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Code cleanup

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This commit is contained in:
Joel Collins 2020-10-14 14:56:29 +00:00
parent 2bfb988460
commit 994e83dbeb
46 changed files with 261 additions and 318 deletions
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44
openflexure_microscope/api/default_extensions/scan.py
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@ -14,7 +14,7 @@ from labthings import (
update_action_progress,
)
from labthings.extensions import BaseExtension
from labthings.views import ActionView, View
from labthings.views import ActionView
from openflexure_microscope.captures.capture_manager import generate_basename
from openflexure_microscope.devel import abort
@ -74,10 +74,13 @@ class ScanExtension(BaseExtension):
use_video_port: bool = False,
resize: Tuple[int, int] = None,
bayer: bool = False,
metadata: dict = {},
annotations: dict = {},
tags: list = [],
metadata: dict = None,
annotations: dict = None,
tags: list = None,
):
metadata = metadata or {}
annotations = annotations or {}
tags = tags or []
# Construct a tile filename
if namemode == "coordinates":
@ -117,18 +120,22 @@ class ScanExtension(BaseExtension):
basename: str = None,
namemode: str = "coordinates",
temporary: bool = False,
stride_size: int = [2000, 1500, 100],
grid: list = [3, 3, 5],
stride_size: list = (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 = {},
annotations: dict = {},
tags: list = [],
metadata: dict = None,
annotations: dict = None,
tags: list = None,
):
metadata = metadata or {}
annotations = annotations or {}
tags = tags or []
start = time.time()
# Keep task progress
@ -210,7 +217,7 @@ class ScanExtension(BaseExtension):
# If we're not doing a z-stack, just capture
if grid[2] <= 1:
capture(
self.capture(
microscope,
basename,
namemode=namemode,
@ -250,7 +257,7 @@ class ScanExtension(BaseExtension):
microscope.stage.move_abs(initial_position)
end = time.time()
logging.info(f"Scan took {end - start} seconds")
logging.info("Scan took %s seconds", end - start)
def stack(
self,
@ -264,24 +271,27 @@ class ScanExtension(BaseExtension):
use_video_port: bool = False,
resize: Tuple[int, int] = None,
bayer: bool = False,
metadata: dict = {},
annotations: dict = {},
tags: list = [],
metadata: dict = None,
annotations: dict = None,
tags: list = None,
):
metadata = metadata or {}
annotations = annotations or {}
tags = tags or []
# Store initial position
initial_position = microscope.stage.position
logging.debug(f"Starting z-stack from position {microscope.stage.position}")
logging.debug("Starting z-stack from position %s", microscope.stage.position)
with microscope.lock:
# Move to center scan
logging.debug("Moving to z-stack starting position")
microscope.stage.move_rel([0, 0, int((-step_size * steps) / 2)])
logging.debug(f"Starting scan from position {microscope.stage.position}")
logging.debug("Starting scan from position %s", microscope.stage.position)
for i in range(steps):
time.sleep(0.1)
logging.debug(f"Capturing from position {microscope.stage.position}")
logging.debug("Capturing from position %s", microscope.stage.position)
self.capture(
microscope,
basename,