bugfixed python code generation

clij · Aug 15, 2020 · ffb0996 · ffb0996
1 parent 556bc80
commit ffb0996
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Showing 3 changed files with 14 additions and 8 deletions.
diff --git a/src/main/java/net/haesleinhuepf/clijx/incubator/scriptgenerator/PyclesperantoGenerator.java b/src/main/java/net/haesleinhuepf/clijx/incubator/scriptgenerator/PyclesperantoGenerator.java
@@ -34,7 +34,7 @@ public String push(ImagePlus source) {
                 "image = imread(\"" + filename.replace("\\", "/") + "\")\n\n"+
 
                 "# Push " + source.getTitle() + " to GPU memory\n" +
-                "image1 = cle.push(image)\n";
+                makeImageID(source) + " = cle.push(image)\n";
 
 
         program = program.replace("\n", "\n" + line_start );
@@ -84,9 +84,14 @@ public String execute(IncubatorPlugin plugin) {
         program = program + methodName + "(" + image1 + ", " + image2 + call + ")\n";
 
         if (use_napari) {
+            String scale = calibration.pixelHeight + ", " + calibration.pixelWidth;
+            if (plugin.getTarget().getNSlices() > 1) {
+                scale = calibration.pixelDepth + ", " + calibration.pixelHeight + ", " + calibration.pixelWidth;
+            }
+
             program = program +
                     "# show result\n\n" +
-                    "viewer.add_image(cle.pull(" + image2 + "), scale=(" + calibration.pixelDepth + ", " + calibration.pixelHeight + ", " + calibration.pixelWidth + "))\n\n";
+                    "viewer.add_image(cle.pull(" + image2 + "), scale=(" + scale + "))\n\n";
         } else {
             program = program +
             "# show result\n\n" +
@@ -123,10 +128,11 @@ public String header() {
                 "#  > conda activate te_oki \n" +
                 "# install dependencies: \n" +
                 "#  > pip install pyopencl napari matplotlib numpy pyclesperanto_prototype \n" +
+                "# Also make sure conda is part of the PATH variable.\n" +
                 "# \n" +
-                "# If you want to run it from Fiji, configure conda in Fijis main menu \n" +
+                "# If you want to run it from Fiji and you're using a different conda environment, you can configure it in Fijis main menu \n" +
                 "# Plugins > ImageJ on GPU (CLIJx-Incubator) > Options >Conda configuration (Te Oki) \n" +
-                "# Furtermore, activate the scripting language Te Oki in Fijis script editor to run this script.\n\n" +
+                "# Furthermore, activate the scripting language Te Oki in Fijis script editor to run this script.\n\n" +
                 "# Stay tuned and check out http://clesperanto.net to learn more." +
                 "\n\n" +
                 "import pyclesperanto_prototype as cle\n";

diff --git a/src/main/java/net/haesleinhuepf/clijx/te_oki/TeOkiConfigurationDialog.java b/src/main/java/net/haesleinhuepf/clijx/te_oki/TeOkiConfigurationDialog.java
@@ -8,15 +8,15 @@ public class TeOkiConfigurationDialog implements PlugIn {
     @Override
     public void run(String arg) {
         GenericDialogPlus gdp = new GenericDialogPlus("Te Oki Configuration");
-        gdp.addDirectoryField("Conda directory", TeOkiEngine.conda_directory);
+        //gdp.addDirectoryField("Conda directory", TeOkiEngine.conda_directory);
         gdp.addStringField("Conda environment", TeOkiEngine.conda_env);
         gdp.showDialog();
 
         if (gdp.wasCanceled()) {
             return;
         }
 
-        TeOkiEngine.conda_directory = gdp.getNextString();
+        //TeOkiEngine.conda_directory = gdp.getNextString();
         TeOkiEngine.conda_env = gdp.getNextString();
     }
 }
diff --git a/src/main/java/net/haesleinhuepf/clijx/te_oki/TeOkiEngine.java b/src/main/java/net/haesleinhuepf/clijx/te_oki/TeOkiEngine.java
@@ -49,7 +49,7 @@
 public class TeOkiEngine extends IJ1MacroEngine {
 
 	public static String teOkiDirectory = null;
-	public static String conda_directory = "C:\\Users\\rober\\miniconda3";
+	//public static String conda_directory = "";
 	public static String conda_env = "te_oki";
 
 
@@ -76,7 +76,7 @@ public void run() {
 				String conda_code;
 
 				if (isWindows) {
-					conda_code = "call " + conda_directory + "\\Scripts\\activate.bat " + conda_directory + "\n" +
+					conda_code = //"call " + conda_directory + "\\Scripts\\activate.bat " + conda_directory + "\n" +
 							"call conda activate " + conda_env + "\n" +
 							"cd " + directory + "\n" +
 							"ipython --gui=qt temp.py";