如何保存多个摘要文件批处理宏imageJ [英] how to save multiple summary files batch process macro imageJ

问题描述

对于imageJ中的批处理图像处理，我还很陌生.我有一个宏，可让我在单个目录中处理多个图像.问题在于该宏为每个处理的图像生成一个单独的摘要窗口，让我手动将所有输出数据编译为单个.csv或.xls.我希望将所有摘要数据自动编译到一个文件中.虽然我发现了一些资料显示如何执行此操作，但是对于我的情况，它并不是特别有用.

I am pretty new to batch image processing in imageJ. I have a macro that allows me to process several images in a single directory. The problem is that the macro generates an individual summary window for each processed image, leaving me to manually compile all the output data into a single .csv or .xls. I would prefer that all the summary data be automatically compiled into one file. While I have found several sources showing how to do this, it has not been particularly helpful in my situation.

如果能帮助您，我将不胜感激.

If you could help, I'd be very grateful.

以下是该代码的缩写示例:

Here is an abbreviated example of the code:

        dir1 = getDirectory("Choose Source Directory ");
        dir2 = getDirectory("Choose Destination directory");
        list = getFileList(dir1);

        setBatchMode(true);

        for (i=0; i<list.length; i++){
        print (list[i]);
        open(dir1+list[i]);
        name=File.nameWithoutExtension;
        //Prepare the image by removing any scale and making 8-bit
       run("Set Scale...", "distance=237.3933 known=1 pixel=1 unit=cm 
       global");            

        makeRectangle(4068, 5940, 1572, 1320);
        run("Crop");
        // Convert the image into RGB channels for proper thresholding
        run("RGB Stack");
        setSlice(3);
        //Threshold
        setAutoThreshold("Default");
        // Analyze particles
        // Provides total area of number of cotyledons in image
        run("Analyze Particles...", "size=60-Infinity pixel display include 
        summarize");
        run("Revert");
 }
 //Save the results
 selectWindow("Summary");
 saveAs("Results", dir2+"Results.xls"); 

推荐答案

在我的测试中(在macOS 10.12.6上使用ImageJ 2.0.0-rc-61/1.51n)，重复执行带有"summary"选项选中的"Analyze Particles"将摘要添加到现有的摘要"窗口中，然后可以在末尾将其另存为单个文件.

In my tests (with ImageJ 2.0.0-rc-61/1.51n on macOS 10.12.6), repeatedly executing Analyze Particles with the summarize option checked appends the summary to the existing Summary window, which can then be saved as a single file at the end.

例如，以下宏生成两条摘要行，然后保存它们:

For example, the following macro generates two summary lines and then saves them:

setBatchMode(true);
run("Blobs (25K)");
setAutoThreshold("Default");
run("Analyze Particles...", "size=60-Infinity pixel display include summarize");
run("Boats (356K)");
setAutoThreshold("Default");
run("Analyze Particles...", "size=60-Infinity pixel display include summarize");
selectWindow("Summary");
saveAs("Results", "/Users/curtis/Desktop/Results.xls"); 

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