Adding "None" as a permitted value in all plotting scripts

NeuralEnsemble · Mar 20, 2024 · 19bab7c · 19bab7c
1 parent 9a68772
commit 19bab7c
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Showing 3 changed files with 8 additions and 6 deletions.
diff --git a/cobrawap/pipeline/stage02_processing/scripts/logMUA_estimation.py b/cobrawap/pipeline/stage02_processing/scripts/logMUA_estimation.py
@@ -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")

diff --git a/cobrawap/pipeline/stage02_processing/scripts/plot_processed_trace.py b/cobrawap/pipeline/stage02_processing/scripts/plot_processed_trace.py
@@ -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,
@@ -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")

diff --git a/cobrawap/pipeline/stage04_wave_detection/scripts/time_slice.py b/cobrawap/pipeline/stage04_wave_detection/scripts/time_slice.py
@@ -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__':