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feat: Use image color when add layer to napari #1200

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Merged
merged 10 commits into from
Sep 27, 2024
Merged

feat: Use image color when add layer to napari #1200

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edc344f
Use image color when add layer to napari
Czaki Sep 26, 2024
24f781f
fix condition in adjust_color and add type annotation
Czaki Sep 26, 2024
d7ce992
add coments with clarification
Czaki Sep 26, 2024
8e1eb08
improve tests to handle color clipping
Czaki Sep 26, 2024
92950aa
fix mn req case
Czaki Sep 27, 2024
bab3447
add information about channel colors in preview of image maetadata
Czaki Sep 27, 2024
6aa5593
fix merging of channels and skip min_req test
Czaki Sep 27, 2024
d34bc47
improve `adjust_color`function
Czaki Sep 27, 2024
fe7a8f8
fix tests
Czaki Sep 27, 2024
21813e7
explain why keep unused parameters
Czaki Sep 27, 2024
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6 changes: 5 additions & 1 deletion package/PartSeg/common_gui/advanced_tabs.py
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Original file line number Diff line number Diff line change
Expand Up @@ -275,4 +275,8 @@ def __init__(self, settings: PartSettings, parent=None):

def update_metadata(self):
self._dict_viewer.set_data(self.settings.image.metadata)
self.channel_info.setText(f"Channels: {self.settings.image.channel_names}")
text = ", ".join(
f"{name}: {color}"
for name, color in zip(self.settings.image.channel_names, self.settings.image.get_colors())
)
self.channel_info.setText(f"Channels with colors: {text}")
45 changes: 45 additions & 0 deletions package/PartSegCore/napari_plugins/loader.py
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Original file line number Diff line number Diff line change
@@ -1,10 +1,54 @@
import typing
from importlib.metadata import version

import numpy as np
from packaging.version import parse as parse_version

from PartSegCore.analysis import ProjectTuple
from PartSegCore.io_utils import LoadBase, WrongFileTypeException
from PartSegCore.mask.io_functions import MaskProjectTuple
from PartSegImage import Image


@typing.overload
def adjust_color(color: str) -> str: ...


@typing.overload
def adjust_color(color: typing.List[int]) -> typing.List[float]: ...


def adjust_color(color: typing.Union[str, typing.List[int]]) -> typing.Union[str, typing.List[float]]:
# as napari ignore alpha channel in color, and adding it to
# color cause that napari fails to detect that such colormap is already present
# in this function I remove alpha channel if it is present
if isinstance(color, str) and color.startswith("#"):
if len(color) == 9:
# case when color is in format #RRGGBBAA
return color[:7]
if len(color) == 5:
# case when color is in format #RGBA
return color[:4]
elif isinstance(color, list):
return [color[i] / 255 for i in range(3)]
# If not fit to an earlier case, return as is.
# Maybe napari will handle it
return color


if parse_version(version("napari")) >= parse_version("0.4.19a1"):

def add_color(image: Image, idx: int) -> dict:
return {
"colormap": adjust_color(image.get_colors()[idx]),
}

else:

def add_color(image: Image, idx: int) -> dict: # noqa: ARG001
# Do nothing, as napari is not able to pass hex color to image
# the image and idx are present to keep the same signature
return {}


def _image_to_layers(project_info, scale, translate):
Expand All @@ -27,6 +71,7 @@ def _image_to_layers(project_info, scale, translate):
"blending": "additive",
"translate": translate,
"metadata": project_info.image.metadata,
**add_color(project_info.image, i),
},
"image",
)
Expand Down
12 changes: 8 additions & 4 deletions package/PartSegImage/image.py
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Original file line number Diff line number Diff line change
Expand Up @@ -393,6 +393,7 @@ def merge(self, image: Image, axis: str) -> Image:
self._channel_arrays + [self.reorder_axes(x, image.array_axis_order) for x in image._channel_arrays]
)
channel_names = self._merge_channel_names(self.channel_names, image.channel_names)
color_map = self.default_coloring + image.default_coloring
else:
index = self.array_axis_order.index(axis)
data = self._image_data_normalize(
Expand All @@ -402,8 +403,11 @@ def merge(self, image: Image, axis: str) -> Image:
]
)
channel_names = self.channel_names
color_map = self.default_coloring

return self.substitute(data=data, ranges=self.ranges + image.ranges, channel_names=channel_names)
return self.substitute(
data=data, ranges=self.ranges + image.ranges, channel_names=channel_names, default_coloring=color_map
)

@property
def channel_names(self) -> list[str]:
Expand Down Expand Up @@ -494,7 +498,7 @@ def substitute(
channel_names = self.channel_names if channel_names is None else channel_names

channel_info = [
ChannelInfoFull(name=name, color_map=color, contrast_limits=contrast_limits)
ChannelInfo(name=name, color_map=color, contrast_limits=contrast_limits)
for name, color, contrast_limits in zip_longest(channel_names, default_coloring, ranges)
]

Expand Down Expand Up @@ -973,9 +977,9 @@ def _hex_to_rgb(hex_code: str) -> tuple[int, int, int]:
"""
hex_code = hex_code.lstrip("#")

if len(hex_code) == 3:
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suggestion: Improve handling of hex codes with alpha channels

While the function now accepts 4-digit and 8-digit hex codes, it still only returns RGB values, discarding any alpha information. Consider extending the function to handle and return alpha channel information when present.

def hex_to_rgb(hex_code):
    """Convert hex color code to RGB tuple."""
    hex_code = hex_code.lstrip("#")

    if len(hex_code) in {3, 4, 6, 8}:
        if len(hex_code) < 5:
            hex_code = "".join([c * 2 for c in hex_code])
        rgb = tuple(int(hex_code[i:i+2], 16) for i in (0, 2, 4))
        if len(hex_code) == 8:
            return rgb + (int(hex_code[6:8], 16),)
        return rgb

if len(hex_code) in {3, 4}:
hex_code = "".join([c * 2 for c in hex_code])
elif len(hex_code) != 6:
elif len(hex_code) not in {6, 8}:
raise ValueError(f"Invalid hex code format: {hex_code}")

return int(hex_code[:2], 16), int(hex_code[2:4], 16), int(hex_code[4:6], 16)
Expand Down
21 changes: 17 additions & 4 deletions package/tests/conftest.py
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Original file line number Diff line number Diff line change
Expand Up @@ -25,7 +25,7 @@
from PartSegCore.roi_info import ROIInfo
from PartSegCore.segmentation.restartable_segmentation_algorithms import BorderRim, LowerThresholdAlgorithm
from PartSegCore.segmentation.segmentation_algorithm import ThresholdAlgorithm
from PartSegImage import Image
from PartSegImage import ChannelInfo, Image


@pytest.fixture(scope="module")
Expand Down Expand Up @@ -69,20 +69,33 @@ def image2(image, tmp_path):
def image2d(tmp_path):
data = np.zeros([20, 20], dtype=np.uint8)
data[10:-1, 1:-1] = 20
return Image(data, (10**-3, 10**-3), axes_order="YX", file_path=str(tmp_path / "test.tiff"))
return Image(data, spacing=(10**-3, 10**-3), axes_order="YX", file_path=str(tmp_path / "test.tiff"))


@pytest.fixture
def stack_image():
data = np.zeros([20, 40, 40, 2], dtype=np.uint8)
data = np.zeros([20, 40, 40, 3], dtype=np.uint8)
for x, y in itertools.product([0, 20], repeat=2):
data[1:-1, x + 2 : x + 18, y + 2 : y + 18] = 100
for x, y in itertools.product([0, 20], repeat=2):
data[3:-3, x + 4 : x + 16, y + 4 : y + 16] = 120
for x, y in itertools.product([0, 20], repeat=2):
data[5:-5, x + 6 : x + 14, y + 6 : y + 14] = 140

return MaskProjectTuple("test_path", Image(data, (2, 1, 1), axes_order="ZYXC", file_path="test_path"))
return MaskProjectTuple(
"test_path",
Image(
data,
spacing=(2, 1, 1),
axes_order="ZYXC",
file_path="test_path",
channel_info=[
ChannelInfo(name="channel 1", color_map="#00FF00FF"),
ChannelInfo(name="channel 2", color_map="#00FF"),
ChannelInfo(name="channel 3", color_map="#FF0000"),
],
),
)


@pytest.fixture
Expand Down
6 changes: 3 additions & 3 deletions package/tests/test_PartSeg/test_viewer.py
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Original file line number Diff line number Diff line change
Expand Up @@ -75,13 +75,13 @@ def test_base(self, image, analysis_segmentation2, tmp_path):
assert len(viewer.layers) == 2
settings.image = analysis_segmentation2.image
viewer.create_initial_layers(True, True, True, True)
assert len(viewer.layers) == 2
assert len(viewer.layers) == 3
settings.roi = analysis_segmentation2.roi_info.roi
viewer.create_initial_layers(True, True, True, True)
assert len(viewer.layers) == 3
assert len(viewer.layers) == 4
settings.mask = analysis_segmentation2.mask
viewer.create_initial_layers(True, True, True, True)
assert len(viewer.layers) == 4
assert len(viewer.layers) == 5
viewer.close()

def test_points(self, image, tmp_path, qtbot):
Expand Down
37 changes: 29 additions & 8 deletions package/tests/test_PartSegCore/test_napari_plugins.py
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Original file line number Diff line number Diff line change
@@ -1,10 +1,12 @@
# pylint: disable=no-self-use

import os
from importlib.metadata import version

import numpy as np
import pytest
from napari.layers import Image, Labels, Layer
from packaging.version import parse as parse_version

from PartSegCore.analysis import ProjectTuple
from PartSegCore.mask.io_functions import LoadROIFromTIFF
Expand All @@ -27,20 +29,39 @@
def test_project_to_layers_analysis(analysis_segmentation):
analysis_segmentation.roi_info.alternative["test"] = np.zeros(analysis_segmentation.image.shape, dtype=np.uint8)
res = project_to_layers(analysis_segmentation)
assert len(res) == 4
assert len(res) == 5
l1 = Layer.create(*res[0])
assert isinstance(l1, Image)
assert l1.name == "channel 1"
assert np.allclose(l1.scale[1:] / 1e9, analysis_segmentation.image.spacing)
l2 = Layer.create(*res[2])
assert isinstance(l2, Labels)
assert l2.name == "ROI"
assert np.allclose(l2.scale[1:] / 1e9, analysis_segmentation.image.spacing)
l3 = Layer.create(*res[3])
assert isinstance(l3, Labels)
assert l3.name == "test"
assert l3.name == "ROI"
assert np.allclose(l3.scale[1:] / 1e9, analysis_segmentation.image.spacing)
assert not l3.visible
l4 = Layer.create(*res[4])
assert isinstance(l4, Labels)
assert l4.name == "test"
assert np.allclose(l4.scale[1:] / 1e9, analysis_segmentation.image.spacing)
assert not l4.visible


@pytest.mark.skipif(
parse_version(version("napari")) < parse_version("0.4.19a16"), reason="not supported by old napari versions"
)
def test_passing_colormap(analysis_segmentation):
res = project_to_layers(analysis_segmentation)
l1 = Layer.create(*res[0])
assert isinstance(l1, Image)
assert l1.name == "channel 1"
assert l1.colormap.name == "green"
l2 = Layer.create(*res[1])
assert isinstance(l2, Image)
assert l2.name == "channel 2"
assert l2.colormap.name == "blue"
l2 = Layer.create(*res[2])
assert isinstance(l2, Image)
assert l2.name == "channel 3"
assert l2.colormap.name == "red"


def test_project_to_layers_roi():
Expand All @@ -55,7 +76,7 @@ def test_project_to_layers_roi():

def test_project_to_layers_mask(stack_segmentation1):
res = project_to_layers(stack_segmentation1)
assert len(res) == 3
assert len(res) == 4
assert res[0][2] == "image"


Expand Down
4 changes: 3 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 @@ -700,11 +700,13 @@ def test_merge_channel_props_with_none(channel_name, default_coloring, ranges):

def test_hex_to_rgb():
assert _hex_to_rgb("#ff0000") == (255, 0, 0)
assert _hex_to_rgb("#ff0000ff") == (255, 0, 0)
assert _hex_to_rgb("#00FF00") == (0, 255, 0)
assert _hex_to_rgb("#b00") == (187, 0, 0)
assert _hex_to_rgb("#b00f") == (187, 0, 0)
assert _hex_to_rgb("#B00") == (187, 0, 0)
with pytest.raises(ValueError, match="Invalid hex code format"):
_hex_to_rgb("#b000")
_hex_to_rgb("#b0000")


def test_name_to_rgb():
Expand Down
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