Open xp1632 opened 10 months ago
xp1632
commented
10 months ago xp1632
commented
10 months ago Ref : https://imagej.net/libs/scijava#services
ImageJ2 encapsulates its various parts as separate “services” that provide related state functionality and track related program state.
An instance of the net.imagej.ImageJ class is nothing more than a collection of these services; this instance is referred to as the “application gateway.”
Services are defined as interfaces, with concrete implementations as plugins. This design provides seams in the right places so that behavior at every level can be customized and overridden.
xp1632
commented
10 months ago %classpath config resolver scijava.public https://maven.scijava.org/content/groups/public
%classpath add mvn sc.fiji fiji 2.0.0-pre-9
ij = new net.imagej.ImageJ()the gate way from sciJava Gateway is not steady every time.
Sometimes we need to restart the kernel and the gateway several times and wait.
I was considering to add imageJ JAR files to classpath manually as copilot suggests:
Yes, you can import the ImageJ API in other ways besides using the SciJava Gateway. One way to do this is to add the ImageJ JAR files to your classpath manually.
Here's an example code snippet that demonstrates how to add the ImageJ JAR files to your classpath in a Groovy script using the BeakerX Groovy kernel:
// Add the ImageJ JAR files to the classpath
%classpath add jar /path/to/imagej-common-<version>.jar
%classpath add jar /path/to/imagej-legacy-<version>.jar
%classpath add jar /path/to/imagej-ops-<version>.jar
%classpath add jar /path/to/imagej-tensorflow-<version>.jar
// Import the required classes
import net.imagej.ImageJ
import net.imagej.ops.OpService
import net.imagej.ops.segment.SegmentRegionCount
import net.imglib2.type.numeric.real.DoubleType
// Create an instance of ImageJ
def ij = new ImageJ()
// Get the OpService
def ops = ij.op()
// Load an input image
def input = ij.io().open("path/to/input/image.tif")
// Set the parameters for the SegmentRegionCount operation
def threshold = 0.5
def connectivity = 4
// Create an instance of the SegmentRegionCount operation
def segment = ops.segment().regionCount(input, threshold, connectivity)
// Get the output as a DoubleType
def output = ops.convert().float64(segment)
// Display the output image
ij.ui().show("Output", output)In this example, the ImageJ JAR files are added to the classpath using the %classpath add jar command, the required classes are imported, an instance of ImageJ is created, the OpService is obtained, an input image is loaded, the parameters for the SegmentRegionCount operation are set, an instance of the SegmentRegionCount operation is created, the operation is applied to the input image, the output is converted to a DoubleType, and the output image is displayed.
Note that you will need to replace /path/to/imagej-common-<version>.jar, /path/to/imagej-legacy-<version>.jar, /path/to/imagej-ops-<version>.jar, and /path/to/imagej-tensorflow-<version>.jar with the actual paths to the ImageJ JAR files on your system.
xp1632
commented
10 months ago At first we add ImageJ through remote scijava maven repo by
Only ImageJ
//load ImageJ
%classpath config resolver imagej.public https://maven.imagej.net/content/groups/public
%classpath add mvn net.imagej imagej 2.0.0-rc-71
//create ImageJ object
ij = new net.imagej.ImageJ()%classpath config resolver scijava.public https://maven.scijava.org/content/groups/public
%classpath add mvn sc.fiji fiji 2.0.0-pre-9
ij = new net.imagej.ImageJ()Thus, we use the local jar gateway instead:
%classpath add jar 'C:/Users/59803/Downloads/fiji-win64/Fiji.app/jars/*'
%classpath add jar 'C:/Users/59803/Downloads/fiji-win64/Fiji.app/jars/bio-formats/*'
%classpath add jar 'C:/Users/59803/Downloads/fiji-win64/Fiji.app/plugins/*'
// import net.imagej.Imagej;
ij = new net.imagej.ImageJ()
"ImageJ v${ij.getVersion()} is ready to go."ImageJ1 sometimes is inactive in jupyterlab's Groovy kernel
Some dependency issues that should be solved by maven
xp1632
commented
9 months ago After some testing, fiji gateway could not be stably resolved
while imageJ2 could
also the kotlin dependency issues could be caused by too high version
with version 2.0.0-rc-71, it works just fine:
with version even 2.1.0, kotlin dependency doesn't work
The ImageJ2 gateway is a Java-based API that provides a bridge between ImageJ and other image processing libraries and frameworks. The ImageJ2 gateway allows developers to use ImageJ as a front-end for other image processing libraries, such as OpenCV, ITK, and more.
The ImageJ2 gateway provides a set of classes and methods for converting between ImageJ data structures and other image processing libraries, as well as for registering and executing algorithms from those libraries within the ImageJ framework. The gateway also provides a set of tools for working with metadata, such as image dimensions, pixel sizes, and calibration information, which can be important for integrating data from different sources.
The ImageJ2 gateway is designed to be flexible and extensible, and provides a framework for building custom image processing workflows and applications that combine the strengths of ImageJ with other image processing libraries. The gateway is open source and freely available, and is widely used in scientific research and industry for a variety of image processing tasks.
Note that the ImageJ2 gateway is part of the ImageJ2 project, which is a major update to the original ImageJ software. ImageJ2 is designed to be more modular, extensible, and scalable than the original ImageJ, and provides a wide range of new features and capabilities for working with images and performing image processing tasks.