def png(self, width=None):
"""Return png string of image.
:param width: integer specifying the desired width
:returns: png as a string
"""
skimage.io.use_plugin('freeimage')
def resize(im, width):
x, y = im.shape[:2]
f = float(width) / float(x)
scale_factors = [1.0 for i in range(len(im.shape))]
scale_factors[0] = f
scale_factors[1] = f
ar = scipy.ndimage.zoom(im, scale_factors, order=0)
return Image.from_array(ar, log_in_history=False)
safe_range_im = self
if self.dtype != np.uint8:
safe_range_im = 255 * normalise(self)
if width is not None:
safe_range_im = resize(safe_range_im, width)
with _TemporaryFilePath(suffix='.png') as tmp:
safe_range_im_uint8 = safe_range_im.astype(np.uint8)
skimage.io.imsave(tmp.fpath, safe_range_im_uint8, "freeimage")
with open(tmp.fpath, 'rb') as fh:
return fh.read()
def png(self, width=None):
"""Return png string of image.
:param width: integer specifying the desired width
:returns: png as a string
"""
skimage.io.use_plugin('freeimage')
def resize(im, width):
x, y = im.shape[:2]
f = float(width) / float(x)
scale_factors = [1.0 for i in range(len(im.shape))]
scale_factors[0] = f
scale_factors[1] = f
ar = scipy.ndimage.zoom(im, scale_factors, order=0)
return Image.from_array(ar, log_in_history=False)
safe_range_im = self
if self.dtype != np.uint8:
safe_range_im = 255 * normalise(self)
if width is not None:
safe_range_im = resize(safe_range_im, width)
with _TemporaryFilePath(suffix='.png') as tmp:
safe_range_im_uint8 = safe_range_im.astype(np.uint8)
skimage.io.imsave(tmp.fpath, safe_range_im_uint8, "freeimage")
with open(tmp.fpath, 'rb') as fh:
return fh.read()
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 annotate(image, segmentation):
"""Return annotated image."""
uint8_normalised = normalise(image) * 255
annotation = AnnotatedImage.from_grayscale(uint8_normalised)
for i in segmentation.identifiers:
region = segmentation.region_by_identifier(i)
annotation.mask_region(region.dilate(1).border,
color=pretty_color(i))
return annotation
def annotate(input_file, output_dir):
"""Write an annotated image to disk."""
logger.info("---")
logger.info('Input image: "{}"'.format(os.path.abspath(input_file)))
image = Image.from_file(input_file)
intensity = mean_intensity_projection(image)
norm_intensity = normalise(intensity)
norm_rgb = np.dstack([norm_intensity, norm_intensity, norm_intensity])
name = fpath2name(input_file)
png_name = name + ".png"
csv_name = name + ".csv"
png_path = os.path.join(output_dir, png_name)
csv_path = os.path.join(output_dir, csv_name)
tubes = find_tubes(input_file, output_dir)
grains, difficult = find_grains(input_file, output_dir)
tubes = remove_tubes_not_touching_grains(tubes, grains)
tubes = remove_tubes_that_are_grains(tubes, grains)
ann = AnnotatedImage.from_grayscale(intensity)
num_grains = 0
for n, i in enumerate(grains.identifiers):
n = n + 1
region = grains.region_by_identifier(i)
ann.mask_region(region.inner.inner.inner.border.dilate(),
color=(0, 255, 0))
num_grains = n
num_tubes = 0
for n, i in enumerate(tubes.identifiers):
n = n + 1
region = tubes.region_by_identifier(i)
highlight = norm_rgb * pretty_color(i)
ann[region] = highlight[region]
ann.mask_region(region.dilate(3).border.dilate(3),
color=pretty_color(i))
num_tubes = n
ann.text_at("Num grains: {:3d}".format(num_grains), (10, 10),
antialias=True, color=(0, 255, 0), size=48)
logger.info("Num grains: {:3d}".format(num_grains))
ann.text_at("Num tubes : {:3d}".format(num_tubes), (60, 10),
antialias=True, color=(255, 0, 255), size=48)
logger.info("Num tubes : {:3d}".format(num_tubes))
logger.info('Output image: "{}"'.format(os.path.abspath(png_path)))
with open(png_path, "wb") as fh:
fh.write(ann.png())
logger.info('Output csv: "{}"'.format(os.path.abspath(csv_path)))
with open(csv_path, "w") as fh:
fh.write("{},{},{}\n".format(png_name, num_grains, num_tubes))
return png_name, num_grains, num_tubes
def to_directory(self, directory):
"""Write slices from 3D image to directory.
"""
if not os.path.isdir(directory):
os.mkdir(directory)
xdim, ydim, zdim = self.shape
num_digits = Image3D._num_digits(zdim-1)
ar = normalise(self) * 255
ar = ar.astype(np.uint8)
for z in range(zdim):
num = str(z).zfill(num_digits)
fname = "z{}.png".format(num)
fpath = os.path.join(directory, fname)
skimage.io.imsave(fpath, ar[:, :, z], "freeimage")
def annotate_segmentation(image, segmentation):
grayscale = normalise(image) * 255
canvas = AnnotatedImage.from_grayscale(grayscale)
for i in segmentation.identifiers:
region = segmentation.region_by_identifier(i)
outline = region.inner.border.dilate()
color = pretty_color_from_identifier(i)
canvas.mask_region(outline, color=color)
fpath = os.path.join(AutoName.directory, "segmentation.png")
with open(fpath, "wb") as fh:
fh.write(canvas.png())
def to_directory(self, directory):
"""Write slices from 3D image to directory.
"""
if not os.path.isdir(directory):
os.mkdir(directory)
xdim, ydim, zdim = self.shape
num_digits = Image3D._num_digits(zdim - 1)
ar = normalise(self) * 255
ar = ar.astype(np.uint8)
for z in range(zdim):
num = str(z).zfill(num_digits)
fname = "z{}.png".format(num)
fpath = os.path.join(directory, fname)
skimage.io.imsave(fpath, ar[:, :, z], "freeimage")
def test_normalise_123(self):
from jicbioimage.core.util.array import normalise
ar = np.array([1,2,3], dtype=np.uint8)
normed = normalise(ar)
expected = np.array([0., .5, 1.], dtype=np.float)
self.assertTrue( np.array_equiv(normed, expected) )
def test_only_negative(self):
from jicbioimage.core.util.array import normalise
zeros = np.zeros(5, dtype=np.float)
normed = normalise(zeros - 1.)
self.assertTrue( np.array_equiv(normed, zeros) )
def test_only_positive(self):
from jicbioimage.core.util.array import normalise
ones = np.ones(5, dtype=np.float)
normed = normalise(ones + 3.)
self.assertTrue( np.array_equiv(normed, ones) )
def test_normalise_returns_float_array(self):
from jicbioimage.core.util.array import normalise
zeros = np.array([1,2,3], dtype=np.uint8)
normed = normalise(zeros)
self.assertEqual(normed.dtype, np.float)