cobrawap_publication_code/cobrawap_output/IDIBAPS_WBS_WT4/stage01_data_entry/working_config.yaml

# Config file for Stage 1 - Data Entry

# Name of stage, must be identical with folder name
STAGE_NAME: stage01_data_entry

# The profile name is the key for this parameter configuration. Results are stored in output_path/<PROFILE>/ (output_path is defined in settings.py)
PROFILE: IDIBAPS_WBS_WT4

# Name of stage output file.
STAGE_OUTPUT: data.nix

# File format in which all intermediate neo objects are stored
NEO_FORMAT: nix

# If True (default), the output file of a stage is created as symbolic link
# to the last block output. If False, a duplicate is created (e.g. for cloud
# application, where sym-links are not supported).
USE_LINK_AS_STAGE_OUTPUT: true

# Datasets which should be processed with identical settings.
# To set as key-value pairs
# Name_of_dataset: /path/to/data/files/
DATA_SETS:
    IDIBAPS_WBS_WT4: 
        /home/rgutzen/Sciebo/Slow_Wave_Analysis_Pipeline/Data/IDIBAPS_WBS/data-originals/WBS/WT/cond-WBS_type-WT_sub-4/hbp-01853_cond-WBS_type-WT_sub-4_chs-32_area-ALL_hem-RH_ana-K100M13_stim-SPN.smr
    # IDIBAPS_WBS_WT4: '/projects/wavescalephant/Data/IDIBAPS_WBS/data-originals/WBS/WT/cond-WBS_type-WT_sub-4/hbp-01853_cond-WBS_type-WT_sub-4_chs-32_area-ALL_hem-RH_ana-K100M13_stim-SPN.smr'

CURATION_SCRIPT: curate_IDIBAPS_data.py

# Plot settings
PLOT_TSTART: 0  # in s
PLOT_TSTOP: 10  # in s
PLOT_CHANNELS: [1, 2, 3] # int, list of ints, or 'None' (default) -> picks channel by random
PLOT_FORMAT: png

# pixel size
SPATIAL_SCALE: 0.55  # mm

# specified in the data file
SAMPLING_RATE: None   # Hz

# time slice in s
# if None, the entire recording is used
T_START: None
T_STOP: None

# recommend top: ventral
ORIENTATION_TOP: ventral
# recommended right: 'lateral' for right hemisphere, 'medial' for left hemisphere
ORIENTATION_RIGHT: lateral

# Metadata
ANNOTATIONS:
    technique: ecog
    doi: 10.25493/DZWT-1T8
    anesthetic: ketamine-medetomidine
    concentration: 100 & 13 mg/kg
    disease_model: WBS
    model_type: WT

ARRAY_ANNOTATIONS: None

# The keyword arguments are passed as key value pairs.
# Keywords must only contain letters, numbers, underscores, and spaces.
# Values can be strings, int, float, bool, or None.
# Values can also be aranged in 1D objects such as lists, or tuples
# It is possible to specify nested subdict.
KWARGS:
    ELECTRODE_ANNOTATION_NAME: phy_chan
    NAME2COORDS:
        0: (0,1)
        1: (6,4)
        2: (3,3)
        3: (4,3)
        4: (5,3)
        5: (6,3)
        6: (7,3)
        7: (8,3)
        8: (1,2)
        9: (2,2)
        10: (3,2)
        11: (4,2)
        12: (5,2)
        13: (6,2)
        14: (7,2)
        15: (8,2)
        16: (7,0)
        17: (1,1)
        18: (2,1)
        19: (3,1)
        20: (4,1)
        21: (5,1)
        22: (6,1)
        23: (7,1)
        24: (8,1)
        25: (0,0)
        26: (1,0)
        27: (2,0)
        28: (3,0)
        29: (4,0)
        30: (5,0)
        31: (6,0)
    ELECTRODE_LOCATION:
        Visual Cortex: [1, 4, 5, 6, 7, 12, 13, 14, 15, 21, 22, 23, 24]
        Retrospenial Cortex: [16, 31, 30, 29]
        Parietal Association Cortex: [3, 11, 20]
        Somatosensory Cortex: [2, 8, 9, 10, 17, 18, 19]
        Motor Cortex: [0, 25, 26, 27, 28]
    ELECTRODE_COLOR: # color scheme to match to figures in publication
        Visual Cortex: '#0C6BB1'
        Retrospenial Cortex: '#422F58'
        Parietal Association Cortex: '#01B24E'
        Somatosensory Cortex: '#F92600'
        Motor Cortex: '#EF6700'

# dictionary mapping the channels (ELECTRODE_ANNOTATION_NAME) to their coordiantes on the grid (grid_size)
STAGES:
    - stage01_data_entry
    - stage02_processing
    - stage03_trigger_detection
    - stage04_wave_detection
    - stage05_wave_characterization
QUALITY: 5
SCALE_X: 720
SCALE_Y: 720
FPS: 18
BITRATE: 20M
FRAME_RATE: None
COLORMAP: twilight
PLOT_EVENT: wavefronts
MARKER_COLOR: r
STAGE_INPUT: