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- # Config file for Stage 2 - Processing
- # Name of stage, must be identical with folder name
- STAGE_NAME: 'stage02_processing'
- # 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: 'LENS|macrodim9'
- # Name of the output file
- STAGE_OUTPUT: "processed_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
- # Plotting parameters
- PLOT_TSTART: 0 # in s
- PLOT_TSTOP: 10 # in s
- PLOT_CHANNELS: [11, 33, 55] # int or None. default 'None' -> randomly selected
- PLOT_FORMAT: 'png'
- # The block order determines which processing steps (blocks) will be applied
- # and in which order. Execution order is from first to last entry.
- # The available blocks are:
- # 'background_subtraction', 'frequency_filter', 'normalization', 'detrending',
- # 'roi_selection', 'logMUA_estimation', 'phase_transform', 'zscore', 'spatial_downsampling'
- BLOCK_ORDER: ['spatial_downsampling', 'roi_selection', 'background_subtraction', 'detrending',
- 'normalization', 'frequency_filter', 'zscore']
- # To make sure that the processing blocks are always executed in the correct
- # order that results from previous runs don't confound the workflow, all blocks
- # are rerun upon each execution. To turn this off, e.g., because the block order
- # didn't change, set to False (do with care!).
- RERUN_MODE: False
- # BLOCK - background_subtraction
- #################################
- # No parameters needed
- # BLOCK - spatial_downsampling
- #################################
- MACRO_PIXEL_DIM: 9
- # BLOCK - normalization
- #######################
- # Normalize the data (devide channels-wise) by either:
- # 'mean', 'median', 'max'
- NORMALIZE_BY: 'max'
- # BLOCK - frequency_filter
- ##########################
- # parameters to be passed to the butterworth frequency filter
- # function by elephant
- HIGHPASS_FREQUENCY: 0.1 # in Hz
- LOWPASS_FREQUENCY: 5 # in Hz
- FILTER_ORDER: 2
- # filter function used in scipy backend.
- # options: ‘filtfilt’, 'lfilter’, ‘sosfiltfilt’
- FILTER_FUNCTION: 'sosfiltfilt'
- # Plotting parameters for the power spectrum
- PSD_FREQUENCY_RESOLUTION: 5 # in Hz
- PSD_OVERLAP: 0.5
- # BLOCK - detrending
- ####################
- # Detrending: 0 - mean detrending;
- # 1 - mean and slope detrending (linear): this should be the default.
- DETRENDING_ORDER: 1
- # BLOCK - subsampling
- #####################
- TARGET_RATE: 200 # in Hz
- # BLOCK - img_roi_selection
- ###########################
- # Threshold below which the pixels are discarded (set to nan).
- # Given in percent of the range between minimum and maximum intensity.
- INTENSITY_THRESHOLD: 0.5
- CROP_TO_SELECTION: True
- # BLOCK - logMUA_estimation
- ########################
- MUA_HIGHPASS_FREQUENCY: 200 # in Hz
- MUA_LOWPASS_FREQUENCY: 1500 # in Hz
- # Rate of the logMUA signal. Must be <= the original sampling rate
- # in Hz (default: 'None', takes highpass_freq)
- logMUA_RATE: 100
- # Length of time slice (in s) to estimate the local power spectrum
- # default 'None', takes minimum number of samples determined
- # by the lower bound of the frequency band
- FFT_SLICE: 0.1
- # PSD_OVERLAP: determined by setting in block frequency_filter
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