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I hava some errors when I load ImageJ RoiSet.zip #71

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FengZhiheng opened this issue Oct 24, 2019 · 9 comments

Contributor

FengZhiheng commented Oct 24, 2019

error information is

'self.run(para)
File "C:\Users\XXX\Desktop\ImagePy-64\ImagePy\programs\lib\site-packages\imagepy\menus\File\Import\roi_plg.py", line 30, in run
img[polygon(ls[i]['y'], ls[i]['x'], img.shape)] = int(i)
KeyError: 'y''

Contributor

BioinfoTongLI commented Oct 30, 2019

Hi, @FengZhiheng,
Thank you for filing the issue.
It seems that some features such as "x" and "y" are not saved when you save the roiset in ij.
Can you maybe send an example of your RoiSet.zip?
Tong

Contributor Author

FengZhiheng commented Oct 31, 2019

Hi, @FengZhiheng,
Thank you for filing the issue.
It seems that some features such as "x" and "y" are not saved when you save the roiset in ij.
Can you maybe send an example of your RoiSet.zip?
Tong

Ok! It's very kind of you for helping me out.

Contributor

BioinfoTongLI commented Oct 31, 2019

I successfully opened the RoiSet.zip you sent to me. Is it the same one that caused the error? It seems that the one you sent to me has no problem.

Contributor Author

FengZhiheng commented Oct 31, 2019

RoiSet1.zip
Please try this one. This one can cause the error I met a few days ago. I used Fiji ROI manager and saves this ROI.zip file.

Contributor

BioinfoTongLI commented Oct 31, 2019

Ok, I confirm it's a glitch. By default, imagepy takes the xy coordinates to draw a polygon. However, IJ sometimes save the bounding box instead of the coordinates. @yxdragon , is there a way to draw a polygon with bounding box?

Member

yxdragon commented Nov 3, 2019

just using slice to fill bounding box, such as img[top:bot, left:right] = lab.
the trouble is, bounding boxes may cross with each other, but for the labled image, one pixel just has one value.

Member

yxdragon commented Nov 4, 2019

I saw the roi file is a collection of oval object like this:
{'type': 'oval', 'left': 154, 'top': 115, 'width': 39, 'height': 38, 'name': '0134-0173', 'position': 0}
It is not a polygon object, so we need draw it by skimage.draw.ellipse

rs, cs = ellipse(top+height/2, left+width/2, height/2, width/2)
img[rs, cs] = lab

Contributor

BioinfoTongLI commented Nov 4, 2019

#72 (comment)
PR created for a quick-fix
@FengZhiheng

Member

yxdragon commented Nov 5, 2019

@FengZhiheng merged, have a try.
@BioinfoTongLI ellipse method need a shape parameter to cut the rs, cs out of image to make sure that img[rs, cs] is safe.

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