Contents
Effect of imaging conditions
%matplotlib ipympl
import numpy as np
import matplotlib.pyplot as plt
import seaborn as sns
import pickle
from itertools import product
from functools import reduce
from ipywidgets import Select, SelectMultiple, FloatRangeSlider, Label, Layout
from IPython.display import display
from ipywidgets import HBox, VBox
plt.rcParams["legend.frameon"] = False
plt.rcParams["legend.fontsize"] = 6
plt.rcParams["legend.title_fontsize"] = 6
plt.rcParams["xtick.labelsize"] = 6
plt.rcParams["ytick.labelsize"] = 6def reduction(series, mode):
match mode:
case "mean":
return series.mean()
case "min":
return series.min()
case "max":
return series.max()
case "median":
return series.median()
case _:
return ValueError
def n_image_select():
return SelectMultiple(
options=[64, 128, 256, 512],
value=[64, 128, 256, 512],
rows=4,
# description="Number of training images",
disabled=False,
layout={"width": "100px", "height":"88px"},
)
def pretrain_lr_select():
return SelectMultiple(
options=["1e-3", "1e-4"],
value=["1e-3", "1e-4"],
rows=2,
# description="Pretrain LRs",
disabled=False,
layout={"width": "100px"},
)
def transfer_lr_select():
return SelectMultiple(
options=["1e-4", "1e-5"],
value=["1e-4", "1e-5"],
rows=2,
# description="Transfer LRs",
disabled=False,
layout={"width": "100px"},
)
def weight_freezing_select():
return SelectMultiple(
options=["none", "decoder", "encoder"],
value=["none", "decoder", "encoder"],
# description="Weight freezing",
rows=3,
disabled=False,
layout={"width": "100px"},
)
def reduction_select():
return Select(
options=["min", "mean", "median", "max"],
value="mean",
rows=4,
# description="Data Reduction",
disabled=False,
layout={"width": "100px"},
)
with open("mini_df.pkl", "rb") as f:
df = pickle.load(f)640 / (3.4 * 1.1) 171.12299465240642def get_plot_data(local_df, reduction_mode):
p_heatmap = np.zeros((5, 11))
t_heatmap = np.zeros((5, 11))
common_defoci = [-100, -50, 0, 50, 100]
all_defoci = np.arange(-250, 300, 50)
for i, starting_df in enumerate(common_defoci):
p_df = local_df.query(f"pretrain_defocus == {starting_df}")
for j, transfer_df in enumerate(all_defoci):
p_heatmap[i, j] = reduction(
p_df[f"best_pretrain_val_{transfer_df}"], reduction_mode
)
t_df = p_df.query(f"transfer_defocus=={transfer_df}")
if len(t_df) > 0:
t_heatmap[i, j] = reduction(
t_df[f"best_transfer_performance_{transfer_df}"], reduction_mode
)
else:
t_heatmap[i, j] = p_heatmap[i, j]
return p_heatmap, t_heatmap
### Get plot data
# p_heatmap, t_heatmap = get_plot_data(df, reduction_mode)
### Figure set up
ratio = 1.8
# height = 3.4
dpi = 168
width = 640 / dpi
height = width / ratio
fig_style = {
"figsize": (width, height), # inches
"constrained_layout": True,
"dpi":dpi
}
fig = plt.figure(**fig_style)
gs = fig.add_gridspec(
8,
31,
left=0.2,
right=0.6,
hspace=0.0,
# wspace=-0.5,
)
ax_p = fig.add_subplot(gs[:4, 5:27])
ax_t = fig.add_subplot(gs[4:, 5:27])
ax_colorbar = fig.add_axes(
[ax_p.get_position().x1+0.155, ax_p.get_position().y0+0.1425, 0.025, 0.27]
)
# ax_colorbar = fig.add_subplot(gs[0:4, 27])
cmap = sns.color_palette("crest_r", as_cmap=True)
ndata_select = n_image_select()
ptlr_select = pretrain_lr_select()
tllr_select = transfer_lr_select()
freeze_select = weight_freezing_select()
rmode_select = reduction_select()
prange_select = FloatRangeSlider(
value=(0.0, 0.1), min=0, max=0.2, step=0.01, layout={'width':'135px'}
)
center_align = Layout(align_items="center")
ptlr_box = VBox([Label("Pretrain LR"), ptlr_select], layout=center_align)
tllr_box = VBox([Label("Transfer LR"), tllr_select], layout=center_align)
ndata_box = VBox([Label("# of transfer images"), ndata_select], layout=center_align)
freeze_box = VBox([Label("Weight Freezing"), freeze_select], layout=center_align)
left_box = VBox([ndata_box, freeze_box], layout={"align_items": "center", "width": "150px"})
right_box = VBox(
[
ptlr_box,
tllr_box,
],
layout={"align_items": "center", "width": "150px"},
)
rmode_box = VBox(
[
Label("Reduction Mode"),
rmode_select,
Label("Color scale"),
prange_select,
],
layout={"align_items": "center", "width": "150px"},
)
full_box = HBox([left_box, right_box, rmode_box])
display(full_box)
def update_plot(*args):
N_points = ndata_select.value
weight_freezing = freeze_select.value
pretrain_lrs = ptlr_select.value
transfer_lrs = tllr_select.value
reduction_mode = rmode_select.value
active_lr_pairs = tuple(product(pretrain_lrs, transfer_lrs))
lr_query = reduce(
lambda x, y: f"{x} or {y}",
(f"(pretrain_lr == {x} and transfer_lr == {y})" for x, y in active_lr_pairs),
)
plot_df = df.query(
f"N_tl_training_points in {N_points} and freeze_option in {weight_freezing}"
).query(lr_query)
p_heatmap, t_heatmap = get_plot_data(plot_df, reduction_mode)
pmin = prange_select.value[0]
pmax = prange_select.value[1]
cim = ax_p.matshow(p_heatmap, cmap=cmap, vmin=pmin, vmax=pmax)
ax_t.matshow(t_heatmap, cmap=cmap, vmin=pmin, vmax=pmax)
ax_p.set_xticks([])
ax_colorbar.clear()
fig.colorbar(cim, cax=ax_colorbar, use_gridspec=True)
ax_colorbar.set_ylabel("Loss", fontsize=6)
ax_colorbar.tick_params(labelsize=6)
for ax in [ax_p, ax_t]:
ax.set_yticks([0, 2, 4])
ax.set_yticklabels([-10, 0, 10], fontsize=6)
ax.set_xticks([1, 3, 5, 7, 9])
ax.set_xticklabels([-20, -10, 0, 10, 20], rotation=0, fontsize=6)
ax.xaxis.set_ticks_position("bottom")
fig.supylabel("Pretrain defocus (nm)", fontsize=6, x=0.25)
_ = [plt.setp(ax.spines.values(), linewidth=0.75) for ax in (ax_p, ax_t, ax_colorbar)]
ax_p.set_title("After pretraining", fontsize=6)
ax_t.set_title("After transfer learning", fontsize=6)
ax_t.set_xlabel("Target/transfer defocus (nm)", fontsize=6)
update_plot()
ndata_select.observe(update_plot, "value")
ptlr_select.observe(update_plot, "value")
tllr_select.observe(update_plot, "value")
rmode_select.observe(update_plot, "value")
freeze_select.observe(update_plot, "value")
prange_select.observe(
update_plot, "value"
) # This can be made faster to avoid re-querying the dataframeLoading...
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