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Commit c5af5c0e authored by Christopher Schmied's avatar Christopher Schmied
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Added and tested resaving of output files

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spim_registration/timelapse/Snakefile
+ 23
− 24
View file @ c5af5c0e
......@@ -112,7 +112,6 @@ rule hdf5_xml:
-Dtimepoints_per_partition={timepoints_per_partition} \
-Dsetups_per_partition={setups_per_partition} \
-Drun_only_job_number=0 \
-Djob_type=xml \
-- --no-splash {path_bsh}""",
config["common"],
config["define_xml_czi"],
......@@ -148,7 +147,6 @@ rule resave_hdf5:
-Dtimepoints_per_partition={timepoints_per_partition} \
-Dsetups_per_partition={setups_per_partition} \
-Drun_only_job_number={job_number} \
-Djob_type=hdf5 \
-- --no-splash {path_bsh}""", # the & submits everyting at once
config["common"],
config["define_xml_czi"],
......@@ -379,39 +377,38 @@ rule deconvolution:
rule define_output:
input: glob.glob('TP*')
output: config["hdf5_output"]["output_xml"] + ".xml"
output: config["hdf5_output"]["output_xml"].strip('\"') + ".xml"
log: "define_xml_tif.log"
run:
cmd_string = produce_string(
"""{fiji-prefix} {fiji-app} \
-Dimage_file_directory={jdir} \
-Dtimepoints={output_timepoints} \
-Dacquisition_angles={acquisition_angles} \
-Dchannels={output_channels} \
-Dimage_file_pattern={output_image_file_pattern} \
-Dpixel_distance_x={output_pixel_distance_x} \
-Dpixel_distance_y={output_pixel_distance_y} \
-Dpixel_distance_z={output_pixel_distance_z} \
-Dpixel_unit={output_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} \
-Dxml_filename={output_xml} \
-Dtype_of_dataset={output_type_of_dataset} \
-Dmultiple_timepoints={output_multiple_timepoints} \
-Dmultiple_channels={output_multiple_channels} \
-Dmultiple_illumination_directions={output_illumination_directions} \
-Dmultiple_angles={output_multiple_angles} \
-Dimglib_container={output_imglib_container} \
-- --no-splash {path_bsh}""",
config["common"],
config["define_xml_tif"],
config["hdf5_output"],
jdir=JOBDIR,
path_bsh=config["common"]["bsh_directory"] + config["define_xml_tif"]["bsh_file"])
path_bsh=config["common"]["bsh_directory"] + config["hdf5_output"]["bsh_file_define"])
cmd_string +=" > {log} 2>&1"
shell(cmd_string)
# create mother .xml/.h5
rule hdf5_xml_output:
input: config["hdf5_output"]["output_xml"] + ".xml"
input: config["hdf5_output"]["output_xml"].strip('\"') + ".xml"
output: expand("{dataset}.{suffix}",dataset=[ config["hdf5_output"]["output_hdf5_xml"].strip('\"')], suffix=["xml","h5"]),
[ item+"_output" for item in datasets ]
log: "hdf5_xml.log"
......@@ -419,8 +416,8 @@ rule hdf5_xml_output:
part_string = produce_string(
"""{fiji-prefix} {fiji-app} \
-Dimage_file_directory={jdir} \
-Dfirst_xml_filename={first_xml_filename} \
-Dhdf5_xml_filename={hdf5_xml_filename} \
-Dfirst_xml_filename={output_xml} \
-Dhdf5_xml_filename={output_hdf5_xml} \
-Dresave_angle={resave_angle} \
-Dresave_channel={resave_channel} \
-Dresave_illumination={resave_illumination} \
......@@ -430,10 +427,11 @@ rule hdf5_xml_output:
-Dtimepoints_per_partition={timepoints_per_partition} \
-Dsetups_per_partition={setups_per_partition} \
-Drun_only_job_number=0 \
-Djob_type=xml \
-Doutput_data_type={output_data_type} \
-Dconvert_32bit={convert_32bit}\
-- --no-splash {path_bsh}""",
config["common"],
config["define_xml_czi"],
config["hdf5_output"],
config["resave_hdf5"],
jdir=JOBDIR,
path_bsh=config["common"]["bsh_directory"] + config["resave_hdf5"]["bsh_file"])
......@@ -444,13 +442,13 @@ rule hdf5_xml_output:
rule resave_hdf5_output:
input: rules.hdf5_xml_output.output
output: "{xml_base}-{file_id,\d+}-00.h5_output_hdf5"
log: "resave_hdf5-{file_id}.log"
log: "resave_output-{file_id}.log"
run:
part_string = produce_string(
"""{fiji-prefix} {fiji-app} \
-Dimage_file_directory={jdir} \
-Dfirst_xml_filename={first_xml_filename} \
-Dhdf5_xml_filename={input_xml_base} \
-Dfirst_xml_filename={output_xml} \
-Dhdf5_xml_filename={output_hdf5_xml} \
-Dresave_angle={resave_angle} \
-Dresave_channel={resave_channel} \
-Dresave_illumination={resave_illumination} \
......@@ -460,10 +458,11 @@ rule resave_hdf5_output:
-Dtimepoints_per_partition={timepoints_per_partition} \
-Dsetups_per_partition={setups_per_partition} \
-Drun_only_job_number={job_number} \
-Djob_type=hdf5 \
-- --no-splash {path_bsh}""", # the & submits everyting at once
-Doutput_data_type={output_data_type} \
-Dconvert_32bit={convert_32bit}\
-- --no-splash {path_bsh}""",
config["common"],
config["define_xml_czi"],
config["hdf5_output"],
config["resave_hdf5"],
jdir=JOBDIR,
path_bsh=config["common"]["bsh_directory"] + config["resave_hdf5"]["bsh_file"],
......
spim_registration/timelapse/define_output.bsh 0 → 100755
+ 107
− 0
View file @ c5af5c0e
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
System.out.println("Start loading parameters");
// Directory
System.out.println("=========================================================");
System.out.println("Directory:");
image_file_directory = System.getProperty( "image_file_directory" );
xml_filename = System.getProperty( "xml_filename" );
System.out.println( "image_file_directory = " + image_file_directory );
System.out.println( "xml_filename = " + xml_filename );
// Dataset settings
System.out.println("=========================================================");
System.out.println("Dataset:");
timepoints = System.getProperty( "timepoints" );
image_file_pattern = System.getProperty( "image_file_pattern" );
type_of_dataset = System.getProperty( "type_of_dataset" );
multiple_timepoints = System.getProperty( "multiple_timepoints" );
multiple_illumination_directions = System.getProperty( "multiple_illumination_directions" );
multiple_angles = System.getProperty( "multiple_angles" );
imglib_container = System.getProperty( "imglib_container" );
System.out.println( "timepoints = " + timepoints );
System.out.println( "image_file_pattern = " + image_file_pattern );
System.out.println( "type_of_dataset = " + type_of_dataset );
System.out.println( "multiple_timepoints = " + multiple_timepoints );
System.out.println( "multiple_illumination_directions = " + multiple_illumination_directions );
System.out.println( "multiple_angles = " + multiple_angles );
System.out.println( "imglib_container = " + imglib_container );
// Calibaration
System.out.println("=========================================================");
System.out.println("Calibration:");
float pixel_distance_x = Float.parseFloat( System.getProperty( "pixel_distance_x" ) );
float pixel_distance_y = Float.parseFloat( System.getProperty( "pixel_distance_y" ) );
float pixel_distance_z = Float.parseFloat( System.getProperty( "pixel_distance_z" ) );
pixel_unit = System.getProperty( "pixel_unit" );
System.out.println( "pixel_distance_x = " + pixel_distance_x );
System.out.println( "pixel_distance_y = " + pixel_distance_y );
System.out.println( "pixel_distance_z = " + pixel_distance_z );
System.out.println( "pixel_unit = " + pixel_unit );
// Channel Switch
System.out.println("=========================================================");
System.out.println("Channel Switch:");
multiple_channels = System.getProperty( "multiple_channels" );
System.out.println( "multiple_channels = " + multiple_channels );
channels = System.getProperty( "channels" );
IJ.run("Define Multi-View Dataset , type_of_dataset=[" + type_of_dataset + "] " +
"xml_filename=[" + xml_filename + ".xml] " +
"multiple_timepoints=[" + multiple_timepoints + "] " +
"multiple_channels=[" + multiple_channels + "] " +
"_____multiple_illumination_directions=[" + multiple_illumination_directions + "] " +
"multiple_angles=[" + multiple_angles + "] " +
"image_file_directory=" + image_file_directory + " " +
"image_file_pattern=" + image_file_pattern + " " +
"timepoints_=" + timepoints + " " +
channels +
"calibration_type=[Same voxel-size for all views] calibration_definition=[User define voxel-size(s)]" + " " +
"imglib2_data_container=[" + imglib_container + "] " +
"pixel_distance_x=" + pixel_distance_x + " " +
"pixel_distance_y=" + pixel_distance_y + " " +
"pixel_distance_z=" + pixel_distance_z + " " +
"pixel_unit=" + pixel_unit + "");
// Executes Fiji plugin
System.out.println("=========================================================");
System.out.println("Start plugin:");
IJ.run("Define Multi-View Dataset",
"type_of_dataset=[" + type_of_dataset + "] " +
"xml_filename=[" + xml_filename + ".xml] " +
"multiple_timepoints=[" + multiple_timepoints + "] " +
"multiple_channels=[" + multiple_channels + "] " +
"_____multiple_illumination_directions=[" + multiple_illumination_directions + "] " +
"multiple_angles=[" + multiple_angles + "] " +
"image_file_directory=" + image_file_directory + " " +
"image_file_pattern=" + image_file_pattern + " " +
"timepoints_=" + timepoints + " " +
channels +
"calibration_type=[Same voxel-size for all views] calibration_definition=[User define voxel-size(s)]" + " " +
"imglib2_data_container=[" + imglib_container + "] " +
"pixel_distance_x=" + pixel_distance_x + " " +
"pixel_distance_y=" + pixel_distance_y + " " +
"pixel_distance_z=" + pixel_distance_z + " " +
"pixel_unit=" + pixel_unit + "");
/* shutdown */
runtime.exit(0);
spim_registration/timelapse/export.bsh
+ 0
− 3
View file @ c5af5c0e
......@@ -52,9 +52,6 @@ System.out.println( "hdf5_chunk_sizes=" + hdf5_chunk_sizes );
System.out.println( "timepoints_per_partition=" + timepoints_per_partition );
System.out.println( "setups_per_partition=" + setups_per_partition );
// job switch
int run_only_job_number = Integer.parseInt( System.getProperty( "run_only_job_number" ) );
System.out.println( "run_only_job_number=" + run_only_job_number );
......
spim_registration/timelapse/tomancak_czi.json
+ 3
− 2
View file @ c5af5c0e
......@@ -175,7 +175,7 @@
"hdf5_output" :
{
"output_image_file_pattern" : "TP{t}_Ch{c}_Ill0_Ang0,72,144,216,288.tif",
"output_image_file_pattern" : "TP{{t}}_Ch{{c}}_Ill0_Ang0,72,144,216,288.tif",
"output_data_type" : "32Bit",
"output_xml" : "\"fused_Dual_Channel\"",
"output_hdf5_xml" : "\"hdf5_fused_Stock68\"",
......@@ -191,7 +191,8 @@
"output_multiple_angles" : "\"NO (one angle)\"",
"output_type_of_dataset" : "\"Image Stacks (ImageJ Opener)\"",
"output_imglib_container" : "\"ArrayImg (faster)\"",
"bsh_file" : "/export_output.bsh",
"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)]\""
}
......
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