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New logic for plot limits #48

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merged 6 commits into from
Jul 18, 2024
Merged

New logic for plot limits #48

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9a68772
Updates the PR according to the presence of robust_t novel function i…
cosimolupo Mar 20, 2024
19bab7c
Adding "None" as a permitted value in all plotting scripts
cosimolupo Mar 20, 2024
991ea39
Minor change in config template files
cosimolupo Mar 22, 2024
afec0a3
Merge branch 'master' into plot_limits_PR
cosimolupo Mar 22, 2024
3ff1ad7
Fix for extra spacings added when merging PR #61
cosimolupo Mar 22, 2024
49e4da7
Merge NeuralEnsemble:cobrawap/master into this branch
cosimolupo Jun 25, 2024
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4 changes: 2 additions & 2 deletions cobrawap/pipeline/configs/config_template.yaml
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Expand Up @@ -19,8 +19,8 @@ NEO_FORMAT: 'nix'
USE_LINK_AS_STAGE_OUTPUT: True

# Plotting parameters
PLOT_TSTART: 0 # in s
PLOT_TSTOP: 10 # in s
PLOT_TSTART: 0 # float (in s) or 'None' -> T_START of the input signal is used
PLOT_TSTOP: 10 # float (in s) or 'None' -> T_STOP of the input signal is used
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Here and in the following, does T_START refer to t_start of the Neo object? In that case I would suggest

Suggested change
PLOT_TSTART: 0 # float (in s) or 'None' -> T_START of the input signal is used
PLOT_TSTOP: 10 # float (in s) or 'None' -> T_STOP of the input signal is used
PLOT_TSTART: 0 # float (in s) or 'None' -> t_start of the input signal is used
PLOT_TSTOP: 10 # float (in s) or 'None' -> t_stop of the input signal is used

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@cosimolupo cosimolupo Mar 21, 2024 •
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Yes, they refer to the attributes of the neo object. I used the uppercase notation as in the config files they are introduced this way. Anyway, let's decide if switch to the lowercase version, and then I will fix them coherently.

PLOT_CHANNELS: 'None' # int or None. default 'None' -> randomly selected
# Note that when using the None option, the automatic creation of reports will fail
PLOT_FORMAT: 'png'
4 changes: 2 additions & 2 deletions cobrawap/pipeline/stage01_data_entry/configs/config_template.yaml
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Expand Up @@ -69,7 +69,7 @@ KWARGS: 'None'
# Plotting parameters
# These parameters are used to create an example plot to get a first view
# on the signals and ensure that the data was loaded and annotated correctly
PLOT_TSTART: 0 # in s
PLOT_TSTOP: 10 # in s
PLOT_TSTART: 0 # float (in s) or 'None' -> T_START of the input signal is used
PLOT_TSTOP: 10 # float (in s) or 'None' -> T_STOP of the input signal is used
PLOT_CHANNELS: 'None' # int, or list of int, or 'None' -> randomly chosen channel
PLOT_FORMAT: 'png' # file extension for storing the plot
6 changes: 3 additions & 3 deletions cobrawap/pipeline/stage01_data_entry/scripts/plot_traces.py
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Expand Up @@ -9,16 +9,16 @@
import seaborn as sns
from utils.io_utils import load_neo, save_plot
from utils.neo_utils import time_slice
from utils.parse import parse_plot_channels, none_or_int
from utils.parse import parse_plot_channels, none_or_int, none_or_float

CLI = argparse.ArgumentParser()
CLI.add_argument("--data", nargs='?', type=Path, required=True,
help="path to input data in neo format")
CLI.add_argument("--output", nargs='?', type=Path, required=True,
help="path of output figure")
CLI.add_argument("--t_start", nargs='?', type=float, default=0,
CLI.add_argument("--t_start", nargs='?', type=none_or_float, default=0,
help="start time in seconds")
CLI.add_argument("--t_stop", nargs='?', type=float, default=10,
CLI.add_argument("--t_stop", nargs='?', type=none_or_float, default=10,
help="stop time in seconds")
CLI.add_argument("--channels", nargs='+', type=none_or_int, default=0,
help="list of channels to plot")
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4 changes: 2 additions & 2 deletions cobrawap/pipeline/stage02_processing/configs/config_template.yaml
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Expand Up @@ -18,8 +18,8 @@ NEO_FORMAT: 'nix'
USE_LINK_AS_STAGE_OUTPUT: True

# Plotting parameters
PLOT_TSTART: 0 # in s
PLOT_TSTOP: 10 # in s
PLOT_TSTART: 0 # float (in s) or 'None' -> T_START of the input signal is used
PLOT_TSTOP: 10 # float (in s) or 'None' -> T_STOP of the input signal is used
PLOT_CHANNELS: 'None' # int or None. default 'None' -> randomly selected
PLOT_FORMAT: 'png'

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4 changes: 2 additions & 2 deletions cobrawap/pipeline/stage02_processing/scripts/logMUA_estimation.py
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Expand Up @@ -37,9 +37,9 @@
help="overlap parameter for Welch's algorithm [0-1]")
CLI.add_argument("--fft_slice", nargs='?', type=none_or_float, default=None,
help="time window length used for power spectrum estimate, in s")
CLI.add_argument("--plot_tstart", nargs='?', type=float, default=0,
CLI.add_argument("--plot_tstart", nargs='?', type=none_or_float, default=0,
help="start time in seconds")
CLI.add_argument("--plot_tstop", nargs='?', type=float, default=10,
CLI.add_argument("--plot_tstop", nargs='?', type=none_or_float, default=10,
help="stop time in seconds")
CLI.add_argument("--plot_channels", nargs='+', type=none_or_int, default=None,
help="list of channels to plot")
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5 changes: 3 additions & 2 deletions cobrawap/pipeline/stage02_processing/scripts/plot_processed_trace.py
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Expand Up @@ -8,6 +8,7 @@
import os
from utils.io_utils import load_neo, save_plot
from utils.neo_utils import time_slice
from utils.parse import none_or_float

CLI = argparse.ArgumentParser()
CLI.add_argument("--original_data", nargs='?', type=str, required=True,
Expand All @@ -19,9 +20,9 @@
CLI.add_argument("--img_name", nargs='?', type=str,
default='processed_trace_channel0.png',
help='example filename for channel 0')
CLI.add_argument("--t_start", nargs='?', type=float, default=0,
CLI.add_argument("--t_start", nargs='?', type=none_or_float, default=0,
help="start time in seconds")
CLI.add_argument("--t_stop", nargs='?', type=float, default=10,
CLI.add_argument("--t_stop", nargs='?', type=none_or_float, default=10,
help="stop time in seconds")
CLI.add_argument("--channels", nargs='+', type=int, default=0,
help="channel to plot")
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4 changes: 2 additions & 2 deletions cobrawap/pipeline/stage03_trigger_detection/configs/config_template.yaml
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Expand Up @@ -18,8 +18,8 @@ NEO_FORMAT: 'nix'
USE_LINK_AS_STAGE_OUTPUT: True

# Plotting parameters
PLOT_TSTART: 0 # in s
PLOT_TSTOP: 10 # in s
PLOT_TSTART: 0 # float (in s) or 'None' -> T_START of the input signal is used
PLOT_TSTOP: 10 # float (in s) or 'None' -> T_STOP of the input signal is used
PLOT_CHANNELS: 'None' # int or None. default 'None' -> randomly selected
PLOT_FORMAT: 'png'

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4 changes: 2 additions & 2 deletions cobrawap/pipeline/stage04_wave_detection/configs/config_template.yaml
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Expand Up @@ -18,8 +18,8 @@ NEO_FORMAT: 'nix'
USE_LINK_AS_STAGE_OUTPUT: True

# Plotting parameters
PLOT_TSTART: 0 # in s
PLOT_TSTOP: 10 # in s
PLOT_TSTART: 0 # float (in s) or 'None' -> T_START of the input signal is used
PLOT_TSTOP: 10 # float (in s) or 'None' -> T_STOP of the input signal is used
PLOT_CHANNELS: 'None' # int or None. default 'None' -> randomly selected
PLOT_FORMAT: 'png'

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5 changes: 3 additions & 2 deletions cobrawap/pipeline/stage04_wave_detection/scripts/time_slice.py
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Expand Up @@ -6,15 +6,16 @@
import quantities as pq
from utils.io_utils import load_neo, write_neo
from utils.neo_utils import time_slice
from utils.parse import none_or_float

CLI = argparse.ArgumentParser()
CLI.add_argument("--data", nargs='?', type=str, required=True,
help="path to input data in neo format")
CLI.add_argument("--output", nargs='?', type=str, required=True,
help="path of output file")
CLI.add_argument("--t_start", nargs='?', type=float, default=0,
CLI.add_argument("--t_start", nargs='?', type=none_or_float, default=0,
help="new starting time in s")
CLI.add_argument("--t_stop", nargs='?', type=float, default=10,
CLI.add_argument("--t_stop", nargs='?', type=none_or_float, default=10,
help="new stopping time in s")

if __name__ == '__main__':
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4 changes: 2 additions & 2 deletions cobrawap/pipeline/stage05_channel_wave_characterization/configs/config_template.yaml
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Expand Up @@ -15,8 +15,8 @@ STAGE_OUTPUT: 'channel-wise_measures.csv'
USE_LINK_AS_STAGE_OUTPUT: True

# Plotting parameters
PLOT_TSTART: 0 # in s
PLOT_TSTOP: 10 # in s
PLOT_TSTART: 0 # float (in s) or 'None' -> T_START of the input signal is used
PLOT_TSTOP: 10 # float (in s) or 'None' -> T_STOP of the input signal is used
PLOT_CHANNELS: 'None' # int or None. default 'None' -> randomly selected
PLOT_FORMAT: 'png'

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4 changes: 2 additions & 2 deletions cobrawap/pipeline/stage05_wave_characterization/configs/config_template.yaml
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Expand Up @@ -15,8 +15,8 @@ STAGE_OUTPUT: 'wave-wise_measures.csv'
USE_LINK_AS_STAGE_OUTPUT: True

# Plotting parameters
PLOT_TSTART: 0 # in s
PLOT_TSTOP: 10 # in s
PLOT_TSTART: 0 # float (in s) or 'None' -> T_START of the input signal is used
PLOT_TSTOP: 10 # float (in s) or 'None' -> T_STOP of the input signal is used
PLOT_CHANNELS: 'None' # int or None. default 'None' -> randomly selected
PLOT_FORMAT: 'png'

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4 changes: 2 additions & 2 deletions cobrawap/pipeline/stageXY_template/configs/config_template.yaml
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Expand Up @@ -20,7 +20,7 @@ OFFSET: 20
A: 'a'

# Plotting parameters
PLOT_TSTART: 0 # in s
PLOT_TSTOP: 10 # in s
PLOT_TSTART: 0 # float (in s) or 'None' -> T_START of the input signal is used
PLOT_TSTOP: 10 # float (in s) or 'None' -> T_STOP of the input signal is used
PLOT_CHANNELS: 'None' # int or None. default 'None' -> randomly selected
PLOT_FORMAT: 'png'