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    Jan Eglinger
    @imagejan
    I opened a PR enabling Deflate (zlib) support for TIFFFormat.Writer: scifio/scifio#455
    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 : )
    Curtis Rueden
    @ctrueden
    @imagejan Reviewed, merged, and released with scifio 0.42.0. Cheers. :beers:
    Let me know if you also need it uploaded to the Java-8 update site.
    Jan Eglinger
    @imagejan
    @ctrueden thanks a lot! Uploading to the Java-8 site would be great, I can do it myself as well, I think. But I also wouldn’t mind waiting for another concerted pom-scijava update if that is planned.
    Curtis Rueden
    @ctrueden
    There will be another pom-scijava update, but probably not for at least 3-4 weeks. Uploading it in the meantime, as long as you do some light testing first of SCIFIO-related features, would be great.
    Jan Eglinger
    @imagejan
    :+1:
    Jan Eglinger
    @imagejan

    @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 more

    Is 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 :-)

    Jan Eglinger
    @imagejan
    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?!
    Curtis Rueden
    @ctrueden
    @imagejan I was going to upload it from here, but it looks like someone (you?) already uploaded it?
    Jan Eglinger
    @imagejan
    Yes, it worked from outside my institute network, see my last comment. Sorry for the buzz :-/
    Curtis Rueden
    @ctrueden
    No worries. I am not sure how to improve the error message, but it's a little surprising that the HTTP proxy settings weren't effective for uploading. Not the first time people haven't been able to upload from behind firewalls, though.
    Jean-Yves Tinevez
    @tinevez
    Indeed, we had the same issue in Janelia Farm back in 2016.
    Jan Eglinger
    @imagejan
    @ctrueden @hinerm concerning the 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!
    Curtis Rueden
    @ctrueden
    @imagejan I added it to my "imagej community" tab group for later!
    Jan Eglinger
    @imagejan
    Thanks! Must be a full tab by now :-D
    Curtis Rueden
    @ctrueden
    I accidentally lost all my tabs awhile back (:cry:) which slimmed it down some, but it's getting pretty fat again. <_< >_>
    Ella H
    @EllaHir
    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?
    Curtis Rueden
    @ctrueden
    @EllaHir Thanks for the detailed report! Did you also try with Bio-Formats? File > Import > Bio-Formats works for me with that dataset.

    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.
    Curtis Rueden
    @ctrueden
    @EllaHir I filed #459 and #460 relating to these problems. My lab will have some students working on SCIFIO over the summer, so perhaps these can be fixed as part of that work. In the meantime, I hope using Bio-Formats instead works OK for you.
    Ella H
    @EllaHir
    @ctrueden I didn't try it with Bio-Formats yet, thanks for the hint and for filing the issues!
    Curtis Rueden
    @ctrueden
    :+1:
    Jan Eglinger
    @imagejan
    Bio-Formats works well with the DEMO 0002 dataset.