petebankhead · February 20, 2018 20:11 · DavidMHaumann · Feb 23, 2018 · petebankhead · Feb 23, 2018
diff --git a/QuPath_Combine_measurement_tables.groovy b/QuPath_Combine_measurement_tables.groovy
 /**
 * Script to combine results tables exported by QuPath.
 *
 * This is particularly intended to deal with the fact that results tables of annotations can produce results
 * with different column names, numbers and orders - making them awkward to combine later manually.
 *
 * It prompts for a directory containing exported text files, and then writes a new file in the same directory.
 * The name of the new file can be modified - see the first lines below.
 *
 * Note: This hasn't been tested very extensively - please check the results carefully, and report any problems so they
 * can be fixed!
 *
 * @author Pete Bankhead
 */

 import qupath.lib.gui.QuPathGUI

 // Some parameters you might want to change...
 String ext = '.txt' // File extension to search for
 String delimiter = '\t' // Use tab-delimiter (this is for the *input*, not the output)
 String outputName = 'Combined_results.txt' // Name to use for output; use .csv if you really want comma separators

 // Prompt for directory containing the results
 def dirResults = QuPathGUI.getSharedDialogHelper().promptForDirectory()
 if (dirResults == null)
    return
 def fileResults = new File(dirResults, outputName)

 // Get a list of all the files to merge
 def files = dirResults.listFiles({
    File f -> f.isFile() &&
            f.getName().toLowerCase().endsWith(ext) &&
            f.getName() != outputName} as FileFilter)
 if (files.size() <= 1) {
    print 'At least two results files needed to merge!'
    return
 } else
    print 'Will try to merge ' + files.size() + ' files'

 // Represent final results as a 'list of maps'
 def results = new ArrayList<Map<String, String>>()

 // Store all column names that we see - not all files necessarily have all columns
 def allColumns = new LinkedHashSet<String>()
 allColumns.add('File name')

 // Loop through the files
 for (file in files) {
    // Check if we have anything to read
    def lines = file.readLines()
    if (lines.size() <= 1) {
        print 'No results found in ' + file
        continue
    }
    // Get the header columns
    def iter = lines.iterator()
    def columns = iter.next().split(delimiter)
    allColumns.addAll(columns)
    // Create the entries
    while (iter.hasNext()) {
        def line = iter.next()
        if (line.isEmpty())
            continue
        def map = ['File name': file.getName()]
        def values = line.split(delimiter)
        // Check if we have the expected number of columns
        if (values.size() != columns.size()) {
            print String.format('Number of entries (%d) does not match the number of columns (%d)!', columns.size(), values.size())
            print('I will stop processing ' + file.getName())
            break
        }
        // Store the results
        for (int i = 0; i < columns.size(); i++)
            map[columns[i]] = values[i]
        results.add(map)
    }
 }

 // Create a new results file - using a comma delimiter if the extension is csv
 if (outputName.toLowerCase().endsWith('.csv'))
    delimiter = ','
 int count = 0
 fileResults.withPrintWriter {
    def header = String.join(delimiter, allColumns)
    it.println(header)
    // Add each of the results, with blank columns for missing values
    for (result in results) {
        for (column in allColumns) {
            it.print(result.getOrDefault(column, ''))
            it.print(delimiter)
        }
        it.println()
        count++
    }
 }

 // Success!  Hopefully...
 print 'Done! ' + count + ' result(s) written to ' + fileResults.getAbsolutePath()
	/**
	* Script to combine results tables exported by QuPath.
	*
	* This is particularly intended to deal with the fact that results tables of annotations can produce results
	* with different column names, numbers and orders - making them awkward to combine later manually.
	*
	* It prompts for a directory containing exported text files, and then writes a new file in the same directory.
	* The name of the new file can be modified - see the first lines below.
	*
	* Note: This hasn't been tested very extensively - please check the results carefully, and report any problems so they
	* can be fixed!
	*
	* @author Pete Bankhead
	*/

	import qupath.lib.gui.QuPathGUI

	// Some parameters you might want to change...
	String ext = '.txt' // File extension to search for
	String delimiter = '\t' // Use tab-delimiter (this is for the input, not the output)
	String outputName = 'Combined_results.txt' // Name to use for output; use .csv if you really want comma separators

	// Prompt for directory containing the results
	def dirResults = QuPathGUI.getSharedDialogHelper().promptForDirectory()
	if (dirResults == null)
	return
	def fileResults = new File(dirResults, outputName)

	// Get a list of all the files to merge
	def files = dirResults.listFiles({
	File f -> f.isFile() &&
	f.getName().toLowerCase().endsWith(ext) &&
	f.getName() != outputName} as FileFilter)
	if (files.size() <= 1) {
	print 'At least two results files needed to merge!'
	return
	} else
	print 'Will try to merge ' + files.size() + ' files'

	// Represent final results as a 'list of maps'
	def results = new ArrayList<Map<String, String>>()

	// Store all column names that we see - not all files necessarily have all columns
	def allColumns = new LinkedHashSet<String>()
	allColumns.add('File name')

	// Loop through the files
	for (file in files) {
	// Check if we have anything to read
	def lines = file.readLines()
	if (lines.size() <= 1) {
	print 'No results found in ' + file
	continue
	}
	// Get the header columns
	def iter = lines.iterator()
	def columns = iter.next().split(delimiter)
	allColumns.addAll(columns)
	// Create the entries
	while (iter.hasNext()) {
	def line = iter.next()
	if (line.isEmpty())
	continue
	def map = ['File name': file.getName()]
	def values = line.split(delimiter)
	// Check if we have the expected number of columns
	if (values.size() != columns.size()) {
	print String.format('Number of entries (%d) does not match the number of columns (%d)!', columns.size(), values.size())
	print('I will stop processing ' + file.getName())
	break
	}
	// Store the results
	for (int i = 0; i < columns.size(); i++)
	map[columns[i]] = values[i]
	results.add(map)
	}
	}

	// Create a new results file - using a comma delimiter if the extension is csv
	if (outputName.toLowerCase().endsWith('.csv'))
	delimiter = ','
	int count = 0
	fileResults.withPrintWriter {
	def header = String.join(delimiter, allColumns)
	it.println(header)
	// Add each of the results, with blank columns for missing values
	for (result in results) {
	for (column in allColumns) {
	it.print(result.getOrDefault(column, ''))
	it.print(delimiter)
	}
	it.println()
	count++
	}
	}

	// Success! Hopefully...
	print 'Done! ' + count + ' result(s) written to ' + fileResults.getAbsolutePath()
No results found