red:
+            color = "R"
+        else:
+            color = "B"
+        return ("[node "
+                + str(self.start) + " -> " + str(self.end) + " "
+                + color + "]")
+
+class RBTree(object):
+    """Red/Black tree"""
+
+    # Init
+    def __init__(self):
+        self.nil = RBNode(start = sys.float_info.min,
+                           end = sys.float_info.min)
+        self.nil.left = self.nil
+        self.nil.right = self.nil
+        self.nil.parent = self.nil
+        self.nil.nil = True
+
+        self.root = RBNode(start = sys.float_info.max,
+                           end = sys.float_info.max)
+        self.root.left = self.nil
+        self.root.right = self.nil
+        self.root.parent = self.nil
+
+    # Rotations and basic operations
+    def __rotate_left(self, x):
+        y = x.right
+        x.right = y.left
+        if y.left is not self.nil:
+            y.left.parent = x
+        y.parent = x.parent
+        if x is x.parent.left:
+            x.parent.left = y
+        else:
+            x.parent.right = y
+        y.left = x
+        x.parent = y
+
+    def __rotate_right(self, y):
+        x = y.left
+        y.left = x.right
+        if x.right is not self.nil:
+            x.right.parent = y
+        x.parent = y.parent
+        if y is y.parent.left:
+            y.parent.left = x
+        else:
+            y.parent.right = x
+        x.right = y
+        y.parent = x
+
+    def __successor(self, x):
+        """Returns the successor of RBNode x"""
+        y = x.right
+        if y is not self.nil:
+            while y.left is not self.nil:
+                y = y.left
+        else:
+            y = x.parent
+            while x is y.right:
+                x = y
+                y = y.parent
+            if y is self.root:
+                return self.nil
+        return y
+
+    def _predecessor(self, x):
+        """Returns the predecessor of RBNode x"""
+        y = x.left
+        if y is not self.nil:
+            while y.right is not self.nil:
+                y = y.right
+        else:
+            y = x.parent
+            while x is y.left:
+                if y is self.root:
+                    y = self.nil
+                    break
+                x = y
+                y = y.parent
+        return y
+
+    # Insertion
+    def insert(self, z):
+        """Insert RBNode z into RBTree and rebalance as necessary"""
+        z.left = self.nil
+        z.right = self.nil
+        y = self.root
+        x = self.root.left
+        while x is not self.nil:
+            y = x
+            if (x.start > z.start or (x.start == z.start and x.end > z.end)):
+                x = x.left
+            else:
+                x = x.right
+        z.parent = y
+        if (y is self.root or
+            (y.start > z.start or (y.start == z.start and y.end > z.end))):
+            y.left = z
+        else:
+            y.right = z
+        # relabel/rebalance
+        self.__insert_fixup(z)
+
+    def __insert_fixup(self, x):
+        """Rebalance/fix RBTree after a simple insertion of RBNode x"""
+        x.red = True
+        while x.parent.red:
+            if x.parent is x.parent.parent.left:
+                y = x.parent.parent.right
+                if y.red:
+                    x.parent.red = False
+                    y.red = False
+                    x.parent.parent.red = True
+                    x = x.parent.parent
+                else:
+                    if x is x.parent.right:
+                        x = x.parent
+                        self.__rotate_left(x)
+                    x.parent.red = False
+                    x.parent.parent.red = True
+                    self.__rotate_right(x.parent.parent)
+            else: # same as above, left/right switched
+                y = x.parent.parent.left
+                if y.red:
+                    x.parent.red = False
+                    y.red = False
+                    x.parent.parent.red = True
+                    x = x.parent.parent
+                else:
+                    if x is x.parent.left:
+                        x = x.parent
+                        self.__rotate_right(x)
+                    x.parent.red = False
+                    x.parent.parent.red = True
+                    self.__rotate_left(x.parent.parent)
+        self.root.left.red = False
+
+    # Deletion
+    def delete(self, z):
+        if z.left is None or z.right is None:
+            raise AttributeError("you can only delete a node object "
+                                 + "from the tree; use find() to get one")
+        if z.left is self.nil or z.right is self.nil:
+            y = z
+        else:
+            y = self.__successor(z)
+        if y.left is self.nil:
+            x = y.right
+        else:
+            x = y.left
+        x.parent = y.parent
+        if x.parent is self.root:
+            self.root.left = x
+        else:
+            if y is y.parent.left:
+                y.parent.left = x
+            else:
+                y.parent.right = x
+        if y is not z:
+            # y is the node to splice out, x is its child
+            y.left = z.left
+            y.right = z.right
+            y.parent = z.parent
+            z.left.parent = y
+            z.right.parent = y
+            if z is z.parent.left:
+                z.parent.left = y
+            else:
+                z.parent.right = y
+            if not y.red:
+                y.red = z.red
+                self.__delete_fixup(x)
+            else:
+                y.red = z.red
+        else:
+            if not y.red:
+                self.__delete_fixup(x)
+
+    def __delete_fixup(self, x):
+        """Rebalance/fix RBTree after a deletion.  RBNode x is the
+        child of the spliced out node."""
+        rootLeft = self.root.left
+        while not x.red and x is not rootLeft:
+            if x is x.parent.left:
+                w = x.parent.right
+                if w.red:
+                    w.red = False
+                    x.parent.red = True
+                    self.__rotate_left(x.parent)
+                    w = x.parent.right
+                if not w.right.red and not w.left.red:
+                    w.red = True
+                    x = x.parent
+                else:
+                    if not w.right.red:
+                        w.left.red = False
+                        w.red = True
+                        self.__rotate_right(w)
+                        w = x.parent.right
+                    w.red = x.parent.red
+                    x.parent.red = False
+                    w.right.red = False
+                    self.__rotate_left(x.parent)
+                    x = rootLeft # exit loop
+            else: # same as above, left/right switched
+                w = x.parent.left
+                if w.red:
+                    w.red = False
+                    x.parent.red = True
+                    self.__rotate_right(x.parent)
+                    w = x.parent.left
+                if not w.left.red and not w.right.red:
+                    w.red = True
+                    x = x.parent
+                else:
+                    if not w.left.red:
+                        w.right.red = False
+                        w.red = True
+                        self.__rotate_left(w)
+                        w = x.parent.left
+                    w.red = x.parent.red
+                    x.parent.red = False
+                    w.left.red = False
+                    self.__rotate_right(x.parent)
+                    x = rootLeft # exit loop
+        x.red = False
+
+    # Rendering
+    def __render_dot_node(self, node, max_depth = 20):
+        from printf import sprintf
+        """Render a single node and its children into a dot graph fragment"""
+        if max_depth == 0:
+            return ""
+        if node is self.nil:
+            return ""
+        def c(red):
+            if red:
+                return 'color="#ff0000", style=filled, fillcolor="#ffc0c0"'
+            else:
+                return 'color="#000000", style=filled, fillcolor="#c0c0c0"'
+        s = sprintf("%d [label=\"%g\\n%g\", %s];\n",
+                    id(node),
+                    node.start, node.end,
+                    c(node.red))
+
+        if node.left is self.nil:
+            s += sprintf("L%d [label=\"-\", %s];\n", id(node), c(False))
+            s += sprintf("%d -> L%d [label=L];\n", id(node), id(node))
+        else:
+            s += sprintf("%d -> %d [label=L];\n", id(node), id(node.left))
+        if node.right is self.nil:
+            s += sprintf("R%d [label=\"-\", %s];\n", id(node), c(False))
+            s += sprintf("%d -> R%d [label=R];\n", id(node), id(node))
+        else:
+            s += sprintf("%d -> %d [label=R];\n", id(node), id(node.right))
+        s += self.__render_dot_node(node.left, max_depth-1)
+        s += self.__render_dot_node(node.right, max_depth-1)
+        return s
+
+    def render_dot(self, title = "RBTree"):
+        """Render the entire RBTree as a dot graph"""
+        return ("digraph rbtree {\n"
+                + self.__render_dot_node(self.root.left)
+                + "}\n");
+
+    def render_dot_live(self, title = "RBTree"):
+        """Render the entire RBTree as a dot graph, live GTK view"""
+        import gtk
+        import gtk.gdk
+        sys.path.append("/usr/share/xdot")
+        import xdot
+        xdot.Pen.highlighted = lambda pen: pen
+        s = ("digraph rbtree {\n"
+             + self.__render_dot_node(self.root)
+             + "}\n");
+        window = xdot.DotWindow()
+        window.set_dotcode(s)
+        window.set_title(title + " - any key to close")
+        window.connect('destroy', gtk.main_quit)
+        def quit(widget, event):
+            if not event.is_modifier:
+                window.destroy()
+                gtk.main_quit()
+        window.widget.connect('key-press-event', quit)
+        gtk.main()
+
+    # Walking, searching
+    def __iter__(self):
+        return self.inorder(self.root.left)
+
+    def inorder(self, x = None):
+        """Generator that performs an inorder walk for the tree
+        starting at RBNode x"""
+        if x is None:
+            x = self.root.left
+        while x.left is not self.nil:
+            x = x.left
+        while x is not self.nil:
+            yield x
+            x = self.__successor(x)
+
+    def __find_all(self, start, end, x):
+        """Find node with the specified (start,end) key.
+        Also returns the largest node less than or equal to key,
+        and the smallest node greater or equal to than key."""
+        if x is None:
+            x = self.root.left
+        largest = self.nil
+        smallest = self.nil
+        while x is not self.nil:
+            if start < x.start:
+                smallest = x
+                x = x.left # start <
+            elif start == x.start:
+                if end < x.end:
+                    smallest = x
+                    x = x.left # start =, end <
+                elif end == x.end: # found it
+                    smallest = x
+                    largest = x
+                    break
+                else:
+                    largest = x
+                    x = x.right # start =, end >
+            else:
+                largest = x
+                x = x.right # start >
+        return (x, smallest, largest)
+
+    def find(self, start, end, x = None):
+        """Find node with the key == (start,end), or None"""
+        y = self.__find_all(start, end, x)[1]
+        return y if y is not self.nil else None
+
+    def find_right(self, start, end, x = None):
+        """Find node with the smallest key >= (start,end), or None"""
+        y = self.__find_all(start, end, x)[1]
+        return y if y is not self.nil else None
+
+    def find_left(self, start, end, x = None):
+        """Find node with the largest key <= (start,end), or None"""
+        y = self.__find_all(start, end, x)[2]
+        return y if y is not self.nil else None
+
+    # Intersections
+    def intersect(self, start, end):
+        """Generator that returns nodes that overlap the given
+        (start,end) range, for the tree rooted at RBNode x.
+
+        NOTE: this assumes non-overlapping intervals."""
+        # Start with the leftmost node before the starting point
+        n = self.find_left(start, start)
+        # If we didn't find one, look for the leftmode node before the
+        # ending point instead.
+        if n is None:
+            n = self.find_left(end, end)
+        # If we still didn't find it, there are no intervals that intersect.
+        if n is None:
+            return none
+
+        # Now yield this node and all successors until their endpoints
+
+        if False:
+            yield
+        return

setup.cfg

@@ -12,6 +12,7 @@ stop=
 verbosity=2
 #tests=tests/test_cmdline.py
 #tests=tests/test_layout.py
+#tests=tests/test_rbtree.py
 tests=tests/test_interval.py
 #tests=tests/test_client.py
 #tests=tests/test_timestamper.py

tests/renderdot.py

@@ -1,73 +0,0 @@
-import sys
-
-class Renderer(object):
-
-    def __init__(self, getleft, getright,
-                 getred, getstart, getend, nil):
-        self.getleft = getleft
-        self.getright = getright
-        self.getred = getred
-        self.getstart = getstart
-        self.getend = getend
-        self.nil = nil
-
-    # Rendering
-    def __render_dot_node(self, node, max_depth = 20):
-        from nilmdb.printf import sprintf
-        """Render a single node and its children into a dot graph fragment"""
-        if max_depth == 0:
-            return ""
-        if node is self.nil:
-            return ""
-        def c(red):
-            if red:
-                return 'color="#ff0000", style=filled, fillcolor="#ffc0c0"'
-            else:
-                return 'color="#000000", style=filled, fillcolor="#c0c0c0"'
-        s = sprintf("%d [label=\"%g\\n%g\", %s];\n",
-                    id(node),
-                    self.getstart(node), self.getend(node),
-                    c(self.getred(node)))
-
-        if self.getleft(node) is self.nil:
-            s += sprintf("L%d [label=\"-\", %s];\n", id(node), c(False))
-            s += sprintf("%d -> L%d [label=L];\n", id(node), id(node))
-        else:
-            s += sprintf("%d -> %d [label=L];\n",
-                         id(node),id(self.getleft(node)))
-        if self.getright(node) is self.nil:
-            s += sprintf("R%d [label=\"-\", %s];\n", id(node), c(False))
-            s += sprintf("%d -> R%d [label=R];\n", id(node), id(node))
-        else:
-            s += sprintf("%d -> %d [label=R];\n",
-                         id(node), id(self.getright(node)))
-        s += self.__render_dot_node(self.getleft(node), max_depth-1)
-        s += self.__render_dot_node(self.getright(node), max_depth-1)
-        return s
-
-    def render_dot(self, rootnode, title = "Tree"):
-        """Render the entire tree as a dot graph"""
-        return ("digraph rbtree {\n"
-                + self.__render_dot_node(rootnode)
-                + "}\n");
-
-    def render_dot_live(self, rootnode, title = "Tree"):
-        """Render the entiretree as a dot graph, live GTK view"""
-        import gtk
-        import gtk.gdk
-        sys.path.append("/usr/share/xdot")
-        import xdot
-        xdot.Pen.highlighted = lambda pen: pen
-        s = ("digraph rbtree {\n"
-             + self.__render_dot_node(rootnode)
-             + "}\n");
-        window = xdot.DotWindow()
-        window.set_dotcode(s)
-        window.set_title(title + " - any key to close")
-        window.connect('destroy', gtk.main_quit)
-        def quit(widget, event):
-            if not event.is_modifier:
-                window.destroy()
-                gtk.main_quit()
-        window.widget.connect('key-press-event', quit)
-        gtk.main()

tests/test_interval.py

@@ -20,6 +20,7 @@ def makeset(string):
     [ = interval start
     | = interval end + adjacent start
     ] = interval end
+    . = zero-width interval (identical start and end)
     anything else is ignored
     """
     iset = IntervalSet()
@@ -33,6 +34,8 @@ def makeset(string):
         elif (c == "]"):
             iset += Interval(start, day)
             del start
+        elif (c == "."):
+            iset += Interval(day, day)
     return iset
 
 class TestInterval:
@@ -68,7 +71,7 @@ class TestInterval:
         assert(Interval(d1, d3) < Interval(d2, d3))
         assert(Interval(d2, d2) > Interval(d1, d3))
         assert(Interval(d3, d3) == Interval(d3, d3))
-        with assert_raises(AttributeError):
+        with assert_raises(TypeError): # was AttributeError, that's wrong
             x = (i == 123)
 
         # subset
@@ -182,7 +185,7 @@ class TestInterval:
 
     def test_intervalset_intersect(self):
         # Test intersection (&)
-        with assert_raises(AttributeError):
+        with assert_raises(TypeError): # was AttributeError
             x = makeset("[--]") & 1234
 
         assert(makeset("[---------]") &
@@ -197,10 +200,18 @@ class TestInterval:
                makeset(" [-----]   ") ==
                makeset("    [--]   "))
 
+        assert(makeset(" [--]  [--]") &
+               makeset("  [------] ") ==
+               makeset("  [-]  [-] "))
+
         assert(makeset("      [---]") &
                makeset(" [--]      ") ==
                makeset("           "))
 
+        assert(makeset("      [---]") &
+               makeset(" [----]    ") ==
+               makeset("      .    "))
+
         assert(makeset("    [-|---]") &
                makeset(" [-----|-] ") ==
                makeset("    [----] "))
@@ -211,8 +222,9 @@ class TestInterval:
 
         assert(makeset(" [----][--]") &
                makeset("[-] [--] []") ==
-               makeset(" [] [-]  []"))
+               makeset(" [] [-]. []"))
 
+class TestIntervalDB:
     def test_dbinterval(self):
         # Test DBInterval class
         i = DBInterval(100, 200, 100, 200, 10000, 20000)
@@ -255,8 +267,9 @@ class TestInterval:
         for i in IntervalSet(iseta.intersection(Interval(125,250))):
             assert(isinstance(i, DBInterval))
 
-class TestIntervalShape:
+class TestIntervalTree:
-    def test_interval_shape(self):
+
+    def test_interval_tree(self):
         import random
         random.seed(1234)
 
@@ -267,49 +280,34 @@ class TestIntervalShape:
             interval = Interval(i, i+1)
             iset += interval
 
-        # Plot it
+        # remove about half of them
-        import renderdot
+        for i in random.sample(xrange(j),j):
-        r = renderdot.Renderer(lambda node: node.cleft,
+            if random.randint(0,1):
-                               lambda node: node.cright,
+                iset -= Interval(i, i+1)
-                               lambda node: False,
-                               lambda node: node.start,
-                               lambda node: node.end,
-                               iset.tree.emptynode())
-        r.render_dot_live(iset.tree.rootnode(), "Random")
 
-        # make a set of 500 intervals, inserted in order
+        # try removing an interval that doesn't exist
-        iset = IntervalSet()
+        with assert_raises(IntervalError):
-        j = 500
+            iset -= Interval(1234,5678)
-        for i in xrange(j):
-            interval = Interval(i, i+1)
-            iset += interval
 
-        # Plot it
+        # show the graph
-        import renderdot
+        if False:
-        r = renderdot.Renderer(lambda node: node.cleft,
+            iset.tree.render_dot_live()
-                               lambda node: node.cright,
-                               lambda node: False,
-                               lambda node: node.start,
-                               lambda node: node.end,
-                               iset.tree.emptynode())
-        r.render_dot_live(iset.tree.rootnode(), "In-order")
-
-        assert(False)
 
 class TestIntervalSpeed:
-    #@unittest.skip("this is slow")
+    @unittest.skip("this is slow")
     def test_interval_speed(self):
         import yappi
         import time
         import aplotter
+        import random
 
         print
         yappi.start()
         speeds = {}
-        for j in [ 2**x for x in range(5,22) ]:
+        for j in [ 2**x for x in range(5,18) ]:
             start = time.time()
             iset = IntervalSet()
-            for i in xrange(j):
+            for i in random.sample(xrange(j),j):
                 interval = Interval(i, i+1)
                 iset += interval
             speed = (time.time() - start) * 1000000.0
@@ -318,3 +316,4 @@ class TestIntervalSpeed:
         aplotter.plot(speeds.keys(), speeds.values(), plot_slope=True)
         yappi.stop()
         yappi.print_stats(sort_type=yappi.SORTTYPE_TTOT, limit=10)
+

tests/test_rbtree.py

@@ -0,0 +1,75 @@
+# -*- coding: utf-8 -*-
+
+import nilmdb
+from nilmdb.printf import *
+
+from nose.tools import *
+from nose.tools import assert_raises
+
+from nilmdb.rbtree import RBTree, RBNode
+
+from test_helpers import *
+import unittest
+
+render = False
+
+class TestRBTree:
+    def test_rbtree(self):
+        rb = RBTree()
+        rb.insert(RBNode(None, 10000, 10001))
+        rb.insert(RBNode(None, 10004, 10007))
+        rb.insert(RBNode(None, 10001, 10002))
+        s = rb.render_dot()
+        # There was a typo that gave the RBTree a loop in this case.
+        # Verify that the dot isn't too big.
+        assert(len(s.splitlines()) < 30)
+
+    def test_rbtree_big(self):
+        import random
+        random.seed(1234)
+
+        # make a set of 500 intervals, inserted in order
+        rb = RBTree()
+        j = 500
+        for i in xrange(j):
+            rb.insert(RBNode(None, i, i+1))
+
+        # show the graph
+        if render:
+            rb.render_dot_live("in-order insert")
+
+        # remove about half of them
+        for i in random.sample(xrange(j),j):
+            if random.randint(0,1):
+                rb.delete(rb.find(i, i+1))
+
+        # show the graph
+        if render:
+            rb.render_dot_live("in-order insert, random delete")
+
+        # make a set of 500 intervals, inserted at random
+        rb = RBTree()
+        j = 500
+        for i in random.sample(xrange(j),j):
+            rb.insert(RBNode(None, i, i+1))
+
+        # show the graph
+        if render:
+            rb.render_dot_live("random insert")
+
+        # remove about half of them
+        for i in random.sample(xrange(j),j):
+            if random.randint(0,1):
+                rb.delete(rb.find(i, i+1))
+
+        # show the graph
+        if render:
+            rb.render_dot_live("random insert, random delete")
+
+        # in-order insert of 250 more
+        for i in xrange(250):
+            rb.insert(RBNode(None, i+500, i+501))
+
+        # show the graph
+        if render:
+            rb.render_dot_live("random insert, random delete, in-order insert")

time-bxintersect

@@ -0,0 +1,54 @@
+nosetests
+
+32: 386 μs (12.0625 μs each)
+64: 672.102 μs (10.5016 μs each)
+128: 1510.86 μs (11.8036 μs each)
+256: 2782.11 μs (10.8676 μs each)
+512: 5591.87 μs (10.9216 μs each)
+1024: 12812.1 μs (12.5119 μs each)
+2048: 21835.1 μs (10.6617 μs each)
+4096: 46059.1 μs (11.2449 μs each)
+8192: 114127 μs (13.9315 μs each)
+16384: 181217 μs (11.0606 μs each)
+32768: 419649 μs (12.8067 μs each)
+65536: 804320 μs (12.2729 μs each)
+131072: 1.73534e+06 μs (13.2396 μs each)
+262144: 3.74451e+06 μs (14.2842 μs each)
+524288: 8.8694e+06 μs (16.917 μs each)
+1048576: 1.69993e+07 μs (16.2118 μs each)
+2097152: 3.29387e+07 μs (15.7064 μs each)
+   |                                                                            
+   +3.29387e+07                                                             *   
+   |                                                                    ----    
+   |                                                               -----        
+   |                                                           ----             
+   |                                                      -----                 
+   |                                                 -----                      
+   |                                             ----                           
+   |                                        -----                               
+   |                                   -----                                    
+   |                               ----                                         
+   |                          -----                                             
+   |                      ----                                                  
+   |                 -----                                                      
+   |              ---                                                           
+   |           ---                                                              
+   |        ---                                                                 
+   | -------                                                                    
+---+386---------------------------------------------------------------------+---
+   +32                                                          +2.09715e+06    
+
+name                                 #n            tsub      ttot      tavg
+..vl/lees/bucket/nilm/nilmdb/nilmdb/interval.py.__iadd__:184  4194272          10.025323     30.262723     0.000007    
+..evl/lees/bucket/nilm/nilmdb/nilmdb/interval.py.__init__:27  4194272          24.715377     24.715377     0.000006    
+../lees/bucket/nilm/nilmdb/nilmdb/interval.py.intersects:239  4194272          6.705053      12.577620     0.000003    
+..im/devl/lees/bucket/nilm/nilmdb/tests/aplotter.py.plot:404  1                0.000048      0.001412      0.001412    
+../lees/bucket/nilm/nilmdb/tests/aplotter.py.plot_double:311  1                0.000106      0.001346      0.001346    
+..vl/lees/bucket/nilm/nilmdb/tests/aplotter.py.plot_data:201  1                0.000098      0.000672      0.000672    
+..vl/lees/bucket/nilm/nilmdb/tests/aplotter.py.plot_line:241  16               0.000298      0.000496      0.000031    
+..jim/devl/lees/bucket/nilm/nilmdb/nilmdb/printf.py.printf:4  17               0.000252      0.000334      0.000020    
+..vl/lees/bucket/nilm/nilmdb/tests/aplotter.py.transposed:39  1                0.000229      0.000235      0.000235    
+..vl/lees/bucket/nilm/nilmdb/tests/aplotter.py.y_reversed:45  1                0.000151      0.000174      0.000174    
+
+name           tid              fname                      ttot      scnt
+_MainThread           47269783682784        ..b/python2.7/threading.py.setprofile:88  64.746000     1