org.hkijena.jipipe.plugins.cellpose.utils

Class CellposeUtils

java.lang.Object

org.hkijena.jipipe.plugins.cellpose.utils.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 CellposeModelInfo	createModelInfo(List<JIPipeTextAnnotation> textAnnotations, CellposeModelData modelData, Path workDirectory, JIPipeProgressInfo modelProgress)
static ij.ImagePlus	extractImageFromInfo(CellposeImageInfo imageInfo, Path ioPath, String basePathSuffix, boolean useBioFormats, JIPipeProgressInfo progressInfo)
static ROI2DListData	extractROIFromInfo(CellposeImageInfo imageInfo, Path ioPath)
static String	getCellposeCustomCode()
static void	runCellpose(PythonEnvironment environment, List<String> arguments, boolean suppressLogs, JIPipeProgressInfo progressInfo)
static void	saveInputImages(JIPipeInputDataSlot inputSlot, Set<Integer> inputRows, boolean enable3D, boolean enableMultiChannel, Path io2DPath, Path io3DPath, List<CellposeImageInfo> runWith2D, List<CellposeImageInfo> runWith3D, JIPipeGraphNode executingNode, 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()

cellposeROIJsonToImageJ

public static ROI2DListData cellposeROIJsonToImageJ(Path file)

Converts ROI in a custom Json format to ROI2DListData

Parameters:

file - the ROI file

Returns:

ImageJ ROI

saveInputImages

public static void saveInputImages(JIPipeInputDataSlot inputSlot,
                                   Set<Integer> inputRows,
                                   boolean enable3D,
                                   boolean enableMultiChannel,
                                   Path io2DPath,
                                   Path io3DPath,
                                   List<CellposeImageInfo> runWith2D,
                                   List<CellposeImageInfo> runWith3D,
                                   JIPipeGraphNode executingNode,
                                   JIPipeProgressInfo progressInfo)

createModelInfo

public static CellposeModelInfo createModelInfo(List<JIPipeTextAnnotation> textAnnotations,
                                                CellposeModelData modelData,
                                                Path workDirectory,
                                                JIPipeProgressInfo modelProgress)

extractImageFromInfo

public static ij.ImagePlus extractImageFromInfo(CellposeImageInfo imageInfo,
                                                Path ioPath,
                                                String basePathSuffix,
                                                boolean useBioFormats,
                                                JIPipeProgressInfo progressInfo)

extractROIFromInfo

public static ROI2DListData extractROIFromInfo(CellposeImageInfo imageInfo,
                                               Path ioPath)