From f06a63e990c7318fbdb1e8f42b674dd7b9c62f04 Mon Sep 17 00:00:00 2001
From: Christopher Schmied <schmied@mpi-cbg.de>
Date: Wed, 15 Jul 2015 17:51:53 +0200
Subject: [PATCH] Fixed broken .yaml file
---
spim_registration/timelapse/single.yaml | 350 +++++++++++++++++++++++-
1 file changed, 346 insertions(+), 4 deletions(-)
mode change 100644 => 100755 spim_registration/timelapse/single.yaml
diff --git a/spim_registration/timelapse/single.yaml b/spim_registration/timelapse/single.yaml
old mode 100644
new mode 100755
index fdd6ccd..d6eef5f
--- a/spim_registration/timelapse/single.yaml
+++ b/spim_registration/timelapse/single.yaml
@@ -1,4 +1,346 @@
-Unstaged changes after reset:
-M spim_registration/timelapse/dual_OneChannel.yaml
-M spim_registration/timelapse/single.yaml
-M spim_registration/timelapse/single_test.yaml
+common: {
+ # ============================================================================
+ #
+ # yaml example file for single channel processing
+ #
+ # General settings for processing
+ # 2015-04-01_LZ2_Stock46
+ # Dpse_Dip3_VK33
+ #
+ # ============================================================================
+ # 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/2015-06-30_Fiji.app.cuda/ImageJ-linux64",
+ fiji-prefix: "/sw/users/schmied/packages/xvfb-run -a", # calls xvfb for Fiji headless mode
+ # ============================================================================
+ # Processing switches
+ # Description: Use switches to decide which processing steps you need:
+ #
+ # Options:
+ # 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
+ #
+ # Switches between content based fusion and deconvoltion
+ # "deconvolution" > for deconvolution
+ # "fusion" > for content based fusion
+ # ============================================================================
+ #
+ # Transformation switch:
+ transformation_switch: "timelapse",
+ # Fusion switch:
+ fusion_switch: "fusion",
+ # ============================================================================
+ # xml file names
+ #
+ # xml file names without .xml suffix
+ # ============================================================================
+ first_xml_filename: 'Dpse_Dip3_VK33', # Name of the xml file for the .czi or .tif files
+ hdf5_xml_filename: '"hdf5_Dpse_Dip3_VK33"', # Name of .xml file for the hdf5 data after resave_hdf5
+ merged_xml: 'hdf5_Dpse_Dip3_VK33_merge', # Name of .xml file after merge
+ # ============================================================================
+ # Describe the dataset
+ #
+ # Options: number of timepoints
+ # angles
+ # channels
+ # illuminations
+ # pixel size
+ # ============================================================================
+ ntimepoints: 72, # number of timepoints of dataset
+ angles: "0,72,144,216,288", # angles
+ channels: "green", # channels
+ illumination: "0", # illuminations
+ # ----------------------------------------------------------------------------
+ # For .czi datasets
+ # master .czi file
+ first_czi: "2015-04-01_LZ2_Stock46.czi",
+ # ----------------------------------------------------------------------------
+ # For .tif datasets
+ # file pattern of .tif files:
+ # for multi channel give spim_TL{tt}_Angle{a}_Channel{c}.tif
+ # for padded zeros use tt
+ # specify calibration
+ image_file_pattern: 'img_TL{{t}}_Angle{{a}}.tif',
+ pixel_distance_x: '0.285901069641113', # Manual calibration x
+ pixel_distance_y: '0.285901069641113', # Manual calibration y
+ pixel_distance_z: '1.500000000000000', # Manual calibration z
+ pixel_unit: "um", # unit of manual calibration
+ # ============================================================================
+ # Detection and registration
+ #
+ # Description: settings for interest point detection and registration
+ # Options: Single channel and dual channel processing
+ # Difference-of-mean or difference-of-gaussian detection
+ # ============================================================================
+ # 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"',
+ #
+ # Dual channel 1 Channel contains the beads: which 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-Gaussian"',
+ # 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: '1.3',
+ threshold_gaussian: '0.025',
+ # ============================================================================
+ # Timelapse registration
+ #
+ # Description: settings for timelapse registration
+ # Options: reference timepoint
+ # ============================================================================
+ reference_timepoint: '40', # Reference timepoint
+ # ============================================================================
+ # Content-based multiview fusion
+ #
+ # Description: settings for content-based multiview fusion
+ # Options: downsampling
+ # Cropping parameters based on full resolution
+ # ============================================================================
+ downsample: '1', # set downsampling
+ minimal_x: '237', # Cropping parameters of full resolution
+ minimal_y: '-16',
+ minimal_z: '-292',
+ maximal_x: '1041',
+ maximal_y: '1853',
+ maximal_z: '509',
+ # ============================================================================
+ # Multiview deconvolution
+ #
+ # Description: settings for multiview deconvolution
+ # Options: number of iterations
+ # Cropping parameters taking downsampling into account
+ # Channel settings for deconvolution
+ # ============================================================================
+ iterations: '1', # number of iterations
+ minimal_x_deco: '237', # Cropping parameters: take downsampling into account
+ minimal_y_deco: '-16',
+ minimal_z_deco: '-292',
+ maximal_x_deco: '1041',
+ maximal_y_deco: '1853',
+ maximal_z_deco: '509',
+ #
+ # 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: '"beads"',
+ #
+ # ============================================================================
+ # Resave output
+ #
+ # Description: writes new hdf5 dataset for fusion output
+ # Options: Naming pattern of output based on channel number
+ # Channel settings
+ # File name for resaving output into hdf5
+ # Pixel size > isotropic resolution
+ # Image type (16Bit from content-based fusion, 32Bit from deconvolution)
+ # ============================================================================
+ # Number of timepoints
+ output_timepoints: '0-71', # Timepoints format: '1-2'
+ #
+ # Naming pattern:
+ # 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:
+ # Single channel: '"NO (one channel)"'
+ # Dual channel: '"YES (one file per channel)"'
+ output_multiple_channels: '"NO (one channel)"',
+ output_channels: "green",
+ #
+ # .xml file names
+ output_xml: '"fused_Dpse_Dip3_VK33"',
+ output_hdf5_xml: '"hdf5_fused_Dpse_Dip3_VK33"',
+ #
+ # pixel size of output: take downsampling into account!
+ output_pixel_distance_x: 0.285901069641113,
+ output_pixel_distance_y: 0.285901069641113,
+ output_pixel_distance_z: 0.285901069641113,
+ output_pixel_unit: 'um',
+ #
+ # File type
+ output_data_type: "16Bit" # "32Bit" or "16Bit"
+ }
+ # ============================================================================
+ # Advanced settings
+ # ============================================================================
+
+define_xml_czi: {
+ manual_calibration_czi: "Yes", # calibration override: No or Yes
+ czi_pixel_distance_x: '0.285901069641113', # Manual calibration x
+ czi_pixel_distance_y: '0.285901069641113', # Manual calibration y
+ czi_pixel_distance_z: '1.500000000000000', # Manual calibration z
+ czi_pixel_unit: "um", # unit of manual calibration
+ rotation_around: "X-Axis", # axis of acquistion
+ bsh_file: "define_czi.bsh" # .bsh script for defining .czi file
+ }
+
+define_xml_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: {
+ # Processing setting for Difference-of-Gaussian detection
+ # compute_on:'"GPU accurate (Nvidia CUDA via JNA)"'
+ compute_on: '"CPU (Java)"',
+ separableconvolution: '"libSeparableConvolutionCUDALib.so"',
+ # Downsampling settings
+ downsample_detection: "Yes", # "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: {
+ # 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: {
+ # 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: {
+ # 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: {
+ # 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
+ }
+
--
GitLab