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Commit a49ba248 authored by Christopher Schmied's avatar Christopher Schmied
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updated .bsh files for define xml

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spim_registration/timelapse/Snakefile 100644 → 100755
+ 8
− 12
View file @ a49ba248
......@@ -7,8 +7,8 @@ if JOBDIR[-1] != "/": # this checks if jobdir ends with slash if not it adds a s
JOBDIR+="/"
#data specific config file, expected to be inside JOBDIR
configfile: "tomancak_test_cluster.json"
# configfile: "tomancak_test_cluster.yaml"
# configfile: "tomancak_test_cluster.json"
configfile: "tomancak_test_cluster.yaml"
padding_format = "{0:0"+str(padding_of_file_id(int(config["common"]["ntimepoints"])))+"d}"
......@@ -34,20 +34,15 @@ rule define_xml_czi:
cmd_string = produce_string("""{fiji-prefix} {fiji-app} \
-Dimage_file_directory={jdir} \
-Dfirst_czi={first_czi} \
-Dangle_1={angle_1} \
-Dangle_2={angle_2} \
-Dangle_3={angle_3} \
-Dangle_4={angle_4} \
-Dangle_5={angle_5} \
-Dchannel_1={channel_1} \
-Dchannel_2={channel_2} \
-Dillumination_1={illumination_1} \
-Drotation_around={rotation_around} \
-Dangles={angles} \
-Dchannels={channels} \
-Dillumination={illumination} \
-Dpixel_distance_x={pixel_distance_x} \
-Dpixel_distance_y={pixel_distance_y} \
-Dpixel_distance_z={pixel_distance_z} \
-Dpixel_unit={pixel_unit} \
-Dfirst_xml_filename={first_xml_filename} \
-Drotation_around={rotation_around} \
-- --no-splash {path_bsh}""",
config["common"],
config["define_xml_czi"],
......@@ -68,8 +63,9 @@ rule define_xml_tif:
"""{fiji-prefix} {fiji-app} \
-Dimage_file_directory={jdir} \
-Dtimepoints={timepoints} \
-Dacquisition_angles={acquisition_angles} \
-Dangles={angles} \
-Dchannels={channels} \
-Dillumination={illumination} \
-Dimage_file_pattern={image_file_pattern} \
-Dpixel_distance_x={pixel_distance_x} \
-Dpixel_distance_y={pixel_distance_y} \
......
spim_registration/timelapse/define_czi.bsh 100644 → 100755
+ 104
− 26
View file @ a49ba248
......@@ -26,25 +26,93 @@ System.out.println( "first_czi_path = " + image_file_directory + first_czi );
// Dataset settings
System.out.println("---------------------------------------------------------");
System.out.println("Dataset:");
angle_1 = System.getProperty( "angle_1" );
angle_2 = System.getProperty( "angle_2" );
angle_3 = System.getProperty( "angle_3" );
angle_4 = System.getProperty( "angle_4" );
angle_5 = System.getProperty( "angle_5" );
channel_1 = System.getProperty( "channel_1" );
channel_2 = System.getProperty( "channel_2" );
illumination_1 = System.getProperty( "illumination_1" );
rotation_around = System.getProperty( "rotation_around" );
System.out.println("Angle Settings:");
// Angle settings
// Parses angles and determines the number of angles
// uses tokens of string angles to assemble the string for angle_string
// via StringBuilder
angles = System.getProperty( "angles" );
System.out.println( "Angles = " + angles );
// Parses string angles
String delims = "[,]";
String[] angle_token = angles.split(delims);
// Builds string using the number of tokens and inserts the tokens in the string
StringBuilder angle_string = new StringBuilder();
String angle_part;
for ( int angle = 0; angle < angle_token.length; angle++) {
int num_angles = angle + 1;
angle_part = "angle_" + num_angles + "=" + angle_token[angle];
angle_string.append(angle_part);
angle_string.append(" ");
}
System.out.println( angle_string );
System.out.println("---------------------------------------------------------");
System.out.println("Channel Settings:");
// Channel settings
// This parses channels and determines the number of channels
// then uses the tokens of channels to assemble the necessary string
// for channel_string via StringBuilder
channels = System.getProperty( "channels" );
System.out.println( "Channel Names = " + channels );
// Parses string channel_names
String delims = "[,]";
String[] channel_token = channels.split(delims);
// Builds string using the number of tokens and inserts the tokens in the string
StringBuilder channel_string = new StringBuilder();
String channel_part;
for ( int channel = 0; channel < channel_token.length; channel++) {
int num_channel = channel + 1;
channel_part = "channel_" + num_channel + "=" + channel_token[channel];
channel_string.append(channel_part);
channel_string.append(" ");
}
System.out.println( "Channel String = " + channel_string );
System.out.println("---------------------------------------------------------");
System.out.println("Illumination Settings:");
// Illuminatin settings
// This parses illumination and determines the number of illuminations
// then uses the tokens of illuminations to assemble the string for
// illum_string via StringBuilder
illumination = System.getProperty( "illumination" );
System.out.println( "Illumination = " + illumination );
// Parses string illumination
String delims = "[,]";
String[] illum_token = illumination.split(delims);
// Builds string using the number of tokens and inserts the tokens in the string
StringBuilder illum_string = new StringBuilder();
String illum_part;
System.out.println( "angle_1 = " + angle_1 );
System.out.println( "angle_2 = " + angle_2 );
System.out.println( "angle_3 = " + angle_3 );
System.out.println( "angle_4 = " + angle_4 );
System.out.println( "angle_5 = " + angle_5 );
System.out.println( "channel_1 = " + channel_1 );
System.out.println( "channel_2 = " + channel_2 );
System.out.println( "illumination_1 = " + illumination_1 );
for ( int illum= 0; illum< illum_token.length; illum++) {
int num_illum = illum + 1;
illum_part = "_______illumination_" + num_illum + "=" + illum_token[illum];
illum_string.append(illum_part);
illum_string.append(" ");
}
System.out.println( illum_string );
System.out.println("---------------------------------------------------------");
System.out.println("Rotation setting:");
rotation_around = System.getProperty( "rotation_around" );
System.out.println( "rotation_around = " + rotation_around );
// Calibaration
......@@ -63,19 +131,29 @@ System.out.println( "pixel_unit = " + pixel_unit );
// Executes Fiji plugin
System.out.println("=========================================================");
System.out.println("Start plugin:");
System.out.println("Define Multi-View Dataset type_of_dataset=[Zeiss Lightsheet Z.1 Dataset (LOCI Bioformats)] " +
"xml_filename=" + first_xml_filename + ".xml " +
"browse=" + image_file_directory + first_czi + " " +
"first_czi=" + image_file_directory + first_czi + " " +
angle_string +
channel_string +
illum_string +
"modify_calibration " +
"modify_rotation_axis " +
"pixel_distance_x=" + pixel_distance_x + " " +
"pixel_distance_y=" + pixel_distance_y + " " +
"pixel_distance_z=" + pixel_distance_z + " " +
"pixel_unit=" + pixel_unit + " " +
"rotation_around=" + rotation_around + "");
IJ.run("Define Multi-View Dataset",
"type_of_dataset=[Zeiss Lightsheet Z.1 Dataset (LOCI Bioformats)] " +
"xml_filename=" + first_xml_filename + ".xml " +
"browse=" + image_file_directory + first_czi + " " +
"first_czi=" + image_file_directory + first_czi + " " +
"angle_1=" + angle_1 + " " +
"angle_2=" + angle_2 + " " +
"angle_3=" + angle_3 + " " +
"angle_4=" + angle_4 + " " +
"angle_5=" + angle_5 + " " +
"channel_1=" + channel_1 + " " +
// "channel_2=" + channel_2 + " " + // for dual channel comment out if single channel
"_______illumination_1=" + illumination_1 + " " +
angle_string +
channel_string +
illum_string +
"modify_calibration " +
"modify_rotation_axis " +
"pixel_distance_x=" + pixel_distance_x + " " +
......
spim_registration/timelapse/define_tif_zip.bsh 100644 → 100755
+ 94
− 10
View file @ a49ba248
......@@ -24,28 +24,91 @@ System.out.println( "xml_filename = " + xml_filename );
// Dataset settings
System.out.println("=========================================================");
System.out.println("Dataset:");
timepoints = System.getProperty( "timepoints" );
channels = System.getProperty( "channels" );
acquisition_angles = System.getProperty( "acquisition_angles" );
image_file_pattern = System.getProperty( "image_file_pattern" );
type_of_dataset = System.getProperty( "type_of_dataset" );
timepoints = System.getProperty( "timepoints" );
angles = System.getProperty( "angles" );
System.out.println( "image_file_pattern = " + image_file_pattern );
System.out.println( "type_of_dataset = " + type_of_dataset );
System.out.println( "timepoints = " + timepoints );
System.out.println( "angles = " + angles );
multiple_timepoints = System.getProperty( "multiple_timepoints" );
multiple_channels = System.getProperty( "multiple_channels" );
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( "channels = " + channels );
System.out.println( "acquisition_angles = " + acquisition_angles );
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_channels = " + multiple_channels );
System.out.println( "multiple_illumination_directions = " + multiple_illumination_directions );
System.out.println( "multiple_angles = " + multiple_angles );
System.out.println( "imglib_container = " + imglib_container );
System.out.println("---------------------------------------------------------");
System.out.println("Channel setting:");
// Channel switch: parses channels and determines if Single or Multi Channel
// assembles the appropriate string for the channel setting
channels = System.getProperty( "channels" );
String channel_string = null;
String delims = "[,]";
String[] channel_token = channels.split(delims);
if (channels.equalsIgnoreCase(""))
{
System.out.println("Warning: There are no channels set");
}
else if ( channel_token.length == 1 )
{
channel_string="";
System.out.println("Single Channel");
}
else if ( channel_token.length > 1)
{
channel_string = "channels_=" + channels + " ";
System.out.println("Multi Channel");
}
System.out.println( "Channels = " + channel_string );
System.out.println("---------------------------------------------------------");
System.out.println("Illumination setting:");
// Illuminatin switch: parses illumination and determines if there is a single
// or multiple illumination sides and then assembles the illum_string
illumination = System.getProperty( "illumination" );
String illum_string = null;
String delims = "[,]";
String[] illum_token = illumination.split(delims);
if (illumination.equalsIgnoreCase(""))
{
System.out.println("Warning: There are no illuminations set");
}
else if ( illum_token.length == 1 )
{
illum_string="";
System.out.println("One illumination side or fused illumination");
}
else if ( illum_token.length > 1)
{
illum_string = "illumination_=" + illumination + " ";
System.out.println("Dual Illumination sides");
}
System.out.println( "Illuminations = " + illum_string );
// Calibaration
System.out.println("=========================================================");
System.out.println("Calibration:");
......@@ -59,6 +122,26 @@ 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 );
System.out.println("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 + " " +
channel_string +
illum_string +
"acquisition_angles_=" + acquisition_angles + " " +
"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:");
......@@ -72,8 +155,9 @@ IJ.run("Define Multi-View Dataset",
"image_file_directory=" + image_file_directory + " " +
"image_file_pattern=" + image_file_pattern + " " +
"timepoints_=" + timepoints + " " +
// "channels_=" + channels + " " + // for dual channel comment out if single channel
"acquisition_angles_=" + acquisition_angles + " " +
channel_string +
illum_string +
"acquisition_angles_=" + angles + " " +
"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 + " " +
......
spim_registration/timelapse/tomancak_test_cluster.yaml 100644 → 100755
+ 108
− 123
View file @ a49ba248
common:
{
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",
bsh_directory: "/projects/pilot_spim/Christopher/snakemake-workflows/spim_registration/timelapse/",
directory_cuda: "/sw/users/schmied/packages/2015-06-08_Fiji.app.cuda/lib/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",
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',
ntimepoints: 5,
angles: "0,72,144,216,288",
channels: "green",
illumination: "0",
pixel_distance_x: '0.28590106964',
pixel_distance_y: '0.28590106964',
pixel_distance_z: '1.50000',
pixel_unit: "um",
rotation_around: "X-Axis"
fusion_switch: "deconvolution"
}
define_xml_czi: {
first_czi: "2015-04-11_LZ2_Stock68_3.czi",
rotation_around: "X-Axis",
bsh_file: "define_czi.bsh"
}
define_xml_tif:
{
acquisition_angles: '0,72,144,216,288',
bsh_file: "define_tif_zip.bsh",
channels: '0',
define_xml_tif: {
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)"'
type_of_dataset: '"Image Stacks (ImageJ Opener)"',
bsh_file: "define_tif_zip.bsh"
}
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'
}
external_transform:
{
registration: {
algorithm: '"Fast 3d geometric hashing (rotation invariant)"',
allowed_error_for_ransac: '5',
angle: '"All angles"',
apply_transformation: '"Current view transformations
(appends to current transforms)"',
bsh_file: "transform.bsh",
bsh_file: "registration.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"'
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"'
}
xml_merge: {
bsh_file: "xml_merge.bsh"
}
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)"'
}
fusion: {
......@@ -113,6 +109,46 @@ fusion: {
process_views_in_paralell: '"All"',
xml_output: '"Save every XML with user-provided unique id"'
}
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"'
}
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)"'
}
hdf5_output: {
bsh_file_define: "define_output.bsh",
......@@ -133,57 +169,6 @@ hdf5_output: {
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"
output_xml: '"fused_Dual_Channel"'
}
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