Commit 677b08d5 authored by Joel Collins's avatar Joel Collins
Browse files

Restructured scan extension

parent 43c16f1b

openflexure_microscope/api/default_extensions/scan.py

+24 −33
Original line number Diff line number Diff line
@@ -8,12 +8,12 @@ from functools import reduce 
from openflexure_microscope.captures.capture_manager import generate_basename

from labthings.server.find import find_component, find_extension

from labthings.server.extensions import BaseExtension

from labthings.server.decorators import use_args, ThingAction

from labthings.server.decorators import use_args

from labthings.server import fields



from openflexure_microscope.devel import abort, update_task_progress



from labthings.server.view import View

from labthings.server.view import View, ActionView

import time
@@ -54,18 +54,6 @@ def flatten_grid(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
@@ -99,10 +87,20 @@ def capture( 
    )





### Scanning

class ScanExtension(BaseExtension):

    def __init__(self):

        self._images_to_be_captured: int = 1

        self._images_captured_so_far: int = 0

        return BaseExtension.__init__(self, "org.openflexure.scan", version="2.0.0")



    def progress(self):

        progress = (self._images_captured_so_far / self._images_to_be_captured) * 100

        logging.info(progress)

        return progress

        

    ### Scanning

    def tile(

        self,

        microscope,

        basename: str = None,

        temporary: bool = False,
@@ -118,12 +116,9 @@ def tile( 
        annotations: dict = {},

        tags: list = [],

    ):

    global _images_to_be_captured

    global _images_captured_so_far



        # Keep task progress

    _images_to_be_captured = reduce((lambda x, y: x * y), grid)

    _images_captured_so_far = 0

        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:
@@ -210,11 +205,11 @@ def tile( 
                        tags=tags,

                    )

                    # Update task progress

                _images_captured_so_far += 1

                update_task_progress(progress())

                    self._images_captured_so_far += 1

                    update_task_progress(self.progress())

                else:

                    logging.debug("Entering z-stack")

                stack(

                    self.stack(

                        microscope=microscope,

                        basename=basename,

                        temporary=temporary,
@@ -235,6 +230,7 @@ def tile( 




    def stack(

        self,

        microscope,

        basename: str = None,

        temporary: bool = False,
@@ -248,7 +244,6 @@ def stack( 
        annotations: dict = {},

        tags: list = [],

    ):

    global _images_captured_so_far



        # Store initial position

        initial_position = microscope.stage.position
@@ -275,8 +270,8 @@ def stack( 
                    tags=tags,

                )

                # Update task progress

            _images_captured_so_far += 1

            update_task_progress(progress())

                self._images_captured_so_far += 1

                update_task_progress(self.progress())



                if i != steps - 1:

                    logging.debug("Moving z by {}".format(step_size))
@@ -286,11 +281,9 @@ def stack( 
                microscope.stage.move_abs(initial_position)





### Web views



scan_extension_v2 = ScanExtension()



@ThingAction

class TileScanAPI(View):

class TileScanAPI(ActionView):

    @use_args(

        {

            "filename": fields.String(missing=None, example=None),
@@ -328,7 +321,7 @@ class TileScanAPI(View): 
        logging.info("Running tile scan...")



        # return a handle on the scan task

        return tile(

        return scan_extension_v2.tile(

            microscope,

            basename=args.get("filename"),

            temporary=args.get("temporary"),
@@ -345,6 +338,4 @@ class TileScanAPI(View): 
        )





scan_extension_v2 = BaseExtension("org.openflexure.scan", version="2.0.0")



scan_extension_v2.add_view(TileScanAPI, "/tile", endpoint="tile")