diff --git a/spim_registration/timelapse/Snakefile b/spim_registration/timelapse/Snakefile index 6436496508748ecedbaff133509b683555ed0efa..f7211ce48505bc7396ac0bb0229d30df15118706 100755 --- a/spim_registration/timelapse/Snakefile +++ b/spim_registration/timelapse/Snakefile @@ -7,9 +7,9 @@ if JOBDIR[-1] != "/": # this checks if jobdir ends with slash if not it adds a s JOBDIR+="/" # Test config file single Channel: -configfile: "single_test.yaml" +# configfile: "single_test.yaml" # Test config file dual channel one channel contains beads: -# configfile: "dual_OneChannel.yaml" +configfile: "dual_OneChannel.yaml" # data specific config file, expected to be inside JOBDIR # configfile: "tomancak_test_cluster.yaml" @@ -266,8 +266,8 @@ rule timelapse: rule duplicate_transformations: input: rules.timelapse.output, merged_xml="{xml_base}_merge.xml" - output: rules.timelapse.output[0] + "_dublicate" - log: "{xml_base}_dublicate_transformations.log" + output: rules.timelapse.output[0] + "_duplicate" + log: "{xml_base}_duplicate_transformations.log" run: cmd_string = produce_string( """{fiji-prefix} {fiji-app} \ diff --git a/spim_registration/timelapse/cluster.json b/spim_registration/timelapse/cluster.json index 00b1765aec32bb087004aecfff9f3281ee576c20..7f13c62a6e51384d597d272137c18db3a2f97eb6 100755 --- a/spim_registration/timelapse/cluster.json +++ b/spim_registration/timelapse/cluster.json @@ -27,7 +27,7 @@ "fusion" : { - "lsf_extra" : "-n 7 -R \"span[hosts=1] rusage[mem=100000]\"" + "lsf_extra" : "-n 12 -R \"span[hosts=1] rusage[mem=100000]\"" }, "deconvolution" : diff --git a/spim_registration/timelapse/dual_OneChannel.yaml b/spim_registration/timelapse/dual_OneChannel.yaml index b0095960b0242d6a250f8854b9e2866500793375..239f9dfd3b117367df8297cf56f13414c695f349 100755 --- a/spim_registration/timelapse/dual_OneChannel.yaml +++ b/spim_registration/timelapse/dual_OneChannel.yaml @@ -29,7 +29,7 @@ common: { # Switches between content based fusion and deconvoltion # "deconvolution" > for deconvolution # "fusion" > for content based fusion - fusion_switch: "deconvolution" + fusion_switch: "fusion" } define_xml_czi: { diff --git a/spim_registration/timelapse/fusion.bsh b/spim_registration/timelapse/fusion.bsh index e6050025af0a6dff457f6b50afdf1f14b2cad9d5..945556cf0c05b6e5cec8419eb89815cc3b504338 100755 --- a/spim_registration/timelapse/fusion.bsh +++ b/spim_registration/timelapse/fusion.bsh @@ -98,7 +98,7 @@ IJ.run("Fuse/Deconvolve Dataset", "imglib2_container=" + imglib2_container_fusion + " " + "process_views_in_paralell=All " + "interpolation=[" + interpolation + "] " + - //"blend " + + "blend " + "content-based " + "output_file_directory=" + image_file_directory + " " + "lossless " + diff --git a/spim_registration/timelapse/single_test.yaml b/spim_registration/timelapse/single_test.yaml index 5cf7c442522c9af81fed403730c5fb71b59a5d32..e89c1f77f7960d3f25caad97663c72ae7d67bf2f 100755 --- a/spim_registration/timelapse/single_test.yaml +++ b/spim_registration/timelapse/single_test.yaml @@ -229,8 +229,8 @@ hdf5_output: { output_multiple_channels: '"NO (one channel)"', # '"YES (one file per channel)"' or '"NO (one channel)"' output_channels: "green", # .xml file names - output_xml: '"fused_Dual_Channel"', - output_hdf5_xml: '"hdf5_fused_Dual_Channel"', + output_xml: '"fused_Single"', + output_hdf5_xml: '"hdf5_fused_Single"', output_timepoints: '0-1', # Timepoints format: '1-2' # pixel size of output: take downsampling into account! output_pixel_distance_x: 0.28590106964,