From 455f7ce274ca49affa98dd7cdd42c755efc09e5c Mon Sep 17 00:00:00 2001
From: Christopher Schmied <schmied@mpi-cbg.de>
Date: Wed, 27 May 2015 17:34:38 +0200
Subject: [PATCH] 1. successful trial run
---
spim_registration/timelapse/Snakefile | 10 ++++----
spim_registration/timelapse/export.bsh | 24 ++++++++++---------
spim_registration/timelapse/tomancak_czi.json | 10 ++++----
3 files changed, 23 insertions(+), 21 deletions(-)
diff --git a/spim_registration/timelapse/Snakefile b/spim_registration/timelapse/Snakefile
index a40074c..778c1e2 100755
--- a/spim_registration/timelapse/Snakefile
+++ b/spim_registration/timelapse/Snakefile
@@ -93,7 +93,7 @@ ruleorder: define_xml_tif > define_xml_czi
rule hdf5_xml:
input: config["common"]["first_xml_filename"] + ".xml"
output: expand("{dataset}.{suffix}",dataset=[ config["common"]["hdf5_xml_filename"].strip('\"')], suffix=["xml","h5"]),
- [ item+"_empty" for item in datasets ]
+ [ item+"_xml" for item in datasets ]
log: "hdf5_xml.log"
run:
part_string = produce_string(
@@ -128,8 +128,8 @@ rule hdf5_xml:
# resave .czi/.tif dataset as hdf5
rule resave_hdf5:
- input: "{xml_base}-{file_id,\d+}-00.h5_empty" # rules.hdf5_xml.output
- output: "{xml_base}-{file_id,\d+}-00.h5"
+ input: rules.hdf5_xml.output # "{xml_base}-{file_id,\d+}-00.h5_xml"
+ output: "{xml_base}-{file_id,\d+}-00.h5", "{xml_base}-{file_id,\d+}-00.h5_hdf5"
log: "resave_hdf5-{file_id}.log"
run:
part_string = produce_string(
@@ -154,8 +154,8 @@ rule resave_hdf5:
jdir=JOBDIR,
path_bsh=config["common"]["bsh_directory"] + config["resave_hdf5"]["bsh_file"],
input_xml_base="{wildcards.xml_base}",
- job_number=int(wildcards.file_id)+1) # problematic calculation not possible in cannot deal wiht wildcards file_id
- part_string += " > {log} 2>&1"
+ job_number=int(wildcards.file_id)+1)
+ part_string += " > {log} 2>&1 && touch {output}"
shell(part_string)
rule registration:
diff --git a/spim_registration/timelapse/export.bsh b/spim_registration/timelapse/export.bsh
index 9722eb6..9905b6e 100755
--- a/spim_registration/timelapse/export.bsh
+++ b/spim_registration/timelapse/export.bsh
@@ -61,16 +61,18 @@ System.out.println( "run_only_job_number=" + run_only_job_number );
job_type = System.getProperty( "job_type" );
System.out.println( "Job type = " + job_type );
-if ( job_type.equalsIgnoreCase( "xml" ) )
- {
- job_number = 0;
- }
-else if ( job_type.equalsIgnoreCase( "hdf5" ) )
- {
- job_number = run_only_job_number + 1;
- }
-
-System.out.println( "Job Number = " + job_number );
+//
+//if ( job_type.equalsIgnoreCase( "xml" ) )
+// {
+// job_number = 0;
+// }
+//else if ( job_type.equalsIgnoreCase( "hdf5" ) )
+// {
+// job_number = run_only_job_number + 1;
+// }
+//
+//System.out.println( "Job Number = " + job_number );
+
// Activate cluster processing
System.out.println("=========================================================");
try{
@@ -98,7 +100,7 @@ IJ.run("As HDF5",
"split_hdf5 " +
"timepoints_per_partition=" + timepoints_per_partition + " " +
"setups_per_partition=" + setups_per_partition + " " +
- "run_only_job_number=" + job_number + " " +
+ "run_only_job_number=" + run_only_job_number + " " +
"use_deflate_compression " +
"export_path=" + image_file_directory + hdf5_xml_filename );
}
diff --git a/spim_registration/timelapse/tomancak_czi.json b/spim_registration/timelapse/tomancak_czi.json
index 5a46e1c..b1dbb8e 100755
--- a/spim_registration/timelapse/tomancak_czi.json
+++ b/spim_registration/timelapse/tomancak_czi.json
@@ -33,10 +33,10 @@
"define_xml_tif" :
{
- "timepoints" : "1-2",
- "acquisition_angles" : "1,2,3,4,5",
- "channels" : "0,1",
- "image_file_pattern" : "spim_TL{{tt}}_Angle{{a}}.tif",
+ "timepoints" : "0-1",
+ "acquisition_angles" : "0,72,144,216,288",
+ "channels" : "0",
+ "image_file_pattern" : "img_TL{{t}}_Angle{{a}}.tif",
"pixel_distance_x" : "0.2875535786151886",
"pixel_distance_y" : "0.2875535786151886",
"pixel_distance_z" : "1.50000",
@@ -70,7 +70,7 @@
"illuminations" : "\"All illuminations\"",
"angle" : "\"All angles\"",
"channel" : "\"All channels\"",
- "proc-ch" : "\"channel 1\"",
+ "proc-ch" : "\"channel 0\"",
"algorithm" : "\"Fast 3d geometric hashing (rotation invariant)\"",
"label_interest_points" : "\"beads\"",
"type_of_registration" : "\"Register timepoints individually\"",
--
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