From 4a77aa40c89ea580599f7e251187dc6b7900e637 Mon Sep 17 00:00:00 2001
From: Christopher Schmied <schmied@mpi-cbg.de>
Date: Wed, 27 May 2015 19:16:23 +0200
Subject: [PATCH] Added resaving of output: hdf5_xml_output, resave_hdf5_output
---
spim_registration/timelapse/Snakefile | 78 +++++++++++++++++++++++----
1 file changed, 69 insertions(+), 9 deletions(-)
diff --git a/spim_registration/timelapse/Snakefile b/spim_registration/timelapse/Snakefile
index b912717..66ddfed 100755
--- a/spim_registration/timelapse/Snakefile
+++ b/spim_registration/timelapse/Snakefile
@@ -17,8 +17,8 @@ xml_merge_in = produce_xml_merge_job_files(datasets)
rule done:
#input: [ ds+"_fusion" for ds in datasets ]
#input: [ ds + "_" + config["common"]["fusion_switch"] for ds in datasets ]
- #input: [ ds + "_" + config["common"]["fusion_switch"] for ds in datasets ]
- input: config["hdf5_output"]["output_xml"] + ".xml"
+ #input: config["hdf5_output"]["output_xml"] + ".xml"
+ input: [ ds + "_output_hdf5" for ds in datasets ]
rule resave_prepared:
input: expand("{dataset}.{suffix}",dataset=[ config["common"]["hdf5_xml_filename"] ], suffix=["xml","h5"])
@@ -385,14 +385,14 @@ rule define_output:
cmd_string = produce_string(
"""{fiji-prefix} {fiji-app} \
-Dimage_file_directory={jdir} \
- -Dtimepoints={timepoints} \
+ -Dtimepoints={output_timepoints} \
-Dacquisition_angles={acquisition_angles} \
- -Dchannels={channels} \
- -Dimage_file_pattern={image_file_pattern} \
- -Dpixel_distance_x={pixel_distance_x} \
- -Dpixel_distance_y={pixel_distance_y} \
- -Dpixel_distance_z={pixel_distance_z} \
- -Dpixel_unit={pixel_unit} \
+ -Dchannels={output_channels} \
+ -Dimage_file_pattern={output_image_file_pattern} \
+ -Dpixel_distance_x={output_pixel_distance_x} \
+ -Dpixel_distance_y={output_pixel_distance_y} \
+ -Dpixel_distance_z={output_pixel_distance_z} \
+ -Dpixel_unit={output_pixel_unit} \
-Dxml_filename={first_xml_filename} \
-Dtype_of_dataset={type_of_dataset} \
-Dmultiple_timepoints={multiple_timepoints} \
@@ -409,8 +409,68 @@ rule define_output:
cmd_string +=" > {log} 2>&1"
shell(cmd_string)
+# create mother .xml/.h5
+rule hdf5_xml_output:
+ input: config["hdf5_output"]["output_xml"] + ".xml"
+ output: expand("{dataset}.{suffix}",dataset=[ config["hdf5_output"]["output_hdf5_xml"].strip('\"')], suffix=["xml","h5"]),
+ [ item+"_output" for item in datasets ]
+ log: "hdf5_xml.log"
+ run:
+ part_string = produce_string(
+ """{fiji-prefix} {fiji-app} \
+ -Dimage_file_directory={jdir} \
+ -Dfirst_xml_filename={first_xml_filename} \
+ -Dhdf5_xml_filename={hdf5_xml_filename} \
+ -Dresave_angle={resave_angle} \
+ -Dresave_channel={resave_channel} \
+ -Dresave_illumination={resave_illumination} \
+ -Dresave_timepoint={resave_timepoint} \
+ -Dsubsampling_factors={subsampling_factors} \
+ -Dhdf5_chunk_sizes={hdf5_chunk_sizes} \
+ -Dtimepoints_per_partition={timepoints_per_partition} \
+ -Dsetups_per_partition={setups_per_partition} \
+ -Drun_only_job_number=0 \
+ -Djob_type=xml \
+ -- --no-splash {path_bsh}""",
+ config["common"],
+ config["define_xml_czi"],
+ config["resave_hdf5"],
+ jdir=JOBDIR,
+ path_bsh=config["common"]["bsh_directory"] + config["resave_hdf5"]["bsh_file"])
+ part_string += " > {log} 2>&1 && touch {output}"
+ shell(part_string)
+rule resave_hdf5_output:
+ input: rules.hdf5_xml_output.output
+ output: "{xml_base}-{file_id,\d+}-00.h5_output_hdf5"
+ log: "resave_hdf5-{file_id}.log"
+ run:
+ part_string = produce_string(
+ """{fiji-prefix} {fiji-app} \
+ -Dimage_file_directory={jdir} \
+ -Dfirst_xml_filename={first_xml_filename} \
+ -Dhdf5_xml_filename={input_xml_base} \
+ -Dresave_angle={resave_angle} \
+ -Dresave_channel={resave_channel} \
+ -Dresave_illumination={resave_illumination} \
+ -Dresave_timepoint={resave_timepoint} \
+ -Dsubsampling_factors={subsampling_factors} \
+ -Dhdf5_chunk_sizes={hdf5_chunk_sizes} \
+ -Dtimepoints_per_partition={timepoints_per_partition} \
+ -Dsetups_per_partition={setups_per_partition} \
+ -Drun_only_job_number={job_number} \
+ -Djob_type=hdf5 \
+ -- --no-splash {path_bsh}""", # the & submits everyting at once
+ config["common"],
+ config["define_xml_czi"],
+ config["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)
+ part_string += " > {log} 2>&1 && touch {output}"
+ shell(part_string)
rule distclean:
--
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