diff --git a/spim_registration/timelapse/Snakefile b/spim_registration/timelapse/Snakefile
index 67ce937470dde80cbde41811569d8ec106d33270..3edf065d5926533f4b629d084e1320b203c51ec6 100644
--- a/spim_registration/timelapse/Snakefile
+++ b/spim_registration/timelapse/Snakefile
@@ -1,23 +1,25 @@
-import os, glob, sys
-
-#where are we
-if "datadir" not in config.keys():
- JOBDIR=os.path.abspath(os.path.curdir)
-else:
- if os.path.isdir(config['datadir']):
- JOBDIR=config['datadir']
- else:
- print("given data dir does not exist {data}".format(data=config['datadir']))
- sys.exit(1)
+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] != "/":
JOBDIR+="/"
-
-datasets = glob.glob('*00.h5')
-#data specific config file
+#data specific config file, expected to be inside JOBDIR
configfile: "tomancak.json"
+
+datasets = glob.glob('*00.h5')
+#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')
+xml_merge_in = []
+for ds in datasets:
+ bn = os.path.basename(ds)
+ bn_res = fre.search(bn)
+ xml_base,file_id = bn_res.group('xml_base'),bn_res.group('file_id')
+ xml_merge_in.append("{xbase}.job_{fid}.xml".format(xbase=xml_base, fid=file_id))
+
+#TODO: this should go into a python module in this path
def produce_string(_fstring, *args, **kwargs):
contents = dict()
for item in args:
@@ -28,12 +30,11 @@ def produce_string(_fstring, *args, **kwargs):
return _fstring.format(**contents)
rule done:
- input: [ ds+"-deconvolved" for ds in datasets ]
-
+ input: [ ds+"_deconvolved" for ds in datasets ]
+
rule registration:
input: "{xml_base}-{file_id,\d+}-00.h5"
- output: "{xml_base}-{file_id,\d+}-00.h5_registered", #convenience files
- "{xml_base}.job_{file_id,\d+}.xml"
+ output: "{xml_base}.job_{file_id,\d+}.xml"
log: "{xml_base}-{file_id,\d+}-registration.log"
run:
cmd_string = produce_string(
@@ -73,30 +74,31 @@ rule registration:
jdir=JOBDIR,
input_xml="{wildcards.xml_base}")
cmd_string += "> {log} 2>&1 && touch {output}"
+
shell(cmd_string)
#shell("touch {output}")
rule xml_merge:
- input: [ item+"_registered" for item in datasets ]
+ input: xml_merge_in
output: "{xml_base}_merge.xml"
log: "{xml_base}_merge.log"
run:
- cmd_string = produce_string("{fiji-prefix} {fiji-app} -Dimage_file_directory={jdir} -Dmerged_xml={merged_xml} -- --no-splash {bsh_file} > {log} 2>&1",
+ cmd_string = produce_string("{fiji-prefix} {fiji-app} -Dimage_file_directory={jdir} -Dmerged_xml={output} -- --no-splash {bsh_file} > {log} 2>&1",
config["common"],
config["xml_merge"],
log="{log}",
- jdir=JOBDIR)
+ jdir=JOBDIR,
+ output="{output}")
shell(cmd_string)
rule external_trafo:
input: rules.xml_merge.output
output: rules.xml_merge.output[0] + "_external_trafo"
log: "external_trafo.log"
-# message: "etrafo {input} -> {output}"
run:
cmd_string = produce_string("""{fiji-prefix} {fiji-app} \
-Dimage_file_directory={jdir} \
--Dmerged_xml={merged_xml} \
+ -Dmerged_xml={input} \
-Dtransform_angle={angle} \
-Dtransform_channel={channel} \
-Dtransform_illumination={illumination} \
@@ -108,19 +110,20 @@ rule external_trafo:
-- --no-splash {bsh_file}""",
config["common"],
config["external_transform"],
- jdir=JOBDIR)
+ jdir=JOBDIR,
+ input="{input}")
cmd_string += "> {log} 2>&1 && touch {output}"
shell(cmd_string)
rule deconvolution:
- input: rules.external_trafo.output, "{xml_base}-{file_id,\d+}-00.h5"
- output: "{xml_base}-{file_id,\d+}-00.h5-deconvolved"
- log: "{xml_base}-{file_id,\d+}-00.h5-deconvolution.log"
+ input: rules.external_trafo.output, "{xml_base}-{file_id,\d+}-00.h5", merged_xml="{xml_base}_merge.xml"
+ output: "{xml_base}-{file_id,\d+}-00.h5_deconvolved"
+ log: "{xml_base}-{file_id,\d+}-00-deconvolution.log"
run:
cmd_string = produce_string("""{fiji-prefix} {fiji-app} \
-Dimage_file_directory={jdir} \
-Ddeco_output_file_directory={jdir} \
--Dmerged_xml={merged_xml} \
+ -Dmerged_xml={merged_xml_file} \
-Dparallel_timepoints={file_id_w} \
-Dprocess_timepoint={process_timepoint} \
-Dprocess_channel={process_channel} \
@@ -145,13 +148,15 @@ rule deconvolution:
-Dpsf_size_y={psf_size_y} \
-Dpsf_size_z={psf_size_z} \
-Diterations={iterations} \
--- --no-splash {bsh_file}""",
+ -- --no-splash {bsh_file}""",
config["common"],
config["deconvolution"],
file_id_w="{wildcards.file_id}",
- jdir=JOBDIR)
+ jdir=JOBDIR,
+ merged_xml_file="{input.merged_xml}"
+ )
cmd_string += "> {log} 2>&1 && touch {output}"
shell(cmd_string)
-rule clean:
- shell : "rm -rf *registered"
+rule distclean:
+ shell : "rm -rf *registered *tif "+str(" ".join(xml_merge_in))
diff --git a/spim_registration/timelapse/cluster.json b/spim_registration/timelapse/cluster.json
index da4af2839fa3d0b8715104330ba43809865b3c87..41d4c6e10b872ec111453d5bad1663c6a3c72e3b 100644
--- a/spim_registration/timelapse/cluster.json
+++ b/spim_registration/timelapse/cluster.json
@@ -1,22 +1,23 @@
{
"__default__" :
{
- "fiji-app" : "/projects/pilot_spim/Christopher/Test_pipeline_3.0/test_unicore/unicore_jobs/Fiji.app.cuda_new/ImageJ-linux64",
- "fiji-good-4-resave" : "/sw/users/schmied/lifeline/Fiji.app.lifeline2/ImageJ-linux64",
- "fiji-good-4-deconv" : "/projects/pilot_spim/Christopher/Test_pipeline_3.0/test_unicore/unicore_jobs/Fiji.app.cuda_new/ImageJ-linux64",
- "fiji-prefix" : "/sw/bin/xvfb-run -a",
"lsf_extra" : "-R span[hosts=1]",
- "lsf_queue" : "short"
+ "lsf_q" : "short"
},
"registration" :
{
- "lsf_extra" : "-R span[hosts=1] -R rusage[mem=100000]",
- "lsf_queue" : "gpu"
+ "lsf_extra" : "-R span[hosts=1] -R rusage[mem=100000]"
},
- "produce" :
+ "external_trafo" :
{
- "lsf_queue" : "short"
+ "lsf_extra" : "-R span[hosts=1] -R rusage[mem=10000]"
+ },
+
+ "deconvolution" :
+ {
+ "lsf_extra" : "-n 7 -R span[hosts=1] -R rusage[mem=50000]",
+ "lsf_q" : "gpu"
}
}