Cannot use "Bio Formats Importer" FIJI plugin

[tomerfried]

I'm trying to use "Bio Formats Importer" by running macros with pyimagej. this is the code:

import imagej
from scyjava import jimport
from skimage import io

ij = imagej.init('C:/Users/Tomer/Desktop/Hereon Project/Fiji.app')
WindowManager = jimport('ij.WindowManager')
macrotest = """
run("Bio-Formats Importer", "open=[C:/Users/Tomer/Desktop/Hereon Project/pyimagej/a.tif] autoscale color_mode=Default rois_import=[ROI manager] view=Hyperstack stack_order=XYCZT");
"""
ij.py.run_macro(macrotest)
img = WindowManager.getCurrentImage()
ij.py.show(img)

and this is the error:

[java.lang.Enum.toString] Macro Error: Unrecognized command: "Bio-Formats Importer" in line 2

run ( "Bio-Formats Importer" , "open=[C:/Users/Tomer/Desktop/Hereon Project/pyimagej/a.tif] autoscale color_mode=Defaul...[java.lang.Enum.toString] 

---------------------------------------------------------------------------
TypeError                                 Traceback (most recent call last)
~\AppData\Local\Temp/ipykernel_3740/809048045.py in <module>
      6 ij.py.run_macro(macrotest)
      7 img = WindowManager.getCurrentImage()
----> 8 ij.py.show(img)

~\Desktop\Hereon Project\pyimagej\lib\site-packages\imagej\__init__.py in show(self, image, cmap)
    608             """
    609             if image is None:
--> 610                 raise TypeError('Image must not be None')
    611 
    612             # NB: Import this only here on demand, rather than above.

Iv'e tried using run_plugin() but the error is the same.

Is there a solution for this? because I didn't find any in previous topics online. Basically, all I need is a good images importer for tiff files, captured from a microscope for a biological research. It is important that there would not be a loss of data when importing.

I'd like to hear any alternatives for Bio Formats if you guys know something

Thank you

[ctrueden]

@tomerfried This is probably the same issue as #129. I'll investigate when I have time!

[hinerm]

@ctrueden @elevans so far I have confirmed that there is a negative interaction with the Bio-Formats plugins.config. The importer sets Location=[Local machine] windowless=false and if I instead pass an empty string, the Importer command is suddenly discovered within PyImageJ.

Other commands are similarly missing: Bio-Formats, Bio-Formats (Windowless) and Bio-Formats Windowless Importer (the latter two being the same command)

Oddly, the Bio-Formats (Remote) commands are both present.

To summarize the state of plugins.config:

• Commands with Location=[Local machine] are not found, but Location=[Internet] are (problem a space in the value?)
• If there is a trailing space in the string the command is not discovered ("Location=[Internet]" is OK but not "Location=[Internet] ") 💥

So I guess the next step is to understand where these params are actually being parsed and interpreted. 😿

[hinerm]

@tomerfried so part of the problem is that ImageJ 1.x's plugin structure is entirely directory based and even though you are specifying a local app, ImageJ 1.x is unable to fully connect the dots to where your plugins are.

With a local Fiji.app you can work around this by doing one of:

• Starting python in a terminal from your Fiji.app directory
• Setting the plugins.dir to your Fiji.app\plugins directory, e.g.:

  
  import imagej
  from scyjava import jimport
  from scyjava import sj
  from skimage import io

sj.config.add_option('-Dplugins.dir=C:/Users/Tomer/Desktop/Hereon Project/Fiji.app/plugins') ij = imagej.init('C:/Users/Tomer/Desktop/Hereon Project/Fiji.app')

@elevans @ctrueden

This also works with a `jgo` initialization but it's kind of dumb since you have to know the jgo directory ahead of time.. e.g.:

import imagej import scyjava as sj sj.config.add_option('-Dplugins.dir=C:\Users\hiner\.jgo\net.imglib2\imglib2-imglyb\1.0.0+net.imagej-imagej-legacy-RELEASE+sc.fiji-fiji-RELEASE') ij = imagej.init('sc.fiji:fiji', headless=False) ij.ui().showUI()

If necessary we could add a bit of code to auto-set `plugins.dir` based on the initialization, but at least we have a workaround for now.

I'm now going to try and understand the mechanism behind the "best effort" plugin detection that still seems to be in play when `plugins.dir` is *not* set.

[hinerm]

I'm now going to try and understand the mechanism behind the "best effort" plugin detection that still seems to be in play when plugins.dir is not set.

It's in imagej-legacy, of course.

This pattern is too restrictive. 👿