From fdf6dafe0210f0c6ebf4a81546e146eb0a7ffb5b Mon Sep 17 00:00:00 2001
From: Christopher Schmied <schmied@mpi-cbg.de>
Date: Tue, 30 Jun 2015 15:17:16 +0200
Subject: [PATCH] Set up tests for snakemake pipeline
---
.../timelapse/SingleChannel.yaml | 189 -------------
spim_registration/timelapse/Snakefile | 10 +-
.../timelapse/dual_OneChannel.yaml | 260 ++++++++++++++++++
spim_registration/timelapse/single_test.yaml | 260 ++++++++++++++++++
spim_registration/timelapse/tomancak.json | 88 ------
spim_registration/timelapse/tomancak_czi.json | 204 --------------
.../timelapse/tomancak_test_cluster.json | 202 --------------
.../timelapse/tomancak_test_cluster.yaml | 11 +-
8 files changed, 533 insertions(+), 691 deletions(-)
delete mode 100755 spim_registration/timelapse/SingleChannel.yaml
create mode 100755 spim_registration/timelapse/dual_OneChannel.yaml
create mode 100755 spim_registration/timelapse/single_test.yaml
delete mode 100644 spim_registration/timelapse/tomancak.json
delete mode 100644 spim_registration/timelapse/tomancak_czi.json
delete mode 100644 spim_registration/timelapse/tomancak_test_cluster.json
diff --git a/spim_registration/timelapse/SingleChannel.yaml b/spim_registration/timelapse/SingleChannel.yaml
deleted file mode 100755
index 60b1688..0000000
--- a/spim_registration/timelapse/SingleChannel.yaml
+++ /dev/null
@@ -1,189 +0,0 @@
-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/",
- 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,
- 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",
- # 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",
- rotation_around: "X-Axis",
- bsh_file: "define_czi.bsh"
- }
-
-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)"',
- type_of_dataset: '"Image Stacks (ImageJ Opener)"',
- bsh_file: "define_tif_zip.bsh"
- }
-
-resave_hdf5: {
- 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',
- 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_timepoint: '"Single Timepoint (Select from List)"',
- reg_process_angle: '"All angles"',
- reg_process_illumination: '"All illuminations"',
- subpixel_localization: '"3-dimensional quadratic fit"',
- detection_min_max: "find_maxima",
- type_of_registration: '"Register timepoints individually"',
- algorithm: '"Fast 3d geometric hashing (rotation invariant)"',
- transformation_model: "Affine",
- allowed_error_for_ransac: '5',
- significance: '10',
- fix_tiles: '"Fix first tile"',
- map_back_tiles: '"Map back to first tile using rigid model"',
- model_to_regularize_with: "Rigid",
- lambda: '0.10',
- imglib_container: '"ArrayImg (faster)"',
- bsh_file: "registration.bsh"
- }
-
-xml_merge: {
- bsh_file: "xml_merge.bsh"
- }
-
-timelapse: {
- reference_timepoint: '0',
- 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",
- duplicate_which_transformations: '"Replace all transformations"',
- bsh_file: "Dublicate_transformations.bsh"
- }
-
-fusion: {
- bsh_file: "fusion.bsh",
- downsample: '4',
- 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"'
- }
-
-external_transform: {
- # channel setting: '"all_channels"'
- channel_setting: '"green"',
- transform_timepoint: '"All Timepoints"',
- transform_angle: '"All angles"',
- transform_channel: '"All channels"',
- # illumination setting only one illumination side
- 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"',
- 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',
- detections_to_extract_psf_for_channel: '"beads"',
- process_timepoint: '"Single Timepoint (Select from List)"',
- process_angle: '"All angles"',
- process_channel: '"All channels"',
- process_illumination: '"All illuminations"',
- Tikhonov_parameter: '0.0006',
- compute: '"in 512x512x512 blocks"',
- compute_on: '"GPU (Nvidia CUDA via JNA)"',
- imglib2_container: '"ArrayImg"',
- osem_acceleration: '"1 (balanced)"',
- 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)"',
- bsh_file: "deconvolution_GPU.bsh"
- }
-
-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"',
- 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_pixel_unit: 'um',
- output_channels: "green",
- output_data_type: "32Bit",
- 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}} }}"',
- # chunk_sizes_output: '"{{ {{16,16,16}}, {{16,16,16}} }}"',
- bsh_file_define: "define_output.bsh",
- bsh_file_hdf5: "export_output.bsh"
- }
-
diff --git a/spim_registration/timelapse/Snakefile b/spim_registration/timelapse/Snakefile
index 46f603e..5518ba9 100755
--- a/spim_registration/timelapse/Snakefile
+++ b/spim_registration/timelapse/Snakefile
@@ -6,8 +6,12 @@ JOBDIR=os.path.abspath(os.path.curdir)
if JOBDIR[-1] != "/": # this checks if jobdir ends with slash if not it adds a slash
JOBDIR+="/"
-#data specific config file, expected to be inside JOBDIR
-# configfile: "tomancak_test_cluster.json"
+# Test config file single Channel:
+# configfile: single_test.yaml
+# Test config file dual channel one channel contains beads:
+# configfile: dual_OneChannel.yaml
+
+# data specific config file, expected to be inside JOBDIR
configfile: "tomancak_test_cluster.yaml"
@@ -260,7 +264,7 @@ rule timelapse:
cmd_string += " > {log} 2>&1 && touch {output}"
shell(cmd_string)
-rule dublicate_transformations:
+rule duplicate_transformations:
input: rules.timelapse.output, merged_xml="{xml_base}_merge.xml"
output: rules.timelapse.output[0] + "_dublicate"
log: "{xml_base}_dublicate_transformations.log"
diff --git a/spim_registration/timelapse/dual_OneChannel.yaml b/spim_registration/timelapse/dual_OneChannel.yaml
new file mode 100755
index 0000000..b009596
--- /dev/null
+++ b/spim_registration/timelapse/dual_OneChannel.yaml
@@ -0,0 +1,260 @@
+common: {
+ # directory that contains the bean shell scripts and Snakefile
+ bsh_directory: "/projects/pilot_spim/Christopher/snakemake-workflows/spim_registration/timelapse/",
+ # Directory that contains the cuda libraries
+ directory_cuda: "/sw/users/schmied/cuda/",
+ # Directory that contains the current working Fiji
+ #fiji-app: "/sw/users/schmied/packages/2015-06-08_Fiji.app.cuda/ImageJ-linux64",
+ fiji-app: "/sw/users/schmied/packages/2015-05-29_Fiji_2.3.9_SNAP.app.cuda/ImageJ-linux64",
+ fiji-prefix: "/sw/bin/xvfb-run -a", # calls xvfb for Fiji headless mode
+ # xml file names without .xml suffix
+ first_xml_filename: "Dual_Channel", # Name of the xml file for the .czi or .tif files
+ hdf5_xml_filename: '"hdf5_Dual_Channel"', # Name of .xml file for the hdf5 data after resave_hdf5
+ merged_xml: "hdf5_Dual_Channel_merge", # Name of .xml file after merge
+ # Describe the dataset
+ ntimepoints: 2, # number of timepoints of dataset
+ angles: "0,72,144,216,288", # angles
+ channels: "green,red", # channels
+ illumination: "0", # illuminations
+ pixel_distance_x: '0.28590', # Manual calibration x
+ pixel_distance_y: '0.28590', # Manual calibration y
+ pixel_distance_z: '1.50000', # Manual calibration z
+ pixel_unit: "um", # unit of manual calibration
+ # Use switches to decide which processing steps you need:
+ # transformation_switch: "timelapse" standard processing
+ # after timelapse registration directly goes into fusion, timelapse_duplicate
+ # "timelapse_duplicate" for dual channel processing one channel contains the beads
+ # duplicates transformations
+ transformation_switch: "timelapse_duplicate",
+ # Switches between content based fusion and deconvoltion
+ # "deconvolution" > for deconvolution
+ # "fusion" > for content based fusion
+ fusion_switch: "deconvolution"
+ }
+
+define_xml_czi: {
+ first_czi: "2015-02-20_LZ2_Stock48_Stock58.czi", # master .czi file
+ rotation_around: "X-Axis", # axis of acquistion
+ bsh_file: "define_czi.bsh" # .bsh script for defining .czi file
+ }
+
+define_xml_tif: {
+ # file pattern of .tif files
+ # for multi channel give spim_TL{tt}_Angle{a}_Channel{c}.tif
+ # # SPIM file pattern: for padded zeros use tt
+ image_file_pattern: 'img_TL{{t}}_Angle{{a}}.tif',
+ # Settings for ImageJ Opener
+ type_of_dataset: '"Image Stacks (ImageJ Opener)"',
+ multiple_timepoints: '"YES (one file per time-point)"', # or NO (one time-point)
+ multiple_angles: '"YES (one file per angle)"', # or NO (one angle)
+ multiple_channels: '"NO (one channel)"', # or "\"NO (one channel)\""
+ multiple_illumination_directions: '"NO (one illumination direction)"', # or YES (one file per illumination direction)
+ imglib_container: '"ArrayImg (faster)"', # '"ArrayImg (faster)"'
+ bsh_file: "define_tif_zip.bsh"
+ }
+
+resave_hdf5: {
+ # Resaves .tif or .czi data into hdf5
+ # Subsampling and resolution settings for hdf5: data dependent
+ hdf5_chunk_sizes: '"{{ {{32,32,4}}, {{32,32,4}}, {{16,16,16}}, {{16,16,16}} }}"',
+ subsampling_factors: '"{{ {{1,1,1}}, {{2,2,1}}, {{4,4,1}}, {{8,8,1}} }}"',
+ # Standard settings for cluster processing
+ setups_per_partition: '0',
+ timepoints_per_partition: '1',
+ resave_timepoint: '"All Timepoints"',
+ resave_angle: '"All angles"',
+ resave_channel: '"All channels"',
+ resave_illumination: '"All illuminations"',
+ bsh_file: "export.bsh"
+ }
+
+registration: {
+ # reg_process_channel:
+ # # Single Channel: '"All channels"'
+ # Dual Channel: '"All channels"'
+ # Dual Channel one Channel contains beads: '"Single channel (Select from List)"'
+ reg_process_channel: '"Single channel (Select from List)"',
+ # reg_processing_channel:
+ # Dual Channel setting for 1 Channel contains the beads
+ reg_processing_channel: '"red"',
+ # reg_interest_points_channel:
+ # Single Channel: '"beads"'
+ # Dual Channel: '"beads,beads"'
+ # Dual Channel: Channel does not contain the beads '"[DO NOT register this channel],beads"'
+ reg_interest_points_channel: '"beads"',
+ # type of detection: '"Difference-of-Mean (Integral image based)"' or '"Difference-of-Gaussian"'
+ type_of_detection: '"Difference-of-Mean (Integral image based)"',
+ # Settings for Difference-of-Mean
+ # For multiple channels 'value1,value2' delimiter is ,
+ reg_radius_1: '2',
+ reg_radius_2: '3',
+ reg_threshold: '0.005',
+ # Settings for Difference-of-Gaussian
+ # For multiple channels 'value1,value2' delimiter is ,
+ sigma: '1.8',
+ threshold_gaussian: '0.0080',
+ # Processing setting for Difference-of-Gaussian detection
+ # compute_on:
+ compute_on: '"GPU accurate (Nvidia CUDA via JNA)"',
+ separableconvolution: '"libSeparableConvolutionCUDALib.so"',
+ # Downsampling settings
+ downsample_detection: "No", # "No" or "Yes"
+ downsample_xy: '"Match Z Resolution (less downsampling)"',
+ downsample_z: "1x",
+ # Standard Settings for bead based registration
+ label_interest_points: '"beads"',
+ reg_process_timepoint: '"Single Timepoint (Select from List)"',
+ reg_process_angle: '"All angles"',
+ reg_process_illumination: '"All illuminations"',
+ subpixel_localization: '"3-dimensional quadratic fit"',
+ detection_min_max: "find_maxima",
+ type_of_registration: '"Register timepoints individually"',
+ algorithm: '"Fast 3d geometric hashing (rotation invariant)"',
+ transformation_model: "Affine",
+ allowed_error_for_ransac: '5',
+ significance: '10',
+ fix_tiles: '"Fix first tile"',
+ map_back_tiles: '"Map back to first tile using rigid model"',
+ model_to_regularize_with: "Rigid",
+ lambda: '0.10',
+ imglib_container: '"ArrayImg (faster)"',
+ bsh_file: "registration.bsh" # .bsh script for registration
+ }
+
+xml_merge: {
+ bsh_file: "xml_merge.bsh"
+ }
+
+timelapse: {
+ reference_timepoint: '0', # Reference timepoint
+ # Standard settings for timelapse registration
+ type_of_registration_timelapse: '"Match against one reference timepoint (no global optimization)"',
+ timelapse_process_timepoints: '"All Timepoints"',
+ bsh_file: "timelapse_registration.bsh"
+ }
+
+dublicate_transformations: {
+ # If dual channel processing and only one channel contains beads
+ # this allows you to dublicate the transformation for the
+ # channel that does not contain beas
+ source_dublication: "red", # source channel
+ target_dublication: "green", # target channel
+ duplicate_which_transformations: '"Replace all transformations"', # mode of dublication
+ bsh_file: "dublicate_transformations.bsh" # .bsh script for dublication
+ }
+
+fusion: {
+ # content based multiview fusion
+ # supports multi channel without new settings
+ downsample: '1', # set downsampling
+ # Cropping parameters of full resolution
+ minimal_x: '220',
+ minimal_y: '40',
+ minimal_z: '-290',
+ maximal_x: '976',
+ maximal_y: '1892',
+ maximal_z: '472',
+ # fused_image: '"Append to current XML Project"', does not work yet
+ process_timepoint: '"Single Timepoint (Select from List)"',
+ process_angle: '"All angles"',
+ process_channel: '"All channels"',
+ process_illumination: '"All illuminations"',
+ imglib2_container_fusion: '"ArrayImg"',
+ interpolation: '"Linear Interpolation"',
+ pixel_type: '"16-bit unsigned integer"',
+ imglib2_data_container: '"ArrayImg (faster)"',
+ process_views_in_paralell: '"All"',
+ xml_output: '"Save every XML with user-provided unique id"',
+ bsh_file: "fusion.bsh"
+ }
+
+external_transform: {
+ # Downsamples for deconvolution
+ # BUG: external transformation breaks .xml file
+ # channel setting: '"all_channels"'
+ channel_setting: '"green,red"',
+ transform_timepoint: '"All Timepoints"',
+ transform_angle: '"All angles"',
+ transform_channel: '"All channels"',
+ transform_illumination: '"All illuminations"',
+ apply_transformation: '"Current view transformations (appends to current transforms)"',
+ define_mode_transform: '"Matrix"',
+ # Matrix for downsampling
+ 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"',
+ transformation: '"Rigid"',
+ bsh_file: "transform.bsh"
+ }
+
+deconvolution: {
+ iterations: '1', # number of iterations
+ # Cropping parameters: take downsampling into account
+ minimal_x_deco: '190',
+ minimal_y_deco: '-16',
+ minimal_z_deco: '-348',
+ maximal_x_deco: '1019',
+ maximal_y_deco: '1941',
+ maximal_z_deco: '486',
+ # Channel settings for deconvolution
+ # Single Channel: '"beads"'
+ # Dual Channel: '"beads,beads"'
+ # Dual Channel one channel contains beads: '"[Same PSF as channel red],beads"'
+ detections_to_extract_psf_for_channel: '"[Same PSF as channel red],beads"',
+ # Settings for GPU or CPU processing
+ # '"CPU (Java)"' or '"GPU (Nvidia CUDA via JNA)"'
+ compute_on: '"GPU (Nvidia CUDA via JNA)"',
+ cudafourierconvolution: "libFourierConvolutionCUDALib.so", # GPU processing name of cuda library
+ # Standard settings for deconvolution
+ process_timepoint: '"Single Timepoint (Select from List)"',
+ process_angle: '"All angles"',
+ process_channel: '"All channels"',
+ process_illumination: '"All illuminations"',
+ type_of_iteration: '"Efficient Bayesian - Optimization I (fast, precise)"',
+ Tikhonov_parameter: '0.0006',
+ compute: '"in 512x512x512 blocks"',
+ osem_acceleration: '"1 (balanced)"',
+ psf_estimation: '"Extract from beads"',
+ psf_size_x: '19',
+ psf_size_y: '19',
+ psf_size_z: '25',
+ imglib2_container: '"ArrayImg"',
+ bsh_file: "deconvolution.bsh"
+ }
+
+hdf5_output: {
+ # writes new hdf5 dataset for fusion output: will be obsolete
+ # Naming pattern of output
+ # Single Channel: TP{t}_Chgreen_Ill0_Ang0,72,144,216,288.tif > Ch{name} is added here
+ # Dual Channel: TP{t}_Ch{0}_Ill0_Ang0,72,144,216,288.tif > Ch{name} is added here
+ output_image_file_pattern: 'TP{{t}}_Ch{{c}}_Ill0_Ang0,72,144,216,288.tif',
+ # channel setting
+ output_multiple_channels: '"YES (one file per channel)"', # '"YES (one file per channel)"' or '"NO (one channel)"'
+ output_channels: "green,red",
+ # .xml file names
+ output_xml: '"fused_Dual_Channel"',
+ output_hdf5_xml: '"hdf5_fused_Dual_Channel"',
+ output_timepoints: '0-1', # Timepoints format: '1-2'
+ # pixel size of output: take downsampling into account!
+ output_pixel_distance_x: 0.28590,
+ output_pixel_distance_y: 0.28590,
+ output_pixel_distance_z: 0.28590,
+ output_pixel_unit: 'um',
+ # give if 16Bit data or 32Bit data
+ # output of fusion is 16Bit, of deconvolution it is 32Bit
+ output_data_type: "16Bit", # "32Bit" or "16Bit"
+ # if data is 32Bit then the data is converted into 16Bit data
+ convert_32bit: '"[Use min/max of first image (might saturate intenities over time)]"',
+ # subsampling and chunk size settings: dataset dependent
+ 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}} }}"',
+ # Standard settings for hdf5_output
+ 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)"',
+ bsh_file_define: "define_output.bsh", # .bsh script for defining the dataset
+ bsh_file_hdf5: "export_output.bsh" # .bsh script for resaving into hdf5
+ }
+
diff --git a/spim_registration/timelapse/single_test.yaml b/spim_registration/timelapse/single_test.yaml
new file mode 100755
index 0000000..acc996e
--- /dev/null
+++ b/spim_registration/timelapse/single_test.yaml
@@ -0,0 +1,260 @@
+common: {
+ # directory that contains the bean shell scripts and Snakefile
+ bsh_directory: "/projects/pilot_spim/Christopher/snakemake-workflows/spim_registration/timelapse/",
+ # Directory that contains the cuda libraries
+ directory_cuda: "/sw/users/schmied/cuda/",
+ # Directory that contains the current working Fiji
+ #fiji-app: "/sw/users/schmied/packages/2015-06-08_Fiji.app.cuda/ImageJ-linux64",
+ fiji-app: "/sw/users/schmied/packages/2015-05-29_Fiji_2.3.9_SNAP.app.cuda/ImageJ-linux64",
+ fiji-prefix: "/sw/bin/xvfb-run -a", # calls xvfb for Fiji headless mode
+ # xml file names without .xml suffix
+ first_xml_filename: "single", # Name of the xml file for the .czi or .tif files
+ hdf5_xml_filename: '"hdf5_single"', # Name of .xml file for the hdf5 data after resave_hdf5
+ merged_xml: "hdf5_single_merge", # Name of .xml file after merge
+ # Describe the dataset
+ ntimepoints: 2, # number of timepoints of dataset
+ angles: "0,72,144,216,288", # angles
+ channels: "green", # channels
+ illumination: "0", # illuminations
+ pixel_distance_x: '0.28590106964', # Manual calibration x
+ pixel_distance_y: '0.28590106964', # Manual calibration y
+ pixel_distance_z: '1.50000', # Manual calibration z
+ pixel_unit: "um", # unit of manual calibration
+ # Use switches to decide which processing steps you need:
+ # transformation_switch: "timelapse" standard processing
+ # after timelapse registration directly goes into fusion, timelapse_duplicate
+ # "timelapse_duplicate" for dual channel processing one channel contains the beads
+ # duplicates transformations
+ transformation_switch: "timelapse",
+ # Switches between content based fusion and deconvoltion
+ # "deconvolution" > for deconvolution
+ # "fusion" > for content based fusion
+ fusion_switch: "deconvolution"
+ }
+
+define_xml_czi: {
+ first_czi: "2015-04-11_LZ2_Stock68_3.czi", # master .czi file
+ rotation_around: "X-Axis", # axis of acquistion
+ bsh_file: "define_czi.bsh" # .bsh script for defining .czi file
+ }
+
+define_xml_tif: {
+ # file pattern of .tif files
+ # for multi channel give spim_TL{tt}_Angle{a}_Channel{c}.tif
+ # # SPIM file pattern: for padded zeros use tt
+ image_file_pattern: 'img_TL{{t}}_Angle{{a}}.tif',
+ # Settings for ImageJ Opener
+ type_of_dataset: '"Image Stacks (ImageJ Opener)"',
+ multiple_timepoints: '"YES (one file per time-point)"', # or NO (one time-point)
+ multiple_angles: '"YES (one file per angle)"', # or NO (one angle)
+ multiple_channels: '"NO (one channel)"', # or "\"NO (one channel)\""
+ multiple_illumination_directions: '"NO (one illumination direction)"', # or YES (one file per illumination direction)
+ imglib_container: '"ArrayImg (faster)"', # '"ArrayImg (faster)"'
+ bsh_file: "define_tif_zip.bsh"
+ }
+
+resave_hdf5: {
+ # Resaves .tif or .czi data into hdf5
+ # Subsampling and resolution settings for hdf5: data dependent
+ hdf5_chunk_sizes: '"{{ {{32,32,4}}, {{32,32,4}}, {{16,16,16}}, {{16,16,16}} }}"',
+ subsampling_factors: '"{{ {{1,1,1}}, {{2,2,1}}, {{4,4,1}}, {{8,8,1}} }}"',
+ # Standard settings for cluster processing
+ setups_per_partition: '0',
+ timepoints_per_partition: '1',
+ resave_timepoint: '"All Timepoints"',
+ resave_angle: '"All angles"',
+ resave_channel: '"All channels"',
+ resave_illumination: '"All illuminations"',
+ bsh_file: "export.bsh"
+ }
+
+registration: {
+ # reg_process_channel:
+ # # Single Channel: '"All channels"'
+ # Dual Channel: '"All channels"'
+ # Dual Channel one Channel contains beads: '"Single channel (Select from List)"'
+ reg_process_channel: '"All channels"',
+ # reg_processing_channel:
+ # Dual Channel setting for 1 Channel contains the beads
+ reg_processing_channel: '"green"',
+ # reg_interest_points_channel:
+ # Single Channel: '"beads"'
+ # Dual Channel: '"beads,beads"'
+ # Dual Channel: Channel does not contain the beads '"[DO NOT register this channel],beads"'
+ reg_interest_points_channel: '"beads"',
+ # type of detection: '"Difference-of-Mean (Integral image based)"' or '"Difference-of-Gaussian"'
+ type_of_detection: '"Difference-of-Mean (Integral image based)"',
+ # Settings for Difference-of-Mean
+ # For multiple channels 'value1,value2' delimiter is ,
+ reg_radius_1: '2',
+ reg_radius_2: '3',
+ reg_threshold: '0.005',
+ # Settings for Difference-of-Gaussian
+ # For multiple channels 'value1,value2' delimiter is ,
+ sigma: '1.8',
+ threshold_gaussian: '0.0080',
+ # Processing setting for Difference-of-Gaussian detection
+ # compute_on:
+ compute_on: '"GPU accurate (Nvidia CUDA via JNA)"',
+ separableconvolution: '"libSeparableConvolutionCUDALib.so"',
+ # Downsampling settings
+ downsample_detection: "No", # "No" or "Yes"
+ downsample_xy: '"Match Z Resolution (less downsampling)"',
+ downsample_z: "1x",
+ # Standard Settings for bead based registration
+ label_interest_points: '"beads"',
+ reg_process_timepoint: '"Single Timepoint (Select from List)"',
+ reg_process_angle: '"All angles"',
+ reg_process_illumination: '"All illuminations"',
+ subpixel_localization: '"3-dimensional quadratic fit"',
+ detection_min_max: "find_maxima",
+ type_of_registration: '"Register timepoints individually"',
+ algorithm: '"Fast 3d geometric hashing (rotation invariant)"',
+ transformation_model: "Affine",
+ allowed_error_for_ransac: '5',
+ significance: '10',
+ fix_tiles: '"Fix first tile"',
+ map_back_tiles: '"Map back to first tile using rigid model"',
+ model_to_regularize_with: "Rigid",
+ lambda: '0.10',
+ imglib_container: '"ArrayImg (faster)"',
+ bsh_file: "registration.bsh" # .bsh script for registration
+ }
+
+xml_merge: {
+ bsh_file: "xml_merge.bsh"
+ }
+
+timelapse: {
+ reference_timepoint: '0', # Reference timepoint
+ # Standard settings for timelapse registration
+ type_of_registration_timelapse: '"Match against one reference timepoint (no global optimization)"',
+ timelapse_process_timepoints: '"All Timepoints"',
+ bsh_file: "timelapse_registration.bsh"
+ }
+
+dublicate_transformations: {
+ # If dual channel processing and only one channel contains beads
+ # this allows you to dublicate the transformation for the
+ # channel that does not contain beas
+ source_dublication: "red", # source channel
+ target_dublication: "green", # target channel
+ duplicate_which_transformations: '"Replace all transformations"', # mode of dublication
+ bsh_file: "dublicate_transformations.bsh" # .bsh script for dublication
+ }
+
+fusion: {
+ # content based multiview fusion
+ # supports multi channel without new settings
+ downsample: '1', # set downsampling
+ # Cropping parameters of full resolution
+ minimal_x: '190',
+ minimal_y: '-16',
+ minimal_z: '-348',
+ maximal_x: '1019',
+ maximal_y: '1941',
+ maximal_z: '486',
+ # fused_image: '"Append to current XML Project"', does not work yet
+ process_timepoint: '"Single Timepoint (Select from List)"',
+ process_angle: '"All angles"',
+ process_channel: '"All channels"',
+ process_illumination: '"All illuminations"',
+ imglib2_container_fusion: '"ArrayImg"',
+ interpolation: '"Linear Interpolation"',
+ pixel_type: '"16-bit unsigned integer"',
+ imglib2_data_container: '"ArrayImg (faster)"',
+ process_views_in_paralell: '"All"',
+ xml_output: '"Save every XML with user-provided unique id"',
+ bsh_file: "fusion.bsh"
+ }
+
+external_transform: {
+ # Downsamples for deconvolution
+ # BUG: external transformation breaks .xml file
+ # channel setting: '"all_channels"'
+ channel_setting: '"green"',
+ transform_timepoint: '"All Timepoints"',
+ transform_angle: '"All angles"',
+ transform_channel: '"All channels"',
+ transform_illumination: '"All illuminations"',
+ apply_transformation: '"Current view transformations (appends to current transforms)"',
+ define_mode_transform: '"Matrix"',
+ # Matrix for downsampling
+ 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"',
+ transformation: '"Rigid"',
+ bsh_file: "transform.bsh"
+ }
+
+deconvolution: {
+ iterations: '5', # number of iterations
+ # Cropping parameters: take downsampling into account
+ minimal_x_deco: '190',
+ minimal_y_deco: '-16',
+ minimal_z_deco: '-348',
+ maximal_x_deco: '1019',
+ maximal_y_deco: '1941',
+ maximal_z_deco: '486',
+ # Channel settings for deconvolution
+ # Single Channel: '"beads"'
+ # Dual Channel: '"beads,beads"'
+ # Dual Channel one channel contains beads: '"[Same PSF as channel red],beads"'
+ detections_to_extract_psf_for_channel: '"[Same PSF as channel red],beads"',
+ # Settings for GPU or CPU processing
+ # '"CPU (Java)"' or '"GPU (Nvidia CUDA via JNA)"'
+ compute_on: '"GPU (Nvidia CUDA via JNA)"',
+ cudafourierconvolution: "libFourierConvolutionCUDALib.so", # GPU processing name of cuda library
+ # Standard settings for deconvolution
+ process_timepoint: '"Single Timepoint (Select from List)"',
+ process_angle: '"All angles"',
+ process_channel: '"All channels"',
+ process_illumination: '"All illuminations"',
+ type_of_iteration: '"Efficient Bayesian - Optimization I (fast, precise)"',
+ Tikhonov_parameter: '0.0006',
+ compute: '"in 512x512x512 blocks"',
+ osem_acceleration: '"1 (balanced)"',
+ psf_estimation: '"Extract from beads"',
+ psf_size_x: '19',
+ psf_size_y: '19',
+ psf_size_z: '25',
+ imglib2_container: '"ArrayImg"',
+ bsh_file: "deconvolution.bsh"
+ }
+
+hdf5_output: {
+ # writes new hdf5 dataset for fusion output: will be obsolete
+ # Naming pattern of output
+ # Single Channel: TP{t}_Chgreen_Ill0_Ang0,72,144,216,288.tif > Ch{name} is added here
+ # Dual Channel: TP{t}_Ch{0}_Ill0_Ang0,72,144,216,288.tif > Ch{name} is added here
+ output_image_file_pattern: 'TP{t}_Chgreen_Ill0_Ang0,72,144,216,288.tif',
+ # channel setting
+ output_multiple_channels: '"NO (one channel)"', # '"YES (one file per channel)"' or '"NO (one channel)"'
+ output_channels: "green",
+ # .xml file names
+ output_xml: '"fused_Dual_Channel"',
+ output_hdf5_xml: '"hdf5_fused_Dual_Channel"',
+ output_timepoints: '0-1', # Timepoints format: '1-2'
+ # pixel size of output: take downsampling into account!
+ output_pixel_distance_x: 0.28590106964,
+ output_pixel_distance_y: 0.28590106964,
+ output_pixel_distance_z: 0.28590106964,
+ output_pixel_unit: 'um',
+ # give if 16Bit data or 32Bit data
+ # output of fusion is 16Bit, of deconvolution it is 32Bit
+ output_data_type: "32Bit", # "32Bit" or "16Bit"
+ # if data is 32Bit then the data is converted into 16Bit data
+ convert_32bit: '"[Use min/max of first image (might saturate intenities over time)]"',
+ # subsampling and chunk size settings: dataset dependent
+ 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}} }}"',
+ # Standard settings for hdf5_output
+ 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)"',
+ bsh_file_define: "define_output.bsh", # .bsh script for defining the dataset
+ bsh_file_hdf5: "export_output.bsh" # .bsh script for resaving into hdf5
+ }
+
diff --git a/spim_registration/timelapse/tomancak.json b/spim_registration/timelapse/tomancak.json
deleted file mode 100644
index 0215784..0000000
--- a/spim_registration/timelapse/tomancak.json
+++ /dev/null
@@ -1,88 +0,0 @@
-{
- "common" :
- {
- "fiji-app" : "/projects/hpcsupport/steinbac/unicore/christopher/unicore_jobs/Fiji.app.cuda_new/ImageJ-linux64",
- "fiji-prefix" : "/sw/bin/xvfb-run -a",
- "directory_cuda" : "/lustre/projects/hpcsupport/steinbac/unicore/christopher/unicore_jobs/Fiji.app.cuda_new/lib/",
- "merged_xml" : "hdf5_test_unicore_merge"
- },
-
- "registration" :
- {
- "timepoint" : "\"Single Timepoint (Select from List)\"",
- "illuminations" : "\"All illuminations\"",
- "angle" : "\"All angles\"",
- "channel" : "\"All channels\"",
- "proc-ch" : "\"channel 1\"",
- "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\"" ,
- "map_back_tiles" : "\"Map back to first tile using rigid model\"",
- "transformation_model" : "Affine",
- "model_to_regularize_with" : "Rigid",
- "lambda" : "0.10" ,
- "allowed_error_for_ransac" : "5",
- "detection_min_max" : "find_maxima",
- "initial_sigma" : "1.8",
- "threshold_gaussian" : "0.0080",
- "bsh_file" : "registration.bsh"
- },
-
- "xml_merge" :
- {
- "bsh_file" : "xml_merge.bsh"
- },
-
- "external_transform" :
- {
- "bsh_file" : "transform.bsh",
- "angle" : "\"All angles\"",
- "channel" : "\"All channels\"",
- "illumination" : "\"All illuminations\"",
- "timepoint" : "\"All Timepoints\"",
- "transformation" : "\"Rigid\"",
- "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\""
- },
-
- "deconvolution" :
- {
-
- "bsh_file" : "deconvolution_GPU.bsh",
- "process_timepoint" : "\"Single Timepoint (Select from List)\"",
- "process_channel" : "\"All channels\"",
- "process_illumination" : "\"All illuminations\"",
- "process_angle" : "\"All angles\"",
- "minimal_x" : "76",
- "minimal_y" : "4",
- "minimal_z" : "-192",
- "maximal_x" : "488",
- "maximal_y" : "956",
- "maximal_z" : "214",
- "imglib2_container" : "\"ArrayImg \"",
- "type_of_iteration" : "\"Efficient Bayesian - Optimization I (fast, precise)\"",
- "osem_acceleration" : "\"1 (balanced)\"",
- "Tikhonov_parameter" : "0.0006",
- "compute" : "\"in 512x512x512 blocks\"",
- "compute_on" : "\"GPU (Nvidia CUDA via JNA)\"",
- "psf_estimation" : "\"Extract from beads\"",
- "iterations" : "5",
- "detections_to_extract_psf_for_channel_0" : "\"beads\"",
- "detections_to_extract_psf_for_channel_1" : "\"beads\"",
- "psf_size_x" : "19",
- "psf_size_y" : "19",
- "psf_size_z" : "25"
- }
-
-}
diff --git a/spim_registration/timelapse/tomancak_czi.json b/spim_registration/timelapse/tomancak_czi.json
deleted file mode 100644
index 9a2445f..0000000
--- a/spim_registration/timelapse/tomancak_czi.json
+++ /dev/null
@@ -1,204 +0,0 @@
-{
- "common" :
- {
- "fiji-app" : "/projects/hpcsupport/steinbac/unicore/christopher/unicore_jobs/Fiji.app.cuda_new/ImageJ-linux64",
- "fiji-prefix" : "/sw/bin/xvfb-run -a",
- "directory_cuda" : "/lustre/projects/hpcsupport/steinbac/unicore/christopher/unicore_jobs/Fiji.app.cuda_new/lib/",
- "merged_xml" : "hdf5_test_unicore_merge",
- "bsh_directory" : "/home/steinbac/development/cschmied-snakemake-workflows/spim_registration/timelapse/",
- "first_xml_filename" : "test_unicore",
- "hdf5_xml_filename" : "\"hdf5_test_unicore\"",
- "fusion_switch" : "deconvolution",
- "ntimepoints" : 3
- },
-
- "define_xml_czi" :
- {
- "pixel_distance_x" : "0.2875535786151886",
- "pixel_distance_y" : "0.2875535786151886",
- "pixel_distance_z" : "1.50000",
- "pixel_unit" : "um",
- "first_czi" : "2015-02-21_LZ1_Stock68_3.czi",
- "channel_1" : "green",
- "channel_2" : "red",
- "angle_1" : "0",
- "angle_2" : "72",
- "angle_3" :"144",
- "angle_4" :"216",
- "angle_5" : "288",
- "illumination_1" : "0",
- "rotation_around" : "X-Axis",
- "bsh_file" : "define_czi.bsh"
- },
-
- "define_xml_tif" :
- {
- "timepoints" : "0-1",
- "acquisition_angles" : "0,72,144,216,288",
- "channels" : "0",
- "image_file_pattern" : "img_TL{{t}}_Angle{{a}}.tif",
- "pixel_distance_x" : "0.2875535786151886",
- "pixel_distance_y" : "0.2875535786151886",
- "pixel_distance_z" : "1.50000",
- "pixel_unit" : "um",
- "multiple_timepoints" : "\"YES (one file per time-point)\"",
- "multiple_channels" : "\"NO (one channel)\"",
- "multiple_illumination_directions" : "\"NO (one illumination direction)\"",
- "multiple_angles" : "\"YES (one file per angle)\"",
- "type_of_dataset" : "\"Image Stacks (ImageJ Opener)\"",
- "imglib_container" : "\"ArrayImg (faster)\"",
- "bsh_file" : "define_tif_zip.bsh"
- },
-
- "resave_hdf5" :
- {
- "parallel_timepoints" : "3",
- "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)\"",
- "illuminations" : "\"All illuminations\"",
- "angle" : "\"All angles\"",
- "channel" : "\"All channels\"",
- "proc-ch" : "\"channel 0\"",
- "algorithm" : "\"Fast 3d geometric hashing (rotation invariant)\"",
- "label_interest_points" : "\"beads\"",
- "type_of_registration" : "\"Register timepoints individually\"",
- "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" : "\"beads\"",
- "interest_points_channel_1" : "\"beads\"",
- "fix_tiles" : "\"Fix first tile\"",
- "map_back_tiles" : "\"Map back to first tile using rigid model\"",
- "transformation_model" : "Affine",
- "model_to_regularize_with" : "Rigid",
- "lambda" : "0.10" ,
- "allowed_error_for_ransac" : "5",
- "significance" : "10",
- "detection_min_max" : "find_maxima",
- "initial_sigma" : "1.8",
- "threshold_gaussian" : "0.0080",
- "bsh_file" : "registration.bsh"
- },
-
- "xml_merge" :
- {
- "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" :
- {
- "bsh_file" : "transform.bsh",
- "angle" : "\"All angles\"",
- "channel" : "\"All channels\"",
- "illumination" : "\"All illuminations\"",
- "timepoint" : "\"All Timepoints\"",
- "transformation" : "\"Rigid\"",
- "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\""
- },
-
- "fusion" :
- {
- "minimal_x" : "128",
- "minimal_y" : "-13",
- "minimal_z" : "-407",
- "maximal_x" : "986",
- "maximal_y" : "1927",
- "maximal_z" : "498",
- "downsample" : "1",
- "process_timepoint" : "\"Single Timepoint (Select from List)\"",
- "process_channel" : "\"All channels\"",
- "process_illumination" : "\"All illuminations\"",
- "process_angle" : "\"All angles\"",
- "xml_output" : "\"Save every XML with user-provided unique id\"",
- "fused_image" : "\"Append to current XML Project\"",
- "pixel_type" : "\"16-bit unsigned integer\"",
- "imglib2_container_fusion" : "\"ArrayImg\"",
- "process_views_in_paralell" : "\"All\"",
- "interpolation" : "\"Linear Interpolation\"",
- "imglib2_data_container" : "\"ArrayImg (faster)\"",
- "bsh_file" : "fusion.bsh"
- },
-
- "deconvolution" :
- {
-
- "bsh_file" : "deconvolution_GPU.bsh",
- "process_timepoint" : "\"Single Timepoint (Select from List)\"",
- "process_channel" : "\"All channels\"",
- "process_illumination" : "\"All illuminations\"",
- "process_angle" : "\"All angles\"",
- "minimal_x" : "76",
- "minimal_y" : "4",
- "minimal_z" : "-192",
- "maximal_x" : "488",
- "maximal_y" : "956",
- "maximal_z" : "214",
- "imglib2_container" : "\"ArrayImg \"",
- "type_of_iteration" : "\"Efficient Bayesian - Optimization I (fast, precise)\"",
- "osem_acceleration" : "\"1 (balanced)\"",
- "Tikhonov_parameter" : "0.0006",
- "compute" : "\"in 512x512x512 blocks\"",
- "compute_on" : "\"GPU (Nvidia CUDA via JNA)\"",
- "psf_estimation" : "\"Extract from beads\"",
- "iterations" : "5",
- "detections_to_extract_psf_for_channel_0" : "\"beads\"",
- "detections_to_extract_psf_for_channel_1" : "\"beads\"",
- "psf_size_x" : "19",
- "psf_size_y" : "19",
- "psf_size_z" : "25"
- },
-
- "hdf5_output" :
- {
- "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\"",
- "output_multiple_channels" : "\"NO (one channel)\"",
- "output_timepoints" : "0-1",
- "output_channels" : "green",
- "output_pixel_distance_x" : "0.5718",
- "output_pixel_distance_y" : "0.5718",
- "output_pixel_distance_z" : "0.5718",
- "output_pixel_unit" : "um",
- "output_multiple_timepoints" : "\"YES (one file per time-point)\"",
- "output_illumination_directions" : "\"NO (one illumination direction)\"",
- "output_multiple_angles" : "\"NO (one angle)\"",
- "output_type_of_dataset" : "\"Image Stacks (ImageJ Opener)\"",
- "output_imglib_container" : "\"ArrayImg (faster)\"",
- "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)]\""
-
- }
-
-
-
-
-
-}
diff --git a/spim_registration/timelapse/tomancak_test_cluster.json b/spim_registration/timelapse/tomancak_test_cluster.json
deleted file mode 100644
index 44899c5..0000000
--- a/spim_registration/timelapse/tomancak_test_cluster.json
+++ /dev/null
@@ -1,202 +0,0 @@
-{
- "common" :
- {
- "fiji-app" : "/projects/hpcsupport/steinbac/unicore/christopher/unicore_jobs/Fiji.app.cuda_new/ImageJ-linux64",
- "fiji-prefix" : "/sw/bin/xvfb-run -a",
- "directory_cuda" : "/lustre/projects/hpcsupport/steinbac/unicore/christopher/unicore_jobs/Fiji.app.cuda_new/lib/",
- "merged_xml" : "hdf5_test_unicore_merge",
- "bsh_directory" : "/home/steinbac/development/schmied-snakemake-workflows/spim_registration/timelapse/",
- "first_xml_filename" : "test_unicore",
- "hdf5_xml_filename" : "\"hdf5_test_unicore\"",
- "fusion_switch" : "deconvolution",
- "ntimepoints" : 5
- },
-
- "define_xml_czi" :
- {
- "pixel_distance_x" : "0.28590106964",
- "pixel_distance_y" : "0.28590106964",
- "pixel_distance_z" : "1.50000",
- "pixel_unit" : "um",
- "first_czi" : "2015-04-11_LZ2_Stock68_3.czi",
- "channel_1" : "green",
- "channel_2" : "red",
- "angle_1" : "0",
- "angle_2" : "72",
- "angle_3" : "144",
- "angle_4" : "216",
- "angle_5" : "288",
- "illumination_1" : "0",
- "rotation_around" : "X-Axis",
- "bsh_file" : "define_czi.bsh"
- },
-
- "define_xml_tif" :
- {
- "acquisition_angles" : "0,72,144,216,288",
- "channels" : "0",
- "image_file_pattern" : "img_TL{{t}}_Angle{{a}}.tif",
- "pixel_distance_x" : "0.28590106964",
- "pixel_distance_y" : "0.28590106964",
- "pixel_distance_z" : "1.50000",
- "pixel_unit" : "um",
- "multiple_timepoints" : "\"YES (one file per time-point)\"",
- "multiple_channels" : "\"NO (one channel)\"",
- "multiple_illumination_directions" : "\"NO (one illumination direction)\"",
- "multiple_angles" : "\"YES (one file per angle)\"",
- "type_of_dataset" : "\"Image Stacks (ImageJ Opener)\"",
- "imglib_container" : "\"ArrayImg (faster)\"",
- "bsh_file" : "define_tif_zip.bsh"
- },
-
- "resave_hdf5" :
- {
- "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)\"",
- "illuminations" : "\"All illuminations\"",
- "angle" : "\"All angles\"",
- "channel" : "\"All channels\"",
- "proc-ch" : "\"channel 0\"",
- "algorithm" : "\"Fast 3d geometric hashing (rotation invariant)\"",
- "label_interest_points" : "\"beads\"",
- "type_of_registration" : "\"Register timepoints individually\"",
- "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" : "\"beads\"",
- "interest_points_channel_1" : "\"beads\"",
- "fix_tiles" : "\"Fix first tile\"",
- "map_back_tiles" : "\"Map back to first tile using rigid model\"",
- "transformation_model" : "Affine",
- "model_to_regularize_with" : "Rigid",
- "lambda" : "0.10" ,
- "allowed_error_for_ransac" : "5",
- "significance" : "10",
- "detection_min_max" : "find_maxima",
- "initial_sigma" : "1.8",
- "threshold_gaussian" : "0.0080",
- "bsh_file" : "registration.bsh"
- },
-
- "xml_merge" :
- {
- "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" :
- {
- "bsh_file" : "transform.bsh",
- "angle" : "\"All angles\"",
- "channel" : "\"All channels\"",
- "illumination" : "\"All illuminations\"",
- "timepoint" : "\"All Timepoints\"",
- "transformation" : "\"Rigid\"",
- "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\""
- },
-
- "fusion" :
- {
- "minimal_x" : "190",
- "minimal_y" : "-16",
- "minimal_z" : "-348",
- "maximal_x" : "1019",
- "maximal_y" : "1941",
- "maximal_z" : "486",
- "downsample" : "1",
- "process_timepoint" : "\"Single Timepoint (Select from List)\"",
- "process_channel" : "\"All channels\"",
- "process_illumination" : "\"All illuminations\"",
- "process_angle" : "\"All angles\"",
- "xml_output" : "\"Save every XML with user-provided unique id\"",
- "fused_image" : "\"Append to current XML Project\"",
- "pixel_type" : "\"16-bit unsigned integer\"",
- "imglib2_container_fusion" : "\"ArrayImg\"",
- "process_views_in_paralell" : "\"All\"",
- "interpolation" : "\"Linear Interpolation\"",
- "imglib2_data_container" : "\"ArrayImg (faster)\"",
- "bsh_file" : "fusion.bsh"
- },
-
- "deconvolution" :
- {
-
- "bsh_file" : "deconvolution_GPU.bsh",
- "process_timepoint" : "\"Single Timepoint (Select from List)\"",
- "process_channel" : "\"All channels\"",
- "process_illumination" : "\"All illuminations\"",
- "process_angle" : "\"All angles\"",
- "minimal_x" : "95",
- "minimal_y" : "-8",
- "minimal_z" : "-174",
- "maximal_x" : "509",
- "maximal_y" : "970",
- "maximal_z" : "243",
- "imglib2_container" : "\"ArrayImg \"",
- "type_of_iteration" : "\"Efficient Bayesian - Optimization I (fast, precise)\"",
- "osem_acceleration" : "\"1 (balanced)\"",
- "Tikhonov_parameter" : "0.0006",
- "compute" : "\"in 512x512x512 blocks\"",
- "compute_on" : "\"GPU (Nvidia CUDA via JNA)\"",
- "psf_estimation" : "\"Extract from beads\"",
- "iterations" : "5",
- "detections_to_extract_psf_for_channel_0" : "\"beads\"",
- "detections_to_extract_psf_for_channel_1" : "\"beads\"",
- "psf_size_x" : "19",
- "psf_size_y" : "19",
- "psf_size_z" : "25"
- },
-
- "hdf5_output" :
- {
- "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\"",
- "output_multiple_channels" : "\"NO (one channel)\"",
- "output_timepoints" : "0-4",
- "output_channels" : "green",
- "output_pixel_distance_x" : "0.5718",
- "output_pixel_distance_y" : "0.5718",
- "output_pixel_distance_z" : "0.5718",
- "output_pixel_unit" : "um",
- "output_multiple_timepoints" : "\"YES (one file per time-point)\"",
- "output_illumination_directions" : "\"NO (one illumination direction)\"",
- "output_multiple_angles" : "\"NO (one angle)\"",
- "output_type_of_dataset" : "\"Image Stacks (ImageJ Opener)\"",
- "output_imglib_container" : "\"ArrayImg (faster)\"",
- "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)]\""
-
- }
-
-
-
-
-
-}
diff --git a/spim_registration/timelapse/tomancak_test_cluster.yaml b/spim_registration/timelapse/tomancak_test_cluster.yaml
index dd9a3a9..b009596 100755
--- a/spim_registration/timelapse/tomancak_test_cluster.yaml
+++ b/spim_registration/timelapse/tomancak_test_cluster.yaml
@@ -22,16 +22,16 @@ common: {
pixel_unit: "um", # unit of manual calibration
# Use switches to decide which processing steps you need:
# transformation_switch: "timelapse" standard processing
- # after timelapse registration directly goes into fusion, timelapse_dublicate
- # "timelapse_dublicate" for dual channel processing one channel contains the beads
- # dublicates transformations
- transformation_switch: "timelapse_dublicate",
+ # after timelapse registration directly goes into fusion, timelapse_duplicate
+ # "timelapse_duplicate" for dual channel processing one channel contains the beads
+ # duplicates transformations
+ transformation_switch: "timelapse_duplicate",
# Switches between content based fusion and deconvoltion
# "deconvolution" > for deconvolution
# "fusion" > for content based fusion
fusion_switch: "deconvolution"
}
-
+
define_xml_czi: {
first_czi: "2015-02-20_LZ2_Stock48_Stock58.czi", # master .czi file
rotation_around: "X-Axis", # axis of acquistion
@@ -54,6 +54,7 @@ define_xml_tif: {
}
resave_hdf5: {
+ # Resaves .tif or .czi data into hdf5
# Subsampling and resolution settings for hdf5: data dependent
hdf5_chunk_sizes: '"{{ {{32,32,4}}, {{32,32,4}}, {{16,16,16}}, {{16,16,16}} }}"',
subsampling_factors: '"{{ {{1,1,1}}, {{2,2,1}}, {{4,4,1}}, {{8,8,1}} }}"',
--
GitLab