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Merged
merged 5 commits into from
Sep 23, 2024
Merged

chore: Add missed code from #1191 #1197

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f174e95
Add mised code from #1191
Czaki Sep 22, 2024
f9ff1f2
improve code
Czaki Sep 23, 2024
60f536d
update tests
Czaki Sep 23, 2024
a6355d6
fix skipif
Czaki Sep 23, 2024
51def5b
change to proper importskip
Czaki Sep 23, 2024
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78 changes: 41 additions & 37 deletions package/PartSegImage/image.py
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Original file line number Diff line number Diff line change
Expand Up @@ -250,9 +250,11 @@ def __init__(

@staticmethod
def _adjust_channel_info(
channel_info: list[ChannelInfo | ChannelInfoFull] | None, channel_array: list[np.ndarray]
channel_info: list[ChannelInfo | ChannelInfoFull] | None,
channel_array: list[np.ndarray],
default_colors=("red", "blue", "green", "yellow", "magenta", "cyan"),
) -> list[ChannelInfoFull]:
default_colors = cycle(["red", "blue", "green", "yellow", "magenta", "cyan"])
default_colors = cycle(default_colors)
if channel_info is None:
ranges = [(np.min(x), np.max(x)) for x in channel_array]
return [
Expand All @@ -262,32 +264,28 @@ def _adjust_channel_info(

channel_info = channel_info[: len(channel_array)]

res = []

for i, ch_inf in enumerate(channel_info):
res.append(
ChannelInfoFull(
name=ch_inf.name or f"channel {i+1}",
color_map=(
ch_inf.color_map if ch_inf.color_map is not None else next(default_colors) # skipcq: PTC-W0063
),
contrast_limits=(
ch_inf.contrast_limits
if ch_inf.contrast_limits is not None
else (np.min(channel_array[i]), np.max(channel_array[i]))
),
)
res = [
ChannelInfoFull(
name=ch_inf.name or f"channel {i+1}",
color_map=(
ch_inf.color_map if ch_inf.color_map is not None else next(default_colors) # skipcq: PTC-W0063
),
contrast_limits=(
ch_inf.contrast_limits
if ch_inf.contrast_limits is not None
else (np.min(channel_array[i]), np.max(channel_array[i]))
),
)

for i, arr in enumerate(channel_array[len(res) :], start=len(channel_info)):
res.append(
ChannelInfoFull(
name=f"channel {i+1}",
color_map=next(default_colors), # skipcq: PTC-W0063
contrast_limits=(np.min(arr), np.max(arr)),
)
for i, ch_inf in enumerate(channel_info)
]
res.extend(
ChannelInfoFull(
name=f"channel {i+1}",
color_map=next(default_colors), # skipcq: PTC-W0063
contrast_limits=(np.min(arr), np.max(arr)),
)

for i, arr in enumerate(channel_array[len(res) :], start=len(channel_info))
)
return res

@staticmethod
Expand Down Expand Up @@ -990,19 +988,25 @@ def _name_to_rgb(name: str) -> tuple[int, int, int]:
:param str name: The color name
:return: A tuple containing the RGB values (R, G, B)
"""
name = name.lower()
if name not in _NAMED_COLORS:
raise ValueError(f"Unknown color name: {name}")
return _hex_to_rgb(_NAMED_COLORS[name])


_NAMED_COLORS = {
"red": "#FF0000",
"green": "#00FF00",
"blue": "#0000FF",
"yellow": "#FFFF00",
"cyan": "#00FFFF",
"magenta": "#FF00FF",
"white": "#FFFFFF",
"black": "#000000",
"orange": "#FFA500",
}
try:
from vispy.color import get_color_dict
except ImportError: # pragma: no cover
_NAMED_COLORS = {
"red": "#FF0000",
"green": "#008000",
"blue": "#0000FF",
"yellow": "#FFFF00",
"cyan": "#00FFFF",
"magenta": "#FF00FF",
"white": "#FFFFFF",
"black": "#000000",
"orange": "#FFA500",
}
else:
_NAMED_COLORS = get_color_dict()
23 changes: 22 additions & 1 deletion package/tests/test_PartSegImage/test_image.py
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Original file line number Diff line number Diff line change
Expand Up @@ -6,7 +6,7 @@
from skimage.morphology import diamond

from PartSegImage import Channel, ChannelInfo, Image, ImageWriter, TiffImageReader
from PartSegImage.image import FRAME_THICKNESS, _hex_to_rgb
from PartSegImage.image import FRAME_THICKNESS, _hex_to_rgb, _name_to_rgb


class TestImageBase:
Expand Down Expand Up @@ -705,3 +705,24 @@ def test_hex_to_rgb():
assert _hex_to_rgb("#B00") == (187, 0, 0)
with pytest.raises(ValueError, match="Invalid hex code format"):
_hex_to_rgb("#b000")


def test_name_to_rgb():
assert _name_to_rgb("red") == (255, 0, 0)
assert _name_to_rgb("Red") == (255, 0, 0)
assert _name_to_rgb("RED") == (255, 0, 0)
assert _name_to_rgb("blue") == (0, 0, 255)
assert _name_to_rgb("green") == (0, 128, 0)
assert _name_to_rgb("white") == (255, 255, 255)
assert _name_to_rgb("black") == (0, 0, 0)
assert _name_to_rgb("yellow") == (255, 255, 0)
with pytest.raises(ValueError, match="Unknown color name"):
_name_to_rgb("strange")
with pytest.raises(ValueError, match="Unknown color name"):
_name_to_rgb("")


def test_name_to_rgb_vispy():
# This test check mapping not defined in fallback dictionary
pytest.importorskip("vispy", reason="vispy not installed")
assert _name_to_rgb("lime") == (0, 255, 0)
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