22  输出csv和txt

输出detections的csv和txt格式文件

对于QuPath项目图片的detections结果，有时候因为某种需要，就想输出逗号分隔（comma-separated）的csv格式文件，或者就想输出制表符分隔（tab-separated）的txt格式文件。

1. 输出csv和txt格式文件

参考如下代码：

// QuPath v0.6.0

import qupath.lib.gui.tools.MeasurementExporter

// #########################################
// Export all detections as comma-separated file (.csv)
// #########################################
// Make the current image name as a list
def entryList = [getProjectEntry()]

// If the folder detections exist, do noting; else create the folder
def outputPath = buildFilePath(PROJECT_BASE_DIR, "detections")
mkdirs(outputPath)

// Separate each measurement value in the output file with ","
def separator = ","

def csvName = getCurrentImageName() + "_detections.csv"
def csvOutputFile = new File(buildFilePath(outputPath, csvName))

// Create the measurementExporter and start the export
def exporter = new MeasurementExporter()
    .imageList(entryList)
    .separator(separator)
    .allDetections()
    .exportMeasurements(csvOutputFile)

println "${csvOutputFile} saved."

// #########################################
// Export all detections as tab-separated file (.txt)
// #########################################
def txtName = getCurrentImageName() + "_detections.txt"
def txtOutputFile = new File(buildFilePath(outputPath, txtName))
saveDetectionMeasurements("${txtOutputFile}")

println "${txtOutputFile} saved."

println "Done."

以上代码部分参考自(1)。

确认下文件已经保存成功：

# R v4.5.2
outputPath <- "path/to/detections/"
outputPath |> fs::dir_tree()

path/to/detections/
├── image1_detections.csv
├── image1_detections.txt
├── image2_detections.csv
├── image2_detections.txt
├── image3_detections.csv
├── image3_detections.txt
├── image4_detections.csv
├── image4_detections.txt
├── image5_detections.csv
└── image5_detections.txt

给我买杯茶🍵

References

1.

MicroscopyRA, QuPath: Saving filtered DetectionTable with MeasurementExporter for current image only? (2020). https://forum.image.sc/t/qupath-saving-filtered-detectiontable-with-measurementexporter-for-current-image-only/41328/2.