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[MRG+1] ENH: only call clock() if verbosity level warrants it #10091

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Merged
merged 1 commit into from
Nov 10, 2017
Merged

[MRG+1] ENH: only call clock() if verbosity level warrants it #10091

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46 changes: 28 additions & 18 deletions sklearn/manifold/_barnes_hut_tsne.pyx
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Original file line number Diff line number Diff line change
Expand Up @@ -61,8 +61,9 @@ cdef float compute_gradient(float[:] val_P,
long n_samples = pos_reference.shape[0]
int n_dimensions = qt.n_dimensions
double[1] sum_Q
clock_t t1, t2
clock_t t1 = 0, t2 = 0
float sQ, error
int take_timing = 1 if qt.verbose > 15 else 0

if qt.verbose > 11:
printf("[t-SNE] Allocating %li elements in force arrays\n",
Expand All @@ -71,19 +72,22 @@ cdef float compute_gradient(float[:] val_P,
cdef float* pos_f = <float*> malloc(sizeof(float) * n_samples * n_dimensions)

sum_Q[0] = 0.0
t1 = clock()
if take_timing:
t1 = clock()
compute_gradient_negative(pos_reference, neg_f, qt, sum_Q,
dof, theta, start, stop)
t2 = clock()
if qt.verbose > 15:
if take_timing:
t2 = clock()
printf("[t-SNE] Computing negative gradient: %e ticks\n", ((float) (t2 - t1)))
sQ = sum_Q[0]
t1 = clock()

if take_timing:
t1 = clock()
error = compute_gradient_positive(val_P, pos_reference, neighbors, indptr,
pos_f, n_dimensions, dof, sQ, start,
qt.verbose)
t2 = clock()
if qt.verbose > 15:
if take_timing:
t2 = clock()
printf("[t-SNE] Computing positive gradient: %e ticks\n", ((float) (t2 - t1)))
for i in range(start, n_samples):
for ax in range(n_dimensions):
Expand Down Expand Up @@ -118,9 +122,10 @@ cdef float compute_gradient_positive(float[:] val_P,
float C = 0.0
float exponent = (dof + 1.0) / -2.0
float[3] buff
clock_t t1, t2
clock_t t1 = 0, t2 = 0

t1 = clock()
if verbose > 10:
t1 = clock()
for i in range(start, n_samples):
# Init the gradient vector
for ax in range(n_dimensions):
Expand All @@ -140,9 +145,9 @@ cdef float compute_gradient_positive(float[:] val_P,
/ max(qij, FLOAT32_TINY))
for ax in range(n_dimensions):
pos_f[i * n_dimensions + ax] += dij * buff[ax]
t2 = clock()
dt = ((float) (t2 - t1))
if verbose > 10:
t2 = clock()
dt = ((float) (t2 - t1))
printf("[t-SNE] Computed error=%1.4f in %1.1e ticks\n", C, dt)
return C

Expand Down Expand Up @@ -170,7 +175,8 @@ cdef void compute_gradient_negative(float[:, :] pos_reference,
double qijZ
float[1] iQ
float[3] force, neg_force, pos
clock_t t1, t2, t3
clock_t t1 = 0, t2 = 0, t3 = 0
int take_timing = 1 if qt.verbose > 20 else 0

summary = <float*> malloc(sizeof(float) * n * offset)

Expand All @@ -183,9 +189,11 @@ cdef void compute_gradient_negative(float[:, :] pos_reference,
iQ[0] = 0.0
# Find which nodes are summarizing and collect their centers of mass
# deltas, and sizes, into vectorized arrays
t1 = clock()
if take_timing:
t1 = clock()
idx = qt.summarize(pos, summary, theta*theta)
t2 = clock()
if take_timing:
t2 = clock()
# Compute the t-SNE negative force
# for the digits dataset, walking the tree
# is about 10-15x more expensive than the
Expand All @@ -200,12 +208,14 @@ cdef void compute_gradient_negative(float[:, :] pos_reference,
mult = size * qijZ * qijZ
for ax in range(n_dimensions):
neg_force[ax] += mult * summary[j * offset + ax]
t3 = clock()
if take_timing:
t3 = clock()
for ax in range(n_dimensions):
neg_f[i * n_dimensions + ax] = neg_force[ax]
dta += t2 - t1
dtb += t3 - t2
if qt.verbose > 20:
if take_timing:
dta += t2 - t1
dtb += t3 - t2
if take_timing:
printf("[t-SNE] Tree: %li clock ticks | ", dta)
printf("Force computation: %li clock ticks\n", dtb)

Expand Down