diff --git a/spim_registration/timelapse/Snakefile b/spim_registration/timelapse/Snakefile
old mode 100644
new mode 100755
index 50f2e0ab03c7404d8293e599a9ee5fb2ad93e244..e018c86443ab0ad1dc6e23abcc4f38d47402abd6
--- a/spim_registration/timelapse/Snakefile
+++ b/spim_registration/timelapse/Snakefile
@@ -26,7 +26,7 @@ xml_merge_in = produce_xml_merge_job_files(datasets)
rule done:
input: [ ds + "_output_hdf5" for ds in datasets ]
-localrules: define_xml_czi, define_xml_tif, hdf5_xml, xml_merge, timelapse,
+localrules: define_xml_czi, define_xml_tif, xml_merge, timelapse,
duplicate_transformations, external_transform, define_output,
hdf5_xml_output
@@ -109,7 +109,7 @@ rule hdf5_xml:
log: "logs/b1_hdf5_xml.log"
run:
part_string = produce_string(
- """{fiji-prefix} {fiji-app} \
+ """{fiji-prefix} {sysconfcpus} {num_cores_hdf5_xml} {fiji-app} \
-Dimage_file_directory={jdir} \
-Dfirst_xml_filename={first_xml_filename} \
-Dhdf5_xml_filename={hdf5_xml_filename} \
@@ -139,7 +139,7 @@ rule resave_hdf5:
log: "logs/b2_resave_hdf5-{file_id}.log"
run:
part_string = produce_string(
- """{fiji-prefix} sysconfcpus -n 2 {fiji-app} \
+ """{fiji-prefix} {sysconfcpus} {num_cores_resave_hdf5} {fiji-app} \
-Dimage_file_directory={jdir} \
-Dfirst_xml_filename={first_xml_filename} \
-Dhdf5_xml_filename={input_xml_base} \
@@ -168,7 +168,7 @@ rule registration:
log: "logs/c_{xml_base}-{file_id}-registration.log"
run:
cmd_string = produce_string(
- """{fiji-prefix} sysconfcpus -n 2 {fiji-app} \
+ """{fiji-prefix} {sysconfcpus} {num_cores_reg} {fiji-app} \
-Dparallel_timepoints={file_id_w} \
-Dimage_file_directory={jdir} \
-Dxml_filename={input_xml} \
@@ -300,7 +300,7 @@ rule fusion:
log: "logs/e1_{xml_base}-{file_id,\d+}-00-fusion.log"
run:
cmd_string = produce_string(
- """{fiji-prefix} sysconfcpus -n 6 {fiji-app} \
+ """{fiji-prefix} {sysconfcpus} {num_cores_fusion} {fiji-app} \
-Dimage_file_directory={jdir} \
-Dparallel_timepoints={file_id_w} \
-Dmerged_xml={merged_xml_file} \
@@ -371,7 +371,7 @@ rule deconvolution:
log: "logs/e2_{xml_base}-{file_id,\d+}-00-deconvolution.log"
run:
cmd_string = produce_string(
- """{fiji-prefix} sysconfcpus -n 2 {fiji-app} \
+ """{fiji-prefix} {sysconfcpus} {num_cores_deco} {fiji-app} \
-Dimage_file_directory={jdir} \
-Ddeco_output_file_directory={jdir} \
-Dmerged_xml={merged_xml_file} \
@@ -451,7 +451,7 @@ rule hdf5_xml_output:
log: "logs/f2_output_hdf5_xml.log"
run:
part_string = produce_string(
- """{fiji-prefix} {fiji-app} \
+ """{fiji-prefix} {sysconfcpus} {num_cores_hdf5_xml_output} {fiji-app} \
-Dimage_file_directory={jdir} \
-Dfirst_xml_filename={output_xml} \
-Dhdf5_xml_filename={output_hdf5_xml} \
@@ -482,7 +482,7 @@ rule resave_hdf5_output:
log: "logs/f3_resave_output-{file_id}.log"
run:
part_string = produce_string(
- """{fiji-prefix} sysconfcpus -n 2 {fiji-app} \
+ """{fiji-prefix} {sysconfcpus} {num_cores_resave_hdf5_output} {fiji-app} \
-Dimage_file_directory={jdir} \
-Dfirst_xml_filename={output_xml} \
-Dhdf5_xml_filename={output_hdf5_xml} \
diff --git a/spim_registration/timelapse/fusion.bsh b/spim_registration/timelapse/fusion.bsh
index 945556cf0c05b6e5cec8419eb89815cc3b504338..cdc86a08d41b30884a62c11866fbe425819ea747 100644
--- a/spim_registration/timelapse/fusion.bsh
+++ b/spim_registration/timelapse/fusion.bsh
@@ -99,7 +99,7 @@ IJ.run("Fuse/Deconvolve Dataset",
"process_views_in_paralell=All " +
"interpolation=[" + interpolation + "] " +
"blend " +
- "content-based " +
+ //"content-based " +
"output_file_directory=" + image_file_directory + " " +
"lossless " +
"imglib2_data_container=[" + imglib2_data_container + "]");
diff --git a/spim_registration/timelapse/single_test.yaml b/spim_registration/timelapse/single_test.yaml
old mode 100644
new mode 100755
index 3171fb1cfc1a09b4422865dfb382d7a003661149..63f96c470e109f88939d314ee5f06329fe821770
--- a/spim_registration/timelapse/single_test.yaml
+++ b/spim_registration/timelapse/single_test.yaml
@@ -13,6 +13,7 @@ common: {
# Directory that contains the current working Fiji
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
+ sysconfcpus: "sysconfcpus -n",
# ============================================================================
# Processing switches
# Description: Use switches to decide which processing steps you need:
@@ -208,6 +209,8 @@ resave_hdf5: {
resave_angle: '"All angles"',
resave_channel: '"All channels"',
resave_illumination: '"All illuminations"',
+ num_cores_hdf5_xml: "2",
+ num_cores_resave_hdf5: "2",
bsh_file: "export.bsh"
}
@@ -237,6 +240,7 @@ registration: {
model_to_regularize_with: "Rigid",
lambda: '0.10',
imglib_container: '"ArrayImg (faster)"',
+ num_cores_reg: "2",
bsh_file: "registration.bsh" # .bsh script for registration
}
@@ -273,6 +277,7 @@ fusion: {
imglib2_data_container: '"ArrayImg (faster)"',
process_views_in_paralell: '"All"',
xml_output: '"Save every XML with user-provided unique id"',
+ num_cores_fusion: "6",
bsh_file: "fusion.bsh"
}
@@ -312,6 +317,7 @@ deconvolution: {
psf_size_y: '19',
psf_size_z: '25',
imglib2_container: '"ArrayImg"',
+ num_cores_deco: "7",
bsh_file: "deconvolution.bsh"
}
@@ -329,6 +335,8 @@ hdf5_output: {
output_multiple_angles: '"NO (one angle)"',
output_illumination_directions: '"NO (one illumination direction)"',
output_imglib_container: '"ArrayImg (faster)"',
+ num_cores_hdf5_xml_output: "2",
+ num_cores_resave_hdf5_output: "2",
bsh_file_define: "define_output.bsh", # .bsh script for defining the dataset
bsh_file_hdf5: "export_output.bsh" # .bsh script for resaving into hdf5
}