From 0e19239eefe6eebff32e835d3fb9b8d8a33eba4d Mon Sep 17 00:00:00 2001
From: Rohan Girish <rohangirishrao@gmail.com>
Date: Wed, 29 Oct 2025 11:22:34 +0100
Subject: [PATCH 1/2] Add example to docstring for clarity

---
 src/imcflibs/imagej/omerotools.py | 9 +++++++++
 1 file changed, 9 insertions(+)

diff --git a/src/imcflibs/imagej/omerotools.py b/src/imcflibs/imagej/omerotools.py
index 31f4bdd4..7dad756f 100644
--- a/src/imcflibs/imagej/omerotools.py
+++ b/src/imcflibs/imagej/omerotools.py
@@ -47,6 +47,15 @@ def parse_url(client, omero_str):
     -------
     list(fr.igred.omero.repository.ImageWrapper)
         List of ImageWrappers parsed from the string.
+
+    Examples
+    --------
+    >>> from fr.igred.omero import Client
+    >>> client = Client()
+    >>> OMERO_LINK = "123456"
+    >>> img_wrappers = omerotools.parse_url(client, OMERO_LINK)
+    >>> for wrapper in img_wrappers:
+    >>>    imp = wpr.toImagePlus(client)
     """
     image_ids = []
     dataset_ids = []

From 7834a922ea2f61efc37096cdd5f45ceba9b2144a Mon Sep 17 00:00:00 2001
From: Rohan Girish <rohangirishrao@gmail.com>
Date: Wed, 29 Oct 2025 17:34:48 +0100
Subject: [PATCH 2/2] Add method to save Fiji script parameters to file

Calls on scijava.script.ScriptModule through Python globals to access only the user-given parameters and not other variables at run-time.
---
 src/imcflibs/imagej/misc.py | 33 +++++++++++++++++++++++++++++++++
 1 file changed, 33 insertions(+)

diff --git a/src/imcflibs/imagej/misc.py b/src/imcflibs/imagej/misc.py
index edd4509e..7b972ba2 100644
--- a/src/imcflibs/imagej/misc.py
+++ b/src/imcflibs/imagej/misc.py
@@ -7,6 +7,7 @@
 import subprocess
 import sys
 import time
+from org.scijava.script import ScriptModule
 
 from ij import IJ  # pylint: disable-msg=import-error
 from ij.plugin import Duplicator, ImageCalculator, StackWriter
@@ -701,3 +702,35 @@ def run_imarisconvert(file_path):
         IJ.log("Conversion to .ims is finished.")
     else:
         IJ.log("Conversion failed with error code: %d" % result)
+    
+
+def save_script_parameters(destination, save_file_name="script_parameters.txt"):
+    """Save all Fiji script parameters to a text file.
+
+    Parameters
+    ----------
+    destination : str
+        Directory where the script parameters file will be saved.
+    save_file_name : str, optional
+        Name of the script parameters file, by default "script_parameters.txt".
+    """
+    # Get the ScriptModule object from globals made by Fiji
+    module = globals().get("org.scijava.script.ScriptModule")
+    if module is None:
+        print("No ScriptModule found- skipping saving script parameters.")
+        return
+
+    # Retrieve the input parameters from the scijava module
+    inputs = module.getInputs()
+    destination = str(destination)
+    out_path = os.path.join(destination, save_file_name)
+    
+    # Write the parameters to output file
+    with open(out_path, "w") as f:
+        for key in inputs.keySet():
+            val = inputs.get(key)
+            f.write("%s: %s\n" % (key, str(val)))
+
+    print("Saved script parameters to: %s" % out_path)
+
+