Import Jpk AFM images Matlab?

Hi everybody, I am trying to extract, from AFM data, a number of parameters from different sets of channels ( Height, Lateral deflection, Photo sum Etc. ) and import it into Matlab.

I currently use Gwyddion to do so, save to CSV and import to Matlab.

But as the amount of data is consistent, would anyone know how to read '.jpk' extensions in Matalb so I could write a script to do the analysis directly? Or have a script to at least to open the '.jpk' extensions for import?

Traditional input methods, also through the import tool, don't do the job as some import only the first layer of data.

Thank You all very much. Best.

[kunal Bhardwaj]

hey Robery Could you show me how to extract from AFM data and import into Matlab for analysis?

I am using gwyddion for AFM

thanks

[e-mail]

[Roberto Diego Ortuso]

Dear Bhardwaj,

Sorry, but your question is too vague.

Might I suggest you start from [ http://gwyddion.net/module-list.en.php ] to decode your AFM file format. This repertory is the source list for AFM file import and holds most AFM file types.

The second option is contact your manufacturer and they will most likely provide you with information on file structure and decoding.

Best,

Robert

Answer 1

[Alex Winkel]

Hello Robert

I can give you some detailed info on our file structure if you contact me.

If you can't get a message directly to me through mathworks please comment here.

Best wishes, Alex

Answer 2

[Emanuel Pfitzner]

Hello Robert,

i once started writing a script for that and it's not the nicest to look at. It just loads the Height and auxiliary channel 3 and 4 into Matlab. Using the imfinfo command you get back a more conclusive overview of the *.jpk file content. With that you might get a chance to modify the code below according to your application.

Hope that helps, Emanuel

function [data,X_trace, X_retrace, Y_trace, Y_retrace, topo] = loadJPKAux34(filename,scaling)

          info=imfinfo(filename);

%       Get the indices for the different channels Hieght measured, Aux 3
%       and Aux 4 for trace and retrace.
        for j=1:size(info,1)
            if strcmp(info(j).UnknownTags(3).Value,'Height')
                indexTopo = j;
                scalingTopo = info(j).UnknownTags(37).Value;
                offsetTopo = info(j).UnknownTags(38).Value;
            end
            if ~isempty(strfind(info(j).UnknownTags(4).Value,'channel.name : aux3'))&&~isempty(strfind(info(j).UnknownTags(4).Value,'retrace : false'))
                indexXTrace=j;
                scalingX = info(j).UnknownTags(19).Value;
                offsetX = info(j).UnknownTags(20).Value;
            end
            if ~isempty(strfind(info(j).UnknownTags(4).Value,'channel.name : aux3'))&&~isempty(strfind(info(j).UnknownTags(4).Value,'retrace : true'))
                indexXRetrace=j;
                scalingX = info(j).UnknownTags(19).Value;
                offsetX = info(j).UnknownTags(20).Value;
            end
            if ~isempty(strfind(info(j).UnknownTags(4).Value,'channel.name : aux4'))&&~isempty(strfind(info(j).UnknownTags(4).Value,'retrace : false'))
                indexYTrace=j;
                scalingY = info(j).UnknownTags(19).Value;
                offsetY = info(j).UnknownTags(20).Value;
            end
            if ~isempty(strfind(info(j).UnknownTags(4).Value,'channel.name : aux4'))&&~isempty(strfind(info(j).UnknownTags(4).Value,'retrace : true'))
                indexYRetrace=j;
                scalingY = info(j).UnknownTags(19).Value;
                offsetY = info(j).UnknownTags(20).Value;
            end
        end

          %%%%%%%%%%%%%%%%%%%%%%%%%%%%%
          %load and correct topography%
          %%%%%%%%%%%%%%%%%%%%%%%%%%%%%

%       Load only the trace map of the topography and scale it by its
%       scaling factors and offset.
        topo = scalingTopo.*double(imread(filename,'Index',indexTopo))+offsetTopo;

          %load X trace and average with retrace
          X_trace = (double(imread(filename,'Index',indexXTrace)).*scalingX+offsetX).*scaling;
          X_retrace = (double(imread(filename,'Index',indexXRetrace)).*scalingX+offsetX).*scaling;

          %load Y trace and average with retrace
          Y_trace = (double(imread(filename,'Index',indexYTrace)).*scalingY+offsetY).*scaling;
          Y_retrace = (double(imread(filename,'Index',indexYRetrace)).*scalingY+offsetY).*scaling;

          data.X_trace = X_trace;
          data.Y_trace = Y_trace;
          data.X_retrace = X_retrace;
          data.Y_retrace = Y_retrace;
          data.topo = topo;
  end

Answer 3

[Peter Newman]

Hi Guys,

The 2018 publication together with software package "Fodis" contains a function "readJPK" that does just the above - see: https://github.com/nicolagalvanetto/Fodis