Add method to save Fiji script parameters, and add example to opening an image by rohangirishrao · Pull Request #111 · imcf/python-imcflibs

rohangirishrao · 2025-11-05T08:32:05Z

Safe way of parsing Fiji script params by ignoring the passwords field automatically.

Calls on scijava.script.ScriptModule through Python globals to access only the user-given parameters and not other variables at run-time.

The method now ignores password in a clean way, and skips some other non-essential runtime keys.

codecov · 2025-11-05T08:45:23Z

Codecov Report

❌ Patch coverage is 14.28571% with 18 lines in your changes missing coverage. Please review.
✅ Project coverage is 24%. Comparing base (26f64c9) to head (8145904).
⚠️ Report is 46 commits behind head on devel.

Files with missing lines	Patch %	Lines
src/imcflibs/imagej/misc.py	14%	18 Missing ⚠️

Additional details and impacted files

@@         Coverage Diff          @@
##           devel   #111   +/-   ##
====================================
- Coverage     25%    24%   -1%     
====================================
  Files         25     25           
  Lines       1688   1742   +54     
====================================
+ Hits         421    425    +4     
- Misses      1267   1317   +50

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imagejan · 2025-12-01T14:27:15Z

src/imcflibs/imagej/misc.py

+            # Skip if parameter is declared with style="password"
+            style = item.getWidgetStyle()
+            if style is not None and style.lower() == "password":
+                continue


You could use WidgetStyle.isStyle(ModuleItem<?> item, String target) here:

Suggested change

# Skip if parameter is declared with style="password"

style = item.getWidgetStyle()

if style is not None and style.lower() == "password":

continue

# Skip if parameter is declared with style="password"

if WidgetStyle.isStyle(item, TextWidget.PASSWORD_STYLE):

continue

Note also the use of public constants instead of hard-coded strings here 😉

I like @imagejan's suggestion. @rohangirishrao could you look into it?

src/imcflibs/imagej/omerotools.py

ehrenfeu · 2026-01-14T15:52:14Z

Add to changelog #126

imagejan · 2026-01-14T15:55:22Z

From the GitHub Actions checks:

src/imcflibs/imagej/misc.py:19: in <module>
    from org.scijava.widget import WidgetStyle
E   ModuleNotFoundError: No module named 'org'

Looks like you need to update imcf-fiji-mocks now (and bump its version here) to provide the necessary org.scijava classes.

ehrenfeu · 2026-01-15T13:53:36Z

Yep: https://github.com/imcf/imcf-fiji-mocks/releases/tag/v0.12.0 😁

Thanks for spotting!

From the GitHub Actions checks:
src/imcflibs/imagej/misc.py:19: in <module>
    from org.scijava.widget import WidgetStyle
E   ModuleNotFoundError: No module named 'org'
Looks like you need to update imcf-fiji-mocks now (and bump its version here) to provide the necessary org.scijava classes.

ehrenfeu · 2026-01-16T11:00:22Z

🕵🏼 Need to investigate why Pytest-Python2 is failing, probably the culprit is in src/imcflibs/imagej/misc.py

____________ ERROR collecting tests/bdv/test_define_dataset_auto.py ____________
venv.py2/lib/python2.7/site-packages/_pytest/python.py:507: in _importtestmodule
    mod = self.fspath.pyimport(ensuresyspath=importmode)
venv.py2/lib/python2.7/site-packages/py/_path/local.py:704: in pyimport
    __import__(modname)
venv.py2/lib/python2.7/site-packages/_pytest/assertion/rewrite.py:304: in load_module
    exec(co, mod.__dict__)
tests/bdv/test_define_dataset_auto.py:6: in <module>
    from imcflibs.imagej import bdv
src/imcflibs/imagej/__init__.py:9: in <module>
    from . import misc
E     File "/home/runner/work/python-imcflibs/python-imcflibs/src/imcflibs/imagej/misc.py", line 743
E   SyntaxError: Non-ASCII character '\xe2' in file /home/runner/work/python-imcflibs/python-imcflibs/src/imcflibs/imagej/misc.py on line 743, but no encoding declared; see http://python.org/dev/peps/pep-0263/ for details

Using UTF-8 is still shaky in the Jython 2.7 environment, so if there is no strong need for it, simply stick to ASCII.

Also see imcf#45

ehrenfeu

Ready to be merged.

ehrenfeu · 2026-01-14T11:53:35Z

src/imcflibs/imagej/misc.py

+            # Skip if parameter is declared with style="password"
+            style = item.getWidgetStyle()
+            if style is not None and style.lower() == "password":
+                continue


I like @imagejan's suggestion. @rohangirishrao could you look into it?

ehrenfeu · 2026-01-16T13:18:01Z

src/imcflibs/imagej/misc.py

+                val = inputs.get(key)
+                f.write("%s: %s\n" % (key, str(val)))
+
+    print("Saved script parameters to: %s" % out_path)


rohangirishrao added 6 commits October 29, 2025 11:22

Add example to docstring for clarity

0e19239

Add method to save Fiji script parameters to file

7834a92

Calls on scijava.script.ScriptModule through Python globals to access only the user-given parameters and not other variables at run-time.

Add keys to skip logging

02d84d8

Update method to save Fiji script parameters

c7c0d3e

The method now ignores password in a clean way, and skips some other non-essential runtime keys.

Run black formatter

cdda918

Remove redundant ScriptModule import

eed68d8

rohangirishrao changed the title ~~Add method to save FIji script parameters, and add example to opening an image~~ Add method to save Fiji script parameters, and add example to opening an image Nov 7, 2025

Remove redundant comments

cd9795f

imagejan reviewed Dec 1, 2025

View reviewed changes

ehrenfeu reviewed Jan 14, 2026

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src/imcflibs/imagej/omerotools.py Show resolved Hide resolved

ehrenfeu added this to imcflibs Jan 14, 2026

ehrenfeu added this to the 2.0.0 milestone Jan 14, 2026

ehrenfeu added enhancement New feature or request new-minor Change introduced in PR will require a new minor release. labels Jan 14, 2026

ehrenfeu assigned rohangirishrao Jan 14, 2026

ehrenfeu moved this to In progress in imcflibs Jan 14, 2026

Change from string literal to public constant

1b74c4e

rohangirishrao changed the base branch from master to devel January 14, 2026 13:29

ehrenfeu added the changelog Needs to be mentioned in release changelogs label Jan 14, 2026

Change mocks version to 0.12.0

38376ec

Update poetry.lock for mocks v0.12.0

bf7fd7d

ehrenfeu assigned ehrenfeu and unassigned rohangirishrao Jan 16, 2026

ehrenfeu added 2 commits January 16, 2026 12:08

Replace UTF-8 dash with an ASCII minus

b7e32fb

Using UTF-8 is still shaky in the Jython 2.7 environment, so if there is no strong need for it, simply stick to ASCII.

Use IJ.log() instead of print()

fc32cca

Also see imcf#45

ehrenfeu added 3 commits January 16, 2026 12:10

Minor syntax / rendering fix

1be7625

Update mocks dependency to version to 0.13.0

d50577f

Add instructions for working around poetry's stubborn cache

8145904

ehrenfeu approved these changes Jan 16, 2026

View reviewed changes

ehrenfeu merged commit 499526c into imcf:devel Jan 16, 2026
3 of 5 checks passed

github-project-automation bot moved this from In progress to Done in imcflibs Jan 16, 2026

rohangirishrao mentioned this pull request Jan 21, 2026

Update changelog for 2.0.0 #126

Open

ehrenfeu mentioned this pull request Jan 23, 2026

Issue accessing globals() from library #136

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Add method to save Fiji script parameters, and add example to opening an image#111

Add method to save Fiji script parameters, and add example to opening an image#111
ehrenfeu merged 15 commits intoimcf:develfrom
rohangirishrao:master

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