ExplodeImages.py

#!/usr/bin/env python

import omero.scripts as scripts
from omero.gateway import BlitzGateway
import omero.util.script_utils as script_utils
import omero
from omero.rtypes import *
import os


def planeGen(z, c, t, pixels):
    currentPlane = pixels.getPlane(z, c, t)
    yield currentPlane


def savePlanes(images, conn, dataset, scriptParams):
    for image in images:
        pixels = image.getPrimaryPixels()
        for t in range(image.getSizeT()):
            for z in range(image.getSizeZ()):
                for c in range(image.getSizeC()):
                    i = conn.createImageFromNumpySeq(planeGen(z, c, t, pixels),
                                                     makeImageName(image, z, c, t, scriptParams), 1, 1, 1,
                                                     description=getImageDescription(image, z, c, t), dataset=dataset)


def makeImageName(image, z, c, t, scriptParams):
    if "Base_Image_Path" in scriptParams:
        name = scriptParams["Base_Image_Path"]
    else:
        originalName = image.getName()
        name = os.path.basename(originalName)

    if scriptParams["Image_Order"] == "T-Z-C":
        imgName = "%s_t%02d_z%s_c%s.tiff" % (name, t, z, c)
    elif scriptParams["Image_Order"] == "T-C-Z":
        imgName = "%s_t%02d_c%s_z%s.tiff" % (name, t, c, z)
    elif scriptParams["Image_Order"] == "Z-T-C":
        imgName = "%s_z%s_t%02d_c%s.tiff" % (name, z, t, c)
    elif scriptParams["Image_Order"] == "Z-C-T":
        imgName = "%s_z%s_c%s_t%02d.tiff" % (name, z, c, t)
    elif scriptParams["Image_Order"] == "C-Z-T":
        imgName = "%s_c%s_z%s_t%02d.tiff" % (name, c, z, t)
    elif scriptParams["Image_Order"] == "C-T-Z":
        imgName = "%s_c%s_t%02d_z%s.tiff" % (name, c, t, z)

    i = 1
    name = imgName[:-(len("tiff") + 1)]
    while os.path.exists(imgName):
        imgName = "%s_(%d).%s" % (name, i, "tiff")
        i += 1
    return imgName


def getImageDescription(image, z, c, t):
    originalName = image.getName()
    zString = "Z-Section: %s" % z
    cString = "Channel: %s" % c
    tString = "Timestamp: %s" % t

    return originalName + "\n" + tString + "\n" + zString + "\n" + cString


def runScript():
    """
    The main entry point of the script, as called by the client via the scripting service, passing the required parameters. 
    """

    orders = [rstring('T-Z-C'), rstring('T-C-Z'), rstring('Z-T-C'), rstring('Z-C-T'), rstring('C-Z-T'),
              rstring('C-T-Z')]
    dataTypes = [rstring('Dataset'), rstring('Image')]

    client = scripts.client('ExplodeImages.py',
                            'Explode multiplane/multitemporal images into multiple images, '
                            + 'split based on channels, number of planes, and timestamps.',

                            scripts.String("Data_Type", optional=False, grouping="1",
                                           description="The data you want to work with.", values=dataTypes,
                                           default="Image"),

                            scripts.List("IDs", optional=False, grouping="1.1",
                                         description="List of Dataset IDs or Image IDs").ofType(rlong(0)),

                            scripts.String("Storing_Dataset", optional=False, grouping="2",
                                           description="Name of data set to store images", default='Explode'),

                            scripts.String("Base_Image_Path", grouping="2.1", description="Base name of image."),
                            scripts.String("Image_Order", grouping="2.2",
                                           description="The order in which explosion information is displayed in"
                                                       + " the image name. (T=time, Z=depth, C=color)",
                                           values=orders, default="T-Z-C"),

                            version="1.0",
                            authors=["WebvalleyTeam 2013"],
                            institutions=["FBK"],
                            contact="webvalley@fbk.eu", )

    try:
        # process the list of args above.
        scriptParams = {}
        for key in client.getInputKeys():
            if client.getInput(key):
                scriptParams[key] = client.getInput(key, unwrap=True)

        # establish connection to omero
        conn = BlitzGateway(client_obj=client)

        #get objects
        objects, logMessage = script_utils.getObjects(conn, scriptParams)

        # gather all images
        images = []

        if (scriptParams["Data_Type"] == "Dataset"):
            for dataSet in objects:
                images.extend(list(dataSet.listChildren()))
            if not images:
                print "No images found in selected dataset."
        else:
            images = objects

        datasetObj = omero.model.DatasetI()
        datasetObj.setName(rstring(scriptParams["Storing_Dataset"]))
        datasetObj = conn.getUpdateService().saveAndReturnObject(datasetObj)

        savePlanes(images, conn, datasetObj, scriptParams)

    finally:
        client.closeSession()


if __name__ == "__main__":
    runScript()