Package qupath.lib.io

Class TMAScoreImporter

java.lang.Object

qupath.lib.io.TMAScoreImporter

public class TMAScoreImporter
extends Object

Helper class for importing data in connection with TMA slides.

Some methods may be changed / moved in the future, e.g. because they are more generally useful, such as those related to parsing CSV data. However, the attempts by these methods to auto-detect numeric data are not entirely robust - so more improvement is needed.

Author:

Pete Bankhead

Constructor Summary

Constructors

Constructor	Description
TMAScoreImporter()

Method Summary

Modifier and Type	Method	Description
static int	importFromCSV(File file, PathObjectHierarchy hierarchy)	Import TMA scores from a file into the TMAGrid of an object hierarchy.
static int	importFromCSV(String text, PathObjectHierarchy hierarchy)	Import TMA scores from a String into the TMAGrid of an object hierarchy.
static double[]	parseNumeric(List<String> list, boolean allOrNothing)	Parse numeric values from a list of strings.
static Map<String,List<String>>	readCSV(File file)	Read CSV data from a file into a map connecting column headers (keys) to lists of Strings (entries).
static Map<String,List<String>>	readCSV(String text)	Read CSV data from a String into a map connecting column headers (keys) to lists of Strings (entries).
static Map<String,List<String>>	readCSV(Scanner scanner)	Read CSV data into a map connecting column headers (keys) to lists of Strings (entries).

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Details

TMAScoreImporter

public TMAScoreImporter()

Method Details

importFromCSV

public static int importFromCSV(File file,
 PathObjectHierarchy hierarchy)
                         throws IOException

Import TMA scores from a file into the TMAGrid of an object hierarchy.

Parameters:

file -

hierarchy -

Returns:

Throws:

IOException

importFromCSV

public static int importFromCSV(String text,
 PathObjectHierarchy hierarchy)

Import TMA scores from a String into the TMAGrid of an object hierarchy.

Parameters:

text -

hierarchy -

Returns:

parseNumeric

public static double[] parseNumeric(List<String> list,
 boolean allOrNothing)

Parse numeric values from a list of strings.

Parameters:

list - list of strings containing the input text. Empty or null strings are treated as missing and returned as NaN.

allOrNothing - is true, the assumption is made that all values will be numeric or none of them will. Consequently, if any non-missing, non-numeric value is found then null is returned. Otherwise, NaNs are returned for any value that couldn't be parsed.

Returns:

readCSV

public static Map<String,List<String>> readCSV(String text)

Read CSV data from a String into a map connecting column headers (keys) to lists of Strings (entries).

Parameters:

text -

Returns:

readCSV

public static Map<String,List<String>> readCSV(File file)
                                        throws IOException

Read CSV data from a file into a map connecting column headers (keys) to lists of Strings (entries).

Parameters:

file -

Returns:

Throws:

IOException

readCSV

public static Map<String,List<String>> readCSV(Scanner scanner)

Read CSV data into a map connecting column headers (keys) to lists of Strings (entries).

Parameters:

scanner -

Returns: