/
MWT_Library.cc
2316 lines (1925 loc) · 80.8 KB
/
MWT_Library.cc
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/* Copyright 2007-2010 Rex A. Kerr, Nicholas A. Swierczek, and HHMI Janelia
* Copyright 2016 Rex A. Kerr and Calico Life Sciences
*
* This file is a part of the Multi-Worm Tracker and is distributed under the
* terms of the GNU Lesser General Public Licence version 2.1 (LGPL 2.1).
* For details, see file LICENSE, or http://www.gnu.org/licences
*/
#include <math.h>
#include <stdio.h>
#include <new>
#include "MWT_Library.h"
/****************************************************************
Useful Utility Methods
****************************************************************/
// Write one line of summary data to disk
void SummaryData::fprint(FILE* f , ManagedList<BlobOriginFate>& mlbof , ManagedList<BlobOutputFate>& mlbf)
{
// Advance to current frame in blob origin/fate list
while (mlbof.current!=NULL && mlbof.i().frame<frame_number)
{
if (!mlbof.advance()) mlbof.current = NULL;
}
while( mlbf.current!=NULL && mlbf.i().frame<frame_number)
{
if(!mlbf.advance()) mlbf.current = NULL;
}
char last_character='\n';
if (
event_list.size > 0 ||
(mlbof.current!=NULL && mlbof.i().frame==frame_number) ||
(mlbf.current!=NULL && mlbf.i().frame==frame_number) ||
dancer_jitter_x != 0 || dancer_jitter_y != 0
) {
last_character = ' ';
}
fprintf(f,"%d %.3f %d %d %.1f %.2f %.3f %.1f %.3f %.1f %.3f %.3f %.3f %.3f %.3f%c",
frame_number,frame_time,
n_dancers_tracked,n_dancers_good,dancer_persistence,
dancer_speed,dancer_angularspeed,
dancer_length,dancer_relativelength,
dancer_width,dancer_relativewidth,
dancer_aspect,dancer_relativeaspect,
dancer_endwiggle,dancer_pixelcount,
last_character
);
if (event_list.size > 0) // More to print
{
fprintf(f,"%%"); // Marker for event list
event_list.start();
while (event_list.advance()) { fprintf(f," 0x%X",event_list.i()); }
}
if (mlbof.current!=NULL && mlbof.i().frame==frame_number) // Yet more to print
{
fprintf(f," %%%%"); // Marker for worm origin/fate list
while (mlbof.current!=NULL && mlbof.i().frame==frame_number)
{
fprintf(f," %d %d",mlbof.i().ID_origin,mlbof.i().ID_fate);
if (!mlbof.advance()) mlbof.current=NULL;
}
}
if( mlbf.current!=NULL && mlbf.i().frame==frame_number) // Even more to print
{
fprintf(f," %%%%%%"); // marker for worm output fate
while( mlbf.current!=NULL && mlbf.i().frame==frame_number)
{
fprintf(f," %d %d.%ld",mlbf.i().blob_ID,mlbf.i().file_ID,mlbf.i().byte_offset);
if( !mlbf.advance()) mlbf.current=NULL;
}
}
if (dancer_jitter_x != 0 || dancer_jitter_y != 0 || dancer_shift_x != 0 || dancer_shift_y != 0) {
fprintf(f, " @ %.3f %.3f %d %d", dancer_jitter_x, dancer_jitter_y, dancer_shift_x, dancer_shift_y);
}
if (last_character!='\n') fprintf(f,"\n");
}
/****************************************************************
TrackerLibrary Methods
****************************************************************/
// Constructor just creates an array of TrackerEntry pointers and sets them to NULL
TrackerLibrary::TrackerLibrary()
: all_trackers(NULL),default_buffer_size(DEFAULT_DEFAULT_SIZE),active_handles(MAX_TRACKER_HANDLES+1,false),lsstore(1024,false)
{
all_trackers = new TrackerEntry*[MAX_TRACKER_HANDLES+1];
for (int i=0 ; i<=MAX_TRACKER_HANDLES ; i++) all_trackers[i] = NULL;
}
// Destructor deletes any handles that are still active
TrackerLibrary::~TrackerLibrary()
{
if (all_trackers==NULL) return;
if (active_handles.size>0)
{
active_handles.start();
while (active_handles.advance())
{
if (all_trackers[active_handles.i()] == NULL) continue;
delete all_trackers[active_handles.i()];
all_trackers[active_handles.i()] = NULL;
active_handles.Backspace();
}
}
delete[] all_trackers;
all_trackers=NULL;
}
// Find the smallest free handle, allocate memory and such for it, and return the handle, or -1 if none are free.
int TrackerLibrary::getNewHandle()
{
int new_handle;
if (active_handles.size==MAX_TRACKER_HANDLES) return -1;
if (active_handles.size==0 || active_handles.h()!=1)
{
new_handle=1;
active_handles.Push(new_handle);
active_handles.start();
active_handles.advance();
}
else
{
new_handle = active_handles.i();
while (active_handles.advance())
{
if (active_handles.i()>new_handle+1) break;
new_handle = active_handles.i();
}
new_handle++;
if (new_handle<active_handles.i())
{
active_handles.Tuck(new_handle);
active_handles.retreat();
}
else if (new_handle <= MAX_TRACKER_HANDLES)
{
active_handles.Append(new_handle);
active_handles.advance();
}
else return -1;
}
if (all_trackers[new_handle] != NULL) delete all_trackers[new_handle];
all_trackers[new_handle] = new TrackerEntry(active_handles.current , default_buffer_size);
return new_handle;
}
// Delete a handle. Return the number of the handle if it exists, or -1 if not.
int TrackerLibrary::killHandle(int victim)
{
if (victim<1 || victim>MAX_TRACKER_HANDLES) return -1;
if (all_trackers[victim]==NULL) return -1;
active_handles.Destroy( all_trackers[victim]->handle );
if (active_handles.size>0) { active_handles.start(); active_handles.advance(); }
delete all_trackers[victim];
all_trackers[victim] = NULL;
return victim;
}
// Set the output type. This should only be done at initialization.
int TrackerLibrary::setCombineBlobs( int handle, bool type )
{
if( handle < 1 || handle > MAX_TRACKER_HANDLES ) return -1;
if( all_trackers[handle] == NULL ) return -1;
all_trackers[handle]->performance.setCombineBlobs( type );
return handle;
}
int TrackerLibrary::setTrackerName(int handle, const char* name) {
if (handle<1 || handle>MAX_TRACKER_HANDLES) return -1;
if (all_trackers[handle]==NULL) return -1;
all_trackers[handle]->setTrackerName(name);
return handle;
}
// Set the date in pieces. Normally, don't do this--just let it pick its own date, or have one or all others adopt the date of one
int TrackerLibrary::setDate(int handle,int year,int month,int day,int hour,int minute,int second,bool is_utc)
{
if (handle<1 || handle>MAX_TRACKER_HANDLES) return -1;
if (all_trackers[handle]==NULL) return -1;
all_trackers[handle]->setDate(year,month,day,hour,minute,second,is_utc);
return handle;
}
// Set the date from another handle
int TrackerLibrary::borrowDate(int handle,int donor_handle)
{
TrackerEntry *te;
if (handle<1 || handle>MAX_TRACKER_HANDLES) return -1;
if (all_trackers[handle]==NULL) return -1;
if (donor_handle<1 || donor_handle>MAX_TRACKER_HANDLES) return -1;
if (all_trackers[donor_handle]==NULL) return -1;
te = all_trackers[donor_handle];
if (te->output_date==NULL)
{
if (all_trackers[handle]->output_date!=NULL) delete all_trackers[handle]->output_date;
all_trackers[handle]->output_date = NULL;
}
else
{
all_trackers[handle]->setDate(te->output_date->tm_year,te->output_date->tm_mon+1,te->output_date->tm_mday,
te->output_date->tm_hour,te->output_date->tm_min,te->output_date->tm_sec,
te->is_utc);
}
return handle;
}
// Make all handles have the same date as this one
int TrackerLibrary::setAllDatesToMine(int handle)
{
if (handle<1 || handle>MAX_TRACKER_HANDLES) return -1;
if (all_trackers[handle]==NULL) return -1;
Listable<int> *iterator;
active_handles.start(iterator);
while (active_handles.advance(iterator))
{
if (handle == iterator->data) continue;
else
{
int i = borrowDate(handle, iterator->data);
if (i != handle) return i;
}
}
return handle;
}
// Set filename stuff, plus say what we want to output
int TrackerLibrary::setOutput(int handle,const char *path,const char *prefix,bool save_obj,bool save_ref,bool save_im)
{
if (handle<1 || handle>MAX_TRACKER_HANDLES) return -1;
if (all_trackers[handle]==NULL) return -1;
TrackerEntry* te = all_trackers[handle];
te->setPath(path);
te->setPrefix(prefix);
te->save_objects = ( save_obj == 1 ) ? true : false;
te->save_refs = ( save_ref == 1 ) ? true : false;
te->save_images = (save_im == 1 ) ? true : false;
te->output_info_known = true;
return handle;
}
// Set whether the times reported are UTC (overwritten if you set the date)
int TrackerLibrary::setUTC(int handle, bool is_utc) {
if (handle < 1 || handle > MAX_TRACKER_HANDLES) return -1;
if (all_trackers[handle] == NULL) return -1;
TrackerEntry* te = all_trackers[handle];
te->is_utc = is_utc;
return handle;
}
// Actually create output directories and get ready to go.
int TrackerLibrary::beginOutput(int handle)
{
if (handle<1 || handle>MAX_TRACKER_HANDLES) return -1;
if (all_trackers[handle]==NULL) return -1;
TrackerEntry* te = all_trackers[handle];
if (!te->output_info_known) return 0;
bool good = te->performance.prepareOutput(
te->tracker_string,te->path_string, te->prefix_string, te->save_objects,
te->save_refs, te->save_images,
te->output_date, te->is_utc
);
if (!good) return 0;
te->output_started = true;
return handle;
}
// Specify some important attributes of the image we'll be dealing with
int TrackerLibrary::setImageInfo(int handle,int bits,int width,int height)
{
if (handle<1 || handle>MAX_TRACKER_HANDLES) return -1;
if (all_trackers[handle]==NULL) return -1;
TrackerEntry* te = all_trackers[handle];
if (bits<1) bits=1;
if (bits>14) bits=14;
te->image_bits = bits;
if (width<1) width=1;
te->image_width = width;
if (height<1) height=1;
te->image_height = height;
te->image_info_known = true;
return handle;
}
// Query the bit depth that the tracker is expecting
// Does NOT return handle; returns bit depth that has been set, or -1 or 0 if error
int TrackerLibrary::getBitDepth(int handle)
{
if (handle<1 || handle>MAX_TRACKER_HANDLES) return -1;
if (all_trackers[handle]==NULL) return -1;
TrackerEntry* te = all_trackers[handle];
if (!te->image_info_known) return 0;
return te->image_bits;
}
// Sets the region of interest to a rectangle
int TrackerLibrary::setRectangle(int handle,int left,int right,int top,int bottom)
{
if (handle<1 || handle>MAX_TRACKER_HANDLES) return -1;
if (all_trackers[handle]==NULL) return -1;
TrackerEntry* te = all_trackers[handle];
if (!te->image_info_known) return 0;
if (right<left) swap(left,right);
if (bottom<top) swap(top,bottom);
if (left<0) left = 0;
if (right>=te->image_width) right = te->image_width-1;
if (top<0) top = 1;
if (bottom>=te->image_height) bottom = te->image_height-1;
te->performance.setROI( Rectangle( Point(left,top) , Point(right,bottom) ) );
return handle;
}
// Sets the region of interest to an ellipse
int TrackerLibrary::setEllipse(int handle,int centerx,int centery,int radiusx,int radiusy)
{
if (handle<1 || handle>MAX_TRACKER_HANDLES) return -1;
if (all_trackers[handle]==NULL) return -1;
TrackerEntry* te = all_trackers[handle];
if (!te->image_info_known) return 0;
if (radiusx<1) radiusx = 1;
if (radiusy<1) radiusy = 1;
if (radiusx>te->image_width+te->image_height) radiusx = te->image_width+te->image_height;
if (radiusy>te->image_height+te->image_width) radiusy = te->image_height+te->image_width;
if (centerx<0) centerx = 0;
if (centery<0) centery = 0;
if (centerx>=te->image_width) centerx = te->image_width-1;
if (centery>=te->image_height) centery = te->image_height-1;
te->performance.setROI( Ellipse( Point(centerx,centery) , Point(radiusx,radiusy) ) );
return handle;
}
// Add a rectangle to the existing region of interest
int TrackerLibrary::addRectangle(int handle,int left,int right,int top,int bottom)
{
if (handle<1 || handle>MAX_TRACKER_HANDLES) return -1;
if (all_trackers[handle]==NULL) return -1;
TrackerEntry* te = all_trackers[handle];
if (!te->image_info_known) return 0;
if (right<left) swap(left,right);
if (bottom<top) swap(top,bottom);
if (left<0) left = 0;
if (right>=te->image_width) right = te->image_width-1;
if (top<0) top = 1;
if (bottom>=te->image_height) bottom = te->image_height-1;
Performance& p = te->performance;
if (p.full_area==NULL) p.setROI( Rectangle( Point(left,top) , Point(right,bottom) ) );
else
{
Mask m( Rectangle( Point(left,top) , Point(right,bottom) ) , &lsstore );
*p.full_area += m;
p.full_area->findBounds();
}
return handle;
}
// Add an ellipse to the region of interest
int TrackerLibrary::addEllipse(int handle,int centerx,int centery,int radiusx,int radiusy)
{
if (handle<1 || handle>MAX_TRACKER_HANDLES) return -1;
if (all_trackers[handle]==NULL) return -1;
TrackerEntry* te = all_trackers[handle];
if (!te->image_info_known) return 0;
if (radiusx<1) radiusx = 1;
if (radiusy<1) radiusy = 1;
if (radiusx>te->image_width+te->image_height) radiusx = te->image_width+te->image_height;
if (radiusy>te->image_height+te->image_width) radiusy = te->image_height+te->image_width;
if (centerx<0) centerx = 0;
if (centery<0) centery = 0;
if (centerx>=te->image_width) centerx = te->image_width-1;
if (centery>=te->image_height) centery = te->image_height-1;
Performance& p = te->performance;
if (p.full_area==NULL) p.setROI( Ellipse( Point(centerx,centery) , Point(radiusx,radiusy) ) );
else
{
Mask m( Ellipse( Point(centerx,centery) , Point(radiusx,radiusy) ) , &lsstore );
*p.full_area += m;
p.full_area->findBounds();
}
return handle;
}
// Remove a rectangle from the region of interest.
int TrackerLibrary::cutRectangle(int handle,int left,int right,int top,int bottom)
{
if (handle<1 || handle>MAX_TRACKER_HANDLES) return -1;
if (all_trackers[handle]==NULL) return -1;
TrackerEntry* te = all_trackers[handle];
if (!te->image_info_known) return 0;
if (right<left) swap(left,right);
if (bottom<top) swap(top,bottom);
if (left<0) left = 0;
if (right>=te->image_width) right = te->image_width-1;
if (top<0) top = 1;
if (bottom>=te->image_height) bottom = te->image_height-1;
Performance& p = te->performance;
if (p.full_area!=NULL) p.setROI( Rectangle(Point(0,0) , Point(te->image_width-1,te->image_height-1) ) );
*p.full_area -= Rectangle( Point(left,top) , Point(right,bottom) );
p.full_area->findBounds();
return handle;
}
// Remove an ellipse from the region of interest.
int TrackerLibrary::cutEllipse(int handle,int centerx,int centery,int radiusx,int radiusy)
{
if (handle<1 || handle>MAX_TRACKER_HANDLES) return -1;
if (all_trackers[handle]==NULL) return -1;
TrackerEntry* te = all_trackers[handle];
if (!te->image_info_known) return 0;
if (radiusx<1) radiusx = 1;
if (radiusy<1) radiusy = 1;
if (radiusx>te->image_width+te->image_height) radiusx = te->image_width+te->image_height;
if (radiusy>te->image_height+te->image_width) radiusy = te->image_height+te->image_width;
if (centerx<0) centerx = 0;
if (centery<0) centery = 0;
if (centerx>=te->image_width) centerx = te->image_width-1;
if (centery>=te->image_height) centery = te->image_height-1;
Performance& p = te->performance;
if (p.full_area!=NULL) p.setROI( Rectangle(Point(0,0) , Point(te->image_width-1,te->image_height-1) ) );
Mask m( Ellipse( Point(centerx,centery) , Point(radiusx,radiusy) ) , &lsstore );
*p.full_area -= m;
p.full_area->findBounds();
return handle;
}
// Draw the region onto an image
int TrackerLibrary::showROI(int handle,Image& im)
{
// WARNING - You must keep this in sync with the 8 bit version BY HAND!!
if (handle<1 || handle>MAX_TRACKER_HANDLES) return -1;
if (all_trackers[handle]==NULL) return -1;
TrackerEntry* te = all_trackers[handle];
short white = (1<<te->image_bits)-1;
short color = te->performance.blob_is_dark ? 1 : white; // Reference object will be oppositely colored from object
im.divide_bg = te->performance.use_division;
te->performance.imprint(&im , 0 , 3 , color , 2 , color , false , color , false , color , 0);
return handle;
}
int TrackerLibrary::showROI8(int handle,Image8& im)
{
// WARNING - You must keep this in sync with the 16 bit version BY HAND!!
if (handle<1 || handle>MAX_TRACKER_HANDLES) return -1;
if (all_trackers[handle]==NULL) return -1;
TrackerEntry* te = all_trackers[handle];
uint8_t white = 255;
uint8_t color = te->performance.blob_is_dark ? 1 : white; // Reference object will be oppositely colored from object
im.divide_bg = te->performance.use_division;
te->performance.imprint8(&im , 0 , 3 , color , 2 , color , false , color , false , color , 0);
return handle;
}
// Copy and resize an image--doesn't actually need a handle
int TrackerLibrary::resizeRescale(int handle,Image& source,Image& dest,Rectangle dest_selection)
{
// WARNING - You must keep this in sync with the 8 bit version BY HAND!!
dest.mimic(source,dest_selection,source.getBounds());
return handle;
}
int TrackerLibrary::resizeRescale8(int handle,Image8& source,Image8& dest,Rectangle dest_selection)
{
// WARNING - You must keep this in sync with the 16 bit version BY HAND!!
dest.mimic(source,dest_selection,source.getBounds());
return handle;
}
// Copy and resize the memory image--does need a handle
int TrackerLibrary::resizeRescaleMemory(int handle,Image& dest,Rectangle dest_selection)
{
// WARNING - You must keep this in sync with the 8 bit version BY HAND!!
if (handle<1 || handle>MAX_TRACKER_HANDLES) return -1;
if (all_trackers[handle]==NULL) return -1;
Performance& p = all_trackers[handle]->performance;
if (p.background==NULL) return 0;
dest.mimic( *p.background , dest_selection , p.background->getBounds() );
return handle;
}
int TrackerLibrary::resizeRescaleMemory8(int handle,Image8& dest,Rectangle dest_selection)
{
// WARNING - You must keep this in sync with the 16 bit version BY HAND!!
if (handle<1 || handle>MAX_TRACKER_HANDLES) return -1;
if (all_trackers[handle]==NULL) return -1;
Performance& p = all_trackers[handle]->performance;
if (p.background==NULL) return 0;
dest.mimic16( *p.background , dest_selection , p.background->getBounds() );
return handle;
}
// Copy and resize the fixed image--needs a handle, and only works after a scanObjects
int TrackerLibrary::resizeRescaleFixed(int handle,Image& dest,Rectangle dest_selection)
{
// WARNING - You must keep this in sync with the 8 bit version BY HAND!!
if (handle<1 || handle>MAX_TRACKER_HANDLES) return -1;
if (all_trackers[handle]==NULL) return -1;
Performance& p = all_trackers[handle]->performance;
if (p.foreground==NULL) return 0;
dest.mimic( *p.foreground , dest_selection , p.foreground->getBounds() );
return handle;
}
int TrackerLibrary::resizeRescaleFixed8(int handle,Image8& dest,Rectangle dest_selection)
{
// WARNING - You must keep this in sync with the 8 bit version BY HAND!!
if (handle<1 || handle>MAX_TRACKER_HANDLES) return -1;
if (all_trackers[handle]==NULL) return -1;
Performance& p = all_trackers[handle]->performance;
if (p.foreground==NULL) return 0;
dest.mimic16( *p.foreground , dest_selection , p.foreground->getBounds() );
return handle;
}
// Set the border around each tracked object so we can follow it moving
int TrackerLibrary::setDancerBorderSize(int handle,int border)
{
if (handle<1 || handle>MAX_TRACKER_HANDLES) return -1;
if (all_trackers[handle]==NULL) return -1;
if (border<1) return 0;
TrackerEntry* te = all_trackers[handle];
te->border_size_known = true;
te->performance.border = border;
return handle;
}
// During load/process cycle, update image a strip at a time; this sets how many strips fit across the image (default is 16)
int TrackerLibrary::setUpdateBandNumber(int handle,int n_bands)
{
if (handle<1 || handle>MAX_TRACKER_HANDLES) return -1;
if (all_trackers[handle]==NULL) return -1;
TrackerEntry* te = all_trackers[handle];
if (n_bands<2) n_bands = 2;
te->performance.n_scan_bands = n_bands;
return handle;
}
// Common bounds etc. checking for edge detection
int TrackerLibrary::checkInImageBounds(int handle, const Rectangle &fromImage, const Rectangle &search, const Point &size) {
if (handle<1 || handle>MAX_TRACKER_HANDLES) return -1;
if (all_trackers[handle]==NULL) return -1;
if (all_trackers[handle]->reference_edges_final) return -2;
if (size.x > search.width() || size.y > search.height()) return -3;
if (!fromImage.contains(search)) return -4;
return 0;
}
// Find a clean set of edges within a region to do automatic jitter-compensation during tracking
// Returns a quality score indicating how "good" the edges are, or NAN to indicate that no edges were found and nothing was added to the list.
float TrackerLibrary::addBestXEdgesInImage(int handle, Image& im, const Rectangle &search, const Point &size) {
int err = checkInImageBounds(handle, im.bounds, search, size); if (err) return err;
TrackerEntry* te = all_trackers[handle];
Profile *p = new (te->reference_edges.Append()) Profile(Rectangle(search.near, search.near + size - 1), Profile::OverY);
float ans = p->best_inside(im, search);
if (p->n_features <= 0) {
te->reference_edges.Truncate();
return NAN;
}
return ans;
}
// Find a clean set of edges within a region to do automatic jitter-compensation during tracking
// Returns a quality score indicating how "good" the edges are, or NAN to indicate that no edges were found and nothing was added to the list.
float TrackerLibrary::addBestYEdgesInImage(int handle, Image& im, const Rectangle &search, const Point &size) {
int err = checkInImageBounds(handle, im.bounds, search, size); if (err) return err;
TrackerEntry* te = all_trackers[handle];
Profile *p = new (te->reference_edges.Append()) Profile(Rectangle(search.near, search.near + size - 1), Profile::OverX);
float ans = p->best_inside(im, search);
if (p->n_features <= 0) {
te->reference_edges.Truncate();
return NAN;
}
return ans;
}
// Find a clean set of edges within a region to do automatic jitter-compensation during tracking
// Returns a quality score indicating how "good" the edges are, or NAN to indicate that no edges were found and nothing was added to the list.
float TrackerLibrary::addBestXEdgesInImage8(int handle, Image8& im, const Rectangle &search, const Point &size) {
int err = checkInImageBounds(handle, im.bounds, search, size); if (err) return err;
TrackerEntry* te = all_trackers[handle];
Profile *p = new (te->reference_edges.Append()) Profile(Rectangle(search.near, search.near + size - 1), Profile::OverY);
float ans = p->best_inside8(im, search);
if (p->n_features <= 0) {
te->reference_edges.Truncate();
return NAN;
}
return ans;
}
// Find a clean set of edges within a region to do automatic jitter-compensation during tracking.
// Returns a quality score indicating how "good" the edges are, or NAN to indicate that no edges were found and nothing was added to the list.
float TrackerLibrary::addBestYEdgesInImage8(int handle, Image8& im, const Rectangle &search, const Point &size) {
int err = checkInImageBounds(handle, im.bounds, search, size); if (err) return err;
TrackerEntry* te = all_trackers[handle];
Profile *p = new (te->reference_edges.Append()) Profile(Rectangle(search.near, search.near + size - 1), Profile::OverX);
float ans = p->best_inside8(im, search);
if (p->n_features <= 0) {
te->reference_edges.Truncate();
return NAN;
}
return ans;
}
// Gets the number of edge profiles already loaded
int TrackerLibrary::loadedProfiles(int handle) {
if (handle<1 || handle>MAX_TRACKER_HANDLES) return -1;
if (all_trackers[handle]==NULL) return -1;
return all_trackers[handle]->reference_edges.size;
}
Profile* TrackerLibrary::getProfileIfValid(int handle, int profile) {
if (handle<1 || handle>MAX_TRACKER_HANDLES) return NULL;
if (all_trackers[handle]==NULL) return NULL;
TrackerEntry *te = all_trackers[handle];
if (profile < 0 || profile >= te->reference_edges.size) return NULL;
if (te->cached_profile_index != profile) {
te->cached_profile = &(te->reference_edges.index(profile));
te->cached_profile_index = profile;
}
return te->cached_profile;
}
// 1 = edge across X; 2 = edge across Y; negative = error
int TrackerLibrary::profileDirection(int handle, int profile) {
Profile* p = getProfileIfValid(handle, profile);
if (p == NULL) return -1;
return (p->direction == Profile::OverX) ? 2 : 1; // Collapse direction is opposite from edge direction
}
// Gets the lower bound of the profile in the x direction
int TrackerLibrary::profileCorner_x0(int handle, int profile) {
Profile* p = getProfileIfValid(handle, profile);
if (p == NULL) return -1;
return p->source.near.x;
}
// Gets the upper bound (inclusive) of the profile in the x direction.
int TrackerLibrary::profileCorner_x1(int handle, int profile) {
Profile* p = getProfileIfValid(handle, profile);
if (p == NULL) return -1;
return p->source.far.x;
}
// Gets the lower bound of the profile in the y direction
int TrackerLibrary::profileCorner_y0(int handle, int profile) {
Profile* p = getProfileIfValid(handle, profile);
if (p == NULL) return -1;
return p->source.near.y;
}
// Gets the upper bound (inclusive) of the profile in the y direction
int TrackerLibrary::profileCorner_y1(int handle, int profile) {
Profile* p = getProfileIfValid(handle, profile);
if (p == NULL) return -1;
return p->source.far.y;
}
// Returns the number of edges associated with a particular profile
int TrackerLibrary::profileEdgeCount(int handle, int profile) {
Profile* p = getProfileIfValid(handle, profile);
if (p == NULL) return -1;
return p->n_features;
}
// Returns 1 if the edge is oriented along x (collapse along y), 2 if along y, otherwise it's an error.
float TrackerLibrary::profileEdgeLocation(int handle, int profile, int edge) {
Profile* p = getProfileIfValid(handle, profile);
if (p == NULL) return NAN;
if (edge < 0 || edge >= p->n_features) return NAN;
return p->features[edge].position;
}
// Returns the absolute position of a particular edge in a particular profile, if it exists; NAN otherwise.
float TrackerLibrary::globalProfileEdgeLocation(int handle, int profile, int edge) {
Profile* p = getProfileIfValid(handle, profile);
if (p == NULL) return NAN;
if (edge < 0 || edge >= p->n_features) return NAN;
return p->features[edge].position + ((p->direction == Profile::OverX) ? p->source.near.y : p->source.near.x);
}
// Returns the strength of a particular edge in a particular profile, if it exists; NAN otherwise
float TrackerLibrary::profileEdgeStrength(int handle, int profile, int edge) {
Profile* p = getProfileIfValid(handle, profile);
if (p == NULL) return NAN;
if (edge < 0 || edge >= p->n_features) return NAN;
return p->features[edge].strength;
}
// Returns the polarity of a particular edge in a particular profile, if it exists; 0 otherwise.
int TrackerLibrary::profileEdgePolarity(int handle, int profile, int edge) {
Profile* p = getProfileIfValid(handle, profile);
if (p == NULL) return 0;
if (edge < 0 || edge >= p->n_features) return 0;
return p->features[edge].sign;
}
// Removes a particular profile (by index), if it exists.
int TrackerLibrary::removeOneProfile(int handle, int profile) {
Profile* p = getProfileIfValid(handle, profile);
if (p == NULL) return -1;
TrackerEntry *te = all_trackers[handle];
if (te->reference_edges_final) return -2;
Listable<Profile> *lp = NULL;
for (te->reference_edges.advance(lp); lp != NULL && &(lp->data) != p; te->reference_edges.advance(lp)) {}
if (lp == NULL) return -3;
te->reference_edges.Destroy(lp);
return 0;
}
// Removes all profiles. Returns the number of profiles removed.
int TrackerLibrary::removeAllProfiles(int handle) {
if (handle<1 || handle>MAX_TRACKER_HANDLES) return -1;
TrackerEntry *te = all_trackers[handle];
if (te == NULL) return -1;
auto n_removed = te->reference_edges.size;
while (te->reference_edges.size > 0) te->reference_edges.Behead();
return n_removed;
}
// Sets whether the profile positions are merely informative or if they actually are used to correct image position
int TrackerLibrary::useProfilesToCorrectImage(int handle, bool use_them) {
if (handle<1 || handle>MAX_TRACKER_HANDLES) return -1;
TrackerEntry *te = all_trackers[handle];
if (te == NULL) return -1;
te->performance.correct_for_jitter = use_them;
return handle;
}
// Set the intensity above or below which we will fill a reference object
int TrackerLibrary::setRefIntensityThreshold(int handle,int intensity_low,int intensity_high)
{
if (handle<1 || handle>MAX_TRACKER_HANDLES) return -1;
if (all_trackers[handle]==NULL) return -1;
TrackerEntry* te = all_trackers[handle];
if (!te->image_info_known) return 0;
if (intensity_low < 1) intensity_low = 1;
if (intensity_high > (1<<te->image_bits)-1) intensity_high = (1<<te->image_bits)-1;
if (intensity_low > intensity_high) intensity_low = intensity_high;
te->reference_intensities_known = true;
te->performance.ref_I = DualRange( Range(intensity_low,intensity_high) );
return handle;
}
// Add a new reference object; must have defined a region of interest
int TrackerLibrary::addReferenceObjectLocation(int handle,int x,int y)
{
if (handle<1 || handle>MAX_TRACKER_HANDLES) return -1;
if (all_trackers[handle]==NULL) return -1;
TrackerEntry* te = all_trackers[handle];
if (!te->image_info_known) return 0;
if (x<0 || y<0 || x>=te->image_width || y>=te->image_height) return 0;
te->reference_objects.Append( Point(x,y) );
return handle;
}
// Remove the last one (I guess we didn't like it)
int TrackerLibrary::removeLastReferenceObject(int handle)
{
if (handle<1 || handle>MAX_TRACKER_HANDLES) return -1;
if (all_trackers[handle]==NULL) return -1;
TrackerEntry* te = all_trackers[handle];
if (te->reference_objects.size==0) return 0;
te->reference_objects.Truncate();
return handle;
}
// Try to find reference objects and return number found (-2 if initialization isn't done)
int TrackerLibrary::scanRefs(int handle,Image& im)
{
// WARNING - You must keep this in sync with the 8 bit version BY HAND!!
if (handle<1 || handle>MAX_TRACKER_HANDLES) return -1;
if (all_trackers[handle]==NULL) return -1;
TrackerEntry* te = all_trackers[handle];
if (!te->image_info_known || !te->reference_intensities_known) return -2;
im.divide_bg = te->performance.use_division;
Performance& p = te->performance;
te->working.imitate( te->reference_objects );
p.initialRefs(&im , te->working , 0.0);
te->references_found = true;
return te->reference_objects.size - te->working.size;
}
int TrackerLibrary::scanRefs8(int handle, Image8& im)
{
// WARNING - You must keep this in sync with the 16 bit version BY HAND!!
if (handle<1 || handle>MAX_TRACKER_HANDLES) return -1;
if (all_trackers[handle]==NULL) return -1;
TrackerEntry* te = all_trackers[handle];
if (!te->image_info_known || !te->reference_intensities_known) return -2;
im.divide_bg = te->performance.use_division;
Performance& p = te->performance;
te->working.imitate( te->reference_objects );
p.initialRefs8(&im , te->working , 0.0);
te->references_found = true;
return te->reference_objects.size - te->working.size;
}
// Show what reference objects were found
int TrackerLibrary::showRefs(int handle,Image& im,bool show_as_white)
{
// WARNING - You must keep this in sync with the 8 bit version BY HAND!!
if (handle<1 || handle>MAX_TRACKER_HANDLES) return -1;
if (all_trackers[handle]==NULL) return -1;
TrackerEntry* te = all_trackers[handle];
if (!te->references_found) return 0;
im.divide_bg = te->performance.use_division;
short color = 1;
if (show_as_white) color = (1<<te->image_bits)-1;
te->performance.imprint(&im , 0 , 3 , (1<<te->image_bits)-1 , 2 , 0 , false , color , true , 0 , 0);
return handle;
}
int TrackerLibrary::showRefs8(int handle,Image8& im,bool show_as_white)
{
// WARNING - You must keep this in sync with the 16 bit version BY HAND!!
if (handle<1 || handle>MAX_TRACKER_HANDLES) return -1;
if (all_trackers[handle]==NULL) return -1;
TrackerEntry* te = all_trackers[handle];
if (!te->references_found) return 0;
im.divide_bg = te->performance.use_division;
uint8_t color = 1;
if (show_as_white) color = 255;
te->performance.imprint8(&im , 0 , 3 , 255 , 2 , 0 , false , color , true , 0 , 0);
return handle;
}
// Set intensity thresholds for moving objects
int TrackerLibrary::setObjectIntensityThresholds(int handle,int intensity_to_fill,int intensity_of_new)
{
if (handle<1 || handle>MAX_TRACKER_HANDLES) return -1;
if (all_trackers[handle]==NULL) return -1;
TrackerEntry* te = all_trackers[handle];
if (!te->image_info_known) return 0;
short white = 2*(1<<te->image_bits)-1;
short gray = 1<<te->image_bits;
if (intensity_to_fill == gray || intensity_of_new==gray) return 0;
else if (intensity_to_fill > gray) // Bright blob
{
if (intensity_of_new < gray) return 0;
if (intensity_of_new > white) intensity_of_new = white;
if (intensity_of_new < intensity_to_fill) intensity_to_fill = intensity_of_new;
te->performance.blob_is_dark = false;
te->performance.fill_I = DualRange( Range(intensity_of_new,white) , Range(intensity_to_fill,white) );
}
else // Standard dark blob
{
if (intensity_of_new > gray) return 0;
if (intensity_of_new < 1) intensity_of_new = 1;
if (intensity_of_new > intensity_to_fill) intensity_to_fill = intensity_of_new;
te->performance.blob_is_dark = true;
te->performance.fill_I = DualRange( Range(1,intensity_of_new) , Range(1,intensity_to_fill) );
}
te->object_intensities_known = true;
return handle;
}
// Set how big the objects are allowed to be
int TrackerLibrary::setObjectSizeThresholds(int handle,int small_size,int small_good_size,int large_good_size,int large_size)
{
if (handle<1 || handle>MAX_TRACKER_HANDLES) return -1;
if (all_trackers[handle]==NULL) return -1;
TrackerEntry* te = all_trackers[handle];
if (small_size<1) small_size = 1;
if (small_good_size<small_size) small_good_size = small_size;
if (large_good_size<small_good_size) large_good_size = small_good_size;
if (large_size<large_good_size) large_size = large_good_size;
te->performance.fill_size = DualRange( Range(small_good_size,large_good_size) , Range(small_size,large_size) );
te->object_sizes_known = true;
return handle;
}
// Set how long we need to track the objects in order to write them out
int TrackerLibrary::setObjectPersistenceThreshold(int handle,int frames)
{
if (handle<1 || handle>MAX_TRACKER_HANDLES) return -1;
if (all_trackers[handle]==NULL) return -1;
TrackerEntry* te = all_trackers[handle];
if (frames<2) frames=2;
te->performance.n_long_enough = frames;