tlambert03 / bioformats_jar Goto Github PK

The majority of formats supported by Bioformats are GPL licensed. However, a subset of them can be used in a BSD licensed package. The subset is small, but it does give access to the OME standard formats and other common formats. Since GPL is particularly aggressive, inclusion of this package is likely a non-starter for many packages.

What could be done is to use the same pipeline/structure as outlined here but use the BSD license formats. I'm not sure of all the details, but there may be interest in such a package.

Hi @tlambert03! 👋

I was wondering if you have considered using the scyjava project to resolve Java dependencies, rather than shipping them in a hardcoded way like this project does?

For PyImageJ, we use scyjava (backed by jpype and jgo) and it lets you customize your classpath from remote Maven artifacts in an extensible way. Without something like this, you'll always run into problems with multiple different needed JARs on the Java classpath across multiple Python-wrappings-of-Java-libraries. Whereas if you use scyjava, we can mix and match things like AICSImageIO[bioformats] with PyImageJ and potentially other Java-backed Python components.

Do you see any reason this wouldn't be a better approach? Happy to discuss further if you have questions or comments about it!

CC @hinerm @elevans

I have folder branch like below:
`.../importer/

• xml.py
• xml_parser folder:
  +CMXLFile.java`

I am using scyjava.jimport to import CMXLFile java class from CMXLFile.java into xml.py My code is below:

`def read_XML_file(xml_file_path):
# initialize ImageJ
ij = imagej.init()
print(f"ImageJ version: {ij.getVersion()}")
# add class path
config.add_classpath("...\Fiji.app\jars\ij-1.53t.jar")

  # xml_file = ij.io().open(xml_file_path)
  
  CXMLFile = jimport('xml_parser.CXMLFile.CXMLFile')
  print(CXMLFile)
  cxmlfile = CXMLFile()
  imp = cxmlfile.Reader(xml_file_path)
  
  return imp

`
I get the error: TypeError: Class xml_parser.CXMLFile.CXMLFile is not found
So, My question is: How to import java class into python?