diff --git a/spim_registration/timelapse/Snakefile b/spim_registration/timelapse/Snakefile
index d61c1391b944bb80d82c854beee20f6a46571795..0e55826ba9bcd6a135ebbf884838654c4e4a92e1 100755
--- a/spim_registration/timelapse/Snakefile
+++ b/spim_registration/timelapse/Snakefile
@@ -8,16 +8,18 @@ if JOBDIR[-1] != "/": # this checks if jobdir ends with slash if not it adds a s
#data specific config file, expected to be inside JOBDIR
configfile: "tomancak_czi.json"
-datasets = glob.glob('*00.h5') # searches JOBDIR for files that match this wildcard expression
+datasets = expand("{xml_base}-{file_id}-00.h5", xml_base=[ config["common"]["hdf5_xml_filename"].strip('\"') ],file_id=range(int(config["common"]["ntimepoints"]))) # 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')
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=int(file_id)))
+ if bn_res:
+ 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=int(file_id)))
#TODO: this should go into a python module in this path
def produce_string(_fstring, *args, **kwargs):
@@ -33,9 +35,12 @@ rule done:
#input: [ ds+"_fusion" for ds in datasets ]
input: [ ds + "_" + config["common"]["fusion_switch"] for ds in datasets ]
+rule resave_prepared:
+ input: expand("{dataset}.{suffix}",dataset=[ config["common"]["hdf5_xml_filename"] ], suffix=["xml","h5"])
+
# defining xml for czi dataset
rule define_xml_czi:
- input: glob.glob('*.czi')
+ input: config["define_xml_czi"]["first_czi"]
output: config["common"]["first_xml_filename"] + ".xml"
message: "Execute define_xml_czi on the following files {input}"
log: "define_xml_czi.log"
@@ -100,20 +105,59 @@ rule define_xml_tif:
cmd_string +="> {log} 2>&1 && touch {output}"
shell(cmd_string)
-
+
+ruleorder: define_xml_tif > define_xml_czi
+
+# create mother .xml/.h5
+rule hdf5_xml:
+ input: config["common"]["first_xml_filename"] + ".xml"
+ output: expand("{dataset}.{suffix}",dataset=[ config["common"]["hdf5_xml_filename"] ], suffix=["xml","h5"]),
+ expand("{xml_base}-{file_id}-00.h5_empty", xml_base=[ config["common"]["hdf5_xml_filename"].strip('\"') ],file_id=range(int(config["common"]["ntimepoints"])))
+
+ 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 \
+ -- --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"])
+
+ part_string += "> {log} 2>&1"
+ shell(part_string)
+
+ #create dummy files according to the number of timepoints found
+ for index in range(int(config["common"]["ntimepoints"])):
+ shell("touch {basename}-{file_id}-00.h5_empty".format(basename=config["common"]["hdf5_xml_filename"],file_id=index))
+
+
# resave .czi dataset as hdf5
rule resave_hdf5:
- input: rules.define_xml_tif.output, glob.glob('*.tif')
- output: "hdf5_test_unicore.xml", "hdf5_test_unicore.h5"
+ input: "{xml_base}-{file_id}-00.h5_empty"
+ output: "{xml_base}-{file_id}-00.h5"
message: "Execute resave_hdf5 on {input}"
threads: int(config["resave_hdf5"]["parallel_timepoints"]) # parallel timepoints should tell me how many timepoints to expect
- log: "resave_hdf5.log"
+ 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={hdf5_xml_filename} \
+ -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} \
@@ -128,14 +172,12 @@ rule resave_hdf5:
config["define_xml_czi"],
config["resave_hdf5"],
jdir=JOBDIR,
- path_bsh=config["common"]["bsh_directory"] + config["resave_hdf5"]["bsh_file"])
-
- cmd_string = ""
- for i in range(int(config["resave_hdf5"]["parallel_timepoints"])):
- cmd_string += part_string.format(job_number=i)
-
- #cmd_string += "> {log} 2>&1 && touch {output}"
- shell(cmd_string)
+ path_bsh=config["common"]["bsh_directory"] + config["resave_hdf5"]["bsh_file"],
+ intput_xml_base="{wildcards.xml_base}",
+ job_number=int("{wildcards.file_id}")+1
+ )
+ part_string += "> {log} 2>&1"
+ shell(part_string)
rule registration:
input: "{xml_base}-{file_id}-00.h5", rules.resave_hdf5.output
diff --git a/spim_registration/timelapse/tomancak_czi.json b/spim_registration/timelapse/tomancak_czi.json
index 21c30f11113c8a63b5429f0ca81f1151b021c656..9f0188921872537cceebc323f02a4388cc9eedd8 100755
--- a/spim_registration/timelapse/tomancak_czi.json
+++ b/spim_registration/timelapse/tomancak_czi.json
@@ -8,7 +8,8 @@
"bsh_directory" : "/projects/pilot_spim/Christopher/snakemake-workflows/spim_registration/timelapse/",
"first_xml_filename" : "test_unicore",
"hdf5_xml_filename" : "\"hdf5_test_unicore\"",
- "fusion_switch" : "deconvolution"
+ "fusion_switch" : "deconvolution",
+ "ntimepoints" : 2
},
"define_xml_czi" :