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- # 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_FXS_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_FXS_WT4: '/projects/wavescalephant/Data/IDIBAPS_FXS/data-originals/FXS/WT/cond-FXS_type-WT_sub-4/hbp-01853_cond-FXS_type-WT_sub-4_chs-32_area-ALL_hem-RH_ana-ISO090_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/ANF9-EG3
- anesthetic: isoflurane
- concentration: 90 mg/kg
- disease_model: 'FXS'
- 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)
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