Combined stack and tile scans (62377623) · Commits · OpenFlexure / openflexure-microscope-server

openflexure_microscope/plugins/default/scan/api.py

+7 −5

Original line number	Diff line number	Diff line
		@@ -10,11 +10,12 @@ class TileScanAPI(MicroscopeViewPlugin):

		# Get params
		name = payload.param('name')
		step_size = payload.param('step_size', default=[2000, 1500], convert=list)
		grid = payload.param('grid', default=[3, 3], convert=list)
		autofocus_dz = payload.param('autofocus_dz', default=20, convert=int)
		step_size = payload.param('step_size', default=[2000, 1500, 100], convert=list)
		grid = payload.param('grid', default=[3, 3, 5], convert=list)
		style = payload.param('style', default='raster', convert=str)
		autofocus_dz = payload.param('autofocus_dz', default=50, convert=int)

		use_video_port = payload.param('use_video_port', default=False, convert=bool)
		use_video_port = payload.param('use_video_port', default=True, convert=bool)
		resize = payload.param('size', default=None)
		if resize:
		if ('width' in resize) and ('height' in resize):
		@@ -22,7 +23,7 @@ class TileScanAPI(MicroscopeViewPlugin):
		else:
		abort(404)

		bayer = payload.param('bayer', default=True, convert=bool)
		bayer = payload.param('bayer', default=False, convert=bool)
		metadata = payload.param('metadata', default={}, convert=dict)
		tags = payload.param('tags', default=[], convert=list)

		@@ -32,6 +33,7 @@ class TileScanAPI(MicroscopeViewPlugin):
		basename=name,
		step_size=step_size,
		grid=grid,
		style=style,
		autofocus_dz=autofocus_dz,
		use_video_port=use_video_port,
		resize=resize,

openflexure_microscope/plugins/default/scan/plugin.py

+91 −24

Original line number	Diff line number	Diff line
		@@ -2,12 +2,44 @@ import time
		import numpy as np
		from typing import Tuple
		import uuid
		import logging

		from openflexure_microscope.camera.base import generate_basename
		from openflexure_microscope.plugins import MicroscopePlugin

		from .api import TileScanAPI, ZStackAPI

		def construct_grid(initial, step_sizes, n_steps, style='raster'):
		"""
		Given an initial position, step sizes, and number of steps,
		construct a 2-dimensional list of scan x-y positions.
		"""
		arr = []

		for i in range(n_steps[0]): # x axis
		arr.append([])
		for j in range(n_steps[1]): # y axis
		# Create a coordinate array
		coord = [initial[ax] + [i, j][ax]*step_sizes[ax] for ax in range(2)]
		# Append coordinate array to position grid
		arr[i].append(tuple(coord))

		# Style modifiers
		if style == 'snake':
		for i, line in enumerate(arr):
		if i % 2 != 0:
		line.reverse()

		return arr

		def flatten_grid(grid):
		"""
		Convert a 3D list of scan positions into a flat list
		of sequential positions.
		"""

		grid = list(itertools.chain(*grid))
		return grid

		class ScanPlugin(MicroscopePlugin):
		"""
		@@ -61,9 +93,10 @@ class ScanPlugin(MicroscopePlugin):
		def tile(
		self,
		basename: str = None,
		step_size: int = [2000, 1500],
		grid: list = [3, 3],
		autofocus_dz: int = 20,
		step_size: int = [2000, 1500, 100],
		grid: list = [3, 3, 5],
		style='raster',
		autofocus_dz: int = 50,
		use_video_port: bool = False,
		resize: Tuple[int, int] = None,
		bayer: bool = False,
		@@ -86,17 +119,38 @@ class ScanPlugin(MicroscopePlugin):
		else:
		autofocus_enabled = False

		xdirection = 1

		with self.microscope.lock:

		for i in range(grid[0]):
		for j in range(grid[1]):
		# Construct an x-y grid (worry about z later)
		x_y_grid = construct_grid(
		initial_position,
		step_size[:2],
		grid[:2],
		style=style
		)

		# Now step through each point in the x-y coordinate array
		for line in x_y_grid:
		# If rastering, rather than snake (or eventually spiral)
		if style == 'raster':
		# Return focus to initial position
		logging.debug("Returning to initial z position")
		self.microscope.stage.move_abs([line[0][0], line[0][1], initial_position[2]])

		for x_y in line:
		current_position = self.microscope.stage.position
		# Move to new grid position without changing z
		logging.debug("Moving to step {}".format([x_y[0], x_y[1], current_position[2]]))
		self.microscope.stage.move_abs([x_y[0], x_y[1], current_position[2]])
		# Refocus
		if autofocus_enabled:
		# TODO: Better autofocus
		logging.debug("Running autofocus")
		self.microscope.plugin.default_autofocus.autofocus(
		range(-2 * autofocus_dz, 3 * autofocus_dz, autofocus_dz))
		range(-3 * autofocus_dz, 4 * autofocus_dz, autofocus_dz))
		logging.debug("Finished autofocus")
		time.sleep(1) # TODO: Remove

		# If we're not doing a z-stack, just capture
		if (grid[2] <= 1):
		self.capture(
		basename,
		scan_id,
		@@ -106,19 +160,28 @@ class ScanPlugin(MicroscopePlugin):
		metadata=metadata,
		tags=tags
		)
		else:
		logging.debug("Entering z-stack")
		self.stack(
		basename=basename,
		scan_id=scan_id,
		step_size=step_size[2],
		steps=grid[2],
		center=True,
		use_video_port=use_video_port,
		resize=resize,
		bayer=bayer,
		metadata=metadata,
		tags=tags
		)

		if j != grid[0] - 1:
		self.microscope.stage.move_rel([step_size[0] * xdirection, 0, 0])

		xdirection *= -1
		if i != grid[1] - 1:
		self.microscope.stage.move_rel([256 * xdirection, step_size[1], 0])

		logging.debug("Returning to {}".format(initial_position))
		self.microscope.stage.move_abs(initial_position)

		def stack(
		self,
		basename: str = None,
		scan_id: str = None,
		step_size: int = 100,
		steps: int = 5,
		center: bool = True,
		@@ -133,6 +196,7 @@ class ScanPlugin(MicroscopePlugin):
		basename = generate_basename()

		# Generate a stack ID
		if not scan_id:
		scan_id = uuid.uuid4().hex

		# Store initial position
		@@ -140,12 +204,13 @@ class ScanPlugin(MicroscopePlugin):

		# Move to center scan
		if center:
		logging.debug("Moving to starting position")
		self.microscope.stage.move_rel([0, 0, int((-step_size * steps) / 2)])

		with self.microscope.lock:

		for i in range(steps):

		logging.debug("Capturing...")
		self.capture(
		basename,
		scan_id,
		@@ -157,6 +222,8 @@ class ScanPlugin(MicroscopePlugin):
		)

		if i != steps - 1:
		logging.debug("Moving z by {}".format(step_size))
		self.microscope.stage.move_rel([0, 0, step_size])

		logging.debug("Returning to {}".format(initial_position))
		self.microscope.stage.move_abs(initial_position)