Import ROI ImageJ error

[pr4deepr]

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

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:

• Windows 10

Details about your Mesmerize install

• Anaconda envt

Cheers Pradeep

[kushalkolar]

This is more of a feature request, see #64

[kushalkolar]

fixed in #68