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| ## Scripting MoBIE Project Creator | ||
| ## Scripting the Java MoBIE Project Creator | ||
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| For datasets with many images, it may be more convenient to use the project | ||
| creator via a script. Here we provide a few examples for using groovy scripting | ||
| within Fiji (this can also be adapted for the other scripting languages within | ||
| Fiji). | ||
| One can create MoBIE projects using Java / Groovy. | ||
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| ### Script editor | ||
| Please note that we also support [creating MoBIE projects in python](https://github.com/mobie/mobie-utils-python?tab=readme-ov-file#mobie-utils-python). | ||
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| In Fiji, click File > New > Script, to open the script editor. Then, in the | ||
| menu at the top of the editor, select Language > Groovy. | ||
| Here are links to example Java / Groovy code: | ||
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| ### Creating a simple project | ||
| Here, we create a project folder, and add a dataset and image: | ||
| - [Create a simple MoBIE project in Java](https://github.com/mobie/mobie-viewer-fiji/blob/main/src/test/java/examples/CreateMoBIEProject.java) | ||
| - [Create a simple MoBIE project in Groovy](https://github.com/mobie/mobie-viewer-fiji/blob/main/src/test/java/examples/CreateMoBIEProject.groovy) | ||
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| ``` | ||
| import ij.IJ; | ||
| import org.embl.mobie.io.ImageDataFormat; | ||
| import org.embl.mobie.viewer.command.OpenMoBIEProjectCommand; | ||
| import org.embl.mobie.viewer.projectcreator.ProjectCreator; | ||
| projectFolder = new File("C:\\Users\\meechan\\Documents\\temp\\test_project") | ||
| dataDirectory = new File(projectFolder, "data"); | ||
| dataDirectory.mkdirs(); | ||
| try { | ||
| projectCreator = new ProjectCreator(dataDirectory); | ||
| // create a 3D dataset called 'testDataset' | ||
| projectCreator.getDatasetsCreator().addDataset("testDataset", false); | ||
| // open an example image to add to project | ||
| currentImage = IJ.openImage("http://imagej.nih.gov/ij/images/mri-stack.zip"); | ||
| // add image to dataset "testDataset" in project with name "testImage" | ||
| projectCreator.getImagesCreator().addImage( currentImage, "testImage", "testDataset", | ||
| ImageDataFormat.BdvN5, ProjectCreator.ImageType.image, | ||
| "images", true ) | ||
| // open it in MoBIE | ||
| openMoBIE = new OpenMoBIEProjectCommand(); | ||
| openMoBIE.projectLocation = projectCreator.getDataLocation().getAbsolutePath(); | ||
| openMoBIE.run(); | ||
| } catch (IOException e) { | ||
| e.printStackTrace(); | ||
| } | ||
| ``` | ||
|
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| ### Datasets | ||
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| You can create a new empty dataset, with a specific name like so: | ||
| ``` | ||
| datasetName = "testDataset" | ||
| is2D = false | ||
| projectCreator.getDatasetsCreator().addDataset( datasetName, is2D ); | ||
| ``` | ||
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| You can rename a dataset like so: | ||
| ``` | ||
| oldName = "testDataset" | ||
| newName = "newDataset" | ||
| // rename 'testDataset' to 'newDataset' | ||
| projectCreator.getDatasetsCreator().renameDataset( oldName, newName ); | ||
| ``` | ||
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| You can set which dataset is shown by default in MoBIE like so: | ||
| ``` | ||
| datasetName = "testDataset" | ||
| projectCreator.getDatasetsCreator().makeDefaultDataset ( datasetName ); | ||
| ``` | ||
|
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| ### Adding ImagePlus images | ||
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| The main function to add images + segmentations is this one: | ||
| ``` | ||
| currentImage = IJ.openImage("http://imagej.nih.gov/ij/images/mri-stack.zip") | ||
| imageName = "testImage" | ||
| datasetName = "testDataset" | ||
| imageFormat = ImageDataFormat.BdvN5 | ||
| imageType = ProjectCreator.ImageType.image | ||
| uiSelectionGroup = "images" | ||
| exclusive = false | ||
| // add image to project | ||
| projectCreator.getImagesCreator().addImage( currentImage, imageName, | ||
| datasetName, imageFormat, imageType, uiSelectionGroup, exclusive ) | ||
| ``` | ||
| which takes the following parameters (in order): | ||
| - image to add, as ImagePlus | ||
| - image name | ||
| - dataset name | ||
| - image format (ImageDataFormat.BdvN5 or ImageDataFormat.OmeZarr) | ||
| - image type - ProjectCreator.ImageType.image or ProjectCreator.ImageType.segmentation | ||
| - ui selection group name - i.e. name of MoBIE drop-down menu to place view in | ||
| - exclusive - Whether to make the view exclusive. | ||
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| If you want more control over the resolution levels / chunking that the | ||
| project creator uses, you can explicitly give these like so: | ||
| ``` | ||
| import org.janelia.saalfeldlab.n5.GzipCompression; | ||
| resolutions = [ [1,1,1], [2,2,2], [4,4,4] ] as int[][] | ||
| subdivisions = [ [64,64,64], [64,64,64], [64,64,64] ] as int[][] | ||
| compression = new GzipCompression() | ||
| // add image with specific resolution levels and chunks | ||
| projectCreator.getImagesCreator().addImage ( currentImage, imageName, | ||
| datasetName, imageFormat, imageType, | ||
| uiSelectionGroup, exclusive, resolutions, | ||
| subdivisions, compression ) | ||
| ``` | ||
| This takes 3 additional parameters to the function above: | ||
| - resolutions - the resolution/downsampling levels to write e.g. | ||
| the example above will write one full resolution level, | ||
| then one 2x downsampled, and one 4x downsampled. The order is {x, y, z}. | ||
| - subdivisions - Chunk size. Must have the same number of entries as 'resolutions'. | ||
| e.g. the example above will use a chunk size of (64, 64. 64) for all levels. | ||
| The order is {x, y, z}. | ||
| - compression - type of compression to use | ||
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| There are also versions of both of these functions, that allow you to specify | ||
| an affine transform for the image. Note that this will be added to the image | ||
| view, and will be added on top of the usual scaling coming from imp.getCalibration(). | ||
| ``` | ||
| import net.imglib2.realtransform.AffineTransform3D; | ||
| // create an affine transform that translates by 2 units in x, y and z | ||
| sourceTransform = new AffineTransform3D(); | ||
| sourceTransform.translate(2,2,2); | ||
| // add image to project with source transform | ||
| projectCreator.getImagesCreator().addImage( currentImage, imageName, datasetName, | ||
| imageFormat, imageType, sourceTransform, uiSelectionGroup, | ||
| exclusive ) | ||
| // add image with specific resolution levels, chunks and source transform | ||
| projectCreator.getImagesCreator().addImage ( currentImage, imageName, | ||
| datasetName, imageFormat, imageType, | ||
| sourceTransform, uiSelectionGroup, exclusive, | ||
| resolutions, subdivisions, compression ) | ||
| ``` | ||
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| ### Adding bdv format images (N5/OME-ZARR) | ||
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| If your image is already in a compatible format (N5 / OME-ZARR), then you can | ||
| also add this directly to your project e.g. for n5: | ||
| ``` | ||
| // use 'copy' add method | ||
| addMethod = ProjectCreator.AddMethod.copy | ||
| imageFormat = ImageDataFormat.BdvN5 | ||
| // copy an existing N5 image into project | ||
| projectCreator.getImagesCreator().addBdvFormatImage ( | ||
| new File("path/to/image.xml"), imageName, datasetName, | ||
| imageType, addMethod, uiSelectionGroup, imageFormat, exclusive ) | ||
| ``` | ||
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| and for ome-zarr: | ||
| ``` | ||
| // use 'copy' add method | ||
| addMethod = ProjectCreator.AddMethod.copy | ||
| imageFormat = ImageDataFormat.OmeZarr | ||
| // copy an existing OME-ZARR image into project | ||
| projectCreator.getImagesCreator().addBdvFormatImage ( | ||
| new File("path/to/image.ome.zarr"), imageName, datasetName, | ||
| imageType, addMethod, uiSelectionGroup, imageFormat, exclusive ) | ||
| ``` | ||
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| This function takes the following parameters (in order): | ||
| - image file location - for n5, location of the xml, for ome-zarr, | ||
| the location of the .ome.zarr directory. | ||
| - image name | ||
| - dataset name | ||
| - image type - ProjectCreator.ImageType.image or ProjectCreator.ImageType.segmentation | ||
| - add method - ProjectCreator.AddMethod.link (leave image as-is, and link to | ||
| this location. Only supported for N5 and local projects), | ||
| ProjectCreator.AddMethod.copy (copy image into project), or | ||
| ProjectCreator.AddMethod.move (move image into project - be careful as this | ||
| will delete the image from its original location!) | ||
| - ui selection group name - i.e. name of MoBIE drop-down menu to place view in | ||
| - image format (ImageDataFormat.BdvN5 or ImageDataFormat.OmeZarr) | ||
| - exclusive - Whether to make the view exclusive. | ||
|
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| ### Adding remote metadata | ||
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| You can generate the remote metadata for a specific image format with: | ||
| ``` | ||
| signingRegion = "us-west-2" | ||
| serviceEndpoint = "https://s3.embl.de" | ||
| bucketName = "bucketName" | ||
| imageFormat = ImageDataFormat.BdvN5S3 // for OME-ZARR use ImageDataFormat.OmeZarrS3 | ||
| projectCreator.getRemoteMetadataCreator().createRemoteMetadata( | ||
| signingRegion, serviceEndpoint, bucketName, imageFormat ) | ||
| ``` | ||
| Note that this will overwrite any existing remote metadata for the | ||
| given image format. | ||
| If you would like to see additional examples please [write on the forum](https://forum.image.sc/) and add the `mobie` tag on your post. |