double ComputeSmoothness(Array * heightMap) {
Array * distances = Make_Array_With_Shape(PLAIN_KIND,UINT32_TYPE,Coord2(heightMap->dims[1], heightMap->dims[0]));
uint32 * distVals = AUINT32(distances);
uint32 * hmVals = AUINT32(heightMap);
Use_Reflective_Boundary();
HeightMapRange range = GetLevelRange(heightMap);
// frame defines the local neighborhood
Frame * f = Make_Frame(heightMap,Coord2(3,3),Coord2(1,1));
Histogram * h = Make_Histogram(UVAL,range.maxLayer,ValU(1),ValU(0));
Place_Frame(f,0);
for (Indx_Type i=0; i< heightMap->size; i++) {
Empty_Histogram(h);
Histagain_Array(h, f, 0);
int middleBin = Value2Bin(h, ValU(hmVals[i])); // To determine the median value of the pixel's neighborhood, we exlude the current pixel i from the histogram
h->counts[middleBin]--;
distVals[i] = std::abs(static_cast<double>(hmVals[i]) - static_cast<double>(Percentile2Bin(h, 0.5)));
}
#ifdef DEVELOP
Write_Image("HeightMapSmoothness", distances, DONT_PRESS);
#endif
Empty_Histogram(h);
Histagain_Array(h, distances, 0);
double meanDistance = Histogram_Mean(h);
std::cout << "Smoothness:\n Mean distance: " << meanDistance << "\n Sd: " << Histogram_Sigma(h) << std::endl;
Free_Histogram(h);
Free_Frame(f);
Free_Array(distances);
return meanDistance;
}
void Segment_Channel(Array *input, Segmentation *seg)
{ double mean, sdev;
int threshc, threshe, sizemin;
Array *labels;
Histogram *hist = Histogram_Array(input,0x100,VALU(1),VALU(0));
mean = Histogram_Mean(hist);
sdev = Histogram_Sigma(hist);
threshc = mean + Get_Double_Arg("-c")*sdev;
threshe = mean + Get_Double_Arg("-e")*sdev;
sizemin = Get_Int_Arg("-s");
#ifdef PROGRESS
printf("\nChannel Segmentation:\n");
printf(" Mean = %.2f Std.Dev = %.2f\n",mean,sdev);
printf(" Thresh-c = %d Thresh-e = %d Size-s = %d\n",threshc,threshe,sizemin);
#ifdef DEBUG
Print_Histogram(hist,stdout,4,BIN_COUNT|CUMULATIVE_COUNT|CLIP_HGRAM,0);
#endif
fflush(stdout);
#endif
Free_Histogram(hist);
labels = Make_Array(PLAIN_KIND,UINT8_TYPE,3,input->dims);
Array_Op_Scalar(labels,SET_OP,UVAL,VALU(0));
SEG_threshc = threshc;
SEG_threshe = threshe;
SEG_sizemin = sizemin;
SEG_values = AUINT16(input);
SEG_labels = AUINT8(labels);
SEG_count = 0;
SEG_coretouch = 0;
SEG_id = 0;
// Mark connected-components of pixels >= threshc that have not less than sizemin pixels
Flood_All(input,0,ISCON2N,NULL,InCore,NULL,CountCore,NULL,GoodCore,NULL,MarkAsIn);
// Mark all connected components of pixels >= threshe that contain a good core as above
Flood_All(input,0,ISCON2N,NULL,InExtend,NULL,TouchCore,NULL,GoodExtend,NULL,SetLabel);
// Capture each labeled region in "labels" with a Region
{ int i, nsegs;
Indx_Type p;
uint8 *val;
Region **segs;
seg->label = labels;
seg->nsegs = nsegs = SEG_id;
seg->segs = segs = (Region **) Guarded_Malloc(sizeof(Region *)*nsegs,Program_Name());
seg->mean = mean;
seg->ethresh = threshe;
seg->cthresh = threshc;
for (i = 0; i < nsegs; i++)
segs[i] = NULL;
val = AUINT8(labels);
for (p = 0; p < labels->size; p++)
{ i = val[p];
if (i > 0 && segs[i-1] == NULL)
segs[i-1] = Record_Basic(labels,0,ISCON2N,p,1,EQ_COMP,VALU(i));
}
}
}
int main(int argc, char *argv[])
{ FILE *output;
Process_Arguments(argc,argv,Spec,0);
#ifdef PROGRESS
printf("\nParameters: c=%g e=%g s=%d\n",
Get_Double_Arg("-c"),Get_Double_Arg("-e"),Get_Int_Arg("-s"));
printf("SubFolder: %s\n",Get_String_Arg("folder"));
printf("CoreName: %s\n",Get_String_Arg("core"));
fflush(stdout);
#endif
RezFolder = strdup(Get_String_Arg("folder"));
if (RezFolder[strlen(RezFolder)-1] == '/')
RezFolder[strlen(RezFolder)-1] = '\0';
if (mkdir(RezFolder,S_IRWXU|S_IRWXG|S_IRWXO))
{ if (errno != EEXIST)
{ fprintf(stderr,"Error trying to create directory %s: %s\n",RezFolder,strerror(errno));
exit (1);
}
}
CoreName = strdup(Get_String_Arg("core"));
sprintf(NameBuf,"%s.neu",CoreName);
output = fopen(NameBuf,"w");
fprintf(output,"NEUSEP: Version 0.9\n");
{ Histogram *hist;
int curchan;
int maxchans;
int i, n;
n = Get_Repeat_Count("inputs");
fwrite(&n,sizeof(int),1,output);
hist = Make_Histogram(UVAL,0x10000,VALU(1),VALU(0));
maxchans = 0;
for (i = 0; i < n; i++)
{
curchan = NumChans;
maxchans = Read_All_Channels(Get_String_Arg("inputs",i),maxchans);
int channelsInCurrentFile=NumChans-curchan;
{ Size_Type sum, max;
Indx_Type p;
int j, wch;
uint16 *val;
max = -1;
for (j = curchan; j < NumChans; j++)
{ val = AUINT16(Images[j]);
sum = 0;
for (p = 0; p < Images[j]->size; p++)
sum += val[p];
if (sum > max)
{ max = sum;
wch = j;
}
}
fprintf(output,"%s\n",Get_String_Arg("inputs",i));
j = wch-curchan;
fwrite(&j,sizeof(int),1,output);
#ifdef PROGRESS
printf("\n Eliminating channel %d from %s\n",j+1,Get_String_Arg("inputs",i));
fflush(stdout);
#endif
{
// Section to write out the reference channel
printf("\n Considering reference channel output, channelsInCurrentFile=%d\n", channelsInCurrentFile);
fflush(stdout);
if (channelsInCurrentFile>2) { // should work with both lsm pair with channels=3, or raw file with channels=4
sprintf(NameBuf,"%s/Reference.tif",RezFolder,CoreName,i);
Write_Image(NameBuf,Images[wch],LZW_PRESS);
}
}
Free_Array(Images[wch]);
NumChans -= 1;
for (j = wch; j < NumChans; j++)
Images[j] = Images[j+1];
}
{ int j, ceil;
Indx_Type p;
uint16 *val;
for (j = curchan; j < NumChans; j++)
{
Histagain_Array(hist,Images[j],0);
ceil = Percentile2Bin(hist,1e-5);
if (ceil==0) {
fprintf(stderr, "Channel must have non-zero values for this program to function\n");
exit(1);
}
#ifdef PROGRESS
printf(" Clipping channel %d at ceil = %d\n",j,ceil); fflush(stdout);
fflush(stdout);
#endif
val = AUINT16(Images[j]);
for (p = 0; p < Images[j]->size; p++)
{
if (val[p] > ceil)
val[p] = ceil;
val[p] = (val[p]*4095)/ceil;
}
// Convert_Array_Inplace(Images[j],PLAIN_KIND,UINT8_TYPE,8,0);
}
}
}
Free_Histogram(hist);
printf("Starting ConsolidatedSignal.tif section\n");
fflush(stdout);
// NA addition: write tif with re-scaled intensities to serve as basis for mask file
{
Array *signalStack;
signalStack = Make_Array(RGB_KIND,UINT8_TYPE,3,Images[0]->dims);
uint8 *sp=AUINT8(signalStack);
int m;
Indx_Type signalIndex;
signalIndex=0;
for (m=0;m<NumChans;m++) {
sprintf(NameBuf, "%s/Signal_%d.tif", RezFolder, m);
printf("Writing 16-bit channel file %s...", NameBuf);
Write_Image(NameBuf, Images[m], LZW_PRESS);
printf("done\n");
uint16 *ip=AUINT16(Images[m]);
Indx_Type channelIndex;
for (channelIndex=0;channelIndex<Images[m]->size;channelIndex++) {
int value=ip[channelIndex]/16;
if (value>255) {
value=255;
}
sp[signalIndex++]=value; // convert 12-bit to 8-bit
}
}
sprintf(NameBuf,"%s/ConsolidatedSignal.tif", RezFolder);
printf("Writing 8-bit consolidated signal file %s...", NameBuf);
Write_Image(NameBuf,signalStack,LZW_PRESS);
printf("done");
//Free_Array(signalStack); - this is causing a bug
}
printf("Finished ConsolidatedSignal.tif section\n");
fflush(stdout);
}
{ int i;
Segmentation *segs;
Overlaps *ovl;
Clusters *clust;
int numneur;
Region **neurons;
segs = (Segmentation *) Guarded_Malloc(sizeof(Segmentation)*NumChans,Program_Name());
for (i = 0; i < NumChans; i++)
{ Segment_Channel(Images[i],segs+i);
if (i == 0)
segs[i].base = 0;
else
segs[i].base = segs[i-1].base + segs[i-1].nsegs;
printf("channel=%d segmentBase=%d\n", i, segs[i].base);
}
ovl = Find_Overlaps(segs);
clust = Merge_Segments(segs,ovl);
neurons = Segment_Clusters(segs,ovl,clust,&numneur);
if (Is_Arg_Matched("-gp"))
Output_Clusters(segs,ovl,clust);
if (Is_Arg_Matched("-nr"))
Output_Neurons(numneur,neurons,1);
// Added for NA
Output_Consolidated_Mask(numneur,neurons,1);
fwrite(&numneur,sizeof(int),1,output);
for (i = 0; i < numneur; i++)
Write_Region(neurons[i],output);
#ifdef PROGRESS
printf("\nProduced %d neurons/fragments in %s.neu\n",numneur,CoreName);
fflush(stdout);
#endif
printf("DEBUG: starting cleanup\n");
fflush(stdout);
for (i = 0; i < numneur; i++) {
printf("DEBUG: calling Kill_Region on neuron=%d\n", i);
fflush(stdout);
Kill_Region(neurons[i]);
}
printf("DEBUG: calling Kill_Clusters\n");
fflush(stdout);
Kill_Clusters(clust);
printf("DEBUG: calling Kill_Overlaps\n");
fflush(stdout);
//Kill_Overlaps(ovl); - causing a bug
printf("DEBUG: starting Kill_Segmentation loop\n");
fflush(stdout);
for (i = 0; i < NumChans; i++) {
printf("DEBUG: Kill_Segmentation on index=%d\n", i);
fflush(stdout);
Kill_Segmentation(segs+i);
}
printf("DEBUG: calling free() on segs\n");
fflush(stdout);
free(segs);
}
printf("DEBUG: starting filestream cleanup\n");
fflush(stdout);
{ int i;
fclose(output);
free(CoreName);
free(RezFolder);
for (i = 0; i < NumChans; i++)
Kill_Array(Images[i]);
free(Images);
}
#ifdef VERBOSE
printf("\nDid I free all arrays?:\n");
Print_Inuse_List(stdout,4);
#endif
exit (0);
}
