These are chat archives for fiji/fiji

1st
Feb 2017
Paula
@paulafaral_twitter
Feb 01 2017 12:09
Hello, good morning... I am having trouble opening a .ssd file with FIJI... is it possible?
Stefan Helfrich
@stelfrich
Feb 01 2017 12:18
@paulafaral_twitter: I don’t think that ssd files are supported by vanilla ImageJ1 or Bio-Formats (according to their list: https://www.openmicroscopy.org/site/support/bio-formats5.3/supported-formats.html)
Paula
@paulafaral_twitter
Feb 01 2017 12:19
yes.. i was just reading a list of programs that support ssd files
very short list
Stefan Helfrich
@stelfrich
Feb 01 2017 12:22
@paulafaral_twitter So ssd is not a life science file format, I guess? Where did you get that data / from software did you get it?
Paula
@paulafaral_twitter
Feb 01 2017 12:23
micrometrics
Stefan Helfrich
@stelfrich
Feb 01 2017 12:26
Do they, by chance, provide a software that you could maybe use to open the images and store them in a more accesible file format, e.g. TIFF?
Paula
@paulafaral_twitter
Feb 01 2017 12:27
yes, the microscope camera comes with the software, but is intalled in a computer in the animal facility at my institut
is not easy for me to access the computer
but i will have to try
Paula
@paulafaral_twitter
Feb 01 2017 12:41
thank you very much
Stefan Helfrich
@stelfrich
Feb 01 2017 12:44
You are welcome! There's not really that much we can do here..
Jean-Yves Tinevez
@tinevez
Feb 01 2017 13:30
Hi all. Can someone points me to an example pom I could use as a base to fix the errors I have when compiling after extending scijava pom?
[INFO] --- maven-enforcer-plugin:1.4.1:enforce (enforce-rules) @ TrackMate_extras ---
[WARNING] Rule 7: org.scijava.maven.plugin.enforcer.RequireElements failed with message:
The following required elements have errors:
* url: element is missing
* inceptionYear: element is missing
* organization: element is missing
* licenses: element is missing
* contributors: element is missing
* mailingLists: element is missing
* issueManagement: element is missing
* ciManagement: element is missing
* properties//license.licenseName: element is missing
* properties//license.copyrightOwners: element is missing
Hadrien Mary
@hadim
Feb 01 2017 13:32
imagej-ops
(I had the issue recently)
Jan Eglinger
@imagejan
Feb 01 2017 14:03
@tinevez you can also look directly in pom-scijava where there are placeholders for some of these.
Seems to be the first problem everyone runs into when upgrading to pom-scijava :smile:
See fiji/Descriptor_based_registration#5
Jean-Yves Tinevez
@tinevez
Feb 01 2017 14:57
Ok thanks!
There are a couple of items I do not find fair.
For instance, I have an empty contributors list, so I put an empty contributors element in the pom. But this gets rejected:
The following required elements have errors:
* contributors: element has no content
* mailingLists: element has no content
* ciManagement: element has no content
That should not cause an error right? It should be ok to have e.g. no ciManagement and to say so.
Curtis Rueden
@ctrueden
Feb 01 2017 15:40
@paulafaral_twitter You could write to the Bio-Formats developers asking them to add support for SSD. Although there are a couple of other major new microscope formats which I know they are working on, so it may be quite a long time before they can accomplish it. I agree with @stelfrich that in the short term, conversion to another format is your best bet.
@tinevez There are dozens of example POMs. Just look at any POM which has already been upgraded to pom-scijava version 12.
That new enforcer check was put in very deliberately. I had to write a custom rule for it. The purpose is to make sure that people actually specify the needed metadata, and do not allow the parent's metadata to inadvertently take precedence (since most XML blocks are inherited).
If you have no <contributors> you can do this.
Curtis Rueden
@ctrueden
Feb 01 2017 15:45
If you have no issueManagement, ciManagement and/or scm then you can do this. Though if your thing is on GitHub, then it will only be the ciManagement that is not already there.
You should put the ImageJ Forum for your mailingLists entry unless that is somehow inappropriate.
I know, I know: it is not a "mailing list"—but it is a support channel.
I am sorry that an empty contributors block does not work, but it seems it is a bug in Maven. It has to do with the inheritance/interpolation of POMs, which to be fair, is non-trivial. Just use the hack above; it's what I do everywhere.
For ciManagement you can use <system>None</system> as linked above.
@tinevez Please let me know if those tricks do not fully solve everything for you.
@imagejan I knew everyone would struggle with it, but I also knew that (nearly) everyone was ignoring the non-mandated requirement spelled out in the previous pom-scijava versions. Too easy to miss, and too easy to make mistakes.
Curtis Rueden
@ctrueden
Feb 01 2017 15:50
The good thing is that once everything is updated to pom-scijava 12+, we will be golden for metadata. It will be much easier to extract metadata from POM files, since you won't have to recurse to the parents. And more importantly, the metadata is much more likely to be correct. And easier for humans to read. And easy to autogenerate wiki templates based on components. Hopefully the advantages are clear.
Jan Eglinger
@imagejan
Feb 01 2017 15:50
:+1: I agree that the switch to the unified pom-scijava is definitely an improvement.
Curtis Rueden
@ctrueden
Feb 01 2017 15:50
<gush> I love the new unified pom-scijava so much you guys. </gush>
Jan Eglinger
@imagejan
Feb 01 2017 15:51
:smile:
Jean-Yves Tinevez
@tinevez
Feb 01 2017 16:08
[INFO] ------------------------------------------------------------------------
[INFO] BUILD SUCCESS
[INFO] ------------------------------------------------------------------------
thanks @ctrueden
Curtis Rueden
@ctrueden
Feb 01 2017 17:05
@tinevez Hooray!