Esempio n. 1
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def test_nuclei():
    io.initialize_paths('20150717', subset='20X_hyb_and_washes/',
                        lasagna_dir='/Volumes/blainey_lab/David/lasagna/')
    master = io.DIR['stacks'][0]

    test_file = io.DIR['stacks'][3]
    data = io.read_stack(test_file, master=master, memmap=False)

    process.DOWNSAMPLE = 2
    n = process.get_nuclei(data[0, 0, :, :])

    return n
Esempio n. 2
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def test_nuclei():
    io.initialize_paths('20150717',
                        subset='20X_hyb_and_washes/',
                        lasagna_dir='/Volumes/blainey_lab/David/lasagna/')
    master = io.DIR['stacks'][0]

    test_file = io.DIR['stacks'][3]
    data = io.read_stack(test_file, master=master, memmap=False)

    process.DOWNSAMPLE = 2
    n = process.get_nuclei(data[0, 0, :, :])

    return n
Esempio n. 3
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def test_nuclei_stitch(well=(('A2',),0)):
    io.initialize_paths('20150716', subset='stitched/',
                        lasagna_dir='/Volumes/blainey_lab/David/lasagna/')

    dict_20X = defaultdict(list)
    [dict_20X[io.get_well_site(f)].append(f) for f in io.DIR['stacks'] if '20X' in f]

    test_files = dict_20X[well]
    print '(well, site) found', dict_20X.keys()
    print 'from', well, 'loading', test_files
    data = {f: io.read_stack(f, memmap=False) for f in test_files}

    offsets = process.register_images(data.values())

    C = io.compose_stacks([io.offset_stack(d, offset)
                           for d, offset in zip(data.values(), offsets)])
    return data, offsets, C
Esempio n. 4
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def test_nuclei_stitch(well=(('A2', ), 0)):
    io.initialize_paths('20150716',
                        subset='stitched/',
                        lasagna_dir='/Volumes/blainey_lab/David/lasagna/')

    dict_20X = defaultdict(list)
    [
        dict_20X[io.get_well_site(f)].append(f) for f in io.DIR['stacks']
        if '20X' in f
    ]

    test_files = dict_20X[well]
    print '(well, site) found', dict_20X.keys()
    print 'from', well, 'loading', test_files
    data = {f: io.read_stack(f, memmap=False) for f in test_files}

    offsets = process.register_images(data.values())

    C = io.compose_stacks(
        [io.offset(d, offset) for d, offset in zip(data.values(), offsets)])
    return data, offsets, C
Esempio n. 5
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def test_nuclei_to_table():
    io.initialize_paths(dataset='20150629/40X_scan',
                        lasagna_dir='/Volumes/blainey_lab/David/lasagna')
    df = process.table_from_nuclei(io.DIR['stacks'][0])
    return df
Esempio n. 6
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def test_nuclei_to_table():
    io.initialize_paths(dataset='20150629/40X_scan',
                        lasagna_dir='/Volumes/blainey_lab/David/lasagna')
    df = process.table_from_nuclei(io.DIR['stacks'][0])
    return df