createImageFromNumpySeq in OMERO Python Blitz Gateway, updated to work in the non-default group (adding self.SERVICE_OPTS to all server calls)

createImageFromNumpySeq.py

    def createImageFromNumpySeq (self, zctPlanes, imageName, sizeZ=1, sizeC=1, sizeT=1, description=None, dataset=None):
        """
        Creates a new multi-dimensional image from the sequence of 2D numpy arrays in zctPlanes.
        zctPlanes should be a generator of numpy 2D arrays of shape (sizeY, sizeX) ordered
        to iterate through T first, then C then Z.
        Example usage:
        original = conn.getObject("Image", 1)
        sizeZ = original.getSizeZ()
        sizeC = original.getSizeC()
        sizeT = original.getSizeT()
        zctList = []
        for z in range(sizeZ):
            for c in range(sizeC):
                for t in range(sizeT):
                    zctList.append( (z,c,t) )
        def planeGen():
            planes = original.getPrimaryPixels().getPlanes(zctList)
            for p in planes:
                # perform some manipulation on each plane
                yield p
        createImageFromNumpySeq (planeGen(), imageName, sizeZ=sizeZ, sizeC=sizeC, sizeT=sizeT

        @param session          An OMERO service factory or equivalent with getQueryService() etc.
        @param zctPlanes        A generator of numpy 2D arrays, corresponding to Z-planes of new image.
        @param imageName        Name of new image
        @param description      Description for the new image
        @param dataset          If specified, put the image in this dataset. omero.model.Dataset object

        @return The new OMERO image: omero.model.ImageI
        """
        queryService = self.getQueryService()
        pixelsService = self.getPixelsService()
        rawPixelsStore = self.c.sf.createRawPixelsStore()    # Make sure we don't get an existing rpStore
        #renderingEngine = self.createRenderingEngine()
        containerService = self.getContainerService()
        updateService = self.getUpdateService()

        def createImage(firstPlane):
            """ Create our new Image once we have the first plane in hand """
            # need to map numpy pixel types to omero - don't handle: bool_, character, int_, int64, object_
            pTypes = {'int8':'int8', 'int16':'int16', 'uint16':'uint16', 'int32':'int32', 'float_':'float', 'float8':'float', 
                        'float16':'float', 'float32':'float', 'float64':'double', 'complex_':'complex', 'complex64':'complex'}
            dType = firstPlane.dtype.name
            if dType not in pTypes: # try to look up any not named above
                pType = dType
            else:
                pType = pTypes[dType]
            pixelsType = queryService.findByQuery("from PixelsType as p where p.value='%s'" % pType, None) # omero::model::PixelsType
            if pixelsType is None:
                raise Exception("Cannot create an image in omero from numpy array with dtype: %s" % dType)
            sizeY, sizeX = firstPlane.shape
            channelList = range(1, sizeC+1)
            iId = pixelsService.createImage(sizeX, sizeY, sizeZ, sizeT, channelList, pixelsType, imageName, description, self.SERVICE_OPTS)
            imageId = iId.getValue()
            return containerService.getImages("Image", [imageId], None, self.SERVICE_OPTS)[0]

        def uploadPlane(plane, z, c, t):
            byteSwappedPlane = plane.byteswap();
            convertedPlane = byteSwappedPlane.tostring();
            rawPixelsStore.setPlane(convertedPlane, z, c, t, self.SERVICE_OPTS)

        image = None
        channelsMinMax = []
        exc = None
        try:
            for theZ in range(sizeZ):
                for theC in range(sizeC):
                    for theT in range(sizeT):
                        plane = zctPlanes.next()
                        if image == None:   # use the first plane to create image.
                            image = createImage(plane)
                            print "new image group:", image.details.group.id.val
                            pixelsId = image.getPrimaryPixels().getId().getValue()
                            rawPixelsStore.setPixelsId(pixelsId, True, self.SERVICE_OPTS)
                        uploadPlane(plane, theZ, theC, theT)
                        # init or update min and max for this channel
                        minValue = plane.min()
                        maxValue = plane.max()
                        if len(channelsMinMax) < (theC +1):     # first plane of each channel
                            channelsMinMax.append( [minValue, maxValue] )
                        else:
                            channelsMinMax[theC][0] = min(channelsMinMax[theC][0], minValue)
                            channelsMinMax[theC][1] = max(channelsMinMax[theC][1], maxValue)
        except Exception, e:
            logger.error("Failed to setPlane() on rawPixelsStore while creating Image", exc_info=True)
            exc = e
        try:
            rawPixelsStore.close(self.SERVICE_OPTS)
        except Exception, e:
            logger.error("Failed to close rawPixelsStore", exc_info=True)
            if exc is None:
                 exc = e
        if exc is not None:
           raise exc

        try:    # simply completing the generator - to avoid a GeneratorExit error.
            zctPlanes.next()
        except StopIteration:
            pass

        for theC, mm in enumerate(channelsMinMax):
            pixelsService.setChannelGlobalMinMax(pixelsId, theC, float(mm[0]), float(mm[1]), self.SERVICE_OPTS)
            #resetRenderingSettings(renderingEngine, pixelsId, theC, mm[0], mm[1])

        # put the image in dataset, if specified.
        if dataset:
            link = omero.model.DatasetImageLinkI()
            link.parent = omero.model.DatasetI(dataset.getId(), False)
            link.child = omero.model.ImageI(image.id.val, False)
            updateService.saveObject(link, self.SERVICE_OPTS)

        return ImageWrapper(self, image)