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This commit is contained in:
Joel Collins 2019-11-06 22:07:16 +00:00
parent be5ddb76ae
commit 4e7606aa0c
24 changed files with 200 additions and 120 deletions
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2
openflexure_microscope/plugins/default/autofocus/api.py
View file

@ -6,7 +6,7 @@ from openflexure_microscope.devel import (
JsonResponse,
request,
jsonify,
taskify
taskify,
)

2
openflexure_microscope/plugins/default/camera_calibration/plugin.py
View file

@ -4,7 +4,7 @@ from openflexure_microscope.devel import (
JsonResponse,
request,
jsonify,
taskify
taskify,
)
import logging

2
openflexure_microscope/plugins/default/scan/api.py
View file

@ -4,7 +4,7 @@ from openflexure_microscope.devel import (
request,
jsonify,
abort,
taskify
taskify,
)
import logging

110
openflexure_microscope/plugins/default/scan/plugin.py
View file

@ -1,13 +1,13 @@
import time
import numpy as np
from typing import Tuple
from functools import reduce
import uuid
import itertools
import logging
from openflexure_microscope.camera.base import generate_basename
from openflexure_microscope.devel import MicroscopePlugin
from openflexure_microscope.devel import MicroscopePlugin, update_task_progress, update_task_data
from .api import TileScanAPI
@ -53,16 +53,26 @@ class ScanPlugin(MicroscopePlugin):
api_views = {"/tile": TileScanAPI}
def __init__(self):
self.images_to_be_captured: int = 1
update_task_data({"images_to_be_captured": self.images_to_be_captured})
@property
def progress(self):
progress = (self.images_captured_so_far / self.images_to_be_captured) * 100
logging.info(progress)
return progress
def capture(
self,
basename,
scan_id,
temporary: bool = False,
use_video_port: bool = False,
resize: Tuple[int, int] = None,
bayer: bool = False,
metadata: dict = {},
tags: list = [],
self,
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
@ -97,21 +107,26 @@ class ScanPlugin(MicroscopePlugin):
output.put_tags(tags)
def tile(
self,
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 = [],
self,
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 = [],
):
# Keep task progress
# TODO: Make this line not nasty
self.images_to_be_captured = reduce((lambda x, y: x * y), grid)
self.images_captured_so_far = 0
# Generate a basename if none given
if not basename:
basename = generate_basename()
@ -123,19 +138,24 @@ class ScanPlugin(MicroscopePlugin):
initial_position = self.microscope.stage.position
# Add scan metadata
if not "time" in metadata:
if "time" not in metadata:
metadata["time"] = generate_basename()
# Check if autofocus is enabled
if autofocus_dz and hasattr(self.microscope.plugin, "default_autofocus"):
if (
autofocus_dz
and hasattr(self.microscope.plugin, "default_autofocus")
and self.microscope.has_real_stage()
and self.microscope.has_real_camera()
):
autofocus_enabled = True
else:
autofocus_enabled = False
if fast_autofocus and not hasattr(
self.microscope.plugin.default_autofocus, "monitor_sharpness"
self.microscope.plugin.default_autofocus, "monitor_sharpness"
):
logging.error(
logging.warning(
"Can't use fast autofocus in the scan - the default plugin doesn't support monitor_sharpness; maybe it is too old?"
)
fast_autofocus = False
@ -198,6 +218,9 @@ class ScanPlugin(MicroscopePlugin):
metadata=metadata,
tags=tags,
)
# Update task progress
self.images_captured_so_far += 1
update_task_progress(self.progress)
else:
logging.debug("Entering z-stack")
self.stack(
@ -218,7 +241,7 @@ class ScanPlugin(MicroscopePlugin):
next_z = self.microscope.stage.position[2]
if fast_autofocus:
next_z += (
autofocus_dz / 2
autofocus_dz / 2
) # Fast autofocus requires us to start at the top of the range
if grid[2] > 1:
next_z -= int(
@ -229,19 +252,19 @@ class ScanPlugin(MicroscopePlugin):
self.microscope.stage.move_abs(initial_position)
def stack(
self,
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 = [],
self,
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 = [],
):
# Generate a basename if none given
@ -278,6 +301,9 @@ class ScanPlugin(MicroscopePlugin):
metadata=metadata,
tags=tags,
)
# Update task progress
self.images_captured_so_far += 1
update_task_progress(self.progress)
if i != steps - 1:
logging.debug("Moving z by {}".format(step_size))