# Copyright (C) 2022 ISIS Rutherford Appleton Laboratory UKRI
# SPDX - License - Identifier: GPL-3.0-or-later
from functools import partial
from mantidimaging.core.data import Images
from mantidimaging.core.operations.base_filter import BaseFilter
from mantidimaging.core.utility.progress_reporting import Progress
[docs]
class ClipValuesFilter(BaseFilter):
"""Clips grey values of the image based on the parameters. Can be used to remove outliers
and noise (e.g. negative values) from reconstructed images.
Intended to be used on: Projections and reconstructed slices
When: To remove a range of pixel values from the data.
Caution: Make sure the value range does not clip information from the sample.
"""
filter_name = "Clip Values"
link_histograms = True
[docs]
@staticmethod
def filter_func(data,
clip_min=None,
clip_max=None,
clip_min_new_value=None,
clip_max_new_value=None,
progress=None) -> Images:
"""Clip values below the min and above the max pixels.
:param data: Input data as a 3D numpy.ndarray.
:param clip_min: The minimum value to be clipped from the data.
If None is provided then no lower threshold is used.
:param clip_max: The maximum value to be clipped from the data.
If None is provided then no upper threshold is used.
:param clip_min_new_value: The value to use when replacing values less than
clip_min.
If None is provided then the value of clip_min
is used.
:param clip_max_new_value: The value to use when replacing values greater
than clip_max.
If None is provided then the value of clip_max
is used.
:return: The processed 3D numpy.ndarray.
"""
# We're using is None because 0.0 is a valid value
if clip_min is None and clip_max is None:
raise ValueError('At least one of clip_min or clip_max must be supplied')
progress = Progress.ensure_instance(progress, num_steps=2, task_name='Clipping Values.')
with progress:
sample = data.data
progress.update(msg="Determining clip min and clip max")
clip_min = clip_min if clip_min is not None else sample.min()
clip_max = clip_max if clip_max is not None else sample.max()
clip_min_new_value = clip_min_new_value if clip_min_new_value is not None else clip_min
clip_max_new_value = clip_max_new_value if clip_max_new_value is not None else clip_max
progress.update(msg=f"Clipping data with values min {clip_min} and max {clip_max}")
# this is the fastest way to clip the values, np.clip does not do
# the clipping in place and ends up copying the data
sample[sample < clip_min] = clip_min_new_value
sample[sample > clip_max] = clip_max_new_value
return data
[docs]
@staticmethod
def register_gui(form, on_change, view):
from mantidimaging.gui.utility import add_property_to_form
value_range = (-10000000, 10000000)
_, clip_min_field = add_property_to_form('Clip Min',
'float',
valid_values=value_range,
form=form,
on_change=on_change,
tooltip="Any pixel with a value below this number will be clipped")
clip_min_field.setDecimals(7)
_, clip_max_field = add_property_to_form('Clip Max',
'float',
valid_values=value_range,
form=form,
on_change=on_change,
tooltip="Any pixel with a value above this number will be clipped")
clip_max_field.setDecimals(7)
_, clip_min_new_value_field = add_property_to_form(
'Min Replacement Value',
'float',
valid_values=value_range,
form=form,
on_change=on_change,
tooltip='The value that will be used to replace pixel values '
'that fall below Clip Min.')
_, clip_max_new_value_field = add_property_to_form(
'Max Replacement Value',
'float',
valid_values=value_range,
form=form,
on_change=on_change,
tooltip='The value that will be used to replace pixel values '
'that are above Clip Max.')
clip_min_new_value_field.setDecimals(7)
clip_max_new_value_field.setDecimals(7)
# Ensures that the new_value fields are set to be clip_min
# or clip_max, unless the user has explicitly changed them
def update_field_on_value_changed(field, field_new_value):
field_new_value.setValue(field.value())
# using lambda we can pass in parameters
clip_min_field.valueChanged.connect(
lambda: update_field_on_value_changed(clip_min_field, clip_min_new_value_field))
clip_max_field.valueChanged.connect(
lambda: update_field_on_value_changed(clip_max_field, clip_max_new_value_field))
return {
"clip_min_field": clip_min_field,
"clip_max_field": clip_max_field,
"clip_min_new_value_field": clip_min_new_value_field,
"clip_max_new_value_field": clip_max_new_value_field
}
[docs]
@staticmethod
def execute_wrapper(clip_min_field=None,
clip_max_field=None,
clip_min_new_value_field=None,
clip_max_new_value_field=None):
clip_min = clip_min_field.value()
clip_max = clip_max_field.value()
clip_min_new_value = clip_min_new_value_field.value()
clip_max_new_value = clip_max_new_value_field.value()
return partial(ClipValuesFilter.filter_func,
clip_min=clip_min,
clip_max=clip_max,
clip_min_new_value=clip_min_new_value,
clip_max_new_value=clip_max_new_value)