Fix for misc.save_script_parameters (Issue #136)

src/imcflibs/imagej/misc.py

@@ -766,3 +766,68 @@ def bytes_to_human_readable(size):
     # If the value is larger than the largest unit, fall back to TB with
     # the current value (already divided accordingly).
     return "%3.1f %s" % (size, "TB")
+
+
+def save_script_parameters(
+    destination, save_file_name="script_parameters.txt", script_globals=None
+):
+    """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".
+    script_globals : dict, optional
+        The globals dictionary from the Fiji script, default None.
+        Must be passed explicitly as ``globals()`` from the script.
+
+    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.
+
+    Examples
+    --------
+    In a Fiji script, you can call this function as follows to save the parameters:
+        save_script_parameters(destination="params.txt", script_globals=globals())
+    """
+    # script_globals must be passed explicitly as globals() from the script.
+    g = script_globals if script_globals is not None else {}
+    module = g.get("org.scijava.script.ScriptModule")
+    if module is None:
+        timed_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)))
+
+    timed_log("Saved script parameters to: %s" % out_path)

tests/interactive-imagej/test_save_params.md

@@ -0,0 +1,18 @@
+# Testing script for misc.save_script_parameters()
+
+```python
+# @ String(label="Password", description="please enter your password", style="password") PASSWORD
+# @ String(label="USERNAME", description="please enter your USR") USERNAME
+# @ File(label="Path for storage", style="directory") outputPath
+# @ Integer threshold
+# @ Boolean taDa
+# @ RoiManager rm
+# @ CommandService command
+# @ LogService sjlog
+
+import os
+from imcflibs.imagej import misc, omerotools
+
+misc.save_script_parameters(outputPath, script_globals=globals())
+print("Saved params")
+```