variable_revision_number = 5
def create_settings(self):
self.image_name = cps.ImageNameSubscriber(
"Select the input image",
cps.NONE, doc=
Select the image with features to be enhanced or suppressed.)self.filtered_image_name = cps.ImageNameProvider(
"Name the output image",
"FilteredBlue", doc=
Enter a name for the feature-enhanced or suppressed image.)
self.method = cps.Choice(
"Select the operation",
[ENHANCE, SUPPRESS], doc=
Select whether you want to enhance or suppress the features you designated.
<ul>
<li><i>%(ENHANCE)s:</i> Produce an image whose intensity is largely
composed of the features of interest.</li>
<li <i>%(SUPPRESS)s:</i> Produce an image with the features largely
removed.</li>
</ul> % globals())
self.enhance_method = cps.Choice(
"Feature type",
[E_SPECKLES, E_NEURITES, E_DARK_HOLES, E_CIRCLES, E_TEXTURE, E_DIC], doc=
<i>(Used only if %(ENHANCE)s is selected)</i><br>
This module can enhance three kinds of image intensity features:
<ul>
<li><i>%(E_SPECKLES)s:</i> A speckle is an area of enhanced intensity
relative to its immediate neighborhood. The module enhances
speckles using a white tophat filter, which is the image minus the
morphological grayscale opening of the image. The opening operation
first suppresses the speckles by applying a grayscale erosion to reduce everything
within a given radius to the lowest value within that radius, then uses
a grayscale dilation to restore objects larger than the radius to an
approximation of their former shape. The white tophat filter enhances
speckles by subtracting the effects of opening from the original image.
</li>
<li><i>%(E_NEURITES)s:</i> Neurites are taken to be long, thin features
of enhanced intensity. Choose this option to enhance the intensity
of the neurites using the %(N_GRADIENT)s or %(N_TUBENESS)s methods
described below.</li>
<li><i>%(E_DARK_HOLES)s:</i> The module uses morphological reconstruction
(the rolling-ball algorithm) to identify dark holes within brighter
areas, or brighter ring shapes. The image is inverted so that the dark holes turn into
bright peaks. The image is successively eroded and the eroded image
is reconstructed at each step, resulting in an image which is
missing the peaks. Finally, the reconstructed image is subtracted
from the previous reconstructed image. This leaves circular bright
spots with a radius equal to the number of iterations performed.
</li>
<li><i>%(E_CIRCLES)s:</i> The module calculates the circular Hough transform of
the image at the diameter given by the feature size. The Hough transform
will have the highest intensity at points that are centered within a ring
of high intensity pixels where the ring diameter is the feature size. You
may want to use the <b>EnhanceEdges</b> module to find the edges of your
circular object and then process the output by enhancing circles. You can
use <b>IdentifyPrimaryObjects</b> to find the circle centers and then use
these centers as seeds in <b>IdentifySecondaryObjects</b> to find whole,
circular objects using a watershed.</li>
<li><i>%(E_TEXTURE)s:</i> <b>EnanceOrSuppressFeatures</b> produces an image
whose intensity is the variance among nearby pixels. This method weights
pixel contributions by distance using a Gaussian to calculate the weighting.
You can use this method to separate foreground from background if the foreground
is textured and the background is not.
</li>
<li><i>%(E_DIC)s:</i> This method recovers the optical density of a DIC image by
integrating in a direction perpendicular to the shear direction of the image.
</li>
</ul>
In addition, this module enables you to suppress certain features (such as speckles)
by specifying the feature size. % globals())
self.object_size = cps.Integer(
"Feature size", 10, 2, doc=
<i>(Used only if circles, speckles or neurites are selected, or if suppressing features)</i><br>
Enter the diameter of the largest speckle, the width of the circle
or the width of the neurites to be enhanced or suppressed, which
will be used to calculate an adequate filter size. %(HELP_ON_MEASURING_DISTANCES)s % globals())
self.hole_size = cps.IntegerRange(
"Range of hole sizes", value=(1, 10), minval=1, doc=
<i>(Used only if %(E_DARK_HOLES)s is selected)</i><br>
The range of hole sizes to be enhanced. The algorithm will
identify only holes whose diameters fall between these two
values. % globals())
self.smoothing = cps.Float(
"Smoothing scale", value=2.0, minval=0, doc=
<i>(Used only for the %(E_TEXTURE)s, %(E_DIC)s or %(E_NEURITES)s methods)</i><br>
<ul>
<li><i>%(E_TEXTURE)s</i>: This is the scale of the texture features, roughly
in pixels. The algorithm uses the smoothing value entered as
the sigma of the Gaussian used to weight nearby pixels by distance
in the variance calculation.</li>
<li><i>%(E_DIC)s:</i> Specifies the amount of smoothing of the image in the direction parallel to the
shear axis of the image. The line integration method will leave
streaks in the image without smoothing as it encounters noisy
pixels during the course of the integration. The smoothing takes
contributions from nearby pixels which decreases the noise but
smooths the resulting image. </li>
<li><i>%(E_DIC)s:</i> Increase the smoothing to
eliminate streakiness and decrease the smoothing to sharpen
the image.</li>
<li><i>%(E_NEURITES)s:</i> The <i>%(N_TUBENESS)s</i> option uses this scale
as the sigma of the Gaussian used to smooth the image prior to
gradient detection.</li>
</ul>
<img src="memory:%(PROTIP_AVOID_ICON)s">
Smoothing can be turned off by entering a value of zero, but this
is not recommended. % globals())
self.angle = cps.Float(
"Shear angle", value=0, doc=
<i>(Used only for the %(E_DIC)s method)</i><br>
The shear angle is the direction of constant value for the
shadows and highlights in a DIC image. The gradients in a DIC
image run in the direction perpendicular to the shear angle.
For example, if the shadows run diagonally from lower left
to upper right and the highlights appear above the shadows,
the shear angle is 45°. If the shadows appear on top,
the shear angle is 180° + 45° = 225°.
% globals())
self.decay = cps.Float(
"Decay", value=0.95, minval=0.1, maxval=1, doc=
<i>(Used only for the %(E_DIC)s method)</i><br>
The decay setting applies an exponential decay during the process
of integration by multiplying the accumulated sum by the decay
at each step. This lets the integration recover from accumulated
error during the course of the integration, but it also results
in diminished intensities in the middle of large objects.
Set the decay to a large value, on the order of 1 - 1/diameter
of your objects if the intensities decrease toward the middle.
Set the decay to a small value if there appears to be a bias
in the integration direction. % globals())
self.neurite_choice = cps.Choice(
"Enhancement method",
[N_TUBENESS, N_GRADIENT], doc=
<i>(Used only for the %(E_NEURITES)s method)</i><br>
After Change
variable_revision_number = 6
def create_settings(self):
super(EnhanceOrSuppressFeatures, self).create_settings()
self.method = cellprofiler.setting.Choice(
"Select the operation",
[ENHANCE, SUPPRESS], doc=
Select whether you want to enhance or suppress the features you designated.
<ul>
<li><i>%(ENHANCE)s:</i> Produce an image whose intensity is largely
composed of the features of interest.</li>
<li <i>%(SUPPRESS)s:</i> Produce an image with the features largely
removed.</li>
</ul> % globals())
self.enhance_method = cellprofiler.setting.Choice(
"Feature type",
[E_SPECKLES, E_NEURITES, E_DARK_HOLES, E_CIRCLES, E_TEXTURE, E_DIC], doc=
<i>(Used only if %(ENHANCE)s is selected)</i><br>
This module can enhance three kinds of image intensity features:
<ul>
<li><i>%(E_SPECKLES)s:</i> A speckle is an area of enhanced intensity
relative to its immediate neighborhood. The module enhances
speckles using a white tophat filter, which is the image minus the
morphological grayscale opening of the image. The opening operation
first suppresses the speckles by applying a grayscale erosion to reduce everything
within a given radius to the lowest value within that radius, then uses
a grayscale dilation to restore objects larger than the radius to an
approximation of their former shape. The white tophat filter enhances
speckles by subtracting the effects of opening from the original image.
</li>
<li><i>%(E_NEURITES)s:</i> Neurites are taken to be long, thin features
of enhanced intensity. Choose this option to enhance the intensity
of the neurites using the %(N_GRADIENT)s or %(N_TUBENESS)s methods
described below.</li>
<li><i>%(E_DARK_HOLES)s:</i> The module uses morphological reconstruction
(the rolling-ball algorithm) to identify dark holes within brighter
areas, or brighter ring shapes. The image is inverted so that the dark holes turn into
bright peaks. The image is successively eroded and the eroded image
is reconstructed at each step, resulting in an image which is
missing the peaks. Finally, the reconstructed image is subtracted
from the previous reconstructed image. This leaves circular bright
spots with a radius equal to the number of iterations performed.
</li>
<li><i>%(E_CIRCLES)s:</i> The module calculates the circular Hough transform of
the image at the diameter given by the feature size. The Hough transform
will have the highest intensity at points that are centered within a ring
of high intensity pixels where the ring diameter is the feature size. You
may want to use the <b>EnhanceEdges</b> module to find the edges of your
circular object and then process the output by enhancing circles. You can
use <b>IdentifyPrimaryObjects</b> to find the circle centers and then use
these centers as seeds in <b>IdentifySecondaryObjects</b> to find whole,
circular objects using a watershed.</li>
<li><i>%(E_TEXTURE)s:</i> <b>EnanceOrSuppressFeatures</b> produces an image
whose intensity is the variance among nearby pixels. This method weights
pixel contributions by distance using a Gaussian to calculate the weighting.
You can use this method to separate foreground from background if the foreground
is textured and the background is not.
</li>
<li><i>%(E_DIC)s:</i> This method recovers the optical density of a DIC image by
integrating in a direction perpendicular to the shear direction of the image.
</li>
</ul>
In addition, this module enables you to suppress certain features (such as speckles)
by specifying the feature size. % globals())
self.object_size = cellprofiler.setting.Integer(
"Feature size", 10, 2, doc=
<i>(Used only if circles, speckles or neurites are selected, or if suppressing features)</i><br>
Enter the diameter of the largest speckle, the width of the circle
or the width of the neurites to be enhanced or suppressed, which
will be used to calculate an adequate filter size. %(HELP_ON_MEASURING_DISTANCES)s % globals())
self.hole_size = cellprofiler.setting.IntegerRange(
"Range of hole sizes", value=(1, 10), minval=1, doc=
<i>(Used only if %(E_DARK_HOLES)s is selected)</i><br>
The range of hole sizes to be enhanced. The algorithm will
identify only holes whose diameters fall between these two
values. % globals())
self.smoothing = cellprofiler.setting.Float(
"Smoothing scale", value=2.0, minval=0, doc=
<i>(Used only for the %(E_TEXTURE)s, %(E_DIC)s or %(E_NEURITES)s methods)</i><br>
<ul>
<li><i>%(E_TEXTURE)s</i>: This is the scale of the texture features, roughly
in pixels. The algorithm uses the smoothing value entered as
the sigma of the Gaussian used to weight nearby pixels by distance
in the variance calculation.</li>
<li><i>%(E_DIC)s:</i> Specifies the amount of smoothing of the image in the direction parallel to the
shear axis of the image. The line integration method will leave
streaks in the image without smoothing as it encounters noisy
pixels during the course of the integration. The smoothing takes
contributions from nearby pixels which decreases the noise but
smooths the resulting image. </li>
<li><i>%(E_DIC)s:</i> Increase the smoothing to
eliminate streakiness and decrease the smoothing to sharpen
the image.</li>
<li><i>%(E_NEURITES)s:</i> The <i>%(N_TUBENESS)s</i> option uses this scale
as the sigma of the Gaussian used to smooth the image prior to
gradient detection.</li>
</ul>
<img src="memory:%(PROTIP_AVOID_ICON)s">
Smoothing can be turned off by entering a value of zero, but this
is not recommended. % globals())
self.angle = cellprofiler.setting.Float(
"Shear angle", value=0, doc=
<i>(Used only for the %(E_DIC)s method)</i><br>
The shear angle is the direction of constant value for the
shadows and highlights in a DIC image. The gradients in a DIC
image run in the direction perpendicular to the shear angle.
For example, if the shadows run diagonally from lower left
to upper right and the highlights appear above the shadows,
the shear angle is 45°. If the shadows appear on top,
the shear angle is 180° + 45° = 225°.
% globals())
self.decay = cellprofiler.setting.Float(
"Decay", value=0.95, minval=0.1, maxval=1, doc=
<i>(Used only for the %(E_DIC)s method)</i><br>
The decay setting applies an exponential decay during the process
of integration by multiplying the accumulated sum by the decay
at each step. This lets the integration recover from accumulated
error during the course of the integration, but it also results
in diminished intensities in the middle of large objects.
Set the decay to a large value, on the order of 1 - 1/diameter
of your objects if the intensities decrease toward the middle.
Set the decay to a small value if there appears to be a bias
in the integration direction. % globals())
self.neurite_choice = cellprofiler.setting.Choice(
"Enhancement method",
[N_TUBENESS, N_GRADIENT], doc=
<i>(Used only for the %(E_NEURITES)s method)</i><br>
