def get_segmentations(experiment_id, mapobject_type_id):
"""
.. http:get:: /api/experiments/(string:experiment_id)/mapobject_types/(string:mapobject_type_id)/segmentations
Get segmentations for each
:class:`Mapobject <tmlib.model.mapobject.Mapobject>` contained within
the specified :class:`Site <tmlib.models.site.Site>`. Segmentations are
provided in form of a 2D labeled array, where pixel values encode
object identity with unsigned integer values and background pixels are
zero.
**Example response**:
.. sourcecode:: http
HTTP/1.1 200 OK
Content-Type: application/json
{
"data": [
[1205, 7042, 4438, 7446, 3213, 8773, 5445, 9884, 8326, 6357],
[4663, 2740, 9954, 5187, 309, 8029, 4502, 4927, 5259, 1802],
[8117, 8489, 8495, 1194, 9788, 8182, 5431, 9969, 5931, 6490],
[7974, 3990, 8892, 1866, 7890, 1147, 9630, 3687, 1565, 3613],
[3977, 7318, 5252, 3270, 6746, 822, 7035, 5184, 7808, 4013],
[4380, 6719, 5882, 4279, 7996, 2139, 1760, 2548, 3753, 5511],
[7829, 8825, 224, 1192, 9296, 1663, 5213, 9040, 463, 9080],
[6922, 6781, 9776, 9002, 6992, 8887, 9672, 8500, 1085, 563]
]
}
:reqheader Authorization: JWT token issued by the server
:statuscode 200: no error
:statuscode 400: malformed request
:query plate_name: name of the plate (required)
:query well_name: name of the well (required)
:query well_pos_x: x-coordinate of the site within the well (required)
:query well_pos_y: y-coordinate of the site within the well (required)
:query tpoint: time point (required)
:query zplane: z-plane (required)
"""
plate_name = request.args.get('plate_name')
well_name = request.args.get('well_name')
well_pos_x = request.args.get('well_pos_x', type=int)
well_pos_y = request.args.get('well_pos_y', type=int)
zplane = request.args.get('zplane', type=int)
tpoint = request.args.get('tpoint', type=int)
align = is_true(request.args.get('align'))
logger.info(
'get segmentations for mapobject type %d of experiment %d at '
'plate "%s", well "%s", well position %d/%d, zplane %d, time point %d',
mapobject_type_id, experiment_id, plate_name, well_name, well_pos_y,
well_pos_x, zplane, tpoint)
with tm.utils.MainSession() as session:
experiment = session.query(tm.ExperimentReference).get(experiment_id)
experiment_name = experiment.name
with tm.utils.ExperimentSession(experiment_id) as session:
site = session.query(tm.Site).\
join(tm.Well).\
join(tm.Plate).\
filter(
tm.Plate.name == plate_name,
tm.Well.name == well_name,
tm.Site.x == well_pos_x, tm.Site.y == well_pos_y
).\
one()
mapobject_type = session.query(tm.MapobjectType).\
get(mapobject_type_id)
polygons = mapobject_type.get_segmentations_per_site(site.id,
tpoint=tpoint,
zplane=zplane)
if len(polygons) == 0:
raise ResourceNotFoundError(tm.MapobjectSegmentation, request.args)
if align:
y_offset, x_offset = site.aligned_offset
height = site.aligned_height
width = site.aligned_width
else:
y_offset, x_offset = site.offset
height = site.height
width = site.width
img = SegmentationImage.create_from_polygons(polygons, y_offset, x_offset,
(height, width))
return jsonify(data=img.array.tolist())
def add_segmentations(experiment_id, mapobject_type_id):
"""
.. http:post:: /api/experiments/(string:experiment_id)/mapobject_types/(string:mapobject_type_id)/segmentations
Provide segmentations in form of a labeled 2D pixels array
for a given :class:`Site <tmlib.models.site.Site>`.
A :class:`Mapobject <tmlib.models.mapobject.Mapobject>` and
:class:`MapobjectSegmentation <tmlib.models.mapobject.MapobjectSegmentation>`
will be created for each labeled connected pixel component in *image*.
:reqheader Authorization: JWT token issued by the server
:statuscode 200: no error
:statuscode 400: malformed request
:query npz_file: npz file containing the segmentation image "segmentation" (required)
:query plate_name: name of the plate (required)
:query well_name: name of the well (required)
:query well_pos_x: x-coordinate of the site within the well (required)
:query well_pos_y: y-coordinate of the site within the well (required)
:query tpoint: time point (required)
:query zplane: z-plane (required)
"""
data = request.get_json()
plate_name = data.get('plate_name')
well_name = data.get('well_name')
well_pos_x = int(data.get('well_pos_x'))
well_pos_y = int(data.get('well_pos_y'))
zplane = int(data.get('zplane'))
tpoint = int(data.get('tpoint'))
align = is_true(request.args.get('align')) # TODO
logger.info(
'add segmentations for mapobject type %d of experiment %d at '
'plate "%s", well "%s", well position %d/%d, zplane %d, time point %d',
mapobject_type_id, experiment_id, plate_name, well_name, well_pos_y,
well_pos_x, zplane, tpoint)
npz_file = base64.b64decode(data.get('npz_file'))
pixels = np.load(BytesIO(npz_file))["segmentation"]
array = np.array(pixels, dtype=np.int32)
labels = np.unique(array[array > 0])
n_objects = len(labels)
with tm.utils.ExperimentSession(experiment_id) as session:
segmentation_layer = session.get_or_create(
tm.SegmentationLayer,
mapobject_type_id=mapobject_type_id,
tpoint=tpoint,
zplane=zplane)
segmentation_layer_id = segmentation_layer.id
site = session.query(tm.Site).\
join(tm.Well).\
join(tm.Plate).\
filter(
tm.Plate.name == plate_name, tm.Well.name == well_name,
tm.Site.y == well_pos_y, tm.Site.x == well_pos_x
).\
one()
if align:
y_offset, x_offset = site.aligned_offset
if array.shape != site.aligned_image_size:
raise MalformedRequestError('Image has wrong dimensions')
else:
y_offset, x_offset = site.offset
if array.shape != site.image_size:
raise MalformedRequestError('Image has wrong dimensions')
site_id = site.id
metadata = SegmentationImageMetadata(mapobject_type_id, site_id,
tpoint, zplane)
image = SegmentationImage(array, metadata)
existing_segmentations_map = dict(
session.query(
tm.MapobjectSegmentation.label,
tm.MapobjectSegmentation.mapobject_id
).\
join(tm.Mapobject).\
filter(
tm.MapobjectSegmentation.label.in_(labels.tolist()),
tm.Mapobject.mapobject_type_id == mapobject_type_id,
tm.MapobjectSegmentation.partition_key == site_id
).\
all()
)
with tm.utils.ExperimentSession(experiment_id, False) as session:
segmentations = list()
for label, polygon in image.extract_polygons(y_offset, x_offset):
mapobject = tm.Mapobject(site_id, mapobject_type_id)
if label in existing_segmentations_map:
# A parent mapobject with the same label may already exist,
# because it got already created for another zplane/tpoint.
# The segmentation for the given zplane/tpoint must not yet
# exist, however. This will lead to an error upon insertion.
mapobject.id = existing_segmentations_map[label]
else:
session.add(mapobject)
session.flush()
s = tm.MapobjectSegmentation(
partition_key=site_id,
mapobject_id=mapobject.id,
geom_polygon=polygon,
geom_centroid=polygon.centroid,
segmentation_layer_id=segmentation_layer_id,
label=label)
segmentations.append(s)
session.bulk_ingest(segmentations)
return jsonify(message='ok')
def get_channel_image_file(experiment_id, channel_id):
"""
.. http:get:: /api/experiments/(string:experiment_id)/channels/(string:channel_id)/image-files
Get a specific image belonging to a channel.
**Example response**:
.. sourcecode:: http
HTTP/1.1 200 OK
Content-Type: image/png
:query plate_name: name of the plate (required)
:query cycle_index: cycle's index (required)
:query well_name: name of the well (required)
:query well_pos_x: x-coordinate of the site within the well (optional)
:query well_pos_y: y-coordinate of the site within the well (optional)
:query tpoint: time point (required)
:query zplane: z-plane (required)
:query illumcorr: correct image for illumination artifacts (optional)
:query align: align image relative to reference cycle (optional)
:reqheader Authorization: JWT token issued by the server
:statuscode 200: no error
:statuscode 404: no matching image found
:statuscode 400: not all query parameters provided
"""
logger.info(
'get image of channel %d from experiment %d', channel_id, experiment_id
)
plate_name = request.args.get('plate_name')
well_name = request.args.get('well_name')
x = request.args.get('well_pos_x', type=int)
y = request.args.get('well_pos_y', type=int)
cycle_index = request.args.get('cycle_index', type=int)
tpoint = request.args.get('tpoint', type=int)
zplane = request.args.get('zplane', type=int)
illumcorr = is_true(request.args.get('correct'))
align = is_true(request.args.get('align'))
with tm.utils.MainSession() as session:
experiment = session.query(tm.ExperimentReference).get(experiment_id)
experiment_name = experiment.name
with tm.utils.ExperimentSession(experiment_id) as session:
site_id = session.query(tm.Site.id).\
join(tm.Well).\
join(tm.Plate).\
filter(
tm.Plate.name == plate_name,
tm.Well.name == well_name,
tm.Site.x == x, tm.Site.y == y
).\
one()[0]
channel = session.query(tm.Channel).get(channel_id)
channel_name = channel.name
image_file = session.query(tm.ChannelImageFile).\
join(tm.Cycle).\
filter(
tm.Cycle.index == cycle_index,
tm.ChannelImageFile.site_id == site_id,
tm.ChannelImageFile.channel_id == channel_id,
tm.ChannelImageFile.tpoint == tpoint,
tm.ChannelImageFile.zplane == zplane
).\
one()
img = image_file.get()
if illumcorr:
# TODO: cache in Redis for a limited amount of time to not having to
# load the file repeatedly when user downloads multiple files of the
# same channel
logger.info('correct image for illumination artefacts')
illumstats_file = session.query(tm.IllumstatsFile).\
filter_by(channel_id=channel_id).\
one_or_none()
if illumstats_file is None:
raise ResourceNotFoundError(
'No illumination statistics file found for channel %d'
% channel_id
)
stats = illumstats_file.get()
img = img.correct(stats)
if align:
img = img.align()
pixels = img.png_encode()
f = StringIO()
f.write(pixels)
f.seek(0)
filename = '%s_%s_%s_y%.3d_x%.3d_z%.3d_t%.3d_%s.png' % (
experiment_name, plate_name, well_name, y, x, zplane, tpoint,
channel_name
)
return send_file(
f,
attachment_filename=secure_filename(filename),
mimetype='image/png',
as_attachment=True
)
def get_channel_image_file(experiment_id, channel_id):
"""
.. http:get:: /api/experiments/(string:experiment_id)/channels/(string:channel_id)/image-files
Get a specific image belonging to a channel.
**Example response**:
.. sourcecode:: http
HTTP/1.1 200 OK
Content-Type: image/png
:query plate_name: name of the plate (required)
:query cycle_index: cycle's index (required)
:query well_name: name of the well (required)
:query well_pos_x: x-coordinate of the site within the well (optional)
:query well_pos_y: y-coordinate of the site within the well (optional)
:query tpoint: time point (required)
:query zplane: z-plane (required)
:query illumcorr: correct image for illumination artifacts (optional)
:query align: align image relative to reference cycle (optional)
:reqheader Authorization: JWT token issued by the server
:statuscode 200: no error
:statuscode 404: no matching image found
:statuscode 400: not all query parameters provided
"""
logger.info('get image of channel %d from experiment %d', channel_id,
experiment_id)
plate_name = request.args.get('plate_name')
well_name = request.args.get('well_name')
x = request.args.get('well_pos_x', type=int)
y = request.args.get('well_pos_y', type=int)
cycle_index = request.args.get('cycle_index', type=int)
tpoint = request.args.get('tpoint', type=int)
zplane = request.args.get('zplane', type=int)
illumcorr = is_true(request.args.get('correct'))
align = is_true(request.args.get('align'))
with tm.utils.MainSession() as session:
experiment = session.query(tm.ExperimentReference).get(experiment_id)
experiment_name = experiment.name
with tm.utils.ExperimentSession(experiment_id) as session:
site_id = session.query(tm.Site.id).\
join(tm.Well).\
join(tm.Plate).\
filter(
tm.Plate.name == plate_name,
tm.Well.name == well_name,
tm.Site.x == x, tm.Site.y == y
).\
one()[0]
channel = session.query(tm.Channel).get(channel_id)
channel_name = channel.name
image_file = session.query(tm.ChannelImageFile).\
join(tm.Cycle).\
filter(
tm.Cycle.index == cycle_index,
tm.ChannelImageFile.site_id == site_id,
tm.ChannelImageFile.channel_id == channel_id,
tm.ChannelImageFile.tpoint == tpoint,
tm.ChannelImageFile.zplane == zplane
).\
one()
img = image_file.get()
if illumcorr:
# TODO: cache in Redis for a limited amount of time to not having to
# load the file repeatedly when user downloads multiple files of the
# same channel
logger.info('correct image for illumination artefacts')
illumstats_file = session.query(tm.IllumstatsFile).\
filter_by(channel_id=channel_id).\
one_or_none()
if illumstats_file is None:
raise ResourceNotFoundError(
'No illumination statistics file found for channel %d' %
channel_id)
stats = illumstats_file.get()
img = img.correct(stats)
if align:
img = img.align()
pixels = img.png_encode()
f = StringIO()
f.write(pixels)
f.seek(0)
filename = '%s_%s_%s_y%.3d_x%.3d_z%.3d_t%.3d_%s.png' % (
experiment_name, plate_name, well_name, y, x, zplane, tpoint,
channel_name)
return send_file(f,
attachment_filename=secure_filename(filename),
mimetype='image/png',
as_attachment=True)
def get_segmentations(experiment_id, mapobject_type_id):
"""
.. http:get:: /api/experiments/(string:experiment_id)/mapobject_types/(string:mapobject_type_id)/segmentations
Get segmentations for each
:class:`Mapobject <tmlib.model.mapobject.Mapobject>` contained within
the specified :class:`Site <tmlib.models.site.Site>`. Segmentations are
provided in form of a 2D labeled array, where pixel values encode
object identity with unsigned integer values and background pixels are
zero.
**Example response**:
.. sourcecode:: http
HTTP/1.1 200 OK
Content-Type: application/json
{
"data": [
[1205, 7042, 4438, 7446, 3213, 8773, 5445, 9884, 8326, 6357],
[4663, 2740, 9954, 5187, 309, 8029, 4502, 4927, 5259, 1802],
[8117, 8489, 8495, 1194, 9788, 8182, 5431, 9969, 5931, 6490],
[7974, 3990, 8892, 1866, 7890, 1147, 9630, 3687, 1565, 3613],
[3977, 7318, 5252, 3270, 6746, 822, 7035, 5184, 7808, 4013],
[4380, 6719, 5882, 4279, 7996, 2139, 1760, 2548, 3753, 5511],
[7829, 8825, 224, 1192, 9296, 1663, 5213, 9040, 463, 9080],
[6922, 6781, 9776, 9002, 6992, 8887, 9672, 8500, 1085, 563]
]
}
:reqheader Authorization: JWT token issued by the server
:statuscode 200: no error
:statuscode 400: malformed request
:query plate_name: name of the plate (required)
:query well_name: name of the well (required)
:query well_pos_x: x-coordinate of the site within the well (required)
:query well_pos_y: y-coordinate of the site within the well (required)
:query tpoint: time point (required)
:query zplane: z-plane (required)
"""
plate_name = request.args.get('plate_name')
well_name = request.args.get('well_name')
well_pos_x = request.args.get('well_pos_x', type=int)
well_pos_y = request.args.get('well_pos_y', type=int)
zplane = request.args.get('zplane', type=int)
tpoint = request.args.get('tpoint', type=int)
align = is_true(request.args.get('align'))
logger.info(
'get segmentations for mapobject type %d of experiment %d at '
'plate "%s", well "%s", well position %d/%d, zplane %d, time point %d',
mapobject_type_id, experiment_id, plate_name, well_name, well_pos_y,
well_pos_x, zplane, tpoint
)
with tm.utils.MainSession() as session:
experiment = session.query(tm.ExperimentReference).get(experiment_id)
experiment_name = experiment.name
with tm.utils.ExperimentSession(experiment_id) as session:
site = session.query(tm.Site).\
join(tm.Well).\
join(tm.Plate).\
filter(
tm.Plate.name == plate_name,
tm.Well.name == well_name,
tm.Site.x == well_pos_x, tm.Site.y == well_pos_y
).\
one()
mapobject_type = session.query(tm.MapobjectType).\
get(mapobject_type_id)
polygons = mapobject_type.get_segmentations_per_site(
site.id, tpoint=tpoint, zplane=zplane
)
if len(polygons) == 0:
raise ResourceNotFoundError(tm.MapobjectSegmentation, request.args)
if align:
y_offset, x_offset = site.aligned_offset
height = site.aligned_height
width = site.aligned_width
else:
y_offset, x_offset = site.offset
height = site.height
width = site.width
img = SegmentationImage.create_from_polygons(
polygons, y_offset, x_offset, (height, width)
)
return jsonify(data=img.array.tolist())
def add_segmentations(experiment_id, mapobject_type_id):
"""
.. http:post:: /api/experiments/(string:experiment_id)/mapobject_types/(string:mapobject_type_id)/segmentations
Provide segmentations in form of a labeled 2D pixels array
for a given :class:`Site <tmlib.models.site.Site>`.
A :class:`Mapobject <tmlib.models.mapobject.Mapobject>` and
:class:`MapobjectSegmentation <tmlib.models.mapobject.MapobjectSegmentation>`
will be created for each labeled connected pixel component in *image*.
:reqheader Authorization: JWT token issued by the server
:statuscode 200: no error
:statuscode 400: malformed request
:query npz_file: npz file containing the segmentation image "segmentation" (required)
:query plate_name: name of the plate (required)
:query well_name: name of the well (required)
:query well_pos_x: x-coordinate of the site within the well (required)
:query well_pos_y: y-coordinate of the site within the well (required)
:query tpoint: time point (required)
:query zplane: z-plane (required)
"""
data = request.get_json()
plate_name = data.get('plate_name')
well_name = data.get('well_name')
well_pos_x = int(data.get('well_pos_x'))
well_pos_y = int(data.get('well_pos_y'))
zplane = int(data.get('zplane'))
tpoint = int(data.get('tpoint'))
align = is_true(request.args.get('align')) # TODO
logger.info(
'add segmentations for mapobject type %d of experiment %d at '
'plate "%s", well "%s", well position %d/%d, zplane %d, time point %d',
mapobject_type_id, experiment_id, plate_name, well_name, well_pos_y,
well_pos_x, zplane, tpoint
)
npz_file = base64.b64decode(data.get('npz_file'))
pixels = np.load(BytesIO(npz_file))["segmentation"]
array = np.array(pixels, dtype=np.int32)
labels = np.unique(array[array > 0])
n_objects = len(labels)
with tm.utils.ExperimentSession(experiment_id) as session:
segmentation_layer = session.get_or_create(
tm.SegmentationLayer,
mapobject_type_id=mapobject_type_id, tpoint=tpoint, zplane=zplane
)
segmentation_layer_id = segmentation_layer.id
site = session.query(tm.Site).\
join(tm.Well).\
join(tm.Plate).\
filter(
tm.Plate.name == plate_name, tm.Well.name == well_name,
tm.Site.y == well_pos_y, tm.Site.x == well_pos_x
).\
one()
if align:
y_offset, x_offset = site.aligned_offset
if array.shape != site.aligned_image_size:
raise MalformedRequestError('Image has wrong dimensions')
else:
y_offset, x_offset = site.offset
if array.shape != site.image_size:
raise MalformedRequestError('Image has wrong dimensions')
site_id = site.id
metadata = SegmentationImageMetadata(
mapobject_type_id, site_id, tpoint, zplane
)
image = SegmentationImage(array, metadata)
existing_segmentations_map = dict(
session.query(
tm.MapobjectSegmentation.label,
tm.MapobjectSegmentation.mapobject_id
).\
join(tm.Mapobject).\
filter(
tm.MapobjectSegmentation.label.in_(labels.tolist()),
tm.Mapobject.mapobject_type_id == mapobject_type_id,
tm.MapobjectSegmentation.partition_key == site_id
).\
all()
)
with tm.utils.ExperimentSession(experiment_id, False) as session:
segmentations = list()
for label, polygon in image.extract_polygons(y_offset, x_offset):
mapobject = tm.Mapobject(site_id, mapobject_type_id)
if label in existing_segmentations_map:
# A parent mapobject with the same label may already exist,
# because it got already created for another zplane/tpoint.
# The segmentation for the given zplane/tpoint must not yet
# exist, however. This will lead to an error upon insertion.
mapobject.id = existing_segmentations_map[label]
else:
session.add(mapobject)
session.flush()
s = tm.MapobjectSegmentation(
partition_key=site_id, mapobject_id=mapobject.id,
geom_polygon=polygon, geom_centroid=polygon.centroid,
segmentation_layer_id=segmentation_layer_id, label=label
)
segmentations.append(s)
session.bulk_ingest(segmentations)
return jsonify(message='ok')