ThreeB 1.1
Classes | Typedefs | Functions
General utility functions.

Classes

struct  MT19937
 Useful wrapper for MT19937 random number generator class. More...
class  Kahan
 Class implementing the Kahan summation algorithm to allow accurate summation of very large numbers of doubles. More...

Typedefs

typedef std::pair
< CVD::ImageRef, CVD::ImageRef > 		BBox

Functions

double ln (double x)
Vector spots_to_Vector (const vector< Vector< 4 > > &s)
vector< Vector< 4 > > spots_to_vector (const Vector<> &s)
Image< byte > scale_to_bytes (const Image< float > &im, float lo, float hi)
Image< byte > scale_to_bytes (const Image< float > &im)
Image< float > average_image (const vector< Image< float > > &ims)
vector< string > split (const string &line)
template<class C >
string xtoa (const C &x)
template<class C >
C atox (const string &s, const string &msg)
set< ImageRef > dilate_mask (const vector< ImageRef > &v, double r)
vector< int > SampledMultispot::sequence (int n)
double sign (double x)
float sq (float f)
const std::vector
< CVD::SubImage< float > > 		sub_images (const std::vector< CVD::Image< float > > &im, CVD::ImageRef pos, CVD::ImageRef size)
std::pair< CVD::ImageRef,
CVD::ImageRef > 		boundingbox (const std::vector< CVD::ImageRef > &all_spots)
template<class Stream >
void open_or_die (Stream &save_spots, const std::string &save_spots_file)

Typedef Documentation

typedef std::pair<CVD::ImageRef, CVD::ImageRef> BBox

Deffinition of a pixel aligned bounding box.

Definition at line 49 of file utility.h.

Function Documentation

double ln ( double  x) [inline]

Computes the natural logarithm, but returns -1e100 instead of inf for an input of 0.

This prevents trapping of FPU exceptions.

Parameters:
xx
Returns:
ln x

Definition at line 15 of file forward_algorithm.h.

Referenced by backward_sampling(), diff_log_log_normal(), forward_algorithm(), forward_algorithm_delta(), forward_algorithm_delta2(), forward_algorithm_hessian(), forward_backward_algorithm(), hess_log_log_normal(), log_log_normal(), and FitSpots::try_modifying_model().

{
    if(x == 0)
        return -1e100;
    else
        return std::log(x);
}
Vector spots_to_Vector ( const vector< Vector< 4 > > &  s)

There are two sensible ways of storing the state vector of spot positions.

This function converts between them. See also spots_to_vector.

Parameters:
slist of spots to convert

Definition at line 99 of file multispot5.cc.

Referenced by FitSpots::optimize_each_spot_in_turn_for_several_passes(), FitSpots::run(), and FitSpots::try_modifying_model().

{
    Vector<> r(s.size()*4);
    for(unsigned int i=0; i < s.size(); i++)
    {
        r[i*4+0] = s[i][0];
        r[i*4+1] = s[i][1];
        r[i*4+2] = s[i][2];
        r[i*4+3] = s[i][3];
    }
    return r;
}
vector<Vector<4> > spots_to_vector ( const Vector<> &  s)

There are two sensible ways of storing the state vector of spot positions.

This function converts between them. See also spots_to_Vector.

Parameters:
slist of spots to convert

Definition at line 116 of file multispot5.cc.

Referenced by NegativeFreeEnergy::compute_with_mask(), generate_state_parameters_ye_olde(), and NegativeFreeEnergy::operator()().

{
    vector<Vector<4> > r(s.size()/4);
    for(unsigned int i=0; i < r.size(); i++)
        r[i] = s.slice<Dynamic, 4>(i*4, 4);
    return r;
}
Image<byte> scale_to_bytes ( const Image< float > &  im,
float  lo,
float  hi 
)

Normalize an image for display purposes.

Definition at line 126 of file multispot5.cc.

{
        Image<byte> out(im.size());
        for(int r=0; r < out.size().y-0; r++)
                for(int c=0; c < out.size().x-0; c++)
                        out[r][c] = (int)floor((im[r][c]-lo)*255/(hi-lo));
        return out;
}
Image<byte> scale_to_bytes ( const Image< float > &  im)

Normalize an image for display purposes.

Definition at line 137 of file multispot5.cc.

{
        float lo = *min_element(im.begin(), im.end());
        float hi = *max_element(im.begin(), im.end());
        Image<byte> out(im.size());
        for(int r=0; r < out.size().y-0; r++)
                for(int c=0; c < out.size().x-0; c++)
                        out[r][c] = (int)floor((im[r][c]-lo)*255/(hi-lo));

        return out;
}
Image<float> average_image ( const vector< Image< float > > &  ims)

Average the input image stack for display purposes.

Definition at line 151 of file multispot5.cc.

References assert_same_size().

{
    assert_same_size(ims);
    Image<float> r(ims[0].size(), 0);

    for(unsigned int i=0; i < ims.size(); i++)
        transform(r.begin(), r.end(), ims[i].begin(), r.begin(), plus<float>());

    transform(r.begin(), r.end(), r.begin(), bind2nd(multiplies<float>(), 1./ims.size()));
    return r;
}
vector<string> split ( const string &  line)

Tokenize a line.

Definition at line 915 of file multispot5.cc.

Referenced by parse_log_file().

{
    vector<string> v;
    istringstream i(line);
    string s;

    while(!i.eof())
    {
        i >> s;
        if(i.fail())
            break;
        v.push_back(s);
    }
    return v;
}
template<class C >
string xtoa ( const C &  x) [inline]

Generic version of itoa.

How many times has this been reimplemented??

Parameters:
xValue to convert to string

Definition at line 935 of file multispot5.cc.

Referenced by parse_log_file().

{
    ostringstream os;
    os << x;
    return os.str();
}
template<class C >
C atox ( const string &  s,
const string &  msg 
) [inline]

Inverse of xtoa() How many times has this been reimplemented??

Parameters:
sString to convert
msgMesage to print on error

Definition at line 947 of file multispot5.cc.

{
    C c;
    istringstream i(s);
    i >> c;
    if(i.fail())
        throw LogFileParseError("Error parsing " + msg + ". Text is `" + s + "'.");
    return c;
}
set<ImageRef> dilate_mask ( const vector< ImageRef > &  v,
double  r 
)

Very simple and inefficient dilation function.

Definition at line 1319 of file multispot5.cc.

{
    vector<ImageRef> m = getDisc(r);

    set<ImageRef> ret;

    for(unsigned int i=0; i < v.size(); i++)
        for(unsigned int j=0; j < m.size(); j++)
            ret.insert(v[i] + m[j]);

    return ret;
}
vector<int> SampledMultispot::sequence ( int  n) [inline]

Create a sequence of integers.

These can be used as observations in an observation class by forward_algorithm() and etc.

Parameters:
nLength of sequence

Definition at line 169 of file sampled_multispot.h.

Referenced by FitSpots::optimize_each_spot_in_turn_for_several_passes().

{
    vector<int> v;
    for(int i=0; i < n; i++)
        v.push_back(i);
    return v;
}
double sign ( double  x) [inline]

computes the sign of x

Parameters:
xx
Returns:
$ \begin{cases} 1 & x \ge 0\\ -1 & x < 0 \end{cases}$

Definition at line 19 of file utility.h.

{
    return x>=0?1:-1;
}
float sq ( float  f) [inline]

The ubiquitous square function.

Parameters:
fNumber to square
Returns:
square of the number

Definition at line 29 of file utility.h.

Referenced by auto_fixed_scaling(), NegativeFreeEnergy::compute_with_mask(), diff_log_log_normal(), hess_log_log_normal(), log_log_normal(), log_normal_std(), log_probability_spot(), log_probability_spot_diff(), log_probability_spot_hess(), NegativeFreeEnergy::operator()(), spot_shape_diff_position(), spot_shape_hess_position(), and NegativeFreeEnergy::variance_from_sample().

{ return f*f; }
const std::vector<CVD::SubImage<float> > sub_images ( const std::vector< CVD::Image< float > > &  im,
CVD::ImageRef  pos,
CVD::ImageRef  size 
)

Cut sub images out of every member of a vector of images.

Parameters:
imImages to be cut
posTop left corner
sizeSize of the patch
Returns:
subimages.

Referenced by test_output_patch_variance().

std::pair<CVD::ImageRef, CVD::ImageRef> boundingbox ( const std::vector< CVD::ImageRef > &  all_spots)

Compute the bounding box of a set of points.

Parameters:
all_spotsList of points

Referenced by mmain(), FitSpots::optimize_each_spot_in_turn_for_several_passes(), and FitSpots::try_modifying_model().

template<class Stream >
void open_or_die ( Stream &  save_spots,
const std::string &  save_spots_file 
)
Parameters:
save_spotsStream
save_spots_fileFile to open

Definition at line 64 of file utility.h.

Referenced by mmain().

{
    using std::cerr;
    using std::endl;
    using std::strerror;
    using std::exit;
    save_spots.open(save_spots_file.c_str());
    int err = errno;

    if(!save_spots.good())
    {
        cerr << "***********************************************************\n";
        cerr << "ERROR: failed to open " << save_spots_file << ": " <<strerror(err) << endl;
        cerr << "***********************************************************\n";
        exit(1);
    }
}
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