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Incomplete attempt to fix affine transform
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@MichaelSNelson
MichaelSNelson committed Jan 26, 2024
1 parent 26a7fcb commit 7b3fdd1
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Showing 3 changed files with 125 additions and 35 deletions.
8 changes: 5 additions & 3 deletions src/main/groovy/qupath/ext/qp_scope/functions/QP_scope_GUI.groovy
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Expand Up @@ -238,8 +238,10 @@ class QP_scope_GUI {
logger.info("user adjusted position of tile at $coordinatesQP")
List currentStageCoordinates_um = UtilityFunctions.runPythonCommand(virtualEnvPath, pythonScriptPath, null)
logger.info("Obtained stage coordinates: $currentStageCoordinates_um")
transformation = TransformationFunctions.updateTransformation(transformation, coordinatesQP as List<String>, currentStageCoordinates_um)

logger.info("QuPath coordinates for selected tile: $coordinatesQP")
logger.info("affine transform before initial alignment: $transformation")
transformation = TransformationFunctions.initialTransformation(transformation, coordinatesQP as List<String>, currentStageCoordinates_um as List<String>)
logger.info("affine transform after initial alignment: $transformation")


// Handle stage alignment for top center tile
Expand Down Expand Up @@ -702,7 +704,7 @@ class QP_scope_GUI {
if (updatePosition.equals("Use adjusted position")) {
// Get access to current stage coordinates and update transformation
List currentStageCoordinates_um = UtilityFunctions.runPythonCommand(virtualEnvPath, pythonScriptPath, null)
transformation = TransformationFunctions.updateTransformation(transformation, expectedStageXYPositionMicrons as List<String>, currentStageCoordinates_um)
transformation = TransformationFunctions.initialTransformation(transformation, expectedStageXYPositionMicrons as List<String>, currentStageCoordinates_um)
}

// Prepare the results to be returned
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144 changes: 116 additions & 28 deletions src/main/groovy/qupath/ext/qp_scope/utilities/TransformationFunctions.groovy
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Expand Up @@ -6,24 +6,41 @@ import qupath.lib.gui.QuPathGUI
import qupath.lib.objects.PathObject

import java.awt.geom.AffineTransform
import java.awt.geom.NoninvertibleTransformException
import java.awt.geom.Point2D
import java.util.regex.Matcher
import java.util.regex.Pattern
import java.util.stream.Collectors

class TransformationFunctions {
static final logger = LoggerFactory.getLogger(TransformationFunctions.class)

//Convert the QuPath pixel based coordinates for a location into the MicroManager micron based stage coordinates

/**
* Transforms coordinates from the QuPath coordinate system to the microscope stage coordinate system.
* This function applies an AffineTransform to a given pair of QuPath coordinates, converting them
* into the corresponding microscope stage coordinates.
*
* @param qpCoordinates The coordinates in the QuPath coordinate system, represented as a list of Double
* where the first element is the x-coordinate and the second is the y-coordinate.
* @param transformation The AffineTransform that defines the conversion from QuPath to microscope stage coordinates.
* @return A list of Double representing the transformed coordinates in the microscope stage coordinate system,
* where the first element is the x-coordinate and the second is the y-coordinate.
*/
static List<Double> QPtoMicroscopeCoordinates(List<Double> qpCoordinates, AffineTransform transformation) {
Point2D.Double sourcePoint = new Point2D.Double(qpCoordinates[0], qpCoordinates[1])
Point2D.Double destPoint = new Point2D.Double()
logger.info("Transforming QP coordinates to microscope coordinates. Input QP Coordinates: ["
+ qpCoordinates.get(0) + ", " + qpCoordinates.get(1) + "]");

Point2D.Double sourcePoint = new Point2D.Double(qpCoordinates.get(0), qpCoordinates.get(1));
Point2D.Double destPoint = new Point2D.Double();

transformation.transform(sourcePoint, destPoint);

transformation.transform(sourcePoint, destPoint)
logger.info("Transformed Microscope Coordinates: [" + destPoint.x + ", " + destPoint.y + "]");

return [destPoint.x, destPoint.y]
return Arrays.asList(destPoint.x, destPoint.y);
}


/**
* Transforms the coordinates in TileConfiguration.txt files located in all child directories
* of a specified parent directory, using an AffineTransform. It reads each file, applies the
Expand Down Expand Up @@ -108,32 +125,103 @@ class TransformationFunctions {
* with microscope stage coordinates after scaling.
*/
//TODO adjust for situations where the macro image is flipped
static AffineTransform updateTransformation(AffineTransform transformation, List<String> coordinatesQP, List<String> coordinatesMM) {
// Convert coordinatesQP and coordinatesMM elements from String to Double
double xQP = coordinatesQP[0].toDouble()
double yQP = coordinatesQP[1].toDouble()
double xMM = coordinatesMM[0].toDouble()
double yMM = coordinatesMM[1].toDouble()

// Apply the existing transformation to the QP coordinates
Point2D.Double transformedPoint = new Point2D.Double()
transformation.transform(new Point2D.Double(xQP, yQP), transformedPoint)

// Calculate the additional translation needed
double additionalXShift = xMM - transformedPoint.x
double additionalYShift = yMM - transformedPoint.y

logger.info("Additional xShift: $additionalXShift")
logger.info("Additional yShift: $additionalYShift")

// Create a new AffineTransform that includes this additional translation
AffineTransform updatedTransformation = new AffineTransform(transformation)
updatedTransformation.translate(additionalXShift, additionalYShift)

return updatedTransformation
// static AffineTransform initialTransformation(AffineTransform transformation, List<String> coordinatesQP, List<String> coordinatesMM) {
// // Convert coordinatesQP and coordinatesMM elements from String to Double
// double xQP = coordinatesQP[0].toDouble()
// double yQP = coordinatesQP[1].toDouble()
// double xMM = coordinatesMM[0].toDouble()
// double yMM = coordinatesMM[1].toDouble()
//
// // Invert the Y-coordinate for the QP coordinates
// yQP = -yQP; // Modify this line based on which system's Y-axis you decide to invert
//
// // Apply the existing transformation to the QP coordinates
// Point2D.Double transformedPointQP = new Point2D.Double()
// transformation.transform(new Point2D.Double(xQP, yQP), transformedPointQP)
// logger.info("Initial transformation - QP point: ${transformedPointQP.x} ${transformedPointQP.y}")
//
// // Attempt to invert the transformation
// try {
// Point2D.Double stagePointInQP = new Point2D.Double(xMM, yMM)
// transformation.inverseTransform(stagePointInQP, stagePointInQP)
//
// // Calculate the additional translation needed
// double additionalXShift = stagePointInQP.x - transformedPointQP.x
// double additionalYShift = stagePointInQP.y - transformedPointQP.y
//
// logger.info("Additional xShift: $additionalXShift")
// logger.info("Additional yShift: $additionalYShift")
//
// // Create a new AffineTransform that includes this additional translation
// AffineTransform updatedTransformation = new AffineTransform(transformation)
// updatedTransformation.translate(additionalXShift, additionalYShift)
//
// // Check if the transformed QP coordinates match the MM coordinates
// Point2D.Double checkTransformedQP = new Point2D.Double(xQP, yQP)
// updatedTransformation.transform(checkTransformedQP, checkTransformedQP)
// logger.info("Transformed QP coordinates with updated transformation: ${checkTransformedQP.x}, ${checkTransformedQP.y}")
// logger.info("Expected MM coordinates: $xMM, $yMM")
// double TOLERANCE = 10
// if (Math.abs(checkTransformedQP.x - xMM) < TOLERANCE && Math.abs(checkTransformedQP.y - yMM) < TOLERANCE) {
// logger.info("Success: Transformed QP coordinates match MM coordinates within tolerance.")
// } else {
// logger.warn("Mismatch: Transformed QP coordinates do not match MM coordinates within tolerance.")
// }
//
// return updatedTransformation
//
// } catch (NoninvertibleTransformException e) {
// logger.error("Transformation is non-invertible: ", e)
// return null;
// }
// }


static AffineTransform initialTransformation(AffineTransform scalingTransform, List<String> qpCoordinatesList, List<String> stageCoordinatesList) {
// Convert input lists to List<Double>, handling both String and Double inputs
List<Double> qpCoordinates = qpCoordinatesList.stream()
.map(coordinate -> Double.parseDouble(coordinate.toString()))
.collect(Collectors.toList());
List<Double> stageCoordinates = stageCoordinatesList.stream()
.map(coordinate -> Double.parseDouble(coordinate.toString()))
.collect(Collectors.toList());

logger.info("Starting calculation of initial AffineTransform");
logger.info("Initial scaling transformation: " + scalingTransform);
logger.info("QuPath coordinates (input): " + qpCoordinates);
logger.info("Stage coordinates (target): " + stageCoordinates);

// Apply scaling and Y-axis inversion to QuPath coordinates
Point2D.Double transformedQP = new Point2D.Double(qpCoordinates.get(0) * scalingTransform.getScaleX(),
qpCoordinates.get(1) * scalingTransform.getScaleY());
logger.info("QuPath coordinates after scaling: [" + transformedQP.x + ", " + transformedQP.y + "]");

// Invert the Y-axis
transformedQP.y = -transformedQP.y;
logger.info("QuPath coordinates after Y-axis inversion: [" + transformedQP.x + ", " + transformedQP.y + "]");

// Calculate translation
double translateX = stageCoordinates.get(0) - transformedQP.x;
double translateY = stageCoordinates.get(1) - transformedQP.y;
logger.info("Calculated translation: [" + translateX + ", " + translateY + "]");

// Create a new AffineTransform with scaling, Y-axis inversion, and translation
AffineTransform newTransform = new AffineTransform(scalingTransform);
newTransform.translate(translateX, translateY);
logger.info("New AffineTransform: " + newTransform);

// Apply the new transformation to the QuPath coordinates to verify the result
Point2D.Double verifiedPoint = new Point2D.Double();
newTransform.transform(new Point2D.Double(qpCoordinates.get(0), qpCoordinates.get(1)), verifiedPoint);
logger.info("Transformed QuPath coordinates using new AffineTransform: [" + verifiedPoint.x + ", " + verifiedPoint.y + "]");
logger.info("Expected Stage coordinates: " + stageCoordinates);

return newTransform;
}



static PathObject getTopCenterTile(Collection<PathObject> detections) {
// Filter out null detections and sort by Y-coordinate
List<PathObject> sortedDetections = detections.findAll { it != null }
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8 changes: 4 additions & 4 deletions src/main/groovy/qupath/ext/qp_scope/utilities/UtilityFunctions.groovy
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Original file line number Diff line number Diff line change
Expand Up @@ -397,10 +397,10 @@ class UtilityFunctions {
//If preferences are null or missing, throw an error and close
//Open to discussion whether scan types should be included here or typed every time, or some other option
//TODO fix the installation to be a folder with an expected .py file target? Or keep as .py file target?
return [pycromanager : "C:\\ImageAnalysis\\QPExtensionTest\\qp_scope\\src\\main\\pythonScripts/4x_bf_scan_pycromanager.py",
environment : "C:\\Anaconda\\envs\\paquo",
projects : "C:\\ImageAnalysis\\QPExtensionTest\\data\\slides",
extensionPath : "C:\\ImageAnalysis\\QPExtensionTest\\qp_scope",
return [pycromanager : "C:\\Users\\lociuser\\Codes\\smart-wsi-scanner\\4x_bf_scan_pycromanager.py",
environment : "C:\\Users\\lociuser\\miniconda3\\envs\\spath",
projects : "C:\\Users\\lociuser\\Codes\\MikeN\\data\\slides",
extensionPath : "C:\\Users\\lociuser\\Codes\\MikeN\\qp_scope",
tissueDetection : "DetectTissue.groovy",
firstScanType : "4x_bf",
secondScanType : "20x_bf",
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