Simplified new configuration and metadata
This commit is contained in:
Joel Collins
parent
5d65c62001
commit
7458d278d8
10 changed files with 214 additions and 216 deletions
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@ -1,6 +1,7 @@
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import itertools
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import logging
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import uuid
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import datetime
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from typing import Tuple
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from functools import reduce
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@ -71,12 +72,12 @@ def progress():
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def capture(
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microscope,
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basename,
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scan_id,
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temporary: bool = False,
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use_video_port: bool = False,
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resize: Tuple[int, int] = None,
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bayer: bool = False,
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metadata: dict = {},
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annotations: dict = {},
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tags: list = [],
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):
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@ -94,16 +95,14 @@ def capture(
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output.file, use_video_port=use_video_port, resize=resize, bayer=bayer
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)
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# Affix metadata
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if "scan" not in tags:
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tags.append("scan")
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# Inject system metadata
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output.put_metadata(microscope.metadata, system=True)
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output.put_metadata({"instrument": microscope.metadata})
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# Insert custom metadata
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output.put_metadata(metadata)
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# Insert custom metadata
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output.put_annotations(annotations)
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# Insert custom tags
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output.put_tags(tags)
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@ -115,7 +114,7 @@ def tile(
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microscope,
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basename: str = None,
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temporary: bool = False,
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step_size: int = [2000, 1500, 100],
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stride_size: int = [2000, 1500, 100],
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grid: list = [3, 3, 5],
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style="raster",
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autofocus_dz: int = 50,
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@ -124,13 +123,13 @@ def tile(
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bayer: bool = False,
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fast_autofocus=False,
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metadata: dict = {},
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annotations: dict = {},
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tags: list = [],
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):
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global _images_to_be_captured
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global _images_captured_so_far
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# Keep task progress
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# TODO: Make this line not nasty
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_images_to_be_captured = reduce((lambda x, y: x * y), grid)
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_images_captured_so_far = 0
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@ -138,28 +137,22 @@ def tile(
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if not basename:
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basename = generate_basename()
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# Generate a stack ID
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scan_id = uuid.uuid4()
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# Store initial position
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initial_position = microscope.stage.position
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# Add scan metadata
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if "time" not in metadata:
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metadata["time"] = generate_basename()
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metadata.update(
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{
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"scan_id": scan_id,
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"basename": basename,
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"scan_parameters": {
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"step_size": step_size,
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"grid": grid,
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"style": style,
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"autofocus_dz": autofocus_dz,
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},
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# Add dataset metadata
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dataset_d = {
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"dataset": {
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"id": uuid.uuid4(),
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"type": "xyzScan",
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"name": basename,
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"acquisitionDate": datetime.datetime.now().isoformat(),
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"strideSize": stride_size,
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"grid": grid,
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"style": style,
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"autofocusDz": autofocus_dz,
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}
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)
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}
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# Check if autofocus is enabled
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autofocus_extension = find_extension("org.openflexure.autofocus")
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@ -174,11 +167,11 @@ def tile(
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autofocus_enabled = False
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z_stack_dz = (
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grid[2] * step_size[2] if grid[2] > 1 else 0
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grid[2] * stride_size[2] if grid[2] > 1 else 0
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) # shorthand for Z stack range
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# Construct an x-y grid (worry about z later)
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x_y_grid = construct_grid(initial_position, step_size[:2], grid[:2], style=style)
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x_y_grid = construct_grid(initial_position, stride_size[:2], grid[:2], style=style)
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# Keep the initial Z position the same as our current position
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next_z = initial_position[2]
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@ -209,26 +202,25 @@ def tile(
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target_z=-z_stack_dz / 2.0, # Finish below the focus
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initial_move_up=False, # We're already at the top of the scan
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)
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# TODO: save the focus data for future reference? Use it for diagnostics?
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else:
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logging.debug("Running autofocus")
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autofocus_extension.autofocus(
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range(-3 * autofocus_dz, 4 * autofocus_dz, autofocus_dz)
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)
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logging.debug("Finished autofocus")
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time.sleep(1) # TODO: Remove
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time.sleep(1)
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# If we're not doing a z-stack, just capture
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if grid[2] <= 1:
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capture(
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microscope,
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basename,
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scan_id,
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temporary=temporary,
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use_video_port=use_video_port,
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resize=resize,
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bayer=bayer,
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metadata=metadata,
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metadata=dataset_d,
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annotations=annotations,
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tags=tags,
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)
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# Update task progress
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@ -240,15 +232,14 @@ def tile(
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microscope=microscope,
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basename=basename,
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temporary=temporary,
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scan_id=scan_id,
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step_size=step_size[2],
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step_size=stride_size[2],
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steps=grid[2],
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center=not fast_autofocus, # fast_autofocus does this for us!
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return_to_start=not fast_autofocus,
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use_video_port=use_video_port,
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resize=resize,
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bayer=bayer,
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metadata=metadata,
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metadata=dataset_d,
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annotations=annotations,
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tags=tags,
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)
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# Make sure we use our current best estimate of focus (i.e. the current position) next point
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@ -259,7 +250,7 @@ def tile(
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) # Fast autofocus requires us to start at the top of the range
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if grid[2] > 1:
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next_z -= int(
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grid[2] / 2.0 * step_size[2]
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grid[2] / 2.0 * stride_size[2]
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) # Z stacking means we're higher up to start with
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logging.debug("Returning to {}".format(initial_position))
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@ -270,39 +261,25 @@ def stack(
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microscope,
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basename: str = None,
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temporary: bool = False,
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scan_id: str = None,
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step_size: int = 100,
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steps: int = 5,
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center: bool = True,
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return_to_start: bool = True,
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use_video_port: bool = False,
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resize: Tuple[int, int] = None,
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bayer: bool = False,
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metadata: dict = {},
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annotations: dict = {},
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tags: list = [],
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):
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global _images_captured_so_far
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# Generate a basename if none given
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if not basename:
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basename = generate_basename()
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# Generate a stack ID
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if not scan_id:
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scan_id = uuid.uuid4()
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# Add scan metadata
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if not "time" in metadata:
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metadata["time"] = generate_basename()
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# Store initial position
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initial_position = microscope.stage.position
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with microscope.lock:
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# Move to center scan
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if center:
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logging.debug("Moving to starting position")
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microscope.stage.move_rel([0, 0, int((-step_size * steps) / 2)])
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logging.debug("Moving to starting position")
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microscope.stage.move_rel([0, 0, int((-step_size * steps) / 2)])
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for i in range(steps):
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time.sleep(0.1)
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@ -310,12 +287,12 @@ def stack(
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capture(
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microscope,
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basename,
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scan_id,
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temporary=temporary,
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use_video_port=use_video_port,
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resize=resize,
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bayer=bayer,
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metadata=metadata,
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annotations=annotations,
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tags=tags,
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)
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# Update task progress
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@ -337,16 +314,18 @@ def stack(
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class TileScanAPI(View):
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@use_args(
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{
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"filename": fields.String(),
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"filename": fields.String(missing=None, example=None),
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"temporary": fields.Boolean(missing=False),
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"step_size": fields.List(fields.Integer, missing=[2000, 1500, 100]),
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"grid": fields.List(fields.Integer, missing=[3, 3, 5]),
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"stride_size": fields.List(
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fields.Integer, missing=[2000, 1500, 100], example=[2000, 1500, 100]
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),
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"grid": fields.List(fields.Integer, missing=[3, 3, 3], example=[3, 3, 3]),
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"style": fields.String(missing="raster"),
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"autofocus_dz": fields.Integer(missing=50),
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"fast_autofocus": fields.Boolean(missing=False),
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"use_video_port": fields.Boolean(missing=False),
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"bayer": fields.Boolean(missing=False),
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"metadata": fields.Dict(missing={}),
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"annotations": fields.Dict(missing={}, example={"Foo": "Bar"}),
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"tags": fields.List(fields.String, missing=[]),
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"resize": fields.Dict(missing=None), # TODO: Validate keys
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}
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@ -373,7 +352,7 @@ class TileScanAPI(View):
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microscope,
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basename=args.get("filename"),
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temporary=args.get("temporary"),
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step_size=args.get("step_size"),
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stride_size=args.get("stride_size"),
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grid=args.get("grid"),
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style=args.get("style"),
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autofocus_dz=args.get("autofocus_dz"),
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@ -381,7 +360,7 @@ class TileScanAPI(View):
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resize=resize,
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bayer=args.get("bayer"),
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fast_autofocus=args.get("fast_autofocus"),
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metadata=args.get("metadata"),
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annotations=args.get("annotations"),
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tags=args.get("tags"),
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)
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