How to fit data when yaxis in log scale and plot the fit?

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Sergii Snegir
Sergii Snegir 2021-3-10
评论： Mathieu NOE 2021-3-17
Dear community please help me to solve the following problem:
I have a set of data plotted in Fig 1 with .YScale='log'. I select the data range and fit it and would like to plot the fir at the same figure 1. But, all the time when I plot the data i have warning "Warning: Negative data ignored".When I checked, I saw that fit generated the negative data...
I assume, I fit the data in some weared way which generates wrong a, b coeficients (y=-ax+b). The outcome , obwiously can not be plotted with log scale...
Please tell, how to solve this issue (how to fitt the data in log scale in fig 1)?!.
The part of the is below
Many thanks
Figure 1
[M,h]=contourf(xbin,ybin,f,cont_lev);
hold on
ax=gca;
ax.YScale='log';
% ------ selecting the data region to fit
m=[];
while true
m=[m,M(:,2:M(2,1)+1)];
M=M(:,M(2,1)+2:end);
if isempty(M);
break;
end
end
m=m';
m=sortrows(m);
idx= 10e-3>m(:,2) & m(:,2)>10e-6;
x=m(idx,1);
y=m(idx,2);
%------------
polyfit(x,y,1)
x1=linspace(0,20,5)
y1=polyval(p,x1)
plot(x1,y1,'--','LineWidth',2)
hold off
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Sergii Snegir
Sergii Snegir 2021-3-16
Here is the code and the data is ettached
clear all
opengl software
% working version V4_2.
smth=1; % k-point mean values for smoothing the data
cont_lev=[.2 .2]; %contour level which is displayed
Imagformat='-dpng'; %format of exported images ('-djpeg' | '-dpng' | '-dtiff' | '-dpdf' | '-deps' | ...)
fit_my=["on"]; %implement this filter. If 'on' - applies fitting, 'off' - no fitting
fig_save=["off"];
timestamp =["20210201101947","20210208115740"];
%% -----
hold on
leg_inf=[];
for i=1:length(timestamp)
% loading the data
filePathName= sprintf('figures\\contours\\%s_from_2D-histo_counts.mat',timestamp(1,i));
load (filePathName);
f=counts';
%----- filter low lewel signal of signal has less than 10% from Max
%conts is is filtered
max_val=max(f(:))
repVal=max(f(:))*.1 % 0.1 = 10% from max value
f(f(:,:)<repVal)=0;
%
f=normalize(f,'range',[0 1]);
f=movmean(f,smth);
max(f(:))
tstapmt=timestamp(1,i);
con_mat_siz=size(counts);
xbin=xbin(1,1:con_mat_siz(1,1))';
ybin=ybin(1,1:con_mat_siz(1,2))';
% plotting contours
plot_cont(f,xbin,ybin,i, cont_lev,tstapmt,smth,x_lim,y_lim,fit_my);
end
hold off
%% functions
function plot_cont(f,xbin,ybin,i,cont_lev,tstapmt,smth,x_lim,y_lim,fit_my)
FonSize=14;
[M,h]=contourf(xbin,ybin,f,cont_lev);
% levels = get(h, 'LevelList')
ax = gca;
ax.XAxis.Label.String ="Bending (\mum)";
ax.YAxis.Label.String ="Conductance (G_0)";
ax.YAxis.TickValues =[1e-6 1e-5 1e-4 1e-3 1e-2 1e-1 1];
ax.LineWidth = 1;
ax.FontSize = FonSize;
ax.YScale='log';
ax.YGrid = 'on';
ax.XGrid = 'on';
ax.Layer = 'top';
ax.GridLineStyle = '-';
ax.GridColor='w';
ax.Color='#0039e6';
ax.LineWidth = 1;
ax.YMinorGrid = 'off';
if i>1
cont_col=["#ff0066","#00ff00","#ffcc00"];
h.LineColor=cont_col(1,i-1);
h.Fill='off';
h.LineWidth=1.5;
end
ax.Box="on";
set(gcf,'PaperUnits','inches','PaperPosition',[0 0 8 6])
legend
ax.Legend.String(1,2*i-1)={tstapmt};
ax.Legend.Title.String = sprintf('con:%s smth:%s',string(cont_lev(1,1)),string(smth));
ax.Legend.Box='off';
ax.Legend.Color='white';
ax.Legend.TextColor='white';
ax.Legend.FontSize=12;
if fit_my=='on'
extr_fit_plot
else
ax.Legend.String(1,i)={tstapmt};
end
% ------------function to extract the data from the counts for fitting sellect data set
function extr_fit_plot
colFitLin=["#00ccff","#ff66ff","#00ff00"];
m=[];
while true
m=[m,M(:,2:M(2,1)+1)];
M=M(:,M(2,1)+2:end);
if isempty(M);
break;
end
end
m=m';
m=sortrows(m);
idx= 10e-3>m(:,2) & m(:,2)>10e-7;
%------------
x=m(idx,1);
y=m(idx,2);
p=polyfit(x,y,1)
x1=linspace(0,x_lim(1,2),5)
y1=polyval(p,x1)
plot(x1,y1,'--','LineWidth',2,"Color",colFitLin(1,i))
a=p(1,1);
b=p(1,2);
% info=sprintf('%.3f*x+%.3f\n',a,b);
info=sprintf('%d*x+%.d\n',a,b)
ax.Legend.String(1,2*i)={info};
end
end

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回答（2 个）

Mathieu NOE
Mathieu NOE 2021-3-16
so this is my proposal - see the lines of your code I modified ; look for comments including :
% modified code
the original lines are still there but commented
one point still I coudn't fix completely, is how to have a better display of the fit function y = 10^(ax+b) in the legend
hope it helps !
clear all
opengl software
% working version V4_2.
smth=1; % k-point mean values for smoothing the data
cont_lev=[.2 .2]; %contour level which is displayed
Imagformat='-dpng'; %format of exported images ('-djpeg' | '-dpng' | '-dtiff' | '-dpdf' | '-deps' | ...)
fit_my=["on"]; %implement this filter. If 'on' - applies fitting, 'off' - no fitting
fig_save=["off"];
timestamp =["20210201101947","20210208115740"];
%% -----
figure(1); % modified code
hold on
leg_inf=[];
for i=1:length(timestamp)
% loading the data
% filePathName= sprintf('figures\\contours\\%s_from_2D-histo_counts.mat',timestamp(1,i));
filePathName= sprintf('%s_from_2D-histo_counts.mat',timestamp(1,i));
load (filePathName);
f=counts';
%----- filter low lewel signal of signal has less than 10% from Max
%conts is is filtered
max_val=max(f(:))
repVal=max(f(:))*.1 % 0.1 = 10% from max value
f(f(:,:)<repVal)=0;
%
f=normalize(f,'range',[0 1]);
f=movmean(f,smth);
max(f(:))
tstapmt=timestamp(1,i);
con_mat_siz=size(counts);
xbin=xbin(1,1:con_mat_siz(1,1))';
ybin=ybin(1,1:con_mat_siz(1,2))';
% plotting contours
plot_cont(f,xbin,ybin,i, cont_lev,tstapmt,smth,x_lim,y_lim,fit_my);
end
hold off
%% functions
function plot_cont(f,xbin,ybin,i,cont_lev,tstapmt,smth,x_lim,y_lim,fit_my)
FonSize=14;
[M,h]=contourf(xbin,ybin,f,cont_lev);
% levels = get(h, 'LevelList')
ax = gca;
ax.XAxis.Label.String ="Bending (\mum)";
ax.YAxis.Label.String ="Conductance (G_0)";
ax.YAxis.TickValues =[1e-6 1e-5 1e-4 1e-3 1e-2 1e-1 1];
ax.LineWidth = 1;
ax.FontSize = FonSize;
ax.YScale='log';
ax.YGrid = 'on';
ax.XGrid = 'on';
ax.Layer = 'top';
ax.GridLineStyle = '-';
ax.GridColor='w';
ax.Color='#0039e6';
ax.LineWidth = 1;
ax.YMinorGrid = 'off';
if i>1
cont_col=["#ff0066","#00ff00","#ffcc00"];
h.LineColor=cont_col(1,i-1);
h.Fill='off';
h.LineWidth=1.5;
end
ax.Box="on";
set(gcf,'PaperUnits','inches','PaperPosition',[0 0 8 6])
legend
ax.Legend.String(1,2*i-1)={tstapmt};
ax.Legend.Title.String = sprintf('con:%s smth:%s',string(cont_lev(1,1)),string(smth));
ax.Legend.Box='off';
ax.Legend.Color='white';
ax.Legend.TextColor='white';
ax.Legend.FontSize=12;
if fit_my=='on'
extr_fit_plot
else
ax.Legend.String(1,i)={tstapmt};
end
% ------------function to extract the data from the counts for fitting sellect data set
function extr_fit_plot
colFitLin=["#00ccff","#ff66ff","#00ff00"];
m=[];
while true
m=[m,M(:,2:M(2,1)+1)];
M=M(:,M(2,1)+2:end);
if isempty(M);
break;
end
end
m=m';
m=sortrows(m);
idx= 10e-3>m(:,2) & m(:,2)>10e-7;
%------------
x=m(idx,1);
y=m(idx,2);
% p=polyfit(x,y,1); % original code
p=polyfit(x,log10(y),1); % modified code / / fit polynomial on log of y
% x1=linspace(0,x_lim(1,2),5); % original code
x1=linspace(0,12,5); % modified code / / to not exceed x = 12 (my very own preference)
y1=polyval(p,x1);
y1= 10.^(y1); % modified code / / go back from log to lin y
plot(x1,y1,'--','LineWidth',2,"Color",colFitLin(1,i))
a=p(1,1);
b=p(1,2);
% info=sprintf('%.3f*x+%.3f\n',a,b);
% info=sprintf('%d*x+%.d\n',a,b) % original code
if b <0 % do not put the '+' in the legend
info=sprintf('y = 10^^( %.3f*x %.3f )',a,b) % modified code / / remove return carriage
else % leave the '+' in the legend
info=sprintf('y = 10^^( %.3f*x+%.3f )',a,b) % modified code / / remove return carriage
end
ax.Legend.String(1,2*i)={info};
end
end
Sergii Snegir
Sergii Snegir 2021-3-17
Dear Methieu,
many, many thanks for your help. All works nice.
Only one question remaines. How to omit this warning in the code????
  1 个评论
Mathieu NOE
Mathieu NOE 2021-3-17
Ok, I finally understood how to get the legend right
had to put the 'Interpreter' from 'text' (default) to 'none'
this is the new code :
clear all
opengl software
% working version V4_2.
smth=1; % k-point mean values for smoothing the data
cont_lev=[.2 .2]; %contour level which is displayed
Imagformat='-dpng'; %format of exported images ('-djpeg' | '-dpng' | '-dtiff' | '-dpdf' | '-deps' | ...)
fit_my=["on"]; %implement this filter. If 'on' - applies fitting, 'off' - no fitting
fig_save=["off"];
timestamp =["20210201101947","20210208115740"];
%% -----
figure(1); % modified code
hold on
leg_inf=[];
for i=1:length(timestamp)
% loading the data
% filePathName= sprintf('figures\\contours\\%s_from_2D-histo_counts.mat',timestamp(1,i));
filePathName= sprintf('%s_from_2D-histo_counts.mat',timestamp(1,i));
load (filePathName);
f=counts';
%----- filter low lewel signal of signal has less than 10% from Max
%conts is is filtered
max_val=max(f(:))
repVal=max(f(:))*.1 % 0.1 = 10% from max value
f(f(:,:)<repVal)=0;
%
f=normalize(f,'range',[0 1]);
f=movmean(f,smth);
max(f(:))
tstapmt=timestamp(1,i);
con_mat_siz=size(counts);
xbin=xbin(1,1:con_mat_siz(1,1))';
ybin=ybin(1,1:con_mat_siz(1,2))';
% plotting contours
plot_cont(f,xbin,ybin,i, cont_lev,tstapmt,smth,x_lim,y_lim,fit_my);
end
hold off
%% functions
function plot_cont(f,xbin,ybin,i,cont_lev,tstapmt,smth,x_lim,y_lim,fit_my)
FonSize=14;
[M,h]=contourf(xbin,ybin,f,cont_lev);
% levels = get(h, 'LevelList')
ax = gca;
ax.XAxis.Label.String ="Bending (\mum)";
ax.YAxis.Label.String ="Conductance (G_0)";
ax.YAxis.TickValues =[1e-6 1e-5 1e-4 1e-3 1e-2 1e-1 1];
ax.LineWidth = 1;
ax.FontSize = FonSize;
ax.YScale='log';
ax.YGrid = 'on';
ax.XGrid = 'on';
ax.Layer = 'top';
ax.GridLineStyle = '-';
ax.GridColor='w';
ax.Color='#0039e6';
ax.LineWidth = 1;
ax.YMinorGrid = 'off';
if i>1
cont_col=["#ff0066","#00ff00","#ffcc00"];
h.LineColor=cont_col(1,i-1);
h.Fill='off';
h.LineWidth=1.5;
end
ax.Box="on";
set(gcf,'PaperUnits','inches','PaperPosition',[0 0 8 6])
legend
ax.Legend.String(1,2*i-1)={tstapmt};
ax.Legend.Title.String = sprintf('con:%s smth:%s',string(cont_lev(1,1)),string(smth));
ax.Legend.Box='off';
ax.Legend.Color='white';
ax.Legend.TextColor='white';
ax.Legend.FontSize=12;
if fit_my=='on'
extr_fit_plot
else
ax.Legend.String(1,i)={tstapmt};
end
% ------------function to extract the data from the counts for fitting sellect data set
function extr_fit_plot
colFitLin=["#00ccff","#ff66ff","#00ff00"];
m=[];
while true
m=[m,M(:,2:M(2,1)+1)];
M=M(:,M(2,1)+2:end);
if isempty(M);
break;
end
end
m=m';
m=sortrows(m);
idx= 10e-3>m(:,2) & m(:,2)>10e-7;
%------------
x=m(idx,1);
y=m(idx,2);
% p=polyfit(x,y,1); % original code
p=polyfit(x,log10(y),1); % modified code / / fit polynomial on log of y
% x1=linspace(0,x_lim(1,2),5); % original code
x1=linspace(0,12,5); % modified code / / to not exceed x = 12 (my very own preference)
y1=polyval(p,x1);
y1= 10.^(y1); % modified code / / go back from log to lin y
plot(x1,y1,'--','LineWidth',2,"Color",colFitLin(1,i))
a=p(1,1);
b=p(1,2);
% info=sprintf('%.3f*x+%.3f\n',a,b);
% info=sprintf('%d*x+%.d\n',a,b) % original code
if b <0 % do not put the '+' in the legend
info=sprintf('y = 10^( %.3f*x %.3f )',a,b) % modified code / / remove return carriage
else % leave the '+' in the legend
info=sprintf('y = 10^( %.3f*x+%.3f )',a,b) % modified code / / remove return carriage
end
ax.Legend.String(1,2*i)={info};
ax.Legend.Interpreter = 'none';
end
end

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