Package qupath.lib.experimental.pixels

Class PixelProcessorUtils

java.lang.Object

qupath.lib.experimental.pixels.PixelProcessorUtils

public class PixelProcessorUtils
extends Object

Utility functions to help with the PixelProcessor class.

Since:

v0.5.0

Constructor Summary

Constructors

Constructor	Description
PixelProcessorUtils()

Method Summary

Modifier and Type	Method	Description
static boolean	containsCentroid(ROI roi, PathObject child)	Check whether a child object's centroid is contained within a ROI.
static double[]	extractMaskedPixels(Parameters<BufferedImage,BufferedImage> params, int channel, Function<PathObject,ROI> roiFunction)	Extract the pixels from one channel of an image using the specified transform, and applying any ROI mask.
static double[]	extractMaskedPixels(Parameters<BufferedImage,BufferedImage> params, String channelName, Function<PathObject,ROI> roiFunction)	Extract the pixels from one channel of an image using the specified transform, and applying any ROI mask.
static double[]	extractMaskedPixels(Parameters<BufferedImage,BufferedImage> params, ColorTransforms.ColorTransform transform, Function<PathObject,ROI> roiFunction)	Extract the pixels from the image using the specified transform, and applying any ROI mask.
static List<PathObject>	maskObject(ROI parentROI, PathObject child)	Apply a ROI mask to an object, ensuring that the child object's ROI does not extend beyond the mask.
static List<PathObject>	maskObjectAndSplit(ROI parentROI, PathObject child)	Apply a ROI mask to an object, ensuring that the child object's ROI does not extend beyond the mask, and splitting the child object's ROI to create multiple objects if it contains disjoint regions.

Methods inherited from class java.lang.Object

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

Constructor Details

PixelProcessorUtils

public PixelProcessorUtils()

Method Details

extractMaskedPixels

public static double[] extractMaskedPixels(Parameters<BufferedImage,BufferedImage> params,
 int channel,
 Function<PathObject,ROI> roiFunction)
                                    throws IOException

Extract the pixels from one channel of an image using the specified transform, and applying any ROI mask.

Parameters:

params - processor parameters

channel - number of the channel to extract (0-based index)

roiFunction - the function used to select a ROI from an object (generally the main ROI or nucleus), or null to use no ROI at all

Returns:

Throws:

IOException

extractMaskedPixels

public static double[] extractMaskedPixels(Parameters<BufferedImage,BufferedImage> params,
 String channelName,
 Function<PathObject,ROI> roiFunction)
                                    throws IOException

Extract the pixels from one channel of an image using the specified transform, and applying any ROI mask.

Parameters:

params - processor parameters

channelName - name of the channel to extract

roiFunction - the function used to select a ROI from an object (generally the main ROI or nucleus), or null to use no ROI at all

Returns:

Throws:

IOException

extractMaskedPixels

public static double[] extractMaskedPixels(Parameters<BufferedImage,BufferedImage> params,
 ColorTransforms.ColorTransform transform,
 Function<PathObject,ROI> roiFunction)
                                    throws IOException

Extract the pixels from the image using the specified transform, and applying any ROI mask.

Parameters:

params - processor parameters

transform - transform to extract single-channel pixels

roiFunction - the function used to select a ROI from an object (generally the main ROI or nucleus), or null to use no ROI at all

Returns:

Throws:

IOException

maskObject

public static List<PathObject> maskObject(ROI parentROI,
 PathObject child)

Apply a ROI mask to an object, ensuring that the child object's ROI does not extend beyond the mask.

Parameters:

parentROI -

child -

Returns:

either an empty or singleton list, depending upon whether the child object has a non-empty ROI after the masking is applied

maskObjectAndSplit

public static List<PathObject> maskObjectAndSplit(ROI parentROI,
 PathObject child)

Apply a ROI mask to an object, ensuring that the child object's ROI does not extend beyond the mask, and splitting the child object's ROI to create multiple objects if it contains disjoint regions.

Parameters:

parentROI -

child -

Returns:

a list of objects, either empty or containing one or more objects

containsCentroid

public static boolean containsCentroid(ROI roi,
 PathObject child)

Check whether a child object's centroid is contained within a ROI.

Parameters:

roi -

child -

Returns: