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Nowadays math.sqrt() is fast than ** 0.5 #42

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9 changes: 5 additions & 4 deletions parsimony/datasets/simulate/grad.py
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Original file line number Diff line number Diff line change
Expand Up @@ -10,6 +10,7 @@
"""
from six import with_metaclass
import abc
import math

import numpy as np

Expand Down Expand Up @@ -333,7 +334,7 @@ def project(self, alpha):
anorm = ax ** 2 + ay ** 2 + az ** 2
i = anorm > 1.0

anorm_i = anorm[i] ** 0.5 # Square root is taken here. Faster.
anorm_i = math.sqrt(anorm[i])
ax[i] = np.divide(ax[i], anorm_i)
ay[i] = np.divide(ay[i], anorm_i)
az[i] = np.divide(az[i], anorm_i)
Expand Down Expand Up @@ -399,7 +400,7 @@ def project(self, a):
anorm = ax ** 2 + ay ** 2 + az ** 2
i = anorm > 1.0

anorm_i = anorm[i] ** 0.5 # Square root is taken here. Faster.
anorm_i = math.sqrt(anorm[i])
ax[i] = np.divide(ax[i], anorm_i)
ay[i] = np.divide(ay[i], anorm_i)
az[i] = np.divide(az[i], anorm_i)
Expand Down Expand Up @@ -429,7 +430,7 @@ def _Nesterov_GroupTV_project(a):
anorm = ax ** 2 + ay ** 2 + az ** 2
i = anorm > 1.0

anorm_i = anorm[i] ** 0.5 # Square root is taken here. Faster.
anorm_i = math.sqrt(anorm[i])
ax[i] = np.divide(ax[i], anorm_i)
ay[i] = np.divide(ay[i], anorm_i)
az[i] = np.divide(az[i], anorm_i)
Expand Down Expand Up @@ -495,7 +496,7 @@ def _Nesterov_TV_project(alpha):
anorm = ax ** 2 + ay ** 2 + az ** 2
i = anorm > 1.0

anorm_i = anorm[i] ** 0.5 # Square root is taken here. Faster.
anorm_i = math.sqrt(anorm[i])
ax[i] = np.divide(ax[i], anorm_i)
ay[i] = np.divide(ay[i], anorm_i)
az[i] = np.divide(az[i], anorm_i)
Expand Down
6 changes: 4 additions & 2 deletions parsimony/functions/nesterov/grouptv.py
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Original file line number Diff line number Diff line change
Expand Up @@ -12,6 +12,8 @@
@email: lofstedt.tommy@gmail.com
@license: BSD 3-clause.
"""
import math

import scipy.sparse as sparse
import numpy as np

Expand Down Expand Up @@ -181,7 +183,7 @@ def project(self, a):
anorm = ax ** 2 + ay ** 2 + az ** 2
i = anorm > 1.0

anorm_i = anorm[i] ** 0.5 # Square root is taken here. Faster.
anorm_i = math.sqrt(anorm[i])
ax[i] = np.divide(ax[i], anorm_i)
ay[i] = np.divide(ay[i], anorm_i)
az[i] = np.divide(az[i], anorm_i)
Expand Down Expand Up @@ -225,7 +227,7 @@ def estimate_mu(self, beta):
ay = A[g + 1].dot(beta_)
az = A[g + 2].dot(beta_)

anorm = (ax ** 2 + ay ** 2 + az ** 2) ** 0.5 # Square root is taken here. Faster.
anorm = math.sqrt(ax ** 2 + ay ** 2 + az ** 2)

max_norm = max(max_norm, np.max(anorm)) # The overall maximum.

Expand Down
2 changes: 1 addition & 1 deletion parsimony/functions/nesterov/l1tv.py
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Original file line number Diff line number Diff line change
Expand Up @@ -232,7 +232,7 @@ def project(self, a):
anorm_tv += a[k] ** 2
i_tv = anorm_tv > 1.0

anorm_tv_i = anorm_tv[i_tv] ** 0.5 # Square root is taken here. Faster.
anorm_tv_i = math.sqrt(anorm_tv[i_tv])
for k in range(1, len(a)):
a[k][i_tv] = np.divide(a[k][i_tv], anorm_tv_i)

Expand Down
4 changes: 2 additions & 2 deletions parsimony/functions/nesterov/tv.py
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Original file line number Diff line number Diff line change
Expand Up @@ -244,7 +244,7 @@ def lambda_max(self):
# anorm = ax ** 2 + ay ** 2 + az ** 2
# i = anorm > 1.0
#
# anorm_i = anorm[i] ** 0.5 # Square root is taken here. Faster.
# anorm_i = math.sqrt(anorm[i])
# ax[i] = np.divide(ax[i], anorm_i)
# ay[i] = np.divide(ay[i], anorm_i)
# az[i] = np.divide(az[i], anorm_i)
Expand All @@ -261,7 +261,7 @@ def project(self, a):
anorm += a[k] ** 2
i = anorm > 1.0

anorm_i = anorm[i] ** 0.5 # Square root is taken here. Faster.
anorm_i = math.sqrt(anorm[i])
for k in range(len(a)):
a[k][i] = np.divide(a[k][i], anorm_i)

Expand Down
3 changes: 2 additions & 1 deletion parsimony/functions/properties.py
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Original file line number Diff line number Diff line change
Expand Up @@ -15,6 +15,7 @@
@license: BSD 3-clause.
"""
import abc
import math
from six import with_metaclass

import numpy as np
Expand Down Expand Up @@ -1042,7 +1043,7 @@ def Ata(self, a):
# anorm = ax ** 2 + ay ** 2 + az ** 2
# i = anorm > 1.0
#
# anorm_i = anorm[i] ** 0.5 # Square root is taken here. Faster.
# anorm_i = math.sqrt(anorm[i])
# ax[i] = np.divide(ax[i], anorm_i)
# ay[i] = np.divide(ay[i], anorm_i)
# az[i] = np.divide(az[i], anorm_i)
Expand Down