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Plotter_multifile_Cluster_20170216.ipf
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Plotter_multifile_Cluster_20170216.ipf
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#pragma rtGlobals=3 // Use modern global access method and strict wave access.
function multiple()
variable numberoffolders=3
make/o/n=(numberoffolders)/T filelist
filelist[0]="RAID:13_02_Cells:20170213_AptPaint_Cell_GS:561_1:0:"
filelist[1]="RAID:13_02_Cells:20170213_AptPaint_Cell_GS:561_2:0:"
filelist[2]="RAID:13_02_Cells:20170213_AptPaint_Cell_GS:561_4:0:"
variable f
for(f=0;f<(numberoffolders);f+=1)
setdatafolder root:
string folder=num2str(f)
PRINT FOLDER
newdatafolder/s $folder
string path=filelist[f]
loadmult(path)
imageclusterplot(path)
clusteranal()
setdatafolder root:
endfor
end
//////////LOAD MULTIPLE FILES////////////
function loadmult(path)
string path
string load1=path+"cluster.txt"
print load1
LoadWave/J/D/W/K=0/A load1
wave xw
duplicate/o xw,cluster
killwaves xw
string load2=path+"fitresults.txt"
print load2
LoadWave/J/D/W/K=0/A load2
end
///////////Output images//////////////
function imageclusterplot(path) // This needs a prior code that outputs all localisations as xw, yw, precision.
string path
wave xw,yw,precision__nm_,cluster
duplicate/o precision__nm_,precision // I only need the x and y-coords and precision values.
variable scale=8 // Change this for different scale.
variable size=scale*512 // This is the size of the matrix to make.
make/o/n=(size,size) Image=0,imagegauss=0 // Make matrices for data.
variable a,b,c // Some originally named variables.
/////////// THIS PART TO PLOT LOCALISATIONS ONLY /////////////////////////
for(a=0;a<(dimsize(xw,0));a+=1) // Go through all of localisations.
if(cluster[a]>0)
variable xcoord=round(scale*(xw[a])) // Multiply by 8 to fit in matrix.
variable ycoord=round(scale*(yw[a]))
image[xcoord][ycoord]+=1 // Add 1 to the matrix- localisation only.
endif
endfor
///// THIS PART FOR 2D GAUSS- width = precision image ///////////////////
make/o/n=(11,11) tempgauss // This is where I'm going to store each Gaussian that's fitted. Need to make an odd number in size to ensure there is a central pixel.
duplicate/o precision,precisionpixel // Notekeeping- I did this just so that I could confirm that the precisions are correct when converted to pixels (from nm)
for(a=0;a<(dimsize(xw,0));a+=1)
if(cluster[a]>0)
xcoord=round(scale*(xw[a]))
ycoord=round(scale*(yw[a]))
variable precis=precision[a]
// Need to convert precision to pixels
variable pixelsize=109 // Change pixel size here if different.
variable pixelsizeinexpanded=109/scale // This is new pixel size with different scale.
variable precispixel=precis/pixelsizeinexpanded // This is now the precision in pixels rather than nm.
precisionpixel[a]=precispixel // Store for notekeeping.
duplicate/o tempgauss,tempfit // I need to make a wave to store the fit in. Idiosynchratic nature of Igor!!
K0 = 0;K1 = 1;K2 = 5;K3 = precispixel;K4 = 5;K5 = precispixel;K6 = 0; // These are the fixed variables to fit the 2D Gaussian to - amplitude = 1, x-width,ywidth = precision (in pixels)
CurveFit/H="1111111"/q Gauss2D tempgauss /D=tempfit // Fit the curve, and output the fit to tempfit wave.
for(b=0;b<11;b+=1) // Place this in the original gaussimage.
for(c=0;c<11;c+=1)
imagegauss[xcoord-5+b][ycoord-5+c]=imagegauss[xcoord-5+b][ycoord-5+c]+tempfit[b][c] // Note that it's an add function - allows gauss to overlap.
endfor
endfor
endif
endfor
string tosave=path+"imagegauss2.txt"
Save/J/M="\n" imagegauss as tosave // Saves the file.
end
///////////////////////////////////////
function load_dan()
LoadWave/J/D/W/K=0/A
wave wave0,wave1,wave2
duplicate/o wave0,xw
duplicate/o wave1,yw
duplicate/o wave2,precision__nm_
end
////// Without clusters
function imageplot() // This needs a prior code that outputs all localisations as xw, yw, precision.
wave xw,yw,precision__nm_
duplicate/o precision__nm_,precision // I only need the x and y-coords and precision values.
variable scale=8 // Change this for different scale.
variable size=scale*512 // This is the size of the matrix to make.
make/o/n=(size,size) Image=0,imagegauss=0 // Make matrices for data.
variable a,b,c // Some originally named variables.
/////////// THIS PART TO PLOT LOCALISATIONS ONLY /////////////////////////
for(a=0;a<(dimsize(xw,0));a+=1) // Go through all of localisations.
variable xcoord=round(scale*(xw[a])) // Multiply by 8 to fit in matrix.
variable ycoord=round(scale*(yw[a]))
image[xcoord][ycoord]+=1 // Add 1 to the matrix- localisation only.
endfor
///// THIS PART FOR 2D GAUSS- width = precision image ///////////////////
make/o/n=(11,11) tempgauss // This is where I'm going to store each Gaussian that's fitted. Need to make an odd number in size to ensure there is a central pixel.
duplicate/o precision,precisionpixel // Notekeeping- I did this just so that I could confirm that the precisions are correct when converted to pixels (from nm)
for(a=0;a<(dimsize(xw,0));a+=1)
xcoord=round(scale*(xw[a]))
ycoord=round(scale*(yw[a]))
variable precis=precision[a]
// Need to convert precision to pixels
variable pixelsize=109 // Change pixel size here if different.
variable pixelsizeinexpanded=109/scale // This is new pixel size with different scale.
variable precispixel=precis/pixelsizeinexpanded // This is now the precision in pixels rather than nm.
precisionpixel[a]=precispixel // Store for notekeeping.
duplicate/o tempgauss,tempfit // I need to make a wave to store the fit in. Idiosynchratic nature of Igor!!
K0 = 0;K1 = 1;K2 = 5;K3 = precispixel;K4 = 5;K5 = precispixel;K6 = 0; // These are the fixed variables to fit the 2D Gaussian to - amplitude = 1, x-width,ywidth = precision (in pixels)
CurveFit/H="1111111"/q Gauss2D tempgauss /D=tempfit // Fit the curve, and output the fit to tempfit wave.
for(b=0;b<11;b+=1) // Place this in the original gaussimage.
for(c=0;c<11;c+=1)
imagegauss[xcoord-5+b][ycoord-5+c]=imagegauss[xcoord-5+b][ycoord-5+c]+tempfit[b][c] // Note that it's an add function - allows gauss to overlap.
endfor
endfor
endfor
Save/J/M="\n" imagegauss // Saves the file.
end
function clusteranal()
wave cluster,xw,yw,precision
variable cl,rows
wavestats cluster
variable length=v_max
make/o/n=(length) numberofpoints
make/o/n=1 temp_prec,temp_x,temp_y
for(cl=0;cl<length;cl+=1)
variable count=0
for(rows=0;rows<(dimsize(cluster,0));rows+=1)
if(cluster[rows]==(cl+1))
redimension/n=(count+1) temp_prec,temp_x,temp_y
temp_prec[count]=precision[rows]
temp_x[count]=xw[rows]
temp_y[count]=yw[rows]
count+=1
endif
endfor
string name1=num2str(cl)+"xw"
string name2=num2str(cl)+"yw"
string name3=num2str(cl)+"precision"
numberofpoints[cl]=count
duplicate/o temp_prec,$name3
duplicate/o temp_x,$name1
duplicate/o temp_y,$name2
endfor
Make/N=25/O numberofpoints_Hist;DelayUpdate
Histogram/B={0,25,25} numberofpoints,numberofpoints_Hist;DelayUpdate
Display numberofpoints_Hist
SetAxis bottom *,1000
ModifyGraph mode=5
print median(numberofpoints)
end
function clusterloaddan()
LoadWave/J/D/W/K=0/A
wave xw
duplicate/o xw,cluster
killwaves xw
LoadWave/J/D/W/K=0/A
wave wave0,wave1,wave2
duplicate/o wave0,xw
duplicate/o wave1,yw
duplicate/o wave2,precision__nm_
end
function plot_number(num)
variable num
string name1=num2str(num)+"xw"
string name2=num2str(num)+"yw"
string name3=num2str(num)+"precision"
duplicate/o $name3,temp_prec
duplicate/o $name1,temp_x
duplicate/o $name2,temp_y
make/o/n=(11,11) tempgauss // This is where I'm going to store each Gaussian that's fitted. Need to make an odd number in size to ensure there is a central pixel.
variable a,b,c,scale=8
make/o/n=(scale*512,scale*512) t_imagegauss=0
duplicate/o temp_prec,precisionpixel // Notekeeping- I did this just so that I could confirm that the precisions are correct when converted to pixels (from nm)
for(a=0;a<(dimsize(temp_x,0));a+=1)
variable xcoord=round(scale*(temp_x[a]))
variable ycoord=round(scale*(temp_y[a]))
variable precis=temp_prec[a]
// Need to convert precision to pixels
variable pixelsize=109 // Change pixel size here if different.
variable pixelsizeinexpanded=109/scale // This is new pixel size with different scale.
variable precispixel=precis/pixelsizeinexpanded // This is now the precision in pixels rather than nm.
precisionpixel[a]=precispixel // Store for notekeeping.
duplicate/o tempgauss,tempfit // I need to make a wave to store the fit in. Idiosynchratic nature of Igor!!
K0 = 0;K1 = 1;K2 = 5;K3 = precispixel;K4 = 5;K5 = precispixel;K6 = 0; // These are the fixed variables to fit the 2D Gaussian to - amplitude = 1, x-width,ywidth = precision (in pixels)
CurveFit/H="1111111"/q Gauss2D tempgauss /D=tempfit // Fit the curve, and output the fit to tempfit wave.
for(b=0;b<11;b+=1) // Place this in the original gaussimage.
for(c=0;c<11;c+=1)
t_imagegauss[xcoord-5+b][ycoord-5+c]=t_imagegauss[xcoord-5+b][ycoord-5+c]+tempfit[b][c] // Note that it's an add function - allows gauss to overlap.
endfor
endfor
endfor
wavestats temp_x
variable xmax=8*v_max
variable xmin=8*v_min
variable xrange=(xmax-xmin)
wavestats temp_y
variable ymax=8*v_max
variable ymin=8*v_min
variable yrange=(xmax-xmin)
if(yrange>xrange)
variable length=yrange
else
length=xrange
endif
newimage t_imagegauss
//AppendImage t_imagegauss
ModifyGraph tick=3,noLabel=2
SetAxis/R top (xmin-40),(xmin+length+40)
SetAxis/R left (ymin-40),(ymin+length+40)
ModifyImage t_imagegauss ctab= {*,*,YellowHot,0}
ModifyGraph width=283.465,height=283.465
end