Updated scanning range to work in macros

Author: DrNjitram

.gitignore

@@ -38,3 +38,4 @@ hs_err_pid*
 /Python Scripts/figures/*
 /Python Scripts/test/results/*
 /test_path/*
+/Python Scripts/figures/*

Python Scripts/figures/figure 2.png

@@ -391,10 +391,11 @@ def run(argument_string = "", max_neighbourhood=None, filter_edges=None, promine
 
     if args.IDE: # change defaults if needed
         args.testing = 0
-        args.show_graph = True
-        args.core_path = r""
-        #args.filenames = "all"
-        args.filenames = ["window100_coronal_top_A_crop", "window300_coronal_top_A_crop"]
+        args.show_graph = False
+        args.core_path = r"D:\Data\2025_KatjaDeadstopPaper\results\input"
+        args.filenames = "all"
+        absolute=True
+        #args.filenames = ["window100_coronal_top_A_crop", "window300_coronal_top_A_crop"]
 
 
     if max_neighbourhood is not None:

Python Scripts/figures/figure 2.svg

@@ -0,0 +1,11 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<module version="4">
+  <component name="AdditionalModuleElements">
+    <content url="file://$MODULE_DIR$" dumb="true">
+      <excludeFolder url="file://$MODULE_DIR$/Matlab" />
+      <excludeFolder url="file://$MODULE_DIR$/Python Scripts" />
+      <excludeFolder url="file://$MODULE_DIR$/Test Images" />
+      <excludeFolder url="file://$MODULE_DIR$/test_path" />
+    </content>
+  </component>
+</module>

Python Scripts/gaussian_order.py

@@ -9,12 +9,12 @@
 	<parent>
 		<groupId>org.scijava</groupId>
 		<artifactId>pom-scijava</artifactId>
-		<version>39.0.0</version>
+		<version>40.0.0</version>
 	</parent>
 
 	<groupId>com.wurgobes</groupId>
 	<artifactId>RFT</artifactId>
-	<version>1.0</version>
+	<version>1.1</version>
 
 
 	<name>Rotated Fourier Transform</name>

RFT.iml

@@ -196,7 +196,9 @@ public void runVector(RFTParameters params){
         if(params.window % 2 == 0)
             params.window += 1;
 
-        setupImage();
+        if(!params.scanning_range)
+            setupImage();
+
         //Non stack version for now
         if(false && imp.hasImageStack()){
             ImageStack input = imp.getStack();
@@ -286,6 +288,8 @@ public void AngleGraph(RFTParameters params){
     }
 
     public void scanWindow(RFTParameters params){
+        setupImage();
+        logService.info("Performing scan: " + params.start + ":" + params.step + ":" + params.end + " on " + imp.getTitle());
         params.scanning_range = Boolean.TRUE;
         ImageStack angle_stack = null;
         for(int i = params.start; i <= params.end; i+=params.step){

pom.xml

@@ -7,7 +7,7 @@
 
 public class Constants {
     static public String softname = "RFT";
-    static public String version = "1.0";
+    static public String version = "1.1";
     static public String date = "1st October 2024";
     static public String author = "Martijn Gobes";
     static public String link = "https://github.com/HohlbeinLab/AnalyseDirectionality";