Skip to content
GitLab
Projects
Groups
Snippets
Help
Loading...
Help
Help
Support
Community forum
Keyboard shortcuts
?
Submit feedback
Contribute to GitLab
Sign in / Register
Toggle navigation
graph-tool
Project overview
Project overview
Details
Activity
Releases
Repository
Repository
Files
Commits
Branches
Tags
Contributors
Graph
Compare
Issues
40
Issues
40
List
Boards
Labels
Service Desk
Milestones
Merge Requests
0
Merge Requests
0
CI / CD
CI / CD
Pipelines
Jobs
Schedules
Operations
Operations
Incidents
Environments
Analytics
Analytics
CI / CD
Repository
Value Stream
Wiki
Wiki
Snippets
Snippets
Members
Members
Collapse sidebar
Close sidebar
Activity
Graph
Create a new issue
Jobs
Commits
Issue Boards
Open sidebar
Tiago Peixoto
graph-tool
Commits
78d42c38
Commit
78d42c38
authored
Jul 22, 2013
by
Tiago Peixoto
Browse files
Options
Browse Files
Download
Email Patches
Plain Diff
Faster Graph copying if filter state is identical
parent
27d059c2
Changes
2
Hide whitespace changes
Inline
Side-by-side
Showing
2 changed files
with
275 additions
and
73 deletions
+275
-73
src/graph/graph_copy.cc
src/graph/graph_copy.cc
+193
-15
src/graph_tool/__init__.py
src/graph_tool/__init__.py
+82
-58
No files found.
src/graph/graph_copy.cc
View file @
78d42c38
...
...
@@ -79,8 +79,169 @@ void copy_property(const Descriptor& src_d, const Descriptor& tgt_d,
throw
ValueException
(
"Cannot find property map type."
);
}
template
<
class
GraphSrc
,
class
GraphTgt
,
class
IndexMap
,
class
SrcIndexMap
,
class
TgtIndexMap
>
struct
copy_vertex_property_dispatch
{
copy_vertex_property_dispatch
(
const
GraphSrc
&
src
,
const
GraphTgt
&
tgt
,
boost
::
any
&
prop_src
,
boost
::
any
&
prop_tgt
,
IndexMap
&
index_map
,
SrcIndexMap
&
src_vertex_index
,
TgtIndexMap
&
tgt_vertex_index
,
bool
&
found
)
:
src
(
src
),
tgt
(
tgt
),
prop_src
(
prop_src
),
prop_tgt
(
prop_tgt
),
index_map
(
index_map
),
src_vertex_index
(
src_vertex_index
),
tgt_vertex_index
(
tgt_vertex_index
),
found
(
found
)
{}
const
GraphSrc
&
src
;
const
GraphTgt
&
tgt
;
boost
::
any
&
prop_src
;
boost
::
any
&
prop_tgt
;
IndexMap
&
index_map
;
SrcIndexMap
&
src_vertex_index
;
TgtIndexMap
&
tgt_vertex_index
;
bool
&
found
;
template
<
class
PropertyMap
>
void
operator
()(
PropertyMap
)
const
{
PropertyMap
*
psrc
=
any_cast
<
PropertyMap
>
(
&
prop_src
);
if
(
psrc
==
NULL
)
return
;
if
(
prop_tgt
.
empty
())
prop_tgt
=
PropertyMap
(
tgt_vertex_index
);
PropertyMap
*
ptgt
=
any_cast
<
PropertyMap
>
(
&
prop_tgt
);
if
(
ptgt
==
NULL
)
return
;
found
=
true
;
typename
PropertyMap
::
unchecked_t
p_src
=
psrc
->
get_unchecked
(
num_vertices
(
src
));
typename
PropertyMap
::
unchecked_t
p_tgt
=
ptgt
->
get_unchecked
(
num_vertices
(
tgt
));
int
i
,
N
=
num_vertices
(
src
);
#pragma omp parallel for default(shared) private(i) schedule(static) if (N > 100)
for
(
i
=
0
;
i
<
N
;
++
i
)
{
typename
graph_traits
<
GraphSrc
>::
vertex_descriptor
v
=
vertex
(
i
,
src
);
if
(
v
==
graph_traits
<
GraphSrc
>::
null_vertex
())
continue
;
typename
graph_traits
<
GraphTgt
>::
vertex_descriptor
new_v
=
vertex
(
index_map
[
i
],
tgt
);
p_tgt
[
new_v
]
=
p_src
[
v
];
}
}
};
template
<
class
PropertyMaps
,
class
GraphSrc
,
class
GraphTgt
,
class
IndexMap
,
class
SrcIndexMap
,
class
TgtIndexMap
>
void
copy_vertex_property
(
boost
::
any
&
prop_src
,
boost
::
any
&
prop_tgt
,
const
GraphSrc
&
src
,
const
GraphTgt
&
tgt
,
IndexMap
&
index_map
,
SrcIndexMap
&
src_vertex_index
,
TgtIndexMap
&
tgt_vertex_index
)
{
bool
found
=
false
;
mpl
::
for_each
<
PropertyMaps
>
(
copy_vertex_property_dispatch
<
GraphSrc
,
GraphTgt
,
IndexMap
,
SrcIndexMap
,
TgtIndexMap
>
(
src
,
tgt
,
prop_src
,
prop_tgt
,
index_map
,
src_vertex_index
,
tgt_vertex_index
,
found
));
if
(
!
found
)
throw
ValueException
(
"Cannot find property map type."
);
}
template
<
class
GraphSrc
,
class
GraphTgt
,
class
IndexMap
,
class
SrcIndexMap
>
struct
copy_edge_property_dispatch
{
copy_edge_property_dispatch
(
const
GraphSrc
&
src
,
const
GraphTgt
&
tgt
,
boost
::
any
&
prop_src
,
boost
::
any
&
prop_tgt
,
IndexMap
&
index_map
,
SrcIndexMap
&
src_edge_index
,
size_t
max_src_edge_index
,
bool
&
found
)
:
src
(
src
),
tgt
(
tgt
),
prop_src
(
prop_src
),
prop_tgt
(
prop_tgt
),
index_map
(
index_map
),
src_edge_index
(
src_edge_index
),
max_src_edge_index
(
max_src_edge_index
),
found
(
found
)
{}
const
GraphSrc
&
src
;
const
GraphTgt
&
tgt
;
boost
::
any
&
prop_src
;
boost
::
any
&
prop_tgt
;
IndexMap
&
index_map
;
SrcIndexMap
&
src_edge_index
;
size_t
max_src_edge_index
;
bool
&
found
;
template
<
class
PropertyMap
>
void
operator
()(
PropertyMap
)
const
{
PropertyMap
*
psrc
=
any_cast
<
PropertyMap
>
(
&
prop_src
);
if
(
psrc
==
NULL
)
return
;
if
(
prop_tgt
.
empty
())
prop_tgt
=
PropertyMap
(
get
(
edge_index_t
(),
tgt
));
PropertyMap
*
ptgt
=
any_cast
<
PropertyMap
>
(
&
prop_tgt
);
if
(
ptgt
==
NULL
)
return
;
found
=
true
;
typename
PropertyMap
::
unchecked_t
p_src
=
psrc
->
get_unchecked
(
max_src_edge_index
+
1
);
typename
PropertyMap
::
unchecked_t
p_tgt
=
ptgt
->
get_unchecked
(
num_edges
(
tgt
));
int
i
,
N
=
num_vertices
(
src
);
#pragma omp parallel for default(shared) private(i) schedule(static) if (N > 100)
for
(
i
=
0
;
i
<
N
;
++
i
)
{
typename
graph_traits
<
GraphSrc
>::
vertex_descriptor
v
=
vertex
(
i
,
src
);
if
(
v
==
graph_traits
<
GraphSrc
>::
null_vertex
())
continue
;
typename
graph_traits
<
GraphSrc
>::
out_edge_iterator
e
,
e_end
;
for
(
tie
(
e
,
e_end
)
=
out_edges
(
v
,
src
);
e
!=
e_end
;
++
e
)
{
typename
graph_traits
<
GraphSrc
>::
vertex_descriptor
s
=
source
(
*
e
,
src
);
typename
graph_traits
<
GraphSrc
>::
vertex_descriptor
t
=
target
(
*
e
,
src
);
if
(
!
is_directed
::
apply
<
GraphSrc
>::
type
::
value
&&
s
>
t
)
continue
;
size_t
ei
=
src_edge_index
[
*
e
];
typename
graph_traits
<
GraphTgt
>::
edge_descriptor
new_e
=
index_map
[
ei
];
p_tgt
[
new_e
]
=
p_src
[
*
e
];
}
}
}
};
template
<
class
PropertyMaps
,
class
GraphSrc
,
class
GraphTgt
,
class
IndexMap
,
class
SrcIndexMap
>
void
copy_edge_property
(
boost
::
any
&
prop_src
,
boost
::
any
&
prop_tgt
,
const
GraphSrc
&
src
,
const
GraphTgt
&
tgt
,
IndexMap
&
index_map
,
SrcIndexMap
&
src_vertex_index
,
size_t
max_src_edge_index
)
{
bool
found
=
false
;
mpl
::
for_each
<
PropertyMaps
>
(
copy_edge_property_dispatch
<
GraphSrc
,
GraphTgt
,
IndexMap
,
SrcIndexMap
>
(
src
,
tgt
,
prop_src
,
prop_tgt
,
index_map
,
src_vertex_index
,
max_src_edge_index
,
found
));
if
(
!
found
)
throw
ValueException
(
"Cannot find property map type."
);
}
struct
do_graph_copy
{
do_graph_copy
(
size_t
max_src_edge_index
)
:
max_src_edge_index
(
max_src_edge_index
)
{}
size_t
max_src_edge_index
;
template
<
class
GraphTgt
,
class
GraphSrc
,
class
TgtVertexIndexMap
,
class
SrcVertexIndexMap
,
class
TgtEdgeIndexMap
,
class
SrcEdgeIndexMap
,
class
OrderMap
>
...
...
@@ -88,7 +249,7 @@ struct do_graph_copy
TgtVertexIndexMap
src_vertex_index
,
SrcVertexIndexMap
tgt_vertex_index
,
TgtEdgeIndexMap
,
SrcEdgeIndexMap
tgt
_edge_index
,
SrcEdgeIndexMap
src
_edge_index
,
OrderMap
vertex_order
,
vector
<
pair
<
reference_wrapper
<
boost
::
any
>
,
reference_wrapper
<
boost
::
any
>
>
>&
vprops
,
vector
<
pair
<
reference_wrapper
<
boost
::
any
>
,
reference_wrapper
<
boost
::
any
>
>
>&
eprops
)
const
...
...
@@ -99,17 +260,20 @@ struct do_graph_copy
{
if
(
src_vertex_index
[
*
v
]
>=
index_map
.
size
())
index_map
.
resize
(
src_vertex_index
[
*
v
]
+
1
);
typename
graph_traits
<
GraphTgt
>::
vertex_descriptor
new_v
=
get
(
vertex_order
,
*
v
);
typename
graph_traits
<
GraphTgt
>::
vertex_descriptor
new_v
=
get
(
vertex_order
,
*
v
);
while
(
new_v
>=
num_vertices
(
tgt
))
add_vertex
(
tgt
);
index_map
[
src_vertex_index
[
*
v
]]
=
tgt_vertex_index
[
new_v
];
for
(
size_t
i
=
0
;
i
<
vprops
.
size
();
++
i
)
copy_property
<
writable_vertex_properties
>
(
*
v
,
new_v
,
vprops
[
i
].
first
.
get
(),
vprops
[
i
].
second
.
get
(),
src
,
tgt
,
tgt_vertex_index
);
}
for
(
size_t
i
=
0
;
i
<
vprops
.
size
();
++
i
)
copy_vertex_property
<
writable_vertex_properties
>
(
vprops
[
i
].
first
.
get
(),
vprops
[
i
].
second
.
get
(),
src
,
tgt
,
index_map
,
src_vertex_index
,
tgt_vertex_index
);
vector
<
typename
graph_traits
<
GraphTgt
>::
edge_descriptor
>
edge_map
(
num_edges
(
src
));
typename
graph_traits
<
GraphSrc
>::
edge_iterator
e
,
e_end
;
for
(
tie
(
e
,
e_end
)
=
edges
(
src
);
e
!=
e_end
;
++
e
)
{
...
...
@@ -118,11 +282,18 @@ struct do_graph_copy
typedef
typename
graph_traits
<
GraphTgt
>::
edge_descriptor
edge_t
;
edge_t
new_e
=
add_edge
(
vertex
(
s
,
tgt
),
vertex
(
t
,
tgt
),
tgt
).
first
;
for
(
size_t
i
=
0
;
i
<
eprops
.
size
();
++
i
)
copy_property
<
writable_edge_properties
>
(
edge_t
(
*
e
),
new_e
,
eprops
[
i
].
first
.
get
(),
eprops
[
i
].
second
.
get
(),
src
,
tgt
,
tgt_edge_index
);
size_t
ei
=
src_edge_index
[
*
e
];
if
(
ei
>=
edge_map
.
size
())
edge_map
.
resize
(
ei
+
1
);
edge_map
[
ei
]
=
new_e
;
}
for
(
size_t
i
=
0
;
i
<
eprops
.
size
();
++
i
)
copy_edge_property
<
writable_edge_properties
>
(
eprops
[
i
].
first
.
get
(),
eprops
[
i
].
second
.
get
(),
src
,
tgt
,
edge_map
,
src_edge_index
,
max_src_edge_index
);
}
};
...
...
@@ -145,6 +316,13 @@ GraphInterface::GraphInterface(const GraphInterface& gi, bool keep_ref,
if
(
keep_ref
)
return
;
if
(
vorder
==
python
::
object
())
{
// simple copying
*
_mg
=
*
gi
.
_mg
;
return
;
}
vector
<
pair
<
reference_wrapper
<
boost
::
any
>
,
reference_wrapper
<
boost
::
any
>
>
>
vprops
;
for
(
int
i
=
0
;
i
<
python
::
len
(
ovprops
);
++
i
)
{
...
...
@@ -161,9 +339,9 @@ GraphInterface::GraphInterface(const GraphInterface& gi, bool keep_ref,
boost
::
any
avorder
=
python
::
extract
<
boost
::
any
>
(
vorder
);
run_action
<>
()
(
const_cast
<
GraphInterface
&>
(
gi
),
bind
<
void
>
(
do_graph_copy
(),
_1
,
ref
(
*
_mg
),
gi
.
_vertex_index
,
_vertex_index
,
gi
.
_edge_index
,
_edge_index
,
_2
,
ref
(
vprops
),
ref
(
eprops
)),
vertex_scalar_properties
())(
avorder
);
bind
<
void
>
(
do_graph_copy
(
gi
.
_mg
->
get_last_index
()
),
_1
,
ref
(
*
_mg
),
gi
.
_vertex_index
,
_vertex_index
,
gi
.
_edge_index
,
_edge_index
,
_2
,
ref
(
vprops
),
ref
(
eprops
)
),
vertex_scalar_properties
())(
avorder
);
// filters will be copied in python
}
src/graph_tool/__init__.py
View file @
78d42c38
...
...
@@ -1060,66 +1060,90 @@ class Graph(object):
vfilt
=
g
.
get_vertex_filter
()[
0
]
efilt
=
g
.
get_edge_filter
()[
0
]
# Copy all internal properties from original graph.
vprops
=
[]
eprops
=
[]
ef_pos
=
vf_pos
=
None
for
k
,
m
in
gv
.
vertex_properties
.
items
():
if
not
vprune
and
m
is
vfilt
:
if
(
vorder
is
None
and
((
g
.
get_vertex_filter
()[
0
]
is
None
and
g
.
get_edge_filter
()[
0
]
is
None
)
or
(
not
vprune
and
not
eprune
))):
# Do a simpler, faster copy.
self
.
__graph
=
libcore
.
GraphInterface
(
gv
.
__graph
,
False
,
[],
[],
None
)
nvfilt
=
nefilt
=
None
for
k
,
m
in
g
.
properties
.
items
():
nmap
=
self
.
copy_property
(
m
,
g
=
gv
)
self
.
properties
[
k
]
=
nmap
if
m
is
vfilt
:
nvfilt
=
nmap
if
m
is
efilt
:
nefilt
=
nmap
if
vfilt
is
not
None
:
if
nvfilt
is
None
:
nvfilt
=
self
.
copy_property
(
vfilt
,
g
=
gv
)
self
.
set_vertex_filter
(
nvfilt
,
g
.
get_vertex_filter
()[
1
])
if
efilt
is
not
None
:
if
nefilt
is
None
:
nefilt
=
self
.
copy_property
(
efilt
,
g
=
gv
)
self
.
set_edge_filter
(
nefilt
,
g
.
get_edge_filter
()[
1
])
else
:
# Copy all internal properties from original graph.
vprops
=
[]
eprops
=
[]
ef_pos
=
vf_pos
=
None
for
k
,
m
in
gv
.
vertex_properties
.
items
():
if
not
vprune
and
m
is
vfilt
:
vf_pos
=
len
(
vprops
)
vprops
.
append
([
_prop
(
"v"
,
gv
,
m
),
libcore
.
any
()])
for
k
,
m
in
gv
.
edge_properties
.
items
():
if
not
eprune
and
m
is
efilt
:
ef_pos
=
len
(
eprops
)
eprops
.
append
([
_prop
(
"e"
,
gv
,
m
),
libcore
.
any
()])
if
not
vprune
and
vf_pos
is
None
and
vfilt
is
not
None
:
vf_pos
=
len
(
vprops
)
vprops
.
append
([
_prop
(
"v"
,
gv
,
m
),
libcore
.
any
()])
for
k
,
m
in
gv
.
edge_properties
.
items
():
if
not
eprune
and
m
is
efilt
:
vprops
.
append
([
_prop
(
"v"
,
gv
,
vfilt
),
libcore
.
any
()])
if
not
eprune
and
ef_pos
is
None
and
efilt
is
not
None
:
ef_pos
=
len
(
eprops
)
eprops
.
append
([
_prop
(
"e"
,
gv
,
m
),
libcore
.
any
()])
if
not
vprune
and
vf_pos
is
None
and
vfilt
is
not
None
:
vf_pos
=
len
(
vprops
)
vprops
.
append
([
_prop
(
"v"
,
gv
,
vfilt
),
libcore
.
any
()])
if
not
eprune
and
ef_pos
is
None
and
efilt
is
not
None
:
ef_pos
=
len
(
eprops
)
eprops
.
append
([
_prop
(
"e"
,
gv
,
efilt
),
libcore
.
any
()])
# The vertex ordering
if
vorder
is
None
:
vorder
=
gv
.
new_vertex_property
(
"int"
)
vorder
.
fa
=
numpy
.
arange
(
gv
.
num_vertices
())
# The actual copying of the graph and property maps
self
.
__graph
=
libcore
.
GraphInterface
(
gv
.
__graph
,
False
,
vprops
,
eprops
,
_prop
(
"v"
,
gv
,
vorder
))
# Put the copied properties in the internal dictionary
for
i
,
(
k
,
m
)
in
enumerate
(
g
.
vertex_properties
.
items
()):
pmap
=
new_vertex_property
(
m
.
value_type
(),
self
.
__graph
.
GetVertexIndex
(),
vprops
[
i
][
1
])
self
.
vertex_properties
[
k
]
=
PropertyMap
(
pmap
,
self
,
"v"
)
for
i
,
(
k
,
m
)
in
enumerate
(
g
.
edge_properties
.
items
()):
pmap
=
new_edge_property
(
m
.
value_type
(),
self
.
__graph
.
GetEdgeIndex
(),
eprops
[
i
][
1
])
self
.
edge_properties
[
k
]
=
PropertyMap
(
pmap
,
self
,
"e"
)
for
k
,
v
in
g
.
graph_properties
.
items
():
new_p
=
self
.
new_graph_property
(
v
.
value_type
())
new_p
[
self
]
=
v
[
g
]
self
.
graph_properties
[
k
]
=
new_p
if
vf_pos
is
not
None
:
pmap
=
new_vertex_property
(
"bool"
,
self
.
__graph
.
GetVertexIndex
(),
vprops
[
vf_pos
][
1
])
pmap
=
PropertyMap
(
pmap
,
self
,
"v"
)
self
.
set_vertex_filter
(
pmap
,
g
.
get_vertex_filter
()[
1
])
if
ef_pos
is
not
None
:
pmap
=
new_edge_property
(
"bool"
,
self
.
__graph
.
GetEdgeIndex
(),
eprops
[
ef_pos
][
1
])
pmap
=
PropertyMap
(
pmap
,
self
,
"e"
)
self
.
set_edge_filter
(
pmap
,
g
.
get_edge_filter
()[
1
])
eprops
.
append
([
_prop
(
"e"
,
gv
,
efilt
),
libcore
.
any
()])
# The vertex ordering
if
vorder
is
None
:
vorder
=
gv
.
new_vertex_property
(
"int"
)
vorder
.
fa
=
numpy
.
arange
(
gv
.
num_vertices
())
# The actual copying of the graph and property maps
self
.
__graph
=
libcore
.
GraphInterface
(
gv
.
__graph
,
False
,
vprops
,
eprops
,
_prop
(
"v"
,
gv
,
vorder
))
# Put the copied properties in the internal dictionary
for
i
,
(
k
,
m
)
in
enumerate
(
g
.
vertex_properties
.
items
()):
pmap
=
new_vertex_property
(
m
.
value_type
(),
self
.
__graph
.
GetVertexIndex
(),
vprops
[
i
][
1
])
self
.
vertex_properties
[
k
]
=
PropertyMap
(
pmap
,
self
,
"v"
)
for
i
,
(
k
,
m
)
in
enumerate
(
g
.
edge_properties
.
items
()):
pmap
=
new_edge_property
(
m
.
value_type
(),
self
.
__graph
.
GetEdgeIndex
(),
eprops
[
i
][
1
])
self
.
edge_properties
[
k
]
=
PropertyMap
(
pmap
,
self
,
"e"
)
for
k
,
v
in
g
.
graph_properties
.
items
():
new_p
=
self
.
new_graph_property
(
v
.
value_type
())
new_p
[
self
]
=
v
[
g
]
self
.
graph_properties
[
k
]
=
new_p
if
vf_pos
is
not
None
:
pmap
=
new_vertex_property
(
"bool"
,
self
.
__graph
.
GetVertexIndex
(),
vprops
[
vf_pos
][
1
])
pmap
=
PropertyMap
(
pmap
,
self
,
"v"
)
self
.
set_vertex_filter
(
pmap
,
g
.
get_vertex_filter
()[
1
])
if
ef_pos
is
not
None
:
pmap
=
new_edge_property
(
"bool"
,
self
.
__graph
.
GetEdgeIndex
(),
eprops
[
ef_pos
][
1
])
pmap
=
PropertyMap
(
pmap
,
self
,
"e"
)
self
.
set_edge_filter
(
pmap
,
g
.
get_edge_filter
()[
1
])
if
not
rprune
:
self
.
set_reversed
(
g
.
is_reversed
())
...
...
Write
Preview
Markdown
is supported
0%
Try again
or
attach a new file
.
Attach a file
Cancel
You are about to add
0
people
to the discussion. Proceed with caution.
Finish editing this message first!
Cancel
Please
register
or
sign in
to comment