diff --git a/spim_registration/timelapse/Snakefile b/spim_registration/timelapse/Snakefile
index 178e91cc79655d23fe520207ae0598a97d84276d..19798e53ed8258cb30911bdb4d00a557d41e85d2 100755
--- a/spim_registration/timelapse/Snakefile
+++ b/spim_registration/timelapse/Snakefile
@@ -260,9 +260,9 @@ rule dublicate_transformations:
log: "{xml_base}_dublicate_transformations.log"
run:
cmd_string = produce_string(
- """{fiji-prefix} {fiji-app}
+ """{fiji-prefix} {fiji-app} \
-Dimage_file_directory={jdir} \
- -Dmerged_xml={merged_xml} \
+ -Dmerged_xml={merged_xml_file} \
-Dprocess_timepoint_timelapse={timelapse_process_timepoints} \
-Dprocess_illumination={reg_process_illumination} \
-Dprocess_angle={reg_process_angle} \
@@ -273,10 +273,9 @@ rule dublicate_transformations:
config["common"],
config["registration"],
config["timelapse"],
- config["dublicate_channel"],
- path_bsh=config["common"]["bsh_directory"] + config["Dublicate_transformations"]["bsh_file"],
+ config["dublicate_transformations"],
+ path_bsh=config["common"]["bsh_directory"] + config["dublicate_transformations"]["bsh_file"],
jdir=JOBDIR,
- file_id_w="{wildcards.file_id}",
merged_xml_file="{input.merged_xml}"
)
cmd_string += " > {log} 2>&1 && touch {output}"
diff --git a/spim_registration/timelapse/dublicate_transformations.bsh b/spim_registration/timelapse/dublicate_transformations.bsh
new file mode 100755
index 0000000000000000000000000000000000000000..e815f3e97f5f98b8b25acbb49a569146e934a6b8
--- /dev/null
+++ b/spim_registration/timelapse/dublicate_transformations.bsh
@@ -0,0 +1,66 @@
+import ij.IJ;
+import ij.Prefs;
+import ij.ImagePlus;
+import java.lang.Runtime;
+import java.io.File;
+import java.io.FilenameFilter;
+
+runtime = Runtime.getRuntime();
+System.out.println(runtime.availableProcessors() + " cores available for multi-threading");
+
+Prefs.setThreads(1); // defines the number of threads allowed
+print("Threads: "+Prefs.getThreads()); // prints thread setting in output
+
+System.out.println("---------------------------------------------------------");
+System.out.println("Xml file:");
+
+xml_path = System.getProperty( "image_file_directory" );
+merged_xml = System.getProperty( "merged_xml" );
+
+System.out.println( "selected_xml = " + xml_path + merged_xml + " ");
+
+// General Registration Parameters and Channel Settings
+System.out.println("---------------------------------------------------------");
+System.out.println( "General parameters: " );
+
+process_timepoint_timelapse = System.getProperty( "process_timepoint_timelapse" );
+process_illumination = System.getProperty( "process_illumination" );
+process_angle = System.getProperty( "process_angle" );
+
+System.out.println( "process_timepoints = " + process_timepoint_timelapse );
+System.out.println( "process_illumination = " + process_illumination );
+System.out.println( "process_angle = " + process_angle );
+
+System.out.println("---------------------------------------------------------");
+System.out.println( "Dublication Parameters: " );
+source_dublication = System.getProperty( "source_dublication" );
+target_dublication = System.getProperty( "target_dublication" );
+
+System.out.println( "source = " + source_dublication );
+System.out.println( "processing_channel = " + target_dublication );
+
+
+System.out.println("=========================================================");
+System.out.println( "Start Dublication : " );
+
+try {
+IJ.run("Duplicate Transformations",
+"apply=[One channel to other channels] " +
+"select_xml=" + xml_path + merged_xml + " " +
+"apply_to_angle=[" + process_angle + "] " +
+"apply_to_illumination=[" + process_illumination + "] " +
+"apply_to_timepoint=[" + process_timepoint_timelapse + "] " +
+"source=" + source_dublication + " " +
+"target=[Single Channel (Select from List)] " +
+"processing_channel=" + target_dublication + " " +
+"duplicate_which_transformations=[Replace all transformations]");
+}
+catch ( e ) {
+
+ print( "[dublicate_transformations] caught exception: "+e );
+ //important to fail the process if exception occurs
+ runtime.exit(1);
+
+}
+/* shutdown */
+runtime.exit(0);
diff --git a/spim_registration/timelapse/tomancak_test_cluster.yaml b/spim_registration/timelapse/tomancak_test_cluster.yaml
index 60b1688d0ca8bac5d1029846f28e22e181895169..eb20c7161a008f36332d020526b3646a7a1251b3 100755
--- a/spim_registration/timelapse/tomancak_test_cluster.yaml
+++ b/spim_registration/timelapse/tomancak_test_cluster.yaml
@@ -1,34 +1,34 @@
common: {
# directory that contains the bean shell scripts
bsh_directory: "/projects/pilot_spim/Christopher/snakemake-workflows/spim_registration/timelapse/",
- directory_cuda: "/sw/users/schmied/packages/2015-06-08_Fiji.app.cuda/lib/",
+ directory_cuda: "/sw/users/schmied/packages/cuda/lib/",
fiji-app: "/sw/users/schmied/packages/2015-06-08_Fiji.app.cuda/ImageJ-linux64",
fiji-prefix: "/sw/bin/xvfb-run -a",
- first_xml_filename: "test_unicore",
- hdf5_xml_filename: '"hdf5_test_unicore"',
- merged_xml: "hdf5_test_unicore_merge",
- ntimepoints: 5,
+ first_xml_filename: "Dual_Channel",
+ hdf5_xml_filename: '"hdf5_Dual_Channel"',
+ merged_xml: "hdf5_Dual_Channel_merge",
+ ntimepoints: 2,
angles: "0,72,144,216,288",
- channels: "green",
+ channels: "green,red",
illumination: "0",
- pixel_distance_x: '0.28590106964',
- pixel_distance_y: '0.28590106964',
+ pixel_distance_x: '0.28590',
+ pixel_distance_y: '0.28590',
pixel_distance_z: '1.50000',
pixel_unit: "um",
- # transformation_switch: "timelapse_dublicate",
- transformation_switch: "timelapse",
+ transformation_switch: "timelapse_dublicate",
+ # transformation_switch: "timelapse",
# fusion_switch: "deconvolution"
fusion_switch: "fusion"
}
define_xml_czi: {
- first_czi: "2015-04-11_LZ2_Stock68_3.czi",
+ first_czi: "2015-02-20_LZ2_Stock48_Stock58.czi", # essential
rotation_around: "X-Axis",
bsh_file: "define_czi.bsh"
}
define_xml_tif: {
- image_file_pattern: 'img_TL{{t}}_Angle{{a}}.tif',
+ image_file_pattern: 'img_TL{{t}}_Angle{{a}}.tif', # essential
imglib_container: '"ArrayImg (faster)"',
multiple_angles: '"YES (one file per angle)"',
multiple_channels: '"NO (one channel)"',
@@ -39,29 +39,28 @@ define_xml_tif: {
}
resave_hdf5: {
- hdf5_chunk_sizes: '"{{ {{32,32,4}}, {{32,32,4}}, {{16,16,16}}, {{16,16,16}} }}"',
+ hdf5_chunk_sizes: '"{{ {{32,32,4}}, {{32,32,4}}, {{16,16,16}}, {{16,16,16}} }}"', # data dependent
+ subsampling_factors: '"{{ {{1,1,1}}, {{2,2,1}}, {{4,4,1}}, {{8,8,1}} }}"', # data dependent
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',
bsh_file: "export.bsh"
}
registration: {
- # "Single Channel" is not a valid choice for "Process_channel"
- reg_process_channel: '"All channels"',
- reg_processing_channel: '"green"',
- reg_interest_points_channel: '"beads"',
- reg_radius_1: '2',
- reg_radius_2: '3',
- reg_threshold: '0.005',
- initial_sigma: '1.8',
- threshold_gaussian: '0.0080',
- type_of_detection: '"Difference-of-Mean (Integral image based)"',
- label_interest_points: '"beads"',
+ reg_process_channel: '"Single channel (Select from List)"', # essential '"All channels"'; '"Single channel (Select from List)"'
+ reg_processing_channel: '"red"', # essential
+ reg_interest_points_channel: '"beads"', # essential
+ reg_radius_1: '2', # essential
+ reg_radius_2: '3', # essential
+ reg_threshold: '0.005', # essential
+ initial_sigma: '1.8', # essetial
+ threshold_gaussian: '0.0080', # essential
+ type_of_detection: '"Difference-of-Mean (Integral image based)"', # switch
+ label_interest_points: '"beads"',
reg_process_timepoint: '"Single Timepoint (Select from List)"',
reg_process_angle: '"All angles"',
reg_process_illumination: '"All illuminations"',
@@ -85,44 +84,45 @@ xml_merge: {
}
timelapse: {
- reference_timepoint: '0',
+ reference_timepoint: '0', # essential
type_of_registration_timelapse: '"Match against one reference timepoint (no global optimization)"',
timelapse_process_timepoints: '"All Timepoints"',
bsh_file: "timelapse_registration.bsh"
}
-Dublicate_transformations: {
- source_dublication: "red",
- target_dublication: "green",
+dublicate_transformations: {
+ source_dublication: "red", # essential for 1 usecase
+ target_dublication: "green", # essential for 1 usecase
duplicate_which_transformations: '"Replace all transformations"',
- bsh_file: "Dublicate_transformations.bsh"
+ bsh_file: "dublicate_transformations.bsh"
}
fusion: {
- bsh_file: "fusion.bsh",
- downsample: '4',
+ downsample: '1', # essential
+ minimal_x: '220', # essential maybe automate
+ minimal_y: '40', # essential maybe automate
+ minimal_z: '-290', # essential maybe automate
+ maximal_x: '976', # essential maybe automate
+ maximal_y: '1892', # essential maybe automate
+ maximal_z: '472', # essential maybe automate
fused_image: '"Append to current XML Project"',
imglib2_container_fusion: '"ArrayImg"',
imglib2_data_container: '"ArrayImg (faster)"',
interpolation: '"Linear Interpolation"',
- minimal_x: '190',
- minimal_y: '-16',
- minimal_z: '-348',
- maximal_x: '1019',
- maximal_y: '1941',
- maximal_z: '486',
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"'
+ xml_output: '"Save every XML with user-provided unique id"',
+ bsh_file: "fusion.bsh"
}
external_transform: {
+ # BUG
# channel setting: '"all_channels"'
- channel_setting: '"green"',
+ channel_setting: '"green,red"',
transform_timepoint: '"All Timepoints"',
transform_angle: '"All angles"',
transform_channel: '"All channels"',
@@ -130,19 +130,19 @@ external_transform: {
transform_illumination: '"All illuminations"',
apply_transformation: '"Current view transformations (appends to current transforms)"',
define_mode_transform: '"Matrix"',
- 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"',
+ 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"', # essential
transformation: '"Rigid"',
bsh_file: "transform.bsh"
}
deconvolution: {
- iterations: '1',
- minimal_x_deco: '190',
- minimal_y_deco: '-16',
- minimal_z_deco: '-348',
- maximal_x_deco: '1019',
- maximal_y_deco: '1941',
- maximal_z_deco: '486',
+ iterations: '1', # essential
+ minimal_x_deco: '190', # essential maybe automate
+ minimal_y_deco: '-16', # essential maybe automate
+ minimal_z_deco: '-348', # essential maybe automate
+ maximal_x_deco: '1019', # essential maybe automate
+ maximal_y_deco: '1941', # essential maybe automate
+ maximal_z_deco: '486', # essential maybe automate
detections_to_extract_psf_for_channel: '"beads"',
process_timepoint: '"Single Timepoint (Select from List)"',
process_angle: '"All angles"',
@@ -162,25 +162,26 @@ deconvolution: {
}
hdf5_output: {
- output_image_file_pattern: 'TP{{t}}_Chgreen_Ill0_Ang0,72,144,216,288.tif',
- output_xml: '"fused_Single_Channel"',
- output_hdf5_xml: '"hdf5_fused_Single_Channel"',
+ # Will be obsolete
+ output_image_file_pattern: 'TP{{t}}_Ch{{c}}_Ill0_Ang0,72,144,216,288.tif',
+ output_xml: '"fused_Dual_Channel"',
+ output_hdf5_xml: '"hdf5_fused_Dual_Channel"',
output_multiple_channels: '"NO (one channel)"',
- output_timepoints: '0-4',
- output_pixel_distance_x: 0.5718,
- output_pixel_distance_y: 0.5718,
- output_pixel_distance_z: 0.5718,
+ output_timepoints: '0-1',
+ output_pixel_distance_x: 0.28590,
+ output_pixel_distance_y: 0.28590,
+ output_pixel_distance_z: 0.28590,
output_pixel_unit: 'um',
- output_channels: "green",
- output_data_type: "32Bit",
+ output_channels: "green,red",
+ output_data_type: "16Bit",
convert_32bit: '"[Use min/max of first image (might saturate intenities over time)]"',
output_type_of_dataset: '"Image Stacks (ImageJ Opener)"',
output_multiple_timepoints: '"YES (one file per time-point)"',
output_multiple_angles: '"NO (one angle)"',
output_illumination_directions: '"NO (one illumination direction)"',
output_imglib_container: '"ArrayImg (faster)"',
- subsampling_output: '"{{ {{1,1,1}}, {{2,2,2}}, {{4,4,4}}, {{8,8,8}} }}"',
- chunk_sizes_output: '"{{ {{16,16,16}}, {{16,16,16}}, {{16,16,16}}, {{16,16,16}} }}"',
+ subsampling_output: '"{{ {{1,1,1}}, {{2,2,2}}, {{4,4,4}}, {{8,8,8}} }}"', # data dependent
+ chunk_sizes_output: '"{{ {{16,16,16}}, {{16,16,16}}, {{16,16,16}}, {{16,16,16}} }}"', # data dependent
# subsampling_output: '"{{ {{1,1,1}}, {{2,2,2}} }}"',
# chunk_sizes_output: '"{{ {{16,16,16}}, {{16,16,16}} }}"',
bsh_file_define: "define_output.bsh",