New logic for plot limits (#48)

* Updates the PR according to the presence of robust_t novel function in neo_utils

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

* Minor change in config template files

* Fix for extra spacings added when merging PR #61

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' -> starting time of the input signal is used
+PLOT_TSTOP: 10  # float (in s) or 'None' -> stopping time 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'

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' -> starting time of the input signal is used
+PLOT_TSTOP: 10  # float (in s) or 'None' -> stopping time 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

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,
+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,
+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")

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' -> starting time of the input signal is used
+PLOT_TSTOP: 10  # float (in s) or 'None' -> stopping time of the input signal is used
 PLOT_CHANNELS: 'None'  # int or None. default 'None' -> randomly selected
 PLOT_FORMAT: 'png'
 

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")

cobrawap/pipeline/stage02_processing/scripts/plot_processed_trace.py

@@ -8,20 +8,21 @@
 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,
                  help="path to input data in neo format")
 CLI.add_argument("--data", nargs='?', type=str, required=True,
                  help="path to input data in neo format")
-CLI.add_argument("--img_dir",  nargs='?', type=str, required=True,
+CLI.add_argument("--img_dir", nargs='?', type=str, required=True,
                  help="path of output figure directory")
 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")

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' -> starting time of the input signal is used
+PLOT_TSTOP: 10  # float (in s) or 'None' -> stopping time of the input signal is used
 PLOT_CHANNELS: 'None'  # int or None. default 'None' -> randomly selected
 PLOT_FORMAT: 'png'
 

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' -> starting time of the input signal is used
+PLOT_TSTOP: 10  # float (in s) or 'None' -> stopping time of the input signal is used
 PLOT_CHANNELS: 'None'  # int or None. default 'None' -> randomly selected
 PLOT_FORMAT: 'png'
 

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__':

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' -> starting time of the input signal is used
+PLOT_TSTOP: 10  # float (in s) or 'None' -> stopping time of the input signal is used
 PLOT_CHANNELS: 'None'  # int or None. default 'None' -> randomly selected
 PLOT_FORMAT: 'png'
 

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' -> starting time of the input signal is used
+PLOT_TSTOP: 10  # float (in s) or 'None' -> stopping time of the input signal is used
 PLOT_CHANNELS: 'None'  # int or None. default 'None' -> randomly selected
 PLOT_FORMAT: 'png'
 

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' -> starting time of the input signal is used
+PLOT_TSTOP: 10  # float (in s) or 'None' -> stopping time of the input signal is used
 PLOT_CHANNELS: 'None'  # int or None. default 'None' -> randomly selected
 PLOT_FORMAT: 'png'