From 361870acbab4a43a3ed282714d20d90918c7ffd5 Mon Sep 17 00:00:00 2001
From: romainGuiet <romain.guiet@epfl.ch>
Date: Mon, 9 Dec 2024 12:45:33 +0100
Subject: [PATCH] update example scripts

---
 resources/scripts/cellpose_macro.ijm     | 4 ++--
 resources/scripts/cellpose_script.groovy | 7 ++++---
 2 files changed, 6 insertions(+), 5 deletions(-)

diff --git a/resources/scripts/cellpose_macro.ijm b/resources/scripts/cellpose_macro.ijm
index 2cec30d..89ae955 100644
--- a/resources/scripts/cellpose_macro.ijm
+++ b/resources/scripts/cellpose_macro.ijm
@@ -1,5 +1,5 @@
-conda_env_path = "D:/conda/conda-envs/cellpose-307-gpu"
+#@File(style="directory" , label="Select conda environment") conda_env_path
 //run("Blobs (25K)"); // uncomment to test
 image_title = getTitle();
 
-run("Cellpose ..." ,"imp="+image_title+" conda_env_path="+conda_env_path+" diameter=30 model=cyto3 model_path= ch1=1 ch2=1 additional_flags=--use_gpu" );
\ No newline at end of file
+run("Cellpose ..." ,"imp="+image_title+" conda_env_path="+conda_env_path+" env_type=conda diameter=30 model=cyto3 model_path= ch1=1 ch2=1 additional_flags=--use_gpu" );
\ No newline at end of file
diff --git a/resources/scripts/cellpose_script.groovy b/resources/scripts/cellpose_script.groovy
index cfea21b..3503514 100644
--- a/resources/scripts/cellpose_script.groovy
+++ b/resources/scripts/cellpose_script.groovy
@@ -11,7 +11,7 @@ IJ.runMacro("close('\\\\Others');")
 
 // cellpose parameters
 def cp = new Cellpose();
-cp.conda_env_path = conda_env_path
+cp.env_path = conda_env_path
 // Or comment the line avove and set the path manually
 // to locate your conda env from a terminal type "conda env list", it will return the path you can paste below
 //cp.conda_env_path = new File ( "D:/conda/conda_envs/cellpose/" ) ;
@@ -20,7 +20,8 @@ cp.diameter = 50;
 cp.model = "cyto3";
 cp.ch1 = 1 ;
 cp.ch2 = 2 ;
-cp.additional_flags= "--use_gpu, --do_3D, --anisotropy, 4 , --restore_type , denoise_cyto3";
+//cp.additional_flags= "--use_gpu, --do_3D, --anisotropy, 4 , --restore_type , denoise_cyto3";
+cp.additional_flags= "--use_gpu,  --restore_type , denoise_cyto3";
 // cellpose run
 cp.run();
 // get the output labels image
@@ -35,4 +36,4 @@ cp_imp.setDisplayRange(0, 12);
 return
 
 import ch.epfl.biop.wrappers.cellpose.ij2commands.Cellpose
-import ij.IJ;
\ No newline at end of file
+import ij.IJ;