Python subprocess.run 参数传递

Question

我正在使用 subprocess.run 在 QuPath 中运行脚本。我的 python 代码在下面，QuPath 脚本在下面。脚本运行但参数未传递。脚本中的第一个代码块打印识别的参数。

当Python代码运行时，QuPath脚本执行成功，但报告没有传递参数，并且脚本由于找不到项目路径而返回。 如果“script”参数放在前面，结果是相同的。 感谢您的想法！

Python代码：

qupath_executable = "C:/path/to/QuPath executable"
script_path = "C:/path/to/script.groovy"
project_path = "C:/path/to/project.qpproj"

command = [
    qupath_executable,
    "-p", project_path,
    "script", script_path,
]
result = subprocess.run(command, capture_output=True, text=True, shell=True)
if result.returncode == 0:
    print("Script executed successfully.")
    print(result.stdout)
else:
    print("Script execution failed.")
    print(result.stderr)

QuPath 脚本：

import java.awt.BasicStroke
import java.awt.Graphics2D
import qupath.ext.stardist.StarDist2D
import qupath.lib.images.servers.ImageServer
import qupath.lib.images.servers.ImageServerProvider

// Print all arguments
println "Arguments passed to the script:"
args.eachWithIndex { arg, index ->
    println "Argument ${index}: ${arg}"
}


// Retrieve the project path from the arguments
def projectPath = null
for (int i = 0; i < args.length; i++) {
    println "Examining argument ${i}: ${args[i]}"
    if (args[i] == "-p" && i + 1 < args.length) {
        projectPath = args[i + 1]
        break
    }
}

if (!projectPath) {
    println "Error: Project path not specified."
    return
}

def annotationOutputPath = projectPath + '/Annotations'
def annotatedImageOutputPath = projectPath + '/AnnotatedImages'
new File(annotationOutputPath).mkdirs()
new File(annotatedImageOutputPath).mkdirs()

def pathModel = projectPath + '/Models/he_heavy_augment.pb'

def stardist = StarDist2D.builder(pathModel)
      .threshold(0.5)              // Prediction threshold
      .normalizePercentiles(1, 99) // Percentile normalization
      .pixelSize(0.5)              // Resolution for detection
      .build()

println 'StarDist model initialized.'

def imageFiles = new File(projectPath + '/Images').listFiles().findAll { it.name.endsWith('.png') || it.name.endsWith('.jpg') }

if (imageFiles.isEmpty()) {
    println "No images found in the project directory."
    return
}

imageFiles.each { file ->
    println "Processing image: ${file.name}"
    
    def server = ImageServerProvider.buildServer(file)
    def imageData = server.readImageData()
    
    def pathObjects = getSelectedObjects()
    if (pathObjects.isEmpty()) {
        println "No objects selected for image: ${file.name}"
        return
    }
    println 'Selected objects: ' + pathObjects.size()
    stardist.detectObjects(imageData, pathObjects)
    println 'Object detection complete for image: ' + file.name
    
    def annotations = imageData.getHierarchy().getAnnotationObjects()
    println 'Number of annotations: ' + annotations.size()
    def json = PathIO.writeObjectToJson(annotations)
    def annotationFile = new File(annotationOutputPath, file.name + '_annotations.json')
    annotationFile.text = json
    println 'Annotations saved to ' + annotationFile.getPath()
    
    def region = RegionRequest.createInstance(server.getPath(), 1, 0, 0, server.getWidth(), server.getHeight())
    def img = ImageIO.read(server.readBufferedImage(region))
    def g2d = img.createGraphics()
    g2d.setColor(Color.RED)
    g2d.setStroke(new BasicStroke(2))
    for (annotation in annotations) {
        def roi = annotation.getROI()
        def shape = roi.getShape()
        g2d.draw(shape)
    }
    g2d.dispose()
    def annotatedImageFile = new File(annotatedImageOutputPath, file.name + '_annotated.png')
    ImageIO.write(img, 'PNG', annotatedImageFile)
    println 'Annotated image saved to ' + annotatedImageFile.getPath()
}

println 'Processing complete.'

Answer 1

您使用了不正确的参数组合：

• args

  是单个字符串并且

  shell=True

  。 shell 解析命令并将其拆分为单独的参数。
• 或

  args

  是args和

  shell=False

  的列表（序列）。