Describe the bug
When importing ImageJ ROIs into MESmerize, it does not read ROIs created by different drawing tools (oval and rectangle) in ImageJ. It recognises freehand ROIs.
To Reproduce
Go to Viewer -> ROI Manager -> Import ROI Manager (attached)
Expected behavior
Ideally, It should import all ROIs regardless of size/type.
Error
I have fixed it by modifying the function import_from_imagej in managers.py. Not the most elegant code, but it works.
Attached ImageJ ROI file for testing.
roi_test.zip
def import_from_imagej(self, path: str):
"""
Uses read-roi package created by Hadrien Mary.
https://pypi.org/project/read-roi/
:param path: Full path to the ImageJ ROIs zip file
"""
ij_roi = read_imagej(path)
for k in ij_roi.keys():
if ij_roi[k]['type'] in ('oval', 'rectangle'):
width=ij_roi[k]['width']
height=ij_roi[k]['height']
left=ij_roi[k]['left']
top=ij_roi[k]['top']
x_center=left+width/2
y_center=top+height/2
if ij_roi[k]['type'] == 'oval':
shape=Ellipse((x_center,y_center),width,height)
vertices_orig=shape.get_path().vertices #get all vertices
vertices = shape.get_patch_transform().transform(vertices_orig)
ps=[tuple(x) for x in vertices]
else:
ps=list(itertools.product((left,left+width),(top,top+height)))
ps[2],ps[3]=ps[3],ps[2] #swap coordinates so it draws coordinates in sequence, must be a better way to do this
else:
xs = ij_roi[k]['x']
ys = ij_roi[k]['y']
ps = list(zip(xs, ys))
roi = ManualROI.from_positions(positions=ps,
curve_plot_item=self.get_plot_item(),
view_box=self.vi.viewer.getView())
self.roi_list.append(roi)
self.roi_list.reindex_colormap()
Operating System & specs (CPU, RAM etc.). Please complete the following information:
Hi
Describe the bug When importing ImageJ ROIs into MESmerize, it does not read ROIs created by different drawing tools (oval and rectangle) in ImageJ. It recognises freehand ROIs.
To Reproduce Go to Viewer -> ROI Manager -> Import ROI Manager (attached)
Expected behavior Ideally, It should import all ROIs regardless of size/type.
Error![image](https://user-images.githubusercontent.com/13831458/133739313-c48b438b-f1c2-4528-bb22-a10798e9d379.png)
I have fixed it by modifying the function import_from_imagej in managers.py. Not the most elegant code, but it works.
Attached ImageJ ROI file for testing. roi_test.zip
Operating System & specs (CPU, RAM etc.). Please complete the following information:
Details about your Mesmerize install
Cheers Pradeep