Hi! The last update on my packaging attempt of FSL was some time ago, so I guess I should do another one. On Thu, Jan 12, 2006 at 02:58:19PM +0100, Andreas Tille wrote: > On Thu, 12 Jan 2006, Michael Hanke wrote: <snip> > >And now for the remaining problems. There is still no official package > >for 'newmat'. Although there has been a RFS lately: > > > >http://lists.debian.org/debian-mentors/2006/01/msg00047.html > > > >I also made an unofficial package of 'newmat', because the above > >packaging attempt did not work with FSL due to some differences in the > >build configuration. I asked the maintainer for the appropriate changes. > >If this is done so I can add this package to the build-dependencies of > >the FSL package. > > If it is in your (=Debian-Med's) interest I would volunteer to sponsor > a newmat package provided that it fits your needs. So if a missing > sponsor for newmat would be the final show stopper for FSL just come > back to me. I did some testing with the newmat package (made by Philippe Coval). It includes a shared library and works pretty well for me. I had a quick look on the package and made some suggestions, but it would be nice if someone more experienced with shared-library packaging could have a look at it (it is available from mentors.d.n). And IIRC the newmat package still needs a sponsor (Andreas?!). > >I was not able to use the Debian version of libgdchart. Neither did > >compiling FSL worked nor was I able to locate the problem. > > Can you specify the problem more detailed? I have no experiences with > libgdchart, but dicussing the problem on debian-devel is very often > helpful. I get a linker error if I use the Debian version of libgdchart: g++ -L/usr/lib -L/home/michael/debian/build-area/fsl-xp/lib -L/usr/lib -L/usr/lib -L/usr/lib -L/usr/lib -L. -L/home/michael/debian/build-area/fsl-xp/lib -L/home/michael/debian/build-area/fsl-xp/lib -o filmbabe halfcosbasisoptions.o filmbabe_manager.o filmbabeoptions.o filmbabe_vb_flobs.o filmbabe.o -lutils -lmiscplot -lmiscpic -lnewimage -lmiscplot -lmiscmaths -lnewmat -lfslio -lniftiio -lprob -lgdc -lgd -lpng -lznz -lz -lm /usr/lib/libgdc.so: undefined reference to `GDCPIE_label_font' /usr/lib/libgdc.so: undefined reference to `GDC_title_ptsize' /usr/lib/libgdc.so: undefined reference to `GDCPIE_3d_angle' f/usr/lib/libgdc.so: undefined reference to `GDCPIE_label_dist' /usr/lib/libgdc.so: undefined reference to `GDCPIE_title_font' /usr/lib/libgdc.so: undefined reference to `GDCPIE_title_size' /usr/lib/libgdc.so: undefined reference to `GDCPIE_percent_labels' /usr/lib/libgdc.so: undefined reference to `GDC_xtitle_ptsize' /usr/lib/libgdc.so: undefined reference to `GDC_annotation_ptsize' /usr/lib/libgdc.so: undefined reference to `GDCPIE_label_line' /usr/lib/libgdc.so: undefined reference to `GDC_title_font' /usr/lib/libgdc.so: undefined reference to `GDC_annotation_font' /usr/lib/libgdc.so: undefined reference to `GDCPIE_label_ptsize' /usr/lib/libgdc.so: undefined reference to `GDCPIE_LineColor' /usr/lib/libgdc.so: undefined reference to `GDC_xtitle_font' /usr/lib/libgdc.so: undefined reference to `GDCPIE_EdgeColor' /usr/lib/libgdc.so: undefined reference to `GDC_ytitle_ptsize' /usr/lib/libgdc.so: undefined reference to `GDCPIE_explode' /usr/lib/libgdc.so: undefined reference to `GDCPIE_3d_depth' /usr/lib/libgdc.so: undefined reference to `GDCPIE_percent_fmt' /usr/lib/libgdc.so: undefined reference to `GDCPIE_other_threshold' /usr/lib/libgdc.so: undefined reference to `GDCPIE_title' /usr/lib/libgdc.so: undefined reference to `GDC_xaxis_ptsize' /usr/lib/libgdc.so: undefined reference to `GDC_xaxis_font' /usr/lib/libgdc.so: undefined reference to `GDCPIE_PlotColor' /usr/lib/libgdc.so: undefined reference to `GDCPIE_missing' /usr/lib/libgdc.so: undefined reference to `GDCPIE_BGColor' /usr/lib/libgdc.so: undefined reference to `GDC_ytitle_font' /usr/lib/libgdc.so: undefined reference to `GDCPIE_title_ptsize' /usr/lib/libgdc.so: undefined reference to `GDCPIE_perspective' /usr/lib/libgdc.so: undefined reference to `GDCPIE_Color' /usr/lib/libgdc.so: undefined reference to `GDCPIE_label_size' collect2: ld returned 1 exit status I compared the included libgdc version with the current Debian one and found no significant differences. I spend some time using Google and only found a single guy with a similar problem, but no solution. My first guess was a possible problem using a C lib in a C++ program. I attached the source code file that seems to cause the problem. I my oppinion this issue has to be solved before considering FSL as a candidate for Debian. > >The last remaining library is CEPHES. There is still no package. But as > >I do not know of any other application that uses this lib, it might be > >ok to keep this one compiled from the FSL source code. > > Well, this depends (as always). If you ask me issuing a RFP or rather > ITP and packaging it from a clean upstream source would be the > clean way to go (TM). If this does not fit your time frame we could > find the intermediate solution to build it from the FSL source code. > But in this case I would strictly vote for building a separate package > for this library if possible in any way. Well, in the meantime I removed the need for half of the CEPHES code. What remains seems to be a customised version that is statically linked against a few parts of FSL. That said, I would not go for a separate package, but rather consider this a part of the FSL source code. I committed some patches concerning GCC4 compatibilty to upstream which are currently inspected and probably integrated in the next FSL release. And finally I started distributing a first version of the package. See here for more information: http://apsy.gse.uni-magdeburg.de/main/index.php?sec=1&page=hm_fsl&lang=en But note, the distributed package is not up-to-date with the GCC4 patches (mentioned above) and the latest packaging improvements. Instead, this package is the best tested one concerning possible side-effect of the packaging on the results produced by the FSL tools. Cheers, Michael -- GPG key: 1024D/3144BE0F Michael Hanke http://apsy.gse.uni-magdeburg.de/hanke ICQ: 48230050
/* miscplot.cc -- miscellaneous plotting functions
Christian F. Beckmann, FMRIB Image Analysis Group
Copyright (C) 1999-2002 University of Oxford */
/* Part of FSL - FMRIB's Software Library
http://www.fmrib.ox.ac.uk/fsl
fsl@fmrib.ox.ac.uk
Developed at FMRIB (Oxford Centre for Functional Magnetic Resonance
Imaging of the Brain), Department of Clinical Neurology, Oxford
University, Oxford, UK
LICENCE
FMRIB Software Library, Release 3.2beta (c) 2004, The University of
Oxford (the "Software")
The Software remains the property of the University of Oxford ("the
University").
The Software is distributed "AS IS" under this Licence solely for
non-commercial use in the hope that it will be useful, but in order
that the University as a charitable foundation protects its assets for
the benefit of its educational and research purposes, the University
makes clear that no condition is made or to be implied, nor is any
warranty given or to be implied, as to the accuracy of the Software,
or that it will be suitable for any particular purpose or for use
under any specific conditions. Furthermore, the University disclaims
all responsibility for the use which is made of the Software. It
further disclaims any liability for the outcomes arising from using
the Software.
The Licensee agrees to indemnify the University and hold the
University harmless from and against any and all claims, damages and
liabilities asserted by third parties (including claims for
negligence) which arise directly or indirectly from the use of the
Software or the sale of any products based on the Software.
No part of the Software may be reproduced, modified, transmitted or
transferred in any form or by any means, electronic or mechanical,
without the express permission of the University. The permission of
the University is not required if the said reproduction, modification,
transmission or transference is done without financial return, the
conditions of this Licence are imposed upon the receiver of the
product, and all original and amended source code is included in any
transmitted product. You may be held legally responsible for any
copyright infringement that is caused or encouraged by your failure to
abide by these terms and conditions.
You are not permitted under this Licence to use this Software
commercially. Use for which any financial return is received shall be
defined as commercial use, and includes (1) integration of all or part
of the source code or the Software into a product for sale or license
by or on behalf of Licensee to third parties or (2) use of the
Software or any derivative of it for research with the final aim of
developing software products for sale or license to a third party or
(3) use of the Software or any derivative of it for research with the
final aim of developing non-software products for sale or license to a
third party, or (4) use of the Software to provide any service to an
external organisation for which payment is received. If you are
interested in using the Software commercially, please contact Isis
Innovation Limited ("Isis"), the technology transfer company of the
University, to negotiate a licence. Contact details are:
innovation@isis.ox.ac.uk quoting reference DE/1112. */
#include <strstream>
#include <stdio.h>
#include "miscplot.h"
#include "miscmaths/miscprob.h"
#include "gdfonts.h"
extern "C" {
#include "gd.h"
#include "gdc.h"
#include "gdchart.h"
}
namespace MISCPLOT{
// MATLAB Line colors
unsigned long sc[64] = {0x8080FF,0x008000,0xFF0000,0x00BFBF,0xBF00BF,0xBFBF00,0x404040,0x0000FF,
0x008000,0xFF0000,0x00BFBF,0xBF00BF,0xBFBF00,0x404040,0x0000FF,0x008000,
0xFF0000,0x00BFBF,0xBF00BF,0xBFBF00,0x404040,0x0000FF,0x008000,0xFF0000,
0x00BFBF,0xBF00BF,0xBFBF00,0x404040,0x0000FF,0x008000,0xFF0000,0x00BFBF,
0xBF00BF,0xBFBF00,0x404040,0x0000FF,0x008000,0xFF0000,0x00BFBF,0xBF00BF,
0xBFBF00,0x404040,0x0000FF,0x008000,0xFF0000,0x00BFBF,0xBF00BF,0xBFBF00,
0x404040,0x0000FF,0x008000,0xFF0000,0x00BFBF,0xBF00BF,0xBFBF00,0x404040,
0x0000FF,0x008000,0xFF0000,0x00BFBF,0xBF00BF,0xBFBF00,0x404040,0x0000FF};
using namespace NEWMAT;
using namespace MISCMATHS;
string int2str(int n)
{
ostrstream os;
os.setf(ios::internal, ios::adjustfield);
os << n << '\0';
return os.str();
}
string float2str(float f, int width, int prec, bool scientif)
{
ostrstream os;
int redw = int(std::abs(std::log10(std::abs(f))))+1;
if(width>0)
os.width(width);
if(scientif)
os.setf(ios::scientific);
os.precision(redw+std::abs(prec));
os.setf(ios::internal, ios::adjustfield);
os << f << '\0';
return os.str();
}
void miscplot::add_legend(void* ptr, unsigned long cmap[], bool inside){
int xsize = gdImagePtr(ptr)->sx;
int ysize = gdImagePtr(ptr)->sy;
int dest_x = 0;
int linebrk = 5;
int space = gdFontSmall->w + 2;
int linelength = 15;
int rlbllength = 0;
for(int ctr= 0; ctr < int(labels.size()); ctr++)
rlbllength = max(rlbllength,int(labels[ctr].length()));
if(explabel.length()>0)
ysize += space + 0*gdFontSmall->h;
if(xlabels.size()>0)
ysize += xlabels.size()*(linebrk + gdFontSmall->h)+linebrk;
if(ylabels.size()>0)
dest_x += ylabels.size()*(linebrk + gdFontSmall->h)+2*linebrk;
if((!inside)&&(labels.size()>0))
xsize += 2*space + linelength + rlbllength * gdFontSmall->w;
xsize += dest_x;
gdImagePtr newim;
newim = gdImageCreate(xsize,ysize);
gdImageCopy(newim,gdImagePtr(ptr),dest_x,0,0,0,gdImagePtr(ptr)->sx,gdImagePtr(ptr)->sy);
int black = gdImageColorResolve(newim, 0, 0, 0);
int ycoor, xcoor, yoffset=0;
//make scale info
if(explabel.length()>0){
yoffset=space;
xcoor=gdImagePtr(ptr)->sx - (4 + explabel.length())*gdFontSmall->w;
ycoor=gdImagePtr(ptr)->sy+linebrk;
char *s = (char*)string("x10").c_str();
gdImageString(newim, gdFontSmall,xcoor,ycoor, (unsigned char*) s, black);
xcoor+=(int)3.5*gdFontSmall->w;
ycoor-=gdFontSmall->h/2;
string s2 = string("-")+explabel;
char *s3 = (char*)s2.c_str();
gdImageString(newim, gdFontSmall,xcoor,ycoor, (unsigned char*) s3, black);
}
// make xlabel
ycoor=gdImagePtr(ptr)->sy+linebrk+yoffset;
for(int ctr=0; ctr < int(xlabels.size()); ctr++){
xcoor = dest_x + gdImagePtr(ptr)->sx/2 - ((int)xlabels[ctr].length())/2*gdFontSmall->w;
char *s = (char*)xlabels[ctr].c_str();
gdImageString(newim, gdFontSmall,xcoor,ycoor, (unsigned char*) s, black);
ycoor+=gdFontSmall->h + linebrk;
}
// make legend
ycoor = 2+2*gdFontSmall->h;
for(int ctr=0; ctr < int(labels.size()); ctr++){
xcoor = dest_x+gdImagePtr(ptr)->sx;
if(inside)
xcoor -= 2*space + linelength + rlbllength * gdFontSmall->w;
int col = gdImageColorResolve(newim, ((cmap[ctr]&PVRED)>>16),((cmap[ctr]&PVGRN)>>8), (cmap[ctr]&0x000000FF));
gdImageLine(newim, xcoor, ycoor + gdFontSmall->h/2, xcoor + linelength, ycoor + gdFontSmall->h/2,col);
gdImageLine(newim, xcoor, ycoor + gdFontSmall->h/2+1, xcoor + linelength, ycoor + gdFontSmall->h/2+1,col);
char *s = (char*)labels[ctr].c_str();
gdImageString(newim, gdFontSmall, xcoor + linelength + space, ycoor, (unsigned char*) s, black);
ycoor += gdFontSmall->h + linebrk;
}
// make ylabel
xcoor=space;
for(int ctr=0; ctr < int(ylabels.size()); ctr++){
int ycoor = 3*gdImagePtr(ptr)->sy/5 + ((int)ylabels[ctr].length())/2*gdFontSmall->w;
char *s = (char*)ylabels[ctr].c_str();
gdImageStringUp(newim, gdFontSmall,xcoor,ycoor, (unsigned char*) s, black);
xcoor+=gdFontSmall->h + linebrk;
}
outim = newim;
}
void miscplot::timeseries(const Matrix& mat, string filename, string title,
float tr, int ysize, int width, int prec, bool sci){
int numlines=mat.Nrows();
int numpoint=mat.Ncols();
float* data = new float[numlines*numpoint];
for(int ctr1=1;ctr1<=numlines; ctr1++){
for(int ctr2=1;ctr2<=numpoint; ctr2++){
data[(ctr1-1)*numpoint + ctr2-1] = mat(ctr1,ctr2);
}
}
int spacing = 1;
if(numpoint>20) spacing = 2;
if(numpoint>40) spacing = 5;
if(numpoint>100) spacing = 10;
if(numpoint>500) spacing = 20;
if(numpoint>1200) spacing = 50;
//if(numpoint>2000) spacing = 100;
char* ctl = new char[numpoint];
if((tr == 0.0)&&(spacing%2 == 1) || (tr > 0.0))
ctl[0] = TRUE;
else
ctl[0] = FALSE;
for(int ctr=1;ctr<numpoint;ctr++)
ctl[ctr]=((((ctr+1)%spacing == 0)&&(tr == 0.0))
||(((ctr)%spacing == 0)&&(tr != 0.0)));
//ctl[numpoint-1]=TRUE;
char** lbls = new char*[numpoint];
string s;
lbls[0] = new char[2];
if(tr == 0.0)
strcpy(lbls[0],string("1").c_str());
else
strcpy(lbls[0],string("0").c_str());
for(int ctr=1;ctr<numpoint;ctr++){
if(ctl[ctr]){
if(tr == 0.0)
s = int2str(ctr+1);
else
s = float2str((ctr)*tr,width,prec,sci);
lbls[ctr] = new char[s.length()+1];
strcpy(lbls[ctr],s.c_str());
}
else{
lbls[ctr] = new char[1];
strcpy(lbls[ctr],string("").c_str());
}
}
{
int tmp = _gdccfoo1;
tmp++;
long unsigned int tmp2 = _gdccfoo2;
tmp2++;
}
GDC_xlabel_ctl = ctl;
GDC_BGColor = 0xFFFFFFL; /* backgound color (white) */
GDC_LineColor = 0x000000L; /* line color (black) */
GDC_SetColor = &(sc[0]); /* MATLAB-like colors */
GDC_title = (char*)title.c_str();
GDC_ticks = GDC_TICK_LABELS;
GDC_grid = GDC_TICK_NONE;
GDC_yaxis = TRUE;
GDC_yaxis2 = FALSE;
GDC_xaxis = TRUE;
GDC_xaxis_angle = 0;
GDC_ylabel_density = 50;
GDC_ylabel_fmt = "%.2f";
GDC_title_size = GDC_SMALL;
int i,j;
GDC_requested_ymax = 1.10*mat.Maximum2(i,j);
GDC_requested_ymin = 1.10*mat.Minimum2(i,j);
int xsize = std::max(4*numpoint,750);
if(xsize>1200) xsize=(int)floor(std::max(xsize/2.0,750.0));
if(req_xsize>0){
xsize=req_xsize;
ysize=req_ysize;
}
//GDC_hard_size = TRUE;
//GDC_hard_xorig = 50;
//GDC_hard_graphwidth = xsize - 65;
if(filename.substr(filename.size()-4,filename.size())!=string(".png"))
filename += string(".png");
FILE *outpng1 = fopen(filename.c_str(), "wb" );
GDC_image_type = GDC_PNG;
if (labels.size()>0||ylabels.size()>0||xlabels.size()>0)
GDC_hold_img = GDC_EXPOSE_IMAGE;
GDC_out_graph( xsize, ysize, outpng1 , GDC_LINE, numpoint, (char**) lbls , numlines, data, NULL );
//GDC_out_graph( xsize, ysize, outpng1 , GDC_LINE, numpoint, NULL , numlines, data, NULL );
fclose( outpng1 );
if (labels.size()>0||ylabels.size()>0||xlabels.size()>0){
outpng1 = fopen(filename.c_str(), "wb" );
add_legend(GDC_image, sc);
gdImagePng(outim, outpng1);
fclose( outpng1 );
GDC_destroy_image(GDC_image);
if(outim) gdImageDestroy(outim);
}
for(int ctr=0;ctr<numpoint;ctr++){
delete [] lbls[ctr];
}
delete [] data;
delete [] ctl;
delete [] lbls;
}
void miscplot::histogram(const Matrix& mat, string filename, string title){
RowVector datam = mat.Row(1);
int numpoint=datam.Ncols();
int i,j;
double scale=std::max(1.0,MISCMATHS::pow((float)10.0,(double)-(std::floor(std::log10(std::min(std::abs(datam.Maximum2(i,j)),std::abs(datam.Minimum2(i,j)))/2.0)))));
//cerr << datam.Maximum2(i,j) << " " << datam.Minimum2(i,j) << scale << endl;
datam *=scale;
if(scale>100)
explabel=num2str(std::log10(scale));
float tmax = datam.Maximum2(i,j);
float tmin = datam.Minimum2(i,j);
float trange = tmax-tmin;
int bins = (int)floor(MISCMATHS::sqrt(numpoint));
float intsize = trange / bins;
int xlint = (int)ceil(trange/6);
int binperint = (int)ceil(xlint / intsize);
//cerr << tmax << " " << tmin << " " << trange << " " << bins << " " << intsize << " " << xlint << " " << binperint << " :" << scale <<endl;
intsize = float(xlint) / float(binperint);
float xmin = ceil(std::abs(1.02*tmin)/intsize)*intsize * sign(tmin);
float xmax = ceil(std::abs(1.02*tmax)/intsize)*intsize * sign(tmax);
bins = (int)((xmax-xmin)/intsize);
Matrix bindata(1,bins);
bindata = 0.0;
double binsize = (xmax-xmin)/std::max(bins,1);
for(int ctr = 1; ctr<= datam.Ncols(); ctr++){
bindata(1,std::max(std::min(int(floor((datam(ctr) - xmin) / binsize) + 1),bins),1))++;
}
//cerr << " calculated bindata " << endl;
int factor = 1;
numpoint = factor * bindata.Ncols();
float* data = new float[numpoint];
for(int ctr1=0;ctr1< numpoint; ctr1++){
data[ctr1] = bindata(1,(int)floor(float(ctr1 / factor + 1)));
}
RowVector xax(numpoint);
for(int ctr1=0;ctr1< numpoint; ctr1++){
xax(ctr1+1) = xmin + (ctr1+ 0.5) * intsize;
}
char* ctl = new char[numpoint];
xlint = (int)ceil((xmax-xmin)/9);
ctl[0]=FALSE;
for(int ctr=1;ctr<numpoint;ctr++){
int lblpoint = (int)(MISCMATHS::round(abs(xax(ctr))/xlint)*xlint);
if(xax(ctr)<0) lblpoint *= -1;
if( (xax(ctr)<lblpoint)&&(xax(ctr+1)>lblpoint) ){
ctl[ctr]=TRUE;
}
else
ctl[ctr]=FALSE;
}
char** lbls = new char*[numpoint];
string s;
for(int ctr=0;ctr<numpoint;ctr++){
if(ctl[ctr]){
if(scale<2||scale>100)
s = float2str((int)MISCMATHS::round(xax(ctr+1)/xlint)*xlint,3,2,false);
else
s = float2str((float)MISCMATHS::round(xax(ctr+1)/xlint)*xlint/scale,3,2,false);
lbls[ctr] = new char[s.length()+1];
strcpy(lbls[ctr],s.c_str());
}
else{
lbls[ctr] = new char[1];
strcpy(lbls[ctr],string("").c_str());
}
}
GDC_xlabel_ctl = ctl;
GDC_BGColor = 0xFFFFFFL; /* backgound color (white) */
GDC_LineColor = 0x000000L; /* line color (black) */
GDC_SetColor = &(sc[0]); /* MATLAB-like colors */
GDC_title = (char*)title.c_str();
GDC_title_size = GDC_SMALL;
GDC_ticks = GDC_TICK_LABELS;
GDC_grid = GDC_TICK_NONE;
GDC_yaxis = ylabels.size()>0;
GDC_yaxis2 = FALSE;
GDC_xaxis = TRUE;
GDC_xaxis_angle = 0;
GDC_bar_width = 75;
GDC_ylabel_density = 50;
GDC_requested_ymax = 1.15*bindata.Maximum2(i,j);
GDC_requested_ymin = 1.15*bindata.Minimum2(i,j);
//int xsize = std::max(4*numpoint,750);
// if(xsize>1200) xsize=(int)floor(std::max(xsize/2.0,750.0));
int xsize = 600;
int ysize = 400;
if(req_xsize>0){
xsize=req_xsize;
ysize=req_ysize;
}
if(filename.substr(filename.size()-4,filename.size())!=string(".png"))
filename += string(".png");
FILE *outpng1 = fopen(filename.c_str(), "wb" );
GDC_image_type = GDC_PNG;
if (labels.size()>0||ylabels.size()>0||xlabels.size()>0||explabel.length()>0)
GDC_hold_img = GDC_EXPOSE_IMAGE;
GDC_out_graph( xsize, ysize, outpng1 , GDC_BAR, numpoint, (char**) lbls , 1, data, NULL );
fclose( outpng1 );
if (labels.size()>0||ylabels.size()>0||xlabels.size()>0||explabel.length()>0){
outpng1 = fopen(filename.c_str(), "wb" );
add_legend(GDC_image, sc);
gdImagePng(outim, outpng1);
fclose( outpng1 );
GDC_destroy_image(GDC_image);
if(outim) gdImageDestroy(outim);
}
for(int ctr=0;ctr<numpoint;ctr++){
delete [] lbls[ctr];
}
delete [] data;
delete [] lbls;
delete [] ctl;
}
void miscplot::gmmfit(const Matrix& mat, Matrix& mu, Matrix& sig,
Matrix& pi, string filename, string title,
bool gammamix, float meanoffset, float detailfactor)
{
RowVector datam = mat.Row(1);
int numpoint=datam.Ncols();
int i,j;
double scale=std::max(1.0,MISCMATHS::pow((float)10.0,(double)-(std::floor(std::log10(std::min(std::abs(datam.Maximum2(i,j)),std::abs(datam.Minimum2(i,j)))/2.0)))));
//cerr << datam.Maximum2(i,j) << " " << datam.Minimum2(i,j) << scale << endl;
datam *=scale; mu *= scale; sig *= scale;
if(scale>100)
explabel=num2str(std::log10(scale));
float tmax = datam.Maximum2(i,j);
float tmin = datam.Minimum2(i,j);
float trange = tmax-tmin;
int bins = (int)floor(MISCMATHS::sqrt(numpoint));
float intsize = trange / bins;
int xlint = (int)ceil(trange/6);
int binperint = (int)ceil(xlint / intsize);
//cerr << tmax << " " << tmin << " " << trange << " " << bins << " " << intsize << " " << xlint << " " << binperint << " :" << scale <<endl;
intsize = float(xlint) / float(binperint);
float xmin = ceil(std::abs(1.02*tmin)/intsize)*intsize * sign(tmin);
float xmax = ceil(std::abs(1.02*tmax)/intsize)*intsize * sign(tmax);
bins = (int)((xmax-xmin)/intsize);
Matrix bindata(1,bins);
bindata = 0.0;
double binsize = (xmax-xmin)/std::max(bins,1);
for(int ctr = 1; ctr<= datam.Ncols(); ctr++){
bindata(1,std::max(std::min(int(floor((datam(ctr) - xmin) / binsize) + 1),bins),1))++;
}
//cerr << " calculated bindata " << endl;
int factor = 5;
bindata = bindata / max(double(factor*bindata.SumAbsoluteValue()),double(1.0));
numpoint = factor * bindata.Ncols();
float* histdata = new float[numpoint];
for(int ctr1=0;ctr1< numpoint; ctr1++){
histdata[ctr1] = bindata(1,(int)floor(float(ctr1 / factor + 1)));
}
RowVector xax(numpoint);
for(int ctr1=0;ctr1< numpoint; ctr1++){
xax(ctr1+1) = xmin + (ctr1+ 0.5) * intsize/factor;
}
char* ctl = new char[numpoint];
xlint = (int)ceil((xmax-xmin)/(factor*5));
ctl[0]=FALSE;
for(int ctr=1;ctr<numpoint;ctr++){
int lblpoint = (int)(MISCMATHS::round(abs(xax(ctr))/xlint)*xlint);
if(xax(ctr)<0) lblpoint *= -1;
if( (xax(ctr)<lblpoint)&&(xax(ctr+1)>lblpoint) ){
ctl[ctr]=TRUE;
}
else
ctl[ctr]=FALSE;
}
char** lbls = new char*[numpoint];
string s;
for(int ctr=0;ctr<numpoint;ctr++){
if(ctl[ctr]){
if(scale<2||scale>100)
s = float2str((int)MISCMATHS::round(xax(ctr+1)/xlint)*xlint,3,2,false);
else
s = float2str((float)MISCMATHS::round(xax(ctr+1)/xlint)*xlint/scale,3,2,false);
lbls[ctr] = new char[s.length()+1];
strcpy(lbls[ctr],s.c_str());
}
else{
lbls[ctr] = new char[1];
strcpy(lbls[ctr],string("").c_str());
}
}
// Calculate lines
int numlines=mu.Ncols()+1;
for(int ctr1=1;ctr1< sig.Ncols(); ctr1++)
if(sig(1,ctr1)<0.000001){
sig(1,ctr1) = 0.000001;
pi(1,ctr1) = 0.0;
}
Matrix fit;
fit = SP(normpdf(xax,mu,sig),pi.t()*ones(1,numpoint));
if(null_shift!=0.0)
fit.Row(1) = pi(1,1)*gammapdf(-(xax + null_shift) + meanoffset, std::abs(mu(1,1) + null_shift), sig(1,1));
if(gammamix){
if(pi(1,2)>0.0001)
fit.Row(2) = pi(1,2)*gammapdf( xax - meanoffset, std::abs(mu(1,2)), sig(1,2));
if(pi(1,3)>0.0001)
fit.Row(3) = pi(1,3)*gammapdf(-xax + meanoffset, std::abs(mu(1,3)), sig(1,3));
}
fit = sum(fit,1) & fit;
fit = fit / fit.Row(1).SumAbsoluteValue();
float* linesdata = new float[(numlines)*numpoint];
for(int ctr1=1;ctr1<=numlines; ctr1++){
for(int ctr2=1;ctr2<=numpoint; ctr2++){
linesdata[(ctr1-1)*numpoint + ctr2-1] = fit(ctr1,ctr2);
}
}
GDC_xlabel_ctl = ctl;
unsigned long* sc2 = new unsigned long[numlines];
for(int ctr=0;ctr<numlines;ctr++) sc2[ctr] = 0xFFDD00;
sc2[0]=0xFF0000;
if(gammamix)
sc2[1]=0x00aa00;
unsigned long sc3[64];
for(int ctr=0;ctr<64;ctr++) sc3[ctr] = sc[ctr];
for(int ctr=0;ctr<numlines;ctr++){
sc3[ctr+1] = sc2[ctr];
}
GDC_BGColor = 0xFFFFFFL; /* backgound color (white) */
GDC_LineColor = 0x000000L; /* line color (black) */
GDC_SetColor = &(sc2[0]); /* MATLAB-like colors */
GDC_title = (char*)title.c_str();
GDC_title_size = GDC_SMALL;
GDC_ticks = GDC_TICK_LABELS;
GDC_grid = GDC_TICK_NONE;
GDC_yaxis = ylabels.size()>0;
GDC_yaxis2 = FALSE;
GDC_xaxis = TRUE;
GDC_xaxis_angle = 0;
GDC_bar_width = 75;
GDC_ylabel_density = 50;
GDC_requested_ymax = 1.15*bindata.Maximum2(i,j);
GDC_requested_ymin = 1.15*bindata.Minimum2(i,j);
//int xsize = std::max(4*numpoint,750);
// if(xsize>1200) xsize=(int)floor(std::max(xsize/2.0,750.0));
int xsize = 600;
int ysize = 400;
if(req_xsize>0){
xsize=req_xsize;
ysize=req_ysize;
}
if(filename.substr(filename.size()-4,filename.size())!=string(".png"))
filename += string(".png");
FILE *outpng1 = fopen(filename.c_str(), "wb" );
GDC_image_type = GDC_PNG;
if (labels.size()>0||ylabels.size()>0||xlabels.size()>0||explabel.length()>0)
GDC_hold_img = GDC_EXPOSE_IMAGE;
GDC_out_graph( xsize, ysize, outpng1 , GDC_COMBO_LINE_AREA, numpoint, (char**) lbls , numlines, linesdata, histdata );
fclose( outpng1 );
if (labels.size()>0||ylabels.size()>0||xlabels.size()>0||explabel.length()>0){
outpng1 = fopen(filename.c_str(), "wb" );
add_legend(GDC_image, sc3, TRUE);
gdImagePng(outim, outpng1);
fclose( outpng1 );
GDC_destroy_image(GDC_image);
if(outim) gdImageDestroy(outim);
}
if((detailfactor > 0.0)&&(fit.Nrows()>2)){
Matrix tmp(1,fit.Ncols()-2);
tmp=sum(fit.Rows(3,fit.Nrows()),1);
float req_max = detailfactor*tmp.Maximum2(i,j);
if(req_max<0.0000001)
req_max= 1.05*std::max(bindata.Maximum2(i,j),fit.Maximum2(i,j));
for(int ctr1=1;ctr1<=numlines; ctr1++){
for(int ctr2=1;ctr2<=numpoint; ctr2++){
linesdata[(ctr1-1)*numpoint + ctr2-1] = std::min(req_max,linesdata[(ctr1-1)*numpoint + ctr2-1]);
}
}
for(int ctr1=0;ctr1< numpoint; ctr1++){
histdata[ctr1] = std::min(req_max, histdata[ctr1]);
}
GDC_requested_ymax = req_max;
GDC_requested_ymin = float(0.0);
GDC_title = (char*)title.append(" (detail)").c_str();
GDC_title_size = GDC_SMALL;
if(filename.substr(filename.size()-4,filename.size())==string(".png"))
filename = filename.substr(0,filename.size()-4);
FILE *outpng1 = fopen((filename.append("_detail.png")).c_str(), "wb" );
GDC_image_type = GDC_PNG;
if (labels.size()>0||ylabels.size()>0||xlabels.size()>0||explabel.length()>0)
GDC_hold_img = GDC_EXPOSE_IMAGE;
GDC_out_graph( xsize, ysize, outpng1 , GDC_COMBO_LINE_BAR, numpoint, (char**) lbls , numlines, linesdata, histdata);
//GDC_out_graph( xsize, ysize, outpng1 , GDC_COMBO_LINE_BAR, numpoint, NULL , numlines, data, histdata);
fclose( outpng1 );
if (labels.size()>0||ylabels.size()>0||xlabels.size()>0||explabel.length()>0){
outpng1 = fopen(filename.c_str(), "wb" );
add_legend(GDC_image, sc3,TRUE);
gdImagePng(outim, outpng1);
fclose( outpng1 );
GDC_destroy_image(GDC_image);
if(outim) gdImageDestroy(outim);
}
}
for(int ctr=0;ctr<numpoint;ctr++){
delete [] lbls[ctr];
}
delete [] histdata;
delete [] linesdata;
delete [] lbls;
delete [] ctl;
}
}
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