I have two dataframes of different length. dfSamples (63012375 rows) and dfFixations (200000 rows).
dfSamples = pd.DataFrame({'tSample':[4, 6, 8, 10, 12, 14]})
dfFixations = pd.DataFrame({'tStart':[4,12],'tEnd':[8,14]})
I would like to check each value in dfSamples if it is within any two ranges given in dfFixations and then assign a label to this value. I have found this: Check if value in a dataframe is between two values in another dataframe, but the loop solution is terribly slow and I cannot make any other solution work.
Working (but very slow) example:
labels = np.empty_like(dfSamples['tSample']).astype(np.chararray)
for i, fixation in dfFix.iterrows():
log_range = dfSamples['tSample'].between(fixation['tStart'], fixation['tEnd'])
labels[log_range] = 'fixation'
labels[labels != 'fixation'] = 'no_fixation'
dfSamples['labels'] = labels
Following this example: Performance of Pandas apply vs np.vectorize to create new column from existing columns I have tried to vectorize this but with no success.
def check_range(samples, tstart, tend):
log_range = (samples > tstart) & (samples < tend)
return log_range
fixations = list(map(check_range, dfSamples['tSample'], dfFix['tStart'], dfFix['tEnd']))
Would appreciate any help!
CodePudding user response:
Use IntervalIndex.from_arrays
with IntervalIndex.get_indexer
, if not match is returned -1
, so checked and set ouput in numpy.where
:
i = pd.IntervalIndex.from_arrays(dfFixations['tStart'],
dfFixations['tEnd'],
closed="both")
pos = i.get_indexer(dfSamples['tSample'])
dfSamples['labels'] = np.where(pos != -1, "fixation", "no_fixation")
print (dfSamples)
tSample labels
0 4 fixation
1 6 fixation
2 8 fixation
3 10 no_fixation
4 12 fixation
5 14 fixation
Performance: In ideal nice sorted not overlap data, in real should be performance different, the best test it.
dfSamples = pd.DataFrame({'tSample':range(10000)})
dfFixations = pd.DataFrame({'tStart':range(0, 10000, 5),'tEnd':range(2, 10000, 5)})
In [165]: %%timeit
...: labels = np.empty_like(dfSamples['tSample']).astype(np.chararray)
...: for i, fixation in dfFixations.iterrows():
...: log_range = dfSamples['tSample'].between(fixation['tStart'], fixation['tEnd'])
...: labels[log_range] = 'fixation'
...: labels[labels != 'fixation'] = 'no_fixation'
...: dfSamples['labels'] = labels
...:
...:
1.25 s ± 52.7 ms per loop (mean ± std. dev. of 7 runs, 1 loop each)
In [168]: %%timeit
...: ii = pd.IntervalIndex.from_arrays(dfFixations['tStart'], dfFixations['tEnd'], closed="both")
...: dfSamples["labels1"] = np.where(dfSamples["tSample"].apply(ii.contains).apply(any), "fixation", "no_fixation")
...:
315 ms ± 18.2 ms per loop (mean ± std. dev. of 7 runs, 1 loop each)
In [170]: %%timeit
...: ii = pd.IntervalIndex.from_arrays(dfFixations['tStart'], dfFixations['tEnd'], closed="both")
...: contained = np.logical_or.reduce(piso.contains(ii, dfSamples["tSample"], include_index=False), axis=0)
...: dfSamples["labels1"] = np.where(contained, "fixation", "no_fixation")
...:
82.4 ms ± 213 µs per loop (mean ± std. dev. of 7 runs, 10 loops each)
In [166]: %%timeit
...: s = pd.IntervalIndex.from_arrays(dfFixations['tStart'], dfFixations['tEnd'], closed="both")
...: pos = s.get_indexer(dfSamples['tSample'])
...: dfSamples['labels'] = np.where(pos != -1, "fixation", "no_fixation")
...:
27.8 ms ± 1.51 ms per loop (mean ± std. dev. of 7 runs, 10 loops each)
CodePudding user response:
setup
dfSamples = pd.DataFrame({'tSample':[4, 6, 8, 10, 12, 14]})
dfFixations = pd.DataFrame({'tStart':[4,12],'tEnd':[8,14]})
solution
Create an interval index from your start and end points
ii = pd.IntervalIndex.from_arrays(dfFixations['tStart'], dfFixations['tEnd'], closed="both")
ii.contains
is a method which checks if a point is contained by each interval in the interval index, eg
dfSamples["tSample"].apply(ii.contains)
gives
0 [True, False]
1 [True, False]
2 [True, False]
3 [False, False]
4 [False, True]
5 [False, True]
Name: tSample, dtype: object
We're going to take this result, apply any
function to each element (a list) to get a pandas.Series
of booleans, which we can then use with numpy.where
dfSamples["labels"] = np.where(dfSamples["tSample"].apply(ii.contains).apply(any), "fixation", "no_fixation")
the result
tSample labels
0 4 fixation
1 6 fixation
2 8 no_fixation
3 10 no_fixation
4 12 fixation
5 14 no_fixation
edit: faster version
Using piso
v0.6.0
import piso
import numpy as np
ii = pd.IntervalIndex.from_arrays(dfFixations['tStart'], dfFixations['tEnd'], closed="both")
contained = np.logical_or.reduce(piso.contains(ii, dfSamples["tSample"], include_index=False), axis=0)
dfSamples["labels"] = np.where(contained, "fixation", "no_fixation")
This will run in a similar time to @jezrael's solution, however it can handle cases where intervals overlaps eg
dfFixations = pd.DataFrame({'tStart':[4,5,12],'tEnd':[8,9,14]})