15034886290

Committed 15 May 2025 01:54AM UTC coverage: 19.059%. First build

Build # 15034886290

Build Type

push

github

Committed by

web-flow

Commit Message

Merge pull request #29 from pinneylab/binding-processing-refactor

Binding processing refactor

Coverage Stats

31 of 65 new or added lines in 2 files covered. (47.69%)

470 of 2466 relevant lines covered (19.06%)

0.76 hits per line

Source File
Press 'n' to go to next uncovered line, 'b' for previous

0.0

/src/htbam_analysis/scripts/corner_picker.py

import argparse
from bokeh.models import ColumnDataSource
from bokeh.plotting import figure
from bokeh.layouts import gridplot, column
import numpy as np
from PIL import Image

from bokeh.io import curdoc
from bokeh.events import Tap
from bokeh.models import Slider
from bokeh.models import Div

"""

"""

def compute_corner_slices(stitched_image):
    
    fraction = 1/8
    height, width = stitched_image.shape
    h_crop = int(height * fraction)
    w_crop = int(width * fraction)

    slices = [
        (slice(0, h_crop), slice(0, w_crop)),                            # Top-left
        (slice(0, h_crop), slice(width - w_crop, width)),               # Top-right
        (slice(height - h_crop, height), slice(0, w_crop)),            # Bottom-left
        (slice(height - h_crop, height), slice(width - w_crop, width)) # Bottom-right
    ]

    return slices

# init parser
parser = argparse.ArgumentParser(description='Launches corner-picking GUI')
parser.add_argument("stitched_image", type=str, help='Path to a stitched image.')
args = parser.parse_args()
stitched_image = np.array(Image.open(args.stitched_image)).astype(float)

# grab corners
corners = ['Top-Left', 'Top-Right', 'Bottom-Left', 'Bottom-Right']
corner_slices = compute_corner_slices(stitched_image)

plots = []
click_sources = []
corner_coords = [None] * 4
coord_display = Div(text="COPY/PASTE ME INTO PROCESSING NOTEBOOK: (None, None), (None, None), (None, None), (None, None)", styles={"font-size": "20px"})

image_sources = []  # To store the original cropped images
image_renderers = []  # To update image brightness later

for idx, s in enumerate(corner_slices):

    # Load and convert to NumPy
    corner_image = stitched_image[s]
    height, width = corner_image.shape
    x0, y0 = s[0].start, s[1].start
    dw, dh = s[1].stop - s[1].start, s[0].stop - s[0].start

    # Click source for recording clicks
    source = ColumnDataSource(data=dict(x=[], y=[], index=[]))
    click_sources.append(source)

    # Set up plot
    # TODO: make width and height more flexible
    p = figure(
        title=corners[idx],
        width=800, height=800,
        tools="tap",
        x_range=(s[1].start, s[1].stop),
        y_range=(s[0].stop, s[0].start)
    )

    # Store for brightness adjustments
    img_cropped_original = corner_image.copy()
    image_sources.append(img_cropped_original)

    renderer = p.image(image=[corner_image], x=y0, y=x0, dw=dw, dh=dh, palette="Greys256")
    image_renderers.append(renderer)

    p.scatter('x', 'y', size=5, color='red', alpha=0.6, source=source)
    
    def make_callback(i, src):
        def on_tap(event):
            # Save coordinate
            src.data = dict(x=[event.x], y=[event.y])

            y_offset = 0
            x_offset = 0
            corner_coords[i] = (event.x + x_offset, event.y + y_offset)

            formatted = "COPY/PASTE ME INTO PROCESSING NOTEBOOK: " + ", ".join(
                f"(({f'{pt[0]:.0f}' if pt is not None else 'None'}, {f'{pt[1]:.0f}' if pt is not None else 'None'}))"
                for pt in corner_coords
            )

            coord_display.text = formatted
        return on_tap

    p.on_event(Tap, make_callback(idx, source))

    plots.append(p)

def update_brightness(attr, old, new):
    scale = brightness_slider.value
    for i in range(4):
        tmp = image_sources[i].copy()
        adjusted = np.clip(tmp * scale, 0, 255)
        image_renderers[i].data_source.data = dict(
            image=[adjusted],
            x=[image_renderers[i].glyph.x],
            y=[image_renderers[i].glyph.y],
            dw=[image_renderers[i].glyph.dw],
            dh=[image_renderers[i].glyph.dh]
        )

brightness_slider = Slider(start=0.1, end=5.0, value=1.0, step=0.1, title="Brightness", width=800, styles={"font-size": "20px"})
brightness_slider.on_change("value", update_brightness)

# Arrange in a 2x2 grid
grid = gridplot([[plots[0], plots[1]], [plots[2], plots[3]]])
curdoc().add_root(column(grid, brightness_slider, coord_display))

1	import argparse	×
2	from bokeh.models import ColumnDataSource	×
3	from bokeh.plotting import figure	×
4	from bokeh.layouts import gridplot, column	×
5	import numpy as np	×
6	from PIL import Image	×
7
8	from bokeh.io import curdoc	×
9	from bokeh.events import Tap	×
10	from bokeh.models import Slider	×
11	from bokeh.models import Div	×
12
13	"""
14
15	"""
16
17	def compute_corner_slices(stitched_image):	×
18
19	fraction = 1/8	×
20	height, width = stitched_image.shape	×
21	h_crop = int(height * fraction)	×
22	w_crop = int(width * fraction)	×
23
24	slices = [	×
25	(slice(0, h_crop), slice(0, w_crop)), # Top-left
26	(slice(0, h_crop), slice(width - w_crop, width)), # Top-right
27	(slice(height - h_crop, height), slice(0, w_crop)), # Bottom-left
28	(slice(height - h_crop, height), slice(width - w_crop, width)) # Bottom-right
29	]
30
31	return slices	×
32
33	# init parser
34	parser = argparse.ArgumentParser(description='Launches corner-picking GUI')	×
35	parser.add_argument("stitched_image", type=str, help='Path to a stitched image.')	×
36	args = parser.parse_args()	×
37	stitched_image = np.array(Image.open(args.stitched_image)).astype(float)	×
38
39	# grab corners
40	corners = ['Top-Left', 'Top-Right', 'Bottom-Left', 'Bottom-Right']	×
41	corner_slices = compute_corner_slices(stitched_image)	×
42
43	plots = []	×
44	click_sources = []	×
45	corner_coords = [None] * 4	×
46	coord_display = Div(text="COPY/PASTE ME INTO PROCESSING NOTEBOOK: (None, None), (None, None), (None, None), (None, None)", styles={"font-size": "20px"})	×
47
48	image_sources = [] # To store the original cropped images	×
49	image_renderers = [] # To update image brightness later	×
50
51	for idx, s in enumerate(corner_slices):	×
52
53	# Load and convert to NumPy
54	corner_image = stitched_image[s]	×
55	height, width = corner_image.shape	×
56	x0, y0 = s[0].start, s[1].start	×
57	dw, dh = s[1].stop - s[1].start, s[0].stop - s[0].start	×
58
59	# Click source for recording clicks
60	source = ColumnDataSource(data=dict(x=[], y=[], index=[]))	×
61	click_sources.append(source)	×
62
63	# Set up plot
64	# TODO: make width and height more flexible
65	p = figure(	×
66	title=corners[idx],
67	width=800, height=800,
68	tools="tap",
69	x_range=(s[1].start, s[1].stop),
70	y_range=(s[0].stop, s[0].start)
71	)
72
73	# Store for brightness adjustments
74	img_cropped_original = corner_image.copy()	×
75	image_sources.append(img_cropped_original)	×
76
77	renderer = p.image(image=[corner_image], x=y0, y=x0, dw=dw, dh=dh, palette="Greys256")	×
78	image_renderers.append(renderer)	×
79
80	p.scatter('x', 'y', size=5, color='red', alpha=0.6, source=source)	×
81
82	def make_callback(i, src):	×
83	def on_tap(event):	×
84	# Save coordinate
85	src.data = dict(x=[event.x], y=[event.y])	×
86
87	y_offset = 0	×
88	x_offset = 0	×
89	corner_coords[i] = (event.x + x_offset, event.y + y_offset)	×
90
NEW 91	formatted = "COPY/PASTE ME INTO PROCESSING NOTEBOOK: " + ", ".join(	×
92	f"(({f'{pt[0]:.0f}' if pt is not None else 'None'}, {f'{pt[1]:.0f}' if pt is not None else 'None'}))"
93	for pt in corner_coords
94	)
95
96	coord_display.text = formatted	×
97	return on_tap	×
98
99	p.on_event(Tap, make_callback(idx, source))	×
100
101	plots.append(p)	×
102
103	def update_brightness(attr, old, new):	×
104	scale = brightness_slider.value	×
105	for i in range(4):	×
106	tmp = image_sources[i].copy()	×
107	adjusted = np.clip(tmp * scale, 0, 255)	×
108	image_renderers[i].data_source.data = dict(	×
109	image=[adjusted],
110	x=[image_renderers[i].glyph.x],
111	y=[image_renderers[i].glyph.y],
112	dw=[image_renderers[i].glyph.dw],
113	dh=[image_renderers[i].glyph.dh]
114	)
115
116	brightness_slider = Slider(start=0.1, end=5.0, value=1.0, step=0.1, title="Brightness", width=800, styles={"font-size": "20px"})	×
117	brightness_slider.on_change("value", update_brightness)	×
118
119	# Arrange in a 2x2 grid
120	grid = gridplot([[plots[0], plots[1]], [plots[2], plots[3]]])	×
121	curdoc().add_root(column(grid, brightness_slider, coord_display))	×

pinneylab / htbam_analysis / 15034886290

Source File Press 'n' to go to next uncovered line, 'b' for previous

Source File
Press 'n' to go to next uncovered line, 'b' for previous