rahix/openflexure-microscope-server
1
0
Fork 0
Code Issues Pull requests Projects Releases Packages Wiki Activity Actions

Simplified new configuration and metadata

Browse source
This commit is contained in:
Joel Collins 2020-01-29 15:36:57 +00:00
parent 5d65c62001
commit 7458d278d8
10 changed files with 214 additions and 216 deletions
Download patch file Download diff file Expand all files Collapse all files

8
openflexure_microscope/api/app.py
View file

@ -19,7 +19,7 @@ from openflexure_microscope.paths import (
OPENFLEXURE_VAR_PATH,
OPENFLEXURE_EXTENSIONS_PATH,
settings_file_path,
logs_file_path
logs_file_path,
)
from labthings.server.quick import create_app
@ -92,7 +92,7 @@ labthing.add_root_link(views.CaptureList, "captures")
labthing.add_view(views.CaptureView, f"/captures/<id>")
labthing.add_view(views.CaptureDownload, f"/captures/<id>/download/<filename>")
labthing.add_view(views.CaptureTags, f"/captures/<id>/tags")
labthing.add_view(views.CaptureMetadata, f"/captures/<id>/metadata")
labthing.add_view(views.CaptureAnnotations, f"/captures/<id>/annotations")
# Attach settings and status resources
labthing.add_view(views.SettingsProperty, f"/settings")
@ -101,6 +101,10 @@ labthing.add_view(views.NestedSettingsProperty, "/settings/<path:route>")
labthing.add_view(views.StatusProperty, "/status")
labthing.add_view(views.NestedStatusProperty, "/status/<path:route>")
labthing.add_root_link(views.StatusProperty, "status")
labthing.add_view(views.ConfigurationProperty, "/configuration")
labthing.add_view(views.NestedConfigurationProperty, "/configuration/<path:route>")
labthing.add_root_link(views.ConfigurationProperty, "configuration")
# Attach streams resources
labthing.add_view(views.MjpegStream, f"/streams/mjpeg")

101
openflexure_microscope/api/default_extensions/scan.py
View file

@ -1,6 +1,7 @@
import itertools
import logging
import uuid
import datetime
from typing import Tuple
from functools import reduce
@ -71,12 +72,12 @@ def progress():
def capture(
microscope,
basename,
scan_id,
temporary: bool = False,
use_video_port: bool = False,
resize: Tuple[int, int] = None,
bayer: bool = False,
metadata: dict = {},
annotations: dict = {},
tags: list = [],
):
@ -94,16 +95,14 @@ def capture(
output.file, use_video_port=use_video_port, resize=resize, bayer=bayer
)
# Affix metadata
if "scan" not in tags:
tags.append("scan")
# Inject system metadata
output.put_metadata(microscope.metadata, system=True)
output.put_metadata({"instrument": microscope.metadata})
# Insert custom metadata
output.put_metadata(metadata)
# Insert custom metadata
output.put_annotations(annotations)
# Insert custom tags
output.put_tags(tags)
@ -115,7 +114,7 @@ def tile(
microscope,
basename: str = None,
temporary: bool = False,
step_size: int = [2000, 1500, 100],
stride_size: int = [2000, 1500, 100],
grid: list = [3, 3, 5],
style="raster",
autofocus_dz: int = 50,
@ -124,13 +123,13 @@ def tile(
bayer: bool = False,
fast_autofocus=False,
metadata: dict = {},
annotations: dict = {},
tags: list = [],
):
global _images_to_be_captured
global _images_captured_so_far
# Keep task progress
# TODO: Make this line not nasty
_images_to_be_captured = reduce((lambda x, y: x * y), grid)
_images_captured_so_far = 0
@ -138,28 +137,22 @@ def tile(
if not basename:
basename = generate_basename()
# Generate a stack ID
scan_id = uuid.uuid4()
# Store initial position
initial_position = microscope.stage.position
# Add scan metadata
if "time" not in metadata:
metadata["time"] = generate_basename()
metadata.update(
{
"scan_id": scan_id,
"basename": basename,
"scan_parameters": {
"step_size": step_size,
"grid": grid,
"style": style,
"autofocus_dz": autofocus_dz,
},
# Add dataset metadata
dataset_d = {
"dataset": {
"id": uuid.uuid4(),
"type": "xyzScan",
"name": basename,
"acquisitionDate": datetime.datetime.now().isoformat(),
"strideSize": stride_size,
"grid": grid,
"style": style,
"autofocusDz": autofocus_dz,
}
)
}
# Check if autofocus is enabled
autofocus_extension = find_extension("org.openflexure.autofocus")
@ -174,11 +167,11 @@ def tile(
autofocus_enabled = False
z_stack_dz = (
grid[2] * step_size[2] if grid[2] > 1 else 0
grid[2] * stride_size[2] if grid[2] > 1 else 0
) # shorthand for Z stack range
# Construct an x-y grid (worry about z later)
x_y_grid = construct_grid(initial_position, step_size[:2], grid[:2], style=style)
x_y_grid = construct_grid(initial_position, stride_size[:2], grid[:2], style=style)
# Keep the initial Z position the same as our current position
next_z = initial_position[2]
@ -209,26 +202,25 @@ def tile(
target_z=-z_stack_dz / 2.0, # Finish below the focus
initial_move_up=False, # We're already at the top of the scan
)
# TODO: save the focus data for future reference? Use it for diagnostics?
else:
logging.debug("Running autofocus")
autofocus_extension.autofocus(
range(-3 * autofocus_dz, 4 * autofocus_dz, autofocus_dz)
)
logging.debug("Finished autofocus")
time.sleep(1) # TODO: Remove
time.sleep(1)
# If we're not doing a z-stack, just capture
if grid[2] <= 1:
capture(
microscope,
basename,
scan_id,
temporary=temporary,
use_video_port=use_video_port,
resize=resize,
bayer=bayer,
metadata=metadata,
metadata=dataset_d,
annotations=annotations,
tags=tags,
)
# Update task progress
@ -240,15 +232,14 @@ def tile(
microscope=microscope,
basename=basename,
temporary=temporary,
scan_id=scan_id,
step_size=step_size[2],
step_size=stride_size[2],
steps=grid[2],
center=not fast_autofocus, # fast_autofocus does this for us!
return_to_start=not fast_autofocus,
use_video_port=use_video_port,
resize=resize,
bayer=bayer,
metadata=metadata,
metadata=dataset_d,
annotations=annotations,
tags=tags,
)
# Make sure we use our current best estimate of focus (i.e. the current position) next point
@ -259,7 +250,7 @@ def tile(
) # Fast autofocus requires us to start at the top of the range
if grid[2] > 1:
next_z -= int(
grid[2] / 2.0 * step_size[2]
grid[2] / 2.0 * stride_size[2]
) # Z stacking means we're higher up to start with
logging.debug("Returning to {}".format(initial_position))
@ -270,39 +261,25 @@ def stack(
microscope,
basename: str = None,
temporary: bool = False,
scan_id: str = None,
step_size: int = 100,
steps: int = 5,
center: bool = True,
return_to_start: bool = True,
use_video_port: bool = False,
resize: Tuple[int, int] = None,
bayer: bool = False,
metadata: dict = {},
annotations: dict = {},
tags: list = [],
):
global _images_captured_so_far
# Generate a basename if none given
if not basename:
basename = generate_basename()
# Generate a stack ID
if not scan_id:
scan_id = uuid.uuid4()
# Add scan metadata
if not "time" in metadata:
metadata["time"] = generate_basename()
# Store initial position
initial_position = microscope.stage.position
with microscope.lock:
# Move to center scan
if center:
logging.debug("Moving to starting position")
microscope.stage.move_rel([0, 0, int((-step_size * steps) / 2)])
logging.debug("Moving to starting position")
microscope.stage.move_rel([0, 0, int((-step_size * steps) / 2)])
for i in range(steps):
time.sleep(0.1)
@ -310,12 +287,12 @@ def stack(
capture(
microscope,
basename,
scan_id,
temporary=temporary,
use_video_port=use_video_port,
resize=resize,
bayer=bayer,
metadata=metadata,
annotations=annotations,
tags=tags,
)
# Update task progress
@ -337,16 +314,18 @@ def stack(
class TileScanAPI(View):
@use_args(
{
"filename": fields.String(),
"filename": fields.String(missing=None, example=None),
"temporary": fields.Boolean(missing=False),
"step_size": fields.List(fields.Integer, missing=[2000, 1500, 100]),
"grid": fields.List(fields.Integer, missing=[3, 3, 5]),
"stride_size": fields.List(
fields.Integer, missing=[2000, 1500, 100], example=[2000, 1500, 100]
),
"grid": fields.List(fields.Integer, missing=[3, 3, 3], example=[3, 3, 3]),
"style": fields.String(missing="raster"),
"autofocus_dz": fields.Integer(missing=50),
"fast_autofocus": fields.Boolean(missing=False),
"use_video_port": fields.Boolean(missing=False),
"bayer": fields.Boolean(missing=False),
"metadata": fields.Dict(missing={}),
"annotations": fields.Dict(missing={}, example={"Foo": "Bar"}),
"tags": fields.List(fields.String, missing=[]),
"resize": fields.Dict(missing=None), # TODO: Validate keys
}
@ -373,7 +352,7 @@ class TileScanAPI(View):
microscope,
basename=args.get("filename"),
temporary=args.get("temporary"),
step_size=args.get("step_size"),
stride_size=args.get("stride_size"),
grid=args.get("grid"),
style=args.get("style"),
autofocus_dz=args.get("autofocus_dz"),
@ -381,7 +360,7 @@ class TileScanAPI(View):
resize=resize,
bayer=args.get("bayer"),
fast_autofocus=args.get("fast_autofocus"),
metadata=args.get("metadata"),
annotations=args.get("annotations"),
tags=args.get("tags"),
)

7
openflexure_microscope/api/v2/views/actions/camera.py
View file

@ -36,7 +36,7 @@ class CaptureAPI(View):
"bayer": fields.Boolean(
missing=False, description="Store raw bayer data in file"
),
"metadata": fields.Dict(missing={}, example={"Client": "SwaggerUI"}),
"annotations": fields.Dict(missing={}, example={"Client": "SwaggerUI"}),
"tags": fields.List(fields.String, missing=[], example=["docs"]),
"resize": fields.Dict(
missing=None, example={"width": 640, "height": 480}
@ -75,11 +75,10 @@ class CaptureAPI(View):
)
# Inject system metadata
output.put_metadata(microscope.metadata, system=True)
output.put_metadata({"instrument": microscope.metadata})
# Insert custom metadata
output.put_metadata(args.get("metadata"))
output.put_annotations(args.get("annotations"))
# Insert custom tags
output.put_tags(args.get("tags"))

22
openflexure_microscope/api/v2/views/captures.py
View file

@ -39,10 +39,12 @@ class CaptureSchema(Schema):
"mimetype": "application/json",
**description_from_view(CaptureTags),
},
"metadata": {
"href": url_for(CaptureMetadata.endpoint, id=data.id, _external=True),
"annotations": {
"href": url_for(
CaptureAnnotations.endpoint, id=data.id, _external=True
),
"mimetype": "application/json",
**description_from_view(CaptureMetadata),
**description_from_view(CaptureAnnotations),
},
"download": {
"href": url_for(
@ -62,6 +64,9 @@ capture_schema = CaptureSchema()
capture_list_schema = CaptureSchema(many=True)
from pprint import pprint
@ThingProperty
@Tag("captures")
class CaptureList(View):
@ -197,10 +202,10 @@ class CaptureTags(View):
@Tag("captures")
class CaptureMetadata(View):
class CaptureAnnotations(View):
def get(self, id):
"""
Get metadata associated with a single image capture
Get annotations associated with a single image capture
"""
microscope = find_component("org.openflexure.microscope")
capture_obj = microscope.camera.image_from_id(id)
@ -208,7 +213,7 @@ class CaptureMetadata(View):
if not capture_obj:
return abort(404) # 404 Not Found
return jsonify(capture_obj.metadata)
return jsonify(capture_obj.annotations)
def put(self, id):
"""
@ -226,7 +231,6 @@ class CaptureMetadata(View):
if type(data_dict) != dict:
return abort(400)
# TODO: Allow putting system metadata maybe?
capture_obj.put_metadata(data_dict)
capture_obj.put_annotations(data_dict)
return jsonify(capture_obj.metadata)
return jsonify(capture_obj.annotations)

32
openflexure_microscope/api/v2/views/state.py
View file

@ -78,7 +78,7 @@ class StatusProperty(View):
Show current read-only state of the microscope
"""
microscope = find_component("org.openflexure.microscope")
return jsonify(microscope.status)
return jsonify(microscope.state)
@Tag("properties")
@ -92,7 +92,35 @@ class NestedStatusProperty(View):
keys = route.split("/")
try:
value = get_by_path(microscope.status, keys)
value = get_by_path(microscope.state, keys)
except KeyError:
return abort(404)
return jsonify(value)
@ThingProperty
class ConfigurationProperty(View):
def get(self):
"""
Show current read-only state of the microscope
"""
microscope = find_component("org.openflexure.microscope")
return jsonify(microscope.configuration)
@Tag("properties")
class NestedConfigurationProperty(View):
@doc_response(404, description="Configuration key cannot be found")
def get(self, route):
"""
Show a nested section of the current microscope state
"""
microscope = find_component("org.openflexure.microscope")
keys = route.split("/")
try:
value = get_by_path(microscope.configuration, keys)
except KeyError:
return abort(404)