%This code is modified from: %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% % This work by EPFL STI IBI LBNI is licensed under % a Creative Commons Attribution-NonCommercial-ShareAlike 3.0 Unported License. % Based on a work at http://lbni.epfl.ch/. %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% function [img, s] = open_nanoscope(fname,channel,error) pft=1; file_name = fname; % Generates the filname to open for this particular iteration % Read in DI Image and image propreties This code is mostly from Jaco De Groot at University College London searchstring(1).label='@2:Z scale:'; searchstring(2).label='Samps'; searchstring(3).label='Lines:'; searchstring(4).label='Data offset'; searchstring(5).label='Image Data:'; searchstring(6).label='\Scan Size:'; searchstring(7).label='@Sens. Zsens:'; searchstring(8).label='@Z magnify:'; searchstring(9).label='Scan Rate:'; searchstring(10).label='@Sens. DeflSens: V'; searchstring(11).label='@2:CantFrequency: V'; searchstring(12).label='@2:CantDrive: V'; searchstring(13).label='@2:TMSetAmplitude: V'; searchstring(14).label='@Sens. ZsensSens: V'; searchstring(15).label='@Sens. Amplitude Error: V'; searchstring(16).label='@Sens. Amplitude: V'; searchstring(17).label='@Sens. ForceDeflSens: V'; searchstring(18).label='Aspect Ratio:'; searchstring(19).label='Capture direction:'; fid = fopen(file_name,'r'); [message,errnum] = ferror(fid); if(errnum) fprintf(1,'I/O Error %d \t %s',[errnum,message]); end header_end=0; eof = 0; counter = 1; byte_location = 0; nstrings=size(searchstring,2); parcounter = ones(nstrings,1); paramters = struct('trace',cell(1,nstrings),'values',cell(1,nstrings),'channel',cell(1,nstrings)); for ij=1:nstrings parcounter(ij)=1; parameters(ij).trace=0; end while( and( ~eof, ~header_end ) ) byte_location = ftell(fid); line = regexprep(fgets(fid),'Zscan','Zsens'); for ij=1:nstrings if strfind(lower(line),lower(searchstring(ij).label)) if (extract_num(line)) b = strfind(line, 'LSB'); if (b>0) parameters(ij).values(parcounter(ij))=extract_num(line(b(1):end)); else parameters(ij).values(parcounter(ij))=extract_num(line); end elseif strcmp(searchstring(ij).label,'Aspect Ratio:') b= strfind(line,':'); parameters(ij).values(parcounter(ij))=extract_num(line(b(1):b(2)-1)); elseif strcmp(searchstring(ij).label,'Capture direction:') b= strfind(line,':'); parameters(ij).values(parcounter(ij)) = strcmp(line(b(1)+2),'D'); else b= strfind(line,'"'); if (b>0) parameters(ij).channel(parcounter(ij)).name=line(b(1)+1:b(2)-1); else if (strfind(line,'Trace')>0) parameters(ij).trace=1; end end end parcounter(ij)=parcounter(ij)+1; end end if( (-1)==line ) eof = 1; end if ~isempty( strfind( line, '\*File list end' ) ) header_end = 1; end counter=counter+1; end fclose(fid); fid = fopen(file_name,'r'); C = textscan(fid, '%s', 3,'delimiter','\n'); fclose(fid); C = C{1}; C = char(C(3)); s.Time = C(8:end); param = parameters; scaling = param(1).values; % Scaling parameters spl = param(2).values(1); % Samples per line s.line_no = param(3).values(1); % No of lines image_pos = param(4).values; % Data position if param(6).values(1) <= 100 s.ScanSize = param(6).values(2); else s.ScanSize = param(6).values(1); end s.Z_Sensitivity = param(7).values; s.Z_Magnification = param(8).values; s.Scan_Rate = param(9).values(1); s.Defl_Sens = param(10).values; s.Drive_Freq = param(11).values; s.Drive_Amp = param(12).values; s.Amp_Set_Point = param(13).values; s.Z_sensor_sens = param(14).values; s.Amp_sens = max([param(15).values,param(16).values]); if s.Amp_sens == 1 s.Amp_sens = 1000*s.Amp_sens; end s.SpringConst = param(17).values; s.AspectRatio = param(18).values; s.Direction = param(19).values; %[~, remain] = strtok(fname,'.'); %file_number = str2double(remain(2:4)); L = length(image_pos); % Sets the number of image channels channel_info = struct('Trace',cell(L,1),'Name',cell(L,1),'Finalscaling',cell(L,1),'Unit',cell(L,1)); finalscaling = zeros(L,1); i=0; for im=1:L % Loops for the number of channels channel_info(im).Trace = char((param(6).trace)*'Trace '+(1-param(6).trace)*'Retrace'); % Determines if Channel is Trace or Retrace channel_info(im).Name = param(5).channel(im).name; % Name of channel 1 channel_info(im).Finalscaling(im) = param(8).values(im)*param(1).values(im); % Computes some of the scaling paramters if im >1 if contains({channel_info(im).Name}, s.channels) s.channels{im} = 'Height Retrace'; else s.channels{im} = channel_info(im).Name; end else s.channels{im} = channel_info(im).Name; end if strcmp(channel,s.channels{im}) i =im; switch channel_info(im).Name % Sets Units according to recorded channel case 'Height' % If height... channel_info(im).Unit='nm' ; % Units are nm channel_info(im).Finalscaling(im)=param(7).values*param(8).values(im)*param(1).values(im); % Sets final scaling value finalscaling(im)=(scaling(im)*s.Z_Sensitivity)/(2^16); case 'Height Retrace' % If height... channel_info(im).Unit='nm' ; % Units are nm channel_info(im).Finalscaling(im)=param(7).values*param(8).values(im)*param(1).values(im); % Sets final scaling value finalscaling(im)=(scaling(im)*s.Z_Sensitivity)/(2^16); % Sets bit scaling case 'Height Sensor' % If height... channel_info(im).Unit='nm' ; % Units are nm channel_info(im).Finalscaling(im)=param(8).values(im)*param(1).values(im); % Sets final scaling value finalscaling(im)=(scaling(im))*s.Z_sensor_sens/(2^16); case 'Deflection' % If Deflection... if s.Defl_Sens == 1 channel_info(im).Unit='V'; else channel_info(im).Unit='nm'; % Units are V end finalscaling(im)=(scaling(im))*s.Defl_Sens/(2^16); % Sets bit scaling case 'Deflection Error' % If Deflection... if s.Defl_Sens == 1 channel_info(im).Unit='V'; else channel_info(im).Unit='nm'; % Units are V end finalscaling(im)=(scaling(im))*s.Defl_Sens/(2^16); % Sets bit scaling case 'Phase' % If Phase... channel_info(im).Unit='Degree'; % Units are degrees finalscaling(im)=(scaling(im))/(2^16); % Sets bit scaling case 'Amplitude' % If Potential... if s.Amp_sens == 1000 channel_info(im).Unit='mV'; s.Amp_sens = s.Amp_sens/1000; else channel_info(im).Unit='nm'; % Units are V s.Amp_sens = s.Amp_sens/1000; end channel_info(im).Finalscaling(im)=param(8).values(im)*param(1).values(im); % Sets final scaling value finalscaling(im)=(scaling(im)*s.Amp_sens)/(2^16); case 'Amplitude Error' % If Potential... if s.Amp_sens == 1000 channel_info(im).Unit='mV'; s.Amp_sens = s.Amp_sens/1000; else channel_info(im).Unit='nm'; s.Amp_sens = s.Amp_sens/1000; end % Units are V channel_info(im).Finalscaling(im)=param(8).values(im)*param(1).values(im); % Sets final scaling value finalscaling(im)=(scaling(im)*s.Amp_sens)/(2^16); case 'Potential' % If Potential... channel_info(im).Unit='V'; % Units are V channel_info(im).Finalscaling(im)=param(8).values(im)*param(1).values(im); % Sets final scaling value finalscaling(im)=(scaling(im))/(2^16); % Sets bit scaling case 'Peak Force Error' % If height... channel_info(im).Unit='nN' ; % Units are nm channel_info(im).Finalscaling(im)=param(7).values*param(8).values(im)*param(1).values(im); % Sets final scaling value finalscaling(im)=(scaling(im)*s.Z_Sensitivity)/(2^16); case 'DMTModulus' % If height... channel_info(im).Unit='MPa' ; % Units are nm channel_info(im).Finalscaling(im)=param(7).values*param(8).values(im)*param(1).values(im); % Sets final scaling value finalscaling(im)=(scaling(im)*s.Z_Sensitivity)/(2^16); case 'LogDMTModulus' % If height... channel_info(im).Unit='log(MPa)' ; % Units are nm channel_info(im).Finalscaling(im)=param(7).values*param(8).values(im)*param(1).values(im); % Sets final scaling value finalscaling(im)=(scaling(im)*s.Z_Sensitivity)/(2^16); case 'Adhesion' % If height... channel_info(im).Unit='nN ' ; % Units are nm channel_info(im).Finalscaling(im)=param(7).values*param(8).values(im)*param(1).values(im); % Sets final scaling value finalscaling(im)=(scaling(im)*s.Z_Sensitivity)/(2^16); case 'Deformation' % If height... channel_info(im).Unit='nm' ; % Units are nm channel_info(im).Finalscaling(im)=param(7).values*param(8).values(im)*param(1).values(im); % Sets final scaling value finalscaling(im)=(scaling(im)*s.Z_Sensitivity)/(2^16); case 'Dissipation' % If height... channel_info(im).Unit='eV' ; % Units are nm channel_info(im).Finalscaling(im)=param(7).values*param(8).values(im)*param(1).values(im); % Sets final scaling value finalscaling(im)=(scaling(im)*s.Z_Sensitivity)/(2^16); % case 'Input1' % If height... % channel_info(im).Unit='nm' ; % Units are nm % channel_info(im).Finalscaling(im)=param(7).values*param(8).values(im)*param(1).values(im); % finalscaling(im)=(scaling(im)*Z_Sensitivity*Defl_Sens)/(2^16); % case 'Input2' channel_info(im).Unit='nm' ; channel_info(im).Finalscaling(im)=param(7).values*param(8).values(im)*param(1).values(im); finalscaling(im)=-1*(scaling(im)*s.Z_Sensitivity*1000)/(2^16); otherwise channel_info(im).Unit='V'; channel_info(im).Finalscaling(im)=param(8).values(im)*param(1).values(im); finalscaling(im)=(scaling(im))/(2^16); end end end % Loops for the number of channels c1 = any(strcmp(s.channels, 'Height Sensor')); c2 = any(strcmp(s.channels, 'Peak Force Error')); c3 = any(strcmp(s.channels, 'Height')); if c1 && c2 pft=2; end if error pft=2; end % if c1 && ~c3 % pft=2; % end % if i ==0 % i=1; % im=1; % channel_info(im).Unit='nm' ; % Units are nm % channel_info(im).Finalscaling(im)=param(8).values(im)*param(1).values(im); % Sets final scaling value % finalscaling(im)=(scaling(im))*s.Z_sensor_sens/(2^16); % end fid = fopen(file_name,'r'); fseek(fid,image_pos(i),-1); A = fread(fid, [spl s.line_no],'int16'); images = rot90(finalscaling(i)*A); [~, fre] = mode(images(:)); img = images; sz = size(img,1)*size(img,2); fre = fre/sz; %pft = 2 if fre > 0.48 || pft ==2 img=[]; fid = fopen(file_name,'r'); fseek(fid,image_pos(i),-1); A = fread(fid, [2*spl s.line_no],'int16'); images = rot90(finalscaling(i)*A); images = images-median(reshape(images,size(images,1)*size(images,2),1)); img = images(:,pft:2:end); end sd = std(img(:)); if sd>1000 || sd< 0.01 img = images(:,pft+1:2:end); end if spl >= size(img,2)-3 && spl <= size(img,2)+3 else img=[]; fid = fopen(file_name,'r'); images = zeros(s.line_no, 2*spl); fseek(fid,image_pos(i),-1); A = fread(fid, [2*spl s.line_no],'int16'); images = rot90(finalscaling(i)*A); images = images-median(reshape(images,size(images,1)*size(images,2),1)); img = images(:,2:2:end); end end %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% % This code has been adapted from the ALEX toolbox and incorporated into this m-file. % The original free source code, which is copywritten by Claudio Rivetti and Mark Young % for ALEX is available at www.mathtools.net. % %This function/script is authorized for use in government and academic %research laboratories and non-profit institutions only. Though this %function has been tested prior to its posting, it may contain mistakes or %require improvements. In exchange for use of this free product, we %request that its use and any issues relating to it be reported to us. %Comments and suggestions are therefore welcome and should be sent to %Prof. Robert Carpick , Engineering Physics %Department, UW-Madison. %Date posted: 7/8/2004 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% function val = extract_num(str) eos = 0; R = str; while(~eos) [T,R] = strtok(str); if( length(R) == 0) eos = 1; end I = find( (T>=48) & (T<=57) | 101==T | 69==T | T==173 | T== 45 | T==46 | T==40); LT = length(T); LI = length(I); if( LI == LT ) J = find(T~='('); val = str2num(T(J)); break end str =R; end end