Fixed broken .yaml file

spim_registration/timelapse/single.yaml

-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
+  }
+