Read ImageJ's ROI files

readroi.py

# UPDATE IN 2020
# You almost always will want to use the version at
# https://github.com/luispedro/imread, which is
# up-to-date and works with Python 3





# Copyright: Luis Pedro Coelho <luis@luispedro.org>, 2012
# License: MIT
import numpy as np

def read_roi(fileobj):
    '''
    points = read_roi(fileobj)

    Read ImageJ's ROI format
    '''
# This is based on:
# http://rsbweb.nih.gov/ij/developer/source/ij/io/RoiDecoder.java.html
# http://rsbweb.nih.gov/ij/developer/source/ij/io/RoiEncoder.java.html


    SPLINE_FIT = 1
    DOUBLE_HEADED = 2
    OUTLINE = 4
    OVERLAY_LABELS = 8
    OVERLAY_NAMES = 16
    OVERLAY_BACKGROUNDS = 32
    OVERLAY_BOLD = 64
    SUB_PIXEL_RESOLUTION = 128
    DRAW_OFFSET = 256


    pos = [4]
    def get8():
        pos[0] += 1
        s = fileobj.read(1)
        if not s:
            raise IOError('readroi: Unexpected EOF')
        return ord(s)

    def get16():
        b0 = get8()
        b1 = get8()
        return (b0 << 8) | b1

    def get32():
        s0 = get16()
        s1 = get16()
        return (s0 << 16) | s1

    def getfloat():
        v = np.int32(get32())
        return v.view(np.float32)

    magic = fileobj.read(4)
    if magic != 'Iout':
        raise IOError('Magic number not found')
    version = get16()

    # It seems that the roi type field occupies 2 Bytes, but only one is used
    roi_type = get8()
    # Discard second Byte:
    get8()

    if not (0 <= roi_type < 11):
        raise ValueError('roireader: ROI type %s not supported' % roi_type)

    if roi_type != 7:
        raise ValueError('roireader: ROI type %s not supported (!= 7)' % roi_type)

    top = get16()
    left = get16()
    bottom = get16()
    right = get16()
    n_coordinates = get16()

    x1 = getfloat() 
    y1 = getfloat() 
    x2 = getfloat() 
    y2 = getfloat()
    stroke_width = get16()
    shape_roi_size = get32()
    stroke_color = get32()
    fill_color = get32()
    subtype = get16()
    if subtype != 0:
        raise ValueError('roireader: ROI subtype %s not supported (!= 0)' % subtype)
    options = get16()
    arrow_style = get8()
    arrow_head_size = get8()
    rect_arc_size = get16()
    position = get32()
    header2offset = get32()

    if options & SUB_PIXEL_RESOLUTION:
        getc = getfloat
        points = np.empty((n_coordinates, 2), dtype=np.float32)
    else:
        getc = get16
        points = np.empty((n_coordinates, 2), dtype=np.int16)
    points[:,1] = [getc() for i in xrange(n_coordinates)]
    points[:,0] = [getc() for i in xrange(n_coordinates)]
    points[:,1] += left
    points[:,0] += top
    points -= 1
    return points

def read_roi_zip(fname):
    import zipfile
    with zipfile.ZipFile(fname) as zf:
        return [read_roi(zf.open(n))
                    for n in zf.namelist()]

super helpful; thanks for posting this!

one note: the first column of points will hold y values and the second column will hold x values!

Sweet! saves me quite some time 👍

This is very nice. Where did you get the info to about the .roi file?

I have some files whose roi_type was 0, so this code didn't work. I commented lines 62 and 63 and it works now.

I've packaged this gist into a pypi package: https://github.com/tdsmith/ijroi, https://pypi.python.org/pypi/ijroi

Nice, thanks! Do you happen to have code for writing ROI by any chance?

See this one too : https://github.com/hadim/read-roi

This old gist does not work with Python 3, but I have now folded the code into the imread project and updated it to work with both Python 2 & 3:

https://github.com/luispedro/imread

Nice, thanks! Do you happen to have code for writing ROI by any chance?

I have the same question. Any one knows how to write ROI? I want to generate some region and go back to image J to edit. Thanks!

The above code does not work in python 3.6.