Merge pull request #36 from AminAlam/dev

BUG FIX - channels_list and ignore_channels in command line

elecphys/data_io.py

@@ -71,12 +71,11 @@ def load_all_npz_files(npz_folder: str, ignore_channels: [
             files_list.remove(file_name)
     files_list = utils.sort_file_names(files_list)
     all_channels_in_folder = list(range(0, len(files_list)))
+    channels_list = utils.convert_string_to_list(channels_list)
     if channels_list is None:
         channels_list = all_channels_in_folder
-    else:
-        channels_list = utils.convert_string_to_list(channels_list)
+    ignore_channels = utils.convert_string_to_list(ignore_channels)
     if ignore_channels is not None:
-        ignore_channels = utils.convert_string_to_list(ignore_channels)
         ignore_channels = [i - 1 for i in ignore_channels]
     else:
         ignore_channels = []

elecphys/fourier_analysis.py

@@ -403,7 +403,7 @@ def freq_bands_power_over_time(
         ----------
             input_npz_folder: str
                 path to input npz folder containing signal npz files (in time domain)
-            freq_bands: tuple
+            freq_bands: tuple, list
                 tuple or list of frequency bands to calculate power over time for. It should be a tuple or list of lists, where each list contains two elements: the lower and upper frequency bounds of the band (in Hz). For example, freq_bands = [[1, 4], [4, 8], [8, 12]] would calculate power over time for the delta, theta, and alpha bands.
             channels_list: str
                 list of channels to include in analysis
@@ -427,10 +427,8 @@ def freq_bands_power_over_time(
         Returns
         ----------
     """
-    if channels_list is not None:
-        channels_list = utils.convert_string_to_list(channels_list)
-    if ignore_channels is not None:
-        ignore_channels = utils.convert_string_to_list(ignore_channels)
+    channels_list = utils.convert_string_to_list(channels_list)
+    ignore_channels = utils.convert_string_to_list(ignore_channels)
 
     data_all, fs, channels_map = data_io.load_all_npz_files(input_npz_folder, ignore_channels, channels_list)
     # if freq_bands only has one list, we should make sure it is a list of lists

elecphys/main.py

@@ -176,9 +176,9 @@ def normalize_npz(ctx, input_npz_folder: str,
               required=True, type=str, default='output_npz_avg_rereferenced', show_default=True)
 @click.option('--ignore_channels',
               '-ic',
-              help='List of channels to ignore (e.g EMG, EOG, etc.). If None, then no channels will be ignored',
+              help='List of channels to ignore (e.g EMG, EOG, etc.). If None, then no channels will be ignored (e.g. --ignore_channels "[1,2,3]").',
               required=False,
-              type=list,
+              type=str,
               default=None,
               show_default=True)
 @click.option('--rr_channel',
@@ -191,7 +191,7 @@ def normalize_npz(ctx, input_npz_folder: str,
 @click.pass_context
 @error_handler
 def re_reference_npz(ctx, input_npz_folder: str, output_npz_folder: str = 'output_npz_avg_rereferenced',
-                     ignore_channels: list = None, rr_channel: int = None) -> None:
+                     ignore_channels: str = None, rr_channel: int = None) -> None:
     """ Re-references NPZ files and save them as NPZ files
 
         Parameters
@@ -200,7 +200,7 @@ def re_reference_npz(ctx, input_npz_folder: str, output_npz_folder: str = 'outpu
             path to input npz folder
         output_npz_folder: str
             path to output npz folder. If the folder already exists, it will be overwritten. If not specified, the default value is 'output_npz_avg_rereferenced'
-        ignore_channels: list
+        ignore_channels: str
             list of channels to ignore (e.g EMG, EOG, etc.). If None, then no channels will be ignored. Either a list of channel indexes or a string of channel indexes separated by commas
         rr_channel: int
             channel to re-reference signals to. If None, signals will be re-referenced to the average of all channels. If not specified, the default value is None
@@ -357,13 +357,18 @@ def frequncy_domain_filter(ctx, input_npz_folder: str, output_npz_folder: str =
               type=str)
 @click.option('--channels_list',
               '-cl',
-              help='List of channels to compute power for. If None, then all of the channels will be used. It should be a string of comma-separated channel numbers (e.g. "[1,2,3]").',
+              help='List of channels to compute power for. If None, then all of the channels will be used. It should be a string of comma-separated channel numbers (e.g. --channels_list "[1,2,3]").',
+              required=False,
+              type=str,
+              default=None,
+              show_default=True)
+@click.option('--ignore_channels',
+              '-ic',
+              help='List of channels to ignore. If None, then no channels will be ignored (e.g. --ignore_channels "[1,2,3]").',
               required=False,
               type=str,
               default=None,
               show_default=True)
-@click.option('--ignore_channels', '-ic', help='List of channels to ignore. If None, then no channels will be ignored',
-              required=False, type=str, default=None, show_default=True)
 @click.option('--window_size', '-w', help='Window size in seconds',
               required=False, type=float, default=1, show_default=True)
 @click.option('--overlap', '-ov', help='Overlap in seconds',
@@ -546,7 +551,7 @@ def plot_avg_stft(
         t_max: float = None,
         db_min: float = None,
         db_max: float = None,
-        channels_list: list = None) -> None:
+        channels_list: str = None) -> None:
     """ Plots average STFT from NPZ files
 
         Parameters
@@ -567,7 +572,7 @@ def plot_avg_stft(
             minimum dB to plot. If not specified, the default value is None and the minimum dB will be the minimum dB of the signal
         db_max: float
             maximum dB to plot. If not specified, the default value is None and the maximum dB will be the maximum dB of the signal
-        channels_list: list
+        channels_list: str
             list of channels to plot. either a string of comma-separated channel numbers or a list of integers. If not specified, the default value is None and all of the channels will be plotted.
 
         Returns
@@ -597,8 +602,13 @@ def plot_avg_stft(
               required=False, type=float, default=None, show_default=True)
 @click.option('--t_max', '-tmax', help='End of time interval to plot',
               required=False, type=float, default=None, show_default=True)
-@click.option('--channels_list', '-cl', help='List of channels to plot, if None then all of the channels will be plotted',
-              required=False, type=list, default=None, show_default=True)
+@click.option('--channels_list',
+              '-cl',
+              help='List of channels to plot, if None then all of the channels will be plotted (e.g. --channels_list "[1,2,3]").',
+              required=False,
+              type=str,
+              default=None,
+              show_default=True)
 @click.option('--normalize', '-n', help='Normalize signals. If true, each channel will be normalized',
               required=False, type=bool, default=False, show_default=True)
 @click.option('--scale_bar', '-sb', help='Scale bar. If true, a scale bar will be added to the plot',
@@ -612,7 +622,7 @@ def plot_avg_stft(
               show_default=True)
 @click.option('--ignore_channels',
               '-ic',
-              help='List of channels to ignore (e.g EMG, EOG, etc.). If None, then no channels will be ignored',
+              help='List of channels to ignore (e.g EMG, EOG, etc.). If None, then no channels will be ignored (e.g. --ignore_channels "[1,2,3]").',
               required=False,
               type=str,
               default=None,
@@ -632,7 +642,7 @@ def plot_signal(
         output_plot_file: str,
         t_min: float = None,
         t_max: float = None,
-        channels_list: list = None,
+        channels_list: str = None,
         normalize: bool = False,
         scale_bar: bool = True,
         re_reference: bool = False,
@@ -650,7 +660,7 @@ def plot_signal(
             Start of time interval to plot. If not specified, the default value is None and the minimum time will be 0 seconds
         t_max: float
             End of time interval to plot. If not specified, the default value is None and the maximum time will be the total duration of the signal
-        channels_list: list
+        channels_list: str
             list of channels to plot. either a string of comma-separated channel numbers or a list of integers. If not specified, the default value is None and all of the channels will be plotted.
         normalize: bool
             normalize signals. If true, each channel will be normalized. If not specified, the default value is False.
@@ -696,8 +706,13 @@ def plot_signal(
               required=False, type=float, default=None, show_default=True)
 @click.option('--f_max', '-fmax', help='Maximum frequency to plot in Hz',
               required=False, type=float, default=None, show_default=True)
-@click.option('--channels_list', '-cl', help='List of channels to plot, if None then all of the channels will be plotted',
-              required=False, type=list, default=None, show_default=True)
+@click.option('--channels_list',
+              '-cl',
+              help='List of channels to plot, if None then all of the channels will be plotted (e.g. --channels_list "[1,2,3]").',
+              required=False,
+              type=str,
+              default=None,
+              show_default=True)
 @click.option('--plot_type',
               '-pt',
               help='Plot type. If "all_channels", then all channels will be plotted in one figure. If "average_of_channels", then average of channels will be plotted in one figure with errorbar',
@@ -710,7 +725,7 @@ def plot_signal(
 @click.pass_context
 @error_handler
 def plot_dft(ctx, input_npz_folder: str, output_plot_file: str, f_min: float = None, f_max: float = None,
-             channels_list: list = None, plot_type: str = 'average_of_channels', conv_window_size: int = None) -> None:
+             channels_list: str = None, plot_type: str = 'average_of_channels', conv_window_size: int = None) -> None:
     """ Plots DFT from NPZ file
 
         Parameters
@@ -723,7 +738,7 @@ def plot_dft(ctx, input_npz_folder: str, output_plot_file: str, f_min: float = N
             minimum frequency to plot in Hz. If not specified, the default value is None and the minimum frequency will be 0 Hz
         f_max: float
             maximum frequency to plot in Hz. If not specified, the default value is None and the maximum frequency will be the Nyquist frequency
-        channels_list: list
+        channels_list: str
             list of channels to plot. either a string of comma-separated channel numbers or a list of integers. If not specified, the default value is None and all of the channels will be plotted.
         plot_type: str
             plot type. If not specified, the default value is 'average_of_channels'. It should be 'all_channels' or 'average_of_channels'
@@ -817,12 +832,17 @@ def plot_filter_freq_response(ctx, filter_type: str = 'LPF', freq_cutoff: str =
               type=bool,
               default=False,
               show_default=True)
-@click.option('--channels_list', '-cl', help='List of channels to apply PCA, if None then all of the channels will be applied',
-              required=False, type=list, default=None, show_default=True)
+@click.option('--channels_list',
+              '-cl',
+              help='List of channels to apply PCA, if None then all of the channels will be applied (e.g. --channels_list "[1,2,3]").',
+              required=False,
+              type=list,
+              default=None,
+              show_default=True)
 @click.pass_context
 @error_handler
 def pca_from_npz(ctx, input_npz_folder: str, output_npz_folder: str = 'output_npz_pca',
-                 n_components: int = None, matrix_whitenning: bool = False, channels_list: list = None) -> None:
+                 n_components: int = None, matrix_whitenning: bool = False, channels_list: str = None) -> None:
     """ Computes PCA from NPZ files
 
         Parameters
@@ -835,7 +855,7 @@ def pca_from_npz(ctx, input_npz_folder: str, output_npz_folder: str = 'output_np
             number of components to keep after applying the PCA. If not specified, the default value is None
         matrix_whitenning: bool
             matrix whitening boolean. If true, the singular values are divided by n_samples. If not specified, the default value is False
-        channels_list: list
+        channels_list: str
             list of channels to apply PCA. either a string of comma-separated channel numbers or a list of integers. If not specified, the default value is None and all of the channels will be applied.
 
         Returns

elecphys/preprocessing.py

@@ -142,7 +142,7 @@ def re_reference_npz(input_npz_folder: str, output_npz_folder: str, ignore_chann
             path to input npz folder
         output_npz_folder: str
             path to output npz folder
-        ignore_channels: list
+        ignore_channels: list, str
             list of channels to be ignored. Either a list of channel indexes or a string of channel indexes separated by commas. If None, no channels will be ignored
         rr_channel: int
             channel to be used as reference. If None, average re-referencing will be used
@@ -171,7 +171,7 @@ def re_reference(data: np.ndarray, ignore_channels: [
         ----------
         data: numpy.ndarray
             data to be re-referenced. Shape: (n_channels, n_samples)
-        ignore_channels: list
+        ignore_channels: str, list
             list of channels to be ignored. Either a list of channel indexes or a string of channel indexes separated by commas. If None, no channels will be ignored
         rr_channel: int
             channel to be used as reference. If None, average re-referencing will be used
@@ -181,15 +181,14 @@ def re_reference(data: np.ndarray, ignore_channels: [
         data_rereferenced: numpy.ndarray
             re-referenced data. Shape: (n_channels, n_samples)
     """
+    ignore_channels = utils.convert_string_to_list(ignore_channels)
     if ignore_channels is not None:
-        ignore_channels = utils.convert_string_to_list(ignore_channels)
         ignore_channels = [i - 1 for i in ignore_channels]
         channels_list = [
             i for i in range(
                 data.shape[0]) if i not in ignore_channels]
     else:
         channels_list = [i for i in range(data.shape[0])]
-
     rr_channel = rr_channel - 1 if rr_channel is not None else None
     data_rereferenced = data.copy()
     if rr_channel is not None:

elecphys/utils.py

@@ -107,7 +107,7 @@ def convert_string_to_list(string):
         output: list
             converted list
     """
-    if string is None:
+    if string is None or string == '' or string == 'None':
         return None
     if not isinstance(string, str):
         string = remove_non_numeric(string)

elecphys/visualization.py

@@ -95,11 +95,10 @@ def plot_avg_stft_from_npz(npz_folder_path: str, output_plot_file: str, f_min: i
 
     npz_files = os.listdir(npz_folder_path)
     npz_files = utils.sort_file_names(npz_files)
-
+    channels_list = utils.convert_string_to_list(channels_list)
     if channels_list is None:
         channels_list = tuple(range(1, len(npz_files) + 1))
     else:
-        channels_list = utils.convert_string_to_list(channels_list)
         channels_list = sorted(channels_list)
 
     for channel_index, channel in enumerate(channels_list):
@@ -246,11 +245,10 @@ def plot_signals_from_npz(
     npz_files = os.listdir(npz_folder_path)
     # remove non-NPZ files
     npz_files = utils.sort_file_names(npz_files)
-
+    channels_list = utils.convert_string_to_list(channels_list)
     if channels_list is None:
         channels_list = tuple(range(1, len(npz_files) + 1))
     else:
-        channels_list = utils.convert_string_to_list(channels_list)
         channels_list = sorted(channels_list)
 
     if len(channels_list) > 20:
@@ -269,29 +267,12 @@ def plot_signals_from_npz(
     else:
         ax = fig.subplots(len(channels_list), 1, sharex=True)
 
-    for row_no, channel_index in enumerate(channels_list):
-        channel_index = channel_index - 1
-        npz_file = npz_files[channel_index]
-        signal_chan, fs = data_io.load_npz(
-            os.path.join(npz_folder_path, npz_file))
-        if normalize:
-            signal_chan = preprocessing.normalize(signal_chan)
-        t = np.linspace(0, len(signal_chan) / fs, len(signal_chan))
-        if t_min is None:
-            t_min = np.min(t)
-        if t_max is None:
-            t_max = np.max(t)
-
-        desired_time_index_low = np.where(
-            np.min(abs(t - t_min)) == abs(t - t_min))[0][0]
-        desired_time_index_high = np.where(
-            np.min(abs(t - t_max)) == abs(t - t_max))[0][0]
-        signal_chan = signal_chan[desired_time_index_low:desired_time_index_high]
-        t = t[desired_time_index_low:desired_time_index_high]
-        if channel_index == 0:
-            data_all = np.zeros((len(channels_list), len(signal_chan)))
-        data_all[row_no, :] = signal_chan
-
+    data_all, fs, channels_map = data_io.load_all_npz_files(npz_folder_path, channels_list=channels_list)
+    t = np.arange(0, data_all.shape[1] / fs, 1 / fs)
+    if t_min is None:
+        t_min = np.min(t)
+    if t_max is None:
+        t_max = np.max(t)
     if _rereference_args is not None:
         ignore_channels = _rereference_args['ignore_channels']
         rr_channel = _rereference_args['rr_channel']
@@ -307,7 +288,7 @@ def plot_signals_from_npz(
         data_all = preprocessing.re_reference(
             data_all, ignore_channels, rr_channel)
 
-    for row_no, channel_index in enumerate(channels_list):
+    for row_no, channel_index in enumerate(channels_map):
         signal_chan = data_all[row_no, :]
         if not scale_bar:
             ax[row_no].plot(t, signal_chan, color='k')
@@ -393,11 +374,10 @@ def plot_dft_from_npz(npz_folder_path: str, output_plot_file: str, f_min: int, f
     npz_files = os.listdir(npz_folder_path)
     npz_files = utils.keep_npz_files(npz_files)
     npz_files = utils.sort_file_names(npz_files)
-
+    channels_list = utils.convert_string_to_list(channels_list)
     if channels_list is None:
         channels_list = tuple(range(1, len(npz_files) + 1))
     else:
-        channels_list = utils.convert_string_to_list(channels_list)
         channels_list = sorted(channels_list)
 
     if len(channels_list) > 20:

setup.py

@@ -26,7 +26,7 @@ def read_description():
 
 setup(
     name="ElecPhys",
-    version="0.0.54",
+    version="0.0.55",
     author='Amin Alam',
     description='Electrophysiology data processing',
     long_description=read_description(),