diff --git a/spim_registration/timelapse/Snakefile b/spim_registration/timelapse/Snakefile
index 0431faad2c1a19570722fa6c6e1b0778d551ebb0..5faec2cf7f7fc810f44db01f2adbf48b5281ed2d 100755
--- a/spim_registration/timelapse/Snakefile
+++ b/spim_registration/timelapse/Snakefile
@@ -63,7 +63,7 @@ rule define_xml_czi:
jdir=JOBDIR,
path_bsh=config["common"]["bsh_directory"] + config["define_xml_czi"]["bsh_file"])
- cmd_string += "> {log} 2>&1"
+ cmd_string += "> {log} 2>&1 && touch {output}"
shell(cmd_string)
# defining xml for tif dataset
@@ -74,24 +74,24 @@ rule define_xml_tif:
log: "define_xml_tif.log"
run:
cmd_string = produce_string(
- """{fiji-prefix} {fiji-app} \
- -Dimage_file_directory={jdir} \
- -Dtimepoints={timepoints} \
- -Dacquisition_angles={acquisition_angles} \
- -Dchannels={channels} \
- -Dimage_file_pattern={image_file_pattern} \
- -Dpixel_distance_x={pixel_distance_x} \
- -Dpixel_distance_y={pixel_distance_y} \
- -Dpixel_distance_z={pixel_distance_z} \
- -Dpixel_unit={pixel_unit} \
- -Dxml_filename={first_xml_filename} \
- -Dtype_of_dataset={type_of_dataset} \
- -Dmultiple_timepoints={multiple_timepoints} \
- -Dmultiple_channels={multiple_channels} \
- -Dmultiple_illumination_directions={multiple_illumination_directions} \
- -Dmultiple_angles={multiple_angles} \
- -Dimglib_container={imglib_container} \
- -- --no-splash {path_bsh}""",
+ """{fiji-prefix} {fiji-app} \
+ -Dimage_file_directory={jdir} \
+ -Dtimepoints={timepoints} \
+ -Dacquisition_angles={acquisition_angles} \
+ -Dchannels={channels} \
+ -Dimage_file_pattern={image_file_pattern} \
+ -Dpixel_distance_x={pixel_distance_x} \
+ -Dpixel_distance_y={pixel_distance_y} \
+ -Dpixel_distance_z={pixel_distance_z} \
+ -Dpixel_unit={pixel_unit} \
+ -Dxml_filename={first_xml_filename} \
+ -Dtype_of_dataset={type_of_dataset} \
+ -Dmultiple_timepoints={multiple_timepoints} \
+ -Dmultiple_channels={multiple_channels} \
+ -Dmultiple_illumination_directions={multiple_illumination_directions} \
+ -Dmultiple_angles={multiple_angles} \
+ -Dimglib_container={imglib_container} \
+ -- --no-splash {path_bsh}""",
config["common"],
config["define_xml_tif"],
jdir=JOBDIR,
@@ -101,13 +101,16 @@ rule define_xml_tif:
# resave .czi dataset as hdf5
rule resave_czi_hdf5:
- input: rules.define_xml_czi.output, glob.glob('*.czi')
- output: "hdf5_Stock68.h5", "hdf5_Stock68.xml"
+# input: config["common"]["first_xml_filename"] + ".xml"
+ input: rules.define_xml_tif.output, glob.glob('*.tif')
+# output: "hdf5_Stock68.h5", "hdf5_Stock68.xml"
+ output: config["common"]["hdf5_xml_filename"] + ".xml", config["common"]["hdf5_xml_filename"] + ".h5"
message: "Execute resave_hdf5 on {input}"
# threads: int(config["resave_hdf5"]["parallel_timepoints"]) # parallel timepoints should tell me how many timepoints to expect
log: "export_czi.log"
run:
- part_string = produce_string("""{fiji-prefix} {fiji-app} \
+ part_string = produce_string(
+ """{fiji-prefix} {fiji-app} \
-Dimage_file_directory={jdir} \
-Dfirst_xml_filename={first_xml_filename} \
-Dhdf5_xml_filename={hdf5_xml_filename} \
@@ -140,38 +143,39 @@ rule registration:
run:
cmd_string = produce_string(
"""{fiji-prefix} {fiji-app} \
--Dparallel_timepoints={file_id_w} \
--Dimage_file_directory={jdir} \
--Dxml_filename={input_xml} \
--Dprocess_timepoint={timepoint} \
--Dprocess_channel={channel} \
--Dprocess_illumination={illuminations} \
--Dprocess_angle={angle} \
--Dprocessing_channel={proc-ch} \
--Dlabel_interest_points={label_interest_points} \
--Dtype_of_registration={type_of_registration} \
--Dtype_of_detection={type_of_detection} \
--Dsubpixel_localization={subpixel_localization} \
--Dimglib_container={imglib_container} \
--Dradius_1={radius_1} \
--Dradius_2={radius_2} \
--Dthreshold={threshold} \
--Dinitial_sigma={initial_sigma} \
--Dthreshold_gaussian={threshold_gaussian} \
--Dregistration_algorithm={algorithm} \
--Dinterest_points_channel_0={interest_points_channel_0} \
--Dinterest_points_channel_1={interest_points_channel_1} \
--Dfix_tiles={fix_tiles} \
--Dmap_back_tiles={map_back_tiles} \
--Dtransformation_model={transformation_model} \
--Dmodel_to_regularize_with={model_to_regularize_with} \
--Dlambda={lambda} \
--Dallowed_error_for_ransac={allowed_error_for_ransac} \
--Ddetection_min_max={detection_min_max} \
--- --no-splash {bsh_file}""",
+ -Dparallel_timepoints={file_id_w} \
+ -Dimage_file_directory={jdir} \
+ -Dxml_filename={input_xml} \
+ -Dprocess_timepoint={timepoint} \
+ -Dprocess_channel={channel} \
+ -Dprocess_illumination={illuminations} \
+ -Dprocess_angle={angle} \
+ -Dprocessing_channel={proc-ch} \
+ -Dlabel_interest_points={label_interest_points} \
+ -Dtype_of_registration={type_of_registration} \
+ -Dtype_of_detection={type_of_detection} \
+ -Dsubpixel_localization={subpixel_localization} \
+ -Dimglib_container={imglib_container} \
+ -Dradius_1={radius_1} \
+ -Dradius_2={radius_2} \
+ -Dthreshold={threshold} \
+ -Dinitial_sigma={initial_sigma} \
+ -Dthreshold_gaussian={threshold_gaussian} \
+ -Dregistration_algorithm={algorithm} \
+ -Dinterest_points_channel_0={interest_points_channel_0} \
+ -Dinterest_points_channel_1={interest_points_channel_1} \
+ -Dfix_tiles={fix_tiles} \
+ -Dmap_back_tiles={map_back_tiles} \
+ -Dtransformation_model={transformation_model} \
+ -Dmodel_to_regularize_with={model_to_regularize_with} \
+ -Dlambda={lambda} \
+ -Dallowed_error_for_ransac={allowed_error_for_ransac} \
+ -Ddetection_min_max={detection_min_max} \
+ -- --no-splash {path_bsh}""",
config["common"],
config["registration"],
file_id_w="{wildcards.file_id}",
+ path_bsh=config["common"]["bsh_directory"] + config["registration"]["bsh_file"],
jdir=JOBDIR,
input_xml="{wildcards.xml_base}")
cmd_string += "> {log} 2>&1 && touch {output}"
@@ -184,17 +188,56 @@ rule xml_merge:
output: "{xml_base}_merge.xml"
log: "{xml_base}_merge.log"
run:
- cmd_string = produce_string("{fiji-prefix} {fiji-app} -Dimage_file_directory={jdir} -Dmerged_xml={output} -- --no-splash {bsh_file} > {log} 2>&1",
+ cmd_string = produce_string(
+ """{fiji-prefix} {fiji-app} \
+ -Dimage_file_directory={jdir} \
+ -Dmerged_xml={output} \
+ -- --no-splash {path_bsh}""",
config["common"],
config["xml_merge"],
log="{log}",
+ path_bsh=config["common"]["bsh_directory"] + config["xml_merge"]["bsh_file"],
jdir=JOBDIR,
output="{output}")
+ cmd_string += "> {log} 2>&1 && touch {output}"
shell(cmd_string)
-rule external_trafo:
+rule timelapse:
input: rules.xml_merge.output
- output: rules.xml_merge.output[0] + "_external_trafo"
+ output: rules.xml_merge.output[0] + "_timelapse"
+ log: "timelapse.log"
+ run:
+ cmd_string = produce_string(
+ """{fiji-prefix} {fiji-app} \
+ -Dimage_file_directory={jdir} \
+ -Dmerged_xml={input} \
+ -Dtimelapse_process_timepoints={timelapse_process_timepoints} \
+ -Dprocess_channel_timelapse={channel} \
+ -Dprocess_illumination={illuminations} \
+ -Dprocess_angle={angle} \
+ -Dreference_timepoint={reference_timepoint} \
+ -Dchannel_1={proc-ch} \
+ -Dtype_of_registration_timelapse={type_of_registration_timelapse} \
+ -Dregistration_algorithm={registration_algorithm} \
+ -Dreg_1_interest_points_channel={interest_points_channel_0} \
+ -Dreg_2_interest_points_channel={interest_points_channel_1} \
+ -Dtransformation_model={transformation_model} \
+ -Dmodel_to_regularize_with={model_to_regularize_with} \
+ -Dlambda={lambda} \
+ -Dallowed_error_for_ransac={allowed_error_for_ransac} \
+ -Dsignificance={significance} \
+ -- --no-splash {path_bsh}""",
+ config["common"],
+ config["registration"],
+ config["timelapse"],
+ input="{input}",
+ path_bsh=config["common"]["bsh_directory"] + config["timelapse"]["bsh_file"],
+ jdir=JOBDIR)
+ shell(cmd_string)
+
+rule external_trafo:
+ input: rules.timelapse.output
+ output: rules.timelapse.output[0] + "_external_trafo"
log: "external_trafo.log"
run:
cmd_string = produce_string("""{fiji-prefix} {fiji-app} \
@@ -208,9 +251,10 @@ rule external_trafo:
-Dapply_transformation={apply_transformation} \
-Ddefine_mode_transform={define_mode_transform} \
-Dmatrix_transform={matrix_transform} \
--- --no-splash {bsh_file}""",
+-- --no-splash {path_bsh}""",
config["common"],
config["external_transform"],
+ path_bsh=config["common"]["bsh_directory"] + config["external_trafo"]["bsh_file"],
jdir=JOBDIR,
input="{input}")
cmd_string += "> {log} 2>&1 && touch {output}"
@@ -249,10 +293,11 @@ rule deconvolution:
-Dpsf_size_y={psf_size_y} \
-Dpsf_size_z={psf_size_z} \
-Diterations={iterations} \
- -- --no-splash {bsh_file}""",
+ -- --no-splash {path_bsh}""",
config["common"],
config["deconvolution"],
file_id_w="{wildcards.file_id}",
+ path_bsh=config["common"]["bsh_directory"] + config["deconvolution"]["bsh_file"],
jdir=JOBDIR,
merged_xml_file="{input.merged_xml}"
)
diff --git a/spim_registration/timelapse/timelapse_registration.bsh b/spim_registration/timelapse/timelapse_registration.bsh
new file mode 100755
index 0000000000000000000000000000000000000000..e27c1fbb018bc512c33d13eff552cdaf15a8cb68
--- /dev/null
+++ b/spim_registration/timelapse/timelapse_registration.bsh
@@ -0,0 +1,92 @@
+// Load Fiji dependencies
+import ij.IJ; // calls imagej
+import ij.Prefs; // calls imagej settings
+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
+
+// Load xml file
+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 + ".xml");
+
+// General Registration Parameters and Channel Settings
+System.out.println("---------------------------------------------------------");
+System.out.println( "General parameters: " );
+timelapse_process_timepoints = System.getProperty( "timelapse_process_timepoints" );
+process_channel_timelapse = System.getProperty( "process_channel_timelapse" );
+process_illumination = System.getProperty( "process_illumination" );
+process_angle = System.getProperty( "process_angle" );
+channel_1 = System.getProperty( "channel_1" );
+channel_2 = System.getProperty( "channel_2" );
+
+System.out.println( "process_timepoints = " + timelapse_process_timepoints );
+System.out.println( "process_channel = " + process_channel_timelapse );
+System.out.println( "process_illumination = " + process_illumination );
+System.out.println( "process_angle = " + process_angle );
+System.out.println( "channel_1 = " + channel_1 );
+System.out.println( "channel_2 = " + channel_2 );
+
+// Timelapse registration Parameter
+System.out.println("---------------------------------------------------------");
+System.out.println( "Timelapse Registration: " );
+
+reference_timepoint = System.getProperty( "reference_timepoint" );
+System.out.println( "reference_timepoint=" + reference_timepoint );
+
+type_of_registration_timelapse = System.getProperty( "type_of_registration_timelapse" );
+registration_algorithm = System.getProperty( "registration_algorithm" );
+reg_1_interest_points_channel = System.getProperty( "reg_1_interest_points_channel" );
+reg_2_interest_points_channel = System.getProperty( "reg_2_interest_points_channel" ); // Dual Channel
+
+System.out.println( "type_of_registration = " + type_of_registration_timelapse );
+System.out.println( "registration_algorithm = " + registration_algorithm );
+System.out.println( "interest_points_channel_" + channel_1 + " = " + reg_1_interest_points_channel );
+System.out.println( "interest_points_channel_" + channel_2 + " = " + reg_2_interest_points_channel );
+
+transformation_model = System.getProperty( "transformation_model" );
+model_to_regularize_with = System.getProperty( "model_to_regularize_with" );
+float lambda = Float.parseFloat( System.getProperty( "lambda" ) );
+int allowed_error_for_ransac = Integer.parseInt( System.getProperty( "allowed_error_for_ransac" ) );
+significance = System.getProperty( "significance" );
+
+System.out.println( "transformation = " + transformation );
+System.out.println( "model_to_regularize_with = " + model_to_regularize_with );
+System.out.println( "lambda = " + lambda );
+System.out.println( "allowed_error_for_ransac = " + allowed_error_for_ransac );
+System.out.println( "significance = " + significance );
+
+System.out.println( "=======================================================" );
+System.out.println( "Starting Timelapse Registration" );
+IJ.run("Register Dataset based on Interest Points",
+ "select_xml=" + xml_path + merged_xml + ".xml " +
+ "process_angle=[" + process_angle + "] " +
+ "process_channel=[" + process_channel_timelapse + "] " +
+ "process_illumination=[" + process_illumination + "] " +
+ "process_timepoint=[" + timelapse_process_timepoints + "] " +
+ "registration_algorithm=[" + registration_algorithm + "] " +
+ "type_of_registration=[" + type_of_registration_timelapse + "] " +
+ "interest_points_channel_" + channel_1 + "=" + reg_1_interest_points_channel + " " +
+// "interest_points_channel_" + channel_2 + "=" + reg_2_interest_points_channel + " " + // Dual Channel
+ "reference=" + reference_timepoint + " " +
+ "consider_each_timepoint_as_rigid_unit " +
+ "transformation=" + transformation_model + " " +
+ "regularize_model " +
+ "model_to_regularize_with=" + model_to_regularize_with + " " +
+ "lamba=" + lambda + " " +
+ "allowed_error_for_ransac=" + allowed_error_for_ransac + " " +
+ "significance=" + significance + "");
+
+/* shutdown */
+runtime.exit(0);
diff --git a/spim_registration/timelapse/tomancak_czi.json b/spim_registration/timelapse/tomancak_czi.json
index 16e167b908b48317fd6cbc500293ed76906eb368..7a5d46f710ed22805805c561d4bc47df4754a50d 100755
--- a/spim_registration/timelapse/tomancak_czi.json
+++ b/spim_registration/timelapse/tomancak_czi.json
@@ -29,20 +29,6 @@
"bsh_file" : "define_czi.bsh"
},
- "resave_czi_hdf5" :
- {
- "parallel_timepoints" : "2",
- "resave_angle" : "\"All angles\"",
- "resave_channel" : "\"All channels\"",
- "resave_illumination" : "\"All illuminations\"",
- "resave_timepoint" : "\"All Timepoints\"",
- "subsampling_factors" : "\"{{ {{1,1,1}}, {{2,2,1}}, {{4,4,1}}, {{8,8,1}} }}\"",
- "hdf5_chunk_sizes" : "\"{{ {{32,32,4}}, {{32,32,4}}, {{16,16,16}}, {{16,16,16}} }}\"",
- "timepoints_per_partition" : "1",
- "setups_per_partition" : "0",
- "bsh_file" : "export.bsh"
- },
-
"define_xml_tif" :
{
"timepoints" : "1-2",
@@ -62,6 +48,20 @@
"bsh_file" : "define_tif_zip.bsh"
},
+ "resave_czi_hdf5" :
+ {
+ "parallel_timepoints" : "2",
+ "resave_angle" : "\"All angles\"",
+ "resave_channel" : "\"All channels\"",
+ "resave_illumination" : "\"All illuminations\"",
+ "resave_timepoint" : "\"All Timepoints\"",
+ "subsampling_factors" : "\"{{ {{1,1,1}}, {{2,2,1}}, {{4,4,1}}, {{8,8,1}} }}\"",
+ "hdf5_chunk_sizes" : "\"{{ {{32,32,4}}, {{32,32,4}}, {{16,16,16}}, {{16,16,16}} }}\"",
+ "timepoints_per_partition" : "1",
+ "setups_per_partition" : "0",
+ "bsh_file" : "export.bsh"
+ },
+
"registration" :
{
"timepoint" : "\"Single Timepoint (Select from List)\"",
@@ -72,16 +72,15 @@
"algorithm" : "\"Fast 3d geometric hashing (rotation invariant)\"",
"label_interest_points" : "\"beads\"",
"type_of_registration" : "\"Register timepoints individually\"",
- "type_of_registration_timelapse" : "\"Match against one reference timepoint (no global optimization)\"",
"type_of_detection" : "\"Difference-of-Mean (Integral image based)\"" ,
"subpixel_localization" : "\"3-dimensional quadratic fit\"",
"imglib_container" : "\"ArrayImg (faster)\"",
"radius_1" : "2",
"radius_2" : "3",
"threshold" : "0.005",
- "interest_points_channel_0" : "\"[DO NOT register this channel]\"" ,
- "interest_points_channel_1" : "\"beads\"",
- "fix_tiles" : "\"Fix first tile\"" ,
+ "interest_points_channel_0" : "\"beads\"",
+ "interest_points_channel_1" : "\"[DO NOT register this channel]\"",
+ "fix_tiles" : "\"Fix first tile\"",
"map_back_tiles" : "\"Map back to first tile using rigid model\"",
"transformation_model" : "Affine",
"model_to_regularize_with" : "Rigid",
@@ -97,6 +96,14 @@
{
"bsh_file" : "xml_merge.bsh"
},
+
+ "timelapse" :
+ {
+ "reference_timepoint" : "0",
+ "timelapse_process_timepoints" : "\"All Timepoints\"",
+ "type_of_registration_timelapse" : "\"Match against one reference timepoint (no global optimization)\"",
+ "bsh_file" : "timelapse_registration.bsh"
+ },
"external_transform" :
{