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batch_create_histograms.py
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import pandas as pd,argparse,glob,statistics as stat,matplotlib.pyplot as plt,numpy as np,operator
'''
ex:
python3 upload_code/compare_with_cue_info_chinanteco.py -i /Users/spanta/Desktop/jon_code_test/upload_code/chinanteco_aeneas/lang_code_epo -o /Users/spanta/Desktop/jon_code_test/upload_code/chinanteco_aeneas -book_find_string MRC -synced_silence -write_audition_format -print_chapter 3 -extract_verse_timing
'''
#Make sure for chinanteco line comparison the cue info first liine is taken care of
parser = argparse.ArgumentParser(
description='This function gives quality control metric between cue info and aeneas. Assumes only one book in aeneas.csv, assumes that each line in core script is translated'
'to cue info and aeneas, otherwise script fails')
required_args = parser.add_argument_group('required arguments')
required_args.add_argument(
'-i', required=True, nargs=1, type=str, help='Input dir that contains aeneas.csv *aeneas*.txt/*adjusted.txt and *cue_info*.txt')
required_args.add_argument(
'-o', required=True, nargs=1, type=str, help='Output dir')
required_args.add_argument(
'-book_find_string', required=True, nargs=1, type=str, help='EX: MRK to get MRK1,ESV_MRK_01 etc.')
required_args.add_argument(
'-sab_timings_find_string', required=True, nargs=1, type=str, help='EX: MRK to get MRK1,ESV_MRK_01 etc.')
optional_args=parser.add_argument_group('optional arguments')
optional_args.add_argument('-strict_comparison', type=int,choices=[1,2], help='1-Compare aeneas and qinfo start boundaries. 2- Compare verse duration and 1')
optional_args.add_argument('-extract_verse_timing', action='store_true', help='Compare verse timing info.')
optional_args.add_argument('-synced_silence', action='store_true', help='Indicate whether the output from aeneas timing was fully synced with silence adjustment')
optional_args.add_argument('-synced_qinfo', action='store_true', help='Indicate whether the output from aeneas timing was fully synced with qinfo')
optional_args.add_argument('-print_chapter', nargs=1, type=str,default=['9'],help='Print chapter')
optional_args.add_argument('-write_audition_format', action='store_true', help='Write output to audition tab csv format')
optional_args.add_argument('-check_secs', nargs=1, type=str,default=['1'],help='Mark if above check secs')
args = parser.parse_args()
input_dir=args.i[0]
output_dir=args.o[0]
book_find_string=args.book_find_string[0]
if args.strict_comparison is not None: strict_comparison=args.strict_comparison
else:strict_comparison=1
print_chapter=args.print_chapter[0]
sab_find_string=args.sab_timings_find_string[0]
print(args)
input_file='aeneas.csv'
df=(pd.read_csv(input_dir+'/'+input_file, encoding='utf-8')).astype(str)
#Get unique book and chapters
book_list=df['book'].unique()
chapter_list=df['chapter'].unique()
target='line_number'
if args.synced_silence: aeneas_adjusted_file='*_sync_adjusted.txt'
elif args.synced_qinfo:aeneas_adjusted_file='*_qinfo_adjusted.txt'
else:aeneas_adjusted_file='*_adjusted.txt'
#get column indexes
target_index=df.columns.get_loc(target)
qc_data=dict()
median_dict=dict()
std_dev_dict=dict()
for each_chapter in chapter_list:
#target_list=df[target][df['chapter'] == str(each_chapter)]
target_list=df[target][(df['chapter'] == str(each_chapter))]
dummy_target_list=df[target][(df['verse_number'] != str(0)) & (df['chapter'] == str(each_chapter))]
uniq_target=dummy_target_list.unique()
if each_chapter==str(1): print('target_list', target_list,'uniq',uniq_target)
if float(each_chapter)<10:
#Get cue info file
cue_info_chapter_file=glob.glob(input_dir+'/*'+sab_find_string+'-'+'0'+str(each_chapter)+'*timing.txt')[0]
print(cue_info_chapter_file)
#Get aeneas silence adjusted file
#aeneas_chapter_file=glob.glob(input_dir+'/*'+'0'+str(each_chapter)+'_'+book_find_string+'*'+aeneas_adjusted_file)[0]
aeneas_chapter_file = glob.glob(input_dir + '/*' + book_find_string + '_'+'0' + str(each_chapter)+'*' + aeneas_adjusted_file)[0]
else:
#Get cue info file
cue_info_chapter_file=glob.glob(input_dir+'/*'+sab_find_string+'-'+str(each_chapter)+'*timing.txt')[0]
print(cue_info_chapter_file)
#Get aeneas silence adjusted file
#aeneas_chapter_file=glob.glob(input_dir+'/*'+str(each_chapter)+'_'+book_find_string+'*'+aeneas_adjusted_file)[0]
aeneas_chapter_file = glob.glob(input_dir + '/*' + book_find_string + '_'+ str(each_chapter)+'*' + aeneas_adjusted_file)[0]
if args.write_audition_format:
audition_file_name = (aeneas_chapter_file.split('/')[-1]).split('_sync_adjusted.txt')[0] + target.split('_')[0]+'_audition_markers.csv'
#print(aeneas_chapter_file.split('/')[-1],(aeneas_chapter_file.split('/')[-1]).split('_sync_adjusted.txt')[0],audition_file_name)
audition_file = input_dir + '/' + audition_file_name
#Read cue info and aeneas for iteration in the foll. for loop
aeneas_target = open(aeneas_chapter_file).readlines()
cue_target=open(cue_info_chapter_file,'r',encoding='utf-8').readlines()
ind=0
difference_list=list()
with open(audition_file,'w') as aud:
# Since we cant read cue info last verse, we will remove the last element from uniq_target
# uniq_target=uniq_target[:-1]
for each_target in uniq_target:
ind+=1
#print(ind)
if ind<=len(open(cue_info_chapter_file).readlines( )):
cue_times=((cue_target[ind-1]).strip('\n')).split('\t')
cue_duration=float(cue_times[1])-float(cue_times[0])
cue_start=float(cue_times[0])
indices=[i for i,val in enumerate(target_list) if val==each_target]
if each_chapter==str(1):print('indices',indices)
#print(each_target)
#print(indices)
aeneas_duration = 0
counter=0
aud_duration=0
aud_text=''
# print(((aeneas_target[0]).strip('\n')).split('\t'))
# print(((aeneas_target[1]).strip('\n')).split('\t'))
# print(((aeneas_target[58]).strip('\n')).split('\t'))
for each_index in indices:
#print(each_index)
aeneas_times = ((aeneas_target[each_index]).strip('\n')).split('\t')
#print('aen_times',aeneas_times)
aeneas_duration = float(aeneas_times[1]) - float(aeneas_times[0])
#print('aen_dur',aeneas_duration)
aud_duration=aeneas_duration
aud_text+=aeneas_times[-1][1:]
if counter==0:
aeneas_start=float(((aeneas_target[each_index]).strip('\n')).split('\t')[0])
aud_start=aeneas_start
counter+=1
# print(aeneas_times,aeneas_duration,cue_duration)
# print(each_chapter,each_target, each_index,cue_times, aeneas_times)
#if int(each_chapter) == 16:print(cue_duration,aeneas_duration)
difference = (round(abs(cue_duration - aeneas_duration), 1))
#print(difference)
# if each_chapter==print_chapter:
#print('AUD->', each_chapter, each_target, each_index, aud_start, aud_duration, aeneas_times[2],aud_text)
if strict_comparison==1:
difference=(round(abs(cue_start - aeneas_start), 1))
#print(each_chapter)
if each_chapter==str(1): print(each_target, cue_start, aeneas_start,difference)
elif strict_comparison==2:difference=(round(abs(cue_start - aeneas_start), 1))+(round(abs(cue_duration - aeneas_duration), 1))
# print(difference)
difference_list.append(difference)
if difference>=1:print('aeneas_chapter_file',aeneas_chapter_file,'chapter',each_chapter,'each_target',each_target,'diff',difference,'aen',aeneas_times,aeneas_duration,'time',cue_times,cue_duration)
# if each_chapter==print_chapter: print(cue_start,aeneas_start)
if difference > float(args.check_secs[0]):
marker_name = 'A1_Check Marker '
else:
marker_name = 'A1_Marker '
if ind==1:
# Write to adobe audition file
aud.write(
'Name' + '\t' + 'Start' + '\t' + 'Duration' + '\t' + 'Time Format' + '\t' + 'Type' + '\t' + 'Description' + '\n')
aud.write(marker_name + '0'+str(each_target) + '\t' + '0:' + str(round(aud_start, 3)) + '\t' + '0:' + str(
round(aud_duration, 3)) + '\t' + 'decimal' + '\t' + 'Cue' + '\t' +aud_text+'\n')
# print('aud text->',aud_text)
else:
if int( str(each_target ).split('-')[0] )<10:marker_number='0'+str(each_target)
else:marker_number=str(each_target)
aud.write(marker_name + marker_number + '\t' + '0:' + str(round(aud_start, 3)) + '\t' + '0:' + str(
round(aud_duration, 3)) + '\t' + 'decimal' + '\t' + 'Cue' + '\t' +aud_text+'\n')
# print('aud text->', aud_text)
target1='verse_number'
#target1_list = df[target1][df['chapter'] == str(each_chapter)]
# target1_list = df[target][(df['verse_number'] != str(0)) & (df['chapter'] == str(each_chapter))]
# uniq1_target = target1_list.unique()
target1_list=df[target1][(df['chapter'] == str(each_chapter))]
dummy_target1_list=df[target1][(df['verse_number'] != str(0)) & (df['chapter'] == str(each_chapter))]
uniq1_target=dummy_target1_list.unique()
if args.write_audition_format:
audition_file_name = (aeneas_chapter_file.split('/')[-1]).split('_sync_adjusted.txt')[0] + target1.split('_')[0]+'_audition_markers.csv'
#print(aeneas_chapter_file.split('/')[-1],(aeneas_chapter_file.split('/')[-1]).split('_sync_adjusted.txt')[0],audition_file_name)
audition_file = input_dir + '/' + audition_file_name
#Read cue info and aeneas for iteration in the foll. for loop
aeneas_target = open(aeneas_chapter_file).readlines()
ind=0
with open(audition_file,'w') as aud:
# Since we cant read cue info last verse, we will remove the last element from uniq_target
# uniq_target=uniq_target[:-1]
for each_target in uniq1_target:
ind+=1
indices=[i for i,val in enumerate(target1_list) if val==each_target]
aeneas_duration = 0
counter=0
aud_duration=0
aud_text=''
for each_index in indices:
aeneas_times = ((aeneas_target[each_index]).strip('\n')).split('\t')
aeneas_duration += float(aeneas_times[1]) - float(aeneas_times[0])
aud_duration=aeneas_duration
aud_text+=aeneas_times[-1][1:]
if counter==0:
aeneas_start=float(((aeneas_target[each_index]).strip('\n')).split('\t')[0])
aud_start=aeneas_start
counter+=1
marker_name = 'A1_Marker '
if ind==1:
# Write to adobe audition file
#print(marker_name + str(each_target) + '\t' + '0:' + str(round(aud_start, 3)) + '\t' + '0:' + str(round(aud_duration, 3)) + '\t' + 'decimal' + '\t' + 'Cue' + '\t' +aud_text+'\n')
aud.write(
'Name' + '\t' + 'Start' + '\t' + 'Duration' + '\t' + 'Time Format' + '\t' + 'Type' + '\t' + 'Description' + '\n')
aud.write(marker_name + '0'+str(each_target) + '\t' + '0:' + str(round(aud_start, 3)) + '\t' + '0:' + str(
round(aud_duration, 3)) + '\t' + 'decimal' + '\t' + 'Cue' + '\t' +aud_text+'\n')
# print('aud text->',aud_text)
else:
if int( str(each_target).split('-')[0] ) < 10:
marker_number = '0' + str(each_target)
else:
marker_number = str(each_target)
aud_text=aud_text[1:]
#print(aud_text)
#print(marker_name + str(each_target) + '\t' + '0:' + str(round(aud_start, 3)) + '\t' + '0:' + str(round(aud_duration, 3)) + '\t' + 'decimal' + '\t' + 'Cue' + '\t' +aud_text+'\n')
aud.write(marker_name + marker_number + '\t' + '0:' + str(round(aud_start, 3)) + '\t' + '0:' + str(
round(aud_duration, 3)) + '\t' + 'decimal' + '\t' + 'Cue' + '\t' +aud_text+'\n')
# print('aud text->', aud_text)
qc_data[each_chapter]=difference_list
if each_chapter==20 : print('chapter',each_chapter,'diff',difference_list)
median_dict[each_chapter]=np.median(difference_list)
std_dev_dict[each_chapter]=np.std(difference_list)
target1='verse_number'
#target1_list = df[target1][df['chapter'] == str(each_chapter)]
# target1_list = df[target][(df['verse_number'] != str(0)) & (df['chapter'] == str(each_chapter))]
# #print('target1_list',type(target1_list))
# uniq1_target = target1_list.unique()
target1_list=df[target1][(df['chapter'] == str(each_chapter))]
dummy_target1_list=df[target1][(df['verse_number'] != str(0)) & (df['chapter'] == str(each_chapter))]
uniq1_target=dummy_target1_list.unique()
#print('uniq1_target',type(uniq1_target))
target2='verse_number'
#target2_list = df[target2][df['chapter'] == str(each_chapter)]
# target2_list = df[target][(df['verse_number'] != str(0)) & (df['chapter'] == str(each_chapter))]
# uniq2_target = target2_list.unique()
target2_list=df[target2][(df['chapter'] == str(each_chapter))]
dummy_target2_list=df[target2][(df['verse_number'] != str(0)) & (df['chapter'] == str(each_chapter))]
uniq2_target=dummy_target2_list.unique()
line_cue_target = open(cue_info_chapter_file).readlines()
# if each_chapter==print_chapter:
# print(uniq1_target,uniq2_target)
if args.write_audition_format:
audition_file_name = (aeneas_chapter_file.split('/')[-1]).split('_sync_adjusted.txt')[0] + '_'+target1.split('_')[0]+'_curated_audition_markers.csv'
#print(aeneas_chapter_file.split('/')[-1],(aeneas_chapter_file.split('/')[-1]).split('_sync_adjusted.txt')[0],audition_file_name)
audition_file = input_dir + '/' + audition_file_name
silence_file=glob.glob(input_dir+'/'+(aeneas_chapter_file.split('/')[-1]).split('_sync_adjusted.txt')[0]+'*silence*')[0]
#Read cue info and aeneas for iteration in the foll. for loop
aeneas_target = open(aeneas_chapter_file).readlines()
ind=0
with open(audition_file,'w') as aud:
# Since we cant read cue info last verse, we will remove the last element from uniq_target
# uniq_target=uniq_target[:-1]
for each_target in uniq1_target:
ind+=1
indices=[i for i,val in enumerate(target1_list) if val==each_target]
#Find the next verse index
for k,kval in enumerate(target1_list):
if int( str(kval).split('-')[0] )==(int( str(each_target).split('-')[0] )+1):
next_verse_index=k
break
# Find the previous verse index
for k, kval in enumerate(target1_list):
if int( str(kval).split('-')[0] ) == (int( str(each_target).split('-')[0] ) - 1):
previous_verse_index = k
break
# if each_chapter==print_chapter:
# print(int(each_target)+1,next_verse_index)
aeneas_duration = 0
counter=0
aud_duration=0
aud_text=''
for g,each_index in enumerate(indices):
aeneas_times = ((aeneas_target[each_index]).strip('\n')).split('\t')
aeneas_duration += float(aeneas_times[1]) - float(aeneas_times[0])
aud_duration=aeneas_duration
aud_text=aud_text+' '+aeneas_times[-1][1:]
if counter==0:
aeneas_start=float(((aeneas_target[each_index]).strip('\n')).split('\t')[0])
# aeneas_start_next=float(((aeneas_target[each_index+1]).strip('\n')).split('\t')[0])
aud_start=aeneas_start
if ind>1 and (float( str(target2_list.iloc[each_index]).split('-')[0] )-float( str(target2_list.iloc[each_index-1]).split('-')[0] ))==1 :
# if each_chapter==print_chapter:
# print(each_target,target2_list.iloc[each_index])
#print(len(uniq2_target))
#Get adjustboundary1
for i,each_line in enumerate(uniq2_target):
if each_line==target2_list.iloc[each_index]:
# if each_chapter==print_chapter:
# print("chapter-{0},verse_num-{1},verse index-{2},line_num-{3}".format(each_chapter,each_target,each_index, float(target2_list.iloc[each_index])))
#print('i',i,'each_chapter',each_chapter)
adjust_boundary1=float( ((line_cue_target[i-1]).split('\t')[0] ) )
# if each_chapter==print_chapter:
# print(each_target, each_line,adjust_boundary1)
break
if each_chapter==print_chapter:
aeneas_start_next = float(
((aeneas_target[next_verse_index]).strip('\n')).split('\t')[0])
#Read silence file
silence_split_field=','
with open(silence_file,'r') as s:
for silence_bounds in s:
silence_start=float(silence_bounds.split(silence_split_field)[0])
silence_end=float(silence_bounds.split(silence_split_field)[1])
#if boundary falls inside silence, move it to silence region mid point
if ind<len(aeneas_target):
aeneas_start_next = float(
((aeneas_target[next_verse_index]).strip('\n')).split('\t')[0])
aeneas_start_previous=float(
((aeneas_target[previous_verse_index]).strip('\n')).split('\t')[0])
# if each_chapter==print_chapter and int(each_target)==14:
# print(each_target, aeneas_start, int(each_target) + 1, aeneas_start_next)
# if each_chapter==print_chapter:
# print('adjust_boundary1->{0},next_verse_start_time->{1},each_target_verse->{2}'.format(adjust_boundary1,aeneas_start_next,each_target))
if silence_end - silence_start >= 0.4 and silence_start <= adjust_boundary1 <= silence_end and aeneas_start_previous<adjust_boundary1 < aeneas_start_next :
#if each_chapter == print_chapter:
#print("chapter-{0},verse_num-{1},verse index-{2},line_num-{3}".format(
#each_chapter, each_target, each_index,
#float(target2_list.iloc[each_index])))
#print('hey its chapt 3', each_target, adjust_boundary1, aeneas_start_next)
adjust_boundary1 = (silence_start + silence_end) / 2
aud_start = adjust_boundary1
delta = aud_start - adjust_boundary1
#print('previous_verse_index',delta,'chapter',each_chapter)
# aud_duration=aud_duration-delta
break
else:
if silence_end - silence_start >= 0.4 and silence_start <= adjust_boundary1 <= silence_end:
#if each_chapter == print_chapter:
#print("chapter-{0},verse_num-{1},verse index-{2},line_num-{3}".format(
#each_chapter, each_target, each_index,
#float(target2_list.iloc[each_index])))
#print('hey its chapt 3', each_target, adjust_boundary1, aeneas_start_next)
adjust_boundary1 = (silence_start + silence_end) / 2
aud_start = adjust_boundary1
delta = aud_start - adjust_boundary1
#print('previous_verse_index', delta, 'chapter', each_chapter)
# aud_duration=aud_duration-delta
break
s.close()
counter += 1
marker_name = 'A1_Marker '
if ind==1:
# Write to adobe audition file
aud.write(
'Name' + '\t' + 'Start' + '\t' + 'Duration' + '\t' + 'Time Format' + '\t' + 'Type' + '\t' + 'Description' + '\n')
aud.write(marker_name + '0'+str(each_target) + '\t' + '0:' + str(round(aud_start, 3)) + '\t' + '0:' + str(
round(aud_duration, 3)) + '\t' + 'decimal' + '\t' + 'Cue' + '\t' +aud_text+'\n')
else:
if int( str(each_target).split('-')[0] ) < 10:
marker_number = '0' + str(each_target)
else:
marker_number = str(each_target)
# print(aud_start)
aud.write(marker_name + marker_number + '\t' + '0:' + str(round(aud_start, 3)) + '\t' + '0:' + str(
round(aud_duration, 3)) + '\t' + 'decimal' + '\t' + 'Cue' + '\t' +aud_text+'\n')
#Makers have been adjusted , now adjust durations to match the markers
#Load audition verse file to update duration
#print(audition_file)
aud_df=pd.read_csv(audition_file, encoding='utf-8',sep='\t')
verses=open(audition_file).readlines()
conv_string_to_secs = [60, 1]
for i,each_verse in enumerate(verses):
if 0<i<len(verses)-1:
verse_num=(each_verse.split('\t')[0])
timestr=(each_verse.split('\t')[1])
current_verse_start_time=sum([a * b for a, b in zip(conv_string_to_secs, map(float, timestr.split(':')))])
timestr = (each_verse.split('\t')[2])
current_verse_duration=sum([a * b for a, b in zip(conv_string_to_secs, map(float, timestr.split(':')))])
current_verse_end_time=current_verse_start_time+current_verse_duration
#Get next verse begin time
next_verse=verses[i+1]
timestr = (next_verse.split('\t')[1])
next_verse_start_time = sum([a * b for a, b in zip(conv_string_to_secs, map(float, timestr.split(':')))])
# if each_chapter==print_chapter:
# print(each_chapter, verse_num, current_verse_start_time, current_verse_end_time, next_verse_start_time)
delta = next_verse_start_time - current_verse_end_time
# if each_chapter==print_chapter:
# print(each_verse,current_verse_end_time,next_verse_start_time)
if next_verse_start_time!=current_verse_end_time:
if delta>60: print(each_chapter,verse_num,delta,current_verse_start_time,current_verse_end_time,next_verse_start_time,"CHECK delta is >60")
new_current_verse_duration=current_verse_duration+delta
new_current_verse_duration=round(new_current_verse_duration,3)
if new_current_verse_duration<10:
new_current_verse_duration='0:0'+str(new_current_verse_duration)
else:
new_current_verse_duration = '0:' + str(new_current_verse_duration)
aud_df['Duration'][i-1]=new_current_verse_duration
if float( (aud_df['Duration'][i]).split(':')[1] )<0:
print(each_chapter,delta,current_verse_duration,aud_df['Duration'][i-1])
#print(aud_df['Duration'][i])
#if each_chapter==print_chapter:
#print(aud_df['Duration'])
aud_df.to_csv(audition_file,encoding='utf-8',sep='\t',index=False)
sorted_median = sorted(median_dict, key=median_dict.get, reverse=True)
n=round(len(chapter_list)/4)
print(n)
i=0
for c in range(1,len(chapter_list)+1):
i+=1
plt.subplot(n,n,c)
g=sorted_median[i-1]
plt.text(0.5, 0.5, 'chap '+str(g)+' ,med=' + str(round(median_dict[g],2)) + ' ,std=' + str(round(std_dev_dict[g],2)),
fontsize=10, ha='left')
plt.hist(qc_data[g])
# plt.show(block=True)
# plt.interactive(False)
plt.show()