pyimagej
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imagej
ImageJ initialisation taking forever?
Hi - I'm trying to use ImageJ from python to run a macro, but I can't seem to initialise it, as it takes forever:
This is my code:
import imagej
print("initializing imageJ, this can take a bit of time...")
ij = imagej.init('/Applications/Fiji.app', headless=False)
print("imageJ successfully initialised.")
and my console has been on "initializing fiji, this can take a bit of time' for about an hour!
I expect that this would take some time as when I run it for the first time it will install lots of JARs, , but it has been running for hours, not sure what might be causing this/how to fix it.
@u2056710 Hello!
What system are you on? I just replicated your code with a fresh download of Fiji and everything is fine on my end (Ubuntu 20.04 LTS).
Some things to try:
- Download a fresh copy of Fiji and try that instead of your existing installation.
- Do you need your local version specifically? You can let pyimagej use the latest and greatest by initializing like so:
ij = imagej.init()
Actually I ran into the same issue, running the initialization on Win 10 64x. I tried using a fresh local version and also initializing without parsing arguments. In both cases the process takes indefinitely long (> 10 min). Any hints on what may cause this would be great.
Sorry for the delayed reply @elevans. I am working on MacOS Catalina. I have tried using the latest and it still does not load.
@StudDavid I have not been able to sort it out yet but will let you know if I do!
Best wishes
This error messages I just got could be helpful:
File "test_imagej.py", line 6, in <module> ij = imagej.init("Fiji.app", headless=False) File "C:\anaconda3\envs\pyimagej\lib\site-packages\imagej\__init__.py", line 168, in init ij = ImageJ() java.lang.IllegalArgumentException: java.lang.IllegalArgumentException: Invalid service: sc.fiji.filamentdetector.gui.GUIStatusService
It occurred, when passing the local installation folder as an argument.
But it runs successfully, when initializing without an argument.
I reinstalled Java and started the basic script from a anaconda console inside the provided anaconda environment. The sample image is shown, but still got an error message stating
log4j:WARN No appenders could be found for logger (org.bushe.swing.event.EventService). log4j:WARN Please initialize the log4j system properly. log4j:WARN See http://logging.apache.org/log4j/1.2/faq.html#noconfig for more info.
After deleting the FilamentDetector-1.0.0.jar from the /jars subfolder, it works also with the locally installed Fiji version.
The same here, regardless of which of those inits I try:
import imagej
# ij = imagej.init('/Applications/Fiji.app')
# ij = imagej.init()
ij = imagej.init('sc.fiji:fiji:2.0.0-pre-10')
it takes forever to do anything and does nothing. No error message, no warning, just runs in the kernel of Jupyter notebook.
Version '1.0.0' of imagej, running Mac Big Sur 11.2.1.
I would like to make it easier to debug this sort of problem in a future version of pyimagej. For now, here is some information about the two major initialization cases:
Using a remote endpoint such as sc.fiji:fiji
The first time you run e.g. ij = imagej.init('sc.fiji:fiji:2.1.1'), PyImageJ downloads Fiji in the background, which can take some time; if it hangs beyond a minute or two though, you can check whether your Maven installation was able to find the artifacts using this command in a separate terminal with your conda environment active:
mvn -B -f ~/.jgo/net.imglib2/imglib2-imglyb/1.0.0+net.imagej-imagej-legacy-RELEASE+sc.fiji-fiji-2.1.1/pom.xml dependency:resolve
The above assumes you are using Fiji at version 2.1.1, the newest usable version as of this writing. If you use a different version, the string above will need to be tweaked accordingly.
Alternately, it's possible to enable debug mode for jgo (the library that's doing the downloading) via:
import jgo, logging, sys
jgo.jgo._logger.addHandler(logging.StreamHandler(sys.stderr))
jgo.jgo._logger.setLevel(logging.DEBUG)
Followed by the usual import imagej and ij = imagej.init(...) call. You should see a lot more stuff get printed to the console, indicating what's happening with jgo. May or may not be useful, but at least it's more detail. :smile:
Using a local installation
The fact that you are seeing hangs with both local and remote installations suggests that it's not an issue with jgo or downloading remote JAR files. With local installations, you may be bit by the problem with Fiji.app/jars/FilamentDetector-1.0.0.jar mentioned by @StudDavid; try deleting that file before initializing from Python and see if that avoids the problem.
You can also try enabling debugging output during ImageJ/Fiji initialization as follows:
import os
os.environ['DEBUG'] = '1'
import imagej
ij = imagej.init('/Applications/Fiji.app')
And you should see a lot of debugging information get printed to the terminal about what's happening as ImageJ spins up.
@jankaWIS @u2056710 Please let us know if any of the above gives any further clues on the issues you're experiencing.
Hi, I also have this problem. I installed from conda forge as instructed from the readme of the this project.
import imageJ seems to work, but imagej.init('sc.fiji:fiji:2.1.1') seems to hang forever.
I did the mvn command suggested above:
(bjorn38) bjorn@bjorn-ThinkPad-T450s:~$ mvn -B -f ~/.jgo/net.imglib2/imglib2-imglyb/1.0.0+net.imagej-imagej-legacy-RELEASE+sc.fiji-fiji-2.1.1/pom.xml dependency:resolve
[INFO] Scanning for projects...
[WARNING]
[WARNING] Some problems were encountered while building the effective model for net.imglib2-BOOTSTRAPPER:imglib2-imglyb-BOOTSTRAPPER:jar:0
[WARNING] 'dependencies.dependency.version' for net.imagej:imagej-legacy:jar is either LATEST or RELEASE (both of them are being deprecated) @ line 10, column 222
[WARNING]
[WARNING] It is highly recommended to fix these problems because they threaten the stability of your build.
[WARNING]
[WARNING] For this reason, future Maven versions might no longer support building such malformed projects.
[WARNING]
...
[INFO]
[INFO] --- maven-dependency-plugin:2.8:resolve (default-cli) @ imglib2-imglyb-BOOTSTRAPPER ---
[INFO] Downloading from central: https://repo.maven.apache.org/maven2/org/apache/maven/maven-settings/2.0.9/maven-settings-2.0.9.pom
mamba list output:
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reportlab 3.5.51 py38he152a6b_0 conda-forge
reproc 14.2.1 h36c2ea0_0 conda-forge
reproc-cpp 14.2.1 h58526e2_0 conda-forge
requests 2.24.0 pyh9f0ad1d_0 conda-forge
requests-mock 1.8.0 pyh9f0ad1d_0 conda-forge
requests-oauthlib 1.3.0 pyh9f0ad1d_0 conda-forge
requests-toolbelt 0.9.1 py_0 conda-forge
rfc3986 1.4.0 pyh9f0ad1d_0 conda-forge
rope 0.17.0 pyh9f0ad1d_0 conda-forge
rsa 4.6 pyh9f0ad1d_0 conda-forge
rtree 0.9.4 py38h08f867b_1 conda-forge
ruamel_yaml 0.15.80 py38h1e0a361_1002 conda-forge
scikit-learn 0.23.2 py38h5d63f67_3 conda-forge
scipy 1.5.2 py38h8c5af15_0 conda-forge
scyjava 1.1.0 pyhd8ed1ab_0 conda-forge
secretstorage 3.1.2 py38h32f6830_1 conda-forge
seguid-calculator 1.1.0 dev_0 <develop>
send2trash 1.5.0 py38_0 defaults
setuptools 52.0.0 py38h06a4308_0 defaults
setuptools-scm 4.1.2 pyh9f0ad1d_0 conda-forge
setuptools_scm 4.1.2 0 conda-forge
simplejson 3.17.2 py38h1e0a361_0 conda-forge
six 1.15.0 pyh9f0ad1d_0 conda-forge
smmap 3.0.4 pyh9f0ad1d_0 conda-forge
snapgene-reader 0.1.18 pypi_0 pypi
snowballstemmer 2.0.0 py_0 conda-forge
sortedcontainers 2.2.2 pyh9f0ad1d_0 conda-forge
soupsieve 2.0.1 py_1 conda-forge
sphinx 3.2.1 py_0 conda-forge
sphinxcontrib-applehelp 1.0.2 py_0 conda-forge
sphinxcontrib-devhelp 1.0.2 py_0 conda-forge
sphinxcontrib-htmlhelp 1.0.3 py_0 conda-forge
sphinxcontrib-jsmath 1.0.1 py_0 conda-forge
sphinxcontrib-qthelp 1.0.3 py_0 conda-forge
sphinxcontrib-serializinghtml 1.1.4 py_0 conda-forge
spyder-kernels 1.10.1 py38h578d9bd_0 conda-forge
sqlite 3.33.0 h4cf870e_0 conda-forge
stapler 1.0.0 pypi_0 pypi
style 1.1.0 pypi_0 pypi
sympy 1.6.2 py38h32f6830_0 conda-forge
termcolor 1.1.0 py38_1 defaults
terminado 0.8.3 py38h32f6830_1 conda-forge
testpath 0.4.4 py_0 conda-forge
texlive-core 20180414 pl526hc0a3334_3 conda-forge
threadpoolctl 2.1.0 pyh5ca1d4c_0 conda-forge
tk 8.6.10 hed695b0_0 conda-forge
toml 0.10.1 pyh9f0ad1d_0 conda-forge
tornado 6.0.4 py38h1e0a361_1 conda-forge
tqdm 4.54.0 pyhd8ed1ab_0 conda-forge
traitlets 4.3.3 py38h32f6830_1 conda-forge
twine 3.2.0 py38h32f6830_0 conda-forge
typed-ast 1.4.1 pypi_0 pypi
typing-extensions 3.7.4.3 pypi_0 pypi
tzlocal 2.1 pypi_0 pypi
ujson 3.2.0 py38h950e882_0 conda-forge
update 0.0.1 pypi_0 pypi
uritemplate 3.0.1 py_0 conda-forge
urllib3 1.25.10 py_0 conda-forge
virtualenv 20.2.1 py38h578d9bd_0 conda-forge
watchdog 0.10.3 py38h32f6830_1 conda-forge
wcwidth 0.2.5 pyh9f0ad1d_1 conda-forge
webencodings 0.5.1 py_1 conda-forge
wheel 0.35.1 pyh9f0ad1d_0 conda-forge
widgetsnbextension 3.5.1 py38h32f6830_1 conda-forge
wikidpadmp 2.4a1.dev2 dev_0 <develop>
wkhtmltopdf 0.12.4 1 conda-forge
wrapt 1.11.2 py38h1e0a361_0 conda-forge
wurlitzer 2.0.0 py38h32f6830_1 conda-forge
wxpython 4.1.0 py38h725c64c_0 conda-forge
x264 1!152.20180806 h14c3975_0 conda-forge
xarray 0.16.2 pyhd8ed1ab_0 conda-forge
xmltodict 0.12.0 pypi_0 pypi
xorg-fixesproto 5.0 h14c3975_1002 conda-forge
xorg-inputproto 2.3.2 h14c3975_1002 conda-forge
xorg-kbproto 1.0.7 h14c3975_1002 conda-forge
xorg-libice 1.0.10 h516909a_0 conda-forge
xorg-libsm 1.2.3 h84519dc_1000 conda-forge
xorg-libx11 1.6.12 h516909a_0 conda-forge
xorg-libxau 1.0.9 h14c3975_0 conda-forge
xorg-libxdmcp 1.1.3 h516909a_0 conda-forge
xorg-libxext 1.3.4 h516909a_0 conda-forge
xorg-libxfixes 5.0.3 h516909a_1004 conda-forge
xorg-libxi 1.7.10 h516909a_0 conda-forge
xorg-libxrender 0.9.10 h516909a_1002 conda-forge
xorg-libxtst 1.2.3 h516909a_1002 conda-forge
xorg-recordproto 1.14.2 h516909a_1002 conda-forge
xorg-renderproto 0.11.1 h14c3975_1002 conda-forge
xorg-xextproto 7.3.0 h14c3975_1002 conda-forge
xorg-xproto 7.0.31 h14c3975_1007 conda-forge
xz 5.2.5 h516909a_1 conda-forge
yaml 0.2.5 h516909a_0 conda-forge
yapf 0.30.0 pyh9f0ad1d_0 conda-forge
yarl 1.5.1 py38h1e0a361_0 conda-forge
youtube-dl 2020.11.1.1 pypi_0 pypi
zeromq 4.3.2 he1b5a44_3 conda-forge
zipp 3.1.0 py_0 conda-forge
zlib 1.2.11 h516909a_1009 conda-forge
zstd 1.4.5 h6597ccf_2 conda-forge
I would like to make it easier to debug this sort of problem in a future version of pyimagej. For now, here is some information about the two major initialization cases:
Using a remote endpoint such as
sc.fiji:fijiThe first time you run e.g.
ij = imagej.init('sc.fiji:fiji:2.1.1'), PyImageJ downloads Fiji in the background, which can take some time; if it hangs beyond a minute or two though, you can check whether your Maven installation was able to find the artifacts using this command in a separate terminal with your conda environment active:mvn -B -f ~/.jgo/net.imglib2/imglib2-imglyb/1.0.0+net.imagej-imagej-legacy-RELEASE+sc.fiji-fiji-2.1.1/pom.xml dependency:resolveThe above assumes you are using Fiji at version 2.1.1, the newest usable version as of this writing. If you use a different version, the string above will need to be tweaked accordingly.
Alternately, it's possible to enable debug mode for jgo (the library that's doing the downloading) via:
import jgo, logging, sys jgo.jgo._logger.addHandler(logging.StreamHandler(sys.stderr)) jgo.jgo._logger.setLevel(logging.DEBUG)Followed by the usual
import imagejandij = imagej.init(...)call. You should see a lot more stuff get printed to the console, indicating what's happening with jgo. May or may not be useful, but at least it's more detail. 😄Using a local installation
The fact that you are seeing hangs with both local and remote installations suggests that it's not an issue with jgo or downloading remote JAR files. With local installations, you may be bit by the problem with
Fiji.app/jars/FilamentDetector-1.0.0.jarmentioned by @StudDavid; try deleting that file before initializing from Python and see if that avoids the problem.You can also try enabling debugging output during ImageJ/Fiji initialization as follows:
import os os.environ['DEBUG'] = '1' import imagej ij = imagej.init('/Applications/Fiji.app')And you should see a lot of debugging information get printed to the terminal about what's happening as ImageJ spins up.
@jankaWIS @u2056710 Please let us know if any of the above gives any further clues on the issues you're experiencing.
I actually do not know what happened. Once I tried:
import os
os.environ['DEBUG'] = '1'
import imagej
ij = imagej.init('/Applications/Fiji.app')
it worked, now I tried again and I'm getting:
---------------------------------------------------------------------------
TypeError Traceback (most recent call last)
<ipython-input-53-c2c4f57e3a60> in <module>
2 os.environ['DEBUG'] = '1'
3 import imagej
----> 4 ij = imagej.init('/Applications/Fiji.app')
~/anaconda3/lib/python3.8/site-packages/imagej/__init__.py in init(ij_dir_or_version_or_endpoint, headless)
212 """
213 raise ImportError("Your ImageJ installation does not support IJ1. This function does not work.")
--> 214 WindowManager = JObject(_WindowManager)
215
216 class ImageJPython:
~/anaconda3/lib/python3.8/site-packages/jpype/_jobject.py in __new__(cls, *args, **kwargs)
57 if len(args) == 0:
58 return _jpype._java_lang_Object()
---> 59 return _JObjectFactory(*args, **kwargs)
60
61
~/anaconda3/lib/python3.8/site-packages/jpype/_jobject.py in _JObjectFactory(v, tp)
109 # Given a Java class
110 if isinstance(tp, _jpype._JClass):
--> 111 return tp._cast(v)
112
113 raise TypeError("Invalid type conversion to %s requested." % tp)
TypeError: Unable to cast 'type' to java type 'java.lang.Class'
And at this moment, this works:
import imagej
ij = imagej.init()
ij.getVersion() #'2.2.0/1.53c'
Update 23.2. None of the above works anymore, now I'm getting:
JVMNotFoundException Traceback (most recent call last)
<ipython-input-2-c2c4f57e3a60> in <module>
2 os.environ['DEBUG'] = '1'
3 import imagej
----> 4 ij = imagej.init('/Applications/Fiji.app')
~/anaconda3/lib/python3.8/site-packages/imagej/__init__.py in init(ij_dir_or_version_or_endpoint, headless)
160 sj.config.add_endpoints('net.imagej:imagej:' + version)
161
--> 162 sj.start_jvm()
163
164 JObjectArray = JArray(JObject)
~/anaconda3/lib/python3.8/site-packages/scyjava/__init__.py in start_jvm(options)
54
55 # initialize JPype JVM
---> 56 jpype.startJVM(*options)
57
58 # grab needed Java classes
~/anaconda3/lib/python3.8/site-packages/jpype/_core.py in startJVM(*args, **kwargs)
185 jvmpath = kwargs.pop('jvmpath')
186 if not jvmpath:
--> 187 jvmpath = getDefaultJVMPath()
188
189 # Classpath handling
~/anaconda3/lib/python3.8/site-packages/jpype/_jvmfinder.py in getDefaultJVMPath()
72 else:
73 finder = LinuxJVMFinder()
---> 74 return finder.get_jvm_path()
75
76
~/anaconda3/lib/python3.8/site-packages/jpype/_jvmfinder.py in get_jvm_path(self)
210 if jvm_notsupport_ext is not None:
211 raise jvm_notsupport_ext
--> 212 raise JVMNotFoundException("No JVM shared library file ({0}) "
213 "found. Try setting up the JAVA_HOME "
214 "environment variable properly."
JVMNotFoundException: No JVM shared library file (libjli.dylib) found. Try setting up the JAVA_HOME environment variable properly.
I have not changed anything in my installations except that FiJi/ImageJ got some update yesterday or the day before. Can that be a cause for the change in the error message, @ctrueden, @elevans?
@BjornFJohansson @jankaWIS Sorry for the long delay in reply. Did you manage to get it working, ever?
I wonder if these hangs are caused by firewall issues? If you still care, could you try:
import os
os.environ["JAVA_TOOL_OPTIONS"] = "-Djava.net.useSystemProxies=true"
Before running imagej.init?
Theoretically, this will cause Maven to use your system proxy settings when querying and downloading from the remote Maven repository.
Or if you need to set proxy settings manually:
import os
mydomain = "example.com" # replace with your proxy server
myport = 8080 # replace with your proxy server's port
os.environ["JAVA_TOOL_OPTIONS"] = (
f"-Dhttp.proxyHost={mydomain}"
+ f" -Dhttp.proxyPort={myport}"
+ f" -Dhttps.proxyHost={mydomain}"
+ f" -Dhttps.proxyPort={myport}"
)
It may not be a firewall issue, though, in which case I would suggest running that mvn invocation again from the command line. @BjornFJohansson based on your output pasted above, it looks like that command was hanging for you? If so, you could try running mvn with the -X flag to enable more verbose debugging output. You can also press Ctrl+</kbd> once it hangs to get a Java stack trace, which might tell us where the code is hanging.
Since writing the above reply, I have now enhanced the Troubleshooting guide in the documentation to talk about ways to control the proxy settings:
https://github.com/imagej/pyimagej/blob/718097feec82fb2353168dbbeb26afad187206a7/doc/Troubleshooting.md#common-errors
I also wrote a troubleshooting analysis tool (not yet part of a PyImageJ release) which you can run like so:
python -c 'import imagej.doctor; imagej.doctor.checkup()'
Or if that doesn't work, download and run the latest version of it directly:
curl -fsLO https://raw.githubusercontent.com/imagej/pyimagej/master/src/imagej/doctor.py; python doctor.py
Right now the doctor is focused on validating your installation, but it does not yet check for proxy settings, and it does not yet warn if the Java version is too old (although it does report it).
I'm closing this due to inactivity, hoping that everyone's setups are happily working. If not, please feel welcome to reopen with details, and we will keep trying to help!