update project creator javadoc

src/main/java/org/embl/mobie/lib/create/DatasetJsonCreator.java

@@ -54,20 +54,46 @@
 
 import static org.embl.mobie.lib.create.ProjectCreatorHelper.imageFormatToFolderName;
 
+/**
+ * Class to create and modify the metadata stored in dataset Json files
+ */
 public class DatasetJsonCreator {
 
     ProjectCreator projectCreator;
 
+    /**
+     * Make a datasetJsonCreator - includes all functions for creating and modifying metadata
+     * stored in dataset Json files
+     * @param projectCreator projectCreator
+     */
     public DatasetJsonCreator( ProjectCreator projectCreator ) {
         this.projectCreator = projectCreator;
     }
 
+    /**
+     * Create dataset Json for new dataset
+     * @param datasetName dataset name
+     * @param is2D whether dataset only contains 2D images
+     */
     public void addDataset( String datasetName, boolean is2D ) {
         Dataset dataset = new Dataset();
         dataset.is2D( is2D );
         writeDatasetJson( datasetName, dataset );
     }
 
+    /**
+     * Add named image to dataset Json (including a view with the image name and sensible defaults)
+     * @param imageName image name
+     * @param datasetName dataset name
+     * @param uiSelectionGroup name of ui selection group to add image view to i.e. the name of the MoBIE dropdown
+     *                         menu it will appear in
+     * @param imageDataFormat image data format
+     * @param contrastLimits contrast limits for image view
+     * @param colour colour for image view
+     * @param exclusive whether the image view is exclusive or not i.e. when viewed, does it first remove all current
+     *                  images from the viewer?
+     * @param sourceTransform affine transform of image view
+     */
     public void addImage(String imageName, String datasetName,
                          String uiSelectionGroup,
                          ImageDataFormat imageDataFormat, double[] contrastLimits, String colour, boolean exclusive, AffineTransform3D sourceTransform ) {
@@ -87,6 +113,17 @@ public void addImage(String imageName, String datasetName,
         writeDatasetJson( datasetName, dataset );
     }
 
+    /**
+     * Add named segmentation to dataset Json (including a view with the segmentation name and sensible defaults)
+     * @param imageName segmentation name
+     * @param datasetName dataset name
+     * @param uiSelectionGroup name of ui selection group to add segmentation view to i.e. the name of the MoBIE
+     *                         dropdown menu it will appear in
+     * @param imageDataFormat segmentation image data format
+     * @param exclusive whether the segmentation view is exclusive or not i.e. when viewed, does it first
+     *                  remove all current images from the viewer?
+     * @param sourceTransform affine transform of segmentation view
+     */
     public void addSegmentation(String imageName, String datasetName, String uiSelectionGroup, ImageDataFormat imageDataFormat, boolean exclusive, AffineTransform3D sourceTransform ) {
         Dataset dataset = fetchDataset( datasetName );
 
@@ -104,6 +141,11 @@ public void addSegmentation(String imageName, String datasetName, String uiSelec
         writeDatasetJson( datasetName, dataset );
     }
 
+    /**
+     * Make named dataset 2D in the dataset Json
+     * @param datasetName dataset name
+     * @param is2D whether dataset only contains 2D images
+     */
     public void makeDataset2D( String datasetName, boolean is2D ) {
         Dataset dataset = projectCreator.getDataset( datasetName );
         dataset.is2D( is2D );
@@ -222,6 +264,11 @@ private View createSegmentationView( String imageName, String uiSelectionGroup,
         }
     }
 
+    /**
+     * Write the provided dataset to a dataset Json file
+     * @param datasetName dataset name
+     * @param dataset dataset
+     */
     public void writeDatasetJson ( String datasetName, Dataset dataset ) {
         try {
             String datasetJsonPath = IOHelper.combinePath( projectCreator.getProjectLocation().getAbsolutePath(),

src/main/java/org/embl/mobie/lib/create/DatasetsCreator.java

@@ -34,6 +34,9 @@
 import java.io.File;
 import java.util.List;
 
+/**
+ * Class to create and modify MoBIE datasets
+ */
 public class DatasetsCreator {
 
     static { net.imagej.patcher.LegacyInjector.preinit(); }

src/main/java/org/embl/mobie/lib/create/ImagesCreator.java

@@ -82,12 +82,19 @@
 import static org.embl.mobie.lib.create.ProjectCreatorHelper.isImageValid;
 import static org.embl.mobie.lib.create.ProjectCreatorHelper.isSpimData2D;
 
+/**
+ * Class to add images and segmentations to MoBIE projects in the correct file formats
+ */
 public class ImagesCreator {
 
     static { net.imagej.patcher.LegacyInjector.preinit(); }
 
     ProjectCreator projectCreator;
 
+    /**
+     * Make an imagesCreator - includes all functions for adding images and segmentations to MoBIE projects
+     * @param projectCreator projectCreator
+     */
     public ImagesCreator( ProjectCreator projectCreator ) {
         this.projectCreator = projectCreator;
     }
@@ -125,32 +132,129 @@ private String getDefaultTablePath( String datasetName, String imageName ) {
         return IOHelper.combinePath( getDefaultTableDirPath(datasetName, imageName), "default.tsv" );
     }
 
+    /**
+     * Check if named image exists within dataset
+     * @param datasetName dataset name
+     * @param imageName image name
+     * @param imageDataFormat image data format - ImageDataFormat.BdvN5 or ImageDataFormat.OmeZarr
+     * @return whether the image exists or not
+     */
     public boolean imageExists( String datasetName, String imageName, ImageDataFormat imageDataFormat ) {
         // either xml file path or zarr file path depending on imageDataFormat
         String filePath = getDefaultLocalImagePath( datasetName, imageName, imageDataFormat );
         return new File (filePath).exists();
     }
 
+    /**
+     * Add ImagePlus image to MoBIE project. Resolutions, subdivisions and compression of converted image will be
+     * set to sensible defaults.
+     * @param imp ImagePlus image
+     * @param imageName image name
+     * @param datasetName dataset name
+     * @param imageDataFormat image data format to convert to - ImageDataFormat.BdvN5 or ImageDataFormat.OmeZarr
+     * @param imageType image type i.e. image or segmentation
+     * @param sourceTransform Affine transform of image
+     * @param uiSelectionGroup name of ui selection group to add image view to i.e. the name of the MoBIE dropdown
+     *                         menu it will appear in
+     * @throws SpimDataException
+     * @throws IOException
+     */
     public void addImage ( ImagePlus imp, String imageName, String datasetName, ImageDataFormat imageDataFormat, ProjectCreator.ImageType imageType, AffineTransform3D sourceTransform, String uiSelectionGroup ) throws SpimDataException, IOException
     {
         addImage( imp, imageName, datasetName, imageDataFormat, imageType, sourceTransform, uiSelectionGroup, false, null, null, null );
     }
 
+    /**
+     * Add ImagePlus image to MoBIE project. Resolutions, subdivisions and compression of converted image will be
+     * set to sensible defaults.
+     * @param imp ImagePlus image
+     * @param imageName image name
+     * @param datasetName dataset name
+     * @param imageDataFormat image data format to convert to - ImageDataFormat.BdvN5 or ImageDataFormat.OmeZarr
+     * @param imageType image type i.e. image or segmentation
+     * @param sourceTransform Affine transform of image
+     * @param uiSelectionGroup name of ui selection group to add image view to i.e. the name of the MoBIE dropdown
+     *                         menu it will appear in
+     * @param exclusive whether the image view is exclusive or not i.e. when viewed, does it first remove all current
+     *                  images from the viewer?
+     * @throws SpimDataException
+     * @throws IOException
+     */
     public void addImage ( ImagePlus imp, String imageName, String datasetName, ImageDataFormat imageDataFormat, ProjectCreator.ImageType imageType, AffineTransform3D sourceTransform, String uiSelectionGroup, boolean exclusive ) throws SpimDataException, IOException
     {
         addImage( imp, imageName, datasetName, imageDataFormat, imageType, sourceTransform, uiSelectionGroup, exclusive, null, null, null );
     }
 
+    /**
+     * Add ImagePlus image to MoBIE project. Resolutions, subdivisions and compression of converted image will be
+     * set to sensible defaults.
+     * @param imp ImagePlus image
+     * @param imageName image name
+     * @param datasetName dataset name
+     * @param imageDataFormat image data format to convert to - ImageDataFormat.BdvN5 or ImageDataFormat.OmeZarr
+     * @param imageType image type i.e. image or segmentation
+     * @param uiSelectionGroup name of ui selection group to add image view to i.e. the name of the MoBIE dropdown
+     *                         menu it will appear in
+     * @param exclusive whether the image view is exclusive or not i.e. when viewed, does it first remove all current
+     *                  images from the viewer?
+     * @throws SpimDataException
+     * @throws IOException
+     */
     public void addImage ( ImagePlus imp, String imageName, String datasetName, ImageDataFormat imageDataFormat, ProjectCreator.ImageType imageType, String uiSelectionGroup, boolean exclusive ) throws SpimDataException, IOException
     {
         addImage( imp, imageName, datasetName, imageDataFormat, imageType, new AffineTransform3D(), uiSelectionGroup, exclusive, null, null, null );
     }
 
+    /**
+     * Add ImagePlus image to MoBIE project. Resolutions, subdivisions and compression of converted image must be
+     * provided directly.
+     * @param imp ImagePlus image
+     * @param imageName image name
+     * @param datasetName dataset name
+     * @param imageDataFormat image data format to convert to - ImageDataFormat.BdvN5 or ImageDataFormat.OmeZarr
+     * @param imageType image type i.e. image or segmentation
+     * @param uiSelectionGroup name of ui selection group to add image view to i.e. the name of the MoBIE dropdown
+     *                         menu it will appear in
+     * @param exclusive whether the image view is exclusive or not i.e. when viewed, does it first remove all current
+     *                  images from the viewer?
+     * @param resolutions Resolution levels to use for converted image e.g. [ [1,1,1], [2,2,2], [4,4,4] ] will
+     *                    write one full resolution level, then one 2x downsampled, and one 4x downsampled.
+     *                    The order is [x, y, z].
+     * @param subdivisions Subdivisions/chunk size to use for converted image. This must have the same number of
+     *                    entries as 'resolutions'. e.g. [ [64,64,64], [64,64,64], [64,64,64] ] will use a chunk size
+     *                    of (64, 64, 64) for all levels. The order is [x, y, z].
+     * @param compression Type of compression to use for converted image.
+     * @throws SpimDataException
+     * @throws IOException
+     */
     public void addImage ( ImagePlus imp, String imageName, String datasetName, ImageDataFormat imageDataFormat, ProjectCreator.ImageType imageType, String uiSelectionGroup, boolean exclusive, int[][] resolutions, int[][] subdivisions, Compression compression ) throws SpimDataException, IOException
     {
         addImage( imp, imageName, datasetName, imageDataFormat, imageType, new AffineTransform3D(), uiSelectionGroup, exclusive, resolutions, subdivisions, compression );
     }
 
+    /**
+     * Add ImagePlus image to MoBIE project. Resolutions, subdivisions and compression of converted image must be
+     * provided directly.
+     * @param imp ImagePlus image
+     * @param imageName image name
+     * @param datasetName dataset name
+     * @param imageDataFormat image data format to convert to - ImageDataFormat.BdvN5 or ImageDataFormat.OmeZarr
+     * @param imageType image type i.e. image or segmentation
+     * @param sourceTransform Affine transform of image
+     * @param uiSelectionGroup name of ui selection group to add image view to i.e. the name of the MoBIE dropdown
+     *                         menu it will appear in
+     * @param exclusive whether the image view is exclusive or not i.e. when viewed, does it first remove all current
+     *                  images from the viewer?
+     * @param resolutions Resolution levels to use for converted image e.g. [ [1,1,1], [2,2,2], [4,4,4] ] will
+     *                    write one full resolution level, then one 2x downsampled, and one 4x downsampled.
+     *                    The order is [x, y, z].
+     * @param subdivisions Subdivisions/chunk size to use for converted image. This must have the same number of
+     *                     entries as 'resolutions'. e.g. [ [64,64,64], [64,64,64], [64,64,64] ] will use a chunk size
+     *                     of (64, 64, 64) for all levels. The order is [x, y, z].
+     * @param compression Type of compression to use for converted image.
+     * @throws IOException
+     * @throws SpimDataException
+     */
     public void addImage( ImagePlus imp, String imageName, String datasetName, ImageDataFormat imageDataFormat, ProjectCreator.ImageType imageType, AffineTransform3D sourceTransform, String uiSelectionGroup, boolean exclusive, int[][] resolutions, int[][] subdivisions, Compression compression ) throws IOException, SpimDataException
     {
         // either xml file path or zarr file path depending on imageDataFormat
@@ -310,6 +414,25 @@ private void deleteImageFiles( String datasetName, String imageName, ImageDataFo
         }
     }
 
+    /**
+     * Add BigDataViewer (Bdv) format image to MoBIE project e.g. one already in n5/ome-zarr.
+     * @param fileLocation image file location - for n5, location of the xml, for ome-zarr,
+     *                     location of the .ome.zarr directory.
+     * @param imageName image name
+     * @param datasetName dataset name
+     * @param imageType image type i.e. image or segmentation
+     * @param addMethod link, copy or move the image - link (leave image as-is, and link to this location. Only
+     *                  supported for N5 and local projects), copy (copy image into project),
+     *                  or move (move image into project - be careful as this will delete the image
+     *                  from its original location!)
+     * @param uiSelectionGroup name of ui selection group to add image view to i.e. the name of the MoBIE dropdown
+     *                         menu it will appear in
+     * @param imageDataFormat  image data format of image - ImageDataFormat.BdvN5 or ImageDataFormat.OmeZarr
+     * @param exclusive whether the image view is exclusive or not i.e. when viewed, does it first remove all current
+     *                  images from the viewer?
+     * @throws SpimDataException
+     * @throws IOException
+     */
     public void addBdvFormatImage ( File fileLocation, String imageName, String datasetName, ProjectCreator.ImageType imageType, ProjectCreator.AddMethod addMethod, String uiSelectionGroup, ImageDataFormat imageDataFormat, boolean exclusive ) throws SpimDataException, IOException {
 
         if ( fileLocation.exists() ) {
@@ -321,6 +444,24 @@ public void addBdvFormatImage ( File fileLocation, String imageName, String data
         }
     }
 
+    /**
+     * Add BigDataViewer (Bdv) format image to MoBIE project e.g. one already in n5/ome-zarr.
+     * @param spimData spim data object for image
+     * @param imageName image name
+     * @param datasetName dataset name
+     * @param imageType image type i.e. image or segmentation
+     * @param addMethod link, copy or move the image - link (leave image as-is, and link to this location. Only
+     *                  supported for N5 and local projects), copy (copy image into project),
+     *                  or move (move image into project - be careful as this will delete the image
+     *                  from its original location!)
+     * @param uiSelectionGroup name of ui selection group to add image view to i.e. the name of the MoBIE dropdown
+     *                         menu it will appear in
+     * @param imageDataFormat image data format of image - ImageDataFormat.BdvN5 or ImageDataFormat.OmeZarr
+     * @param exclusive whether the image view is exclusive or not i.e. when viewed, does it first remove all current
+     *                  images from the viewer?
+     * @throws SpimDataException
+     * @throws IOException
+     */
     public void addBdvFormatImage ( SpimData spimData, String imageName, String datasetName,
 									ProjectCreator.ImageType imageType, ProjectCreator.AddMethod addMethod, String uiSelectionGroup, ImageDataFormat imageDataFormat, boolean exclusive ) throws SpimDataException, IOException {
 

src/main/java/org/embl/mobie/lib/create/ProjectCreator.java

@@ -49,6 +49,9 @@
 
 import static org.embl.mobie.lib.create.ProjectCreatorHelper.getGroupToViewsMap;
 
+/**
+ * Class to create and edit MoBIE projects.
+ */
 public class ProjectCreator {
 
     static { LegacyInjector.preinit(); }
@@ -80,6 +83,12 @@ public enum AddMethod {
         move
     }
 
+    /**
+     * Make a projectCreator - main entry point to create + edit MoBIE projects.
+     * This will create the project directory (if it doesn't exist).
+     * @param projectLocation Filepath of project directory
+     * @throws IOException
+     */
     public ProjectCreator( File projectLocation ) throws IOException {
         this.projectLocation = projectLocation;
         if ( ! projectLocation.exists() )
@@ -114,6 +123,10 @@ public Project getProject() {
 
     public File getProjectJson() { return projectJson; }
 
+    /**
+     * Reload project by directly reading the project json
+     * @throws IOException
+     */
     public void reloadProject() throws IOException {
         this.project = new ProjectJsonParser().parseProject( projectJson.getAbsolutePath() );
     }
@@ -139,6 +152,11 @@ public Dataset getDataset( String datasetName ) {
         }
     }
 
+    /**
+     * Get all ui selection groups (i.e. MoBIE dropdown menu names) used by views in the named dataset
+     * @param datasetName dataset name
+     * @return array of ui selection group names
+     */
     public String[] getGroups( String datasetName ) {
         if ( !datasetName.equals(currentDatasetName) ) {
             getDataset( datasetName );
@@ -152,6 +170,12 @@ public String[] getGroups( String datasetName ) {
         return groups;
     }
 
+    /**
+     * Get all view names within the given dataset and ui selection group (i.e. MoBIE dropdown menu)
+     * @param datasetName dataset name
+     * @param uiSelectionGroup ui selection group name
+     * @return array of view names
+     */
     public String[] getViews( String datasetName, String uiSelectionGroup ) {
         if ( !datasetName.equals(currentDatasetName) ) {
             getDataset( datasetName );
@@ -164,6 +188,7 @@ public String[] getViews( String datasetName, String uiSelectionGroup ) {
 
         return views;
     }
+
     public String getVoxelUnit() {
         return voxelUnit;
     }
@@ -172,6 +197,10 @@ public void setVoxelUnit(String voxelUnit) {
         this.voxelUnit = voxelUnit;
     }
 
+    /**
+     * Reload dataset by directly reading the dataset json
+     * @throws IOException
+     */
     public void reloadCurrentDataset() throws IOException {
         if ( currentDatasetName != null ) {
             this.currentDataset = new DatasetJsonParser().parseDataset(currentDatasetJson.getAbsolutePath());