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This commit is contained in:
Joel Collins 2019-11-06 22:13:39 +00:00
parent 4e7606aa0c
commit dd82528d78
3 changed files with 51 additions and 49 deletions
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4
openflexure_microscope/api/app.py
View file

@ -90,7 +90,9 @@ api_microscope.attach(api_camera, api_stage)
# Restore loaded capture array to camera object # Restore loaded capture array to camera object
logging.debug("Restoring captures...") logging.debug("Restoring captures...")
api_microscope.camera.images = build_captures_from_exif(api_microscope.camera.paths["default"]) api_microscope.camera.images = build_captures_from_exif(
api_microscope.camera.paths["default"]
)
logging.debug("Microscope successfully attached!") logging.debug("Microscope successfully attached!")

8
openflexure_microscope/microscope.py
View file

@ -143,17 +143,13 @@ class Microscope:
self.attach_plugins(self.plugin_maps) self.attach_plugins(self.plugin_maps)
def has_real_stage(self): def has_real_stage(self):
if hasattr(self, "stage") and not isinstance( if hasattr(self, "stage") and not isinstance(self.stage, MockStage):
self.stage, MockStage
):
return True return True
else: else:
return False return False
def has_real_camera(self): def has_real_camera(self):
if hasattr(self, "camera") and not isinstance( if hasattr(self, "camera") and not isinstance(self.camera, MockStreamer):
self.camera, MockStreamer
):
return True return True
else: else:
return False return False

88
openflexure_microscope/plugins/default/scan/plugin.py
View file

@ -7,7 +7,11 @@ import logging
from openflexure_microscope.camera.base import generate_basename from openflexure_microscope.camera.base import generate_basename
from openflexure_microscope.devel import MicroscopePlugin, update_task_progress, update_task_data from openflexure_microscope.devel import (
MicroscopePlugin,
update_task_progress,
update_task_data,
)
from .api import TileScanAPI from .api import TileScanAPI
@ -64,15 +68,15 @@ class ScanPlugin(MicroscopePlugin):
return progress return progress
def capture( def capture(
self, self,
basename, basename,
scan_id, scan_id,
temporary: bool = False, temporary: bool = False,
use_video_port: bool = False, use_video_port: bool = False,
resize: Tuple[int, int] = None, resize: Tuple[int, int] = None,
bayer: bool = False, bayer: bool = False,
metadata: dict = {}, metadata: dict = {},
tags: list = [], tags: list = [],
): ):
# Construct a tile filename # Construct a tile filename
@ -107,19 +111,19 @@ class ScanPlugin(MicroscopePlugin):
output.put_tags(tags) output.put_tags(tags)
def tile( def tile(
self, self,
basename: str = None, basename: str = None,
temporary: bool = False, temporary: bool = False,
step_size: int = [2000, 1500, 100], step_size: int = [2000, 1500, 100],
grid: list = [3, 3, 5], grid: list = [3, 3, 5],
style="raster", style="raster",
autofocus_dz: int = 50, autofocus_dz: int = 50,
use_video_port: bool = False, use_video_port: bool = False,
resize: Tuple[int, int] = None, resize: Tuple[int, int] = None,
bayer: bool = False, bayer: bool = False,
fast_autofocus=False, fast_autofocus=False,
metadata: dict = {}, metadata: dict = {},
tags: list = [], tags: list = [],
): ):
# Keep task progress # Keep task progress
@ -143,17 +147,17 @@ class ScanPlugin(MicroscopePlugin):
# Check if autofocus is enabled # Check if autofocus is enabled
if ( if (
autofocus_dz autofocus_dz
and hasattr(self.microscope.plugin, "default_autofocus") and hasattr(self.microscope.plugin, "default_autofocus")
and self.microscope.has_real_stage() and self.microscope.has_real_stage()
and self.microscope.has_real_camera() and self.microscope.has_real_camera()
): ):
autofocus_enabled = True autofocus_enabled = True
else: else:
autofocus_enabled = False autofocus_enabled = False
if fast_autofocus and not hasattr( if fast_autofocus and not hasattr(
self.microscope.plugin.default_autofocus, "monitor_sharpness" self.microscope.plugin.default_autofocus, "monitor_sharpness"
): ):
logging.warning( logging.warning(
"Can't use fast autofocus in the scan - the default plugin doesn't support monitor_sharpness; maybe it is too old?" "Can't use fast autofocus in the scan - the default plugin doesn't support monitor_sharpness; maybe it is too old?"
@ -241,7 +245,7 @@ class ScanPlugin(MicroscopePlugin):
next_z = self.microscope.stage.position[2] next_z = self.microscope.stage.position[2]
if fast_autofocus: if fast_autofocus:
next_z += ( next_z += (
autofocus_dz / 2 autofocus_dz / 2
) # Fast autofocus requires us to start at the top of the range ) # Fast autofocus requires us to start at the top of the range
if grid[2] > 1: if grid[2] > 1:
next_z -= int( next_z -= int(
@ -252,19 +256,19 @@ class ScanPlugin(MicroscopePlugin):
self.microscope.stage.move_abs(initial_position) self.microscope.stage.move_abs(initial_position)
def stack( def stack(
self, self,
basename: str = None, basename: str = None,
temporary: bool = False, temporary: bool = False,
scan_id: str = None, scan_id: str = None,
step_size: int = 100, step_size: int = 100,
steps: int = 5, steps: int = 5,
center: bool = True, center: bool = True,
return_to_start: bool = True, return_to_start: bool = True,
use_video_port: bool = False, use_video_port: bool = False,
resize: Tuple[int, int] = None, resize: Tuple[int, int] = None,
bayer: bool = False, bayer: bool = False,
metadata: dict = {}, metadata: dict = {},
tags: list = [], tags: list = [],
): ):
# Generate a basename if none given # Generate a basename if none given