From 0d0dcea5978dfb9c4af3676933ef4199fd09dd95 Mon Sep 17 00:00:00 2001
From: Christopher Schmied <schmied@mpi-cbg.de>
Date: Fri, 22 May 2015 12:47:54 +0200
Subject: [PATCH] Added define_xml_czi to snakemake workflow
---
spim_registration/timelapse/Snakefile | 26 +++++++++----------
spim_registration/timelapse/tomancak_czi.json | 25 +++++++++---------
2 files changed, 26 insertions(+), 25 deletions(-)
diff --git a/spim_registration/timelapse/Snakefile b/spim_registration/timelapse/Snakefile
index 69a0716..a3ab631 100755
--- a/spim_registration/timelapse/Snakefile
+++ b/spim_registration/timelapse/Snakefile
@@ -2,13 +2,13 @@ import os, glob, sys, re
#where are we (can be configured through -d/--directory flag)
JOBDIR=os.path.abspath(os.path.curdir)
-if JOBDIR[-1] != "/":
+if JOBDIR[-1] != "/": # this checks if jobdir ends with slash if not it adds a slash
JOBDIR+="/"
#data specific config file, expected to be inside JOBDIR
configfile: "tomancak_czi.json"
-datasets = glob.glob('*00.h5')
+datasets = glob.glob('*00.h5') # searches JOBDIR for files that match this wildcard expression
#TODO: this should go into a python module in this path
fre = re.compile(r'(?P<xml_base>\w+)-(?P<file_id>\d+)-00.h5')
@@ -33,14 +33,15 @@ rule done:
input: [ ds+"_deconvolved" for ds in datasets ]
# add part for defining xml file on czi dataset
-rule define_xml:
- input: "{czi_base}.czi"
- output: "{xml_name}.xml"
- threads: 1
- message: "Execute define xml with {threads} threads on the following files {input}"
- log: "define_xml.log"
- run: cmd_string = produce_string("""{fiji-prefix} {fiji-app} \
- -Dimage_file_directory={jdir}\
+rule define_xml_czi:
+ input: glob.glob('*.czi')
+ output: config["define_xml_czi"]["first_xml_filename"] + ".xml"
+ threads: 1
+ message: "Execute define xml with {threads} threads on the following files {input}"
+ log: "define_xml.log"
+ run:
+ cmd_string = produce_string("""{fiji-prefix} {fiji-app} \
+ -Dimage_file_directory={jdir} \
-Dfirst_czi={first_czi} \
-Dangle_1={angle_1} \
-Dangle_2={angle_2} \
@@ -59,10 +60,9 @@ rule define_xml:
-- --no-splash {bsh_file}""",
config["common"],
config["define_xml_czi"],
- jdir=JOBDIR,
- output="{output}")
+ jdir=JOBDIR)
- shell(cmd_string)
+ shell(cmd_string)
rule registration:
input: "{xml_base}-{file_id}-00.h5"
diff --git a/spim_registration/timelapse/tomancak_czi.json b/spim_registration/timelapse/tomancak_czi.json
index d5e2031..a328e67 100755
--- a/spim_registration/timelapse/tomancak_czi.json
+++ b/spim_registration/timelapse/tomancak_czi.json
@@ -9,18 +9,19 @@
"define_xml_czi" :
{
- "pixel_distance_x" : "0.2875535786151886" # Manual calibration x
- "pixel_distance_y" : "0.2875535786151886" # Manual calibration y
- "pixel_distance_z" : "1.50000" # Manual calibration z
- "pixel_unit" : "um" # unit of manual calibration
- "first_czi" : "2015-02-21_LZ1_Stock68_3.czi"
- "angle_1" : "0"
- "angle_2" : "72"
- "angle_3" :"144"
- "angle_4" :"216"
- "angle_5" : "288"
- "illumination_1" : "0"
- "bsh_file" : "define_czi.bsh"
+ "first_xml_filename" : "\"Stock68\"",
+ "pixel_distance_x" : "0.2875535786151886",
+ "pixel_distance_y" : "0.2875535786151886",
+ "pixel_distance_z" : "1.50000",
+ "pixel_unit" : "um",
+ "first_czi" : "2015-02-21_LZ1_Stock68_3.czi",
+ "angle_1" : "0",
+ "angle_2" : "72",
+ "angle_3" :"144",
+ "angle_4" :"216",
+ "angle_5" : "288",
+ "illumination_1" : "0",
+ "bsh_file" : "define_czi.bsh"
},
"registration" :
--
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