Error when visualizing a CachedCellImg with BigDataViewer

albertcardona · November 26, 2020, 6:14pm

When running this script: https://github.com/acardona/scripts/blob/01cd9c723d0a07fe1acadd255812699b68ba0161/python/imagej/examples/imglib2_load_4D_CachedCellImg_from_3D_filepaths.py , I get an error at line:

bdv = BdvFunctions.show(cachedCellImg, "4D volume")

The error: lacking field list. Any clues?

Traceback (most recent call last):
  File "/home/albert/lab/scripts/python/imagej/examples/imglib2_load_4D_CachedCellImg_from_3D_filepaths.py", line 82, in <module>
    bdv = BdvFunctions.show(cachedCellImg, "4D volume", Bdv.options())
	at bdv.viewer.BasicViewerState.notifyListeners(BasicViewerState.java:1622)
	at bdv.viewer.BasicViewerState.addSources(BasicViewerState.java:724)
	at bdv.viewer.SynchronizedViewerState.addSources(SynchronizedViewerState.java:496)
	at bdv.viewer.state.ViewerState.<init>(ViewerState.java:81)
	at bdv.viewer.ViewerPanel.<init>(ViewerPanel.java:248)
	at bdv.viewer.ViewerFrame.<init>(ViewerFrame.java:103)
	at bdv.BigDataViewer.<init>(BigDataViewer.java:335)
	at bdv.util.BdvHandleFrame.createViewer(BdvHandleFrame.java:91)
	at bdv.util.BdvHandle.add(BdvHandle.java:142)
	at bdv.util.BdvFunctions.addRandomAccessibleInterval(BdvFunctions.java:449)
	at bdv.util.BdvFunctions.show(BdvFunctions.java:86)
	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.lang.reflect.Method.invoke(Method.java:498)
java.lang.NoSuchFieldError: java.lang.NoSuchFieldError: list

NicoKiaru · November 26, 2020, 8:03pm

There was an old issue related to this error:

But it should be solved now.
Which versions do you have for imglib2, bdv-core and bdv-vistools ? Do you have update sites enabled ?

albertcardona · November 26, 2020, 9:16pm

Thanks, good catch. I do have update sites enabled, but I had just updated Fiji, which should also update jars from update sites.

I’ve now unticked the update site BigVolumeViewer, but the error persists.

I have:

Fiji.app/jars$ ls big*
bigdataviewer-core-9.0.5.jar
bigdataviewer-vistools-1.0.0-beta-20.jar
bigvolumeviewer-0.1.8.jar

/Fiji.app/jars$ ls scijava-listeners*
scijava-listeners-1.0.0-beta-3.jar

Fiji.app/plugins$ ls big
bigdataviewer_fiji-6.2.0.jar
bigwarp_fiji-6.0.2.jar

Are any of these not up to date? They ought to be, as per the Fiji updater.

albertcardona · November 26, 2020, 9:21pm

Found a solution: uninstall the SciView update site.

NicoKiaru · November 26, 2020, 9:26pm

You should have bdv-vistools v>=1.0.0-beta-21 to have the issue fixed : https://github.com/bigdataviewer/bigdataviewer-vistools/issues/46

albertcardona · November 26, 2020, 9:28pm

Thanks. Do you know who is in charge of SciView? Their Bdv tools have this issue. @tpietzsch @kephale?

kephale · November 26, 2020, 9:34pm

One moment please! Let me check. I’ll try to cut a release early. The SciView-Unstable site should be working with a more recent vistools in the meantime.

kephale · November 26, 2020, 9:37pm

Aha, the latest pom-scijava still seems to use 1.0.0-beta-20

kephale · November 26, 2020, 9:44pm

Currently waiting on a SciView-Unstable CI update. @albertcardona I’ll test your script when that is ready and follow up after that.

albertcardona · November 26, 2020, 9:46pm

Thanks! the data for that script is here:

… and requires the SiMView update site for the KLB file format reader.

kephale · November 26, 2020, 11:04pm

Okey doke, working for me with the SciView-Unstable update site. We’ll propagate this to the primary SciView update site soon

albertcardona · November 26, 2020, 11:36pm

For the record, the whole script is here:

github.com

acardona/scripts/blob/c50db26d8387d22cc5d3aeaee75e45f560eb97cd/python/imagej/examples/imglib2_load_4D_CachedCellImg_from_3D_filepaths.py

import os, re
from jarray import array
# Must have enabled the "SiMView" update site from the Keller lab at Janelia
from org.janelia.simview.klb import KLB
from net.imglib2.img.cell import CellGrid, Cell
from net.imglib2.cache import CacheLoader
from net.imagej import ImgPlus
from net.imglib2.util import Intervals
from net.imglib2.cache.ref import SoftRefLoaderCache
from net.imglib2.img.basictypeaccess.volatiles.array import VolatileByteArray, VolatileShortArray,\
                                                            VolatileFloatArray, VolatileLongArray  
from net.imglib2.cache.img import ReadOnlyCachedCellImgFactory as Factory, \
                                  ReadOnlyCachedCellImgOptions as Options

# Get this data set of 11 stacks at:
# https://www.dropbox.com/sh/dcp0coglw1ym6nb/AABVY8I1RenMq4kDN1RByLZTa?dl=0
source_dir = "/home/albert/lab/presentations/20201130_I2K_Janelia/data/"
series4D_dir = os.path.join(source_dir, "4D-series/")

# One 3D stack (in KLB format) per time point in this 4D volume

This file has been truncated. show original

… and showcases:

How to read a series of 3D stacks as a 4D volume using ImgLib2’s CachedCellImg.
How to view the volume in an ImageJ VirtualStack and with the BigDataViewer, properly setting a display range (min and max values) for best initial visualization.
How to write the volume in N5 format.
How to read the N5 formatted-volume into an ImgLib2 image, and then view it either with a VirtualStack or a BigDataViewer, showcasing:
A) How the N5 format with an appropriate GZIP compression level compares in file storage requirements to e.g. the highly compressed KLB (584 MB for GZIP=4 N5 versus 407 MB for KLB).
B) How the N5 format with a relatively small block size (2 MB) enables fast random access on the volume.

This will be part of the python (jython) tutorial on exploring large datasets at #I2K2020 on December 1st.

kephale · November 27, 2020, 7:08am

Sounds very complementary to the volumetric data segment of the sciview I2K tutorial! Good thing the update sites wont clash now