416 lines
15 KiB
Python
416 lines
15 KiB
Python
import datetime
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import logging
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import time
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import uuid
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from functools import reduce
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from typing import Dict, List, Optional, Tuple
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from labthings import (
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current_action,
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fields,
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find_component,
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find_extension,
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update_action_progress,
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)
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from labthings.extensions import BaseExtension
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from labthings.views import ActionView
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from typing_extensions import Literal
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from openflexure_microscope.api.v2.views.actions.camera import FullCaptureArgs
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from openflexure_microscope.captures.capture_manager import generate_basename
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from openflexure_microscope.devel import abort
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from openflexure_microscope.microscope import Microscope
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# Type alias for convenience
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XyCoordinate = Tuple[int, int]
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XyzCoordinate = Tuple[int, int, int]
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### Grid construction
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def construct_grid(
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initial: XyCoordinate,
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step_sizes: XyCoordinate,
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n_steps: XyCoordinate,
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style: Literal["raster", "snake", "spiral"] = "raster",
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):
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"""
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Given an initial position, step sizes, and number of steps,
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construct a 2-dimensional list of scan x-y positions.
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"""
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arr: List[List[XyCoordinate]] = [] # 2D array of coordinates
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if style == "spiral":
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# deal with the centre image immediately
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coord = initial
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arr.append([initial])
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# for spiral, n_steps is the number of shells, and so only requires n_steps[0]
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for i in range(2, n_steps[0] + 1):
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arr.append([]) # Append new shell holder
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side_length = (2 * i) - 1
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# Iteratively generate the next location to append
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# Start coordinate of the shell
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# We create a copy of coord so that the new value of coord doesn't depend on itself
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# Otherwise we create a generator, not a tuple, which makes type checking angry
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last_coordinate: XyCoordinate = coord
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coord = (
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last_coordinate[0] + [-1, 1][0] * step_sizes[0],
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last_coordinate[1] + [-1, 1][1] * step_sizes[1],
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)
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for direction in ([1, 0], [0, -1], [-1, 0], [0, 1]):
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for _ in range(side_length - 1):
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last_coordinate = coord
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coord = (
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last_coordinate[0] + direction[0] * step_sizes[0],
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last_coordinate[1] + direction[1] * step_sizes[1],
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)
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arr[i - 1].append(coord)
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# If raster or snake
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else:
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for i in range(n_steps[0]): # x axis
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arr.append([])
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for j in range(n_steps[1]): # y axis
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# Create a coordinate tuple
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coord = (
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initial[0] + [i, j][0] * step_sizes[0],
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initial[1] + [i, j][1] * step_sizes[1],
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)
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# Append coordinate array to position grid
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arr[i].append(coord)
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# Style modifiers
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if style == "snake":
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# For each line (row) in the coordinate array
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for i, line in enumerate(arr):
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# If it's an odd row
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if i % 2 != 0:
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# Reverse the list of coordinates
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line.reverse()
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return arr
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### Capturing
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class ScanExtension(BaseExtension):
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def __init__(self):
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BaseExtension.__init__(self, "org.openflexure.scan", version="2.0.0")
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self._images_to_be_captured: int = 1
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self._images_captured_so_far: int = 0
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self.add_view(TileScanAPI, "/tile", endpoint="tile")
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def capture(
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self,
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microscope: Microscope,
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basename: Optional[str],
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namemode: str = "coordinates",
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temporary: bool = False,
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use_video_port: bool = False,
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resize: Optional[Tuple[int, int]] = None,
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bayer: bool = False,
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metadata: Optional[dict] = None,
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annotations: Optional[Dict[str, str]] = None,
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tags: Optional[List[str]] = None,
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dataset: Optional[Dict[str, str]] = None,
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):
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metadata = metadata or {}
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annotations = annotations or {}
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tags = tags or []
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# Construct a tile filename
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if namemode == "coordinates":
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filename = "{}_{}_{}_{}".format(basename, *microscope.stage.position)
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else:
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filename = "{}_{}".format(
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basename,
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str(self._images_captured_so_far).zfill(
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len(str(self._images_to_be_captured))
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),
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)
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folder = "SCAN_{}".format(basename)
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# Do capture
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return microscope.capture(
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filename=filename,
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folder=folder,
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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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annotations=annotations,
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tags=tags,
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dataset=dataset,
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metadata=metadata,
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cache_key=folder,
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)
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def progress(self):
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progress = (self._images_captured_so_far / self._images_to_be_captured) * 100
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logging.info(progress)
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return progress
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### Scanning
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def tile(
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self,
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microscope: Microscope,
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basename: Optional[str] = None,
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namemode: str = "coordinates",
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temporary: bool = False,
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stride_size: XyzCoordinate = (2000, 1500, 100),
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grid: XyzCoordinate = (3, 3, 5),
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style="raster",
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autofocus_dz: int = 50,
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use_video_port: bool = False,
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resize: Optional[Tuple[int, int]] = None,
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bayer: bool = False,
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fast_autofocus: bool = False,
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metadata: Optional[dict] = None,
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annotations: Optional[Dict[str, str]] = None,
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tags: Optional[List[str]] = None,
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):
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metadata = metadata or {}
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annotations = annotations or {}
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tags = tags or []
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start = time.time()
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# Keep task progress
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self._images_to_be_captured = reduce((lambda x, y: x * y), grid)
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self._images_captured_so_far = 0
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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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# Store initial position
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initial_position = microscope.stage.position
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# Add dataset metadata
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dataset_d = {
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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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# Check if autofocus is enabled
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autofocus_extension = find_extension("org.openflexure.autofocus")
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if (
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autofocus_dz
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and autofocus_extension
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and microscope.has_real_stage()
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and microscope.has_real_camera()
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):
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autofocus_enabled = True
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else:
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autofocus_enabled = False
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# Construct an x-y grid (worry about z later)
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x_y_grid = construct_grid(
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initial_position[:2], stride_size[:2], grid[:2], style=style
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)
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# Keep the initial Z position the same as our current position
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initial_z = initial_position[2]
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next_z = initial_z # Save this value for use in raster scans
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# Now step through each point in the x-y coordinate array
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for line in x_y_grid:
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# If rastering, rather than snake (or eventually spiral)
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# Return focus to initial position
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if style == "raster":
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next_z = initial_z # Reset z position at start of each new row
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logging.debug("Returning to initial z position")
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microscope.stage.move_abs(
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(line[0][0], line[0][1], next_z)
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) # RWB: I think this line is redundant
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for x_y in line:
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# Move to new grid position without changing z
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logging.debug("Moving to step %s", ([x_y[0], x_y[1], next_z]))
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microscope.stage.move_abs((x_y[0], x_y[1], next_z))
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# Refocus
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if autofocus_enabled:
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if fast_autofocus:
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# Run fast autofocus. Client should provide dz ~ 2000
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autofocus_extension.fast_autofocus(microscope, dz=autofocus_dz)
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else:
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# Run slow autofocus. Client should provide dz ~ 50
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autofocus_extension.autofocus(
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microscope,
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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)
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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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self.capture(
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microscope,
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basename,
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namemode=namemode,
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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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dataset=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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self._images_captured_so_far += 1
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update_action_progress(self.progress())
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else:
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logging.debug("Entering z-stack")
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self.stack(
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microscope=microscope,
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basename=basename,
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namemode=namemode,
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temporary=temporary,
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step_size=stride_size[2],
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steps=grid[2],
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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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dataset=dataset_d,
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annotations=annotations,
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tags=tags,
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)
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if current_action() and current_action().stopped:
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return
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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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next_z = microscope.stage.position[2]
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logging.debug("Returning to %s", (initial_position))
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microscope.stage.move_abs(initial_position)
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end = time.time()
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logging.info("Scan took %s seconds", end - start)
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def stack(
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self,
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microscope: Microscope,
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basename: Optional[str] = None,
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namemode: str = "coordinates",
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temporary: bool = False,
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step_size: int = 100,
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steps: int = 5,
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return_to_start: bool = True,
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use_video_port: bool = False,
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resize: Optional[Tuple[int, int]] = None,
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bayer: bool = False,
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metadata: Optional[dict] = None,
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annotations: Optional[Dict[str, str]] = None,
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dataset: Optional[Dict[str, str]] = None,
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tags: Optional[List[str]] = None,
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):
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metadata = metadata or {}
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annotations = annotations or {}
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tags = tags or []
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# Store initial position
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initial_position = microscope.stage.position
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logging.debug("Starting z-stack from position %s", microscope.stage.position)
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with microscope.lock:
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# Move to center scan
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logging.debug("Moving to z-stack starting position")
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microscope.stage.move_rel((0, 0, int((-step_size * steps) / 2)))
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logging.debug("Starting scan from position %s", microscope.stage.position)
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for i in range(steps):
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time.sleep(0.1)
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logging.debug("Capturing from position %s", microscope.stage.position)
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self.capture(
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microscope,
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basename,
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namemode=namemode,
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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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dataset=dataset,
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tags=tags,
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)
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# Update task progress
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self._images_captured_so_far += 1
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update_action_progress(self.progress())
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if current_action() and current_action().stopped:
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return
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if i != steps - 1:
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logging.debug("Moving z by %s", (step_size))
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microscope.stage.move_rel((0, 0, step_size))
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if return_to_start:
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logging.debug("Returning to %s", (initial_position))
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microscope.stage.move_abs(initial_position)
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class TileScanArgs(FullCaptureArgs):
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namemode = fields.String(missing="coordinates", example="coordinates")
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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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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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class TileScanAPI(ActionView):
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args = TileScanArgs()
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# Allow 10 seconds to stop upon DELETE request
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# Gives fast-autofocus time to finish if it's running
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default_stop_timeout = 10
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def post(self, args):
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microscope = find_component("org.openflexure.microscope")
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if not microscope:
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abort(503, "No microscope connected. Unable to autofocus.")
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resize = args.get("resize", None)
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if resize:
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if ("width" in resize) and ("height" in resize):
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resize = (
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int(resize["width"]),
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int(resize["height"]),
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) # Convert dict to tuple
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else:
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abort(404)
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logging.info("Running tile scan...")
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# Acquire microscope lock with 1s timeout
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with microscope.lock(timeout=1):
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# Run scan_extension_v2
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return self.extension.scan_extension_v2.tile(
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microscope,
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basename=args.get("filename"),
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namemode=args.get("namemode"),
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temporary=args.get("temporary"),
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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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use_video_port=args.get("use_video_port"),
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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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annotations=args.get("annotations"),
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tags=args.get("tags"),
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)
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