FijiScriptHelloWorld.imjoy.html

<docs>
A hello world example for running fiji script in ImJoy.
</docs>

<config lang="json">
{
  "name": "FijiScriptHelloWorld",
  "type": "scijava",
  "tags": [],
  "ui": "",
  "version": "0.1.0",
  "cover": "",
  "description": "A hello world example for running fiji script in ImJoy.",
  "icon": "extension",
  "inputs": null,
  "outputs": null,
  "api_version": "0.1.8",
  "env": "",
  "permissions": [],
  "requirements": [],
  "dependencies": ["https://gist.githubusercontent.com/oeway/157b970d2ab993084a2ac650197c077c/raw/SciJavaEngine.imjoy.html"]
}
</config>

<script lang="ijm">
 
#@ String name
#@ int age
#@ String city
#@output Object greeting
greeting = "Hi " + name + ". You are " + age + " years old, and live in " + city + "."

</script>

SciJavaEngine.imjoy.html

<docs lang="markdown">
## SciJava Engine

Support running scijava/Fiji/ImageJ scripts as a plugin

</docs>

<config lang="json">
{
    "name": "SciJava Engine",
    "type": "native-python",
    "version": "0.1.7",
    "api_version": "0.1.2",
    "description": "Support running SciJava/Fiji/ImageJ scripts as a plugin",
    "tags": [],
    "ui": "",
    "inputs": null,
    "outputs": null,
    "flags": ["engine"],
    "icon": "extension",
    "env": ["conda create -n imagej", {"type": "binder", "spec": "oeway/pyimagej-binder-image/master", "skip_requirements": true}],
    "requirements": ["conda: openjdk=8", "conda: -c conda-forge pyimagej", "pip: scikit-image pillow"],
    "dependencies": [],
    "runnable": false
}
</config>

<script lang="python">
from imjoy import api
import imagej
import numpy as np
import skimage
from skimage import io
import numpy as np
from PIL import Image
import base64
from io import BytesIO
ij = imagej.init('sc.fiji:fiji:2.0.0-pre-10')

from jnius import autoclass
ScriptInfo = autoclass('org.scijava.script.ScriptInfo')
StringReader = autoclass('java.io.StringReader')


def get_module_info(custom_script, name=None):
    name = name or "scijava_script"
    moduleinfo = ScriptInfo(ij.getContext(), name, StringReader(custom_script))
    inputs = []
    outputs = []
    
    for inp in ij.py.from_java(moduleinfo.inputs()):
        input_type = inp.getType().getName()
        input_name = inp.getName()
        print(input_type, input_name)
        inputs.append({"name": input_name, "type": input_type})

    for outp in ij.py.from_java(moduleinfo.outputs()):
        output_type = outp.getType().getName()
        output_name = outp.getName()
        outputs.append({"name": output_name, "type": output_type})

    return {'id': moduleinfo.getIdentifier(), "outputs": outputs, "inputs": inputs }

def connect():
    return True

def disconnect():
    pass

def heartbeat():
    return True

SchemaIOTypeMapping = {
    "boolean": "checkbox",
    "byte": "number",
    "short": "number",
    "int": "number",
    "long": "number",
    "char": "text",
    "java.lang.Boolean": "checkbox",
    "java.lang.Byte": "number",
    "java.lang.Short": "number",
    "java.lang.Int": "number",
    "java.lang.Long": "number",
    "java.lang.Float": "number",
    "java.lang.String": "text",
    "java.lang.Character": "text",
    # TODO: BigInteger | BigDecimal
    # TODO: Dataset | ImagePlus	(>=2 images) triggers a dropdown list	
    # TODO: ColorRGB	color chooser	
    # TODO: Date	date chooser	
    # TODO: File	file chooser
}

async def start_plugin(config, imjoy_interface, engine_utils):
    script = config["scripts"][0]["content"]
    language_extension = config["scripts"][0]["attrs"]["lang"]
    module_info = get_module_info(script)
    def setup():
        api.showMessage('Plugin initialized: ' + config['name'])

    async def run(ctx):
        # args = {}
        fields = []
        for inp in module_info['inputs']:
            widget_type = SchemaIOTypeMapping[inp["type"]]
            if widget_type in ['text', 'number']:
                fields.append({"type": "input", "inputType": widget_type, "label": inp["name"], "model": inp["name"]})
            else:
                fields.append({"type": widget_type, "label": inp["name"], "model": inp["name"]})
            # args[inp['name']] = await api.prompt("What is your " + inp["name"] + "("+ inp["type"] + ")")
        
        dialog = await api.showDialog({
            "type": 'imjoy/schema-io',
            "name": config["name"],
            "data": {
                "id": 0,
                "type": 'form',
                "schema": {
                    "fields": fields
                },
                "data": {},
                "options": {
                    "validateAfterLoad": True,
                    "validateAfterChanged": True
                },
                "description": "",
                "buttons": [{"label": 'Run', "event_id": 'run', "class": 'md-primary md-raised'}]
            }
        })

        def run_script(args):
            dialog.close()
            output_name = module_info['outputs'][0]['name']
            result = ij.py.run_script(language_extension, script, args).getOutput(output_name)
            api.alert(result)
    
        dialog.on('run', run_script)

    return {"_rintf": True, "setup": setup, "run": run}

async def setup():
    await api.register({
        "_rintf": True,
        "type": "engine",
        "pluginType": "scijava",
        "icon": "🚀",
        "name": 'scijava',
        "url": 'imagej.net',
        "connect": connect,
        "disconnect": disconnect,
        "startPlugin": start_plugin,
        "heartbeat": heartbeat
    })
    
api.export({"setup": setup})
</script>