def test_erode_binary(self):
from jicbioimage.transform import erode_binary
from jicbioimage.core.image import Image
array = np.array([[0, 0, 0, 0, 0], [0, 0, 1, 0, 0], [0, 1, 1, 1, 0],
[0, 0, 1, 0, 0], [0, 0, 0, 0, 0]],
dtype=np.bool)
expected = np.array([[0, 0, 0, 0, 0], [0, 0, 0, 0, 0], [0, 0, 1, 0, 0],
[0, 0, 0, 0, 0], [0, 0, 0, 0, 0]],
dtype=np.bool)
eroded = erode_binary(array)
self.assertTrue(np.array_equal(expected, eroded))
self.assertTrue(isinstance(eroded, Image))
# The erode_binary function only makes sense on dtype bool.
with self.assertRaises(TypeError):
erode_binary(array.astype(np.uint8))
def find_grains(input_file, output_dir=None):
"""Return tuple of segmentaitons (grains, difficult_regions)."""
name = fpath2name(input_file)
name = "grains-" + name + ".png"
if output_dir:
name = os.path.join(output_dir, name)
image = Image.from_file(input_file)
intensity = mean_intensity_projection(image)
image = remove_scalebar(intensity, np.mean(intensity))
image = threshold_abs(image, 75)
image = invert(image)
image = fill_holes(image, min_size=500)
image = erode_binary(image, selem=disk(4))
image = remove_small_objects(image, min_size=500)
image = dilate_binary(image, selem=disk(4))
dist = distance(image)
seeds = local_maxima(dist)
seeds = dilate_binary(seeds) # Merge spurious double peaks.
seeds = connected_components(seeds, background=0)
segmentation = watershed_with_seeds(dist, seeds=seeds, mask=image)
# Need a copy to avoid over-writing original.
initial_segmentation = np.copy(segmentation)
# Remove spurious blobs.
segmentation = remove_large_segments(segmentation, max_size=3000)
segmentation = remove_small_segments(segmentation, min_size=500)
props = skimage.measure.regionprops(segmentation)
segmentation = remove_non_round(segmentation, props, 0.6)
difficult = initial_segmentation - segmentation
return segmentation, difficult
def find_grains(input_file, output_dir=None):
"""Return tuple of segmentaitons (grains, difficult_regions)."""
name = fpath2name(input_file)
name = "grains-" + name + ".png"
if output_dir:
name = os.path.join(output_dir, name)
image = Image.from_file(input_file)
intensity = mean_intensity_projection(image)
# Median filter seems more robust than Otsu.
# image = threshold_otsu(intensity)
image = threshold_median(intensity, scale=0.8)
image = invert(image)
image = erode_binary(image, selem=disk(2))
image = dilate_binary(image, selem=disk(2))
image = remove_small_objects(image, min_size=200)
image = fill_holes(image, min_size=50)
dist = distance(image)
seeds = local_maxima(dist)
seeds = dilate_binary(seeds) # Merge spurious double peaks.
seeds = connected_components(seeds, background=0)
segmentation = watershed_with_seeds(dist, seeds=seeds, mask=image)
# Remove spurious blobs.
segmentation = remove_large_segments(segmentation, max_size=3000)
segmentation = remove_small_segments(segmentation, min_size=100)
return segmentation
def analyse_image(image):
image = normalise(image) * 255
canvas = AnnotatedImage.from_grayscale(image)
image = smooth_gaussian(image.astype(float), 5)
image = threshold_abs(image, 30)
image = erode_binary(image)
image = remove_small_objects(image, 5)
salem = skimage.morphology.disk(2)
image = dilate_binary(image, salem)
segmentation = connected_components(image, background=0)
for i in segmentation.identifiers:
color = pretty_color_from_identifier(i)
region = segmentation.region_by_identifier(i)
convex_hull = region.convex_hull
outline = convex_hull.inner.border.dilate()
canvas.mask_region(outline, color=color)
return canvas
def generate_cross_section_mask(image):
image = find_edges_sobel(image)
image = threshold_otsu(image)
image = dilate_binary(image, selem=skimage.morphology.disk(5))
image = remove_small_objects(image, 5000)
image = fill_holes(image, 50000)
image = erode_binary(image, selem=skimage.morphology.disk(10))
image = remove_small_objects(image, 50000)
return image
def generate_mask(image):
mask = threshold_abs(image, 6500)
mask = remove_small_objects(mask, 50)
mask = fill_holes(mask, 5)
selem = disk(3)
mask = erode_binary(mask, selem)
mask = dilate_binary(mask, selem)
return mask
def segment(image):
cross_section_mask = generate_cross_section_mask(image)
seeds = threshold_adaptive_median(image, 51)
seeds = clip_mask(seeds, cross_section_mask)
seeds = fill_holes(seeds, 10000)
seeds = erode_binary(seeds)
seeds = remove_small_objects(seeds, 10)
seeds = connected_components(seeds, connectivity=1, background=0)
cells = watershed_with_seeds(image, seeds=seeds, mask=cross_section_mask)
return cells
def find_tubes(input_file, output_dir=None):
"""Return pollen tube segmentation."""
name = fpath2name(input_file)
name = "tubes-" + name + ".png"
if output_dir:
name = os.path.join(output_dir, name)
image = Image.from_file(input_file)
intensity = mean_intensity_projection(image)
image = find_edges_sobel(intensity)
image = remove_scalebar(image, 0)
image = threshold_otsu(image)
image = dilate_binary(image, selem=disk(3))
image = erode_binary(image, selem=disk(3))
image = remove_small_objects(image, min_size=500)
image = fill_holes(image, min_size=500)
image = erode_binary(image, selem=disk(3))
image = remove_small_objects(image, min_size=200)
segmentation = connected_components(image, background=0)
return segmentation
def analyse_file_org(fpath, output_directory):
"""Analyse a single file."""
logging.info("Analysing file: {}".format(fpath))
image = Image.from_file(fpath)
image = identity(image)
image = select_red(image)
image = invert(image)
image = threshold_otsu(image)
seeds = remove_small_objects(image, min_size=1000)
seeds = fill_small_holes(seeds, min_size=1000)
seeds = erode_binary(seeds, selem=disk(30))
seeds = connected_components(seeds, background=0)
watershed_with_seeds(-image, seeds=seeds, mask=image)
def test_erode_binary_with_selem(self):
from jicbioimage.transform import erode_binary
selem = np.ones((3, 3))
array = np.array([[0, 0, 0, 0, 0, 0, 0], [0, 1, 0, 1, 1, 1, 0],
[0, 1, 1, 1, 1, 1, 0], [0, 1, 1, 1, 1, 1, 0],
[0, 1, 1, 1, 1, 1, 0], [0, 1, 1, 1, 1, 1, 0],
[0, 0, 0, 0, 0, 0, 0]],
dtype=np.bool)
expected = np.array([[0, 0, 0, 0, 0, 0, 0], [0, 0, 0, 0, 0, 0, 0],
[0, 0, 0, 0, 1, 0, 0], [0, 0, 1, 1, 1, 0, 0],
[0, 0, 1, 1, 1, 0, 0], [0, 0, 0, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 0, 0]],
dtype=np.bool)
eroded = erode_binary(array, selem=selem)
self.assertTrue(np.array_equal(expected, eroded))
def segment(image):
"""Return field plots."""
red = red_channel(image)
green = green_channel(image)
image = difference(red, green)
mask = threshold_otsu(image)
mask = remove_small_objects(mask, min_size=1000)
mask = fill_small_holes(mask, min_size=100)
seeds = erode_binary(mask, selem=disk(10))
seeds = remove_small_objects(seeds, min_size=100)
seeds = connected_components(seeds, background=0)
return watershed_with_seeds(-image, seeds=seeds, mask=mask)
def segment(image, seeds=None):
"""Return field plots."""
green = green_channel(image)
image = sklocal(green)
image = skmean(image)
mask = threshold_otsu(image)
mask = remove_small_objects(mask, min_size=1000)
mask = fill_small_holes(mask, min_size=100)
dist = distance_transform(mask)
if seeds is None:
seeds = erode_binary(mask, selem=disk(10))
seeds = remove_small_objects(seeds, min_size=100)
seeds = connected_components(seeds, background=0)
return watershed_with_seeds(image, seeds=seeds, mask=mask)
def segment_cells(wall_projection, surface, mask, **kwargs):
"""Return segmented cells as SegmentedImage."""
seeds = threshold_adaptive_median(
wall_projection,
block_size=kwargs["wall_threshold_adaptive_block_size"])
seeds = remove_small_objects(
seeds, min_size=kwargs["wall_remove_small_objects_in_cell_min_size"])
seeds = invert(seeds)
if "wall_erode_step" in kwargs and kwargs["wall_erode_step"]:
seeds = erode_binary(seeds)
seeds = remove_small_objects(
seeds, min_size=kwargs["wall_remove_small_objects_in_wall_min_size"])
seeds = connected_components(seeds, connectivity=1, background=0)
cells = watershed_with_seeds(-wall_projection, seeds=seeds)
cells = remove_cells_not_in_mask(cells, mask)
return cells
