From 0e19239eefe6eebff32e835d3fb9b8d8a33eba4d Mon Sep 17 00:00:00 2001 From: Rohan Girish Date: Wed, 29 Oct 2025 11:22:34 +0100 Subject: [PATCH 1/7] 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 Date: Wed, 29 Oct 2025 17:34:48 +0100 Subject: [PATCH 2/7] 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) + + From 02d84d8346eb9c1895e83d1d1652ffa83bb6eb1f Mon Sep 17 00:00:00 2001 From: Rohan Girish Date: Tue, 4 Nov 2025 14:40:05 +0100 Subject: [PATCH 3/7] Add keys to skip logging --- src/imcflibs/imagej/misc.py | 3 +++ 1 file changed, 3 insertions(+) diff --git a/src/imcflibs/imagej/misc.py b/src/imcflibs/imagej/misc.py index 7b972ba2..1cbf9dac 100644 --- a/src/imcflibs/imagej/misc.py +++ b/src/imcflibs/imagej/misc.py @@ -726,8 +726,11 @@ def save_script_parameters(destination, save_file_name="script_parameters.txt"): out_path = os.path.join(destination, save_file_name) # Write the parameters to output file + skip_keys = ["PASSWORD", "USERNAME", "SJLOG", "COMMAND", "RM"] with open(out_path, "w") as f: for key in inputs.keySet(): + if any(s in key.upper() for s in skip_keys): + continue val = inputs.get(key) f.write("%s: %s\n" % (key, str(val))) From c7c0d3e89befac5e6a00b605b071d195dbf59ba8 Mon Sep 17 00:00:00 2001 From: Rohan Girish Date: Wed, 5 Nov 2025 09:30:44 +0100 Subject: [PATCH 4/7] Update method to save Fiji script parameters The method now ignores password in a clean way, and skips some other non-essential runtime keys. --- src/imcflibs/imagej/misc.py | 44 ++++++++++++++++++++++++++++--------- 1 file changed, 34 insertions(+), 10 deletions(-) diff --git a/src/imcflibs/imagej/misc.py b/src/imcflibs/imagej/misc.py index 1cbf9dac..1af50fcd 100644 --- a/src/imcflibs/imagej/misc.py +++ b/src/imcflibs/imagej/misc.py @@ -713,27 +713,51 @@ def save_script_parameters(destination, save_file_name="script_parameters.txt"): 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: - print("No ScriptModule found- skipping saving script parameters.") + 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 - skip_keys = ["PASSWORD", "USERNAME", "SJLOG", "COMMAND", "RM"] + + # Access script metadata and parameter map + script_info = module.getInfo() + inputs = module.getInputs() + + # Keys to skip explicitly (case-insensitive match) + skip_keys = ["USERNAME", "SJLOG", "COMMAND", "RM"] + with open(out_path, "w") as f: - for key in inputs.keySet(): - if any(s in key.upper() for s in skip_keys): + 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 - val = inputs.get(key) - f.write("%s: %s\n" % (key, str(val))) + + # Skip if parameter is declared with style="password" + style = item.getWidgetStyle() + if style is not None and style.lower() == "password": + continue + + # Write all other parameters + if inputs.containsKey(key): + val = inputs.get(key) + f.write("%s: %s\n" % (key, str(val))) print("Saved script parameters to: %s" % out_path) + From cdda918932d3502d7695cdb49cc27594a0c776c1 Mon Sep 17 00:00:00 2001 From: Rohan Girish Date: Wed, 5 Nov 2025 09:35:23 +0100 Subject: [PATCH 5/7] Run black formatter --- src/imcflibs/imagej/misc.py | 9 +++------ 1 file changed, 3 insertions(+), 6 deletions(-) diff --git a/src/imcflibs/imagej/misc.py b/src/imcflibs/imagej/misc.py index 1af50fcd..7568d9e3 100644 --- a/src/imcflibs/imagej/misc.py +++ b/src/imcflibs/imagej/misc.py @@ -702,7 +702,7 @@ 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. @@ -713,9 +713,9 @@ def save_script_parameters(destination, save_file_name="script_parameters.txt"): 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. @@ -758,6 +758,3 @@ def save_script_parameters(destination, save_file_name="script_parameters.txt"): f.write("%s: %s\n" % (key, str(val))) print("Saved script parameters to: %s" % out_path) - - - From eed68d8bc109e5805329c0c8b121834f59040175 Mon Sep 17 00:00:00 2001 From: Rohan Girish Date: Wed, 5 Nov 2025 09:44:28 +0100 Subject: [PATCH 6/7] Remove redundant ScriptModule import --- src/imcflibs/imagej/misc.py | 1 - 1 file changed, 1 deletion(-) diff --git a/src/imcflibs/imagej/misc.py b/src/imcflibs/imagej/misc.py index 7568d9e3..847c6dbf 100644 --- a/src/imcflibs/imagej/misc.py +++ b/src/imcflibs/imagej/misc.py @@ -7,7 +7,6 @@ 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 From cd9795fe217ef7887cd3bcb1948cf21375f17cd4 Mon Sep 17 00:00:00 2001 From: Rohan Girish Date: Wed, 12 Nov 2025 11:23:00 +0100 Subject: [PATCH 7/7] Remove redundant comments --- src/imcflibs/imagej/misc.py | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/src/imcflibs/imagej/misc.py b/src/imcflibs/imagej/misc.py index 847c6dbf..7b9ec0a3 100644 --- a/src/imcflibs/imagej/misc.py +++ b/src/imcflibs/imagej/misc.py @@ -731,11 +731,11 @@ def save_script_parameters(destination, save_file_name="script_parameters.txt"): destination = str(destination) out_path = os.path.join(destination, save_file_name) - # Access script metadata and parameter map + # Access script metadata and inputs script_info = module.getInfo() inputs = module.getInputs() - # Keys to skip explicitly (case-insensitive match) + # Keys to skip explicitly skip_keys = ["USERNAME", "SJLOG", "COMMAND", "RM"] with open(out_path, "w") as f: @@ -751,7 +751,6 @@ def save_script_parameters(destination, save_file_name="script_parameters.txt"): if style is not None and style.lower() == "password": continue - # Write all other parameters if inputs.containsKey(key): val = inputs.get(key) f.write("%s: %s\n" % (key, str(val)))