From b37103c77a91ea43473c5e9734a04c8d86abd3f4 Mon Sep 17 00:00:00 2001
From: Christopher Schmied <schmied@mpi-cbg.de>
Date: Tue, 14 Jul 2015 19:22:34 +0200
Subject: [PATCH] Modified output of GPU/CPU setting in deconvolution.bsh
---
spim_registration/timelapse/deconvolution.bsh | 35 ++++++++++++++++++-
1 file changed, 34 insertions(+), 1 deletion(-)
mode change 100644 => 100755 spim_registration/timelapse/deconvolution.bsh
diff --git a/spim_registration/timelapse/deconvolution.bsh b/spim_registration/timelapse/deconvolution.bsh
old mode 100644
new mode 100755
index 1ecd9b9..4509830
--- a/spim_registration/timelapse/deconvolution.bsh
+++ b/spim_registration/timelapse/deconvolution.bsh
@@ -140,6 +140,7 @@ if (compute_on.equalsIgnoreCase( "GPU (Nvidia CUDA via JNA)" ) )
cuda_settings = "cuda_directory=" + directory_cuda + " " +
"select_native_library_for_cudafourierconvolution=" + cudafourierconvolution + " " +
"gpu_1 ";
+ System.out.println( "cuda_settings=" + cuda_settings );
}
else if (compute_on.equalsIgnoreCase( "CPU (Java)" ) )
@@ -155,11 +156,43 @@ else
}
System.out.println( "compute_string=" + compute_string );
-System.out.println( "cuda_settings=" + cuda_settings );
// Execute Fiji Plugin
System.out.println( "=======================================================" );
System.out.println( "Starting Deconvolution" );
+System.out.println("Fuse/Deconvolve Dataset select_xml=" + image_file_directory + merged_xml + " " +
+ "process_angle=[All angles] " +
+ "process_channel=[All channels] " +
+ "process_illumination=[All illuminations] " +
+ "process_timepoint=[" + process_timepoint + "] " +
+ "processing_timepoint=[Timepoint " + parallel_timepoints + "] " +
+ "type_of_image_fusion=[Multi-view deconvolution] " +
+ "bounding_box=[Define manually] " +
+ "fused_image=[Save as TIFF stack] " +
+ "minimal_x=" + minimal_x_deco + " " +
+ "minimal_y=" + minimal_y_deco + " " +
+ "minimal_z=" + minimal_z_deco + " " +
+ "maximal_x=" + maximal_x_deco + " " +
+ "maximal_y=" + maximal_y_deco + " " +
+ "maximal_z=" + maximal_z_deco + " " +
+ "imglib2_container=" + imglib2_container_deco + " " +
+ "type_of_iteration=[" + type_of_iteration + "] " +
+ "osem_acceleration=[" + osem_acceleration + "] " +
+ "number_of_iterations=" + iterations + " " +
+// "adjust_blending_parameters " +
+ "use_tikhonov_regularization " +
+ "tikhonov_parameter=" + Tikhonov_parameter + " " +
+ "compute=[" + compute + "] " +
+ compute_string +
+ "psf_estimation=[" + psf_estimation + "] " +
+ "psf_display=[Do not show PSFs] " +
+ "output_file_directory=" + deco_output_file_directory + " " +
+ cuda_settings +
+ channel_string +
+ "psf_size_x=" + psf_size_x + " " +
+ "psf_size_y=" + psf_size_y + " " +
+ "psf_size_z=" + psf_size_z + "");
+
try {
IJ.run("Fuse/Deconvolve Dataset",
"select_xml=" + image_file_directory + merged_xml + " " +
--
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