def add_channel(self, can_remove=True):
"""Add another channel to the channels list"""
group = SettingsGroup()
group.can_remove = can_remove
group.append(
"channel_choice",
Integer(
text="Channel number",
value=len(self.channels) + 1,
minval=1,
doc="""\
*(Used only when splitting images)*
This setting chooses a channel to be processed. For example, *1*
is the first
channel in a .TIF or the red channel in a traditional image file.
*2* and *3* are the second and third channels of a TIF or
the green and blue channels in other formats. *4* is the
transparency channel for image formats that support transparency and is
channel # 4 for a .TIF file. **ColorToGray** will fail to process an
image if you select a channel that is not supported by that image, for
example, “5” for a three-channel .PNG file.""",
),
)
group.append(
"contribution",
Float(
"Relative weight of the channel",
1,
0,
doc="""\
*(Used only when combining channels)*
Relative weights: If all relative weights are equal, all three colors
contribute equally in the final image. To weight colors relative to each
other, increase or decrease the relative weights.""",
),
)
group.append(
"image_name",
ImageName(
"Image name",
value="Channel%d" % (len(self.channels) + 1),
doc="""\
*(Used only when splitting images)*
Select the name of the output grayscale image.""",
),
)
if group.can_remove:
group.append(
"remover",
RemoveSettingButton("", "Remove this channel", self.channels, group),
)
self.channels.append(group)
def add_image(self, can_remove=True):
group = SettingsGroup()
group.can_remove = can_remove
if can_remove:
group.append("divider", Divider())
idx = len(self.outputs)
default_name = STAINS_BY_POPULARITY[idx % len(STAINS_BY_POPULARITY)]
default_name = default_name.replace(" ", "")
group.append(
"image_name",
ImageName(
"Name the output image",
default_name,
doc="""\
Use this setting to name one of the images produced by the
module for a particular stain. The image can be used in
subsequent modules in the pipeline.
""",
),
)
choices = list(sorted(STAIN_DICTIONARY.keys())) + [CHOICE_CUSTOM]
group.append(
"stain_choice",
Choice(
"Stain",
choices=choices,
doc="""\
Use this setting to choose the absorbance values for a particular stain.
The stains are:
|Unmix_image0|
(Information taken from `here`_,
`here <http://en.wikipedia.org/wiki/Staining>`__, and
`here <http://stainsfile.info>`__.)
You can choose *{CHOICE_CUSTOM}* and enter your custom values for the
absorbance (or use the estimator to determine values from single-stain
images).
.. _here: http://en.wikipedia.org/wiki/Histology#Staining
.. |Unmix_image0| image:: {UNMIX_COLOR_CHART}
""".format(
**{
"UNMIX_COLOR_CHART":
cellprofiler.gui.help.content.image_resource(
"UnmixColors.png"),
"CHOICE_CUSTOM":
CHOICE_CUSTOM,
}),
),
)
group.append(
"red_absorbance",
Float(
"Red absorbance",
0.5,
0,
1,
doc="""\
*(Used only if "%(CHOICE_CUSTOM)s" is selected for the stain)*
The red absorbance setting estimates the dye’s absorbance of light in
the red channel.You should enter a value between 0 and 1 where 0 is no
absorbance and 1 is complete absorbance. You can use the estimator to
calculate this value automatically.
""" % globals(),
),
)
group.append(
"green_absorbance",
Float(
"Green absorbance",
0.5,
0,
1,
doc="""\
*(Used only if "%(CHOICE_CUSTOM)s" is selected for the stain)*
The green absorbance setting estimates the dye’s absorbance of light in
the green channel. You should enter a value between 0 and 1 where 0 is
no absorbance and 1 is complete absorbance. You can use the estimator to
calculate this value automatically.
""" % globals(),
),
)
group.append(
"blue_absorbance",
Float(
"Blue absorbance",
0.5,
0,
1,
doc="""\
*(Used only if "%(CHOICE_CUSTOM)s" is selected for the stain)*
The blue absorbance setting estimates the dye’s absorbance of light in
the blue channel. You should enter a value between 0 and 1 where 0 is no
absorbance and 1 is complete absorbance. You can use the estimator to
calculate this value automatically.
""" % globals(),
),
)
def on_estimate():
result = self.estimate_absorbance()
if result is not None:
(
group.red_absorbance.value,
group.green_absorbance.value,
group.blue_absorbance.value,
) = result
group.append(
"estimator_button",
DoSomething(
"Estimate absorbance from image",
"Estimate",
on_estimate,
doc="""\
Press this button to load an image of a sample stained only with the dye
of interest. **UnmixColors** will estimate appropriate red, green and
blue absorbance values from the image.
""",
),
)
if can_remove:
group.append(
"remover",
RemoveSettingButton("", "Remove this image", self.outputs,
group),
)
self.outputs.append(group)