Commit 994e83db authored by Joel Collins's avatar Joel Collins
Browse files

Code cleanup

parent 2bfb9884

.gitlab-ci.yml

+40 −0
Original line number Diff line number Diff line 
stages:

  - analysis

  - build

  - deploy
@@ -9,6 +10,45 @@ cache: 
  paths:

  - node_modules/



pylint:

  stage: analysis

  image: python:3.7

  allow_failure: true



  before_script:

    - curl -sSL https://raw.githubusercontent.com/python-poetry/poetry/master/get-poetry.py | python



  script:

    # Install server

    - $HOME/.poetry/bin/poetry install

    # Run static build script

    - $HOME/.poetry/bin/poetry run pylint ./openflexure_microscope/



  only:

    - branches

    - merge_requests

    - tags

    - web



black:

  stage: analysis

  image: python:3.7

  allow_failure: true



  before_script:

    - curl -sSL https://raw.githubusercontent.com/python-poetry/poetry/master/get-poetry.py | python



  script:

    # Install server

    - $HOME/.poetry/bin/poetry install

    # Run static build script

    - $HOME/.poetry/bin/poetry run black --check .



  only:

    - branches

    - merge_requests

    - tags

    - web



# Electron app build

build:

openflexure_microscope/api/app.py

+11 −12
Original line number Diff line number Diff line
@@ -21,7 +21,7 @@ import os 
from datetime import datetime



import pkg_resources

from flask import Flask, abort, send_file

from flask import abort, send_file

from flask_cors import CORS, cross_origin

from labthings import create_app

from labthings.extensions import find_extensions
@@ -34,7 +34,6 @@ from openflexure_microscope.paths import ( 
    OPENFLEXURE_EXTENSIONS_PATH,

    OPENFLEXURE_VAR_PATH,

    logs_file_path,

    settings_file_path,

)



# Handle logging
@@ -72,7 +71,7 @@ root_log.addHandler(fh) 
access_log.addHandler(afh)



# Log server paths being used

logging.info(f"Running with data path {OPENFLEXURE_VAR_PATH}")

logging.info("Running with data path %s", OPENFLEXURE_VAR_PATH)



logging.info("Creating app")

# Create flask app
@@ -103,16 +102,16 @@ for extension in find_extensions(OPENFLEXURE_EXTENSIONS_PATH): 
    labthing.register_extension(extension)



# Attach captures resources

labthing.add_view(views.CaptureList, f"/captures")

labthing.add_view(views.CaptureList, "/captures")

labthing.add_root_link(views.CaptureList, "captures")



labthing.add_view(views.CaptureView, f"/captures/<id>")

labthing.add_view(views.CaptureDownload, f"/captures/<id>/download/<filename>")

labthing.add_view(views.CaptureTags, f"/captures/<id>/tags")

labthing.add_view(views.CaptureAnnotations, f"/captures/<id>/annotations")

labthing.add_view(views.CaptureView, "/captures/<id>")

labthing.add_view(views.CaptureDownload, "/captures/<id>/download/<filename>")

labthing.add_view(views.CaptureTags, "/captures/<id>/tags")

labthing.add_view(views.CaptureAnnotations, "/captures/<id>/annotations")



# Attach settings and state resources

labthing.add_view(views.SettingsProperty, f"/instrument/settings")

labthing.add_view(views.SettingsProperty, "/instrument/settings")

labthing.add_root_link(views.SettingsProperty, "instrumentSettings")

labthing.add_view(views.NestedSettingsProperty, "/instrument/settings/<path:route>")

labthing.add_view(views.StateProperty, "/instrument/state")
@@ -129,8 +128,8 @@ labthing.add_view(views.StageTypeProperty, "/instrument/stage/type") 




# Attach streams resources

labthing.add_view(views.MjpegStream, f"/streams/mjpeg")

labthing.add_view(views.SnapshotStream, f"/streams/snapshot")

labthing.add_view(views.MjpegStream, "/streams/mjpeg")

labthing.add_view(views.SnapshotStream, "/streams/snapshot")



# Attach microscope action resources

labthing.add_view(views.actions.ActionsView, "/actions")
@@ -170,7 +169,7 @@ def err_log(): 


@app.route("/api/v1/", defaults={"path": ""})

@app.route("/api/v1/<path:path>")

def api_v1_catch_all(path):

def api_v1_catch_all(path):  # pylint: disable=W0613

    abort(410, "API v1 is no longer in use. Please upgrade your client.")

openflexure_microscope/api/default_extensions/__init__.py

+4 −2
Original line number Diff line number Diff line
@@ -8,9 +8,11 @@ def handle_extension_error(extension_name): 
    """'gracefully' log an error if an extension fails to load."""

    try:

        yield

    except Exception as e:

    except Exception:  # pylint: disable=W0703

        logging.error(

            f"Exception loading builtin extension {extension_name}: \n{traceback.format_exc()}"

            "Exception loading builtin extension %s: \n%s",

            extension_name,

            traceback.format_exc(),

        )

openflexure_microscope/api/default_extensions/autofocus.py

+9 −17
Original line number Diff line number Diff line
@@ -6,10 +6,10 @@ from threading import Event, Thread 
import numpy as np

from labthings import current_action, fields, find_component

from labthings.extensions import BaseExtension

from labthings.views import ActionView, PropertyView, View

from labthings.views import ActionView, View

from scipy import ndimage



from openflexure_microscope.devel import JsonResponse, abort, request

from openflexure_microscope.devel import abort

from openflexure_microscope.utilities import set_properties



### Autofocus utilities
@@ -36,19 +36,15 @@ class JPEGSharpnessMonitor: 
            return self.background_thread.is_alive()



    def should_stop(self):

        import time



        return time.time() - self.kept_alive > self.timeout



    def keep_alive(self):

        import time



        self.kept_alive = time.time()



    def start(self):

        "Start monitoring sharpness by looking at JPEG size"

        if not self.camera.stream_active:

            logging.warn(

            logging.warning(

                "Autofocus sharpness monitor was started but the camera isn't streaming.  Attempting to start the stream..."

            )

            self.camera.start_stream_recording()
@@ -66,7 +62,7 @@ class JPEGSharpnessMonitor: 
        "Function that runs in a background thread to record sharpness"

        logging.debug("Starting sharpness measurement in background thread")

        self.keep_alive()

        logging.debug(f"_measure_jpegs stop_event: {self.stop_event.is_set()}")

        logging.debug("_measure_jpegs stop_event: %s", self.stop_event.is_set())

        while not self.stop_event.is_set() and not self.should_stop():

            size_now = self.jpeg_size()

            time_now = time.time()
@@ -107,7 +103,7 @@ class JPEGSharpnessMonitor: 
            if np.sum(jpeg_times > stage_times[0]) == 0:

                raise ValueError(

                    "No images were captured during the move of the stage.  Perhaps the camera is not streaming images?"

                )

                ) from e

            else:

                raise e

        if stop < 1:
@@ -119,7 +115,7 @@ class JPEGSharpnessMonitor: 


    def sharpest_z_on_move(self, index):

        """Return the z position of the sharpest image on a given move"""

        jt, jz, js = self.move_data(index)

        _, jz, js = self.move_data(index)

        if len(js) == 0:

            raise ValueError(

                "No images were captured during the move of the stage.  Perhaps the camera is not streaming images?"
@@ -226,7 +222,7 @@ def fast_autofocus(microscope, dz=2000, backlash=None): 
    """Perform a down-up-down-up autofocus"""

    with monitor_sharpness(

        microscope

    ) as m, microscope.camera.lock, microscope.stage.lock:

    ) as m, microscope.camera.lock as _, microscope.stage.lock as _:

        i, z = m.focus_rel(-dz / 2)

        i, z = m.focus_rel(dz)

        fz = m.sharpest_z_on_move(i)
@@ -278,7 +274,7 @@ def fast_up_down_up_autofocus( 
    """

    with monitor_sharpness(

        microscope

    ) as m, microscope.camera.lock, microscope.stage.lock:

    ) as m, microscope.camera.lock as _, microscope.stage.lock as _:

        # Ensure the MJPEG stream has started

        microscope.camera.start_stream_recording()
@@ -291,12 +287,8 @@ def fast_up_down_up_autofocus( 
        i, z = m.focus_rel(-df)

        # now inspect where the sharpest point is, and estimate the sharpness

        # (JPEG size) that we should find at the start of the Z stack

        logging.debug("Get target_s")

        jt, jz, js = m.move_data(i)

        _, jz, js = m.move_data(i)

        best_z = jz[np.argmax(js)]

        target_s = np.interp(

            [best_z + target_z], jz[::-1], js[::-1]

        )  # NB jz is decreasing



        # now move to the start of the z stack

        logging.debug("Move to the start of the z stack")

openflexure_microscope/api/default_extensions/autostorage.py

+5 −15
Original line number Diff line number Diff line 
import logging

import os

from sys import platform



import psutil

from flask import abort
@@ -9,9 +8,7 @@ from labthings.extensions import BaseExtension 
from labthings.views import PropertyView, View



from openflexure_microscope.api.utilities.gui import build_gui

from openflexure_microscope.captures.capture import build_captures_from_exif

from openflexure_microscope.captures.capture_manager import BASE_CAPTURE_PATH

from openflexure_microscope.config import OpenflexureSettingsFile

from openflexure_microscope.paths import check_rw, settings_file_path



AS_SETTINGS_PATH = settings_file_path("autostorage_settings.json")
@@ -97,10 +94,10 @@ class AutostorageExtension(BaseExtension): 


    def on_microscope(self, microscope_obj):

        """Function to automatically call when the parent LabThing has a microscope attached."""

        logging.debug(f"Autostorage extension found microscope {microscope_obj}")

        logging.debug("Autostorage extension found microscope %s", microscope_obj)

        if hasattr(microscope_obj, "captures"):

            logging.debug(

                f"Autostorage extension bound to CaptureManager {self.capture_manager}"

                "Autostorage extension bound to CaptureManager %s", self.capture_manager

            )



            # Store a reference to the CaptureManager
@@ -119,7 +116,8 @@ class AutostorageExtension(BaseExtension): 
        # If preferred path does not exist, or cannot be written to

        if not (os.path.isdir(location) and check_rw(location)):

            logging.error(

                f"Preferred capture path {location} is missing or cannot be written to. Restoring defaults."

                "Preferred capture path %s is missing or cannot be written to. Restoring defaults.",

                location,

            )

            # Reset the storage location to default

            set_current_location(self.capture_manager, get_default_location())
@@ -187,8 +185,6 @@ autostorage_extension_v2 = AutostorageExtension() 


class GetLocationsView(PropertyView):

    def get(self):

        global autostorage_extension_v2



        autostorage_extension_v2.check_location()

        return autostorage_extension_v2.get_locations()
@@ -197,13 +193,10 @@ class PreferredLocationView(PropertyView): 
    schema = fields.String(required=True, example="Default")



    def get(self):

        global autostorage_extension_v2



        autostorage_extension_v2.check_location()

        return autostorage_extension_v2.get_preferred_key()



    def post(self, new_path_key):

        global autostorage_extension_v2

        microscope = find_component("org.openflexure.microscope")



        if not microscope:
@@ -218,13 +211,11 @@ class PreferredLocationGUIView(View): 
    args = {"new_path_title": fields.String(required=True)}



    def post(self, args):

        global autostorage_extension_v2



        new_path_title = args.get("new_path_title")

        logging.debug(new_path_title)



        new_path_key = autostorage_extension_v2.title_to_key(new_path_title)

        logging.debug(f"{new_path_key}")

        logging.debug(new_path_key)



        autostorage_extension_v2.check_location()

        autostorage_extension_v2.set_preferred_key(new_path_key)
@@ -233,7 +224,6 @@ class PreferredLocationGUIView(View): 




def dynamic_form():

    global autostorage_extension_v2

    autostorage_extension_v2.check_location()

    return {

        "icon": "sd_storage",