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Cut and paste app fixes #6

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91f9e03
add tear color option + minor fixes
chiggum Jun 16, 2026
ac6700d
add metadata processing to reproduce cut and paste steps
chiggum Jun 17, 2026
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129 changes: 82 additions & 47 deletions examples/cut_and_paste_app.py
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Original file line number Diff line number Diff line change
Expand Up @@ -5,6 +5,7 @@
from bokeh.plotting import figure, curdoc
from bokeh.models import (
LassoSelectTool,
PolySelectTool,
TapTool,
TextInput,
Button,
Expand Down Expand Up @@ -32,7 +33,6 @@
import vis
from vis import maximize_window


from pyRATS._utils import (
procrustes,
compute_final_embedding,
Expand Down Expand Up @@ -98,32 +98,42 @@ def __init__(
self,
model,
y,
color_of_pts_on_tear,
metadata_fname=None,
metadata_fpath=None,
save_progress_dir="",
cmap_interior="summer",
cmap_tear="jet",
tear_color_eig_inds=[5, 1, 2],
max_refinement_iter=10,
force_compute=False,
):
self.model = model
self.y = y
self.color_of_pts_on_tear = color_of_pts_on_tear
self.pts = None
if metadata_fname is None:
if metadata_fpath is None:
self.metadata = []
else:
self.metadata = read(metadata_fname)
_, self.metadata = read(metadata_fpath)
self.save_progress_dir = save_progress_dir
if self.save_progress_dir:
makedirs(self.save_progress_dir)
self.cur_iter = 0

self.model = model
self.y = y
self.cmap_interior = cmap_interior
self.cmap_tear = cmap_tear
self.tear_color_eig_inds = tear_color_eig_inds
self.max_refinement_iter = max_refinement_iter
self.force_compute = force_compute
self.selected_pts_to_move = np.array([])

if len(self.metadata) > 0:
# simulate cut and paste
print('Simulating cut and paste for', len(self.metadata), 'iterations using previously stored metadata.')
_ = self.get_current_embedding_data()
for i in range(len(self.metadata)):
self.cut_clusters_to_move(None)
self.paste_clusters(None)


def init_metadata_for_current_iter(self):
if len(self.metadata) <= self.cur_iter:
self.metadata.append(
Expand All @@ -136,30 +146,29 @@ def init_metadata_for_current_iter(self):

def get_current_embedding_data(self):
y = self.y.copy()
color_of_pts_on_tear = self.color_of_pts_on_tear.copy()
color_of_pts_on_tear = self.model.compute_color_of_pts_on_tear(y, self.tear_color_eig_inds)
cmap_interior = self.cmap_interior
cmap_tear = self.cmap_tear

matplotlib.use("Agg")
color_of_pts_on_tear = self.color_of_pts_on_tear
pts_on_tear = ~np.isnan(color_of_pts_on_tear[:, -1])

interior_handle, tear_handle = vis.Visualize().global_embedding_for_gui(
y,
y[:, 0],
cmap0=cmap_interior,
color_of_pts_on_tear=color_of_pts_on_tear[:, -1],
color_of_pts_on_tear=color_of_pts_on_tear[:, self.tear_color_eig_inds],
cmap1=cmap_tear,
set_title=True,
figsize=(3, 3),
s=20,
s=40,
)
if self.save_progress_dir:
save_fn = (
self.save_progress_dir
+ "/reg_tear_y_at_iter="
+ str(self.cur_iter)
+ ".png"
+ ".eps"
)
plt.savefig(save_fn, bbox_inches="tight", dpi=400)

Expand Down Expand Up @@ -234,6 +243,7 @@ def paste_clusters(self, final_polyg):
selected_cluster_mask = self.metadata[self.cur_iter]["selected_cluster_mask"]
points_in_selected_clusters = selected_cluster_mask[self.model.c]
y = self.y.copy()

y_new = self.recompute_embedding(
y,
points_in_selected_clusters,
Expand Down Expand Up @@ -278,12 +288,12 @@ def finish_pasting(self, y_new):
)
self.color_of_pts_on_tear = model.compute_color_of_pts_on_tear(self.y)

self.save_buml_obj(
"buml_obj_and_metadata_after_iter=" + str(self.cur_iter) + ".dat",
self.save_model(
"model_and_metadata_after_iter=" + str(self.cur_iter) + ".dat",
)
self.cur_iter += 1

def save_buml_obj(self, fname):
def save_model(self, fname):
if self.save_progress_dir:
new_emb_info = {
"y": self.y,
Expand All @@ -309,7 +319,7 @@ def recompute_embedding(
)
return y

def save_polygon(self, y, y_face_color, y_polyg, stage, s=20):
def save_polygon(self, y, y_face_color, y_polyg, stage, s=40):
assert stage in ["init", "final"]
matplotlib.use("Agg")
_, ax = plt.subplots()
Expand All @@ -320,16 +330,16 @@ def save_polygon(self, y, y_face_color, y_polyg, stage, s=20):
plt.axis("image")
plt.axis("off")
plt.tight_layout()
ax.set_rasterized(True)
save_fn = (
self.save_progress_dir
+ "/"
+ stage
+ "_polyg_at_iter="
+ str(self.cur_iter)
+ ".png"
+ ".eps"
)
plt.savefig(save_fn, bbox_inches="tight", dpi=400)
ax.set_rasterized(True)


def get_convex_covering_polygon(y):
Expand All @@ -339,8 +349,11 @@ def get_convex_covering_polygon(y):

# APP itself
###############################################################
from datetime import datetime

REG_TEAR_TAG = "reg_tear"
# Format as YYYY-MM-DD HH:MM:SS
string_format = datetime.now().strftime("%Y-%m-%d %H:%M:%S")
REG_TEAR_TAG = "reg_tear_" + string_format

# Spinner using CSS
################################################################
Expand Down Expand Up @@ -446,21 +459,26 @@ def print_main_log(message):
################################################################
gen_data_path_input = TextInput(
title="Generated data path",
value="/Users/joshuaoffergeld/Documents/pyRATS/examples",
value="/data2/dhruv/RATS_code/RATS/code/R2OFday1/notebooks/generated_data/",
width=550,
)
cut_and_paste_metadata_path_input = TextInput(
title="Cut and paste metadata path (leave it blank if running for the first time)",
value="/data2/dhruv/RATS_code/RATS/code/R2OFday1/notebooks/generated_data/rats_mishnelab/34_3_reg_tear_2026-06-16 15:04:51/model_and_metadata_after_iter=1.dat",
width=550,
)

algo_input = TextInput(title="Algorithm Name: (for ex: rats)", value="rats")
hyp_param_input = TextInput(title="Hyperparameter: (for ex: 28_5)", value="28_5")
algo_input = TextInput(title="Algorithm Name: (for ex: rats)", value="rats_mishnelab")
hyp_param_input = TextInput(title="Hyperparameter: (for ex: 28_5)", value="34_3")
options_input = TextAreaInput(
title="Additional options:",
value="{'force_compute': True, 'max_refinement_iter': 10, 'cmap_interior': 'summer', 'cmap_tear': 'jet'}",
value="{'force_compute': False, 'max_refinement_iter': 10, 'cmap_interior': 'summer', 'cmap_tear': 'jet', 'tear_color_eig_inds': [5, 2, 3]}",
rows=5,
)

cut_and_paste_obj = None
rot_deg = 5
lasso_tool = LassoSelectTool()
select_tool = PolySelectTool()
tap_tool = TapTool()

update_max_fig_height_button = Button(
Expand All @@ -478,15 +496,16 @@ def print_main_log(message):
)

source = ColumnDataSource(data=dict(x=[], y=[], color=[]))
cluster_patches_source = ColumnDataSource(data=dict(xs=[], ys=[]))
patch_source = ColumnDataSource(data=dict(x=[], y=[]))

MAX_FIG_HEIGHT = 900
MAX_FIG_WIDTH = 900
MAX_FIG_HEIGHT = 200
MAX_FIG_WIDTH = 200

max_fig_height_input = TextInput(title="Max figure height", value=str(MAX_FIG_HEIGHT))
fig = figure(
title="Cut & Paste operation on the embedding",
tools=[lasso_tool],
tools=[select_tool],
x_axis_label="x",
y_axis_label="y",
width=MAX_FIG_HEIGHT,
Expand All @@ -500,22 +519,22 @@ def print_main_log(message):
# Adjust figure size using the scatter x and y coordinates
##############################################################################
def adjust_figure_size():
print(source.data, source)
x_min = 1.25 * np.min(source.data["x"])
x_max = 1.25 * np.max(source.data["x"])
y_min = 1.25 * np.min(source.data["y"])
y_max = 1.25 * np.max(source.data["y"])
scale = 2
x_min = scale * np.min(source.data["x"])
x_max = scale * np.max(source.data["x"])
y_min = scale * np.min(source.data["y"])
y_max = scale * np.max(source.data["y"])
aspect_ratio = (x_max - x_min) / (y_max - y_min)
print("Aspect ratio (x/y) of the embedding: " + str(aspect_ratio))
print("Adjusting figure width based on the aspect ratio.")
print("MAX_FIG_WIDTH = " + str(MAX_FIG_WIDTH))
print("MAX_FIG_HEIGHT = " + str(MAX_FIG_HEIGHT))
if aspect_ratio >= 1:
fig.height = int(1.25 * MAX_FIG_WIDTH / aspect_ratio)
fig.width = int(1.25 * MAX_FIG_WIDTH)
fig.height = int(scale * MAX_FIG_WIDTH / aspect_ratio)
fig.width = int(scale * MAX_FIG_WIDTH)
else:
fig.height = int(1.25 * MAX_FIG_HEIGHT)
fig.width = int(1.25 * aspect_ratio * MAX_FIG_HEIGHT)
fig.height = int(scale * MAX_FIG_HEIGHT)
fig.width = int(scale * aspect_ratio * MAX_FIG_HEIGHT)

fig.x_range = Range1d(x_min, x_max, bounds=(x_min, x_max))
fig.y_range = Range1d(y_min, y_max, bounds=(y_min, y_max))
Expand Down Expand Up @@ -668,26 +687,36 @@ def read(fpath, verbose=True):

def start_main():
gen_data_path = gen_data_path_input.value.strip()
cut_and_paste_metadata_path = cut_and_paste_metadata_path_input.value.strip()
algo = algo_input.value.strip()
hyp_param = hyp_param_input.value.strip()
buml_obj_info_path = (
model_info_path = (
gen_data_path + "/" + algo + "/" + hyp_param + "/" + algo + ".dat"
)
save_dir = gen_data_path + "/" + algo + "/" + hyp_param + "_" + REG_TEAR_TAG
if cut_and_paste_metadata_path != "":
print("cut_and_paste_metadata_path=" + cut_and_paste_metadata_path)
save_dir = gen_data_path + "/" + algo + "/" + cut_and_paste_metadata_path.split('/')[-2]
else:
cut_and_paste_metadata_path = None
save_dir = gen_data_path + "/" + algo + "/" + hyp_param + "_" + REG_TEAR_TAG

options = process_additional_options()
print("buml_obj_info_path=" + buml_obj_info_path)
print("model_info_path=" + model_info_path)
print("save_dir=" + save_dir)
global cut_and_paste_obj
emb_info, metadata = read(buml_obj_info_path)
emb_info, metadata = read(model_info_path)


cut_and_paste_obj = CutAndPaste(
model=emb_info["model"],
y=emb_info["y"],
color_of_pts_on_tear=emb_info["color_of_pts_on_tear"],
metadata_fpath=cut_and_paste_metadata_path,
save_progress_dir=save_dir,
max_refinement_iter=options["max_refinement_iter"],
force_compute=options["force_compute"],
cmap_interior=options["cmap_interior"],
cmap_tear=options["cmap_tear"],
tear_color_eig_inds=options["tear_color_eig_inds"]
)
source.data = cut_and_paste_obj.get_current_embedding_data()

Expand All @@ -698,8 +727,9 @@ def start_end():
cut_button.disabled = False
update_max_fig_height_button.disabled = False
fig.toolbar.active_inspect = None
fig.toolbar.active_drag = lasso_tool
print_main_log("Select region to cut using lasso and then press cut.")
#fig.toolbar.active_drag = select_tool
fig.toolbar.active_tap = select_tool
print_main_log("Select polygonal region to cut (tap at a location to add a vertex), press Enter/Esc to finish selection and then press cut button.")


def start():
Expand All @@ -721,13 +751,16 @@ def on_start_button_click():
# Cut
#######################################
def cut_start():
fig.toolbar.active_drag = None
#fig.toolbar.active_drag = None
fig.toolbar.active_tap = None
cut_button.disabled = True
save_button.disabled = True


def cut_main():
global cut_and_paste_obj
print(source.selected.indices)
print(len(source.selected.indices))
patch_source.data = cut_and_paste_obj.cut_clusters_to_move(source.selected.indices)
source.selected.indices = cut_and_paste_obj.selected_pts_to_move.tolist()
print("len(source.selected.indices) = " + str(len(source.selected.indices)))
Expand Down Expand Up @@ -768,7 +801,8 @@ def paste_end():
cut_button.disabled = False
save_button.disabled = False
patch_source.data = dict(x=[], y=[])
fig.toolbar.active_drag = lasso_tool
#fig.toolbar.active_drag = select_tool
fig.toolbar.active_tap = select_tool


def paste_main():
Expand Down Expand Up @@ -800,7 +834,7 @@ def on_paste_button_click():
def save_():
algo = algo_input.value.strip()
global cut_and_paste_obj
cut_and_paste_obj.save_buml_obj(algo + ".dat")
cut_and_paste_obj.save_model(algo + ".dat")


def on_save_button_click():
Expand Down Expand Up @@ -833,6 +867,7 @@ def on_update_max_fig_height_button_click():
column(
main_log_div,
row(gen_data_path_input),
row(cut_and_paste_metadata_path_input),
row(algo_input, hyp_param_input, options_input, max_fig_height_input),
row(
update_max_fig_height_button,
Expand Down
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