diff --git a/spim_registration/timelapse/Snakefile b/spim_registration/timelapse/Snakefile
index 5518ba99486500147100508e256de95f8a88a16a..6436496508748ecedbaff133509b683555ed0efa 100755
--- a/spim_registration/timelapse/Snakefile
+++ b/spim_registration/timelapse/Snakefile
@@ -7,12 +7,12 @@ 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"
+# configfile: "tomancak_test_cluster.yaml"
padding_format = "{0:0"+str(padding_of_file_id(int(config["common"]["ntimepoints"])))+"d}"
@@ -306,7 +306,6 @@ rule fusion:
-Dprocess_illumination={process_illumination} \
-Dprocess_angle={process_angle} \
-Dxml_output={xml_output} \
- -Dfused_image={fused_image} \
-Dminimal_x={minimal_x} \
-Dminimal_y={minimal_y} \
-Dminimal_z={minimal_z} \
diff --git a/spim_registration/timelapse/cluster.json b/spim_registration/timelapse/cluster.json
index 4b2be746447e0fbd6c2b2892b30e26c895b4b0dd..ab4d912db15f4f01a47972356c2ecff5629b46d6 100755
--- a/spim_registration/timelapse/cluster.json
+++ b/spim_registration/timelapse/cluster.json
@@ -4,7 +4,12 @@
"lsf_extra" : "-R \"span[hosts=1]\"",
"lsf_q" : "short"
},
-
+
+ "resave_hdf5" :
+ {
+ "lsf_extra" : "-n 7 -R \"span[hosts=1] rusage[mem=50000]\""
+ },
+
"registration" :
{
"lsf_extra" : "-R \"span[hosts=1] rusage[mem=100000]\""
@@ -20,6 +25,11 @@
"lsf_extra" : "-R \"span[hosts=1] rusage[mem=10000]\""
},
+ "fusion" :
+ {
+ "lsf_extra" : "-n 6 -R \"span[hosts=1] rusage[mem=100000]\""
+ },
+
"deconvolution" :
{
"lsf_extra" : "-n 7 -R \"span[hosts=1] rusage[mem=50000]\"",
diff --git a/spim_registration/timelapse/define_czi.bsh b/spim_registration/timelapse/define_czi.bsh
index e3e1d30e788e27aa6888ce5a4a7e352162aae4d5..aa6b0526148588817ababb68666eacb6e7529e3e 100755
--- a/spim_registration/timelapse/define_czi.bsh
+++ b/spim_registration/timelapse/define_czi.bsh
@@ -48,7 +48,6 @@ String angle_part;
angle_part = "angle_" + num_angles + "=" + angle_token[angle];
angle_string.append(angle_part);
angle_string.append(" ");
-
}
System.out.println( angle_string );
@@ -76,9 +75,7 @@ String channel_part;
channel_part = "channel_" + num_channel + "=" + channel_token[channel];
channel_string.append(channel_part);
channel_string.append(" ");
-
}
-
System.out.println( "Channel String = " + channel_string );
System.out.println("---------------------------------------------------------");
@@ -104,7 +101,6 @@ String illum_part;
illum_part = "_______illumination_" + num_illum + "=" + illum_token[illum];
illum_string.append(illum_part);
illum_string.append(" ");
-
}
System.out.println( illum_string );
diff --git a/spim_registration/timelapse/single_test.yaml b/spim_registration/timelapse/single_test.yaml
index acc996e9b95134243d735d0ea153bc019dc5c17b..9171d0c8a9537778c6c99f453f9dc12933933e86 100755
--- a/spim_registration/timelapse/single_test.yaml
+++ b/spim_registration/timelapse/single_test.yaml
@@ -4,13 +4,12 @@ common: {
# Directory that contains the cuda libraries
directory_cuda: "/sw/users/schmied/cuda/",
# Directory that contains the current working Fiji
- #fiji-app: "/sw/users/schmied/packages/2015-06-08_Fiji.app.cuda/ImageJ-linux64",
- fiji-app: "/sw/users/schmied/packages/2015-05-29_Fiji_2.3.9_SNAP.app.cuda/ImageJ-linux64",
- fiji-prefix: "/sw/bin/xvfb-run -a", # calls xvfb for Fiji headless mode
+ fiji-app: "/sw/users/schmied/packages/2015-06-30_Fiji.app.cuda/ImageJ-linux64",
+ fiji-prefix: "/sw/users/schmied/packages/xvfb-run -a", # calls xvfb for Fiji headless mode
# xml file names without .xml suffix
- first_xml_filename: "single", # Name of the xml file for the .czi or .tif files
+ first_xml_filename: '"single"', # Name of the xml file for the .czi or .tif files
hdf5_xml_filename: '"hdf5_single"', # Name of .xml file for the hdf5 data after resave_hdf5
- merged_xml: "hdf5_single_merge", # Name of .xml file after merge
+ merged_xml: '"hdf5_single_merge"', # Name of .xml file after merge
# Describe the dataset
ntimepoints: 2, # number of timepoints of dataset
angles: "0,72,144,216,288", # angles
@@ -29,11 +28,11 @@ 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: {
- first_czi: "2015-04-11_LZ2_Stock68_3.czi", # master .czi file
+ first_czi: "2015-02-21_LZ1_Stock68_3.czi", # master .czi file
rotation_around: "X-Axis", # axis of acquistion
bsh_file: "define_czi.bsh" # .bsh script for defining .czi file
}
@@ -146,7 +145,7 @@ dublicate_transformations: {
fusion: {
# content based multiview fusion
# supports multi channel without new settings
- downsample: '1', # set downsampling
+ downsample: '2', # set downsampling
# Cropping parameters of full resolution
minimal_x: '190',
minimal_y: '-16',
@@ -223,9 +222,9 @@ deconvolution: {
hdf5_output: {
# writes new hdf5 dataset for fusion output: will be obsolete
# Naming pattern of output
- # Single Channel: TP{t}_Chgreen_Ill0_Ang0,72,144,216,288.tif > Ch{name} is added here
- # Dual Channel: TP{t}_Ch{0}_Ill0_Ang0,72,144,216,288.tif > Ch{name} is added here
- output_image_file_pattern: 'TP{t}_Chgreen_Ill0_Ang0,72,144,216,288.tif',
+ # Single Channel: TP{{t}}_Chgreen_Ill0_Ang0,72,144,216,288.tif > Ch{name} is added here
+ # Dual Channel: TP{{t}}_Ch{{0}}_Ill0_Ang0,72,144,216,288.tif > Ch{name} is added here
+ output_image_file_pattern: '"TP{{t}}_Chgreen_Ill0_Ang0,72,144,216,288.tif"',
# channel setting
output_multiple_channels: '"NO (one channel)"', # '"YES (one file per channel)"' or '"NO (one channel)"'
output_channels: "green",
@@ -240,7 +239,7 @@ hdf5_output: {
output_pixel_unit: 'um',
# give if 16Bit data or 32Bit data
# output of fusion is 16Bit, of deconvolution it is 32Bit
- output_data_type: "32Bit", # "32Bit" or "16Bit"
+ output_data_type: "16Bit", # "32Bit" or "16Bit"
# if data is 32Bit then the data is converted into 16Bit data
convert_32bit: '"[Use min/max of first image (might saturate intenities over time)]"',
# subsampling and chunk size settings: dataset dependent