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Commit ae77e857 authored by Christopher Schmied's avatar Christopher Schmied
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Added timelapse registration

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spim_registration/timelapse/Snakefile
+ 101
− 56
View file @ ae77e857
......@@ -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}"
)
......
spim_registration/timelapse/timelapse_registration.bsh 0 → 100755
+ 92
− 0
View file @ ae77e857
// 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);
spim_registration/timelapse/tomancak_czi.json
+ 25
− 18
View file @ ae77e857
......@@ -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" :
{
......
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