Static type analysis
This commit is contained in:
Joel Collins
parent
3aebb8bead
commit
7866ec0f47
63 changed files with 1825 additions and 2722 deletions
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@ -3,7 +3,7 @@ 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 Tuple
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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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@ -14,20 +14,32 @@ from labthings import (
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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(initial, step_sizes, n_steps, style="raster"):
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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 = []
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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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@ -35,31 +47,48 @@ def construct_grid(initial, step_sizes, n_steps, style="raster"):
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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([])
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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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coord = [coord[ax] + [-1, 1][ax] * step_sizes[ax] for ax in range(2)]
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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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coord = [
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coord[ax] + direction[ax] * step_sizes[ax] for ax in range(2)
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]
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arr[i - 1].append(tuple(coord))
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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 array
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coord = [initial[ax] + [i, j][ax] * step_sizes[ax] for ax in range(2)]
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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(tuple(coord))
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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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@ -76,16 +105,17 @@ class ScanExtension(BaseExtension):
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def capture(
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self,
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microscope,
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basename,
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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: Tuple[int, int] = None,
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resize: Optional[Tuple[int, int]] = None,
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bayer: bool = False,
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metadata: dict = None,
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annotations: dict = None,
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tags: list = None,
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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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@ -113,6 +143,7 @@ class ScanExtension(BaseExtension):
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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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@ -125,21 +156,21 @@ class ScanExtension(BaseExtension):
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### Scanning
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def tile(
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self,
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microscope,
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basename: str = None,
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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: list = (2000, 1500, 100),
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grid: list = (3, 3, 5),
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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: Tuple[int, int] = None,
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resize: Optional[Tuple[int, int]] = None,
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bayer: bool = False,
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fast_autofocus=False,
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metadata: dict = None,
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annotations: dict = None,
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tags: list = None,
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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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@ -160,16 +191,14 @@ class ScanExtension(BaseExtension):
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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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"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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@ -186,7 +215,7 @@ class ScanExtension(BaseExtension):
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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, stride_size[:2], grid[:2], style=style
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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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@ -201,13 +230,13 @@ class ScanExtension(BaseExtension):
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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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(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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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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@ -232,7 +261,7 @@ class ScanExtension(BaseExtension):
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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=dataset_d,
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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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@ -251,7 +280,7 @@ class ScanExtension(BaseExtension):
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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=dataset_d,
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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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@ -268,19 +297,20 @@ class ScanExtension(BaseExtension):
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def stack(
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self,
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microscope,
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basename: str = None,
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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: Tuple[int, int] = None,
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resize: Optional[Tuple[int, int]] = None,
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bayer: bool = False,
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metadata: dict = None,
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annotations: dict = None,
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tags: list = None,
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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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@ -293,7 +323,7 @@ class ScanExtension(BaseExtension):
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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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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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@ -309,6 +339,7 @@ class ScanExtension(BaseExtension):
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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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@ -319,7 +350,7 @@ class ScanExtension(BaseExtension):
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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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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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