From 39afa828956e05065d12eb80bea3a8e3f3e75433 Mon Sep 17 00:00:00 2001
From: Christopher Schmied <schmied@mpi-cbg.de>
Date: Thu, 11 Jun 2015 14:42:53 +0200
Subject: [PATCH] Added dublicate_transformations.bsh
Added a switch in .yaml file for selecting dublication of transformation
Added a part in the snakefile for dublication of the transformation
in the pipeline
---
spim_registration/timelapse/Snakefile | 34 +++++++++++++++++--
.../timelapse/tomancak_test_cluster.yaml | 9 +++--
2 files changed, 37 insertions(+), 6 deletions(-)
diff --git a/spim_registration/timelapse/Snakefile b/spim_registration/timelapse/Snakefile
index 812dccc..178e91c 100755
--- a/spim_registration/timelapse/Snakefile
+++ b/spim_registration/timelapse/Snakefile
@@ -253,9 +253,37 @@ rule timelapse:
jdir=JOBDIR)
cmd_string += " > {log} 2>&1 && touch {output}"
shell(cmd_string)
-
+
+rule dublicate_transformations:
+ input: rules.timelapse.output, merged_xml="{xml_base}_merge.xml"
+ output: rules.timelapse.output[0] + "_dublicate"
+ log: "{xml_base}_dublicate_transformations.log"
+ run:
+ cmd_string = produce_string(
+ """{fiji-prefix} {fiji-app}
+ -Dimage_file_directory={jdir} \
+ -Dmerged_xml={merged_xml} \
+ -Dprocess_timepoint_timelapse={timelapse_process_timepoints} \
+ -Dprocess_illumination={reg_process_illumination} \
+ -Dprocess_angle={reg_process_angle} \
+ -Dsource_dublication={source_dublication} \
+ -Dtarget_dublication={target_dublication} \
+ -Dduplicate_which_transformations={duplicate_which_transformations} \
+ -- --no-splash {path_bsh}""",
+ config["common"],
+ config["registration"],
+ config["timelapse"],
+ config["dublicate_channel"],
+ path_bsh=config["common"]["bsh_directory"] + config["Dublicate_transformations"]["bsh_file"],
+ jdir=JOBDIR,
+ file_id_w="{wildcards.file_id}",
+ merged_xml_file="{input.merged_xml}"
+ )
+ cmd_string += " > {log} 2>&1 && touch {output}"
+ shell(cmd_string)
+
rule fusion:
- input: rules.timelapse.output, "{xml_base}-{file_id,\d+}-00.h5", merged_xml="{xml_base}_merge.xml"
+ input: [ str("{xml_base}_merge.xml_" + config["common"]["transformation_switch"] ) ], "{xml_base}-{file_id,\d+}-00.h5", merged_xml="{xml_base}_merge.xml" # rules.timelapse.output, "{xml_base}-{file_id,\d+}-00.h5", merged_xml="{xml_base}_merge.xml"
output: "{xml_base}-{file_id,\d+}-00.h5_fusion"
log: "{xml_base}-{file_id,\d+}-00-fusion.log"
run:
@@ -327,7 +355,7 @@ rule external_transform:
shell(cmd_string)
rule deconvolution:
- input: rules.timelapse.output, "{xml_base}-{file_id,\d+}-00.h5", merged_xml="{xml_base}_merge.xml" # rules.external_transform.output, "{xml_base}-{file_id,\d+}-00.h5", merged_xml="{xml_base}_merge.xml"
+ input: [ str("{xml_base}_merge.xml_" + config["common"]["transformation_switch"] ) ], "{xml_base}-{file_id,\d+}-00.h5", merged_xml="{xml_base}_merge.xml" # rules.timelapse.output, "{xml_base}-{file_id,\d+}-00.h5", merged_xml="{xml_base}_merge.xml" # rules.external_transform.output, "{xml_base}-{file_id,\d+}-00.h5", merged_xml="{xml_base}_merge.xml"
output: "{xml_base}-{file_id,\d+}-00.h5_deconvolution"
log: "{xml_base}-{file_id,\d+}-00-deconvolution.log"
run:
diff --git a/spim_registration/timelapse/tomancak_test_cluster.yaml b/spim_registration/timelapse/tomancak_test_cluster.yaml
index 77c7621..60b1688 100755
--- a/spim_registration/timelapse/tomancak_test_cluster.yaml
+++ b/spim_registration/timelapse/tomancak_test_cluster.yaml
@@ -15,8 +15,10 @@ common: {
pixel_distance_y: '0.28590106964',
pixel_distance_z: '1.50000',
pixel_unit: "um",
- fusion_switch: "deconvolution"
- # fusion_switch: "fusion"
+ # transformation_switch: "timelapse_dublicate",
+ transformation_switch: "timelapse",
+ # fusion_switch: "deconvolution"
+ fusion_switch: "fusion"
}
define_xml_czi: {
@@ -92,7 +94,8 @@ timelapse: {
Dublicate_transformations: {
source_dublication: "red",
target_dublication: "green",
- bsh_file: "dublicate_channel.bsh"
+ duplicate_which_transformations: '"Replace all transformations"',
+ bsh_file: "Dublicate_transformations.bsh"
}
fusion: {
--
GitLab