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main_ms_numpress_test.py
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import unittest
import struct
import math
try:
import numpy as np
except:
np = None
from pymzml.ms_numpress import MSNumpress
@unittest.skipIf(np is None, "Numpy is required for this test.")
class test_MSNumpress(unittest.TestCase):
"""
unittest for MSNumpress en- and decoding
"""
def setUp(self):
""" """
self.mz_data = np.asarray([100.1, 100.01, 100.001, 100.0001], dtype=np.float64)
self.i_data = [5e6, 6.5e5, 2e6, 12e6]
self.i_slof_data = [1, 2, 4]
self.integer = 23
# self._encoded_int = bytes([ 0x06, 0x07, 0x01 ])
self.Decoder = MSNumpress()
self.fixed_point = 10000
def test_enc_int_leading_zeros(self):
encoded_integer = self.Decoder._encodeInt(1)
self.assertEqual(encoded_integer[0], 0x07)
encoded_integer = self.Decoder._encodeInt(16)
self.assertEqual(encoded_integer[0], 0x06)
def test_enc_int_leading_ones(self):
bytearray(b"\x08\x0f\x0f\x0f\x0f\x0f\x0f\x0f\x07")
encoded_integer = self.Decoder._encodeInt((2**31) - 1)
self.assertEqual(encoded_integer[0], 0x08)
self.assertEqual(encoded_integer[1], 0x0F)
def test_encodeInt_negative(self):
""" """
negative_integer = -1
encoded_integer = self.Decoder._encodeInt(negative_integer)
# print('encoded', encoded_integer)
self.assertEqual(encoded_integer[0], 0xF)
self.assertEqual(encoded_integer[1], 0xF)
def test_encodeInt_0(self):
encoded_integer = self.Decoder._encodeInt(0)
self.assertEqual(len(encoded_integer), 1, msg="{}".format(encoded_integer))
self.assertEqual(encoded_integer[0], 0x08)
def test_encodeInt_256(self):
encoded_integer = self.Decoder._encodeInt(256)
self.assertEqual(len(encoded_integer), 4)
self.assertEqual(encoded_integer[0], 0x05)
self.assertEqual(encoded_integer[1], 0x00)
self.assertEqual(encoded_integer[2], 0x00)
self.assertEqual(encoded_integer[3], 0x01)
def test_encode_4096(self):
encoded_integer = self.Decoder._encodeInt(4096)
self.assertEqual(len(encoded_integer), 5)
self.assertEqual(encoded_integer[0], 0x04)
self.assertEqual(encoded_integer[1], 0x00)
self.assertEqual(encoded_integer[2], 0x00)
self.assertEqual(encoded_integer[3], 0x00)
self.assertEqual(encoded_integer[4], 0x01)
def test_dec_int_leading_zeros(self):
encoded_integer = bytearray([0x07, 0x01])
decoded_integer = self.Decoder._decodeInt(encoded_integer)
self.assertEqual(decoded_integer, 1)
def test_encode_decode_int(self):
encoded_integer = self.Decoder._encodeInt(200)
# print(encoded_integer)
decoded_integer = self.Decoder._decodeInt(encoded_integer)
self.assertEqual(decoded_integer, 200)
def test_dec_int_leading_ones(self):
encoded_integer = bytearray(b"\x08\n\x03\x04\x01\x05\x03\x07\x07")
decoded_integer = self.Decoder._decodeInt(encoded_integer)
# print(decoded_integer)
self.assertEqual(
decoded_integer,
1999967290,
msg="result: {}\nexpected: {}".format(decoded_integer, hex(1999967290)),
)
def test_dec_int_negative(self):
encoded_negative_int = bytearray([0x0F, 0x0F])
decoded_negative_int = self.Decoder._decodeInt(encoded_negative_int)
self.assertEqual(decoded_negative_int, -1)
def test_encode_slof(self):
self.Decoder.decoded_data = self.i_slof_data
encoded_array = self.Decoder.encode_slof()
self.assertEqual(len(encoded_array), 14)
self.assertEqual(encoded_array[0], 0x40)
self.assertEqual(encoded_array[1], 0xE3)
self.assertEqual(encoded_array[2], 0xE1)
self.assertEqual(encoded_array[3], 0xE0)
self.assertEqual(encoded_array[4], 0x0)
self.assertEqual(encoded_array[5], 0x0)
self.assertEqual(encoded_array[6], 0x0)
self.assertEqual(encoded_array[7], 0x0)
self.assertEqual(encoded_array[8], 0x40)
self.assertEqual(encoded_array[9], 0x6E)
self.assertEqual(encoded_array[10], 0xBE)
self.assertEqual(encoded_array[11], 0xAE)
self.assertEqual(encoded_array[12], 0xFF)
self.assertEqual(encoded_array[13], 0xFF)
def test_decode_slof(self):
test_array = [
0x40,
0xC3,
0x88,
0x0,
0x0,
0x0,
0x0,
0x0,
0x13,
0x1B,
0xEA,
0x2A,
0xDE,
0x3E,
]
test_array = bytearray(test_array)
self.Decoder.encoded_data = test_array
decoded_array = self.Decoder.decode_slof()
for i, dec in enumerate(decoded_array):
self.assertAlmostEqual(dec, self.i_slof_data[i], places=2)
# self.assertCountEqual(decoded_array, self.i_slof_data)
def test_encode_decode_slof(self):
""" """
self.Decoder.decoded_data = self.i_slof_data
self.Decoder.encode_slof()
decoded_array = self.Decoder.decode_slof()
for i, dec in enumerate(decoded_array):
self.assertAlmostEqual(dec, self.i_slof_data[i], places=2)
def test_encode_pic_i_data(self):
self.Decoder.decoded_data = self.i_data
encoded_array = self.Decoder.encode_pic()
self.assertEqual(
len(encoded_array), 14, msg="{}".format([hex(x) for x in encoded_array])
)
self.assertEqual(encoded_array[0], 0x20)
self.assertEqual(encoded_array[1], 0x4B)
self.assertEqual(encoded_array[2], 0x4C)
self.assertEqual(encoded_array[3], 0x43)
self.assertEqual(encoded_array[4], 0x1)
self.assertEqual(encoded_array[5], 0xBE)
self.assertEqual(encoded_array[6], 0x92)
self.assertEqual(encoded_array[7], 0x8)
self.assertEqual(encoded_array[8], 0x48)
self.assertEqual(encoded_array[9], 0xE1)
self.assertEqual(encoded_array[10], 0x20)
self.assertEqual(encoded_array[11], 0xB)
self.assertEqual(encoded_array[12], 0x17)
self.assertEqual(encoded_array[13], 0xB0)
def test_decode_pic_i_data(self):
test_array = [
0x20,
0x4B,
0x4C,
0x43,
0x1,
0xBE,
0x92,
0x8,
0x48,
0xE1,
0x20,
0xB,
0x17,
0xB0,
]
test_array = bytearray(test_array)
self.Decoder.encoded_data = test_array
decoded_array = self.Decoder.decode_pic()
self.assertCountEqual(
decoded_array,
self.i_data,
msg="{}\n{}".format([x for x in decoded_array], [x for x in self.i_data]),
)
def test_encode_decode_pic(self):
""" """
self.Decoder.decoded_data = self.i_slof_data
self.Decoder.encode_pic()
decoded_array = self.Decoder.decode_pic()
self.assertCountEqual(self.i_slof_data, decoded_array)
def test_encode_decode_fixed_point(self):
encoded_fixed_point = self.Decoder._encode_fixed_point(self.fixed_point)
decoded_fixed_point = self.Decoder._decode_fixed_point(encoded_fixed_point)
self.assertEqual(self.fixed_point, decoded_fixed_point)
# def test_encode_linear(self):
# self.Decoder.decoded_data = self.mz_data
# self.Decoder.encoded_data = None
# encoded_array = self.Decoder.encode_linear()
# self.assertEqual(
# len(encoded_array),
# 23,
# msg='{0}\n{1}'.format(
# [hex(x) for x in encoded_array],
# [
# '0x41', '0x74', '0x75', '0xa4', '0x70', '0x0', '0x0',
# '0x0', '0xf6', '0xff', '0xff', '0x7f', '0xc2', '0x89',
# '0xe2', '0x7f', '0x2b', '0xf3', '0x8a', '0x13', '0xdc',
# '0x6a', '0x20'
# ]
# )
# )
# # assert first value
# self.assertEqual(
# 0xff & encoded_array[8],
# 0xf6,
# msg='Fail in value at pos {0}: {1} != {2}'.format(
# 8, hex(0xff & encoded_array[8]), hex(0xf6)
# )
# )
# self.assertEqual(
# 0xff & encoded_array[9],
# 0xff,
# msg='Fail in value at pos {0}: {1} != {2}'.format(
# 9,
# hex(0xff & encoded_array[9]),
# hex(0xff)
# )
# )
# self.assertEqual(
# 0xff & encoded_array[10],
# 0xff,
# msg='Fail in value at pos {0}: {1} != {2}'.format(
# 10,
# hex(0xff & encoded_array[10]),
# hex(0xff)
# )
# )
# self.assertEqual(
# 0xff & encoded_array[11],
# 0x7f,
# msg='Fail in value at pos {0}: {1} != {2}'.format(
# 11,
# hex(0xff & encoded_array[11]),
# hex(0x7f)
# )
# )
# # assert second value
# self.assertEqual(
# 0xff & encoded_array[12],
# 0xc2,
# msg='Fail in value at pos {0}: {1} != {2}'.format(
# 12,
# hex(0xff & encoded_array[12]),
# hex(0xc2)
# )
# )
# self.assertEqual(
# 0xff & encoded_array[13],
# 0x89,
# msg='Fail in value at pos {0}: {1} != {2}'.format(
# 13,
# hex(0xff & encoded_array[13]),
# hex(0x89)
# )
# )
# self.assertEqual(
# 0xff & encoded_array[14],
# 0xe2,
# msg='Fail in value at pos {0}: {1} != {2}'.format(
# 14,
# hex(0xff & encoded_array[14]),
# hex(0xe2)
# )
# )
# self.assertEqual(
# 0xff & encoded_array[15],
# 0x7f,
# msg='Fail in value at pos {0}: {1} != {2}'.format(
# 15,
# hex(0xff & encoded_array[15]),
# hex(0x7f)
# )
# )
# # assert third value
# self.assertEqual(
# 0xff & encoded_array[16],
# 0x2b,
# msg='Fail in value at pos {0}: {1} != {2}'.format(
# 16,
# hex(0xff & encoded_array[16]),
# hex(0x2b)
# )
# )
# self.assertEqual(
# 0xff & encoded_array[17],
# 0xf3,
# msg='Fail in value at pos {0}: {1} != {2}'.format(
# 17,
# hex(0xff & encoded_array[17]),
# hex(0xc2)
# )
# )
# self.assertEqual(
# 0xff & encoded_array[18],
# 0x8a,
# msg='Fail in value at pos {0}: {1} != {2}'.format(
# 18,
# hex(0xff & encoded_array[18]),
# hex(0x8a)
# )
# )
# self.assertEqual(
# 0xff & encoded_array[19],
# 0x13,
# msg='Fail in value at pos {0}: {1} != {2}'.format(
# 19,
# hex(0xff & encoded_array[19]),
# hex(0x13)
# )
# )
# # assert fourth value
# self.assertEqual(
# 0xff & encoded_array[20],
# 0xdc,
# msg='Fail in value at pos {0}: {1} != {2}'.format(
# 19,
# hex(0xff & encoded_array[20]),
# hex(0xdc)
# )
# )
# self.assertEqual(
# 0xff & encoded_array[21],
# 0x6a,
# msg='Fail in value at pos {0}: {1} != {2}'.format(
# 19,
# hex(0xff & encoded_array[21]),
# hex(0x6a)
# )
# )
# # self.assertEqual(
# # 0xff & encoded_array[22],
# # 0x20,
# # msg='Fail in value at pos {0}: {1} != {2}'.format(
# # 19,
# # hex(0xff & encoded_array[22]),
# # hex(0x20)
# # )
# # )
# def test_decode_linear(self):
# # ouput of >>> PyMSNumpress.encode_linear(self.mz_data, enc,
# # self.fixed_point)
# encoded_array = [
# 65, 116, 117, 164, 112, 0, 0, 0, 246, 255,
# 255, 127, 194, 137, 226, 127, 43, 243, 138, 19, 220, 106, 32
# ]
# # make bytearray from hex vals
# encoded_array = bytearray(encoded_array)
# MSNumpress.encoded_data = encoded_array
# # decode bytearray to numpy array
# decoded_array = self.Decoder.decode_linear()
# self.assertIsInstance(decoded_array, np.ndarray)
# self.assertEqual(len(decoded_array), len(self.mz_data))
# for i in range(len(decoded_array)):
# self.assertAlmostEqual(
# decoded_array[i], self.mz_data[i], places=i+1)
def test_encode_decode_linear(self):
""" """
test_array = [
100.00066,
100.00217,
100.00368,
100.00519,
111.73335,
111.73513,
111.73692,
111.7387,
111.74049,
111.74227,
111.74406,
111.74584,
111.74763,
111.74941,
111.7512,
111.75298,
111.75477,
112.00694,
112.00873,
112.01052,
112.01231,
112.0141,
112.01589,
112.01768,
]
self.Decoder.decoded_data = test_array
self.Decoder.encode_linear()
decoded_array = self.Decoder.decode_linear()
for i in range(len(decoded_array)):
self.assertAlmostEqual(
decoded_array[i],
test_array[i],
places=4,
msg="error at pos {0}".format(i),
)
def test_encode_decode_self_mz(self):
self.Decoder.decoded_data = self.mz_data
self.Decoder.encode_linear()
decoded_array = self.Decoder.decode_linear()
for i in range(len(decoded_array)):
self.assertAlmostEqual(
decoded_array[i],
self.mz_data[i],
places=4,
msg="error at pos {0}".format(i),
)
if __name__ == "__main__":
unittest.main(verbosity=3)