Add script for bombyx ipi labelling

IPI_bombyx.py

+import ipi_extract as ipi
+import pandas as pd
+import argparse
+import numpy as np
+import os
+import matplotlib.pyplot as plt
+from functools import partial
+from matplotlib.widgets import Button
+import sys
+
+
+class BetterIter(object):
+    def __init__(self, to_wrap):
+        self.wrapped = iter(to_wrap)
+        self.max_num = len(to_wrap)
+        self.to_wrap = to_wrap
+        self.overlap = False
+
+    def __iter__(self):
+        return self
+
+    def _test_done(self ,list_pass):
+        self.overlap = len(list_pass) >= self.max_num
+
+    def __next__(self):
+        while True:
+            try:
+                val = next(self.wrapped)
+            except StopIteration:
+                self.wrapped = iter(self.to_wrap)
+                val = next(self.wrapped)
+
+            self.done_file.seek(0)
+            list_pass = [int(v) for v in self.done_file.read().split('\n') if len(v)]
+            self._test_done(list_pass)
+            if (val not in list_pass) or self.overlap:
+                break
+        self.current = val
+        return val
+
+
+def _next_file(event, refs, order, df, save, args, outpath, done_file):
+    tmp = pd.DataFrame.from_dict(refs['callback'].df, orient='index')
+    ind = order.current
+    tmp['file'] = df.iloc[ind].filepredmax
+    tmp['passage'] = df.iloc[ind].ipassage
+    tmp['nb_ind'] = df.iloc[ind].nbindiv
+    tmp['pred_max'] = df.iloc[ind].predmax
+    tmp['annotator'] = args.annotator
+    save.append(tmp)
+    df_ann = pd.concat(save)
+    df_ann.to_hdf(outpath, 'df')
+    if len(tmp):
+        done_file.write(f'{df.iloc[ind].ipassage}\n')
+        done_file.flush()
+    ind = order.__next__()
+    try:
+        ipi.reset(refs['callback'], os.path.join(args.wd, df.iloc[ind].filepredmax.strip('/')), args.channel)
+        refs['fig'].canvas.set_window_title('IPI of ' + df.iloc[ind].filepredmax.rsplit('/', 1)[-1])
+    except (RuntimeError,FileNotFoundError) as e:
+        print(e, 'Opening next file')
+        _next_file(event, refs, order, df, save, args, outpath, done_file)
+
+
+
+def main(args):
+    if args.out == '':
+        outpath = args.input.rsplit('.', 1)[0] + f'_{args.annotator}.h5'
+    else:
+        outpath = args.out
+    save = []
+    if os.path.isfile(outpath) and not args.erase:
+        save.append(pd.read_hdf(outpath))
+    df = pd.read_pickle(args.input)
+    done_file = open(args.done_file, 'a+')
+    done_file.seek(0)
+    file_list = [int(v) for v in done_file.read().split('\n') if len(v)]
+    df = df[~df.ipassage.isin(file_list)]
+    overlap = False
+    if not len(df):
+        df = pd.read_pickle(args.input)
+        overlap = True
+    if args.nb_ind != -1:
+        df = df[df.nbindiv <= args.nb_ind]
+    samples_order = BetterIter(np.random.choice(len(df), len(df), replace=False))
+    samples_order.done_file = done_file
+    samples_order.overlap = overlap
+    ind = samples_order.__next__()
+    try:
+        ref_dict = ipi.init(os.path.join(args.wd, df.iloc[ind].filepredmax.strip('/')), args.channel)
+    except(RuntimeError,FileNotFoundError) as e:
+        print(e, 'Opening next file')
+        ind = samples_order.__next__()
+        ref_dict = ipi.init(os.path.join(args.wd, df.iloc[ind].filepredmax.strip('/')), args.channel)
+    next_file = partial(_next_file, refs=ref_dict, order=samples_order, df=df, save=save, args=args, outpath=outpath,
+                        done_file=done_file)
+    next_ax = plt.subplot(ref_dict['gridspec'][-1, -2:])
+    next_button = Button(next_ax, 'Next file')
+    next_button.on_clicked(next_file)
+    plt.draw()
+    plt.pause(0.2)
+    ref_dict['fig'].set_constrained_layout(False)
+    plt.show()
+    tmp = pd.DataFrame.from_dict(ref_dict['callback'].df, orient='index')
+    ind = samples_order.current
+    tmp['file'] = df.iloc[ind].filepredmax
+    tmp['passage'] = df.iloc[ind].ipassage
+    tmp['nb_ind'] = df.iloc[ind].nbindiv
+    tmp['pred_max'] = df.iloc[ind].predmax
+    save.append(tmp)
+    df_ann = pd.concat(save)
+    df_ann['annotator'] = args.annotator
+    df_ann.to_hdf(outpath, 'df')
+    done_file.close()
+    return 0
+
+
+
+if __name__ == '__main__':
+    parser = argparse.ArgumentParser(formatter_class=argparse.ArgumentDefaultsHelpFormatter)
+    parser.add_argument("input", type=str, help="Input metadata file")
+    parser.add_argument("annotator", type=str, help="Your name")
+    parser.add_argument("--out", type=str, default='', help="Output file. Default to the input_path'.annotator.h5'")
+    parser.add_argument("--channel", type=int, default=0, help="Sound channel to be analysed. Indices start from 0.")
+    parser.add_argument("--nb_ind", type=int, default=1, help="Maximum number of individual for each track. -1 for no limit")
+    parser.add_argument("--erase", action='store_true', help="If out file exist and this option is not given,"
+                                                             " the computation will be halted")
+    parser.add_argument("--wd", type=str, default='/nfs/NASDELL/SABIOD/SITE/BOMBYX/', help='Path to root dir'
+                                                                                           ' containing Bombyx files')
+    parser.add_argument("--done_file", type=str,
+                        default='/nfs/NASDELL/SABIOD/SITE/BOMBYX/manip_2021/IPI_scripts/done_file.csv',
+                        help='Path to file listing files done')
+
+    args = parser.parse_args()
+    sys.exit(main(args))
\ No newline at end of file

ipi_extract.py

@@ -5,8 +5,7 @@ import scipy.signal as sg
 import soundfile as sf
 import os
 import sys
-from matplotlib.widgets import Button, Cursor, MultiCursor, CheckButtons, RadioButtons, AxesWidget, TextBox
-from matplotlib.patches import Circle
+from matplotlib.widgets import Button, Cursor, RadioButtons, AxesWidget
 from fractions import Fraction
 from pydub import AudioSegment
 from pydub.playback import play
@@ -422,9 +421,21 @@ class Callback(object):
         self.view_ax[ind][2].set_xlabel(f'Corr man:{dic["ipi_corr_man"]:.3f} auto:{dic["ipi_corr_auto"]:.3f}')
         self.view_ax[ind][3].set_xlabel(f'Ceps man:{dic["ipi_ceps_man"]:.3f} auto:{dic["ipi_ceps_auto"]:.3f}')
 
+    def _set_visible(self, ind=None, state=False):
+        if ind is None:
+            ind = self.curr
+        self.view_data[ind][0][1][0].set_visible(state)
+        self.view_data[ind][0][1][1].set_visible(state)
+        self.view_data[ind][1][1][0].set_visible(state)
+        self.view_data[ind][1][1][1].set_visible(state)
+        self.view_data[ind][2][1].set_visible(state)
+        self.view_data[ind][3][1].set_visible(state)
+
+
     def reset_curr(self, event):
         self.df[self.offset[self.curr_ind[self.curr], 0]] = EMLN.copy()
         self._set_label()
+        self._set_visible()
         plt.draw()
 
     def reset(self, song, sr, song_resample):
@@ -439,8 +450,11 @@ class Callback(object):
         self.scat.set_offsets(self.offset)
         self.curr_ind = 3 * [None]  # Ind of click for each plot
         self.curr_vert = 3 * [0]  # Current vertical line of sig/spec for each  plot
+        for i in range(3):
+            self.view_data[i][1][0].set_clim(2000,2100)
         for i in range(3):
             self._set_label(i, EMLN)
+            self._set_visible(i)
         plt.draw()
 
 
@@ -526,8 +540,9 @@ def init(in_path, channel, low=2e3, high=20e3):
         data_view[i][0][1][0].set_visible(False)
         data_view[i][0][1][1].set_visible(False)
 
-        data_view[i][1][0] = ax_view[i][1].specgram(np.random.normal(0, 1, int(20e-3 * sr)),
+        data_view[i][1][0] = ax_view[i][1].specgram(np.random.normal(0, 1e-6, int(20e-3 * sr)),
                                                     Fs=sr, NFFT=128, noverlap=127, cmap='jet')[-1]
+        data_view[i][1][0].set_clim(2000,2100)
         data_view[i][1][1] = (ax_view[i][1].axvline(0.01, c='k', linestyle='--'), ax_view[i][1].axvline(0.01, c='k'))
         data_view[i][1][1][0].set_visible(False)
         data_view[i][1][1][1].set_visible(False)
@@ -560,10 +575,7 @@ def init(in_path, channel, low=2e3, high=20e3):
         m_cursor[i].linev[0].set_linestyle('--')
         m_cursor[i].linev[1].set_linestyle('--')
     callback.view_data = data_view
-    plt.draw()
-    plt.pause(0.2)
-    fig.set_constrained_layout(False)
-    return {'callback': callback, 'fig': fig, 'buttons':
+    return {'callback': callback, 'fig': fig, 'gridspec': gs, 'buttons':
         {'b_left': b_left, 'b_right': b_right, 'play_b': play_b, 'resize_b': resize_b, 'r_button': r_button,
          'fs_click': cid, 'reset_b': reset_b}}  # Needed to keep the callbacks alive
 
@@ -582,6 +594,9 @@ def main(args):
         print(f'Out file {outpath} already exist and erase option isn\'t set.')
         return 1
     ref_dict = init(args.input, args.channel)
+    plt.draw()
+    plt.pause(0.2)
+    ref_dict['fig'].set_constrained_layout(False)
     plt.show()
     df = pd.DataFrame.from_dict(ref_dict['callback'].df, orient='index')
     df.to_hdf(outpath, 'df')
@@ -593,7 +608,7 @@ if __name__ == '__main__':
     class ArgumentParser(argparse.ArgumentParser):
         def error(self, message):
             if message.startswith('the following arguments are required:'):
-                raise ValueError()
+                raise ValueError(message)
             super(ArgumentParser, self).error(message)
 
     parser = ArgumentParser(formatter_class=argparse.ArgumentDefaultsHelpFormatter)