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bugfix/catch-channel-colors-errors-from-typing #299

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evamaxfield merged 3 commits into from
Aug 23, 2021
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bugfix/catch-channel-colors-errors-from-typing #299

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883d008
Catch bugs for channel colors detected by typing
Aug 23, 2021
a121567
Resolve Madison comments
Aug 23, 2021
12a1ada
Merge branch 'main' into bugfix/catch-bugs-for-channel-colors-from-ty…
Aug 23, 2021
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93 changes: 88 additions & 5 deletions aicsimageio/tests/writers/test_ome_tiff_writer.py
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Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -353,15 +353,98 @@ def test_ome_tiff_writer_multiscene(
["TCZYX", "TCZYX"],
[(1.0, 2.0, 3.0), (4.0, 5.0, 6.0)],
),
(
np.random.rand(3, 16, 16),
"CYX",
types.PhysicalPixelSizes(None, 1.0, 1.0),
["C0", "C1", "C2"],
[[255, 0, 0], [0, 255, 0], [0, 0, 255]],
[(1, 3, 1, 16, 16)],
["TCZYX"],
[(None, 1.0, 1.0)],
),
pytest.param(
np.random.rand(3, 16, 16),
"CYX",
types.PhysicalPixelSizes(None, 1.0, 1.0),
["C0", "C1", "C2"],
[[255, 0, 0], [0, 255, 0], [0, 0, 255], [1, 1, 1]],
[(1, 3, 1, 16, 16)],
["TCZYX"],
[(None, 1.0, 1.0)],
marks=pytest.mark.raises(exception=ValueError),
),
(
[np.random.rand(3, 16, 16)],
["CYX"],
[types.PhysicalPixelSizes(None, 1.0, 1.0)],
[["C0", "C1", "C2"]],
[[[255, 0, 0], [0, 255, 0], [0, 0, 255]]],
[(1, 3, 1, 16, 16)],
["TCZYX"],
[(None, 1.0, 1.0)],
),
(
[np.random.rand(3, 16, 16)],
["CYX"],
[types.PhysicalPixelSizes(None, 1.0, 1.0)],
[["C0", "C1", "C2"]],
[None],
[(1, 3, 1, 16, 16)],
["TCZYX"],
[(None, 1.0, 1.0)],
),
(
[np.random.rand(3, 16, 16), np.random.rand(3, 16, 16)],
"CYX",
types.PhysicalPixelSizes(None, 1.0, 1.0),
["C0", "C1", "C2"],
[[255, 0, 0], [0, 255, 0], [0, 0, 255]],
[(1, 3, 1, 16, 16), (1, 3, 1, 16, 16)],
["TCZYX", "TCZYX"],
[(None, 1.0, 1.0), (None, 1.0, 1.0)],
),
(
[np.random.rand(3, 16, 16), np.random.rand(3, 4, 16, 16)],
["CYX", "CZYX"],
[
types.PhysicalPixelSizes(None, 1.0, 1.0),
types.PhysicalPixelSizes(1.0, 1.0, 1.0),
],
[["C0", "C1", "C2"], ["C4", "C5", "C6"]],
[
[[255, 0, 0], [0, 255, 0], [0, 0, 255]],
[[0, 255, 0], [0, 0, 255], [255, 0, 0]],
],
[(1, 3, 1, 16, 16), (1, 3, 4, 16, 16)],
["TCZYX", "TCZYX"],
[(None, 1.0, 1.0), (1.0, 1.0, 1.0)],
),
(
[np.random.rand(3, 16, 16), np.random.rand(3, 4, 16, 16)],
["CYX", "CZYX"],
[
types.PhysicalPixelSizes(None, 1.0, 1.0),
types.PhysicalPixelSizes(1.0, 1.0, 1.0),
],
[["C0", "C1", "C2"], ["C4", "C5", "C6"]],
[
None,
[[0, 255, 0], [0, 0, 255], [255, 0, 0]],
],
[(1, 3, 1, 16, 16), (1, 3, 4, 16, 16)],
["TCZYX", "TCZYX"],
[(None, 1.0, 1.0), (1.0, 1.0, 1.0)],
),
],
)
@pytest.mark.parametrize("filename", ["e.ome.tiff"])
def test_ome_tiff_writer_common_metadata(
array_data: List[types.ArrayLike],
write_dim_order: List[Optional[str]],
pixel_size: List[types.PhysicalPixelSizes],
channel_names: List[Optional[List[str]]],
channel_colors: List[Optional[List[int]]],
array_data: Union[types.ArrayLike, List[types.ArrayLike]],
write_dim_order: Union[Optional[str], List[Optional[str]]],
pixel_size: Union[types.PhysicalPixelSizes, List[types.PhysicalPixelSizes]],
channel_names: Union[List[str], List[Optional[List[str]]]],
channel_colors: Union[Optional[List[List[int]]], List[Optional[List[List[int]]]]],
read_shapes: List[Tuple[int, ...]],
read_dim_order: List[str],
expected_pixel_size: List[types.PhysicalPixelSizes],
Expand Down
84 changes: 65 additions & 19 deletions aicsimageio/writers/ome_tiff_writer.py
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Original file line number Diff line number Diff line change
Expand Up @@ -39,7 +39,9 @@ def save(
physical_pixel_sizes: Optional[
Union[types.PhysicalPixelSizes, List[types.PhysicalPixelSizes]]
] = None,
channel_colors: Optional[Union[List[int], List[Optional[List[int]]]]] = None,
channel_colors: Optional[
Union[List[List[int]], List[Optional[List[List[int]]]]]
] = None,
**kwargs: Any,
) -> None:
"""
Expand Down Expand Up @@ -88,9 +90,9 @@ def save(
List[types.PhysicalPixelSizes]]]
List of numbers representing the physical pixel sizes in Z, Y, X in microns
Default: None
channel_colors: Optional[Union[List[int], List[Optional[List[int]]]]]
List of rgb color values per channel. These must be values compatible with
the OME spec.
channel_colors: Optional[Union[List[List[int]], List[Optional[List[List[int]]]]]
List of rgb color values per channel or a list of lists for each image.
These must be values compatible with the OME spec.
Default: None

Raises
Expand Down Expand Up @@ -177,15 +179,16 @@ def save(
)
if channel_colors is not None:
if isinstance(channel_colors[0], list):
if len(channel_colors) != num_images:
raise exceptions.ConflictingArgumentsError(
f"OmeTiffWriter received a list of arrays to use as scenes "
f"but the provided list of channel_colors is of different "
f"length. "
f"Number of provided scenes: {num_images}, "
f"Number of provided dimension strings: "
f"{len(channel_colors)}"
)
if not isinstance(channel_colors[0][0], int):
if len(channel_colors) != num_images:
raise exceptions.ConflictingArgumentsError(
f"OmeTiffWriter received a list of arrays to use as "
f"scenes but the provided list of channel_colors is of "
f"different length. "
f"Number of provided scenes: {num_images}, "
f"Number of provided dimension strings: "
f"{len(channel_colors)}"
)

# make sure data is a list
if not isinstance(data, list):
Expand All @@ -205,7 +208,29 @@ def save(
] * num_images
if channel_names is None or isinstance(channel_names[0], str):
channel_names = [channel_names] * num_images # type: ignore
if channel_colors is None or isinstance(channel_colors[0], int):

if channel_colors is not None:
if all(
[
(
channel_colors[img_idx] is None
or isinstance(channel_colors[img_idx], list)
)
for img_idx in range(num_images)
]
):
single_image_channel_colors_provided = False
else:
single_image_channel_colors_provided = True

if (
channel_colors[0] is not None
and isinstance(channel_colors[0], list)
and isinstance(channel_colors[0][0], int)
):
single_image_channel_colors_provided = True

if channel_colors is None or single_image_channel_colors_provided:
channel_colors = [channel_colors] * num_images # type: ignore

xml = b""
Expand Down Expand Up @@ -418,7 +443,7 @@ def _build_ome_image(
None, None, None
),
channel_names: List[str] = None,
channel_colors: List[int] = None,
channel_colors: Optional[List[List[int]]] = None,
) -> Image:
if len(data_shape) < 2 or len(data_shape) > 6:
raise ValueError(f"Bad OME image shape length: {data_shape}")
Expand Down Expand Up @@ -447,7 +472,11 @@ def dim_or_1(dim: str) -> int:
if isinstance(channel_names, list) and len(channel_names) != channel_count:
raise ValueError(f"Wrong number of channel names {len(channel_names)}")
if isinstance(channel_colors, list) and len(channel_colors) != channel_count:
raise ValueError(f"Wrong number of channel colors {len(channel_colors)}")
raise ValueError(
f"Wrong number of channel colors. "
f"Received: {len(channel_colors)} ({channel_colors}) "
f"Expected: {channel_count}."
)

samples_per_pixel = 1
if is_rgb:
Expand Down Expand Up @@ -507,7 +536,24 @@ def dim_or_1(dim: str) -> int:
if channel_colors is not None:
assert len(channel_colors) >= pixels.size_c
for i in range(channel_count):
pixels.channels[i].color = Color(channel_colors[i])
this_channel_color_def = channel_colors[i]
if len(this_channel_color_def) != 3:
raise ValueError(
f"Expected RGB (3) color definition for channel color. "
f"Received {len(this_channel_color_def)} values "
f"({this_channel_color_def}) for image {image_index} "
f"channel {i}."
)
else:
# Handle List[int] -> Tuple[int, int, int] for color def
# Naive cast of tuple(List[int]) generates type: Tuple[int, ...]
this_channel_color = (
this_channel_color_def[0],
this_channel_color_def[1],
this_channel_color_def[2],
)
Comment on lines +550 to +554

@AetherUnbound AetherUnbound Aug 23, 2021

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I think this can just be tuple(this_channel_color_def)

[ins] In [1]: a = [1, 2, 3]

[ins] In [2]: tuple(a)
Out[2]: (1, 2, 3)

@evamaxfield evamaxfield Aug 23, 2021

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See my comment:

# Naive cast of tuple(List[int]) generates type: Tuple[int, ...]

I explicitely can't do that because of typing

@toloudis toloudis Aug 23, 2021

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On the other hand, the way it is written ensures no more than 3 entries even if the color def had too many

@evamaxfield evamaxfield Aug 23, 2021

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It will never reach that because I check for len(this_channel_color_def) != 3 and raise

@toloudis toloudis Aug 23, 2021

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yeah, forget i said anything 🤣

@AetherUnbound AetherUnbound Aug 23, 2021

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Ah, fair. I guess the alternative could be this_channel_color: Tuple[int, int, int] = tuple(this_channel_color_def)?

@evamaxfield evamaxfield Aug 23, 2021

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Nope, even that doesn't work. It raises a expression has different type than expected value type or something.

@AetherUnbound AetherUnbound Aug 23, 2021

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Ah well, disregard then!


pixels.channels[i].color = Color(this_channel_color)

img = Image(
name=image_name,
Expand All @@ -524,7 +570,7 @@ def build_ome(
channel_names: Optional[List[Optional[List[str]]]] = None,
image_name: List[Optional[str]] = None,
physical_pixel_sizes: List[types.PhysicalPixelSizes] = None,
channel_colors: List[Optional[List[int]]] = None,
channel_colors: List[Optional[List[List[int]]]] = None,
) -> OME:
"""

Expand All @@ -547,7 +593,7 @@ def build_ome(
Z,Y, and X physical dimensions of each pixel,
defaulting to microns
channel_colors:
The channel colors to be put into the OME metadata
List of all images channel colors to be put into the OME metadata
is_rgb:
is a S dimension present? S is expected to be the last dim in
the data shape
Expand Down