def tile(mode, project, specimen, block, resource, slide_name, slide_ext,
level, col, row, format):
format = format.lower()
if format != 'jpeg' and format != 'png':
# Not supported by Deep Zoom
return 'bad format'
abort(404)
# Get a project reference, using either local database or remotely supplied dict
pr = dzi_get_project_ref(project)
# Get the raw SVS/tiff file for the slide (the resource should exist,
# or else we will spend a minute here waiting with no response to user)
sr = SlideRef(pr, specimen, block, slide_name, slide_ext)
tiff_file = sr.get_local_copy(resource)
os = None
if mode == 'affine':
os = AffineTransformedOpenSlide(
tiff_file, get_affine_matrix(sr, 'affine', resource, 'image'))
else:
os = OpenSlide(tiff_file)
dz = DeepZoomGenerator(os)
tile = dz.get_tile(level, (col, row))
buf = PILBytesIO()
tile.save(buf, format, quality=75)
resp = make_response(buf.getvalue())
resp.mimetype = 'image/%s' % format
print('PNG size: %d' % (len(buf.getvalue(), )))
return resp
def index_wsi(file_path):
config_map = {
'DEEPZOOM_TILE_SIZE': 'tile_size',
'DEEPZOOM_OVERLAP': 'overlap',
'DEEPZOOM_LIMIT_BOUNDS': 'limit_bounds',
}
opts = dict((v, app.config[k]) for k, v in config_map.items())
slide = open_slide('static/wsi/' + file_path)
app.slides = {
SLIDE_NAME: DeepZoomGenerator(slide, **opts)
}
app.associated_images = []
app.slide_properties = slide.properties
for name, image in slide.associated_images.items():
app.associated_images.append(name)
slug = slugify(name)
app.slides[slug] = DeepZoomGenerator(ImageSlide(image), **opts)
try:
mpp_x = slide.properties[openslide.PROPERTY_NAME_MPP_X]
mpp_y = slide.properties[openslide.PROPERTY_NAME_MPP_Y]
slide_mpp = (float(mpp_x) + float(mpp_y)) / 2
except (KeyError, ValueError):
slide_mpp = 0
slide_url = url_for('dzi', slug=SLIDE_NAME)
return render_template('as_viewer.html', slide_url=slide_url, slide_mpp=slide_mpp, file_name=file_path, dictionary=getDictionary(file_path))
def load_slide():
slidefile = app.config['DEEPZOOM_SLIDE']
if slidefile is None:
raise ValueError('No slide file specified')
config_map = {
'DEEPZOOM_TILE_SIZE': 'tile_size',
'DEEPZOOM_OVERLAP': 'overlap',
'DEEPZOOM_LIMIT_BOUNDS': 'limit_bounds',
}
opts = dict((v, app.config[k]) for k, v in config_map.items())
slide = open_slide(slidefile)
app.slides = {
SLIDE_NAME: DeepZoomGenerator(slide, **opts)
}
app.associated_images = []
app.slide_properties = slide.properties
for name, image in slide.associated_images.items():
app.associated_images.append(name)
slug = slugify(name)
app.slides[slug] = DeepZoomGenerator(ImageSlide(image), **opts)
try:
mpp_x = slide.properties[openslide.PROPERTY_NAME_MPP_X]
mpp_y = slide.properties[openslide.PROPERTY_NAME_MPP_Y]
app.slide_mpp = (float(mpp_x) + float(mpp_y)) / 2
except (KeyError, ValueError):
app.slide_mpp = 0
def ndpi_cut(ndpi_way, x, k, outway, pe): # x = 分割后图片边长 k = ndpi图片的第几个level
# time_start = time.time()
if not os.path.isdir(outway):
os.makedirs(outway)
for files in os.listdir(ndpi_way):
# 当前文件夹所有文件
if files.endswith('.tiff'): # 判断是否以.ndpi结尾 也可以为tiff
slide = op.OpenSlide(ndpi_way + '\\' + files)
# print(slide.level_dimensions)
bigImg = DeepZoomGenerator(slide,
tile_size=x - 2,
overlap=1,
limit_bounds=False)
count = bigImg.level_count - 1
z = count - k # 倒着读取
raw, col = bigImg.level_tiles[z]
# print(raw, col)
(filename, extension) = os.path.splitext(files)
for i in range(raw - 1):
for j in range(col - 1):
try:
img = bigImg.get_tile(z, (j, i))
Img = np.asarray(img)
if Img.shape == (a, a, Img.shape[2]):
p = judge_white.judge_white(Img)
print(p, Img.shape, (a, a, Img.shape[2]))
if p < pe:
outputway = outway + '\\' + filename + r'_{a}_{b}.png'.format(
a=i, b=j)
img.save(outputway)
else:
pass
except ValueError:
break
print(files + ' done')
def get(self, path):
"""
Method for getting slide cache. Has self and path arguments.
"""
with self._lock:
if path in self._cache:
# Move to end of LRU
slide = self._cache.pop(path)
self._cache[path] = slide
return slide
osr = OpenSlide(path)
slide = DeepZoomGenerator(osr, **self.dz_opts)
try:
mpp_x = osr.properties[openslide.PROPERTY_NAME_MPP_X]
mpp_y = osr.properties[openslide.PROPERTY_NAME_MPP_Y]
slide.mpp = (float(mpp_x) + float(mpp_y)) / 2
except (KeyError, ValueError):
slide.mpp = 0
with self._lock:
if path not in self._cache:
if len(self._cache) == self.cache_size:
self._cache.popitem(last=False)
self._cache[path] = slide
return slide
def __init__(self, osr, tile_size=254, overlap=1, limit_bounds=False):
if osr.format in ['.kfb', '.KFB']:
self._dzg = KfbDZG(osr, tile_size, overlap, limit_bounds)
elif osr.format in ['.tmap', '.TMAP']:
self._dzg = TmapDZG(osr, 256, overlap, limit_bounds)
else:
self._dzg = OpenSlideDZG(osr, tile_size, overlap, limit_bounds)
def save_valid_imgs(samples, patch_size=PATCH_SIZE):
num_samples = len(samples)
for idx in range(num_samples):
for _, batch_sample in samples.iloc[idx:idx + 1].iterrows():
slide_path = batch_sample.slide_path
print(slide_path)
slide_name = 's'
slide_contains_tumor = 'pos' in slide_path
with openslide.open_slide(slide_path) as slide:
tiles = DeepZoomGenerator(slide,
tile_size=patch_size,
overlap=0,
limit_bounds=False)
x, y = batch_sample.tile_loc[::-1]
if slide_contains_tumor:
start_x = int(slide.properties.get('openslide.bounds-x', 0))
start_y = int(slide.properties.get('openslide.bounds-y', 0))
start_x = start_x / patch_size
start_y = start_y / patch_size
x += start_x
y += start_y
img = tiles.get_tile(tiles.level_count - 1, (x, y))
img.save('/data/model/patches/val/pos/{}_pos_{}.png'.format(
slide_name, idx))
else:
img = tiles.get_tile(tiles.level_count - 1, (x, y))
img.save('/data/model/patches/val/neg/{}_neg_{}.png'.format(
slide_name, idx))
print('num_samples_val : ', num_samples)
print('val img save completed')
def load_slide(slidefile, tile_size):
print("there is an image")
slide = open_slide(slidefile)
slides = {
"slide": DeepZoomGenerator(slide,
tile_size=tile_size,
overlap=1,
limit_bounds=True)
}
associated_images = []
slide_properties = slide.properties
for name, image in slide.associated_images.items():
associated_images.append(name)
slug = slugify(name)
slides[slug] = DeepZoomGenerator(ImageSlide(image),
tile_size=tile_size,
overlap=1,
limit_bounds=True)
try:
mpp_x = slide.properties[openslide.PROPERTY_NAME_MPP_X]
mpp_y = slide.properties[openslide.PROPERTY_NAME_MPP_Y]
slide_mpp = (float(mpp_x) + float(mpp_y)) / 2
except (KeyError, ValueError):
slide_mpp = 0
return slides, associated_images, slide_properties, slide_mpp
def get(self, path):
with self._lock:
if path in self._cache:
# Move to end of LRU
slide = self._cache.pop(path)
self._cache[path] = slide
return slide
if is_image(path):
#osr = ImageSlide(path)
osr = get_osr(path)
else:
osr = OpenSlide(path)
slide = DeepZoomGenerator(osr, **self.dz_opts)
try:
mpp_x = osr.properties[openslide.PROPERTY_NAME_MPP_X]
mpp_y = osr.properties[openslide.PROPERTY_NAME_MPP_Y]
slide.mpp = (float(mpp_x) + float(mpp_y)) / 2
except (KeyError, ValueError):
slide.mpp = 0
with self._lock:
if path not in self._cache:
if len(self._cache) == self.cache_size:
self._cache.popitem(last=False)
self._cache[path] = slide
return slide
def _serve_tiles(self, request):
tile_config = request.path[len("/data/plugin/WSI/tiles/"):].split("/")
id = int(tile_config[0])
if id == self._cache_slide_id:
slide = self._cache_slide
else:
slide_path = self._cache_slide_prop[id]["slide_path"]
slide = DeepZoomGenerator(open_slide(slide_path))
self._cache_slide = slide
self._cache_slide_id = id
if len(tile_config) <= 2:
response = werkzeug.Response(slide.get_dzi("jpeg"))
response.headers.set('Content-Type', 'application/xml')
return response
else:
level, colrow = tile_config[1:]
level = int(level)
col, row = map(int, colrow[:-1 * len(".jpeg"):].split("_"))
tile = slide.get_tile(level, (col, row))
buf = PILBytesIO()
tile.save(buf, "jpeg", quality=75)
response = werkzeug.Response(buf.getvalue())
response.headers.set('Content-Type', 'image/jpeg')
return response
def getTile(file, level, col, row):
format = 'jpeg'
slide = DeepZoomGenerator(open_slide(file))
tile = slide.get_tile(level, (col, row))
buf = PILBytesIO()
tile.save(buf, format, quality=app.config['DEEPZOOM_TILE_QUALITY'])
return base64.b64encode(buf.getvalue())
def dzi_asso(path, associated_name):
slide = _get_slide(path)
associated_image = slide.osr.associated_images[associated_name]
dzg = DeepZoomGenerator(ImageSlide(associated_image))
format = app.config['DEEPZOOM_FORMAT']
resp = make_response(dzg.get_dzi(format))
resp.mimetype = 'application/xml'
return resp
def slide_dzi(request, pk):
scan = get_object_or_404(Scan, pk=pk)
raw_slide = open_slide(scan.file)
slide = DeepZoomGenerator(
raw_slide,
tile_size=DEEPZOOM_TILE_SIZE,
overlap=DEEPZOOM_OVERLAP,
limit_bounds=DEEPZOOM_LIMIT_BOUNDS,
)
response = slide.get_dzi(DEEPZOOM_FORMAT)
return HttpResponse(response, content_type="application/xml")
def get_tiles(batch_samples, patch_size=256, num_classes=2, convert_to_cat=True):
"""Generator function to yield image and mask tuples,
Parameters
----------
batch_samples: DataFrame
Subsetted dataframe as obtained from get_all_patches_from_slide
patch_size: int
Patch size
convert_to_cat: bool
Should convert to categorical
Returns
-------
X: tensor
Y: tensor
"""
images = []
masks = []
for _, batch_sample in batch_samples.iterrows():
slide_contains_tumor = batch_sample["uid"].startswith("tumor")
with WSIReader(batch_sample.slide_path, 40) as slide:
tiles = DeepZoomGenerator(
slide, tile_size=patch_size, overlap=0, limit_bounds=False
)
tile_loc = batch_sample.tile_loc # [::-1]
if isinstance(tile_loc, six.string_types):
tile_row, tile_col = eval(tile_loc)
else:
tile_row, tile_col = tile_loc
# the get_tile tuple required is (col, row)
img = tiles.get_tile(tiles.level_count - 1, (tile_col, tile_row))
(tile_x, tile_y), tile_level, _ = tiles.get_tile_coordinates(
tiles.level_count - 1, (tile_col, tile_row)
)
if slide_contains_tumor:
json_filepath = batch_sample["json_filepath"]
polygons = get_annotation_polygons(json_filepath, "shapely")
mask = create_tumor_mask_from_tile(tile_x, tile_y, polygons, patch_size)
else:
mask = np.zeros((patch_size, patch_size))
images.append(np.array(img))
masks.append(mask)
X_train = np.array(images)
y_train = np.array(masks)
if convert_to_cat:
y_train = mask_to_categorical(y_train, num_classes, patch_size)
return X_train, y_train
def tile(request, pk, level, col, row):
scan = get_object_or_404(Scan, pk=pk)
raw_slide = open_slide(scan.file)
slide = DeepZoomGenerator(
raw_slide,
tile_size=DEEPZOOM_TILE_SIZE,
overlap=DEEPZOOM_OVERLAP,
limit_bounds=DEEPZOOM_LIMIT_BOUNDS,
)
tile = slide.get_tile(level, (col, row))
buf = BytesIO()
tile.save(buf, DEEPZOOM_FORMAT, quality=DEEPZOOM_TILE_QUALITY)
return HttpResponse(buf.getvalue(), content_type="image/jpeg")
def sample_and_store_patches(self, patch_size, level, progressBar):
start_time = start_timer() # Timer Start
rows_per_txn = 20
tile_size = patch_size
slide = open_slide(self.file_path)
tiles = DeepZoomGenerator(slide,
tile_size=tile_size,
overlap=0,
limit_bounds=True)
if level >= tiles.level_count:
print(
"[error]: requested level does not exist. Number of slide levels: "
+ str(tiles.level_count))
return 0
x_tiles, y_tiles = tiles.level_tiles[level]
x, y = 0, 0
count, batch_count = 0, 0
patches, coords, labels = [], [], []
while y < y_tiles:
while x < x_tiles:
new_tile = np.array(tiles.get_tile(level, (x, y)),
dtype=np.uint8)
# OpenSlide calculates overlap in such a way that sometimes depending on the dimensions, edge
# patches are smaller than the others. We will ignore such patches.
if np.shape(new_tile) == (patch_size, patch_size, 3):
patches.append(new_tile)
coords.append(np.array([x, y]))
count += 1
progressBar.setValue(
int((y * x_tiles + x) * 100 / (x_tiles * y_tiles)))
x += 1
# To save memory, we will save data into the dbs every rows_per_txn rows. i.e., each transaction will commit
# rows_per_txn rows of patches. Write after last row regardless. HDF5 does NOT follow
# this convention due to efficiency.
if (y % rows_per_txn == 0 and y != 0) or y == y_tiles - 1:
self.save_to_disk(patches, coords, labels)
y += 1
x = 0
print("============ Patches Dataset Stats ===========")
print("Total patches sampled: ", count)
print("Patches saved to: ", self.db_location)
print("==============================================")
end_timer(start_time) # Timer Ends
def __init__(self, path: str, tile_size: int = 224):
self.path = path
self.tile_size = tile_size
self.slide = openslide.OpenSlide(self.path)
self.deepzoom_gen = DeepZoomGenerator(self.slide,
tile_size=self.tile_size,
overlap=0,
limit_bounds=False)
self.mpp = (float(
self.slide.properties[openslide.PROPERTY_NAME_MPP_X]),
float(
self.slide.properties[openslide.PROPERTY_NAME_MPP_Y]))
self.level_count = self.deepzoom_gen.level_count
self.level_dimensions = self.deepzoom_gen.level_dimensions
self.level_tiles = self.deepzoom_gen.level_tiles
def ChangeImage(folder, filename):
global imagePathLookupTable
session["ID"] = binascii.hexlify(os.urandom(20))
path = "//home/prosjekt" + imagePathLookupTable[folder + "/" + filename]
image = openslide.OpenSlide(path)
logger.log(
25,
configuration.LogFormat() + current_user.username +
" requested image " + filename)
deepZoomGen = DeepZoomGenerator(image,
tile_size=254,
overlap=1,
limit_bounds=False)
deepZoomList.append(session["ID"], deepZoomGen)
return deepZoomGen.get_dzi("jpeg")
def __init__(self, path):
self.warning = ''
self.path = path
self.reader = None
self.tilesize = 1024
self.ext = check_ext(path)
self.default_dtype = np.uint16
if self.ext == '.ome.tif' or self.ext == '.ome.tiff':
self.io = TiffFile(self.path, is_ome=False)
self.group = zarr.open(self.io.series[0].aszarr())
self.reader = 'tifffile'
self.ome_version = self._get_ome_version()
print("OME ", self.ome_version)
num_channels = self.get_shape()[0]
tile_0 = self.get_tifffile_tile(num_channels, 0, 0, 0, 0, 1024)
if tile_0 is not None:
self.default_dtype = tile_0.dtype
if (num_channels == 3 and tile_0.dtype == 'uint8'):
self.rgba = True
self.rgba_type = '3 channel'
elif (num_channels == 1 and tile_0.dtype == 'uint8'):
self.rgba = True
self.rgba_type = '1 channel'
else:
self.rgba = False
self.rgba_type = None
print("RGB ", self.rgba)
print("RGB type ", self.rgba_type)
elif self.ext == '.svs':
self.io = OpenSlide(self.path)
self.dz = DeepZoomGenerator(self.io,
tile_size=1024,
overlap=0,
limit_bounds=True)
self.reader = 'openslide'
self.rgba = True
self.rgba_type = None
self.default_dtype = np.uint8
print("RGB ", self.rgba)
print("RGB type ", self.rgba_type)
else:
self.reader = None
def slide_to_tiles(slide,
new_mpp=0.5,
tile_size=512,
overlap=0,
return_locations=False):
"""
Convert a slide to tiles with a given mpp and tile size
"""
# Identify appropriate pyramid level for given micron per pixel
mpp = np.float(slide.properties['openslide.mpp-x'])
scale_factor = new_mpp / mpp
offset = math.floor(np.log2((scale_factor + 0.1)))
level_mpp = 2**offset * mpp
scale_from_level = new_mpp / level_mpp
level_tile_size = math.ceil(tile_size * scale_from_level)
generator = DeepZoomGenerator(slide,
tile_size=level_tile_size,
overlap=overlap,
limit_bounds=True)
highest_level = generator.level_count - 1
level = highest_level - offset
cols, rows = generator.level_tiles[level]
# Extract tiles
tiles = []
tile_locations = []
for col in range(cols):
for row in range(rows):
tile = np.array(generator.get_tile(level, (col, row)))
if tile.shape[0] == level_tile_size and tile.shape[
1] == level_tile_size:
tile = cv2.resize(tile, (tile_size, tile_size),
interpolation=cv2.INTER_LINEAR)
tiles.append(tile)
tile_locations.append([row, col])
tiles = np.stack(tiles, axis=0)
tile_locations = np.array(tile_locations)
if return_locations:
return tiles, tile_locations
else:
return tiles
def run_image(self, associated=None):
"""
Run a single image from self.slide.
"""
if associated is None:
image = self.slide
if self.with_viewer:
basename = os.path.join(self.basename, VIEWER_SLIDE_NAME)
else:
basename = self.basename
else:
image = ImageSlide(self.slide.associated_images[associated])
basename = os.path.join(self.basename, self.slugify(associated))
dz = DeepZoomGenerator(image,
self.tile_size,
self.overlap,
limit_bounds=self.limit_bounds)
tiler = DeepZoomImageTiler(dz, basename, self.format, associated,
self.queue, self.slide, self.basename_jpg,
self.xml_file, self.mask_type,
self.xml_label, self.roi_percentage,
self.img_extension, self.save_masks,
self.magnification)
tiler.run()
self.dzi_data[self.url_for(associated)] = tiler.get_dzi()
def _run_image(self, associated=None):
"""Run a single image from self._slide."""
if associated is None:
image = self._slide
if self._with_viewer:
basename = os.path.join(self._basename, VIEWER_SLIDE_NAME)
else:
basename = self._basename
else:
image = ImageSlide(self._slide.associated_images[associated])
basename = os.path.join(self._basename, self._slugify(associated))
print("enter DeepZoomGenerator")
dz = DeepZoomGenerator(image,
self._tile_size,
self._overlap,
limit_bounds=self._limit_bounds)
print("enter DeepZoomImageTiler")
tiler = DeepZoomImageTiler(dz, basename, self._format, associated,
self._queue, self._slide, self._basenameJPG,
self._xmlfile, self._mask_type,
self._xmlLabel, self._ROIpc,
self._ImgExtension, self._SaveMasks,
self._Mag)
tiler.run()
self._dzi_data[self._url_for(associated)] = tiler.get_dzi()
def print_tile_dimensions(self, patch_size=0):
patch_dim = patch_size
level_count = 0
level_tiles = []
level_dimensions = []
# Check that either tile or patch size is set correctly.
if patch_size == 0:
print("[error]: set patch size.")
else:
print("Setting patch size ", patch_dim)
# Open image and return variables.
slide = open_slide(self.file_path)
tiles = DeepZoomGenerator(slide, tile_size=patch_size, overlap=0)
level_count = tiles.level_count
level_tiles = tiles.level_tiles
level_dimensions = tiles.level_dimensions
print("============Tile Dimensions==========")
print("Level count: " + str(level_count))
print("Level tiles: " + str(level_tiles))
print("Level dimensions: " + str(level_dimensions))
print("=====================================")
def get_regions(dz: DZG, i: int, j: int) -> Tuple[List[int], List[int]]:
"""Retourne une région d'intérêt étant donné deux indices i et j.
Paramètres:
i : indice selon la largeur de la lame
j : indice selon la hauteur de la lame
Outputs:
region_0 : liste de 4 entiers (w_0, h_0, t_w, t_h) avec w_0 et h_0
les coordonnées du coin en haut à gauche du patch d'indice
(i, j). t_w et t_h sont la largeur et la hauteur du patch
en pixel. En principe, t_w = t_h sauf pour les patches
présents sur les bordures de la lame. Les coordonnées w_0,
h_0, t_w, t_h sont prises pour le plus haut niveau de
résolution.
region_l : liste de 4 entiers (h_start, h_end, w_start, w_end)
correpondant aux coordonnées du patch équivalent à
un niveau de résolution plus faible (ex. 32). Ces
coordonnées permettront de calculer le pourcentage
de fond blanc sur le patch grâce au masque de segmen-
tation.
"""
# coordonnées dans le niveau de résolution le plus élevé
(w_0_ij, h_0_ij), _, (d_w_0_ij,
d_h_0_ij) = dz.get_tile_coordinates(dz.l0_z, (j, i))
# coordonnées dans le niveau de résolution le plus faible
d_h_l_ij, d_w_l_ij = round(d_h_0_ij / dz.f_h), round(d_w_0_ij / dz.f_w)
start_w_l_ij, start_h_l_ij = round(w_0_ij / dz.f_w), round(h_0_ij / dz.f_h)
region_0 = [w_0_ij, h_0_ij, d_h_0_ij, d_w_0_ij]
region_l = [
start_h_l_ij, start_h_l_ij + d_h_l_ij, start_w_l_ij,
start_w_l_ij + d_w_l_ij
]
return region_0, region_l
def get(self, path):
with self._lock:
if path in self._cache:
# Move to end of LRU
slide = self._cache.pop(path)
self._cache[path] = slide
return slide
if path.endswith('.ndpi') and self.use_ndp_read and os.path.getsize(
path) >= self.ndpi_size_limit:
slide = LargeNDPiDeepZoomGenerator(path, self.dz_opts['tile_size'],
self.dz_opts['overlap'])
else:
osr = OpenSlide(path)
slide = DeepZoomGenerator(osr, **self.dz_opts)
try:
mpp_x = osr.properties[openslide.PROPERTY_NAME_MPP_X]
mpp_y = osr.properties[openslide.PROPERTY_NAME_MPP_Y]
slide.mpp = (float(mpp_x) + float(mpp_y)) / 2
except (KeyError, ValueError):
slide.mpp = 0
with self._lock:
if path not in self._cache:
if len(self._cache) == self.cache_size:
self._cache.popitem(last=False)
self._cache[path] = slide
return slide
def _get_dz(self, associated=None):
if associated is not None:
image = ImageSlide(self._slide.associated_images[associated])
else:
image = self._slide
return DeepZoomGenerator(image, self._tile_size, self._overlap,
limit_bounds=self._limit_bounds)
def load_slide(file):
slidefile = file
if slidefile is None:
raise ValueError('No slide file specified')
config_map = {
'DEEPZOOM_TILE_SIZE': 'tile_size',
'DEEPZOOM_OVERLAP': 'overlap',
'DEEPZOOM_LIMIT_BOUNDS': 'limit_bounds',
}
opts = dict((v, app.config[k]) for k, v in config_map.items())
slide = open_slide(slidefile)
left = slide.properties[
"mirax.NONHIERLAYER_3_LEVEL_0_SECTION.COMPRESSED_STITCHING_ORIG_SLIDE_SCANNED_AREA_IN_PIXELS__LEFT"]
top = slide.properties[
"mirax.NONHIERLAYER_3_LEVEL_0_SECTION.COMPRESSED_STITCHING_ORIG_SLIDE_SCANNED_AREA_IN_PIXELS__TOP"]
app.slides = {
SLIDE_NAME: DeepZoomGenerator(slide, **opts),
'left': left,
'top': top
}
try:
mpp_x = slide.properties[openslide.PROPERTY_NAME_MPP_X]
mpp_y = slide.properties[openslide.PROPERTY_NAME_MPP_Y]
app.slide_mpp = (float(mpp_x) + float(mpp_y)) / 2
return app.slide_mpp
except (KeyError, ValueError):
app.slide_mpp = 0
return 0
def tile_gen(self, state=9):
"""Call this function to divide the slice in tiles, it manage the dimension and the edge cuts.
This function call the method 'manage_process' that create same vectors for the next step, run the theads"""
self.generator = DeepZoomGenerator(self.slide,
tile_size=self.tile_size,
overlap=self.overlap,
limit_bounds=self.limit_bounds)
dim = self.generator.level_dimensions
ntile = self.generator._t_dimensions
for i, a in enumerate(dim):
if self.list_levels[self.lev_sec][1] == a[1] or self.list_levels[
self.lev_sec][1] == (
a[1] -
1) or self.list_levels[self.lev_sec][1] == (a[1] + 1):
self.levi = i
print(
f'found the right level {i} -- rr = {self.list_levels[self.lev_sec][1]} --- a = {a[1]}'
)
print(self.list_levels)
else:
pass
try:
numx, numy = ntile[self.levi]
print('{}---{}'.format(numx, numy))
except IndexError:
numx, numy = ntile[-1]
self.levi = len(ntile) - 1
print(
f'------There is a problem in if, add combinations, max resolution selected------{numx},{numy}'
)
self.ntiles_y = numy
numx_start, numx_stop, list_proc, start_indexs, stop_index = self.manage_process(
numx, numy)
if state == 0:
return numx_start, numx_stop, list_proc, start_indexs, stop_index, numy, self.levi
elif state == 1:
return self.generator
elif state == 2:
return numx
else:
self.start_thread(numx_start, numx_stop, list_proc, start_indexs)
def image(filename):
user = current_user
engine = db.get_engine(bind=user.dbname)
DBSession = sessionmaker(bind=engine)
db_session = DBSession()
annotationsInfo = db_session.query(Annotation).filter_by(pathimage_imageid=filename).all()
slug = slugify(filename)
slidempp = 'slide_mpp'
imagesize = 'imagesize'
if not hasattr(app,'slides'):
app.slides = {}
print('app.slides is null')
if not app.slides.has_key(slug):
print('image not exsits ' + slug)
image = db_session.query(PathImage).filter_by(filename=filename).first()
slidefile = image.filepath
config_map = {
'DEEPZOOM_TILE_SIZE': 'tile_size',
'DEEPZOOM_OVERLAP': 'overlap',
'DEEPZOOM_LIMIT_BOUNDS': 'limit_bounds',
}
opts = dict((v, app.config[k]) for k, v in config_map.items())
if 'kfb' in slidefile:
slide = kfbslide.KfbSlide(slidefile)
deepzoom = kfb_deepzoom.KfbDeepZoomGenerator(slide, **opts)
else:
slide = open_slide(slidefile)
deepzoom = DeepZoomGenerator(slide, **opts)
slideinfo = {SLIDE_NAME: deepzoom}
try:
mpp_x = slide.properties[openslide.PROPERTY_NAME_MPP_X]
mpp_y = slide.properties[openslide.PROPERTY_NAME_MPP_Y]
slideinfo[slidempp] = (float(mpp_x) + float(mpp_y)) / 2
except (KeyError, ValueError):
slideinfo[slidempp] = 0
slideinfo[imagesize] = [int(deepzoom.level_dimensions[-1][0]), int(deepzoom.level_dimensions[-1][1])]
slideinfo['active'] = True
app.slides[slug] = slideinfo
annotaions = getannotations(annotationsInfo, app.slides[slug][imagesize], db_session,user)
db_session.close()
slidename = SLIDE_NAME + slug
slide_url = url_for('dzi', slug=slidename)
return render_template("display.html",
user=user,
slide_url=slide_url,
slide_mpp=app.slides[slug][slidempp],
canlogout=True,
image_name=filename,
annotations=annotaions,
imagesize=app.slides[slug][imagesize]
)
def insertslide(cls, key, sl):
opts = {
'tile_size': settings.DEEPZOOM_TILE_SIZE,
'overlap': settings.DEEPZOOM_OVERLAP
}
with cls._dict_lock:
cls._slides[key] = sl
cls._deepzooms[key] = DeepZoomGenerator(sl, **opts)
def get(self, path):
with self._lock:
if path in self._cache:
# Move to end of LRU
slide = self._cache.pop(path)
self._cache[path] = slide
return slide
osr = OpenSlide(path)
slide = DeepZoomGenerator(osr, **self.dz_opts)
try:
mpp_x = osr.properties[openslide.PROPERTY_NAME_MPP_X]
mpp_y = osr.properties[openslide.PROPERTY_NAME_MPP_Y]
slide.mpp = (float(mpp_x) + float(mpp_y)) / 2
except (KeyError, ValueError):
slide.mpp = 0
with self._lock:
if path not in self._cache:
if len(self._cache) == self.cache_size:
self._cache.popitem(last=False)
self._cache[path] = slide
return slide
class _BoxesDeepZoomTest(object):
def setUp(self):
self.osr = self.CLASS(file_path(self.FILENAME))
self.dz = DeepZoomGenerator(self.osr, 254, 1)
def tearDown(self):
self.osr.close()
def test_repr(self):
self.assertEqual(repr(self.dz),
('DeepZoomGenerator(%r, tile_size=254, overlap=1, ' +
'limit_bounds=False)') % self.osr)
def test_metadata(self):
self.assertEqual(self.dz.level_count, 10)
self.assertEqual(self.dz.tile_count, 11)
self.assertEqual(self.dz.level_tiles,
((1, 1), (1, 1), (1, 1), (1, 1), (1, 1),
(1, 1), (1, 1), (1, 1), (1, 1), (2, 1)))
self.assertEqual(self.dz.level_dimensions,
((1, 1), (2, 1), (3, 2), (5, 4), (10, 8),
(19, 16), (38, 32), (75, 63), (150, 125), (300, 250)))
def test_get_tile(self):
self.assertEqual(self.dz.get_tile(9, (1, 0)).size, (47, 250))
def test_get_tile_bad_level(self):
self.assertRaises(ValueError, lambda: self.dz.get_tile(-1, (0, 0)))
self.assertRaises(ValueError, lambda: self.dz.get_tile(10, (0, 0)))
def test_get_tile_bad_address(self):
self.assertRaises(ValueError, lambda: self.dz.get_tile(0, (-1, 0)))
self.assertRaises(ValueError, lambda: self.dz.get_tile(0, (1, 0)))
def test_get_tile_coordinates(self):
self.assertEqual(self.dz.get_tile_coordinates(9, (1, 0)),
((253, 0), 0, (47, 250)))
def test_get_tile_dimensions(self):
self.assertEqual(self.dz.get_tile_dimensions(9, (1, 0)), (47, 250))
def test_get_dzi(self):
self.assertTrue('http://schemas.microsoft.com/deepzoom/2008' in
self.dz.get_dzi('jpeg'))
#!/usr/local/bin/python
from openslide import OpenSlide
from openslide.deepzoom import DeepZoomGenerator
from PIL import Image
import Thresholding as T, numpy, cv2
slide=DeepZoomGenerator(OpenSlide("/usr/local/OpenSlideServe/data/CarlZeiss/TilOysteinAnalyse/Alphonse.tif"))
tile=slide.get_tile(15,(72,15))
t=""
tile = Image.open("colorwheel-rgb.jpg")
# print tile.getextrema()
# tile.save("orig.tif")
# t=T.Thresholder([[0,255],[0,255],[0,255]],"rgb","hsv")
# th=t.threshold_image(tile)
# th.save("new.tif")
# print th.getextrema()
a=numpy.array([255,255,0,0],dtype=numpy.uint8)
b=numpy.array([200,150,100,50],dtype=numpy.uint8)
print a
print b
print "mask:"
print a
print "image:"
print b
print "result of cv2.bitwise_and(b,b,mask=a):"
im2=cv2.bitwise_and(b,b,mask=a)
print im2
def setUp(self):
self.osr = self.CLASS(file_path(self.FILENAME))
self.dz = DeepZoomGenerator(self.osr, 254, 1)
