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Merge branch 'main' of github.com:NSLS-II-XPD/ae-gpcam into main
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@jklynch
jklynch committed Feb 8, 2021
2 parents 3b5b5c3 + cc15ee0 commit e0196e1
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Showing 14 changed files with 1,608 additions and 96 deletions.
11 changes: 7 additions & 4 deletions ae_gpcam/bluesky_config/ipython/adaptive_gpcam_count.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -45,18 +45,21 @@ def to_recommender(name, doc):
snap_function = snap_factory(single_data, time_tol=None, temp_tol=None, Ti_tol=None)

xrun(
5,
10,
adaptive_plan(
[pe1c],
(24, 340, 30 * 60),
[pe2c],
(18, 400, 7.5 * 60, 1),
to_recommender=to_recommender,
from_recommender=redis_queue,
reccomender_timeout=60,
real_motors=(sample_x, ss_stg2_y),
transform_pair=pair,
snap_function=snap_function,
take_data=stepping_ct,
exposure=5
exposure=20,
max_runs=10000,
rocking_range=0.5,
num=3
),
#print
#lambda name, doc: pprint.pprint(doc) if name == 'start' else None
Expand Down
96 changes: 58 additions & 38 deletions ae_gpcam/bluesky_config/ipython/profile_default/startup/01-adaptive.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -100,22 +100,27 @@ def to_bl_coords(Ti_frac, temperature, annealing_time, thickness):
if Ti_frac > np.max(ti_fractions) or Ti_frac < np.min(ti_fractions):
raise ValueError

d = np.interp(Ti_frac, ti_fractions, cell_positions) + start_distance
print(reference_x, np.cos(angle) * d, reference_y, np.sin(angle) * d)
return reference_x + np.cos(angle) * d, reference_y + np.sin(angle) * d
d = (
np.interp(Ti_frac, ti_fractions, cell_positions)
- start_distance
+ (cell_size / 2)
)

# minus because we index the cells backwards
return reference_x - np.cos(angle) * d, reference_y - np.sin(angle) * d

def to_data_coords(x, y):
x_rel = x - reference_x
# negative because we index the cells backwards
x_rel = -(x - reference_x)
y_rel = y - reference_y

r = np.hypot(x_rel, y_rel)

d_angle = np.arctan2(y_rel, x_rel)
d_angle = -np.arctan2(y_rel, x_rel)

from_center_angle = d_angle - angle

d = np.cos(from_center_angle) * r - start_distance
h = np.sin(from_center_angle) * r
d = np.cos(from_center_angle) * (r + start_distance - (cell_size / 2))
h = -np.sin(from_center_angle) * r

if not (np.min(cell_positions) < d < np.max(cell_positions)):
raise ValueError
Expand Down Expand Up @@ -347,7 +352,7 @@ def l2_norm(strip):
temperature=340,
annealing_time=450,
ti_fractions=[19, 22, 27, 30, 35, 40, 44, 49, 53],
start_distance=18.5,
start_distance=-13.5,
reference_y=0,
reference_x=5,
angle=0,
Expand All @@ -357,7 +362,7 @@ def l2_norm(strip):
temperature=340,
annealing_time=1800,
ti_fractions=[19, 20, 23, 28, 32, 37, 42, 46, 51, 56, 60],
start_distance=14.0,
start_distance=-9.0,
reference_y=0,
reference_x=5,
angle=0,
Expand All @@ -367,7 +372,7 @@ def l2_norm(strip):
temperature=340,
annealing_time=3600,
ti_fractions=[16, 18, 22, 25, 29, 34, 36, 43, 49, 53, 58, 62, 67],
start_distance=9.5,
start_distance=-4.5,
reference_y=0,
reference_x=5,
angle=0,
Expand All @@ -377,7 +382,7 @@ def l2_norm(strip):
temperature=400,
annealing_time=450,
ti_fractions=[17, 20, 23, 27, 31, 36, 41, 46, 51, 56, 61, 65, 69],
start_distance=9.5,
start_distance=-4.5,
reference_y=0,
reference_x=5,
angle=0,
Expand All @@ -387,7 +392,7 @@ def l2_norm(strip):
temperature=400,
annealing_time=1800,
ti_fractions=[20, 23, 27, 32, 37, 42, 47, 51, 57, 63, 67, 71, 75, 78, 81],
start_distance=5,
start_distance=0,
reference_y=0,
reference_x=5,
angle=0,
Expand All @@ -397,7 +402,7 @@ def l2_norm(strip):
temperature=400,
annealing_time=3600,
ti_fractions=[19, 22, 25, 30, 35, 39, 45, 50, 55, 60, 65, 69, 73, 77, 79],
start_distance=5,
start_distance=0,
reference_y=0,
reference_x=5,
angle=0,
Expand All @@ -407,7 +412,7 @@ def l2_norm(strip):
temperature=460,
annealing_time=450,
ti_fractions=[17, 20, 24, 28, 32, 37, 43, 48, 52, 58, 63, 67, 71, 75, 78],
start_distance=5,
start_distance=0,
reference_y=0,
reference_x=5,
angle=0,
Expand All @@ -417,7 +422,7 @@ def l2_norm(strip):
temperature=460,
annealing_time=15 * 60,
ti_fractions=[17, 19, 22, 26, 31, 35, 40, 46, 51, 56, 61, 65, 69, 73, 76],
start_distance=5,
start_distance=0,
reference_y=0,
reference_x=5,
angle=0,
Expand All @@ -427,7 +432,7 @@ def l2_norm(strip):
temperature=460,
annealing_time=30 * 60,
ti_fractions=[15, 18, 21, 25, 28, 33, 38, 43, 48, 53, 58, 63, 67, 71, 75],
start_distance=5,
start_distance=0,
reference_y=0,
reference_x=5,
angle=0,
Expand All @@ -437,7 +442,7 @@ def l2_norm(strip):
temperature=340,
annealing_time=1800,
ti_fractions=[19, 20, 23, 28, 32, 37, 42, 46, 51, 56, 60],
start_distance=14.0,
start_distance=-9.0,
reference_y=0,
reference_x=5,
angle=0,
Expand All @@ -447,7 +452,7 @@ def l2_norm(strip):
temperature=340,
annealing_time=3600,
ti_fractions=[16, 18, 22, 25, 29, 34, 36, 43, 49, 53, 58, 62, 67],
start_distance=9.5,
start_distance=-4.5,
reference_y=0,
reference_x=5,
angle=0,
Expand All @@ -457,7 +462,7 @@ def l2_norm(strip):
temperature=400,
annealing_time=450,
ti_fractions=[17, 20, 23, 27, 31, 36, 41, 46, 51, 56, 61, 65, 69],
start_distance=9.5,
start_distance=-4.5,
reference_y=0,
reference_x=5,
angle=0,
Expand All @@ -467,7 +472,7 @@ def l2_norm(strip):
temperature=400,
annealing_time=1800,
ti_fractions=[20, 23, 27, 32, 37, 42, 47, 51, 57, 63, 67, 71, 75, 78, 81],
start_distance=5,
start_distance=0,
reference_y=0,
reference_x=5,
angle=0,
Expand All @@ -477,7 +482,7 @@ def l2_norm(strip):
temperature=400,
annealing_time=3600,
ti_fractions=[19, 22, 25, 30, 35, 39, 45, 50, 55, 60, 65, 69, 73, 77, 79],
start_distance=5,
start_distance=0,
reference_y=0,
reference_x=5,
angle=0,
Expand All @@ -487,7 +492,7 @@ def l2_norm(strip):
temperature=460,
annealing_time=450,
ti_fractions=[17, 20, 24, 28, 32, 37, 43, 48, 52, 58, 63, 67, 71, 75, 78],
start_distance=5,
start_distance=0,
reference_y=0,
reference_x=5,
angle=0,
Expand All @@ -497,7 +502,7 @@ def l2_norm(strip):
temperature=460,
annealing_time=15 * 60,
ti_fractions=[17, 19, 22, 26, 31, 35, 40, 46, 51, 56, 61, 65, 69, 73, 76],
start_distance=5,
start_distance=0,
reference_y=0,
reference_x=5,
angle=0,
Expand All @@ -507,7 +512,7 @@ def l2_norm(strip):
temperature=460,
annealing_time=30 * 60,
ti_fractions=[15, 18, 21, 25, 28, 33, 38, 43, 48, 53, 58, 63, 67, 71, 75],
start_distance=5,
start_distance=0,
reference_y=0,
reference_x=5,
angle=0,
Expand All @@ -532,7 +537,7 @@ def l2_norm(strip):
# fit the above to a line
fits = [scipy.stats.linregress(sampled_x, m) for m in mpos]
# get the 0 we need to make the start_distance's above make sense
ref_x = 35 - 5 - 2 * 4.5
ref_x = 95 - 1.25

# generate the data by zipping the template + the fit angle and offsets
single_data = [
Expand Down Expand Up @@ -566,14 +571,17 @@ def show_layout(strip_list, ax=None, *, cell_size=4.5):
labels = {}
for strip in strip_list:
cells[strip] = []

pair = single_strip_transform_factory(*astuple(strip))
for j, ti_frac in enumerate(strip.ti_fractions):
color = cmap(norm(ti_frac))
d = strip.start_distance + j * cell_size
x, y = pair.forward(
ti_frac, strip.temperature, strip.annealing_time, strip.thickness
)
d = strip.start_distance - j * cell_size
rect = mpatches.Rectangle(
(
strip.reference_x + d * np.cos(strip.angle),
strip.reference_y - cell_size / 2 + d * np.sin(strip.angle),
x - cell_size / 2,
y - cell_size / 2,
),
cell_size,
cell_size,
Expand All @@ -582,22 +590,21 @@ def show_layout(strip_list, ax=None, *, cell_size=4.5):
ax.add_patch(rect)
cells[strip].append(
ax.text(
strip.reference_x + (d + cell_size / 2) * np.cos(strip.angle),
strip.reference_y + (d + cell_size / 2) * np.sin(strip.angle),
x,
y,
f"{ti_frac}",
ha="center",
va="center",
color="w",
)
)
cells[strip].append(rect)

full_d = strip.start_distance + (j + 1) * cell_size
d = cell_size * (len(strip.ti_fractions) - 0.5) - strip.start_distance
labels[strip] = ax.annotate(
f"{strip.temperature}°C\n{strip.annealing_time}s\n{state_map[strip.thickness]}",
f"{strip.temperature}°C\n{strip.annealing_time}s",
xy=(
strip.reference_x + full_d * np.cos(strip.angle),
strip.reference_y + full_d * np.sin(strip.angle),
strip.reference_x - d - cell_size / 2,
strip.reference_y - np.sin(strip.angle) * d,
),
xytext=(10, 0),
textcoords="offset points",
Expand All @@ -613,6 +620,7 @@ def show_layout(strip_list, ax=None, *, cell_size=4.5):
ax.spines["top"].set_visible(False)
# positive goes down on the beamline
ax.invert_yaxis()
ax.invert_xaxis()
ax.set_aspect("equal")


Expand All @@ -625,5 +633,17 @@ def show_layout(strip_list, ax=None, *, cell_size=4.5):
ax.plot(sampled_x, mpos.T, marker="o", color=".5")

ax.add_patch(
mpatches.Rectangle((28.5, 2.5), 64, 80, color="k", alpha=0.25, zorder=2)
mpatches.Rectangle((95 - 64, 2.5), 64, 80, color="k", alpha=0.25, zorder=2)
)
plt.show()


for strip in single_data:
pair = single_strip_transform_factory(*astuple(strip))
for j, ti_frac in enumerate(strip.ti_fractions[1:-1]):
start = (ti_frac, strip.temperature, strip.annealing_time, strip.thickness)
x, y = pair.forward(
ti_frac, strip.temperature, strip.annealing_time, strip.thickness
)
ret = pair.inverse(np.round(x, 2), y)
assert np.allclose(start, ret, atol=0.01)
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