Python + imageJ 解决方案，采坑记录

Python + imageJ 解决方案，采坑记录

方案一：ImageJ的Python脚本编程

ImageJ的Python脚本编程 | 数字旗手

方案二：jython

建议放弃，因为jython很多包都pip install 不了

方案三：pyimagej（注意不是imagepy，imagepy的作者是闫大），

pyimagej · PyPI

方案四：Python程序，cmd调用imageJ，解析imageJ的宏脚本，是可以做到的

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code如下

def WriteImageJMacroFile(fileRootPath, fileName, ROI):
    fileRootPath = fileRootPath.replace('\\', '/')

    ijmPath = fileRootPath + "/" + fileName[0:-4] + '.ijm'

    p1 = "fileRootPath=\"" + fileRootPath + "\";\n"
    p2 = "fileName=\"" + fileName + "\";\n"
    p3 = "ROI=newArray(" + str(ROI.iloc[0, 0]) + "," + str(ROI.iloc[1, 0]) + "," + str(ROI.iloc[2, 0]) + "," + str(
        ROI.iloc[3, 0]) + ");\n"

    body = """function processFile(fileRootPath, fileName) {
    setBatchMode(true); 
    open(fileRootPath + "/" + fileName);
    id = getImageID();
    selectImage(id);
    makeRectangle(ROI[0], ROI[1], ROI[2], ROI[3]);
    run("Crop");
    run("8-bit");  
    run("Size...", "width=100 height=80 average interpolation=Bilinear");
   outputFileName2 = "Pupil_Crop_"+fileName.substring(0,lengthOf(fileName)-4)+".avi";
   saveAs("avi", fileRootPath+"/"+outputFileName2);   

    run("Close");
}
processFile(fileRootPath,fileName);"""
    macro2 = p1 + p2 + p3 + body
    with open(ijmPath, "w") as f:
        f.write(macro2)
    return ijmPath