Question: Error messages when trying to read and image

[sebi06]

Hi guys,

I just tried to test the python-bioformats library and got stuck with I problem. I am not a programmer, so my question might be silly ...
When I open the file inside Fiji using the BioFormats Importer it works fine, so the file itself is ok. And I also managed to read it using: http://www.lfd.uci.edu/~gohlke/pythonlibs/#bioformats

But when I use python-bioformats I get those error messages:

java.lang.IllegalArgumentException: 0.0 must not be null and positive.
at ome.xml.model.primitives.PositiveFloat.(PositiveFloat.java:41)
at loci.formats.in.MRCReader.initFile(MRCReader.java:286)
at loci.formats.FormatReader.setId(FormatReader.java:1072)
java.lang.NoClassDefFoundError: Glacier2/PermissionDeniedException
Caused by: java.lang.ClassNotFoundException: Glacier2.PermissionDeniedException
at java.net.URLClassLoader$1.run(Unknown Source)
at java.net.URLClassLoader$1.run(Unknown Source)
at java.security.AccessController.doPrivileged(Native Method)
at java.net.URLClassLoader.findClass(Unknown Source)
at java.lang.ClassLoader.loadClass(Unknown Source)
at sun.misc.Launcher$AppClassLoader.loadClass(Unknown Source)
at java.lang.ClassLoader.loadClass(Unknown Source)
Traceback (most recent call last):
File "", line 1, in
File "C:\Python27\lib\site-packages\python_bioformats-0.0.0-py2.7.egg\bioformats\formatreader.py", line 908, in load_using_bioformats
with ImageReader(path=path) as rdr:
File "C:\Python27\lib\site-packages\python_bioformats-0.0.0-py2.7.egg\bioformats\formatreader.py", line 634, in init
self.init_reader()
File "C:\Python27\lib\site-packages\python_bioformats-0.0.0-py2.7.egg\bioformats\formatreader.py", line 675, in init_reader
je, "Glacier2/PermissionDeniedException"):
File "C:\Python27\lib\site-packages\javabridge\jutil.py", line 811, in is_instance_of
raise JavaException(jexception)
javabridge.jutil.JavaException: Glacier2/PermissionDeniedException

Thanks for the help,

Sebastian

[LeeKamentsky]

Hi Sebi - it looks like there's something wrong with the loci_tools.jar file that you're using. You've obviously used the right class path (e.g. javabridge.start_vm(class_path=bioformats.JARS)). Can you send me or post a link to the image you're trying to load? Also, the code you're running through is for an OMERO url and that's a little strange.

Christoph Gohlke is kindly building bioformats for us, so the packages should be roughly equivalent. Perhaps he's a day or two behind.

You can test whether the Bio-Formats JAR loads your image directly from Java. Navigate to the directory containing the JAR (on my system, c:\Python27\Lib\site-packages\bioformats\jars) and type
java -cp loci_tools.jar loci.formats.tools.ImageInfo <your file name here>

If your file doesn't load, it's probably something we have to figure out with Bio-Formats.

[sebi06]

Hi Lee,

well on my PC I have:

C:\Python27\Lib\site-packages\python_bioformats-0.0.0-py2.7.egg\bioformats\jars\loci_tools.jar

When I try

java -cp loci_tools.jar loci.formats.tools.ImageInfo
C:\Users\M1SRH\Documents\Testdata_Zeiss\Zen_Output\Count_Cells_DAPI_10_Frames_with_Fiji.czi

I get the follwoing error: Error: could not open `C:\Program Files
(x86)\Java\jre7\lib\i386\jvm.cfg', which is clear, since I have only
Java64bit installed. Is this some 32/64bit issue with the loci_tools.jar?

By the way, inside Fiji and ImageJ the loci_tools.far was replaced by the
bio_formats_package.jar. And the loci_tools.jar (5.0.0) is way bigger in
file size than the one located here:
C:\Python27\Lib\site-packages\python_bioformats-0.0.0-py2.7.egg\bioformats\jars\loci_tools.jar

When do:

java -cp loci_tools.jar loci.formats.tools.ImageInfo
C:\Python27\Lib\site-packages\bio_formats\loci_tools.jar

I get the exact same error message...

My JAVA_HOME is C:\Program Files\Java\jdk1.7.0_21

I found one jvm.cfg here: C:\Program
Files\Java\jdk1.7.0_21\jre\lib\amd64\jvm.cfg

and also here: C:\Program Files\Java\jre7\lib\amd64\jvm.cfg

Cheers,

Sebi

2014-03-17 13:29 GMT+01:00 LeeKamentsky notifications@github.com:

Hi Sebi - it looks like there's something wrong with the loci_tools.jar
file that you're using. You've obviously used the right class path (e.g.
javabridge.start_vm(class_path=bioformats.JARS)). Can you send me or post
a link to the image you're trying to load? Also, the code you're running
through is for an OMERO url and that's a little strange.

Christoph Gohlke is kindly building bioformats for us, so the packages
should be roughly equivalent. Perhaps he's a day or two behind.

You can test whether the Bio-Formats JAR loads your image directly from
Java. Navigate to the directory containing the JAR (on my system,
c:\Python27\Lib\site-packages\bioformats\jars) and type
java -cp loci_tools.jar loci.formats.tools.ImageInfo

If your file doesn't load, it's probably something we have to figure out
with Bio-Formats.

Reply to this email directly or view it on GitHubhttps://github.com//issues/6#issuecomment-37809707
.

Dr. Sebastian Rhode
Grünwalder Straße 103a
81547 München
Tel: +49 89 4703091
Mobil: +49 151 40767993
sebrhode@gmail.com

[LeeKamentsky]

It sure looks like a 32-bit / 64-bit problem. I'm wondering if CP picked a
32-bit JDK to build against. I'll have more time for this tomorrow.

On Mon, Mar 17, 2014 at 12:45 PM, sebi06 notifications@github.com wrote:

Hi Lee,

well on my PC I have:

C:\Python27\Lib\site-packages\python_bioformats-0.0.0-py2.7.egg\bioformats\jars\loci_tools.jar

When I try

java -cp loci_tools.jar loci.formats.tools.ImageInfo
C:\Users\M1SRH\Documents\Testdata_Zeiss\Zen_Output\Count_Cells_DAPI_10_Frames_with_Fiji.czi

I get the follwoing error: Error: could not open `C:\Program Files
(x86)\Java\jre7\lib\i386\jvm.cfg', which is clear, since I have only
Java64bit installed. Is this some 32/64bit issue with the loci_tools.jar?

By the way, inside Fiji and ImageJ the loci_tools.far was replaced by the
bio_formats_package.jar. And the loci_tools.jar (5.0.0) is way bigger in
file size than the one located here:
C:\Python27\Lib\site-packages\python_bioformats-0.0.0-py2.7.egg\bioformats\jars\loci_tools.jar

When do:

java -cp loci_tools.jar loci.formats.tools.ImageInfo
C:\Python27\Lib\site-packages\bio_formats\loci_tools.jar

I get the exact same error message...

My JAVA_HOME is C:\Program Files\Java\jdk1.7.0_21

I found one jvm.cfg here: C:\Program
Files\Java\jdk1.7.0_21\jre\lib\amd64\jvm.cfg

and also here: C:\Program Files\Java\jre7\lib\amd64\jvm.cfg

Cheers,

Sebi

2014-03-17 13:29 GMT+01:00 LeeKamentsky notifications@github.com:

Hi Sebi - it looks like there's something wrong with the loci_tools.jar
file that you're using. You've obviously used the right class path (e.g.
javabridge.start_vm(class_path=bioformats.JARS)). Can you send me or
post
a link to the image you're trying to load? Also, the code you're running
through is for an OMERO url and that's a little strange.

Christoph Gohlke is kindly building bioformats for us, so the packages
should be roughly equivalent. Perhaps he's a day or two behind.

You can test whether the Bio-Formats JAR loads your image directly from
Java. Navigate to the directory containing the JAR (on my system,
c:\Python27\Lib\site-packages\bioformats\jars) and type
java -cp loci_tools.jar loci.formats.tools.ImageInfo

If your file doesn't load, it's probably something we have to figure out
with Bio-Formats.

Reply to this email directly or view it on GitHub<
https://github.com/CellProfiler/python-bioformats/issues/6#issuecomment-37809707>

.

Dr. Sebastian Rhode
Grünwalder Straße 103a
81547 München
Tel: +49 89 4703091
Mobil: +49 151 40767993
sebrhode@gmail.com

Reply to this email directly or view it on GitHubhttps://github.com//issues/6#issuecomment-37839067
.

[sebi06]

Any news on this issue yet?

[LeeKamentsky]

Sorry to have taken so long, my fault for not remembering to get back to it. We've included an older version of loci_tools.jar which is why it's smaller than Fiji's. I am a bit confused about Error: could not openC:\Program Files (x86)\Java\jre7\lib\i386\jvm.cfg` because you saw that totally outside of Javabridge, using only java. I can't think of why that happened.

Looking at the code and at the loci_tools.jar that's included with Bio-Formats, I am guessing that loci_tools is having some problem opening your file and, in the course of reporting the problem, it tries to use a Java class that's not present in the loci_tools.jar. So what it reports on is not finding the Java class and not on why you couldn't open the file. I'll fix the bug that prevents it from reporting, but I think I still need an example file to determine why we can't open your file.

[sebi06]

Hi Lee,

my Fiji on a Windows7, 64bit is using BioFormats 5.0.0 (see attached screen shot). The File open without any problems there. You can download it with this link:

https://dl.dropboxusercontent.com/u/623476/Count_Cells_DAPI_10_Frames_with_Fiji.czi

Sebi

[LeeKamentsky]

Hi Sebi,
The file was really instructive - I believe there's a bug in the version of Bio-formats that comes with python-bioformats that keeps it from reading the file. I tried bioformats with both the standard loci_tools and with Bio-Formats 5.0.1 and the former fails while the latter succeeds. I downloaded bioformats_package.jar from here:
http://downloads.openmicroscopy.org/bio-formats/5.0.1/artifacts/bioformats_package.jar

Here's a script that will start bioformats appropriately:

# Substitute "path" with the path to bioformats_package.jar on your own system.
path = r"C:\Users\leek\Downloads\bioformats_package.jar"
import javabridge
import bioformats
jars = javabridge.JARS + [path]
javabridge.start_vm(class_path=jars)

And here's your first image:

[sebi06]

Hi Lee,

thanks a lot. Now it works fine.

Sebi