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Fixed imports, and PEP8 styling

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This commit is contained in:
Joel Collins 2019-03-07 10:58:08 +00:00
parent 298bc2ba6a
commit 89ea6a69de
3 changed files with 30 additions and 33 deletions
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2
openflexure_microscope/plugins/default/scan/__init__.py
View file

@ -1 +1 @@
from .plugin import StackPlugin from .plugin import ScanPlugin

47
openflexure_microscope/plugins/default/scan/api.py
View file

@ -1,5 +1,3 @@
import numpy as np
from openflexure_microscope.api.v1.views import MicroscopeViewPlugin from openflexure_microscope.api.v1.views import MicroscopeViewPlugin
from openflexure_microscope.api.utilities import JsonPayload from openflexure_microscope.api.utilities import JsonPayload
@ -9,7 +7,7 @@ from flask import request, jsonify, abort
class TileScanAPI(MicroscopeViewPlugin): class TileScanAPI(MicroscopeViewPlugin):
def post(self): def post(self):
payload = JsonPayload(request) payload = JsonPayload(request)
# Get params # Get params
name = payload.param('name') name = payload.param('name')
step_size = payload.param('step_size', default=[2000, 1500], convert=list) step_size = payload.param('step_size', default=[2000, 1500], convert=list)
@ -31,29 +29,28 @@ class TileScanAPI(MicroscopeViewPlugin):
print("Running tile scan...") print("Running tile scan...")
task = self.microscope.task.start( task = self.microscope.task.start(
self.plugin.tile, self.plugin.tile,
basename = name, basename=name,
step_size = step_size, step_size=step_size,
grid = grid, grid=grid,
autofocus_dz = autofocus_dz, autofocus_dz=autofocus_dz,
use_video_port = use_video_port, use_video_port=use_video_port,
resize = resize, resize=resize,
bayer = bayer, bayer=bayer,
metadata = metadata, metadata=metadata,
tags = tags tags=tags
) )
# return a handle on the autofocus task # return a handle on the autofocus task
return jsonify(task.state, 202) return jsonify(task.state, 202)
class ZStackAPI(MicroscopeViewPlugin): class ZStackAPI(MicroscopeViewPlugin):
def post(self): def post(self):
payload = JsonPayload(request) payload = JsonPayload(request)
# Get params # Get params
name = payload.param('name') name = payload.param('name')
step_size = payload.param('step_size', default=[2000, 1500], convert=list) step_size = payload.param('step_size', default=100, convert=int)
steps = payload.param('steps', default=5, convert=int) steps = payload.param('steps', default=5, convert=int)
center = payload.param('center', default=True, convert=bool) center = payload.param('center', default=True, convert=bool)
@ -72,16 +69,16 @@ class ZStackAPI(MicroscopeViewPlugin):
print("Running tile scan...") print("Running tile scan...")
task = self.microscope.task.start( task = self.microscope.task.start(
self.plugin.stack, self.plugin.stack,
basename = name, basename=name,
step_size = step_size, step_size=step_size,
steps = steps, steps=steps,
center = center, center=center,
use_video_port = use_video_port, use_video_port=use_video_port,
resize = resize, resize=resize,
bayer = bayer, bayer=bayer,
metadata = metadata, metadata=metadata,
tags = tags tags=tags
) )
# return a handle on the autofocus task # return a handle on the autofocus task
return jsonify(task.state, 202) return jsonify(task.state, 202)

14
openflexure_microscope/plugins/default/scan/plugin.py
View file

@ -5,10 +5,10 @@ import uuid
from openflexure_microscope.camera.base import generate_basename from openflexure_microscope.camera.base import generate_basename
from openflexure_microscope.plugins import MicroscopePlugin from openflexure_microscope.plugins import MicroscopePlugin
from openflexure_microscope.utilities import set_properties
from .api import TileScanAPI, ZStackAPI from .api import TileScanAPI, ZStackAPI
class ScanPlugin(MicroscopePlugin): class ScanPlugin(MicroscopePlugin):
""" """
Stack and tile plugin Stack and tile plugin
@ -19,7 +19,6 @@ class ScanPlugin(MicroscopePlugin):
'/stack': ZStackAPI, '/stack': ZStackAPI,
} }
def capture(self, def capture(self,
basename, basename,
scan_id, scan_id,
@ -95,7 +94,8 @@ class ScanPlugin(MicroscopePlugin):
for j in range(grid[1]): for j in range(grid[1]):
if autofocus_enabled: if autofocus_enabled:
self.microscope.plugin.default_autofocus.autofocus(range(-2*autofocus_dz, 3*autofocus_dz, autofocus_dz)) self.microscope.plugin.default_autofocus.autofocus(
range(-2 * autofocus_dz, 3 * autofocus_dz, autofocus_dz))
self.capture( self.capture(
basename, basename,
@ -108,11 +108,11 @@ class ScanPlugin(MicroscopePlugin):
) )
if j != grid[0] - 1: if j != grid[0] - 1:
self.microscope.stage.move_rel([step_size[0]*xdirection, 0, 0]) self.microscope.stage.move_rel([step_size[0] * xdirection, 0, 0])
xdirection *= -1 xdirection *= -1
if i != grid[1] - 1: if i != grid[1] - 1:
self.microscope.stage.move_rel([256*xdirection, step_size[1], 0]) self.microscope.stage.move_rel([256 * xdirection, step_size[1], 0])
self.microscope.stage.move_abs(initial_position) self.microscope.stage.move_abs(initial_position)
@ -120,7 +120,7 @@ class ScanPlugin(MicroscopePlugin):
self, self,
basename: str = None, basename: str = None,
step_size: int = 100, step_size: int = 100,
steps: list = 5, steps: int = 5,
center: bool = True, center: bool = True,
use_video_port: bool = False, use_video_port: bool = False,
resize: Tuple[int, int] = None, resize: Tuple[int, int] = None,
@ -140,7 +140,7 @@ class ScanPlugin(MicroscopePlugin):
# Move to center scan # Move to center scan
if center: if center:
self.microscope.stage.move_rel([0, 0, int((-step_size * steps)/2)]) self.microscope.stage.move_rel([0, 0, int((-step_size * steps) / 2)])
with self.microscope.lock: with self.microscope.lock: