diff --git a/spim_registration/timelapse/deconvolution.bsh b/spim_registration/timelapse/deconvolution.bsh old mode 100644 new mode 100755 index 1ecd9b960e59567c901217e65a0984533574d8b3..4509830467a56fe657c2e7eb9da504bf66f3a2d9 --- 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 + " " +