From 0b1bb5b9f031056f60169ba80b368d97c6db2c8f Mon Sep 17 00:00:00 2001
From: Christopher Schmied <schmied@mpi-cbg.de>
Date: Wed, 1 Jul 2015 16:40:37 +0200
Subject: [PATCH] Tested single channel processing fusion takes to long with
blending and full resolution
---
spim_registration/timelapse/cluster.json | 2 +-
spim_registration/timelapse/fusion.bsh | 2 +-
spim_registration/timelapse/single_test.yaml | 4 ++--
3 files changed, 4 insertions(+), 4 deletions(-)
diff --git a/spim_registration/timelapse/cluster.json b/spim_registration/timelapse/cluster.json
index ab4d912..00b1765 100755
--- a/spim_registration/timelapse/cluster.json
+++ b/spim_registration/timelapse/cluster.json
@@ -27,7 +27,7 @@
"fusion" :
{
- "lsf_extra" : "-n 6 -R \"span[hosts=1] rusage[mem=100000]\""
+ "lsf_extra" : "-n 7 -R \"span[hosts=1] rusage[mem=100000]\""
},
"deconvolution" :
diff --git a/spim_registration/timelapse/fusion.bsh b/spim_registration/timelapse/fusion.bsh
index 945556c..e605002 100755
--- a/spim_registration/timelapse/fusion.bsh
+++ b/spim_registration/timelapse/fusion.bsh
@@ -98,7 +98,7 @@ IJ.run("Fuse/Deconvolve Dataset",
"imglib2_container=" + imglib2_container_fusion + " " +
"process_views_in_paralell=All " +
"interpolation=[" + interpolation + "] " +
- "blend " +
+ //"blend " +
"content-based " +
"output_file_directory=" + image_file_directory + " " +
"lossless " +
diff --git a/spim_registration/timelapse/single_test.yaml b/spim_registration/timelapse/single_test.yaml
index 9171d0c..5cf7c44 100755
--- a/spim_registration/timelapse/single_test.yaml
+++ b/spim_registration/timelapse/single_test.yaml
@@ -7,9 +7,9 @@ common: {
fiji-app: "/sw/users/schmied/packages/2015-06-30_Fiji.app.cuda/ImageJ-linux64",
fiji-prefix: "/sw/users/schmied/packages/xvfb-run -a", # calls xvfb for Fiji headless mode
# xml file names without .xml suffix
- first_xml_filename: '"single"', # Name of the xml file for the .czi or .tif files
+ first_xml_filename: 'single', # Name of the xml file for the .czi or .tif files
hdf5_xml_filename: '"hdf5_single"', # Name of .xml file for the hdf5 data after resave_hdf5
- merged_xml: '"hdf5_single_merge"', # Name of .xml file after merge
+ merged_xml: 'hdf5_single_merge', # Name of .xml file after merge
# Describe the dataset
ntimepoints: 2, # number of timepoints of dataset
angles: "0,72,144,216,288", # angles
--
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