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adding test data folder and unit test for rescale bvec #9

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adding test data folder and unit test for rescale bvec #9

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4e78583
adding test data folder and unit test for rescale bvec
wiltang Sep 30, 2019
8871471
Merge branch 'staging' into WilsonTang
wilttang Sep 30, 2019
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31 changes: 31 additions & 0 deletions tests/test_data/bvec_scaled.bvec
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0.000000000000000000e+00 0.000000000000000000e+00 0.000000000000000000e+00
-2.033253493328788519e-01 5.191425167298733268e-01 -8.301504981881513423e-01
1.977081165290608677e-01 5.196681659363497907e-01 -8.311777775968758331e-01
4.018050792304720953e-01 1.756857064686520586e-01 -8.987141986456009812e-01
-4.031232896024871115e-01 7.315950994365449933e-01 -5.497819784791977415e-01
-2.017372527568954965e-01 9.417546889448769054e-01 -2.690728278746084556e-01
-8.534215120105359542e-01 5.179216878381357470e-01 -5.855636690016949308e-02
-7.312383684642190795e-01 5.197490477110885410e-01 -4.417594095083925421e-01
-4.067892940004660396e-01 1.761111280856997030e-01 -8.963857098654488542e-01
-7.326343113734050672e-01 1.759595287941236319e-01 -6.574839998243049433e-01
-6.505047457118273702e-01 7.302047957321597949e-01 2.089127379939905715e-01
-3.223554568316183144e-01 9.409120901667874515e-01 1.037853459253569310e-01
-3.239056163210728423e-01 5.188188542002923898e-01 7.911460979123651205e-01
-6.499877119641050971e-01 5.198718424278614414e-01 5.543006781037963515e-01
-9.787562000010596730e-01 1.756262202307987685e-01 1.057909813118716735e-01
-8.543251023447319126e-01 1.757810088374901492e-01 4.891110880318884080e-01
7.351200102798949049e-04 7.312280906641346334e-01 6.821326403436903663e-01
1.884360179654446556e-03 9.415929137758602963e-01 3.367480273346800668e-01
6.541350652685095080e-01 5.188895597835903040e-01 5.503280304815979518e-01
3.286347067729832871e-01 5.199866853774535169e-01 7.884244266474781382e-01
1.973678352949524983e-01 -1.753764330242377489e-01 -9.645149269610500120e-01
2.038724103925809439e-01 1.754682642453940788e-01 9.631442926807112226e-01
6.511546289927737652e-01 7.302924301027146070e-01 2.065686706060597677e-01
3.236193315131545289e-01 9.410258404305261726e-01 9.869597718752717852e-02
1.996235361681136800e-01 9.406987842073736283e-01 -2.742922550829809958e-01
4.031232896024871115e-01 7.315950994365449933e-01 -5.497819784791977415e-01
7.319223515982337114e-01 1.758058722731208057e-01 -6.583175271137770013e-01
7.286410965136864704e-01 5.186801579370168280e-01 -4.472728990602538590e-01
8.524194359344654526e-01 5.188670754168032140e-01 -6.448304652838203477e-02
8.572526403435390963e-01 1.761364603732337719e-01 4.838324688889937275e-01
9.793287628014578639e-01 1.755445172664188702e-01 1.004952576366961586e-01
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188 changes: 139 additions & 49 deletions tests/test_scripts/test_rescale_bvec.py
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import pytest
import ndmg
import numpy as np
import warnings

warnings.simplefilter("ignore")
import os.path as op

# def rescale_bvec(bvec, bvec_new):
#
# bv1 = np.array(np.loadtxt(bvec))
# # Enforce proper dimensions
# bv1 = bv1.T if bv1.shape[0] == 3 else bv1
#
# # Normalize values not close to norm 1
# bv2 = [
# b / np.linalg.norm(b) if not np.isclose(np.linalg.norm(b), 0) else b
# for b in bv1
# ]
#
# try:
# assert "bvec" in bvec_new
# np.savetxt(bvec_new, bv2)
# pass
# except AssertionError:
# print(
# "Error: your new b-vector file must have extension .bvec to"
# + " be compatible with the the pipeline."
# )
# pass
# else:
# pass
# pass


def test_rescale_bvec(tmp_path):
d = tmp_path/"sub"
d.mkdir()
test_input = d / "text_input.bvec"
test_output = d / "text_output.bvec"
test_input_array = np.array([[1, 2, 3],
[4, 5, 6],
[7, 8, 9]])
np.savetxt(test_input, test_input_array)
ndmg.preproc.rescale_bvec(str(test_input), str(test_output))
test_output_array = np.array(np.loadtxt(str(test_output)))
b = np.array([[1.230914909793327239e-01, 4.923659639173308955e-01, 8.616404368553290949e-01],
[2.073903389460850510e-01, 5.184758473652126831e-01, 8.295613557843402042e-01],
[2.672612419124243965e-01, 5.345224838248487931e-01, 8.017837257372731896e-01]])
assert np.allclose(test_output_array, b)
from ndmg import preproc as mgp
from ndmg.utils import gen_utils as mgu
from ndmg.register import gen_reg as mgr
from ndmg.track import gen_track as mgt
from ndmg.graph import gen_graph as mgg
from ndmg.utils.bids_utils import name_resource
from unittest.mock import Mock
import numpy as np
import pytest
import os

#requires most up to date pytest for tmp_path to work
def test_rescale_bvac(tmp_path):
#create temp file dir
d = tmp_path/"sub"
d.mkdir()
temp_in1 = d/ "test1.bvec"
temp_in2 = d/ "test2.bvec"

#create temp output dir
temp_out1 = d/ "test1_new.bvec"
temp_out2 = d/ "test2_new.bvec"

#write cases for test1 Test w/ proper dimensions
bvec_test_1 = np.array([[ 0.00000000e+00, -2.03325346e-01, 1.97708115e-01,
4.01805073e-01, -4.03123289e-01, -2.01737255e-01,
-8.53421509e-01, -7.31238365e-01, -4.06789303e-01,
-7.32634306e-01, -6.50504768e-01, -3.22355449e-01,
-3.23905617e-01, -6.49987698e-01, -9.78756189e-01,
-8.54325116e-01, 7.35120033e-04, 1.88436022e-03,
6.54135048e-01, 3.28634709e-01, 1.97367832e-01,
2.03872412e-01, 6.51154637e-01, 3.23619336e-01,
1.99623540e-01, 4.03123289e-01, 7.31922328e-01,
7.28641093e-01, 8.52419436e-01, 8.57252657e-01,
9.79328752e-01],
[ 0.00000000e+00, 5.19142509e-01, 5.19668162e-01,
1.75685704e-01, 7.31595099e-01, 9.41754699e-01,
5.17921686e-01, 5.19749045e-01, 1.76111132e-01,
1.75959527e-01, 7.30204821e-01, 9.40912068e-01,
5.18818855e-01, 5.19871831e-01, 1.75626218e-01,
1.75781012e-01, 7.31228113e-01, 9.41592932e-01,
5.18889546e-01, 5.19986689e-01, -1.75376430e-01,
1.75468266e-01, 7.30292439e-01, 9.41025853e-01,
9.40698802e-01, 7.31595099e-01, 1.75805867e-01,
5.18680155e-01, 5.18867075e-01, 1.76136464e-01,
1.75544515e-01],
[ 0.00000000e+00, -8.30150485e-01, -8.31177771e-01,
-8.98714185e-01, -5.49781978e-01, -2.69072831e-01,
-5.85563667e-02, -4.41759408e-01, -8.96385729e-01,
-6.57483995e-01, 2.08912745e-01, 1.03785343e-01,
7.91146100e-01, 5.54300666e-01, 1.05790980e-01,
4.89111096e-01, 6.82132661e-01, 3.36748034e-01,
5.50328016e-01, 7.88424432e-01, -9.64514911e-01,
9.63144302e-01, 2.06568673e-01, 9.86959785e-02,
-2.74292260e-01, -5.49781978e-01, -6.58317506e-01,
-4.47272897e-01, -6.44830465e-02, 4.83832479e-01,
1.00495256e-01]])
#save file
np.savetxt(temp_in1,bvec_test_1)

#write cases for test2 Test non proper dimensions
bvec_test_2 = np.array([[ 0.00000000e+00, 0.00000000e+00, 0.00000000e+00],
[-2.03325346e-01, 5.19142509e-01, -8.30150485e-01],
[ 1.97708115e-01, 5.19668162e-01, -8.31177771e-01],
[ 4.01805073e-01, 1.75685704e-01, -8.98714185e-01],
[-4.03123289e-01, 7.31595099e-01, -5.49781978e-01],
[-2.01737255e-01, 9.41754699e-01, -2.69072831e-01],
[-8.53421509e-01, 5.17921686e-01, -5.85563667e-02],
[-7.31238365e-01, 5.19749045e-01, -4.41759408e-01],
[-4.06789303e-01, 1.76111132e-01, -8.96385729e-01],
[-7.32634306e-01, 1.75959527e-01, -6.57483995e-01],
[-6.50504768e-01, 7.30204821e-01, 2.08912745e-01],
[-3.22355449e-01, 9.40912068e-01, 1.03785343e-01],
[-3.23905617e-01, 5.18818855e-01, 7.91146100e-01],
[-6.49987698e-01, 5.19871831e-01, 5.54300666e-01],
[-9.78756189e-01, 1.75626218e-01, 1.05790980e-01],
[-8.54325116e-01, 1.75781012e-01, 4.89111096e-01],
[ 7.35120033e-04, 7.31228113e-01, 6.82132661e-01],
[ 1.88436022e-03, 9.41592932e-01, 3.36748034e-01],
[ 6.54135048e-01, 5.18889546e-01, 5.50328016e-01],
[ 3.28634709e-01, 5.19986689e-01, 7.88424432e-01],
[ 1.97367832e-01, -1.75376430e-01, -9.64514911e-01],
[ 2.03872412e-01, 1.75468266e-01, 9.63144302e-01],
[ 6.51154637e-01, 7.30292439e-01, 2.06568673e-01],
[ 3.23619336e-01, 9.41025853e-01, 9.86959785e-02],
[ 1.99623540e-01, 9.40698802e-01, -2.74292260e-01],
[ 4.03123289e-01, 7.31595099e-01, -5.49781978e-01],
[ 7.31922328e-01, 1.75805867e-01, -6.58317506e-01],
[ 7.28641093e-01, 5.18680155e-01, -4.47272897e-01],
[ 8.52419436e-01, 5.18867075e-01, -6.44830465e-02],
[ 8.57252657e-01, 1.76136464e-01, 4.83832479e-01],
[ 9.79328752e-01, 1.75544515e-01, 1.00495256e-01]])
#save file
np.savetxt(temp_in2,bvec_test_2)

# #desired ouput
output = np.array([[ 0.00000000e+00, 0.00000000e+00, 0.00000000e+00],
[-2.03325349e-01, 5.19142517e-01, -8.30150498e-01],
[ 1.97708117e-01, 5.19668166e-01, -8.31177778e-01],
[ 4.01805079e-01, 1.75685707e-01, -8.98714199e-01],
[-4.03123289e-01, 7.31595100e-01, -5.49781978e-01],
[-2.01737253e-01, 9.41754689e-01, -2.69072828e-01],
[-8.53421512e-01, 5.17921688e-01, -5.85563669e-02],
[-7.31238368e-01, 5.19749047e-01, -4.41759410e-01],
[-4.06789294e-01, 1.76111128e-01, -8.96385710e-01],
[-7.32634311e-01, 1.75959528e-01, -6.57484000e-01],
[-6.50504746e-01, 7.30204796e-01, 2.08912738e-01],
[-3.22355457e-01, 9.40912090e-01, 1.03785345e-01],
[-3.23905616e-01, 5.18818854e-01, 7.91146098e-01],
[-6.49987712e-01, 5.19871842e-01, 5.54300678e-01],
[-9.78756200e-01, 1.75626220e-01, 1.05790981e-01],
[-8.54325102e-01, 1.75781009e-01, 4.89111088e-01],
[ 7.35120011e-04, 7.31228091e-01, 6.82132640e-01],
[ 1.88436018e-03, 9.41592914e-01, 3.36748027e-01],
[ 6.54135065e-01, 5.18889560e-01, 5.50328031e-01],
[ 3.28634707e-01, 5.19986685e-01, 7.88424427e-01],
[ 1.97367835e-01, -1.75376433e-01, -9.64514927e-01],
[ 2.03872410e-01, 1.75468264e-01, 9.63144293e-01],
[ 6.51154629e-01, 7.30292430e-01, 2.06568670e-01],
[ 3.23619332e-01, 9.41025840e-01, 9.86959772e-02],
[ 1.99623536e-01, 9.40698784e-01, -2.74292255e-01],
[ 4.03123289e-01, 7.31595100e-01, -5.49781978e-01],
[ 7.31922351e-01, 1.75805873e-01, -6.58317527e-01],
[ 7.28641097e-01, 5.18680158e-01, -4.47272899e-01],
[ 8.52419436e-01, 5.18867075e-01, -6.44830465e-02],
[ 8.57252640e-01, 1.76136461e-01, 4.83832469e-01],
[ 9.79328763e-01, 1.75544517e-01, 1.00495257e-01]])

#run through data
mgp.rescale_bvec(str(temp_in1),str(temp_out1))
mgp.rescale_bvec(str(temp_in2),str(temp_out2))
#open data
test1 = np.loadtxt(str(temp_out1))
test2 = np.loadtxt(str(temp_out2))

assert np.allclose(test1,output)
assert np.allclose(test2,output)