Related
I am continuing my motion-planning algorithm with a recursive Node structure and a boost geometry rtree. However, I'm running into a couple of issues in which the value at a Node pointer keeps changing. Here is a MWE:
#include <algorithm>
#include <iostream>
#include <cmath>
#include <stdlib.h>
#include <stdio.h>
#include <string>
#include <vector>
#include <set>
#include <boost/geometry.hpp>
#include <boost/geometry/geometry.hpp>
#include <boost/geometry/geometries/point.hpp>
#include <boost/geometry/geometries/box.hpp>
#include <boost/geometry/geometries/register/point.hpp>
#include <boost/geometry/index/rtree.hpp>
using namespace std;
namespace bg = boost::geometry;
namespace bgi = boost::geometry::index;
typedef bg::model::point<double, 2, bg::cs::cartesian> point;
struct Node
{
struct Node *parent;
point pos;
int id;
};
typedef pair<Node, unsigned int> ptval;
BOOST_GEOMETRY_REGISTER_POINT_2D_GET_SET(Node, double, bg::cs::cartesian, pos.get<0>, pos.get<1>, pos.set<0>, pos.set<1>);
double px(point& p) {
return pbruh.get<0>();
}
double nx(Node *n) {
return px(n->pos);
}
double py(point& p)
{
return pbruh.get<1>();
}
double ny(Node *n)
{
return py(n->pos);
}
int main() {
point start(0, 0), end(200, 200);
Node *root = new Node;
root->parent = NULL;
root->pos = start;
root->id = 0;
Node *last = root;
bgi::rtree<ptval, bgi::quadratic<16>> pts;
pts.insert(make_pair(*root, 0));
int c = 1; // running count
srand(time(nullptr)); // seed rng
vector<int> pars; // actual parent ids
pars.push_back(-1);
Node *save;
int marker = 500;
while (c<2000)
{
// generate random pos
double xr = ((double)rand() / RAND_MAX) * 200;
double yr = ((double)rand() / RAND_MAX) * 200;
point random(xr, yr);
vector<ptval> res;
pts.query(bgi::nearest(random, 1), back_inserter(res)); // get nearest point in rtree
Node *pnearest = &(res[0].first);
Node *pnew = new Node;
pnew->pos = random;
pnew->parent = pnearest; pnew->id = c; if (c == marker) { save = pnew; }
pars.push_back(pnearest->id);
if (c > marker && c < marker+50 && save->parent->id != pars[marker]) { cout << "CHANGED " << c << " " << pars[marker] << " " << save->parent->id << " " << save->parent << " " << nx(save->parent) << " " << ny(save->parent) << endl; }
pts.insert(make_pair(*pnew, c));
last = pnew;
c++;
}
cout << "ULTIMATE " << pars[marker] << " " << save->parent->id << endl;
return 0;
}
An example output is
CHANGED 501 416 118 0x257c1b0 134.416 103.623
CHANGED 502 416 412 0x257c1b0 187.164 150.841
CHANGED 503 416 190 0x257c1b0 176.128 162.548
CHANGED 504 416 212 0x257c1b0 68.16 167.425
CHANGED 505 416 487 0x257c1b0 0.701926 114.237
CHANGED 506 416 61 0x257c1b0 16.8645 91.7386
CHANGED 507 416 221 0x257c1b0 160.991 62.9841
CHANGED 508 416 439 0x257c1b0 65.627 130.284
CHANGED 509 416 203 0x257c1b0 146.312 189.367
CHANGED 510 416 140 0x257c1b0 164.946 30.2683
CHANGED 511 416 76 0x257c1b0 193.194 146.336
CHANGED 512 416 286 0x257c1b0 29.8898 124.509
CHANGED 513 416 14 0x257c1b0 88.4732 88.3816
CHANGED 514 416 340 0x257c1b0 179.907 93.4538
CHANGED 515 416 409 0x257c1b0 26.5389 94.4609
CHANGED 516 416 488 0x257c1b0 98.8983 12.36
CHANGED 517 416 256 0x257c1b0 141.984 180.651
CHANGED 518 416 256 0x257c1b0 141.984 180.651
CHANGED 519 416 256 0x257c1b0 141.984 180.651
CHANGED 520 416 256 0x257c1b0 141.984 180.651
CHANGED 521 416 256 0x257c1b0 141.984 180.651
CHANGED 522 416 256 0x257c1b0 141.984 180.651
CHANGED 523 416 256 0x257c1b0 141.984 180.651
CHANGED 524 416 256 0x257c1b0 141.984 180.651
CHANGED 525 416 256 0x257c1b0 141.984 180.651
CHANGED 526 416 256 0x257c1b0 141.984 180.651
CHANGED 527 416 256 0x257c1b0 141.984 180.651
CHANGED 528 416 256 0x257c1b0 141.984 180.651
CHANGED 529 416 256 0x257c1b0 141.984 180.651
CHANGED 530 416 256 0x257c1b0 141.984 180.651
CHANGED 531 416 256 0x257c1b0 141.984 180.651
CHANGED 532 416 256 0x257c1b0 141.984 180.651
CHANGED 533 416 256 0x257c1b0 141.984 180.651
CHANGED 534 416 256 0x257c1b0 141.984 180.651
CHANGED 535 416 256 0x257c1b0 141.984 180.651
CHANGED 536 416 256 0x257c1b0 141.984 180.651
CHANGED 537 416 256 0x257c1b0 141.984 180.651
CHANGED 538 416 256 0x257c1b0 141.984 180.651
CHANGED 539 416 256 0x257c1b0 141.984 180.651
CHANGED 540 416 256 0x257c1b0 141.984 180.651
CHANGED 541 416 256 0x257c1b0 141.984 180.651
CHANGED 542 416 256 0x257c1b0 141.984 180.651
CHANGED 543 416 256 0x257c1b0 141.984 180.651
CHANGED 544 416 256 0x257c1b0 141.984 180.651
CHANGED 545 416 256 0x257c1b0 141.984 180.651
CHANGED 546 416 256 0x257c1b0 141.984 180.651
CHANGED 547 416 256 0x257c1b0 141.984 180.651
CHANGED 548 416 256 0x257c1b0 141.984 180.651
CHANGED 549 416 256 0x257c1b0 141.984 180.651
ULTIMATE 416 599
As you can see, for all of these iterations, same->parent->id differs from the actual id of the parent (416) when same was processed on its iteration, and for some reason same->parent->id fluctuates on these first few iterations. However, the pointer address remains the same. What is happening in the heap memory that is causing these values to fluctuate and then stop but still be at the wrong address? This is very weird. I suspect it may have something to do with the Boost RTree as I store a direct reference to each Node in it and Boost may be doing some underlying operations, but that is just a theory. I may also just be a bit misguided on how pointers work.
Does anyone know how to fix the issue?
I'm assuming the missing functions are:
double px(point& p) { return p.get<0>(); }
double py(point& p) { return p.get<1>(); }
double nx(Node* n) { return px(n->pos); }
double ny(Node* n) { return py(n->pos); }
The first real issue I see is:
pts.insert(make_pair(*root, 0));
That inserts a copy of the object pointed to by root. Any references will not point to the copy. root is always leaked for no reason.
This is a better start that might actually work until the tree invalidates references:
pts.insert(std::make_pair(Node{nullptr, start, 0}, 0));
Node const* last = &pts.begin()->first;
Same here:
pts.insert(std::make_pair(*pnew, id));
last = pnew;
*pnew is always leaked, and you didn't want last to point to it. To "fix" it naievely, I'd use a helper function:
auto insert = [&pts](Node n) -> Node const* {
pts.insert(std::make_pair(n, n.id));
auto it = std::find_if(pts.begin(), pts.end(),
[](ptval const& p) { return p.second == n.id; });
return &it->first;
};
Node const* last = insert(Node{nullptr, start, 0});
As others have noted, this is definitely wrong:
ptval res;
pts.query(bgi::nearest(newpos, 1), &res);
Node* pnearest = &(res[0].first);
This by definition takes the address of the local copy of a ptval's Node element. Instead, let's use the same naive (probably enormously inefficient) approach:
auto find = [&pts](int id) -> Node const* {
auto it = std::find_if(pts.begin(), pts.end(),
[id](ptval const& p) { return p.second == id; });
return &it->first;
};
auto insert = [&, find](Node n) -> Node const* {
pts.insert(std::make_pair(n, n.id));
return find(n.id);
};
Now you can have:
Node const* last = insert(Node{nullptr, start, 0}); // insert root
As well as:
ptval res;
pts.query(bgi::nearest(newpos, 1), &res);
Node new_node{find(res.second), newpos, id};
if (id == marker) {
marker_parent = new_node.parent;
}
parents.push_back(new_node.parent->id);
Next up
srand(time(nullptr)); // seed rng
// generate random pos
double xr = ((double)rand() / RAND_MAX) * 200;
double yr = ((double)rand() / RAND_MAX) * 200;
Prefer standard library:
std::mt19937 prng{std::random_device{}()};
std::uniform_real_distribution<double> dist(0, 200);
// generate random pos
double xr = dist(prng);
double yr = dist(prng);
Next up
Node* save;
Prefer to initialize:
Node* save = nullptr;
Know your loops.
int c = 1; // running count
// ...
while (c < 2000) {
//...
c++;
}
Should just be
for (int id = 1; id<2000; ++id) {
//...
}
Note the naming as well.
Don't use using namespace std; (Why is "using namespace std;" considered bad practice?)
Applying all this leads me to:
Live On Compiler Explorer
//#include <algorithm>
#include <iostream>
//#include <cmath>
//#include <stdlib.h>
//#include <stdio.h>
//#include <string>
//#include <vector>
//#include <set>
#include <boost/geometry.hpp>
#include <boost/geometry/geometries/box.hpp>
#include <boost/geometry/geometries/point.hpp>
#include <boost/geometry/geometries/register/point.hpp>
#include <boost/geometry/geometry.hpp>
#include <boost/geometry/index/rtree.hpp>
#include <random>
namespace bg = boost::geometry;
namespace bgi = boost::geometry::index;
typedef bg::model::point<double, 2, bg::cs::cartesian> point;
struct Node {
Node const* parent = nullptr;
point pos = {};
int id = -1;
};
typedef std::pair<Node, int> ptval;
BOOST_GEOMETRY_REGISTER_POINT_2D_GET_SET(Node, double, bg::cs::cartesian,
pos.get<0>, pos.get<1>, pos.set<0>,
pos.set<1>)
double px(point const& p) { return p.get<0>(); }
double py(point const& p) { return p.get<1>(); }
double nx(Node const* n) { return px(n->pos); }
double ny(Node const* n) { return py(n->pos); }
int main(int argc, char** argv) {
point start(0, 0) /*, end(200, 200)*/;
bgi::rtree<ptval, bgi::quadratic<16>> pts;
auto find = [&pts](int id) -> Node const* {
auto it = std::find_if(pts.begin(), pts.end(),
[id](ptval const& p) { return p.second == id; });
return &it->first;
};
auto insert = [&, find](Node n) -> Node const* {
pts.insert(std::make_pair(n, n.id));
return find(n.id);
};
Node const* last = insert(Node{nullptr, start, 0}); // insert root
std::mt19937 prng{argc > 1 ? atoi(argv[1]) : std::random_device{}()};
std::uniform_real_distribution<double> dist(0, 200);
std::vector<int> parents{-1}; // actual parent ids
Node const* marker_parent = nullptr;
int marker = 500;
for (int id = 1; id < 2000; ++id) {
// generate random pos
point newpos(dist(prng), dist(prng));
ptval res;
pts.query(bgi::nearest(newpos, 1), &res);
Node new_node{find(res.second), newpos, id};
if (id == marker) {
marker_parent = new_node.parent;
}
parents.push_back(new_node.parent->id);
if (id > marker && id < marker + 50 &&
marker_parent->id != parents[marker]) {
std::cout << "CHANGED " << id << " " << parents[marker] << " "
<< marker_parent->id << " " << marker_parent
<< " " << nx(marker_parent) << " "
<< ny(marker_parent) << std::endl;
}
last = insert(new_node);
}
std::cout << "ULTIMATE " << parents[marker] << " ";
if (marker_parent)
std::cout << marker_parent->id << std::endl;
else
std::cout << std::endl;
}
Prints (with the seed fixed at 42 for online demo):
ULTIMATE 307 1622
The funny thing is, as far as I can see last is never used. So you can probably do with much simpler and more efficient:
auto insert = [&](Node n) { pts.insert(std::make_pair(n, n.id)); };
Isolating The Bug - Root Cause
Note above when I said "might actually work until the tree invalidates references". Sadly I was unable to find any documentation of reference stability/invalidation guarantees for rtree¹.
With different seeds we still get output like e.g. for seed 47:
CHANGED 501 189 38 0x617000004e30 26.0044 140.042
...
CHANGED 549 189 38 0x617000004e30 26.0044 140.042
ULTIMATE 189 474
Obviously, at least all the lines are identical (except for the running counter 501..549). Comparing seed 40:
CHANGED 517 108 500 0x560957ad1638 109.71 53.341
...
CHANGED 549 108 500 0x560957ad1638 109.71 53.341
ULTIMATE 108 590
Illustrates that sometimes the marker "randomly" changes during the game. The problem then, clearly, is that rtree can reallocate, invalidating Node references.
The number 517 is interesting to me for its relation to 16 in bgi::quadratic<16>. So, I thought to make a much more granular test instead of randomly monitoring the 500th "marker". Why not monitor all parents?
constexpr auto N = 2000;
std::vector<Node const*> parents(N, nullptr); // parents refs
std::vector<int> parent_ids(N, -1); // parent ids
for (int id = 1; id < N; ++id) {
// generate random pos
point newpos(dist(prng), dist(prng));
ptval res;
pts.query(bgi::nearest(newpos, 1), &res);
Node new_node{find(res.second), newpos, id};
parents[id] = new_node.parent;
parent_ids[id] = new_node.parent->id;
bool invalidated = !std::equal(
parents.begin(), parents.end(), parent_ids.begin(),
[](Node const* p, int id) { return !p || p->id == id; });
std::cout << "invalidated: " << std::boolalpha << invalidated << "\n";
//assert(!invalidated);
insert(new_node);
}
Now running this a few hundred times with random seeds shows a pattern of always invalidating after 16 nodes:
$ for a in {1..100}; do ./build/sotest; done | uniq -c | sort | uniq
16 invalidated: false
1983 invalidated: true
1 ULTIMATE 101 1393
1 ULTIMATE 103 262
1 ULTIMATE 103 5
1 ULTIMATE 104 536
1 ULTIMATE 108 1406
1 ULTIMATE 111 111
This confirms beyond any statistical doubt that reallocation is causing the references (i.e. the pointers) to become invalidated.
FIXING
I suggest keeping the parent references by id only. Interestingly, since id is already part of Node you can do without the duplication in std::pair by using a custom ``indexable<>or customIndexableGetter` template argument.
Let's store references to Nodes in the tree, instead, using a custom indexable:
using NodeRef = std::reference_wrapper<Node const>;
struct MyIndexable {
using value_type = NodeRef;
using result_type = Node const&;
result_type operator()(NodeRef r) const { return r; }
};
Now we can trivially build a tree from those:
bgi::rtree<NodeRef, bgi::quadratic<16>, MyIndexable> pts;
All we need is some stable storage for the referenced nodes:
std::deque<Node> storage; // reference stability adding/removing at either end
//std::list<Node> storage; // iterator and reference stability (except removed)
auto insert = [&](Node n) {
storage.push_back(std::move(n));
pts.insert(NodeRef(storage.back()));
};
The rest of the program can remain pretty much the same - except for a few respellings to accomodate NodeRef:
Live On Coliru
#undef NDEBUG
#include <iostream>
#include <boost/geometry.hpp>
#include <boost/geometry/geometries/box.hpp>
#include <boost/geometry/geometries/point.hpp>
#include <boost/geometry/geometries/register/point.hpp>
#include <boost/geometry/geometry.hpp>
#include <boost/geometry/index/rtree.hpp>
#include <random>
namespace bg = boost::geometry;
namespace bgi = boost::geometry::index;
typedef bg::model::point<double, 2, bg::cs::cartesian> point;
struct Node {
Node const* parent = nullptr;
point pos = {};
int id = -1;
};
BOOST_GEOMETRY_REGISTER_POINT_2D_GET_SET(Node, double, bg::cs::cartesian,
pos.get<0>, pos.get<1>, pos.set<0>,
pos.set<1>)
double px(point const& p) { return p.get<0>(); }
double py(point const& p) { return p.get<1>(); }
double nx(Node const* n) { return px(n->pos); }
double ny(Node const* n) { return py(n->pos); }
using NodeRef = std::reference_wrapper<Node const>;
struct MyIndexable {
using value_type = NodeRef;
using result_type = Node const&;
result_type operator()(NodeRef r) const { return r; }
};
int main(int argc, char** argv) {
bgi::rtree<NodeRef, bgi::quadratic<16>, MyIndexable> pts;
std::deque<Node> storage; // reference stability adding/removing at either end
//std::list<Node> storage; // iterator and reference stability (except removed)
auto insert = [&](Node n) {
storage.push_back(std::move(n));
pts.insert(NodeRef(storage.back()));
};
insert({nullptr, point(0, 0), 0}); // insert root
std::mt19937 prng{argc > 1 ? atoi(argv[1]) : std::random_device{}()};
std::uniform_real_distribution<double> dist(0, 200);
constexpr auto N = 2000;
std::vector<NodeRef> parents; // parents refs
std::vector<int> parent_ids; // parent ids
for (int id = 1; id < N; ++id) {
// generate random pos
point newpos(dist(prng), dist(prng));
std::vector<NodeRef> res;
pts.query(bgi::nearest(newpos, 1), back_inserter(res));
Node new_node{&res.front().get(), newpos, id};
parents.push_back(*new_node.parent);
parent_ids.push_back(new_node.parent->id);
bool invalidated =
!std::equal(parents.begin(), parents.end(), parent_ids.begin(),
[](Node const& p, int id) { return p.id == id; });
assert(!invalidated);
insert(std::move(new_node));
}
std::cout << "ULTIMATE " << parent_ids.at(500) << " "
<< parents.at(500).get().id << "\n";
}
Which never trips the assert, and produces stable output like:
for a in {1..50}; do ./a.out; done
ULTIMATE 41 41
ULTIMATE 365 365
ULTIMATE 219 219
ULTIMATE 193 193
ULTIMATE 448 448
ULTIMATE 331 331
ULTIMATE 227 227
ULTIMATE 234 234
ULTIMATE 300 300
ULTIMATE 227 227
ULTIMATE 243 243
ULTIMATE 248 248
ULTIMATE 233 233
ULTIMATE 143 143
ULTIMATE 39 39
ULTIMATE 488 488
ULTIMATE 493 493
ULTIMATE 9 9
ULTIMATE 212 212
ULTIMATE 338 338
ULTIMATE 141 141
ULTIMATE 356 356
ULTIMATE 147 147
ULTIMATE 376 376
ULTIMATE 76 76
ULTIMATE 450 450
ULTIMATE 272 272
ULTIMATE 34 34
ULTIMATE 492 492
ULTIMATE 478 478
ULTIMATE 84 84
ULTIMATE 416 416
ULTIMATE 222 222
ULTIMATE 457 457
ULTIMATE 95 95
ULTIMATE 446 446
ULTIMATE 233 233
ULTIMATE 480 480
ULTIMATE 265 265
ULTIMATE 415 415
ULTIMATE 289 289
ULTIMATE 121 121
ULTIMATE 344 344
ULTIMATE 110 110
ULTIMATE 429 429
ULTIMATE 31 31
ULTIMATE 344 344
ULTIMATE 172 172
ULTIMATE 20 20
ULTIMATE 394 394
Bonus
A version without the now-redundant sanity checks and unused code: Live On Coliru
¹ although there are some notes about iterator invalidation
I'm writing an application in Python that applies a watermark to a font file. The glyphs are non-convex polygons with holes and consist of bezier splines defined in PostScript. The watermark needs to merge with the glyphs, not overlap. I was unable to find a library to do this in Python so I'm using CGAL & C++. I have it working nicely on most glyphs, but it's mysteriously failing on others.
Initially, I was very impressed with CGAL. It looked very comprehensive and sophisticated and seemed to provide all the functionality I needed, but it suffers one fatal flaw - and I almost can't believe it - the library contains no error handling. No error codes, no exceptions, just assertions - but only in the debug build. In the release build you get a nice segmentation fault instead. Furthermore, the assertions reveal nothing about the nature of the problem.
The program fails only on certain glyphs. The letter 'e' works fine, but it crashes on 'a'. The crash occurs when I attempt to compute the union of the glyph with the watermark. There is nothing visibly wrong with the 'a' glyph. My application parses the PostScript correctly and renders it fine on a QGraphicsView.
This program needs to run on a server and its output sent directly to the customer so it must be reliable. I can't recover from an assertion failure or a segfault, so what can I do?
Even if I get it working reliably, how can I trust that it will never fail? If there was some kind of error handling in place, I could just skip the few glyphs that it fails on, leaving them unwatermarked - not ideal, but acceptable. I just don't understand what the authors of this library were thinking; they went to such tremendous effort to make the most comprehensive geometry library available only to ensure that it's completely unfit for purpose.
Currently, it's looking like I'm going to have to modify the code myself to handle the error in a sensible way, but this just seems so ridiculous.
I'm sorry if I come off as impatient, but I'm way past my deadline and my client isn't going to care about or understand these excuses.
The assertion failure is occurring on line 2141 of multiset.h:
CGAL_multiset_precondition (comp_f(object, nodeP->object) != LARGER);
It happens when I call join() on a BezierPolygonSet. My types are as follows:
typedef CGAL::CORE_algebraic_number_traits NtTraits;
typedef NtTraits::Rational Rational;
typedef NtTraits::Algebraic Algebraic;
typedef CGAL::Cartesian<Rational> RatKernel;
typedef CGAL::Cartesian<Algebraic> AlgKernel;
typedef RatKernel::Point_2 BezierRatPoint;
typedef CGAL::Arr_Bezier_curve_traits_2<RatKernel, AlgKernel, NtTraits> Traits;
typedef Traits::Point_2 BezierPoint;
typedef Traits::Curve_2 BezierCurve;
typedef CGAL::Gps_traits_2<Traits> BezierTraits;
typedef BezierTraits::X_monotone_curve_2 BezierXMonotoneCurve;
typedef BezierTraits::General_polygon_2 BezierPolygon;
typedef BezierTraits::General_polygon_with_holes_2 BezierPolygonWithHoles;
typedef CGAL::Gps_default_dcel<BezierTraits> BezierDcelTraits;
typedef CGAL::General_polygon_set_2<BezierTraits, BezierDcelTraits> BezierPolygonSet;
Any help would be much appreciated. Thanks.
EDIT:
I have a module called Geometry which wraps the CGAL code and exposes a bunch of geometric primitives (Point, Curve, LineSegment, CubicBezier, Path) and the functions:
PathList toPathList(const PolyList& polyList);
PolyList toPolyList(const PathList& paths);
The Path class has a method called computeUnion, which looks like this:
PathList Path::computeUnion(const PathList& paths1, const PathList& paths2) {
PolyList polyList1 = toPolyList(paths1);
PolyList polyList2 = toPolyList(paths2);
cgal_wrap::BezierPolygonSet polySet;
for (auto i : polyList1) {
polySet.join(i);
}
for (auto i : polyList2) {
polySet.join(i);
}
PolyList polyList;
polySet.polygons_with_holes(std::back_inserter(polyList));
return toPathList(polyList);
}
The error occurs when I call join(). The polygons are created from paths like so:
PolyList toPolyList(const PathList& paths) {
cgal_wrap::Traits traits;
cgal_wrap::Traits::Make_x_monotone_2 fnMakeXMonotone = traits.make_x_monotone_2_object();
cgal_wrap::RatKernel ratKernel;
cgal_wrap::RatKernel::Equal_2 fnEqual = ratKernel.equal_2_object();
PolyList polyList; // The final polygons with holes
cgal_wrap::BezierPolygon outerPoly;
std::list<cgal_wrap::BezierPolygon> holes;
std::list<cgal_wrap::BezierXMonotoneCurve> monoCurves;
bool first = true;
cgal_wrap::BezierRatPoint firstPoint;
// For each path in the list
for (auto i = paths.begin(); i != paths.end(); ++i) {
const Path& path = *i;
cgal_wrap::BezierRatPoint prevEndPoint;
// For each curve in the path
for (auto j = path.begin(); j != path.end(); ++j) {
const Curve& curve = **j;
std::list<cgal_wrap::BezierRatPoint> points;
if (curve.type() == LineSegment::type) {
const LineSegment& lseg = dynamic_cast<const LineSegment&>(curve);
cgal_wrap::BezierRatPoint A = lseg.A();
if (j != path.begin()) {
if (A != prevEndPoint) {
// TODO
assert(false);
}
A = prevEndPoint;
}
points.push_back(cgal_wrap::BezierRatPoint(A));
points.push_back(cgal_wrap::BezierRatPoint(lseg.B()));
}
else if (curve.type() == CubicBezier::type) {
const CubicBezier& bezier = dynamic_cast<const CubicBezier&>(curve);
cgal_wrap::BezierRatPoint A = bezier.A();
if (j != path.begin()) {
if (A != prevEndPoint) {
// TODO
assert(false);
}
A = prevEndPoint;
}
points.push_back(cgal_wrap::BezierRatPoint(A));
points.push_back(cgal_wrap::BezierRatPoint(bezier.B()));
points.push_back(cgal_wrap::BezierRatPoint(bezier.C()));
points.push_back(cgal_wrap::BezierRatPoint(bezier.D()));
}
bool bClosesCurve = false;
if (!first && Point(points.back()) == Point(firstPoint)) {
points.pop_back();
points.push_back(firstPoint);
bClosesCurve = true;
}
prevEndPoint = points.back();
cgal_wrap::BezierCurve cgalCurve(points.begin(), points.end());
std::list<CGAL::Object> monoObjs;
fnMakeXMonotone(cgalCurve, std::back_inserter(monoObjs));
// Append the x-monotone curves to the list
cgal_wrap::BezierXMonotoneCurve monoCurve;
for (auto o = monoObjs.begin(); o != monoObjs.end(); ++o) {
if (CGAL::assign(monoCurve, *o)) {
monoCurves.push_back(monoCurve);
}
}
if (!first) {
// If this curve closes the current chain, thereby creating a new polygon
if (bClosesCurve) {
// Add the new polygon to the list
cgal_wrap::BezierPolygon subPoly(monoCurves.begin(), monoCurves.end());
if (subPoly.orientation() == CGAL::COUNTERCLOCKWISE) {
if (!outerPoly.is_empty()) {
polyList.push_back(cgal_wrap::BezierPolygonWithHoles(outerPoly, holes.begin(), holes.end()));
holes.clear();
}
outerPoly = subPoly;
}
else {
holes.push_back(subPoly);
}
monoCurves.clear();
first = true;
}
}
else {
// This is the first curve in the chain - store its source point
firstPoint = cgalCurve.control_point(0);
first = false;
}
}
}
polyList.push_back(cgal_wrap::BezierPolygonWithHoles(outerPoly, holes.begin(), holes.end()));
return polyList;
}
Notice that I'm careful to ensure that the polygon boundaries have no gaps by setting the first point of curve n+1 to the last point of curve n in case they were slightly different. I was hoping this would solve the problem, but it didn't. I can't think of any other things that might make the shapes invalid.
Here is the successful merging of the 'e' glyph with the watermark (an X).
Here is what the 'a' glyph looks like. The merging fails on this glyph.
EDIT 2:
Here are the curves that make up the 'a' glyph after parsing it from PostScript. There doesn't appear to be anything wrong with it. As I said, it looks okay when rendered. The error probably occurs during the translation from this data into the CGAL types. The line segments get translated into BezierCurves with 2 control points. I will investigate further.
LineSegment[(344, 0), (409, 0)]
CubicBezier[(409, 0), (403, 24), (400, 68), (400, 161)]
LineSegment[(400, 161), (400, 324)]
CubicBezier[(400, 324), (400, 437), (330, 485), (232, 485)]
CubicBezier[(232, 485), (180, 485), (121, 472), (66, 437)]
LineSegment[(66, 437), (94, 385)]
CubicBezier[(94, 385), (127, 405), (167, 424), (224, 424)]
CubicBezier[(224, 424), (283, 424), (326, 392), (326, 320)]
LineSegment[(326, 320), (326, 290)]
LineSegment[(326, 290), (236, 287)]
CubicBezier[(236, 287), (188, 285), (150, 280), (118, 264)]
CubicBezier[(118, 264), (70, 242), (38, 199), (38, 136)]
CubicBezier[(38, 136), (38, 45), (102, -10), (188, -10)]
CubicBezier[(188, -10), (247, -10), (293, 18), (330, 53)]
LineSegment[(330, 53), (344, 0)]
LineSegment[(326, 234), (326, 114)]
CubicBezier[(326, 114), (304, 91), (260, 52), (201, 52)]
CubicBezier[(201, 52), (147, 52), (113, 88), (113, 140)]
CubicBezier[(113, 140), (113, 171), (127, 198), (154, 213)]
CubicBezier[(154, 213), (175, 224), (202, 230), (243, 231)]
LineSegment[(243, 231), (326, 234)]
EDIT 3:
Here are the 'a' glyph curves after translation into CGAL curves. Notice that they exactly match the curves before translation implying that none of them had to be split into X-monotone subcurves; they must have all been X-monotone already.
Outer boundary:
2 344 0 409 0 [1] | 344 0 --> 409 0
4 409 0 403 24 400 68 400 161 [1] | 409 0 --> 400 161
2 400 161 400 324 [1] | 400 161 --> 400 324
4 400 324 400 437 330 485 232 485 [1] | 400 324 --> 232 485
4 232 485 180 485 121 472 66 437 [1] | 232 485 --> 66 437
2 66 437 94 385 [1] | 66 437 --> 94 385
4 94 385 127 405 167 424 224 424 [1] | 94 385 --> 224 424
4 224 424 283 424 326 392 326 320 [1] | 224 424 --> 326 320
2 326 320 326 290 [1] | 326 320 --> 326 290
2 326 290 236 287 [1] | 326 290 --> 236 287
4 236 287 188 285 150 280 118 264 [1] | 236 287 --> 118 264
4 118 264 70 242 38 199 38 136 [1] | 118 264 --> 38 136
4 38 136 38 45 102 -10 188 -10 [1] | 38 136 --> 188 -10
4 188 -10 247 -10 293 18 330 53 [1] | 188 -10 --> 330 53
2 330 53 344 0 [1] | 330 53 --> 344 0
Holes:
Hole:
2 326 234 326 114 [1] | 326 234 --> 326 114
4 326 114 304 91 260 52 201 52 [1] | 326 114 --> 201 52
4 201 52 147 52 113 88 113 140 [1] | 201 52 --> 113 140
4 113 140 113 171 127 198 154 213 [1] | 113 140 --> 154 213
4 154 213 175 224 202 230 243 231 [1] | 154 213 --> 243 231
2 243 231 326 234 [1] | 243 231 --> 326 234
This polygon causes the assertion failure when added to a BezierPolygonSet. Any ideas?
You can customize error handling; see the manual.
Please attach a complete standalone program. Nothing looks wrong to me with statements you listed.
You can approximate the Bezier curves with polylines and process the whole things using polylines. If the problem is with the handling of Bezier curves, then this would solve it. If this is acceptable, it will also be more efficient.
We have fixed a bug in the CGAL component that handles Bezier curves, namely, Arr_Bezier_curve_traits_2.h.
I have a project where I have to read a vector list from a .txt file and parse it. I have the vector list displaying on the screen but I do not know how to parse it.
#include <iostream>
#include <cstring>
#include <fstream>
#include <conio.h>
using namespace std;
int main() {
ifstream vl;
vl.open("PIXA.txt");
char output[100];
if (vl.is_open()) {
while (!vl.eof()) {
vl >> output;
cout << output;
}
vl >> output;
cout << output;
}
cin.ignore();
cin.get();
vl.close();
return 0;
}
Could someone help out with adding code so that I can parse this .txt file?
Here is what the .txt file looks like:
J
366 -1722 583
366 356 1783
866 789 1033
866 -1289 -167
366 -1722 583
J
-500 -1472 150
0 -1039 -600
0 1039 600
-500 606 1350
-500 -1472 150
J
366 356 1783
-500 606 1350
0 1039 600
866 789 1033
366 356 1783
J
366 -1722 583
866 -1289 -167
0 -1039 -600
-500 -1472 150
366 -1722 583
So, there are two things that can help you here.
Firstly, std::getline can take an optional delimiter parameter. This is handy, because your matrices are delimited by J.
std::string line;
std::getline(in, line, 'J')
This will either leave line empty (for the first entry in your file) or with a long string containing a bunch of space-delimited integers. Note that std::getline will pull the delimiter out of the stream, but not add it to the string argument, so you don't need to worry about the J when it comes to parsing the integer bits.
You can feed that into a std::stringstream, and yank out all the integers in a loop like this:
std::vector<int> matrix;
std::stringstream ss(line);
int i;
while (ss >> i)
matrix.push_back(i);
and you'll get a nice 1-dimensional vector full of all your numbers. Writing a simple indexing function that can convert between a row,column format that you probably want from a matrix, and the offset format you'll need with a vector is left as an exercise to the reader as it is pretty simple. Don't forget to handle the empty-line situation for the very first J!
You can wrap this stuff up in a loop,
while (std::getline(in, line)) { /* ... */ }
easily enough, and do something like generate a vector of vectors that'll be dead easy to work with later in your application.
In a function, I want to generate a list of numbers in range:
(This function will be called only once when executing the program.)
void DataSet::finalize(double trainPercent, bool genValidData)
{
srand(time(0));
printf("%d\n", rand());
// indices = {0, 1, 2, 3, 4, ..., m_train.size()-1}
vector<size_t> indices(m_train.size());
for (size_t i = 0; i < indices.size(); i++)
indices[i] = i;
random_shuffle(indices.begin(), indices.end());
// Output
for (size_t i = 0; i < 10; i++)
printf("%ld ", indices[i]);
puts("");
}
The results are like:
850577673
246 239 7 102 41 201 288 23 1 237
After a few seconds:
856981140
246 239 7 102 41 201 288 23 1 237
And more:
857552578
246 239 7 102 41 201 288 23 1 237
Why the function rand() works properly but `random_shuffle' does not?
random_shuffle() isn't actually specified to use rand() and so srand() may not have any impact. If you want to be sure, you should use one of the C++11 forms, random_shuffle(b, e, RNG) or shuffle(b, e, uRNG).
An alternative would be to use random_shuffle(indices.begin(), indices.end(), rand()); because apparently your implementation of random_shuffle() is not using rand().
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Closed 9 years ago.
I am currently trying to understand how the following code (http://pastebin.com/zTHUrmyx) works, my approach is currently compiling the software in debug and using gdb to step through the code.
However, I'm running into the problem that 'step' does not always tell me what is going on. Particularly unclear to me is the EXECUTE {...} which I cannot step into.
How do I go about learning what the code is doing?
1 /*
2 Copyright 2008 Brain Research Institute, Melbourne, Australia
3
4 Written by J-Donald Tournier, 27/06/08.
5
6 This file is part of MRtrix.
7
8 MRtrix is free software: you can redistribute it and/or modify
9 it under the terms of the GNU General Public License as published by
10 the Free Software Foundation, either version 3 of the License, or
11 (at your option) any later version.
12
13 MRtrix is distributed in the hope that it will be useful,
14 but WITHOUT ANY WARRANTY; without even the implied warranty of
15 MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
16 GNU General Public License for more details.
17
18 You should have received a copy of the GNU General Public License
19 along with MRtrix. If not, see <http://www.gnu.org/licenses/>.
20
21
22 15-10-2008 J-Donald Tournier <d.tournier#brain.org.au>
23 * fix -prs option handling
24 * remove MR::DICOM_DW_gradients_PRS flag
25
26 15-10-2008 J-Donald Tournier <d.tournier#brain.org.au>
27 * add -layout option to manipulate data ordering within the image file
28
29 14-02-2010 J-Donald Tournier <d.tournier#brain.org.au>
30 * fix -coord option so that the "end" keyword can be used
31
32
33 */
34
35 #include "app.h"
36 #include "image/position.h"
37 #include "image/axis.h"
38 #include "math/linalg.h"
39
40 using namespace std;
41 using namespace MR;
42
43 SET_VERSION_DEFAULT;
44
45 DESCRIPTION = {
46 "perform conversion between different file types and optionally extract a subset of the input image.",
47 "If used correctly, this program can be a very useful workhorse. In addition to converting images between different formats, it can be used to extract specific studies from a data set, extract a specific region of interest, flip the images, or to scale the intensity of the images.",
48 NULL
49 };
50
51 ARGUMENTS = {
52 Argument ("input", "input image", "the input image.").type_image_in (),
53 Argument ("ouput", "output image", "the output image.").type_image_out (),
54 Argument::End
55 };
56
57
58 const gchar* type_choices[] = { "REAL", "IMAG", "MAG", "PHASE", "COMPLEX", NULL };
59 const gchar* data_type_choices[] = { "FLOAT32", "FLOAT32LE", "FLOAT32BE", "FLOAT64", "FLOAT64LE", "FLOAT64BE",
60 "INT32", "UINT32", "INT32LE", "UINT32LE", "INT32BE", "UINT32BE",
61 "INT16", "UINT16", "INT16LE", "UINT16LE", "INT16BE", "UINT16BE",
62 "CFLOAT32", "CFLOAT32LE", "CFLOAT32BE", "CFLOAT64", "CFLOAT64LE", "CFLOAT64BE",
63 "INT8", "UINT8", "BIT", NULL };
64
65 OPTIONS = {
66 Option ("coord", "select coordinates", "extract data only at the coordinates specified.", false, true)
67 .append (Argument ("axis", "axis", "the axis of interest").type_integer (0, INT_MAX, 0))
68 .append (Argument ("coord", "coordinates", "the coordinates of interest").type_sequence_int()),
69
70 Option ("vox", "voxel size", "change the voxel dimensions.")
71 .append (Argument ("sizes", "new dimensions", "A comma-separated list of values. Only those values specified will be changed. For example: 1,,3.5 will change the voxel size along the x & z axes, and leave the y-axis voxel size unchanged.")
72 .type_sequence_float ()),
73
74 Option ("datatype", "data type", "specify output image data type.")
75 .append (Argument ("spec", "specifier", "the data type specifier.").type_choice (data_type_choices)),
76
77 Option ("scale", "scaling factor", "apply scaling to the intensity values.")
78 .append (Argument ("factor", "factor", "the factor by which to multiply the intensities.").type_float (NAN, NAN, 1.0)),
79
80 Option ("offset", "offset", "apply offset to the intensity values.")
81 .append (Argument ("bias", "bias", "the value of the offset.").type_float (NAN, NAN, 0.0)),
82
83 Option ("zero", "replace NaN by zero", "replace all NaN values with zero."),
84
85 Option ("output", "output type", "specify type of output")
86 .append (Argument ("type", "type", "type of output.")
87 .type_choice (type_choices)),
88
89 Option ("layout", "data layout", "specify the layout of the data in memory. The actual layout produced will depend on whether the output image format can support it.")
90 .append (Argument ("spec", "specifier", "the data layout specifier.").type_string ()),
91
92 Option ("prs", "DW gradient specified as PRS", "assume that the DW gradients are specified in the PRS frame (Siemens DICOM only)."),
93
94 Option::End
95 };
96
97
98
99 inline bool next (Image::Position& ref, Image::Position& other, const std::vector<int>* pos)
100 {
101 int axis = 0;
102 do {
103 ref.inc (axis);
104 if (ref[axis] < ref.dim(axis)) {
105 other.set (axis, pos[axis][ref[axis]]);
106 return (true);
107 }
108 ref.set (axis, 0);
109 other.set (axis, pos[axis][0]);
110 axis++;
111 } while (axis < ref.ndim());
112 return (false);
113 }
114
115
116
117
118
119 EXECUTE {
120 std::vector<OptBase> opt = get_options (1); // vox
121 std::vector<float> vox;
122 if (opt.size())
123 vox = parse_floats (opt[0][0].get_string());
124
125
126 opt = get_options (3); // scale
127 float scale = 1.0;
128 if (opt.size()) scale = opt[0][0].get_float();
129
130 opt = get_options (4); // offset
131 float offset = 0.0;
132 if (opt.size()) offset = opt[0][0].get_float();
133
134 opt = get_options (5); // zero
135 bool replace_NaN = opt.size();
136
137 opt = get_options (6); // output
138 Image::OutputType output_type = Image::Default;
139 if (opt.size()) {
140 switch (opt[0][0].get_int()) {
141 case 0: output_type = Image::Real; break;
142 case 1: output_type = Image::Imaginary; break;
143 case 2: output_type = Image::Magnitude; break;
144 case 3: output_type = Image::Phase; break;
145 case 4: output_type = Image::RealImag; break;
146 }
147 }
148
149
150
151
152 Image::Object &in_obj (*argument[0].get_image());
153
154 Image::Header header (in_obj);
155
156 if (output_type == 0) {
157 if (in_obj.is_complex()) output_type = Image::RealImag;
158 else output_type = Image::Default;
159 }
160
161 if (output_type == Image::RealImag) header.data_type = DataType::CFloat32;
162 else if (output_type == Image::Phase) header.data_type = DataType::Float32;
163 else header.data_type.unset_flag (DataType::ComplexNumber);
164
165
166 opt = get_options (2); // datatype
167 if (opt.size()) header.data_type.parse (data_type_choices[opt[0][0].get_int()]);
168
169 for (guint n = 0; n < vox.size(); n++)
170 if (isfinite (vox[n])) header.axes.vox[n] = vox[n];
171
172 opt = get_options (7); // layout
173 if (opt.size()) {
174 std::vector<Image::Axis> ax = parse_axes_specifier (header.axes, opt[0][0].get_string());
175 if (ax.size() != (guint) header.axes.ndim())
176 throw Exception (String("specified layout \"") + opt[0][0].get_string() + "\" does not match image dimensions");
177
178 for (guint i = 0; i < ax.size(); i++) {
179 header.axes.axis[i] = ax[i].axis;
180 header.axes.forward[i] = ax[i].forward;
181 }
182 }
183
184
185 opt = get_options (8); // prs
186 if (opt.size() && header.DW_scheme.rows() && header.DW_scheme.columns()) {
187 for (guint row = 0; row < header.DW_scheme.rows(); row++) {
188 double tmp = header.DW_scheme(row, 0);
189 header.DW_scheme(row, 0) = header.DW_scheme(row, 1);
190 header.DW_scheme(row, 1) = tmp;
191 header.DW_scheme(row, 2) = -header.DW_scheme(row, 2);
192 }
193 }
194
195 std::vector<int> pos[in_obj.ndim()];
196
197 opt = get_options (0); // coord
198 for (guint n = 0; n < opt.size(); n++) {
199 int axis = opt[n][0].get_int();
200 if (pos[axis].size()) throw Exception ("\"coord\" option specified twice for axis " + str (axis));
201 pos[axis] = parse_ints (opt[n][1].get_string(), header.dim(axis)-1);
202 header.axes.dim[axis] = pos[axis].size();
203 }
204
205 for (int n = 0; n < in_obj.ndim(); n++) {
206 if (pos[n].empty()) {
207 pos[n].resize (in_obj.dim(n));
208 for (guint i = 0; i < pos[n].size(); i++) pos[n][i] = i;
209 }
210 }
211
212
213 in_obj.apply_scaling (scale, offset);
214
215
216
217
218
219
220 Image::Position in (in_obj);
221 Image::Position out (*argument[1].get_image (header));
222
223 for (int n = 0; n < in.ndim(); n++) in.set (n, pos[n][0]);
224
225 ProgressBar::init (out.voxel_count(), "copying data...");
226
227 do {
228
229 float re, im = 0.0;
230 in.get (output_type, re, im);
231 if (replace_NaN) if (gsl_isnan (re)) re = 0.0;
232 out.re (re);
233
234 if (output_type == Image::RealImag) {
235 if (replace_NaN) if (gsl_isnan (im)) im = 0.0;
236 out.im (im);
237 }
238
239 ProgressBar::inc();
240 } while (next (out, in, pos));
241
242 ProgressBar::done();
243 }
As was noted in the comments, EXECUTE seems to be a macro, apparent from the context a function header (and maybe a bit more, e.g. some global variables and functions), so the part in curly braces is the function body.
To get to the definition of EXECUTE, you will have to examine the headers.
However, if you can reach some part of the code during debugging, you could insert a string or char[] at that point, giving it the stringified version of EXECUTE, so you get whatever the preprocessor will emit for EXECUTE at that position in the code.
#define STR(x) #x
#define STRINGIFY(x) STR(x)
char c[] = STRINGIFY(EXECUTE);
the two macros are a known little macro trick to get the content of any macro as a string literal. Try it out and inspect the char array in your debugger to get the content of execute.
My wild guess here: EXECUTE is the main function or a replacement for it, the OPTIONS and ARGUMENTS describe what arguments the program expects and what command line options you can pass to it. Those macros and some of the used functions and variables (get_options, argument) are part of a little framework that should facilitate the usage, evaluation and user information about command line options.