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Strange error message when using LOCI reader inside script
HI guys,
I am using the LOCI reader inside a python script (latest Fiji from 20150522) and get:
ERROR loci.formats.ImageReader - *** One or more readers is misbehaving. See the debug output for more information. e.g.: loci.formats.in.APLReader@44c82053 -> java.lang.NullPointerException('null') ***
C:\Users\m1srh\Documents\Apeer_Modules\fiji_module_template_b88fae21-a305-4afb-b70b-48c18efc9fa8>docker run -it --rm -v c:\Temp\input:/input -v c:\Temp\output:/output --env-file wfe.env sebi/apeer_test_fijimodule:latest
Java HotSpot(TM) 64-Bit Server VM warning: ignoring option PermSize=128m; support was removed in 8.0
Java HotSpot(TM) 64-Bit Server VM warning: Using incremental CMS is deprecated and will likely be removed in a future release
[INFO] Overriding BIOP Run Macro...; identifier: command:ch.epfl.biop.macrorunner.B_Run_Macro; jar: file:/Fiji.app/plugins/BIOP/B_Run_Macro-1.0.0-SNAPSHOT.jar
[INFO] Overriding Get Spine From Circle Rois; identifier: command:Cirlces_Based_Spine; jar: file:/Fiji.app/plugins/Max_Inscribed_Circles-1.1.0.jar
[INFO] Image Filename : /input/cells.tif
13:19:50.336 [SciJava-563a89b5-Thread-2] ERROR loci.formats.ImageReader - *** One or more readers is misbehaving. See the debug output for more information. e.g.:
loci.formats.in.APLReader@44c82053 -> java.lang.NullPointerException('null') ***
[INFO] Apply Filter : MEDIAN
[INFO] Filter Radius : 5
[INFO] Duration of whole Processing : 2.4412176
[INFO] Saving Filtered Image .../output/cells_FILTERED.ome.tiff
[INFO] Duration of saving as OME.TIFF : 0.5278022
[INFO] Writing output JSON file ...
[INFO] Done.
So what does this mean? The output seems OK ....? Here is the script:
# @LogService log
# required import
import os
import json
from java.lang import Double, Integer
from ij import IJ, ImagePlus, ImageStack, Prefs
from ij.process import ImageProcessor, LUT
from ij.plugin.filter import RankFilters
from loci.plugins import BF
from loci.plugins.in import ImporterOptions
from loci.plugins import LociExporter
from loci.plugins.out import Exporter
from ij.io import FileSaver
import time
# helper function to apply the filetr
def getImageStack(imp):
# get the stacks
try:
stack = imp.getStack() # get the stack within the ImagePlus
nslices = stack.getSize() # get the number of slices
except:
stack = imp.getProcessor()
nslices = 1
return stack, nslices
def apply_filter(imp,
radius=5,
filtertype='MEDIAN'):
# initialize filter
filter = RankFilters()
# create filter dictionary
filterdict = {}
filterdict['MEAN'] = RankFilters.MEAN
filterdict['MIN'] = RankFilters.MIN
filterdict['MAX'] = RankFilters.MAX
filterdict['MEDIAN'] = RankFilters.MEDIAN
filterdict['VARIANCE'] = RankFilters.VARIANCE
filterdict['OPEN'] = RankFilters.OPEN
filterdict['DESPECKLE'] = RankFilters.DESPECKLE
# get the stack and number of slices
stack, nslices = getImageStack(imp)
for index in range(1, nslices + 1):
# get the image processor
ip = stack.getProcessor(index)
# apply filter based on filtertype
filter.rank(ip, radius, filterdict[filtertype])
return imp
#######################################################################
def run(imagefile, useBF=True, series=0):
log.info('Image Filename : ' + imagefile)
if not useBF:
# using IJ static method
imp = IJ.openImage(imagefile)
if useBF:
# initialize the importer options
options = ImporterOptions()
options.setOpenAllSeries(True)
options.setShowOMEXML(False)
options.setConcatenate(True)
options.setAutoscale(True)
options.setId(imagefile)
# open the ImgPlus
imps = BF.openImagePlus(options)
imp = imps[series]
# apply the filter
if FILTERTYPE != 'NONE':
# apply filter
log.info('Apply Filter : ' + FILTERTYPE)
log.info('Filter Radius : ' + str(FILTER_RADIUS))
# apply the filter based on the choosen type
imp = apply_filter(imp,
radius=FILTER_RADIUS,
filtertype=FILTERTYPE)
if FILTERTYPE == 'NONE':
log.info('No filter selected. Do nothing.')
return imp
##################################################################
# Parse Inputs of Module
INPUT_JSON = json.loads(os.environ['WFE_INPUT_JSON'])
IMAGEPATH = INPUT_JSON['IMAGEPATH']
# suffix for the filename of the saved data
SUFFIX_FL = '_FILTERED'
# parameters for filter
FILTERTYPE = INPUT_JSON['FILTERTYPE']
FILTER_RADIUS = INPUT_JSON['FILTER_RADIUS']
SAVEFORMAT = 'ome.tiff'
# define path for the output
outputimagepath = '/output/' + os.path.basename(IMAGEPATH)
basename = os.path.splitext(outputimagepath)[0]
# remove the extra .ome before reassembling the filename
if basename[-4:] == '.ome':
basename = basename[:-4]
log.info('New basename for output :' + basename)
# save processed image
outputimagepath = basename + SUFFIX_FL + '.' + SAVEFORMAT
############# RUN MAIN IMAGE ANALYSIS PIPELINE ##########
# get the starting time of processing pipeline
start = time.clock()
# run image analysis pipeline
filtered_image = run(IMAGEPATH,
useBF=False,
series=0)
# get time at the end and calc duration of processing
end = time.clock()
log.info('Duration of whole Processing : ' + str(end - start))
###########################################################
# save the particle stack
outputimagepath = '/output/' + os.path.basename(IMAGEPATH)
# save processed image in out_dir
outputimagepath = os.path.splitext(outputimagepath)[0] + SUFFIX_FL + '.' + SAVEFORMAT
log.info('Saving Filtered Image ...' + outputimagepath)
# create the argument string for the BioFormats Exporter and save as OME.TIFF
start = time.clock()
paramstring = "outfile=" + outputimagepath + " " + "windowless=true compression=Uncompressed saveROI=false"
plugin = LociExporter()
plugin.arg = paramstring
exporter = Exporter(plugin, filtered_image)
exporter.run()
# get time at the end and calc duration of processing
end = time.clock()
log.info('Duration of saving as OME.TIFF : ' + str(end - start))
# write output JSON
log.info('Writing output JSON file ...')
output_json = {"FILTERED_IMAGE": outputimagepath}
with open("/output/" + INPUT_JSON['WFE_output_params_file'], 'w') as f:
json.dump(output_json, f)
# finish
log.info('Done.')
# finish and exit the script
os._exit()
Hi @sebi06. The error message was added in https://github.com/openmicroscopy/bioformats/pull/3344 to allow execution to continue despite the NullPointerException. You can read more about the root cause in https://github.com/ome/ome-common-java/pull/38 -- but the full solution required more changes than we wanted to attempt for 6.1.0. A workaround to remove the error message is to move the files as @dgault explains in https://forum.image.sc/t/bioformats-importer-issue/25439/2?u=joshmoore
Hope that helps. ~Josh
Thx for the answer. This helps and I can live with this for now easily. The error just popped up when running the script inside a docker on APEER inside the logs.
Josh Moore [email protected] schrieb am Mi. 22. Mai 2019 um 18:22:
Hi @sebi06 https://github.com/sebi06. The error message was added in #3344 https://github.com/openmicroscopy/bioformats/pull/3344 to allow execution to continue despite the NullPointerException. You can read more about the root cause in ome/ome-common-java#38 https://github.com/ome/ome-common-java/pull/38 -- but the full solution required more changes than we wanted to attempt for 6.1.0. A workaround to remove the error message is to move the files as @dgault https://github.com/dgault explains in https://forum.image.sc/t/bioformats-importer-issue/25439/2?u=joshmoore
Hope that helps. ~Josh
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This issue has been mentioned on Image.sc Forum. There might be relevant details there:
https://forum.image.sc/t/error-when-i-open-a-tif-image-in-qupath/70808/2
