Related to https://github.com/openmicroscopy/bioformats/issues/2763

czi.py

#@UIService uiService
#@LogService log

# read in and display ImagePlus object(s)
from loci.plugins import BF
from loci.common import Region
from loci.plugins.in import ImporterOptions
from loci.plugins.util import LociPrefs
from ij import Prefs
from loci.formats import ImageReader
from loci.formats import MetadataTools
from ij import IJ
from ome.units import UNITS
# ZEISS STUFF
from loci.formats.in import ZeissCZIReader
from loci.formats.in import DynamicMetadataOptions

def getImageSeries(imps, series):
    imp = imps[series]
    # get the stack
    imgstack = imp.getImageStack()
    slices = imgstack.getSize()
    width = imgstack.getWidth()
    height = imgstack.getHeight()
    log.info("Show Series #        : " + str(series))
    log.info("ImgStack.getSize()   : " + str(slices))
    log.info("ImgStack.getWidth()  : " + str(width))
    log.info("ImgStack.getHeight() : " + str(height))

    return imp


def getCZIinfo(imagefile,
               showimage=False,
               setflatres=False,
               setreslevel=0,
               openallseries=True,
               showomexml=False,
               stitchtiles=False,
               setconcat=False):

    CZIinfo = {}
    options = DynamicMetadataOptions()
    options.setBoolean("zeissczi.autostitch", stitchtiles)
    options.setBoolean("zeissczi.attachments", False)
    czireader = ZeissCZIReader()
    czireader.setFlattenedResolutions(setflatres)
    czireader.setMetadataOptions(options)
    czireader.setId(imagefile)
    #czireader.setResolution(setreslevel)
    CZIinfo['rescount'] = czireader.getResolutionCount()
    CZIinfo['seriesCount'] = czireader.getSeriesCount()
    CZIinfo['flatres'] = czireader.hasFlattenedResolutions()
    CZIinfo['getreslevel'] = czireader.getResolution()
    # Dimensions
    CZIinfo['SizeT'] = czireader.getSizeT()
    CZIinfo['SizeZ'] = czireader.getSizeZ()
    CZIinfo['SizeC'] = czireader.getSizeC()
    CZIinfo['SizeX'] = czireader.getSizeX()
    CZIinfo['SizeY'] = czireader.getSizeX()
    # check for autostitching and possibility to read attchmenst
    CZIinfo['AllowAutoStitching'] = czireader.allowAutostitching()
    CZIinfo['CanReadAttachments'] = czireader.canReadAttachments()

    # get OME data
    omeMeta = MetadataTools.createOMEXMLMetadata()
    CZIinfo['imageCount_OME'] = omeMeta.getImageCount()

    log.info("Current Image File : " + imagefile)
    log.info("Get Resolution Count    : " + str(CZIinfo['rescount']))
    log.info("Get Resolution Level    : " + str(CZIinfo['getreslevel']))
    log.info("hasFlattenedResolution  : " + str(CZIinfo['flatres']))
    log.info("# of Series (CZIReader) : " + str(CZIinfo['seriesCount']))
    log.info("# of Images (OMEMeta)   : " + str(CZIinfo['imageCount_OME']))
    log.info("SizeT   : " + str(CZIinfo['SizeT']))
    log.info("SizeZ   : " + str(CZIinfo['SizeZ']))
    log.info("SizeC   : " + str(CZIinfo['SizeC']))
    log.info("SizeX   : " + str(CZIinfo['SizeX']))
    log.info("SizeY   : " + str(CZIinfo['SizeY']))
    log.info("AllowAutoStitching : " + str(CZIinfo['AllowAutoStitching']))
    log.info("CanReadAttachments : " + str(CZIinfo['CanReadAttachments']))

    # Set the preferences in the ImageJ plugin
    Prefs.set("bioformats.zeissczi.allow.autostitch",  str(stitchtiles).lower())
    Prefs.set("bioformats.zeissczi.include.attachments", str(True).lower())

    if showimage:

        # read in and display ImagePlus(es) with arguments
        options = ImporterOptions()
        options.setOpenAllSeries(openallseries)
        options.setShowOMEXML(showomexml)
        options.setConcatenate(setconcat)
        options.setId(imagefile)

        log.info("setOpenAllSeries   : " + str(openallseries))
        log.info("setShowOMEXML      : " + str(showomexml))
        log.info("setConcatenate     : " + str(setconcat))

        # open the ImgPlus
        imps = BF.openImagePlus(options)
        
        for series in range(0, CZIinfo['seriesCount']):
            imp = getImageSeries(imps, series)
            imp.show()

    czireader.close()

    return CZIinfo


# clear the console automatically when not in headless mode
uiService.getDefaultUI().getConsolePane().clear()

# define testfile
imagefile = r'/tmp/OverViewScan.czi'
#imagefile = r'c:\Users\m1srh\Documents\Testdata_Zeiss\Castor\EMBL\96well\testwell96_woatt.czi'

info = getCZIinfo(imagefile,
                  showimage=True,
                  setflatres=False,
                  setreslevel=0,
                  openallseries=True,
                  showomexml=False,
                  stitchtiles=False,
                  setconcat=False)

#for x in info.keys():
#    print str(x) +" => " + str(info[x])

Hi,
I have tried to use your code with my own axioscan data, but I still end up not getting the files I need. As you mentioned : "Bio-Formats ImageJ API (BF.openImagePlus) only supports flattened resolutions", which means that even if I can get the series count with the setFlattenedResolutions=False it will simply open the files that correspond to the 0-series count limit of the flattened list not the actual unflattened one.
I was using a macro in imagej that was skipping the in between lower levels of the pyramid, but that only works if the number of levels is consistent between each series and between slides. Do you by chance have any input on how I could solve this problem? If I could find a way to get the number of levels for each series I could use that to loop through and grab only the ones I need, but I could not find a function that would report that.
Thanks, Brigida