def _getTile(self, item, z, x, y, imageArgs):
"""
Get an large image tile.
:param item: the item to get a tile from.
:param z: tile layer number (0 is the most zoomed-out).
.param x: the X coordinate of the tile (0 is the left side).
.param y: the Y coordinate of the tile (0 is the top).
:param imageArgs: additional arguments to use when fetching image data.
:return: a function that returns the raw image data.
"""
try:
x, y, z = int(x), int(y), int(z)
except ValueError:
raise RestException('x, y, and z must be integers', code=400)
if x < 0 or y < 0 or z < 0:
raise RestException('x, y, and z must be positive integers',
code=400)
try:
tileData, tileMime = self.imageItemModel.getTile(
item, x, y, z, **imageArgs)
except TileGeneralException as e:
raise RestException(e.message, code=404)
setResponseHeader('Content-Type', tileMime)
setRawResponse()
return tileData
def thumbnail(self, segmentation, params):
contentDisp = params.get('contentDisposition', None)
if contentDisp is not None and contentDisp not in {'inline', 'attachment'}:
raise ValidationException('Unallowed contentDisposition type "%s".' % contentDisp,
'contentDisposition')
# TODO: convert this to make Segmentation use an AccessControlMixin
image = Image().load(
segmentation['imageId'], level=AccessType.READ, user=self.getCurrentUser(), exc=True)
width = int(params.get('width', 256))
thumbnailImageStream = Segmentation().boundaryThumbnail(segmentation, image, width)
if thumbnailImageStream is None:
raise RestException('This segmentation is failed, and thus has no thumbnail.', code=410)
thumbnailImageData = thumbnailImageStream.getvalue()
# Only setRawResponse now, as this handler may return a JSON error
# earlier
setRawResponse()
setResponseHeader('Content-Type', 'image/jpeg')
contentName = '%s_segmentation_thumbnail.jpg' % image['name']
if contentDisp == 'inline':
setResponseHeader('Content-Disposition', 'inline; filename="%s"' % contentName)
else:
setResponseHeader('Content-Disposition', 'attachment; filename="%s"' % contentName)
setResponseHeader('Content-Length', len(thumbnailImageData))
return thumbnailImageData
def getAnnotationMarkupMask(self, annotation, featureId, params):
self._ensureMarkup(annotation, featureId)
markupFile = Annotation().getMarkupFile(annotation, featureId)
if markupFile:
return File().download(markupFile, headers=True, contentDisposition='inline')
else:
image = Image().load(annotation['imageId'], force=True, exc=True)
markupMask = numpy.zeros(
(
image['meta']['acquisition']['pixelsY'],
image['meta']['acquisition']['pixelsX']
),
dtype=numpy.uint8
)
markupMaskEncodedStream = ScikitSegmentationHelper.writeImage(markupMask, 'png')
markupMaskEncodedData = markupMaskEncodedStream.getvalue()
setRawResponse()
setResponseHeader('Content-Type', 'image/png')
contentName = 'annotation_%s_%s.png' % (
annotation['_id'],
# Rename features to ensure the file is downloadable on Windows
featureId.replace(' : ', ' ; ').replace('/', ',')
)
setResponseHeader('Content-Disposition', 'inline; filename="%s"' % contentName)
setResponseHeader('Content-Length', len(markupMaskEncodedData))
return markupMaskEncodedData
def getAnnotationMarkupRendered(self, annotation, featureId, params):
contentDisp = params.get('contentDisposition', None)
if contentDisp is not None and contentDisp not in {'inline', 'attachment'}:
raise ValidationException('Unallowed contentDisposition type "%s".' % contentDisp,
'contentDisposition')
self._ensureMarkup(annotation, featureId)
renderData = Annotation().renderMarkup(annotation, featureId)
renderEncodedStream = ScikitSegmentationHelper.writeImage(renderData, 'jpeg')
renderEncodedData = renderEncodedStream.getvalue()
# Only setRawResponse now, as this handler may return a JSON error earlier
setRawResponse()
setResponseHeader('Content-Type', 'image/jpeg')
contentName = 'annotation_%s_%s.jpg' % (
annotation['_id'],
# Rename features to ensure the file is downloadable on Windows
featureId.replace(' : ', ' ; ').replace('/', ',')
)
if contentDisp == 'inline':
setResponseHeader(
'Content-Disposition',
'inline; filename="%s"' % contentName)
else:
setResponseHeader(
'Content-Disposition',
'attachment; filename="%s"' % contentName)
setResponseHeader('Content-Length', len(renderEncodedData))
return renderEncodedData
def getTilesRegion(self, item, params):
params = self._parseParams(params, True, [
('left', float, 'region', 'left'),
('top', float, 'region', 'top'),
('right', float, 'region', 'right'),
('bottom', float, 'region', 'bottom'),
('regionWidth', float, 'region', 'width'),
('regionHeight', float, 'region', 'height'),
('units', str, 'region', 'units'),
('width', int, 'output', 'maxWidth'),
('height', int, 'output', 'maxHeight'),
('magnification', float, 'scale', 'magnification'),
('mm_x', float, 'scale', 'mm_x'),
('mm_y', float, 'scale', 'mm_y'),
('exact', bool, 'scale', 'exact'),
('encoding', str),
('jpegQuality', int),
('jpegSubsampling', int),
])
try:
regionData, regionMime = self.imageItemModel.getRegion(
item, **params)
except TileGeneralException as e:
raise RestException(e.message)
except ValueError as e:
raise RestException('Value Error: %s' % e.message)
setResponseHeader('Content-Type', regionMime)
setRawResponse()
return regionData
def testAnalysisXmlDetection(self, params):
"""Return the nuclei detection XML spec as a test case."""
xml_file = os.path.abspath(
os.path.join(os.path.dirname(__file__), '..', 'histomicstk', 'cli',
'NucleiDetection', 'NucleiDetection.xml'))
with open(xml_file) as f:
xml = f.read()
setResponseHeader('Content-Type', 'application/xml')
setRawResponse()
return xml
def testAnalysisXmlFeatures(self, params):
"""Return the nuclei feature classification XML spec as a test case."""
xml_file = os.path.abspath(
os.path.join(os.path.dirname(__file__), '..', 'server',
'ComputeNucleiFeatures', 'ComputeNucleiFeatures.xml'))
with open(xml_file) as f:
xml = f.read()
setResponseHeader('Content-Type', 'application/xml')
setRawResponse()
return xml
def thumbnail(self, image, params):
width = int(params.get('width', 256))
height = int(params.get('height', 256))
thumbData, thumbMime = ImageItem().getThumbnail(image, width=width, height=height)
# Only setRawResponse now, as this handler may return a JSON error
# earlier
setRawResponse()
setResponseHeader('Content-Type', thumbMime)
return thumbData
def thumbnail(self, image, params):
width = int(params.get('width', 256))
height = int(params.get('height', 256))
thumbData, thumbMime = ImageItem().getThumbnail(image, width=width, height=height)
# Only setRawResponse now, as this handler may return a JSON error
# earlier
setRawResponse()
setResponseHeader('Content-Type', thumbMime)
return thumbData
def _forward(self):
"""
Forward a request to the same path with a slash added.
"""
result = '\n'.join([
'<html>', '<head><title>301 Moved Permanently</title></head>',
'<body>', '<center><h1>301 Moved Permanently</h1></center>',
'</body>', '</html>'])
setResponseHeader('Location', cherrypy.request.path_info + '/')
setResponseHeader('Content-Type', 'text/html')
setRawResponse()
cherrypy.response.status = 301
return result.encode('utf8')
def downloadKeyFile(self, file, algo):
self._validateAlgo(algo)
if algo not in file:
raise RestException('This file does not have the %s hash computed.' % algo)
keyFileBody = '%s\n' % file[algo]
name = '.'.join((file['name'], algo))
setResponseHeader('Content-Length', len(keyFileBody))
setResponseHeader('Content-Type', 'text/plain')
setContentDisposition(name)
setRawResponse()
return keyFileBody
def downloadKeyFile(self, file, algo, params):
self._validateAlgo(algo)
if algo not in file:
raise RestException('This file does not have the %s hash computed.' % algo)
hash = file[algo]
name = '.'.join((file['name'], algo))
setResponseHeader('Content-Length', len(hash))
setResponseHeader('Content-Type', 'text/plain')
setResponseHeader('Content-Disposition', 'attachment; filename="%s"' % name)
setRawResponse()
return hash
def downloadKeyFile(self, file, algo):
self._validateAlgo(algo)
if algo not in file:
raise RestException('This file does not have the %s hash computed.' % algo)
keyFileBody = '%s\n' % file[algo]
name = '.'.join((file['name'], algo))
setResponseHeader('Content-Length', len(keyFileBody))
setResponseHeader('Content-Type', 'text/plain')
setContentDisposition(name)
setRawResponse()
return keyFileBody
def _getHdf5Dataset(self, item):
try:
setResponseHeader('Content-Type', 'image/png')
setRawResponse()
hdf5Path = [i for i in item['meta']
if 'hdf5Path' in i.keys()][0]['hdf5Path']
pathInHdf5 = [i for i in item['meta']
if 'pathInHdf5' in i.keys()][0]['pathInHdf5']
figure = render_hdf5_dataset(hdf5Path, pathInHdf5)
buf = BytesIO()
figure.savefig(buf, format='png')
return b64encode(buf.getvalue())
except:
pass
def getTile(self, image, z, x, y, params):
try:
x, y, z = int(x), int(y), int(z)
except ValueError:
raise RestException('x, y, and z must be integers')
if x < 0 or y < 0 or z < 0:
raise RestException('x, y, and z must be positive integers')
try:
tileData, tileMime = ImageItem().getTile(image, x, y, z)
except TileGeneralException as e:
raise RestException(e.message, code=404)
setResponseHeader('Content-Type', tileMime)
setRawResponse()
return tileData
def getTile(self, image, z, x, y, params):
try:
x, y, z = int(x), int(y), int(z)
except ValueError:
raise RestException('x, y, and z must be integers')
if x < 0 or y < 0 or z < 0:
raise RestException('x, y, and z must be positive integers')
try:
tileData, tileMime = ImageItem().getTile(image, x, y, z)
except TileGeneralException as e:
raise RestException(e.message, code=404)
setResponseHeader('Content-Type', tileMime)
setRawResponse()
return tileData
def downloadKeyFile(self, file, algo):
self._validateAlgo(algo)
if algo not in file:
raise RestException('This file does not have the %s hash computed.' % algo)
hash = file[algo]
name = '.'.join((file['name'], algo))
setResponseHeader('Content-Length', len(hash))
setResponseHeader('Content-Type', 'text/plain')
setResponseHeader('Content-Disposition', 'attachment; filename="%s"' % name)
setRawResponse()
return hash
def getDZITile(self, item, level, xandy, params):
_adjustParams(params)
tilesize = int(params.get('tilesize', 256))
if tilesize & (tilesize - 1):
raise RestException('Invalid tilesize', code=400)
overlap = int(params.get('overlap', 0))
if overlap < 0:
raise RestException('Invalid overlap', code=400)
x, y = [int(xy) for xy in xandy.split('.')[0].split('_')]
_handleETag('getDZITile', item, level, xandy, params)
metadata = self.imageItemModel.getMetadata(item, **params)
level = int(level)
maxlevel = int(math.ceil(math.log(max(
metadata['sizeX'], metadata['sizeY'])) / math.log(2)))
if level < 1 or level > maxlevel:
raise RestException('level must be between 1 and the image scale',
code=400)
lfactor = 2 ** (maxlevel - level)
region = {
'left': (x * tilesize - overlap) * lfactor,
'top': (y * tilesize - overlap) * lfactor,
'right': ((x + 1) * tilesize + overlap) * lfactor,
'bottom': ((y + 1) * tilesize + overlap) * lfactor,
}
width = height = tilesize + overlap * 2
if region['left'] < 0:
width += int(region['left'] / lfactor)
region['left'] = 0
if region['top'] < 0:
height += int(region['top'] / lfactor)
region['top'] = 0
if region['left'] >= metadata['sizeX']:
raise RestException('x is outside layer', code=400)
if region['top'] >= metadata['sizeY']:
raise RestException('y is outside layer', code=400)
if region['left'] < metadata['sizeX'] and region['right'] > metadata['sizeX']:
region['right'] = metadata['sizeX']
width = int(math.ceil(float(region['right'] - region['left']) / lfactor))
if region['top'] < metadata['sizeY'] and region['bottom'] > metadata['sizeY']:
region['bottom'] = metadata['sizeY']
height = int(math.ceil(float(region['bottom'] - region['top']) / lfactor))
regionData, regionMime = self.imageItemModel.getRegion(
item,
region=region,
output=dict(maxWidth=width, maxHeight=height),
**params)
setResponseHeader('Content-Type', regionMime)
setRawResponse()
return regionData
def renderAnnotation(self, annotation, params):
contentDisp = params.get('contentDisposition', None)
if contentDisp is not None and contentDisp not in {
'inline', 'attachment'
}:
raise ValidationException(
'Unallowed contentDisposition type "%s".' % contentDisp,
'contentDisposition')
self.requireParams(['featureId'], params)
featureId = params['featureId']
study = Study().load(annotation['meta']['studyId'],
force=True,
exc=True)
featureset = Study().getFeatureset(study)
if not any(featureId == feature['id']
for feature in featureset['localFeatures']):
raise ValidationException('Invalid featureId.', 'featureId')
if Annotation().getState(annotation) != Study().State.COMPLETE:
raise RestException('Only complete annotations can be rendered.')
renderData = Annotation().renderAnnotation(annotation, featureId)
renderEncodedStream = ScikitSegmentationHelper.writeImage(
renderData, 'jpeg')
renderEncodedData = renderEncodedStream.getvalue()
# Only setRawResponse now, as this handler may return a JSON error
# earlier
setRawResponse()
setResponseHeader('Content-Type', 'image/jpeg')
contentName = '%s_%s_annotation.jpg' % (
annotation['_id'],
featureId.replace('/',
',') # TODO: replace with a better character
)
if contentDisp == 'inline':
setResponseHeader('Content-Disposition',
'inline; filename="%s"' % contentName)
else:
setResponseHeader('Content-Disposition',
'attachment; filename="%s"' % contentName)
setResponseHeader('Content-Length', len(renderEncodedData))
return renderEncodedData
def renderAnnotation(self, annotation, params):
Study = self.model('study', 'isic_archive')
Annotation = self.model('annotation', 'isic_archive')
contentDisp = params.get('contentDisposition', None)
if contentDisp is not None and contentDisp not in {'inline', 'attachment'}:
raise ValidationException('Unallowed contentDisposition type "%s".' % contentDisp,
'contentDisposition')
self.requireParams(['featureId'], params)
featureId = params['featureId']
study = Study.load(annotation['meta']['studyId'], force=True, exc=True)
featureset = Study.getFeatureset(study)
if not any(featureId == feature['id'] for feature in featureset['localFeatures']):
raise ValidationException('Invalid featureId.', 'featureId')
if Annotation.getState(annotation) != Study.State.COMPLETE:
raise RestException('Only complete annotations can be rendered.')
renderData = Annotation.renderAnnotation(annotation, featureId)
renderEncodedStream = ScikitSegmentationHelper.writeImage(renderData, 'jpeg')
renderEncodedData = renderEncodedStream.getvalue()
# Only setRawResponse now, as this handler may return a JSON error
# earlier
setRawResponse()
setResponseHeader('Content-Type', 'image/jpeg')
contentName = '%s_%s_annotation.jpg' % (
annotation['_id'],
featureId.replace('/', ',') # TODO: replace with a better character
)
if contentDisp == 'inline':
setResponseHeader(
'Content-Disposition',
'inline; filename="%s"' % contentName)
else:
setResponseHeader(
'Content-Disposition',
'attachment; filename="%s"' % contentName)
setResponseHeader('Content-Length', len(renderEncodedData))
return renderEncodedData
def pathRedirect(self, path):
user = self.getCurrentUser()
# Find the longest path that is a valid resource
used = len(path)
while used:
try:
resource = path_util.lookUpPath('/'.join(path[:used]), user)['document']
break
except path_util.ResourcePathNotFound:
if used == 1:
raise
used -= 1
path = [resource['_modelType'], str(resource['_id'])] + list(path[used:])
path_info = ('/'.join(cherrypy.request.path_info.split('/')[:2] + path))
# This locates the redirected handler
cherrypy.request.get_resource(path_info)
result = cherrypy.request.handler()
setRawResponse()
return result
def getTilesThumbnail(self, item, params):
params = self._parseParams(params, True, [
('width', int),
('height', int),
('jpegQuality', int),
('jpegSubsampling', int),
('encoding', str),
])
try:
result = self.imageItemModel.getThumbnail(item, **params)
except TileGeneralException as e:
raise RestException(e.message)
except ValueError as e:
raise RestException('Value Error: %s' % e.message)
if not isinstance(result, tuple):
return result
thumbData, thumbMime = result
setResponseHeader('Content-Type', thumbMime)
setRawResponse()
return thumbData
def getTilesThumbnail(self, item, params):
params = self._parseParams(params, True, [
('width', int),
('height', int),
('jpegQuality', int),
('jpegSubsampling', int),
('encoding', str),
])
try:
result = self.imageItemModel.getThumbnail(item, **params)
except TileGeneralException as e:
raise RestException(e.message)
except ValueError as e:
raise RestException('Value Error: %s' % e.message)
if not isinstance(result, tuple):
return result
thumbData, thumbMime = result
setResponseHeader('Content-Type', thumbMime)
setRawResponse()
return thumbData
def processTask(self, params=None):
"""
Based on the process name in the URL and JSON in the request body,
create & send a WPS request and pass on the response.
"""
json_body = self.getBodyJson()
process = json.loads(json.dumps(json_body), object_hook=deserialize)
# assume output is GeoJSON or GeoTIFF
process.compute()
if process.output.default_output == gaia.formats.PANDAS:
result = json.loads(process.output.read(format=gaia.formats.JSON))
else:
result = json.loads(process.output.read())
if not isinstance(result, dict):
setRawResponse(True)
cherrypy.response.headers['Content-Type'] = 'image/tiff'
return result
def processTask(self, params):
"""
Based on the process name in the URL and JSON in the request body,
create & send a WPS request and pass on the response.
"""
json_body = self.getBodyJson()
process = json.loads(json.dumps(json_body),
object_hook=deserialize)
# assume output is GeoJSON or GeoTIFF
process.compute()
if process.output.default_output == gaia.formats.PANDAS:
result = json.loads(process.output.read(format=gaia.formats.JSON))
else:
result = json.loads(process.output.read())
if not isinstance(result, dict):
setRawResponse(True)
cherrypy.response.headers['Content-Type'] = 'image/tiff'
return result
def getTilesRegion(self, item, params):
_adjustParams(params)
params = self._parseParams(params, True, [
('left', float, 'region', 'left'),
('top', float, 'region', 'top'),
('right', float, 'region', 'right'),
('bottom', float, 'region', 'bottom'),
('regionWidth', float, 'region', 'width'),
('regionHeight', float, 'region', 'height'),
('units', str, 'region', 'units'),
('unitsWH', str, 'region', 'unitsWH'),
('width', int, 'output', 'maxWidth'),
('height', int, 'output', 'maxHeight'),
('fill', str),
('magnification', float, 'scale', 'magnification'),
('mm_x', float, 'scale', 'mm_x'),
('mm_y', float, 'scale', 'mm_y'),
('exact', bool, 'scale', 'exact'),
('frame', int),
('encoding', str),
('jpegQuality', int),
('jpegSubsampling', int),
('tiffCompression', str),
('style', str),
('resample', 'boolOrInt'),
('contentDisposition', str),
])
_handleETag('getTilesRegion', item, params)
try:
regionData, regionMime = self.imageItemModel.getRegion(
item, **params)
except TileGeneralException as e:
raise RestException(e.args[0])
except ValueError as e:
raise RestException('Value Error: %s' % e.args[0])
self._setContentDisposition(
item, params.get('contentDisposition'), regionMime, 'region')
setResponseHeader('Content-Type', regionMime)
setRawResponse()
return regionData
def thumbnail(self, segmentation, params):
contentDisp = params.get('contentDisposition', None)
if contentDisp is not None and contentDisp not in {
'inline', 'attachment'
}:
raise ValidationException(
'Unallowed contentDisposition type "%s".' % contentDisp,
'contentDisposition')
# TODO: convert this to make Segmentation use an AccessControlMixin
image = Image().load(segmentation['imageId'],
level=AccessType.READ,
user=self.getCurrentUser(),
exc=True)
width = int(params.get('width', 256))
thumbnailImageStream = Segmentation().boundaryThumbnail(
segmentation, image, width)
if thumbnailImageStream is None:
raise RestException(
'This segmentation is failed, and thus has no thumbnail.',
code=410)
thumbnailImageData = thumbnailImageStream.getvalue()
# Only setRawResponse now, as this handler may return a JSON error
# earlier
setRawResponse()
setResponseHeader('Content-Type', 'image/jpeg')
contentName = '%s_segmentation_thumbnail.jpg' % image['name']
if contentDisp == 'inline':
setResponseHeader('Content-Disposition',
'inline; filename="%s"' % contentName)
else:
setResponseHeader('Content-Disposition',
'attachment; filename="%s"' % contentName)
setResponseHeader('Content-Length', len(thumbnailImageData))
return thumbnailImageData
def _getTile(self, item, z, x, y, imageArgs, mayRedirect=False):
"""
Get an large image tile.
:param item: the item to get a tile from.
:param z: tile layer number (0 is the most zoomed-out).
.param x: the X coordinate of the tile (0 is the left side).
.param y: the Y coordinate of the tile (0 is the top).
:param imageArgs: additional arguments to use when fetching image data.
:param mayRedirect: if True or one of 'any', 'encoding', or 'exact',
allow return a response whcih may be a redirect.
:return: a function that returns the raw image data.
"""
try:
x, y, z = int(x), int(y), int(z)
except ValueError:
raise RestException('x, y, and z must be integers', code=400)
if x < 0 or y < 0 or z < 0:
raise RestException('x, y, and z must be positive integers',
code=400)
result = self.imageItemModel._tileFromHash(item,
x,
y,
z,
mayRedirect=mayRedirect,
**imageArgs)
if result is not None:
tileData, tileMime = result
else:
try:
tileData, tileMime = self.imageItemModel.getTile(
item, x, y, z, mayRedirect=mayRedirect, **imageArgs)
except TileGeneralException as e:
raise RestException(e.args[0], code=404)
setResponseHeader('Content-Type', tileMime)
setRawResponse()
return tileData
def getItemXML(self, item):
setResponseHeader('Content-Type', 'application/xml')
setRawResponse()
return CLIItem(item).xml
def getXMLSpecHandler(self, *args, **kwargs):
setResponseHeader('Content-Type', 'application/xml')
setRawResponse()
return str_xml
def getTilesRegion(self, item, params):
_adjustParams(params)
params = self._parseParams(params, True, [
('left', float, 'region', 'left'),
('top', float, 'region', 'top'),
('right', float, 'region', 'right'),
('bottom', float, 'region', 'bottom'),
('regionWidth', float, 'region', 'width'),
('regionHeight', float, 'region', 'height'),
('units', str, 'region', 'units'),
('unitsWH', str, 'region', 'unitsWH'),
('width', int, 'output', 'maxWidth'),
('height', int, 'output', 'maxHeight'),
('fill', str),
('magnification', float, 'scale', 'magnification'),
('mm_x', float, 'scale', 'mm_x'),
('mm_y', float, 'scale', 'mm_y'),
('exact', bool, 'scale', 'exact'),
('frame', int),
('encoding', str),
('jpegQuality', int),
('jpegSubsampling', int),
('tiffCompression', str),
('style', str),
('resample', 'boolOrInt'),
('contentDisposition', str),
('contentDispositionFileName', str)
])
_handleETag('getTilesRegion', item, params)
setResponseTimeLimit(86400)
try:
regionData, regionMime = self.imageItemModel.getRegion(
item, **params)
except TileGeneralException as e:
raise RestException(e.args[0])
except ValueError as e:
raise RestException('Value Error: %s' % e.args[0])
subname = str(int(params.get('region')['left'])) + ',' + str(int(params.get('region')['top']))
self._setContentDisposition(
item, params.get('contentDisposition'), regionMime, subname,
params.get('contentDispositionFilename'))
setResponseHeader('Content-Type', regionMime)
if isinstance(regionData, pathlib.Path):
BUF_SIZE = 65536
def stream():
try:
with regionData.open('rb') as f:
while True:
data = f.read(BUF_SIZE)
if not data:
break
yield data
finally:
regionData.unlink()
return stream
setRawResponse()
return regionData
