Fix RunImageJScript parameter detection, add DOI (#200)

* CP-IJ: fix image parameter detection

Fixes the previous logic to no longer claim every param type as an
image, restricting things appropriately to just the classes defined in
img_strings.

* CP-IJ: fully support parameter deletion

We were tracking input/output params in addition to the overall
settings, so both locations need to be updated when removing.

* Add DOI

---------

Co-authored-by: hinerm <hinerm@gmail.com>

Author: bethac07

active_plugins/runimagejscript.py

@@ -24,6 +24,10 @@
 import skimage.io
 import cpij.bridge as ijbridge, cpij.server as ijserver
 
+imagej_link = "https://doi.org/10.1038/nmeth.2089"
+imagej2_link = "https://doi.org/10.1186/s12859-017-1934-z"
+pyimagej_link = "https://doi.org/10.1038/s41592-022-01655-4"
+
 __doc__ = """\
 RunImageJScript
 =================
@@ -51,6 +55,10 @@
 ^^^^^^^^
 
 ImageJ Scripting: https://imagej.net/Scripting 
+Schneider, C. A., Rasband, W. S., & Eliceiri, K. W. (2012). NIH Image to ImageJ: 25 years of image analysis. Nature Methods, 9(7), 671–675. {imagej_link}
+Rueden, C. T., Schindelin, J., Hiner, M. C., DeZonia, B. E., Walter, A. E., Arena, E. T., & Eliceiri, K. W. (2017). ImageJ2: ImageJ for the next generation of scientific image data. BMC Bioinformatics, 18(1). {imagej2_link}
+Rueden, C.T., Hiner, M.C., Evans, E.L. Pinkart, M.A., Lucas, A.M., Carpenter, A.E., Cimini, B.A., & Eliceiri, K. W. (2022). PyImageJ: A library for integrating ImageJ and Python. Nat Methods 19, 1326–1327 . {pyimagej_link}
+
  
 """
 
@@ -112,6 +120,8 @@ class RunImageJScript(Module):
     variable_revision_number = 3
     category = "Advanced"
 
+    doi = {"If you are using RunImageJScript please cite the following": pyimagej_link }
+
     def __init__(self):
         super().__init__()
         self.parsed_params = False  # Used for validation
@@ -504,6 +514,12 @@ def validate_module_warnings(self, pipeline):
     def run(self, workspace):
         self.init_pyimagej()
 
+        # Unwrap the current settings from their SettingsGroups
+        all_settings = list(map(lambda x: x.settings[0], self.script_parameter_list))
+        # Update the script input/output settings in case any were removed from the GUI
+        self.script_input_settings = {k: v for (k,v) in self.script_input_settings.items() if v in all_settings}
+        self.script_output_settings = {k: v for (k,v) in self.script_output_settings.items() if v in all_settings}
+
         if self.show_window:
             workspace.display_data.script_input_pixels = {}
             workspace.display_data.script_input_dimensions = {}

cpij/server.py

@@ -209,7 +209,7 @@ def set_directory_fn_app(path):
                 browse_msg=f'Choose {param_label} file'
                 )
             return (param_dir, param_file)
-        elif bool((img_string for img_string in img_strings if type_string == img_string)):
+        elif type_string in img_strings:
             return ImageSubscriber(param_label)
     elif OUTPUT_CLASS == param_class:
         if bool((img_string for img_string in img_strings if type_string == img_string)):