def prepare_data(bags, arena, smoothstr, smooth, medfilt, gts,
min_experiment_duration):
RESAMPLE_SPEC = '10L'
found_gts = []
pooldf = DataFrame()
for bag in bags:
df = madplot.load_bagfile_single_dataframe(bag,
arena,
ffill=True,
smooth=smooth)
df = flymad_analysis.resample(df, resample_specifier=RESAMPLE_SPEC)
metadata = filename_regexes.parse_filename(
bag, extract_genotype_and_laser=True)
dateobj = filename_regexes.parse_date(bag)
genotype = metadata['genotype'] + '-' + metadata['laser']
found_gts.append(genotype)
if genotype not in gts:
print "\tskipping genotype", genotype
continue
duration = (df.index[-1] - df.index[0]).total_seconds()
if duration < min_experiment_duration:
print "\tmissing data", bag
continue
print "\t%ss experiment" % duration
#MAXIMUM SPEED = 300:
#df['v'][df['v'] >= 300] = np.nan
#df['v'] = df['v'].fillna(method='ffill')
try:
df = flymad_analysis.align_t_by_laser_on(
df,
min_experiment_duration=min_experiment_duration,
align_first_only=True,
exact_num_ranges=1,
resample_bin=RESAMPLE_SPEC)
except flymad_analysis.AlignError, err:
print "\talign error %s (%s)" % (bag, err)
pass
#median filter
if medfilt:
df['v'] = scipy.signal.medfilt(df['v'].values, medfilt)
df['obj_id'] = calendar.timegm(dateobj)
df['Genotype'] = genotype
pooldf = pd.concat([pooldf, df])
def prepare_data(bags, arena, smoothstr, smooth, medfilt, gts, min_experiment_duration):
RESAMPLE_SPEC = '10L'
found_gts = []
pooldf = DataFrame()
for bag in bags:
df = madplot.load_bagfile_single_dataframe(bag, arena,
ffill=True,
smooth=smooth)
df = flymad_analysis.resample(df, resample_specifier=RESAMPLE_SPEC)
metadata = filename_regexes.parse_filename(bag, extract_genotype_and_laser=True)
dateobj = filename_regexes.parse_date(bag)
genotype = metadata['genotype'] + '-' + metadata['laser']
found_gts.append(genotype)
if genotype not in gts:
print "\tskipping genotype", genotype
continue
duration = (df.index[-1] - df.index[0]).total_seconds()
if duration < min_experiment_duration:
print "\tmissing data", bag
continue
print "\t%ss experiment" % duration
#MAXIMUM SPEED = 300:
#df['v'][df['v'] >= 300] = np.nan
#df['v'] = df['v'].fillna(method='ffill')
try:
df = flymad_analysis.align_t_by_laser_on(
df, min_experiment_duration=min_experiment_duration,
align_first_only=True,
exact_num_ranges=1,
resample_bin=RESAMPLE_SPEC)
except flymad_analysis.AlignError, err:
print "\talign error %s (%s)" % (bag, err)
pass
#median filter
if medfilt:
df['v'] = scipy.signal.medfilt(df['v'].values, medfilt)
df['obj_id'] = calendar.timegm(dateobj)
df['Genotype'] = genotype
pooldf = pd.concat([pooldf, df])
print 'will overwrite output file',out_fname
real_input_mp4s.append( mp4 )
inputmp4s = real_input_mp4s
print 'will score %d mp4 movies'%(len(inputmp4s),)
for mp4 in inputmp4s:
fname = mp4
base_fname = os.path.basename(fname)
out_fname = os.path.join(args.outdir, base_fname+'.csv')
if args.no_merge_bags:
bname = None
else:
try:
mp4time = filename_regexes.parse_date(mp4)
except filename_regexes.RegexError, e:
print "error: incorrectly named mp4 file?", mp4
continue
bname = None
if inputbags:
best_diff = np.inf
for bag in inputbags:
try:
bagtime = filename_regexes.parse_date(bag)
except filename_regexes.RegexError, e:
print "error: incorrectly named bag file?", bag
continue
this_diff = abs(time.mktime(bagtime)-time.mktime(mp4time))
if this_diff < best_diff:
print 'will overwrite output file', out_fname
real_input_mp4s.append(mp4)
inputmp4s = real_input_mp4s
print 'will score %d mp4 movies' % (len(inputmp4s), )
for mp4 in inputmp4s:
fname = mp4
base_fname = os.path.basename(fname)
out_fname = os.path.join(args.outdir, base_fname + '.csv')
if args.no_merge_bags:
bname = None
else:
try:
mp4time = filename_regexes.parse_date(mp4)
except filename_regexes.RegexError, e:
print "error: incorrectly named mp4 file?", mp4
continue
bname = None
if inputbags:
best_diff = np.inf
for bag in inputbags:
try:
bagtime = filename_regexes.parse_date(bag)
except filename_regexes.RegexError, e:
print "error: incorrectly named bag file?", bag
continue
this_diff = abs(
time.mktime(bagtime) - time.mktime(mp4time))
