org.hkijena.jipipe.plugins.cellpose

Class CellposeUtils

java.lang.Object

org.hkijena.jipipe.plugins.cellpose.CellposeUtils

public class CellposeUtils
extends Object

Method Summary

Modifier and Type	Method and Description
static ROI2DListData	cellposeROIJsonToImageJ(Path file) Converts ROI in a custom Json format to ROI2DListData
static ROI2DListData	cellposeROIToImageJ(Path file) Converts a Cellpose ROI to ROI2DListData according to ...
static void	extractCellposeOutputs(JIPipeMultiIterationStep iterationStep, JIPipeProgressInfo progressInfo, Path outputRoiOutline, Path outputLabels, Path outputFlows, Path outputProbabilities, Path outputStyles, List<JIPipeTextAnnotation> annotationList, CellposeSegmentationOutputSettings_Old outputParameters)
static String	getCellposeCustomCode()
static void	runCellpose(PythonEnvironment environment, List<String> arguments, boolean suppressLogs, JIPipeProgressInfo progressInfo)

Methods inherited from class java.lang.Object

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

Method Detail

runCellpose

public static void runCellpose(PythonEnvironment environment,
                               List<String> arguments,
                               boolean suppressLogs,
                               JIPipeProgressInfo progressInfo)

getCellposeCustomCode

public static String getCellposeCustomCode()

cellposeROIToImageJ

public static ROI2DListData cellposeROIToImageJ(Path file)

Converts a Cellpose ROI to ROI2DListData according to ...

Parameters:

file - the Cellpose ROI

Returns:

ImageJ ROI

cellposeROIJsonToImageJ

public static ROI2DListData cellposeROIJsonToImageJ(Path file)

Converts ROI in a custom Json format to ROI2DListData

Parameters:

file - the ROI file

Returns:

ImageJ ROI

extractCellposeOutputs

public static void extractCellposeOutputs(JIPipeMultiIterationStep iterationStep,
                                          JIPipeProgressInfo progressInfo,
                                          Path outputRoiOutline,
                                          Path outputLabels,
                                          Path outputFlows,
                                          Path outputProbabilities,
                                          Path outputStyles,
                                          List<JIPipeTextAnnotation> annotationList,
                                          CellposeSegmentationOutputSettings_Old outputParameters)