Updates the PR according to the presence of robust_t novel function i…

…n neo_utils
APE-group · Mar 20, 2024 · 9a68772 · 9a68772
1 parent 6c1b2f4
commit 9a68772
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Showing 9 changed files with 19 additions and 19 deletions.
diff --git a/cobrawap/pipeline/configs/config_template.yaml b/cobrawap/pipeline/configs/config_template.yaml
@@ -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
 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'
diff --git a/cobrawap/pipeline/stage01_data_entry/configs/config_template.yaml b/cobrawap/pipeline/stage01_data_entry/configs/config_template.yaml
@@ -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
diff --git a/cobrawap/pipeline/stage01_data_entry/scripts/plot_traces.py b/cobrawap/pipeline/stage01_data_entry/scripts/plot_traces.py
@@ -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")

diff --git a/cobrawap/pipeline/stage02_processing/configs/config_template.yaml b/cobrawap/pipeline/stage02_processing/configs/config_template.yaml
@@ -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'
 

diff --git a/cobrawap/pipeline/stage03_trigger_detection/configs/config_template.yaml b/cobrawap/pipeline/stage03_trigger_detection/configs/config_template.yaml
@@ -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'
 

diff --git a/cobrawap/pipeline/stage04_wave_detection/configs/config_template.yaml b/cobrawap/pipeline/stage04_wave_detection/configs/config_template.yaml
@@ -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'
 

diff --git a/cobrawap/pipeline/stage05_channel_wave_characterization/configs/config_template.yaml b/cobrawap/pipeline/stage05_channel_wave_characterization/configs/config_template.yaml
@@ -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'
 

diff --git a/cobrawap/pipeline/stage05_wave_characterization/configs/config_template.yaml b/cobrawap/pipeline/stage05_wave_characterization/configs/config_template.yaml
@@ -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'
 

diff --git a/cobrawap/pipeline/stageXY_template/configs/config_template.yaml b/cobrawap/pipeline/stageXY_template/configs/config_template.yaml
@@ -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'