diff --git a/spim_registration/timelapse/Snakefile b/spim_registration/timelapse/Snakefile
index 95e865b866f6cf44371e02e9544a38d088d2c2a9..7d20dad47afc6e667ccf51e711464dd3cdd4bed9 100644
--- a/spim_registration/timelapse/Snakefile
+++ b/spim_registration/timelapse/Snakefile
@@ -8,6 +8,8 @@ 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_test_cluster.json"
+# configfile: "tomancak_test_cluster.yaml"
+
padding_format = "{0:0"+str(padding_of_file_id(int(config["common"]["ntimepoints"])))+"d}"
ds_format = "-"+padding_format+"-00.h5"
@@ -406,7 +408,7 @@ rule define_output:
rule hdf5_xml_output:
input: config["hdf5_output"]["output_xml"].strip('\"') + ".xml"
output: expand("{dataset}.{suffix}",dataset=[ config["common"]["hdf5_xml_filename"].strip('\"')], suffix=["xml","h5"]),
- [ item+"_output" for item in datasets ] # expand("{dataset}.{suffix}",dataset=[ config["hdf5_output"]["output_hdf5_xml"].strip('\"')], suffix=["xml","h5"]), "{xml_base}-{file_id,\d+}-00.h5_output_hdf5_xml"
+ [ item+"_output" for item in datasets ]
log: "hdf5_xml.log"
run:
part_string = produce_string(
@@ -469,7 +471,7 @@ rule resave_hdf5_output:
rule distclean:
- params : glob.glob(config["common"]["hdf5_xml_filename"].strip('\"')+"*"), glob.glob(config["common"]["first_xml_filename"].strip('\"')+"*"), glob.glob("*registered"), glob.glob("*_fusion"), glob.glob("*_timelapse"), glob.glob("*log"), glob.glob("*_deconvolved"), glob.glob("*.xml~*"),"interestpoints", glob.glob("*empty"), expand("{dataset}.{suffix}",dataset=[ config["common"]["hdf5_xml_filename"].strip('\"')], suffix=["xml","h5"])# xml_merge_in,
+ params : glob.glob(config["common"]["hdf5_xml_filename"].strip('\"')+"*"), glob.glob(config["common"]["first_xml_filename"].strip('\"')+"*"), glob.glob("*registered"), glob.glob("*_fusion"), glob.glob("*_timelapse"), glob.glob("*log"), glob.glob("*_deconvolved"), glob.glob("*.xml~*"),"interestpoints", glob.glob("*empty"), expand("{dataset}.{suffix}",dataset=[ config["common"]["hdf5_xml_filename"].strip('\"')], suffix=["xml","h5"]), glob.glob("*_output_hdf5"), glob.glob("*_output")# xml_merge_in,
message : os.path.abspath(os.path.curdir) + ": rm -rf {params}"
shell : "rm -rf {params}"
diff --git a/spim_registration/timelapse/tomancak.json b/spim_registration/timelapse/tomancak.json
index b1a87ba51d43edd2bb5a778b1680030c116c3688..021578435e6439631f55fdcb0780d5de97888993 100644
--- a/spim_registration/timelapse/tomancak.json
+++ b/spim_registration/timelapse/tomancak.json
@@ -1,7 +1,7 @@
{
"common" :
{
- "fiji-app" : "/projects/hpcsupport/steinbac/unicore/christopher-sandbox/unicore_jobs/Fiji.app.cuda_new/ImageJ-linux64",
+ "fiji-app" : "/projects/hpcsupport/steinbac/unicore/christopher/unicore_jobs/Fiji.app.cuda_new/ImageJ-linux64",
"fiji-prefix" : "/sw/bin/xvfb-run -a",
"directory_cuda" : "/lustre/projects/hpcsupport/steinbac/unicore/christopher/unicore_jobs/Fiji.app.cuda_new/lib/",
"merged_xml" : "hdf5_test_unicore_merge"
diff --git a/spim_registration/timelapse/tomancak_czi.json b/spim_registration/timelapse/tomancak_czi.json
index 7c14583d1bd6ecc7515a1f8f586b8365ab8f38f1..9a2445f03860cec92dec550035d55edcc38ada2e 100644
--- a/spim_registration/timelapse/tomancak_czi.json
+++ b/spim_registration/timelapse/tomancak_czi.json
@@ -1,7 +1,7 @@
{
"common" :
{
- "fiji-app" : "/projects/hpcsupport/steinbac/unicore/christopher-sandbox/unicore_jobs/Fiji.app.cuda_new/ImageJ-linux64",
+ "fiji-app" : "/projects/hpcsupport/steinbac/unicore/christopher/unicore_jobs/Fiji.app.cuda_new/ImageJ-linux64",
"fiji-prefix" : "/sw/bin/xvfb-run -a",
"directory_cuda" : "/lustre/projects/hpcsupport/steinbac/unicore/christopher/unicore_jobs/Fiji.app.cuda_new/lib/",
"merged_xml" : "hdf5_test_unicore_merge",
diff --git a/spim_registration/timelapse/tomancak_test_cluster.json b/spim_registration/timelapse/tomancak_test_cluster.json
index 0559f68e6de60cbf7162561776fb46a2a80e769a..44899c53b1b4dca63946a6b2a9d852faa25c9909 100644
--- a/spim_registration/timelapse/tomancak_test_cluster.json
+++ b/spim_registration/timelapse/tomancak_test_cluster.json
@@ -1,7 +1,7 @@
{
"common" :
{
- "fiji-app" : "/projects/hpcsupport/steinbac/unicore/christopher-sandbox/unicore_jobs/Fiji.app.cuda_new/ImageJ-linux64",
+ "fiji-app" : "/projects/hpcsupport/steinbac/unicore/christopher/unicore_jobs/Fiji.app.cuda_new/ImageJ-linux64",
"fiji-prefix" : "/sw/bin/xvfb-run -a",
"directory_cuda" : "/lustre/projects/hpcsupport/steinbac/unicore/christopher/unicore_jobs/Fiji.app.cuda_new/lib/",
"merged_xml" : "hdf5_test_unicore_merge",
diff --git a/spim_registration/timelapse/tomancak_test_cluster.yaml b/spim_registration/timelapse/tomancak_test_cluster.yaml
new file mode 100644
index 0000000000000000000000000000000000000000..fa7788278a9544938599cef4df97a171c7445811
--- /dev/null
+++ b/spim_registration/timelapse/tomancak_test_cluster.yaml
@@ -0,0 +1,189 @@
+common:
+ {
+ # directory that contains the bean shell scripts
+ bsh_directory: "/home/steinbac/development/schmied-snakemake-workflows/spim_registration/timelapse/",
+ directory_cuda: "/lustre/projects/hpcsupport/steinbac/unicore/christopher/unicore_jobs/Fiji.app.cuda_new/lib/",
+ fiji-app: "/projects/hpcsupport/steinbac/unicore/christopher/unicore_jobs/Fiji.app.cuda_new/ImageJ-linux64",
+ fiji-prefix: "/sw/bin/xvfb-run -a",
+ first_xml_filename: "test_unicore",
+ fusion_switch: "deconvolution",
+ hdf5_xml_filename: '"hdf5_test_unicore"',
+ merged_xml: "hdf5_test_unicore_merge",
+ ntimepoints: 5
+ }
+
+deconvolution:
+ {
+ Tikhonov_parameter: '0.0006',
+ bsh_file: "deconvolution_GPU.bsh",
+ compute: '"in 512x512x512 blocks"',
+ compute_on: '"GPU (Nvidia CUDA via JNA)"',
+ detections_to_extract_psf_for_channel_0: '"beads"',
+ detections_to_extract_psf_for_channel_1: '"beads"',
+ imglib2_container: '"ArrayImg"',
+ iterations: '5',
+ maximal_x: '509',
+ maximal_y: '970',
+ maximal_z: '243',
+ minimal_x: '95',
+ minimal_y: '-8',
+ minimal_z: '-174',
+ osem_acceleration: '"1 (balanced)"',
+ process_angle: '"All angles"',
+ process_channel: '"All channels"',
+ process_illumination: '"All illuminations"',
+ process_timepoint: '"Single Timepoint (Select from List)"',
+ psf_estimation: '"Extract from beads"',
+ psf_size_x: '19',
+ psf_size_y: '19',
+ psf_size_z: '25',
+ type_of_iteration: '"Efficient Bayesian - Optimization I (fast, precise)"'
+ }
+
+define_xml_czi:
+ {
+ angle_1: '0',
+ angle_2: '72',
+ angle_3: '144',
+ angle_4: '216',
+ angle_5: '288',
+ bsh_file: "define_czi.bsh",
+ channel_1: "green",
+ channel_2: "red",
+ first_czi: "2015-04-11_LZ2_Stock68_3.czi",
+ illumination_1: '0',
+ pixel_distance_x: '0.28590106964',
+ pixel_distance_y: '0.28590106964',
+ pixel_distance_z: '1.50000',
+ pixel_unit: "um",
+ rotation_around: "X-Axis"
+ }
+
+define_xml_tif:
+ {
+ acquisition_angles: '0,72,144,216,288',
+ bsh_file: "define_tif_zip.bsh",
+ channels: '0',
+ image_file_pattern: 'img_TL{{t}}_Angle{{a}}.tif',
+ imglib_container: '"ArrayImg (faster)"',
+ multiple_angles: '"YES (one file per angle)"',
+ multiple_channels: '"NO (one channel)"',
+ multiple_illumination_directions: '"NO (one illumination direction)"',
+ multiple_timepoints: '"YES (one file per time-point)"',
+ pixel_distance_x: '0.28590106964',
+ pixel_distance_y: '0.28590106964',
+ pixel_distance_z: '1.50000',
+ pixel_unit: "um",
+ type_of_dataset: '"Image Stacks (ImageJ Opener)"'
+ }
+
+
+external_transform:
+ {
+ angle: '"All angles"',
+ apply_transformation: '"Current view transformations
+ (appends to current transforms)"',
+ bsh_file: "transform.bsh",
+ channel: '"All channels"',
+ define_mode_transform: '"Matrix"',
+ illumination: '"All illuminations"',
+ matrix_transform: '"0.5, 0.0, 0.0, 0.0, 0.0, 0.5, 0.0, 0.0, 0.0, 0.0, 0.5, 0.0"',
+ timepoint: '"All Timepoints"',
+ transformation: '"Rigid"'
+ }
+
+fusion: {
+ bsh_file: "fusion.bsh",
+ downsample: '1',
+ fused_image: '"Append to current XML Project"',
+ imglib2_container_fusion: '"ArrayImg"',
+ imglib2_data_container: '"ArrayImg (faster)"',
+ interpolation: '"Linear Interpolation"',
+ maximal_x: '1019',
+ maximal_y: '1941',
+ maximal_z: '486',
+ minimal_x: '190',
+ minimal_y: '-16',
+ minimal_z: '-348',
+ pixel_type: '"16-bit unsigned integer"',
+ process_angle: '"All angles"',
+ process_channel: '"All channels"',
+ process_illumination: '"All illuminations"',
+ process_timepoint: '"Single Timepoint (Select from List)"',
+ process_views_in_paralell: '"All"',
+ xml_output: '"Save every XML with user-provided unique id"'
+ }
+
+hdf5_output: {
+ bsh_file_define: "define_output.bsh",
+ bsh_file_hdf5: "export_output.bsh",
+ convert_32bit: '"[Use min/max of first image (might saturate intenities over time)]"',
+ output_channels: "green",
+ output_data_type: "32Bit",
+ output_hdf5_xml: '"hdf5_fused_Stock68"',
+ output_illumination_directions: '"NO (one illumination direction)"',
+ output_image_file_pattern: 'TP{{t}}_Ch{{c}}_Ill0_Ang0,72,144,216,288.tif',
+ output_imglib_container: '"ArrayImg (faster)"',
+ output_multiple_angles: '"NO (one angle)"',
+ output_multiple_channels: '"NO (one channel)"',
+ output_multiple_timepoints: '"YES (one file per time-point)"',
+ output_pixel_distance_x: 0.5718,
+ output_pixel_distance_y: 0.5718,
+ output_pixel_distance_z: 0.5718,
+ output_pixel_unit: 'um',
+ output_timepoints: '0-4',
+ output_type_of_dataset: '"Image Stacks (ImageJ Opener)"',
+ output_xml: '"fused_Dual_Channel"'}
+
+registration: {
+ algorithm: '"Fast 3d geometric hashing (rotation invariant)"',
+ allowed_error_for_ransac: '5',
+ angle: '"All angles"',
+ bsh_file: "registration.bsh",
+ channel: '"All channels"',
+ detection_min_max: "find_maxima",
+ fix_tiles: '"Fix first tile"',
+ illuminations: '"All illuminations"',
+ imglib_container: '"ArrayImg (faster)"',
+ initial_sigma: '1.8',
+ interest_points_channel_0: '"beads"',
+ interest_points_channel_1: '"beads"',
+ label_interest_points: '"beads"',
+ lambda: '0.10',
+ map_back_tiles: '"Map back to first tile using rigid model"',
+ model_to_regularize_with: "Rigid",
+ proc-ch: '"channel 0"',
+ radius_1: '2',
+ radius_2: '3',
+ significance: '10',
+ subpixel_localization: '"3-dimensional quadratic fit"',
+ threshold: '0.005',
+ threshold_gaussian: '0.0080',
+ timepoint: '"Single Timepoint (Select from List)"',
+ transformation_model: "Affine",
+ type_of_detection: '"Difference-of-Mean (Integral image based)"',
+ type_of_registration: '"Register timepoints individually"'
+ }
+
+resave_hdf5: {
+ bsh_file: "export.bsh",
+ hdf5_chunk_sizes: '"{{ {{32,32,4}}, {{32,32,4}}, {{16,16,16}}, {{16,16,16}} }}"',
+ resave_angle: '"All angles"',
+ resave_channel: '"All channels"',
+ resave_illumination: '"All illuminations"',
+ resave_timepoint: '"All Timepoints"',
+ setups_per_partition: '0',
+ subsampling_factors: '"{{ {{1,1,1}}, {{2,2,1}}, {{4,4,1}}, {{8,8,1}} }}"',
+ timepoints_per_partition: '1'}
+
+timelapse: {
+ bsh_file: "timelapse_registration.bsh",
+ reference_timepoint: '0',
+ timelapse_process_timepoints: '"All Timepoints"',
+ type_of_registration_timelapse: '"Match against one reference timepoint (no global optimization)"'
+ }
+
+xml_merge: {
+ bsh_file: "xml_merge.bsh"
+ }
+