Pandas tools you didn’t know you needed, part 2: Groupby

Very often, you need to do something to groups of rows of a dataframe that match some condition, for instance a certain mouse or brain region. The most intuitive solution is to use a for loop.

For instance, let's start with this dataframe:

	experiment	brain_region	neuron	Mean ISI
0	bucket_1_m026_1568757659_	pfc	0	3.08281
1	bucket_1_m026_1568757659_	pfc	1	8.37044
2	bucket_1_m026_1568757659_	pfc	2	38.5265
3	bucket_1_m026_1568757659_	pfc	3	31.795
4	bucket_1_m026_1568757659_	pfc	4	3.43186

We can loop over experiments, brain regions, and neuron like so:

log_mean_isi = []
for neuron in df['neuron'].unique():
    for brain_region in df['brain_region'].unique():
        for experiment in df['experiment'].unique():
            sub_df=df[
                (df['experiment']==experiment) & 
                (df['brain_region']==brain_region) & 
                (df['neuron']==neuron) 
            ]
            log_mean_isi.append(np.log(sub_df['Mean ISI']).values)
print(np.hstack(log_mean_isi))

[ 1.12584188  2.19215951 -1.98074317 -0.25722232  2.1247061   0.0063244 0.92415014 -1.93038317  3.6513468   2.28266164  1.39365976 -3.23681353  3.459308    1.48402753 -0.65003803  1.4140086   1.23310109 -0.8740564  1.29957486 -0.60594385 -0.61921541  4.51176028  0.5622578   3.48668087 -1.57394565 -1.15482997  3.62078013 -0.64878302 -2.08398518  0.28354575 -0.92326873 -2.23523802 -1.15944804 -1.16315081  1.29454247 -0.89566237  0.72300259 -1.38527266  1.3694298   2.95919545  3.07555102 -1.38317331  2.3510588  -1.68488011  2.15864159  2.92067342  0.20249933  1.76685816 -1.14606501 -2.54545905  2.17651238  2.49333615 -1.08762839 -1.10690211  1.79675315  1.08438564 -1.61687289  3.64009558  2.50376142  3.53577889 -2.31447026 -0.9560716  ...]

However, nested for loops are evil for many reasons. Let's use the groupby command:

log_mean_isi=[]
for index, sub_df in df.groupby(['neuron', 'brain_region', 'experiment']):
    log_mean_isi.append(np.log(sub_df['Mean ISI']).values)
print(np.hstack(log_mean_isi))

or even in one line:

mean_isi_list=[np.log(sub_df['Mean ISI']).values for index, sub_df in df.groupby(['neuron', 'brain_region', 'experiment'])]
print(np.hstack(mean_isi_list))

Much more readable and efficient! Furthermore, the index part can be used for reconstructing the modified dataframe. I might make a post on that in the future.

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Pandas tools you didn’t know you needed, part 2: Groupby

Max Myroshnychenko

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