StevenVB12
Cropping
Hello,
I'm running patternize on Heliconius wings to get PCA outputs without the androconial region included. It ran just fine when running the whole wing but when using cropoffset with negative values to cut off the androconia the wings didn't seem to align properly (from looking at the stacked plots with patLanRGB). It looks like it's cropping wings (that have slight different orientations) and then aligning them- does that sound right?
Can cropoffset be used to remove part of the wing or would it be better to just remove some landmarks in that region?
Thank you, Lucie
Hi Lucie,
I don’t think the cropOffset will work with negative values. Using patLanRGB, I would advise you to not use the crop, but instead at the end of your analysis draw a mask outline (setMask()) and using that outline to crop everything you are not interested in. Here’s an example of what the code should look like for that:
setMask(summedRaster_XX, IDList_XX, cartoonID = 'XXX, 'mask/mask_XX.txt')
mask_XX <- read.table("mask/mask_XX.txt", h=T)
rasterList_XX_M <-list()
for(e in IDList_XX){
rasterList_XX_M[[e]] <- maskOutline(rasterList_XX[[e]], mask_XX, refShape = 'target',
imageList = imageList_XX)
}
Hope this helps!
Steven
From: LucieMQ [email protected] Sent: Monday, October 28, 2019 1:17:37 PM To: StevenVB12/patternize [email protected] Cc: Subscribed [email protected] Subject: [StevenVB12/patternize] Cropping (#16)
Hello,
I'm running patternize on Heliconius wings to get PCA outputs without the androconial region included. It ran just fine when running the whole wing but when using cropoffset with negative values to cut off the androconia the wings didn't seem to align properly (from looking at the stacked plots with patLanRGB). It looks like it's cropping wings (that have slight different orientations) and then aligning them- does that sound right?
Can cropoffset be used to remove part of the wing or would it be better to just remove some landmarks in that region?
Thank you, Lucie
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