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add a recipe module to modify the origin when needed #1483

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add a recipe module to modify the origin when needed #1483

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3e3cc19
add a recipe module to modify the origin when needed
Yujin-Bao Mar 7, 2024
ec6ea72
set the origin metadata using ModuleBase
Yujin-Bao Mar 8, 2024
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38 changes: 37 additions & 1 deletion PYME/recipes/processing.py
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Original file line number Diff line number Diff line change
Expand Up @@ -2905,4 +2905,40 @@ def applyFilter(self, data, chanNum, i, image0):
if self.offset_selection == 'offset by a constant':
return data - self.offset_constant
elif self.offset_selection == 'offset by minimum':
return data - np.min(data)
return data - np.min(data)


@register_module('SetOriginMetadata')
class SetOriginMetadata(ModuleBase):
"""
Set the origin metadata

Parameters
----------
Origin_x : the origin of x that the image will be set to, float in nm
Origin_y : the origin of y that the image will be set to, float in nm
Origin_z : the origin of z that the image will be set to, float in nm
"""
inputImage = Input('input')
outputImage = Output('output')
Origin_x = Float(37281.0)
Origin_y = Float(33475.5)
Origin_z = Float(0.0)

def run(self, inputImage):
# create a new image, using the data from the old image
# this re-uses the reference to the unmodified image data so we don't need to allocate more memory
# but creates a new, empty, metadata
im = ImageStack(inputImage.data, titleStub=self.outputImage)

# copy the metadata entries from the original image (note, this is not technically required, as the .execute()
# method will automatically copy (merge) the input metadata to the output, but it doesn't hurt to be explicit)
im.mdh.copyEntriesFrom(inputImage.mdh)

# add any module-specific metadata to the output image
im.mdh['Origin.x'] = self.Origin_x
im.mdh['Origin.y'] = self.Origin_y
im.mdh['Origin.z'] = self.Origin_z

# return the new image.
return im