From b826503349f983f23883cac2e9658ff25cab929c Mon Sep 17 00:00:00 2001
From: Christopher Schmied <schmied@mpi-cbg.de>
Date: Wed, 1 Jul 2015 22:39:29 +0200
Subject: [PATCH] Tested Dual Channel Pipeline one channel contains beads
---
spim_registration/timelapse/Snakefile | 8 ++++----
spim_registration/timelapse/cluster.json | 2 +-
spim_registration/timelapse/dual_OneChannel.yaml | 2 +-
spim_registration/timelapse/fusion.bsh | 2 +-
spim_registration/timelapse/single_test.yaml | 4 ++--
5 files changed, 9 insertions(+), 9 deletions(-)
diff --git a/spim_registration/timelapse/Snakefile b/spim_registration/timelapse/Snakefile
index 6436496..f7211ce 100755
--- a/spim_registration/timelapse/Snakefile
+++ b/spim_registration/timelapse/Snakefile
@@ -7,9 +7,9 @@ if JOBDIR[-1] != "/": # this checks if jobdir ends with slash if not it adds a s
JOBDIR+="/"
# Test config file single Channel:
-configfile: "single_test.yaml"
+# configfile: "single_test.yaml"
# Test config file dual channel one channel contains beads:
-# configfile: "dual_OneChannel.yaml"
+configfile: "dual_OneChannel.yaml"
# data specific config file, expected to be inside JOBDIR
# configfile: "tomancak_test_cluster.yaml"
@@ -266,8 +266,8 @@ rule timelapse:
rule duplicate_transformations:
input: rules.timelapse.output, merged_xml="{xml_base}_merge.xml"
- output: rules.timelapse.output[0] + "_dublicate"
- log: "{xml_base}_dublicate_transformations.log"
+ output: rules.timelapse.output[0] + "_duplicate"
+ log: "{xml_base}_duplicate_transformations.log"
run:
cmd_string = produce_string(
"""{fiji-prefix} {fiji-app} \
diff --git a/spim_registration/timelapse/cluster.json b/spim_registration/timelapse/cluster.json
index 00b1765..7f13c62 100755
--- a/spim_registration/timelapse/cluster.json
+++ b/spim_registration/timelapse/cluster.json
@@ -27,7 +27,7 @@
"fusion" :
{
- "lsf_extra" : "-n 7 -R \"span[hosts=1] rusage[mem=100000]\""
+ "lsf_extra" : "-n 12 -R \"span[hosts=1] rusage[mem=100000]\""
},
"deconvolution" :
diff --git a/spim_registration/timelapse/dual_OneChannel.yaml b/spim_registration/timelapse/dual_OneChannel.yaml
index b009596..239f9df 100755
--- a/spim_registration/timelapse/dual_OneChannel.yaml
+++ b/spim_registration/timelapse/dual_OneChannel.yaml
@@ -29,7 +29,7 @@ common: {
# Switches between content based fusion and deconvoltion
# "deconvolution" > for deconvolution
# "fusion" > for content based fusion
- fusion_switch: "deconvolution"
+ fusion_switch: "fusion"
}
define_xml_czi: {
diff --git a/spim_registration/timelapse/fusion.bsh b/spim_registration/timelapse/fusion.bsh
index e605002..945556c 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 5cf7c44..e89c1f7 100755
--- a/spim_registration/timelapse/single_test.yaml
+++ b/spim_registration/timelapse/single_test.yaml
@@ -229,8 +229,8 @@ hdf5_output: {
output_multiple_channels: '"NO (one channel)"', # '"YES (one file per channel)"' or '"NO (one channel)"'
output_channels: "green",
# .xml file names
- output_xml: '"fused_Dual_Channel"',
- output_hdf5_xml: '"hdf5_fused_Dual_Channel"',
+ output_xml: '"fused_Single"',
+ output_hdf5_xml: '"hdf5_fused_Single"',
output_timepoints: '0-1', # Timepoints format: '1-2'
# pixel size of output: take downsampling into account!
output_pixel_distance_x: 0.28590106964,
--
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