Render layout of bxintersect

nilmdb/bxintersect.pyx

@@ -1,7 +1,26 @@
 # cython: profile=False
-# This is based on bxintersect in bx-python 554:07aca5a9f6fc (BSD licensed);
+# This is from bx-python 554:07aca5a9f6fc (BSD licensed), modified to
-# modified to store interval ranges as doubles rather than 32-bit integers,
+# 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
@@ -53,7 +72,7 @@ cdef class IntervalNode:
     cdef public object interval
     cdef public double start, end
     cdef double minend, maxend, minstart
-    cdef IntervalNode cleft, cright, croot
+    cdef public IntervalNode cleft, cright, croot
 
     property left_node:
         def __get__(self):
@@ -175,6 +194,76 @@ 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():
@@ -301,9 +390,15 @@ 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`.
@@ -313,14 +408,8 @@ cdef class IntervalTree:
         else:
             self.root = self.root.insert( start, end, value )
 
-    def delete( self, double start, double end, object value=None ):
+    add = insert
-        """
+
-        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 ):
         """
@@ -330,9 +419,26 @@ 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
@@ -340,6 +446,50 @@ 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

@@ -8,25 +8,20 @@ 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.
 
-# Second version was based on the quicksect implementation from
+# This version is based on the quicksect implementation from python-bx,
-# python-bx, modified slightly to handle floating point intervals.
+# 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(object):
+class Interval(bxintersect.Interval):
     """Represents an interval of time."""
 
     def __init__(self, start, end):
@@ -35,8 +30,7 @@ class Interval(object):
         """
         if start > end:
             raise IntervalError("start %s must precede end %s" % (start, end))
-        self.start = float(start)
+        bxintersect.Interval.__init__(self, start, end)
-        self.end = float(end)
 
     def __repr__(self):
         s = repr(self.start) + ", " + repr(self.end)
@@ -45,20 +39,6 @@ class Interval(object):
     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):
@@ -86,7 +66,6 @@ class DBInterval(Interval):
         end = 150
         db_end = 200, db_endpos = 20000
     """
-
     def __init__(self, start, end,
                  db_start, db_end,
                  db_startpos, db_endpos):
@@ -130,14 +109,12 @@ class IntervalSet(object):
         """
         'source' is an Interval or IntervalSet to add.
         """
-        self.tree = bxinterval.IntervalTree()
+        self.tree = bxintersect.IntervalTree()
         if source is not None:
             self += source
 
     def __iter__(self):
-        for node in self.tree:
+        return self.tree.traverse()
-            if node.obj:
-                yield node.obj
 
     def __len__(self):
         return sum(1 for x in self)
@@ -218,17 +195,6 @@ 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)
@@ -245,12 +211,11 @@ class IntervalSet(object):
         out = IntervalSet()
 
         if not isinstance(other, IntervalSet):
-            for i in self.intersection(other):
+            other = [ other ]
-                out.tree.insert(rbtree.RBNode(i))
+
-        else:
+        for x in other:
-            for x in other:
+            for i in self.intersection(x):
-                for i in self.intersection(x):
+                out.tree.insert_interval(i)
-                    out.tree.insert(rbtree.RBNode(i))
 
         return out
 
@@ -264,30 +229,13 @@ class IntervalSet(object):
         Output intervals are built as subsets of the intervals in the
         first argument (self).
         """
-        if not isinstance(interval, Interval):
+        for i in self.tree.find(interval.start, interval.end):
-            raise TypeError("bad type")
+            if i.start > interval.start and i.end < interval.end:
-        for n in self.tree.intersect(interval.start, interval.end):
+                yield i
-            i = n.obj
+            else:
-            if i:
+                yield i.subset(max(i.start, interval.start),
-                if i.start >= interval.start and i.end <= interval.end:
+                               min(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"""
-        node = self.tree.find_left(other.start, other.end)
+        return len(self.tree.find(other.start, other.end)) > 0
-        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

@@ -1,392 +0,0 @@
-"""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

@@ -12,7 +12,6 @@ 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

@@ -0,0 +1,73 @@
+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

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

@@ -1,75 +0,0 @@
-# -*- 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

@@ -1,54 +0,0 @@
-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