From c3b1a849f3c452cb77bde28bcf3ca383ad9ebd97 Mon Sep 17 00:00:00 2001
From: Christopher Schmied <schmied@mpi-cbg.de>
Date: Mon, 15 Jun 2015 16:34:00 +0200
Subject: [PATCH] Added annotation for .yaml file
---
.../timelapse/tomancak_test_cluster.yaml | 244 +++++++++++-------
1 file changed, 153 insertions(+), 91 deletions(-)
diff --git a/spim_registration/timelapse/tomancak_test_cluster.yaml b/spim_registration/timelapse/tomancak_test_cluster.yaml
index 3bd147a..dd9a3a9 100755
--- a/spim_registration/timelapse/tomancak_test_cluster.yaml
+++ b/spim_registration/timelapse/tomancak_test_cluster.yaml
@@ -1,72 +1,107 @@
common: {
- # directory that contains the bean shell scripts
- bsh_directory: "/projects/pilot_spim/Christopher/snakemake-workflows/spim_registration/timelapse/",
- directory_cuda: "/sw/users/schmied/cuda/",
+ # 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",
- first_xml_filename: "Dual_Channel",
- hdf5_xml_filename: '"hdf5_Dual_Channel"',
- merged_xml: "hdf5_Dual_Channel_merge",
- ntimepoints: 2,
- angles: "0,72,144,216,288",
- channels: "green,red",
- illumination: "0",
- pixel_distance_x: '0.28590',
- pixel_distance_y: '0.28590',
- pixel_distance_z: '1.50000',
- pixel_unit: "um",
- transformation_switch: "timelapse_dublicate",
- # transformation_switch: "timelapse",
+ 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_dublicate
+ # "timelapse_dublicate" for dual channel processing one channel contains the beads
+ # dublicates transformations
+ transformation_switch: "timelapse_dublicate",
+ # Switches between content based fusion and deconvoltion
+ # "deconvolution" > for deconvolution
+ # "fusion" > for content based fusion
fusion_switch: "deconvolution"
- # fusion_switch: "fusion"
}
define_xml_czi: {
- first_czi: "2015-02-20_LZ2_Stock48_Stock58.czi", # essential
- rotation_around: "X-Axis",
- bsh_file: "define_czi.bsh"
+ 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: {
- image_file_pattern: 'img_TL{{t}}_Angle{{a}}.tif', # essential
- 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)"',
+ # 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)"',
- bsh_file: "define_tif_zip.bsh"
+ 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: {
- hdf5_chunk_sizes: '"{{ {{32,32,4}}, {{32,32,4}}, {{16,16,16}}, {{16,16,16}} }}"', # data dependent
- subsampling_factors: '"{{ {{1,1,1}}, {{2,2,1}}, {{4,4,1}}, {{8,8,1}} }}"', # data dependent
+ # 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"',
- resave_timepoint: '"All Timepoints"',
- setups_per_partition: '0',
- timepoints_per_partition: '1',
bsh_file: "export.bsh"
}
registration: {
- reg_process_channel: '"Single channel (Select from List)"', # essential '"All channels"'; '"Single channel (Select from List)"'
- reg_processing_channel: '"red"', # essential
- reg_interest_points_channel: '"beads"', # essential
- type_of_detection: '"Difference-of-Mean (Integral image based)"', # Difference-of-Gaussian
- reg_radius_1: '2', # essential
- reg_radius_2: '3', # essential
- reg_threshold: '0.005', # essential
- sigma: '1.8', # essetial
- threshold_gaussian: '0.0080', # essential
+ # 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"',
- downsample_detection: "No",
+ # Downsampling settings
+ downsample_detection: "No", # "No" or "Yes"
downsample_xy: '"Match Z Resolution (less downsampling)"',
downsample_z: "1x",
- label_interest_points: '"beads"',
+ # 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"',
@@ -82,7 +117,7 @@ registration: {
model_to_regularize_with: "Rigid",
lambda: '0.10',
imglib_container: '"ArrayImg (faster)"',
- bsh_file: "registration.bsh"
+ bsh_file: "registration.bsh" # .bsh script for registration
}
xml_merge: {
@@ -90,108 +125,135 @@ xml_merge: {
}
timelapse: {
- reference_timepoint: '0', # essential
+ 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: {
- source_dublication: "red", # essential for 1 usecase
- target_dublication: "green", # essential for 1 usecase
- duplicate_which_transformations: '"Replace all transformations"',
- bsh_file: "dublicate_transformations.bsh"
+ # 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: {
- downsample: '1', # essential
- minimal_x: '220', # essential maybe automate
- minimal_y: '40', # essential maybe automate
- minimal_z: '-290', # essential maybe automate
- maximal_x: '976', # essential maybe automate
- maximal_y: '1892', # essential maybe automate
- maximal_z: '472', # essential maybe automate
- fused_image: '"Append to current XML Project"',
- imglib2_container_fusion: '"ArrayImg"',
- imglib2_data_container: '"ArrayImg (faster)"',
- interpolation: '"Linear Interpolation"',
- pixel_type: '"16-bit unsigned integer"',
+ # 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"',
- process_timepoint: '"Single Timepoint (Select from List)"',
+ 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: {
- # BUG
+ # 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"',
- # 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"', # essential
+ # 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', # essential
- minimal_x_deco: '190', # essential maybe automate
- minimal_y_deco: '-16', # essential maybe automate
- minimal_z_deco: '-348', # essential maybe automate
- maximal_x_deco: '1019', # essential maybe automate
- maximal_y_deco: '1941', # essential maybe automate
- maximal_z_deco: '486', # essential maybe automate
- detections_to_extract_psf_for_channel: '"beads,beads"',
+ 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"',
- compute_on: '"GPU (Nvidia CUDA via JNA)"',
- cudafourierconvolution: "libFourierConvolutionCUDALib.so",
- 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)"',
+ imglib2_container: '"ArrayImg"',
bsh_file: "deconvolution.bsh"
}
hdf5_output: {
- # Will be obsolete
+ # 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_multiple_channels: '"YES (one file per channel)"', # "\"YES (one file per channel)\"" or "\"NO (one channel)\""
- output_timepoints: '0-1',
- output_pixel_distance_x: 0.28590,
+ 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',
- output_channels: "green,red",
- output_data_type: "16Bit",
+ # 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)"',
- 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}} }}"',
- bsh_file_define: "define_output.bsh",
- bsh_file_hdf5: "export_output.bsh"
+ bsh_file_define: "define_output.bsh", # .bsh script for defining the dataset
+ bsh_file_hdf5: "export_output.bsh" # .bsh script for resaving into hdf5
}
--
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