set half precision for numpy arrays #87
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arnikz
requested changes
Jan 15, 2021
| @@ -74,7 +75,7 @@ def get_windows(carrays_dir, outDir, chrom_list, win, label_file_path, mode, npz | |||
| n_r = 10 ** 5 | |||
| last_t = time() | |||
| i = 1 | |||
| padding = np.zeros(shape=(padding_len, n_channels), dtype=np.float32) | |||
| padding = np.zeros(shape=(padding_len, n_channels), dtype=np.half) | |||
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Is this precision sufficient? I would keep the former.
>>> np.finfo(np.float32).precision
6
>>> np.finfo(np.half).precision
3
``
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From the result on the test data it seems to be sufficient, but I need to try it on the real data.
| @@ -32,7 +32,7 @@ def get_snv_number(query_seq_list, reference_base): | |||
| stop_pos = chrLen | |||
| reference_sequence = twobit.TwoBitFile(itwobit) | |||
| snv_list = ['BQ', 'SNV', 'MAPQ'] | |||
| snv_array = np.zeros(shape=(stop_pos, len(snv_list)), dtype=np.float32) | |||
| snv_array = np.zeros(shape=(stop_pos, len(snv_list)), dtype=np.half) | |||
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Btw aren't all channel values counts only?
|
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It reduces the file size for numpy arrays by setting half precision.