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Plot 2d image from 3D data Mathematica

  1. May 6, 2012 #1
    hello guys,

    I have a CSV file with hyuge set of data devided into 3 cols. Y position X position and corresponding intensity values.

    I want to plot the image , my thesis is laser- microscopy. so a 2D plot ( density plot ) based on these values.

    The following is what I have tried so far!
    plotdata = Import["test2 10 10.csv", "Table"]
    ListPlot3D[plotdata]
    But above results in : is not a rectangular array larger than 2 x 2. >>

    Can anyone help me how to deal with such a huge set of data and how to plot it as 2D image ( Grey scale is also fine )

    Thank you,

    abhi - abikutn@gmail.com
     

    Attached Files:

  2. jcsd
  3. May 6, 2012 #2
    If your complete dataset is a square matrix of {x,y,z} in the same form as your small sample then this may work for you

    xyz = Import["test2 10 10.csv"];
    z = Partition[Map[Last, xyz], 10];
    ArrayPlot[z, ColorFunctionScaling -> True]

    That depends on your data being a square matrix and you need to set the size of the partition to restore your data to be a square matrix of z values.

    This has been done of samples with a million data points and might work with larger values if needed.
     
  4. May 6, 2012 #3
    Thanks for your reply and support

    "That depends on your data being a square matrix and you need to set the size of the partition to restore your data to be a square matrix of z values. "

    by saying this: suppose I have 10 by 10 pixels with some intensity values Z for each pixel.

    So partition meaning I have to split it 10 by 10 so that its a square matrix ?

    and what is the meaning of machine size values ?

    Thank you
     
  5. May 6, 2012 #4
    I suggest you take a look at the CSV file I have attached.

    for example I have y{1->10} and x{1->10}
    The way the values are recording in the CSV is as:

    [step1: y=1, get values for X{1->10}
    step2: increment y and repeat process till Y=max]

    Will this affect in anyway how the plot forms based on its actual X and Y co ordinates ???
    Just a question. I am not sure if you got my understanding.Basically wont the code you gave mix up all Z values with respect to their X and Y ?
     
  6. May 6, 2012 #5
    Remove that "Table" from import, use something like this:
    Code (Text):

    plotdata = Import["test2 10 10.csv"]
    z = GatherBy[plotdata, First][[All, All, 3]]
    ArrayPlot[z, ColorFunction -> "Rainbow"]
     
  7. May 6, 2012 #6
    I did use your CSV file to write and test the example I gave you.
    Thank you for the example data. That makes it much easier to provide correct answers.
    I believe that it does correctly keep the position of the Z values.

    You should ALWAYS carefully test any code to make sure that it is correct.
    Compare your matrix before any changes and after my calculation to verify this.

    I had intended to use an even simpler method of obtaining the Z values but for some reason I just didn't think of a simpler method when I posted my first reply.
     
  8. May 7, 2012 #7
    Thank you! ... That was a good start ...

    in the list density plot how can I change the color variation to grey scale image ? Is there a colorscaling function for grey scale just like how it can be done for RGB with ranibow ?

    Abhi
     
  9. May 7, 2012 #8
    Just remove ColorFunction -> "Rainbow",
    e.g.

    Code (Text):
    ArrayPlot[z]
     
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