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yuzhile moschn ufcolemanlab reconmaster jakirkham tarokiritani cxrodgers tito21 andrewmicallef tom-f-oconnell miroc911

ijroi's Issues

Unsupported ROI types: OVAL

Is there a reason there are only 5 supported ROI types in this package? FREEHAND, TRACED, POLYGON, RECT, and POINT are all supported, but type OVAL (which is common for cell segmentation pipelines), among a few others, raises exceptions.

I haven't looked at this too closely yet, but I assume something about the way ImageJ calculates ovals must be hard to translate to a numpy array?

Unexpected EOF with sub pixel resolution

The ijroi.read_roi() threw this exception when reading a roi file with sub pixel resolution.

  File "<ipython-input-27-1cbaa36a0ba9>", line 2, in <module>
    ijroi.read_roi(f)

  File "C:\Users\kiritani\Documents\data\GitHub\ijroi\ijroi\ijroi.py", line 124, in read_roi
    points[:, 1] = [getc() for i in range(n_coordinates)]

  File "C:\Users\kiritani\Documents\data\GitHub\ijroi\ijroi\ijroi.py", line 124, in <listcomp>
    points[:, 1] = [getc() for i in range(n_coordinates)]

  File "C:\Users\kiritani\Documents\data\GitHub\ijroi\ijroi\ijroi.py", line 61, in getfloat
    v = np.int32(get32())

  File "C:\Users\kiritani\Documents\data\GitHub\ijroi\ijroi\ijroi.py", line 56, in get32
    s0 = get16()

  File "C:\Users\kiritani\Documents\data\GitHub\ijroi\ijroi\ijroi.py", line 51, in get16
    b0 = get8()

  File "C:\Users\kiritani\Documents\data\GitHub\ijroi\ijroi\ijroi.py", line 47, in get8
    raise IOError('readroi: Unexpected EOF')

OSError: readroi: Unexpected EOF

I assume the file's current position is incorrectly set in line 111?

Reading slice # from volumetric data

Hi,

Thanks for this tool. Very helpful!

It would be great if, in addition to the ROI data, this method would also return the slice # that the ROI was taken from in an image stack. Here is an example matlab function that accomplishes this.

Thanks!
Dave

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