SCientific Image Format Input & Output: a flexible, extensible framework for image I/O. *EXPERIMENTAL* All API is subject to change, so depend at your own risk! See also @openmicroscopy/bioformats.
More than six years ago now... 🤯
I tried to work with this commit, in case someone has time let me know what you think: scijava/scijava-common#395
hey everyone! we currently have a strange issue with scifio
[ERROR] Module threw exception
java.lang.NullPointerException
at io.scif.services.DefaultInitializeService.initializeReader(DefaultInitializeService.java:87)
at io.scif.img.ImgOpener.createReader(ImgOpener.java:483)
at io.scif.img.ImgOpener.openImgs(ImgOpener.java:242)
at io.scif.services.DefaultDatasetIOService.open(DefaultDatasetIOService.java:152)
at io.scif.services.DefaultDatasetIOService.open(DefaultDatasetIOService.java:133)
at io.scif.services.DefaultDatasetIOService.open(DefaultDatasetIOService.java:138)
at io.scif.convert.FileToDatasetConverter.convert(FileToDatasetConverter.java:66)
at org.scijava.convert.AbstractConvertService.convert(AbstractConvertService.java:125)
at org.scijava.convert.AbstractDelegateConverter.convert(AbstractDelegateConverter.java:53)
at org.scijava.convert.AbstractConvertService.convert(AbstractConvertService.java:125)
at org.scijava.module.DefaultModuleService.load(DefaultModuleService.java:316)
at org.scijava.module.DefaultModuleService.loadInput(DefaultModuleService.java:544)
at org.scijava.module.DefaultModuleService.lambda$loadInputs$1(DefaultModuleService.java:346)
at java.util.ArrayList.forEach(ArrayList.java:1257)
at java.util.Collections$UnmodifiableCollection.forEach(Collections.java:1080)
at org.scijava.module.DefaultModuleService.loadInputs(DefaultModuleService.java:346)
at org.scijava.module.process.LoadInputsPreprocessor.process(LoadInputsPreprocessor.java:58)
at org.scijava.module.ModuleRunner.preProcess(ModuleRunner.java:102)
at org.scijava.module.ModuleRunner.run(ModuleRunner.java:154)
at org.scijava.module.ModuleRunner.call(ModuleRunner.java:124)
at org.scijava.module.ModuleRunner.call(ModuleRunner.java:63)
at org.scijava.thread.DefaultThreadService.lambda$wrap$2(DefaultThreadService.java:225)
at java.util.concurrent.FutureTask.run(FutureTask.java:266)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
at java.lang.Thread.run(Thread.java:748)
this is triggered by using sciview's Isosurface command, https://github.com/scenerygraphics/sciview/blob/5a09273513df003b53457f99bb3b2a60d08b72c1/src/main/java/sc/iview/commands/process/Isosurface.java, with quite a large selection of TIFF files -- any ideas what could be the root cause there?
@skalarproduktraum it could be that SCIFIO/SciJava is too eagerly trying to convert a
String into a Dataset with the new StringToDatasetConverter in SCIFIO. Can you try whether scifio/scifio#443 fixes your issue?
(or
FileToDatasetConverter actually, just read the stack trace in more detail)
you might need to combine scifio/scifio#443 with scifio/scifio#444 and build yourself though...
@ctrueden @hinerm I’m stuck with a strange SCIFIO issue: scifio/scifio#453
If you find a minute to give me pointers how to solve it, that would be great : )
If you find a minute to give me pointers how to solve it, that would be great : )
@imagejan Update so far: I was able to reproduce by running your Groovy script via
--ij2 --headless --run. I was not yet able to reproduce using jgo to run the SCIFIO command line tool, not at the most recent release, nor the latest SCIFIO snapshot version. I think I'll start digging a bit in Eclipse. Once I have an idea what might be wrong, I'll update here again.
Update 3: In my local fiji/fiji working copy, I checked out tag
fiji-2.1.0. Imported into Eclipse. Launched in debug mode. Loaded the MCVE script into the script editor. Back in Eclipse, navigated to FormatService, getFormat(Location) method. It's an interface, used ctrl+T to bring up implementations, navigated into DefaultFormatService, same method. Saw it delegates to another method, hit F3 to jump there, which led me to this code in scifio 0.41.0 (the version associated with fiji 2.1.0). Put a breakpoint there, ran the script in Fiji, and then back in Eclipse, I see that getFormatList returns null. Hit F8 to continue, then go back to Fiji and run the script again to trigger the breakpoint again. Rinse and repeat while stepping through the code with F5/F6/F7 to learn more about what's going wrong. I know this is a lot of detail, and that @imagejan probably doesn't need it, but I write it here for anyone wondering how we debug this stuff. The Script Editor + IDE combination is very powerful.
It does help to have some prior knowledge—in this case I know that
BioFormatsFormat is supposed to be the format handling STK files, so in the formats for loop, I'm digging in to that one first. Fortunately, it's the first one on the list right now. (If it weren't, you could use a conditional breakpoint to step straight to it by pressing F8.)
Update 4: After working around some bugs in Eclipse's debugger (*sigh* I may bite the bullet and switch to IntelliJ soon; Eclipse seems to be getting buggier, at least for me), I reach the following surprising exception!
java.io.FileNotFoundException: .../benchmark_v1_2018_x64y64z1c2s4t11_w1Laser4054BD4BP.stk (Permission denied)
I think what's going on, at least for me, is that the file is read-only on my file system, but SCIFIO tries to wrap it in a read/write handle. I will see if other problems remain after addressing that.
Update 5: I fixed the read-only file bug, which was a separate issue, with scijava/scijava-common@c4cb3a7. I then continued debugging, and indeed the NPE continues to happen. The problem is:
- SCIFIO's
BioFormatsFormatonly looks at the file contents if theSCIFIOConfig'scheckerIsOpenflag is set totrue, but it isfalseby default; and: - Bio-Formats does not consider the
.stkextension sufficient for theMetamorphReaderto returntruefromisThisType; whenopenisfalse, it simply returnsfalse.
OK @imagejan, I'm done analyzing this issue. I responded on the GitHub issue with a workaround for you, along with a question about if we should change anything in SCIFIO.
@ctrueden @hinerm what’s the status of
scifio-javacv? As far as I can see, the unit test is failing with “data array too small”, and there’s no deployed maven artefact for it. Are there any plans to resurrect it? It would be awesome to have video codec support in SCIFIO.
I opened a PR enabling Deflate (zlib) support for
See also this forum topic.
If you have time to have a look, I’d appreciate if this can be merged and released some time soon, as it will greatly simplify a workflow I’m currently working on : )
TIFFFormat.Writer: scifio/scifio#455See also this forum topic.
If you have time to have a look, I’d appreciate if this can be merged and released some time soon, as it will greatly simplify a workflow I’m currently working on : )
Let me know if you also need it uploaded to the Java-8 update site.
@ctrueden I tried to upload the new scifio-0.42.0.jar after having tested it a bit in Fiji, but I get the following error when uploading (with my account Eglinger):
[ERROR] org.apache.http.conn.HttpHostConnectException: Connect to sites.imagej.net:443 [sites.imagej.net/144.92.48.186] failed: Connection refused: connect
at org.apache.http.impl.conn.DefaultHttpClientConnectionOperator.connect(DefaultHttpClientConnectionOperator.java:156)
at org.apache.http.impl.conn.PoolingHttpClientConnectionManager.connect(PoolingHttpClientConnectionManager.java:376)
at org.apache.http.impl.execchain.MainClientExec.establishRoute(MainClientExec.java:393)
at org.apache.http.impl.execchain.MainClientExec.execute(MainClientExec.java:236)
at org.apache.http.impl.execchain.ProtocolExec.execute(ProtocolExec.java:186)
at org.apache.http.impl.execchain.RetryExec.execute(RetryExec.java:89)
at org.apache.http.impl.execchain.RedirectExec.execute(RedirectExec.java:110)
at org.apache.http.impl.client.InternalHttpClient.doExecute(InternalHttpClient.java:185)
at org.apache.http.impl.client.CloseableHttpClient.execute(CloseableHttpClient.java:83)
at org.apache.http.impl.client.CloseableHttpClient.execute(CloseableHttpClient.java:56)
at net.imagej.plugins.uploaders.webdav.WebDAVUploader.runMethodOnClient(WebDAVUploader.java:525)
at net.imagej.plugins.uploaders.webdav.WebDAVUploader.runMethodOnClient(WebDAVUploader.java:514)
at net.imagej.plugins.uploaders.webdav.WebDAVUploader.lock(WebDAVUploader.java:314)
at net.imagej.plugins.uploaders.webdav.WebDAVUploader.upload(WebDAVUploader.java:202)
at net.imagej.updater.FilesUploader.upload(FilesUploader.java:260)
at net.imagej.ui.swing.updater.UpdaterFrame.upload(UpdaterFrame.java:803)
at net.imagej.ui.swing.updater.UpdaterFrame$5$1.run(UpdaterFrame.java:309)
Caused by: java.net.ConnectException: Connection refused: connect
at java.net.DualStackPlainSocketImpl.connect0(Native Method)
at java.net.DualStackPlainSocketImpl.socketConnect(DualStackPlainSocketImpl.java:79)
at java.net.AbstractPlainSocketImpl.doConnect(AbstractPlainSocketImpl.java:350)
at java.net.AbstractPlainSocketImpl.connectToAddress(AbstractPlainSocketImpl.java:206)
at java.net.AbstractPlainSocketImpl.connect(AbstractPlainSocketImpl.java:188)
at java.net.PlainSocketImpl.connect(PlainSocketImpl.java:172)
at java.net.SocksSocketImpl.connect(SocksSocketImpl.java:392)
at java.net.Socket.connect(Socket.java:589)
at org.apache.http.conn.ssl.SSLConnectionSocketFactory.connectSocket(SSLConnectionSocketFactory.java:368)
at org.apache.http.impl.conn.DefaultHttpClientConnectionOperator.connect(DefaultHttpClientConnectionOperator.java:142)
... 16 moreIs that expected, i.e. wrong account, wrong password? I would have expected a bit informative error message, so I’m unsure if the issue is on my side now, or on the server side :-)
Update: it seems it’s our institute’s restrictive firewall/proxy. From my home network, uploading worked fine. At our institute we have to use a proxy for http and https. The proxy settings in ImageJ work for subscribing to update sites, but apparently not for (webdav) uploading?!
@ctrueden @hinerm concerning the
I pushed my work here: https://github.com/scifio/scifio-javacv/compare/wip
I get a NPE when trying to read, but all I found was that
Here I’m stuck and would need some input :-)
scifio-javacv update to the FileLocation API, I tried to update MovieFormat, but wasn’t able to fix the test (that was failing independently of the FileLocation API changes)…I pushed my work here: https://github.com/scifio/scifio-javacv/compare/wip
I get a NPE when trying to read, but all I found was that
openPlane is never called despite the format matches and setDest is called.Here I’m stuck and would need some input :-)
But feel free to focus on the ImageJ wiki first!
Hi everybody,
I am facing an issue with compressed DICOM files.
As a sample dataset I used DEMO 0002 from http://www.rubomedical.com/dicom_files/. I can’t open a plane for this file, as the process doesn’t come to an end. I tracked the issue back to line 1527 in the DICOMFormat.java file (https://github.com/scifio/scifio/blob/741ac2ac03ec4c566a6612c0f148fdd47bd47d9d/src/main/java/io/scif/formats/DICOMFormat.java#L1527), where the codec should be decompressed. And even more precisely: The while-loop in JPEGCodec.java doesn’t seem to come to an end (https://github.com/scifio/scifio/blob/741ac2ac03ec4c566a6612c0f148fdd47bd47d9d/src/main/java/io/scif/codec/JPEGCodec.java#L109). Can anyone help me with this?
I am facing an issue with compressed DICOM files.
As a sample dataset I used DEMO 0002 from http://www.rubomedical.com/dicom_files/. I can’t open a plane for this file, as the process doesn’t come to an end. I tracked the issue back to line 1527 in the DICOMFormat.java file (https://github.com/scifio/scifio/blob/741ac2ac03ec4c566a6612c0f148fdd47bd47d9d/src/main/java/io/scif/formats/DICOMFormat.java#L1527), where the codec should be decompressed. And even more precisely: The while-loop in JPEGCodec.java doesn’t seem to come to an end (https://github.com/scifio/scifio/blob/741ac2ac03ec4c566a6612c0f148fdd47bd47d9d/src/main/java/io/scif/codec/JPEGCodec.java#L109). Can anyone help me with this?
With SCIFIO (File > Import > Image...) I get a much weirder error:
[ERROR] java.io.IOException: io.scif.img.ImgIOException: java.io.FileNotFoundException: /home/curtis/Downloads/dicom_viewer_0002/0002.DCM (Permission denied)I've not seen this happen before.
OK, I add write permission to the file, which worked around that error. Certainly it's a bug in SCIFIO that the file is being opened read-write just to read it, though. And now, I can reproduce the error you're seeing, @EllaHir.