Renamed LabThing plugins to extensions
This commit is contained in:
jtc42
parent
d96e188d16
commit
2a245185a6
10 changed files with 89 additions and 89 deletions
404
openflexure_microscope/api/default_extensions/scan.py
Normal file
404
openflexure_microscope/api/default_extensions/scan.py
Normal file
|
|
@ -0,0 +1,404 @@
|
|||
import numpy as np
|
||||
import itertools
|
||||
import logging
|
||||
import uuid
|
||||
from typing import Tuple
|
||||
from functools import reduce
|
||||
|
||||
from openflexure_microscope.camera.base import generate_basename
|
||||
from openflexure_microscope.common.flask_labthings.find import find_device, find_extension
|
||||
from openflexure_microscope.common.flask_labthings.extensions import BaseExtension
|
||||
|
||||
from openflexure_microscope.devel import (
|
||||
JsonResponse,
|
||||
request,
|
||||
jsonify,
|
||||
taskify,
|
||||
abort,
|
||||
update_task_progress,
|
||||
update_task_data,
|
||||
)
|
||||
|
||||
from openflexure_microscope.common.flask_labthings.resource import Resource
|
||||
import time
|
||||
|
||||
|
||||
### Grid construction
|
||||
|
||||
|
||||
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
|
||||
|
||||
|
||||
### Progress
|
||||
|
||||
_images_to_be_captured: int = 1
|
||||
_images_captured_so_far: int = 0
|
||||
|
||||
|
||||
def progress():
|
||||
progress = (_images_captured_so_far / _images_to_be_captured) * 100
|
||||
logging.info(progress)
|
||||
return progress
|
||||
|
||||
|
||||
### Capturing
|
||||
|
||||
|
||||
def capture(
|
||||
microscope,
|
||||
basename,
|
||||
scan_id,
|
||||
temporary: bool = False,
|
||||
use_video_port: bool = False,
|
||||
resize: Tuple[int, int] = None,
|
||||
bayer: bool = False,
|
||||
metadata: dict = {},
|
||||
tags: list = [],
|
||||
):
|
||||
|
||||
# Construct a tile filename
|
||||
filename = "{}_{}_{}_{}".format(basename, *microscope.stage.position)
|
||||
folder = "SCAN_{}".format(basename)
|
||||
|
||||
# Create output object
|
||||
output = microscope.camera.new_image(
|
||||
temporary=temporary, filename=filename, folder=folder
|
||||
)
|
||||
|
||||
# Capture
|
||||
microscope.camera.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)
|
||||
|
||||
# Insert custom metadata
|
||||
output.put_metadata(metadata)
|
||||
|
||||
# Insert custom tags
|
||||
output.put_tags(tags)
|
||||
|
||||
|
||||
### Scanning
|
||||
|
||||
|
||||
def tile(
|
||||
microscope,
|
||||
basename: str = None,
|
||||
temporary: bool = False,
|
||||
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,
|
||||
fast_autofocus=False,
|
||||
metadata: 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
|
||||
|
||||
# Generate a basename if none given
|
||||
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,
|
||||
},
|
||||
}
|
||||
)
|
||||
|
||||
# Check if autofocus is enabled
|
||||
autofocus_extension = find_extension("autofocus")
|
||||
if (
|
||||
autofocus_dz
|
||||
and autofocus_extension
|
||||
and microscope.has_real_stage()
|
||||
and microscope.has_real_camera()
|
||||
):
|
||||
autofocus_enabled = True
|
||||
else:
|
||||
autofocus_enabled = False
|
||||
|
||||
z_stack_dz = (
|
||||
grid[2] * step_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)
|
||||
|
||||
# Keep the initial Z position the same as our current position
|
||||
next_z = initial_position[2]
|
||||
if fast_autofocus: # If fast autofocus is enabled, make
|
||||
next_z += autofocus_dz / 2 # sure we start from the top of the range
|
||||
initial_z = next_z # Save this value for use in raster scans
|
||||
|
||||
# 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)
|
||||
# Return focus to initial position
|
||||
if style == "raster":
|
||||
next_z = initial_z
|
||||
logging.debug("Returning to initial z position")
|
||||
microscope.stage.move_abs(
|
||||
[line[0][0], line[0][1], next_z]
|
||||
) # RWB: I think this line is redundant
|
||||
|
||||
for x_y in line:
|
||||
# Move to new grid position without changing z
|
||||
logging.debug("Moving to step {}".format([x_y[0], x_y[1], next_z]))
|
||||
microscope.stage.move_abs([x_y[0], x_y[1], next_z])
|
||||
# Refocus
|
||||
if autofocus_enabled:
|
||||
if fast_autofocus:
|
||||
autofocus_extension.fast_autofocus(
|
||||
dz=autofocus_dz,
|
||||
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
|
||||
|
||||
# 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,
|
||||
tags=tags,
|
||||
)
|
||||
# Update task progress
|
||||
_images_captured_so_far += 1
|
||||
update_task_progress(progress())
|
||||
else:
|
||||
logging.debug("Entering z-stack")
|
||||
stack(
|
||||
microscope=microscope,
|
||||
basename=basename,
|
||||
temporary=temporary,
|
||||
scan_id=scan_id,
|
||||
step_size=step_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,
|
||||
tags=tags,
|
||||
)
|
||||
# Make sure we use our current best estimate of focus (i.e. the current position) next point
|
||||
next_z = microscope.stage.position[2]
|
||||
if fast_autofocus:
|
||||
next_z += (
|
||||
autofocus_dz / 2
|
||||
) # 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]
|
||||
) # Z stacking means we're higher up to start with
|
||||
|
||||
logging.debug("Returning to {}".format(initial_position))
|
||||
microscope.stage.move_abs(initial_position)
|
||||
|
||||
|
||||
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 = {},
|
||||
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)])
|
||||
|
||||
for i in range(steps):
|
||||
time.sleep(0.1)
|
||||
logging.debug("Capturing...")
|
||||
capture(
|
||||
microscope,
|
||||
basename,
|
||||
scan_id,
|
||||
temporary=temporary,
|
||||
use_video_port=use_video_port,
|
||||
resize=resize,
|
||||
bayer=bayer,
|
||||
metadata=metadata,
|
||||
tags=tags,
|
||||
)
|
||||
# Update task progress
|
||||
_images_captured_so_far += 1
|
||||
update_task_progress(progress())
|
||||
|
||||
if i != steps - 1:
|
||||
logging.debug("Moving z by {}".format(step_size))
|
||||
microscope.stage.move_rel([0, 0, step_size])
|
||||
if return_to_start:
|
||||
logging.debug("Returning to {}".format(initial_position))
|
||||
microscope.stage.move_abs(initial_position)
|
||||
|
||||
|
||||
### Web views
|
||||
|
||||
|
||||
class TileScanAPI(Resource):
|
||||
def post(self):
|
||||
payload = JsonResponse(request)
|
||||
microscope = find_device("openflexure_microscope")
|
||||
|
||||
if not microscope:
|
||||
abort(503, "No microscope connected. Unable to autofocus.")
|
||||
|
||||
# Get params
|
||||
filename = payload.param("filename")
|
||||
temporary = payload.param("temporary", default=False, convert=bool)
|
||||
|
||||
step_size = payload.param("step_size", default=[2000, 1500, 100], convert=list)
|
||||
step_size = [int(i) for i in step_size]
|
||||
|
||||
grid = payload.param("grid", default=[3, 3, 5], convert=list)
|
||||
grid = [int(i) for i in grid]
|
||||
|
||||
style = payload.param("style", default="raster", convert=str)
|
||||
autofocus_dz = payload.param("autofocus_dz", default=50, convert=int)
|
||||
fast_autofocus = payload.param("fast_autofocus", 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):
|
||||
resize = (
|
||||
int(resize["width"]),
|
||||
int(resize["height"]),
|
||||
) # Convert dict to tuple
|
||||
else:
|
||||
abort(404)
|
||||
|
||||
bayer = payload.param("bayer", default=False, convert=bool)
|
||||
metadata = payload.param("metadata", default={}, convert=dict)
|
||||
tags = payload.param("tags", default=[], convert=list)
|
||||
|
||||
logging.info("Running tile scan...")
|
||||
task = taskify(tile)(
|
||||
microscope,
|
||||
basename=filename,
|
||||
temporary=temporary,
|
||||
step_size=step_size,
|
||||
grid=grid,
|
||||
style=style,
|
||||
autofocus_dz=autofocus_dz,
|
||||
use_video_port=use_video_port,
|
||||
resize=resize,
|
||||
bayer=bayer,
|
||||
fast_autofocus=fast_autofocus,
|
||||
metadata=metadata,
|
||||
tags=tags,
|
||||
)
|
||||
|
||||
# return a handle on the scan task
|
||||
return jsonify(task.state), 201
|
||||
|
||||
|
||||
scan_extension_v2 = BaseExtension("scan")
|
||||
|
||||
scan_extension_v2.add_view(TileScanAPI, "/tile")
|
||||
scan_extension_v2.register_action(TileScanAPI)
|
||||
Loading…
Add table
Add a link
Reference in a new issue