def __init__(self, root): pn = '/Users/nathaning/Documents/Python/Image Processing/B2 H&E 20X_001.svs' level = 1 i = OpenSlide(pn) # Load an SVS file # dims = i.level_dimensions[level] # k = i.read_region((0,0), level, dims) #Extract the level 1 image as a PIL.Image Object k = i.get_thumbnail(size=(600, 600)) # k.show() self.pi = ImageTk.PhotoImage(k) disp = Label(root, image=self.pi) disp.pack() print 'done'
def get_thumbnail(
slide_path: str,
downsample: int = None,
create_thumbnail: bool = False
) -> Image.Image:
"""Return thumbnail by using openslide or by creating a new one."""
if slide_path.endswith('czi'):
if create_thumbnail:
return generate_thumbnail(slide_path, downsample)
else:
return None
else:
reader = OpenSlide(slide_path)
level_downsamples = [round(x) for x in reader.level_downsamples]
if downsample is None:
downsample = max(level_downsamples)
if downsample in level_downsamples:
level = level_downsamples.index(downsample)
dims = reader.level_dimensions[level]
thumbnail = reader.get_thumbnail(dims)
elif create_thumbnail:
thumbnail = generate_thumbnail(slide_path, downsample)
else:
thumbnail = None
return thumbnail
def get(self, id):
"""
Get slide thumbnail
---
tags:
- Thumbnail
parameters:
- in: path
name: id
description: MonogDB ObjectId -- Example 57bf3c092f9b2e1595b29730
type: string
- in: query
name: size
description: Thumbnail size [small, medium, large]
type: string
responses:
200:
description: Returns the slide information
404:
description: Invalid slide Id or slide not found
"""
if not ObjectId.is_valid(id):
resp = {"status": 404, "message": "Invalid slide Id " + id}
return Response(dumps(resp),
status=404,
mimetype='application/json')
thumbSize = request.args.get("size", "small")
image = self.slides.find_one({'_id': ObjectId(id)})
path = image["path"]
filename = os.path.splitext(
os.path.basename(path))[0] + "." + str(thumbSize) + ".jpg"
if not self.gfs.exists(filename=filename):
width = int(image["scanProperties"]["openslide_level[0]_width"])
height = int(image["scanProperties"]["openslide_level[0]_height"])
thumbHeight = float(self.config["thumb_" + thumbSize + "_height"])
thumbWidth = int(round(thumbHeight / float(height) * int(width)))
try:
osr = OpenSlide(path)
thumb = osr.get_thumbnail((thumbWidth, thumbHeight))
except OpenSlideError, e:
resp = {
"status": 404,
"message": "OpenSlideError: Thumbnail failed to load"
}
return Response(dumps(resp),
status=404,
mimetype='application/json')
except ValueError:
resp = {
"status": 404,
"message": "ValueError: Thumbnail failed to load"
}
return Response(dumps(resp),
status=404,
mimetype='application/json')
def preview_from_queries(
slide: openslide.OpenSlide,
queries: Sequence[Patch],
min_res: int = 512,
color: Tuple[int, int, int] = (255, 255, 0),
thickness: int = 2,
cell_size: int = 20,
size_0: Optional[Coord] = None,
) -> NDByteImage:
"""
Give thumbnail with patches displayed.
Args:
slide: openslide object
queries: patch objects to preview from
min_res: minimum size for the smallest side of the thumbnail (usually the width)
color: rgb color for patch boundaries
thickness: thickness of patch boundaries
cell_size: size of a cell representing a patch in the grid
psize: size of a patch at level 0
Returns:
Thumbnail image with patches displayed.
"""
# get thumbnail first
slide_size = Coord(slide.dimensions)
if size_0 is None:
size_0 = Coord(queries[0].size_0)
thickness = 2 * (thickness // 2) + 1
res = slide_size / size_0 * (thickness + cell_size) + thickness
thumb_w = max(min_res, res.x)
thumb_h = max(min_res, res.y)
image = slide.get_thumbnail((thumb_w, thumb_h))
thumb_size = Coord(image.size)
dsr = slide_size[0] / thumb_size[0]
image = numpy.array(image)[:, :, 0:3]
# get grid
grid = 255 * numpy.ones((thumb_size.y, thumb_size.x), numpy.uint8)
for query in queries:
# position in queries are absolute
x, y = query.position / dsr
dx, dy = query.size_0 / dsr
startx = min(x, thumb_size.x - 1)
starty = min(y, thumb_size.y - 1)
endx = min(x + dx, thumb_size.x - 1)
endy = min(y + dy, thumb_size.y - 1)
# horizontal segments
grid[starty, startx:endx] = 0
grid[endy, startx:endx] = 0
# vertical segments
grid[starty:endy, startx] = 0
grid[starty:endy, endx] = 0
grid = grid < 255
d = disk(thickness//2)
grid = binary_dilation(grid, d)
image[grid] = color
return image
def get_thumbnails():
import os
from openslide import OpenSlide
data_dir = '/media/hui/Local Disk1/work/Data/Liver_Multi_Modality/Pathology/SlideImages/20-1018 PURU_VINOD'
save_dir = '/media/hui/Local Disk1/work/Data/Liver_Multi_Modality/Pathology/thumbnails'
os.makedirs(save_dir, exist_ok=True)
filelist = os.listdir(data_dir)
for file in filelist:
wsi_file = OpenSlide('{:s}/{:s}'.format(data_dir, file))
thumbnail = wsi_file.get_thumbnail((1000, 1000))
thumbnail.save('{:s}/{:s}.png'.format(save_dir, file.split('.')[0]))
def __init__(self, root):
pn = '/Users/nathaning/Documents/Python/Image Processing/B2 H&E 20X_001.svs'
level = 1
i = OpenSlide(pn) # Load an SVS file
# dims = i.level_dimensions[level]
# k = i.read_region((0,0), level, dims) #Extract the level 1 image as a PIL.Image Object
k = i.get_thumbnail(size=(600, 600))
# k.show()
self.pi = ImageTk.PhotoImage(k)
disp = Label(root, image=self.pi)
disp.pack()
print 'done'
def get(self, id):
"""
Get slide thumbnail
---
tags:
- Thumbnail
parameters:
- in: path
name: id
description: MonogDB ObjectId -- Example 57bf3c092f9b2e1595b29730
type: string
- in: query
name: size
description: Thumbnail size [small, medium, large]
type: string
responses:
200:
description: Returns the slide information
404:
description: Invalid slide Id or slide not found
"""
if not ObjectId.is_valid(id):
resp = {"status": 404, "message": "Invalid slide Id " + id}
return Response(dumps(resp), status=404, mimetype='application/json')
thumbSize = request.args.get("size", "small")
image = self.slides.find_one({'_id': ObjectId(id)})
path = image["path"]
filename = os.path.splitext(os.path.basename(path))[0] + "." + str(thumbSize) + ".jpg"
if not self.gfs.exists(filename=filename):
width = int(image["scanProperties"]["openslide_level[0]_width"])
height = int(image["scanProperties"]["openslide_level[0]_height"])
thumbHeight = float(self.config["thumb_" + thumbSize + "_height"])
thumbWidth = int(round(thumbHeight/float(height) * int(width)))
try:
osr = OpenSlide(path)
thumb = osr.get_thumbnail((thumbWidth,thumbHeight))
except OpenSlideError, e:
resp = {"status": 404, "message": "OpenSlideError: Thumbnail failed to load"}
return Response(dumps(resp), status=404, mimetype='application/json')
except ValueError:
resp = {"status": 404, "message": "ValueError: Thumbnail failed to load"}
return Response(dumps(resp), status=404, mimetype='application/json')
def gen_thumbnail_url(request, slide_id):
try:
s = Alopecia.objects.get(pk=slide_id)
except Alopecia.DoesNotExist:
raise Http404
label_name = str(s.LabelUrlPath).split('/')[-1]
if label_name != 'placeholder.png':
return JsonResponse({
'thumbnail':
request.build_absolute_uri(str(s.LabelUrlPath)),
})
else:
if s.SlideType == 1:
ds = pydicom.dcmread(str(s.UrlPath))
thumbnail = get_PIL_image(ds)
response = HttpResponse(content_type='image/png')
thumbnail.thumbnail(MAX_THUMBNAIL_SIZE)
filename = str(s.UrlPath).split('/')[-1]
fWithoutExt = filename.split('.')
fWithoutExt.pop()
fWithoutExt = ''.join(fWithoutExt)
thumbnailName = fWithoutExt + '.thumbnail'
dirPath = settings.STATICFILES_DIRS[0] + '/images/thumbnail'
thumbnail.save(dirPath + '/' + thumbnailName, 'JPEG')
return JsonResponse({
'thumbnail':
request.build_absolute_uri('/static/images/thumbnail/') +
thumbnailName,
})
else:
file = path.join(settings.HISTOSLIDE_SLIDEROOT, str(s.UrlPath))
slide = OpenSlide(file)
thumbnail = slide.get_thumbnail((800, 600))
filename = str(s.UrlPath).split('/')[-1]
fWithoutExt = filename.split('.')
fWithoutExt.pop()
fWithoutExt = ''.join(fWithoutExt)
thumbnailName = fWithoutExt + '.thumbnail'
dirPath = settings.STATICFILES_DIRS[0] + '/images/thumbnail'
thumbnail.save(dirPath + '/' + thumbnailName, 'JPEG')
return JsonResponse({
'thumbnail':
request.build_absolute_uri('/static/images/thumbnail/') +
thumbnailName,
})
def getThumbnail(path):
"""This will return the 0/0 tile later whch in the case of an SVS image is actually the thumbnail..... """
path = os.path.abspath(os.path.join(dz.config['slides_dir'], path))
osr = OpenSlide(path)
format = 'jpeg'
format = format.lower()
if format != 'jpeg' and format != 'png':
# Not supported by Deep Zoom
abort(404)
try:
thumb = osr.get_thumbnail((300, 300))
except ValueError:
# Invalid level or coordinates
abort(404)
buf = PILBytesIO()
thumb.save(buf, 'jpeg', quality=90)
resp = make_response(buf.getvalue())
resp.mimetype = 'image/%s' % format
return resp
def generate_thumbnail(image_filepath, thumbnail_filepath):
'''
Generates a thumbnail from the specified image.
'''
# open image with OpenSlide library
image_file = OpenSlide(image_filepath)
# extract image dimensions
image_dims = image_file.dimensions
# make thumbnail 100 times smaller
thumb_dims = tuple( (x/100 for x in image_dims) )
# create thumbnail
thumb_file = image_file.get_thumbnail(thumb_dims)
# save file with desired path, format
thumb_file.save(thumbnail_filepath, "png")
# cleanup
image_file.close()
def getThumbnail(path):
"""This will return the 0/0 tile later whch in the case of an SVS image is actually the thumbnail..... """
path = os.path.abspath(os.path.join(dz.config['slides_dir'], path))
osr = OpenSlide(path)
format = 'jpeg'
format = format.lower()
if format != 'jpeg' and format != 'png':
# Not supported by Deep Zoom
abort(404)
try:
thumb = osr.get_thumbnail( (300,300))
except ValueError:
# Invalid level or coordinates
abort(404)
buf = PILBytesIO()
thumb.save(buf, 'jpeg', quality=90)
resp = make_response(buf.getvalue())
resp.mimetype = 'image/%s' % format
return resp
def print_slide_details(
wsi: openslide.OpenSlide,
show_thumbnail: bool = True,
max_size: Tuple[int, int] = (1200, 800)) -> None:
"""Informations essentielles de la lame."""
# nombre de pixels par niveaux
n_pixels = [w0 * w1 for (w0, w1) in wsi.level_dimensions]
n_pixels_ = tuple(format(n, ',d').replace(',', ' ') for n in n_pixels)
# taille (Gb) des niveaux
t_pixels = tuple(round(24 * n / 1e9, 2) for n in n_pixels)
# dimensions réelles (cm) de la lame
dim_x = round(
float(wsi.properties['openslide.mpp-x']) * wsi.dimensions[0] / 10000,
2)
dim_y = round(
float(wsi.properties['openslide.mpp-y']) * wsi.dimensions[1] / 10000,
2)
# affichage des informations
print(f"Fichier : {wsi}")
print(
f"Grandissement : {wsi.properties['openslide.objective-power']}x"
)
print(f"Dimensions en pixel : {wsi.dimensions}")
print(f"Dimensions en cm : {(dim_x, dim_y)}")
print(
f"Microns par pixel : {float(wsi.properties['openslide.mpp-x']):.3f}"
)
print(f"Nombre de niveaux de résolution : {wsi.level_count}")
print(f"Grandissement des niveaux : {wsi.level_downsamples}")
print(f"Dimensions des niveaux : {wsi.level_dimensions}")
print(f"Nombre de pixels des niveaux : {n_pixels_}")
print(f"Taille (Gb) par niveaux : {t_pixels}")
print(f"Taille fichier décompressé (Gb) : {round(sum(t_pixels), 2)}")
# optionnel: affiche une image macro de la lame
if show_thumbnail:
display(wsi.get_thumbnail(size=max_size))
from openslide import OpenSlide
svs_path = 'Slide 10.svs'
# Open whole slide image
img = OpenSlide(svs_path)
# Get shape
original_dimensions = img.dimensions
# Get thumbnail image (t times smaller)
t = 512
resize_width = original_dimensions[0] / t
resize_height = original_dimensions[1] / t
resized_img = img.get_thumbnail(
(resize_width, resize_height)) # PIL.Image type
resized_img.save('thumbnail_images_sample/' + svs_path.split('.')[0] + '.png')
# Get a region of the original image (here [10000:10100,10000:10100])
cropped_img = img.read_region((10000, 10000), 0, (100, 100)) # PIL Image RGBA
cropped_img = cropped_img.convert('RGB') # PIL Image RGB
cropped_img.save('tmp.png')