🔀 Merge pull request #156 from rohangirishrao/save-script-params

Rework and generalize `save_script_parameters`

Author: ehrenfeu

CHANGELOG.md

@@ -71,6 +71,9 @@ multiple modules. For detailed information, please refer to the
 * `imcflibs.imagej.misc.run_imarisconvert`:
   * Now allows to select an output folder.
   * Adds pixel calibration to the converted file.
+* `imcflibs.imagej.misc.save_script_parameters` skips only parameters whose
+    whole name is in the skip list (`fusion_format` was skipped because it
+    contains `RM`).
 * `imcflibs.imagej.misc.subtract_images` now validates the slice count is equal
     for both images.
 * `imcflibs.imagej.misc.save_image_with_extension`: fix issue with java path

src/imcflibs/imagej/misc.py

@@ -784,16 +784,17 @@ def _is_password_style(item):  # pragma: no cover (jython)
     return WidgetStyle.isStyle(item, TextWidget.PASSWORD_STYLE)
 
 
-def save_script_parameters(
-    script_globals, destination, save_file_name="script_parameters.txt"
-):
+def save_script_parameters(script_globals, destination="", overwrite=False):
     """Save all Fiji script parameters to a text file.
 
     Record all input parameters defined in the Fiji script header (e.g.
     `#@ String`) to a text file such that they can be stored e.g. next to the
     input data and the analysis results in order to document how a specific
     processing run was executed.
 
+    The file name is generated automatically following the pattern
+    ``<script_name>_run-<timestamp>_params.txt``.
+
     The following parameters are excluded:
 
     - Parameters explicitly declared with `style="password"`.
@@ -808,30 +809,49 @@ def save_script_parameters(
     script_globals : dict
         The globals dictionary from the running Fiji instance. Must be passed
         explicitly as `globals()` by the calling code.
-    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".
+    destination : str, optional
+        Directory where the script parameters file will be saved. If empty
+        (the default), parameter saving is skipped.
+    overwrite : bool, optional
+        If True, use a fixed filename ``<script_name>_params.txt`` that gets
+        overwritten on each run. If False (the default), a timestamp is
+        included in the filename to preserve parameters from each run.
 
     Examples
     --------
     In a Fiji script, you can call this function as follows to save the parameters:
 
     >>> save_script_parameters(script_globals=globals(), destination="/data")
-    Saved script parameters to: /data/script_parameters.txt
+    Saved 2 script parameters to: /data/example1_run-2026-04-10--10-41_params.txt
     """
+    if destination == "":
+        timed_log("No destination provided for saving script parameters - skipping.")
+        return
+
     try:
         module = script_globals.get("org.scijava.script.ScriptModule")
-        # Access script metadata and inputs
         script_info = module.getInfo()
         inputs = module.getInputs()
     except:
         timed_log("ScriptModule inspection failed - skipping saving of parameters.")
         return
 
-    # NOTE: the two parameters are intentionally kept separate for (1) consistency
-    # reasons with other scripts and (b) as this allows for easier modification of just
-    # the output file e.g. in subsequent runs.
+    script_location = script_info.getLocation()
+    if script_location:
+        # getLocation() returns "file:/path/to/script.py"
+        # strip the "file:" prefix to get the actual path
+        if script_location.startswith("file:"):
+            script_location = script_location[5:]
+        script_name = os.path.splitext(os.path.basename(script_location))[0]
+    else:
+        script_name = "script"
+
+    if overwrite:
+        save_file_name = "%s_params.txt" % script_name
+    else:
+        timestamp = time.strftime("%Y-%m-%d--%H-%M")
+        save_file_name = "%s_run-%s_params.txt" % (script_name, timestamp)
+
     destination = str(destination)
     out_path = os.path.join(destination, save_file_name)
 
@@ -843,8 +863,9 @@ def save_script_parameters(
         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):
+            # Skip if the key is in the skip list (whole name, not a substring:
+            # e.g. "FUSION_FORMAT" contains "RM")
+            if key.upper() in skip_keys:
                 log.info("Skipping parameter from skip-list: %s", key)
                 skipped += 1
                 continue
@@ -855,7 +876,6 @@ def save_script_parameters(
                 passwords += 1
                 continue
 
-            # TODO: discuss if this approach is fine within Fiji/Jython
             try:
                 val = inputs.get(key)
                 if val is None:  # required for testing in CPython

tests/test_misc.py

@@ -1,6 +1,7 @@
 """Tests for `imcflibs.imagej.misc` utility functions."""
 
 import logging
+import os
 
 from org.scijava.script import ScriptInfo, ScriptModule
 
@@ -9,15 +10,22 @@
 from imcflibs.imagej.misc import bytes_to_human_readable
 from imcflibs.imagej.misc import save_script_parameters
 
-
 PASSWORD_ITEMS = ["OMERO_PASSWD"]
 
 
-def test_save_script_parameters_fail(caplog):
+def test_save_script_parameters_no_destination(caplog):
+    """Tests save_script_parameters skips saving without a destination."""
+    caplog.clear()
+
+    save_script_parameters(script_globals=None)
+    assert "No destination provided" in caplog.messages[0]
+
+
+def test_save_script_parameters_fail(tmp_path, caplog):
     """Tests save_script_parameters with an invalid script_globals object."""
     caplog.clear()
 
-    save_script_parameters(script_globals=None, destination="")
+    save_script_parameters(script_globals=None, destination=tmp_path)
     assert "ScriptModule inspection failed" in caplog.messages[0]
 
 
@@ -38,19 +46,63 @@ def _is_password_style(item):
         input_names=["AAA", "BBB", "OMERO_PASSWD", "SJLOG", "NOT_THERE"],
         inputs={"AAA": "aaa", "BBB": "bbb", "OMERO_PASSWD": "ultra-secret"},
     )
+    script_module.getInfo().location = "file:/some/path/example1.py"
     script_globals = {"org.scijava.script.ScriptModule": script_module}
-    save_script_parameters(script_globals, destination=base)
+    save_script_parameters(script_globals, destination=base, overwrite=True)
     assert "Skipping parameter from skip-list" in caplog.text
     assert "Skipping password-style parameter" in caplog.text
     assert "Unable to fetch value for parameter: NOT_THERE" in caplog.text
     assert "Saved 2 parameters (skipped 1 password-style and 1 others)." in caplog.text
     assert "Saved 2 script parameters to" in caplog.text
 
-    with open(str(base) + "/script_parameters.txt", "r") as f:
+    with open(str(base) + "/example1_params.txt", "r") as f:
         contents = f.read()
     assert contents == "AAA: aaa\nBBB: bbb\n"
 
 
+def test_save_script_parameters_timestamped(tmp_path, monkeypatch):
+    """Tests save_script_parameters default naming without a script location."""
+
+    def _is_password_style(item):
+        return False
+
+    monkeypatch.setattr(imcflibs.imagej.misc, "_is_password_style", _is_password_style)
+
+    script_module = ScriptModule(input_names=["AAA"], inputs={"AAA": "aaa"})
+    script_globals = {"org.scijava.script.ScriptModule": script_module}
+    save_script_parameters(script_globals, destination=tmp_path)
+
+    # the folder should now contain exactly one file
+    files = os.listdir(str(tmp_path))
+    assert len(files) == 1
+
+    # its name is "script_run-<timestamp>_params.txt"
+    file_name = files[0]
+    assert file_name.startswith("script_run-")
+    assert file_name.endswith("_params.txt")
+
+    with open(os.path.join(str(tmp_path), file_name), "r") as f:
+        assert f.read() == "AAA: aaa\n"
+
+
+def test_save_script_parameters_skip_whole_names(tmp_path, monkeypatch, caplog):
+    """Only whole names are skipped, case insensitive, not substrings."""
+    caplog.set_level(logging.DEBUG)
+    caplog.clear()
+    monkeypatch.setattr(imcflibs.imagej.misc, "_is_password_style", lambda item: False)
+
+    script_module = ScriptModule(
+        input_names=["rm", "fusion_format", "commander"],
+        inputs={"rm": "roimanager", "fusion_format": "TIFF", "commander": "x"},
+    )
+    script_globals = {"org.scijava.script.ScriptModule": script_module}
+    save_script_parameters(script_globals, destination=tmp_path, overwrite=True)
+
+    with open(str(tmp_path) + "/script_params.txt", "r") as f:
+        contents = f.read()
+    assert contents == "fusion_format: TIFF\ncommander: x\n"
+
+
 def test_bytes_to_human_readable_simple():
     """Ensure common sizes are formatted into human-readable strings."""
     assert bytes_to_human_readable(500) == "500.0 bytes"