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

pyproject.toml

@@ -20,7 +20,7 @@ version = "0.0.0"
 # - or: python = ">=3.10"
 
 [tool.poetry.dependencies]
-imcf-fiji-mocks = ">=0.10.0"
+imcf-fiji-mocks = ">=0.13.0"
 python = ">=2.7"
 python-micrometa = "^15.2.2"
 sjlogging = ">=0.5.2"

src/imcflibs/imagej/misc.py

@@ -16,6 +16,9 @@
 from . import bioformats as bf
 from . import prefs
 
+from org.scijava.widget import WidgetStyle
+from org.scijava.widget import TextWidget
+
 
 def show_status(msg):
     """Update the ImageJ status bar and issue a log message.
@@ -701,3 +704,57 @@ 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".
+
+    Notes
+    -----
+    This function records all input parameters defined in the Fiji script header
+    (e.g. `#@ String`) to a text file.
+
+    The following parameters are excluded:
+    - Parameters explicitly declared with `style="password"` are ignored.
+    - Runtime keys (e.g. 'SJLOG', 'COMMAND', 'RM') are also skipped.
+    """
+    # Get the ScriptModule object from globals made by Fiji
+    module = globals().get("org.scijava.script.ScriptModule")
+    if module is None:
+        IJ.log("No ScriptModule found - skipping saving script parameters.")
+        return
+
+    destination = str(destination)
+    out_path = os.path.join(destination, save_file_name)
+
+    # Access script metadata and inputs
+    script_info = module.getInfo()
+    inputs = module.getInputs()
+
+    # Keys to skip explicitly
+    skip_keys = ["USERNAME", "SJLOG", "COMMAND", "RM"]
+
+    with open(out_path, "w") as f:
+        for item in script_info.inputs():
+            key = item.getName()
+
+            # Skip if any keys are in the skip list
+            if any(skip in key.upper() for skip in skip_keys):
+                continue
+
+            # Skip if parameter is declared with password style
+            if WidgetStyle.isStyle(item, TextWidget.PASSWORD_STYLE):
+                continue
+
+            if inputs.containsKey(key):
+                val = inputs.get(key)
+                f.write("%s: %s\n" % (key, str(val)))
+
+    print("Saved script parameters to: %s" % out_path)

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 = []