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Fix MakeRaw #293

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Fix MakeRaw #293

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77 changes: 38 additions & 39 deletions dacapo/utils/pipeline.py
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Original file line number Diff line number Diff line change
Expand Up @@ -83,45 +83,44 @@ class MakeRaw(gp.BatchFilter):
process: Generate the raw image from the labels.
"""

class Pipeline:
def __init__(
self,
raw,
labels,
gaussian_noise_args: Iterable = (0.5, 0.1),
gaussian_noise_lim: float = 0.3,
gaussian_blur_args: Iterable = (0.5, 1.5),
membrane_like=True,
membrane_size=3,
inside_value=0.5,
):
"""
Initialize the Pipeline object.

Args:
raw: The raw data.
labels: The labels data.
gaussian_noise_args: Tuple of two floats representing the mean and standard deviation
of the Gaussian noise to be added to the data. Default is (0.5, 0.1).
gaussian_noise_lim: The limit of the Gaussian noise. Default is 0.3.
gaussian_blur_args: Tuple of two floats representing the mean and standard deviation
of the Gaussian blur to be applied to the data. Default is (0.5, 1.5).
membrane_like: Boolean indicating whether to apply membrane-like transformation to the data.
Default is True.
membrane_size: The size of the membrane. Default is 3.
inside_value: The value to be assigned to the inside of the membrane. Default is 0.5.
Examples:
>>> Pipeline(raw="RAW", labels="LABELS", gaussian_noise_args=(0.5, 0.1), gaussian_noise_lim=0.3,
>>> gaussian_blur_args=(0.5, 1.5), membrane_like=True, membrane_size=3, inside_value=0.5)
"""
self.raw = raw
self.labels = labels
self.gaussian_noise_args = gaussian_noise_args
self.gaussian_noise_lim = gaussian_noise_lim
self.gaussian_blur_args = gaussian_blur_args
self.membrane_like = membrane_like
self.membrane_size = membrane_size
self.inside_value = inside_value
def __init__(
self,
raw,
labels,
gaussian_noise_args: Iterable = (0.5, 0.1),
gaussian_noise_lim: float = 0.3,
gaussian_blur_args: Iterable = (0.5, 1.5),
membrane_like=True,
membrane_size=3,
inside_value=0.5,
):
"""
Initialize the Pipeline object.

Args:
raw: The raw data.
labels: The labels data.
gaussian_noise_args: Tuple of two floats representing the mean and standard deviation
of the Gaussian noise to be added to the data. Default is (0.5, 0.1).
gaussian_noise_lim: The limit of the Gaussian noise. Default is 0.3.
gaussian_blur_args: Tuple of two floats representing the mean and standard deviation
of the Gaussian blur to be applied to the data. Default is (0.5, 1.5).
membrane_like: Boolean indicating whether to apply membrane-like transformation to the data.
Default is True.
membrane_size: The size of the membrane. Default is 3.
inside_value: The value to be assigned to the inside of the membrane. Default is 0.5.
Examples:
>>> Pipeline(raw="RAW", labels="LABELS", gaussian_noise_args=(0.5, 0.1), gaussian_noise_lim=0.3,
>>> gaussian_blur_args=(0.5, 1.5), membrane_like=True, membrane_size=3, inside_value=0.5)
"""
self.raw = raw
self.labels = labels
self.gaussian_noise_args = gaussian_noise_args
self.gaussian_noise_lim = gaussian_noise_lim
self.gaussian_blur_args = gaussian_blur_args
self.membrane_like = membrane_like
self.membrane_size = membrane_size
self.inside_value = inside_value

def setup(self):
"""
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