From df5d0dab68204a95c666fa95dd12d0a601d87ce7 Mon Sep 17 00:00:00 2001
From: Richard Bowman <richard.bowman@cantab.net>
Date: Mon, 8 Feb 2021 20:26:16 +0000
Subject: [PATCH 01/41] Add minimum scan dimension

It doesn't make sense to allow fewer than 1 image in any dimension
of a scan.  Currently, supplying 0 gives a division by zero error.
I've added min="1" to each control.
---
 .../tabContentComponents/captureComponents/paneCapture.vue | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

diff --git a/openflexure_microscope/api/static/src/components/tabContentComponents/captureComponents/paneCapture.vue b/openflexure_microscope/api/static/src/components/tabContentComponents/captureComponents/paneCapture.vue
index 1de921e0..1c3a0c85 100644
--- a/openflexure_microscope/api/static/src/components/tabContentComponents/captureComponents/paneCapture.vue
+++ b/openflexure_microscope/api/static/src/components/tabContentComponents/captureComponents/paneCapture.vue
@@ -155,7 +155,7 @@
                     v-model="scanStepSize.z"
                     class="uk-input uk-form-small"
                     type="number"
-                    name="inputPositionZx"
+                    name="inputPositionZ"
                   />
                 </div>
               </div>
@@ -172,6 +172,7 @@
                     class="uk-input uk-form-small"
                     type="number"
                     name="inputPositionX"
+                    min="1"
                   />
                 </div>
               </div>
@@ -186,6 +187,7 @@
                     class="uk-input uk-form-small"
                     type="number"
                     name="inputPositionY"
+                    min="1"
                   />
                 </div>
               </div>
@@ -199,7 +201,8 @@
                     v-model="scanSteps.z"
                     class="uk-input uk-form-small"
                     type="number"
-                    name="inputPositionZx"
+                    name="inputPositionZ"
+                    min="1"
                   />
                 </div>
               </div>

From 792e782968dc6000acacac98a8951c61417ea505 Mon Sep 17 00:00:00 2001
From: Richard Bowman <richard.bowman@cantab.net>
Date: Tue, 9 Feb 2021 09:21:56 +0000
Subject: [PATCH 02/41] Validate scan shape on the server

The scan API view now uses a schema with validation
constraints to enforce a minimum size of 1 in any dimension.
This requires better error handling in the app, which I've added.
It also needs a fix in LabThings so the error propagates correctly
---
 openflexure_microscope/api/app.py                 | 15 ++++++++++++++-
 .../api/default_extensions/scan.py                |  3 ++-
 2 files changed, 16 insertions(+), 2 deletions(-)

diff --git a/openflexure_microscope/api/app.py b/openflexure_microscope/api/app.py
index 44659886..205e9333 100644
--- a/openflexure_microscope/api/app.py
+++ b/openflexure_microscope/api/app.py
@@ -23,7 +23,7 @@ import os
 from datetime import datetime
 
 import pkg_resources
-from flask import abort, send_file
+from flask import abort, send_file, jsonify
 from flask_cors import CORS, cross_origin
 from labthings import create_app
 from labthings.extensions import find_extensions
@@ -105,6 +105,19 @@ app, labthing = create_app(
 # Enable CORS for some routes outside of LabThings
 cors: CORS = CORS(app)
 
+# Enable correct handling of Marshmallow/Webargs validation errors
+# Return validation errors as JSON 
+# (see  https://webargs.readthedocs.io/en/latest/framework_support.html)
+@app.errorhandler(422)
+@app.errorhandler(400)
+def handle_error(err):
+    headers = err.data.get("headers", None)
+    messages = err.data.get("messages", ["Invalid request."])
+    if headers:
+        return jsonify({"errors": messages}), err.code, headers
+    else:
+        return jsonify({"errors": messages}), err.code
+
 # Use custom JSON encoder
 labthing.json_encoder = JSONEncoder
 app.json_encoder = JSONEncoder
diff --git a/openflexure_microscope/api/default_extensions/scan.py b/openflexure_microscope/api/default_extensions/scan.py
index 5a2365c4..e05f7352 100644
--- a/openflexure_microscope/api/default_extensions/scan.py
+++ b/openflexure_microscope/api/default_extensions/scan.py
@@ -2,6 +2,7 @@ import datetime
 import logging
 import time
 import uuid
+import marshmallow
 from functools import reduce
 from typing import Dict, List, Optional, Tuple
 
@@ -361,7 +362,7 @@ class ScanExtension(BaseExtension):
 
 class TileScanArgs(FullCaptureArgs):
     namemode = fields.String(missing="coordinates", example="coordinates")
-    grid = fields.List(fields.Integer, missing=[3, 3, 3], example=[3, 3, 3])
+    grid = fields.List(fields.Integer(validate=marshmallow.validate.Range(min=1)), missing=[3, 3, 3], example=[3, 3, 3], )
     style = fields.String(missing="raster")
     autofocus_dz = fields.Integer(missing=50)
     fast_autofocus = fields.Boolean(missing=False)

From fc86745006a6e15e2221f4bab122a254d3e4a02a Mon Sep 17 00:00:00 2001
From: Richard Bowman <richard.bowman@cantab.net>
Date: Tue, 9 Feb 2021 10:19:56 +0000
Subject: [PATCH 03/41] Fix whitespace

---
 .../tabContentComponents/aboutComponents/devTools.vue       | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/openflexure_microscope/api/static/src/components/tabContentComponents/aboutComponents/devTools.vue b/openflexure_microscope/api/static/src/components/tabContentComponents/aboutComponents/devTools.vue
index f0372c94..fecf56de 100644
--- a/openflexure_microscope/api/static/src/components/tabContentComponents/aboutComponents/devTools.vue
+++ b/openflexure_microscope/api/static/src/components/tabContentComponents/aboutComponents/devTools.vue
@@ -24,9 +24,9 @@ export default {
   },
 
   mounted() {
-    if (localStorage.overrideOrigin){
+    if (localStorage.overrideOrigin) {
       this.newOrigin = localStorage.overrideOrigin;
-    }else{
+    } else {
       this.newOrigin = "http://microscope.local:5000";
     }
   },
@@ -34,7 +34,7 @@ export default {
   methods: {
     overrideAPIHost: function() {
       this.$store.commit("changeOrigin", this.newOrigin);
-      localStorage.overrideOrigin = this.newOrigin
+      localStorage.overrideOrigin = this.newOrigin;
     }
   }
 };

From 5527c4eb7b27ec88bae26aa75ae1d46b90f7d1db Mon Sep 17 00:00:00 2001
From: Richard Bowman <richard.bowman@cantab.net>
Date: Thu, 11 Feb 2021 14:30:20 +0000
Subject: [PATCH 04/41] Fix auto-exposure and AWB

The previous "auto calibrate" button for the camera relied on a
combination of the built-in autoexposure/AWB and
some JPEG-based tweaks to get the exposure settings right.
This often led to confusing results, e.g. oscillating between green and
 pink images.

 I have rewritten the auto-exposure code to adjust gain and shutter
 speed based on the raw image.  This seems to be
 very reliable, at the expense of being quite slow.  That's a price I'm
 happy to pay.

 I have replaced both the camera's auto white balance and my
 JPEG-based AWB hack with a single-shot AWB method that
 looks at the raw image.
---
 .../picamera_autocalibrate/extension.py       | 177 ++++++++++++----
 .../recalibrate_utils.py                      | 193 ++++++++++++++++--
 2 files changed, 320 insertions(+), 50 deletions(-)

diff --git a/openflexure_microscope/api/default_extensions/picamera_autocalibrate/extension.py b/openflexure_microscope/api/default_extensions/picamera_autocalibrate/extension.py
index 3b7de2ea..5a0f56dc 100644
--- a/openflexure_microscope/api/default_extensions/picamera_autocalibrate/extension.py
+++ b/openflexure_microscope/api/default_extensions/picamera_autocalibrate/extension.py
@@ -1,6 +1,8 @@
 import logging
 from contextlib import contextmanager
 
+import labthings.fields as fields
+import numpy as np
 import picamerax
 from flask import abort
 from labthings import find_component
@@ -13,7 +15,11 @@ from openflexure_microscope.microscope import Microscope
 from .recalibrate_utils import (
     auto_expose_and_freeze_settings,
     flat_lens_shading_table,
+    get_channel_percentiles,
     recalibrate_camera,
+    adjust_shutter_and_gain_from_raw,
+    adjust_white_balance_from_raw,
+    lst_from_camera,
 )
 
 
@@ -61,48 +67,71 @@ class LSTExtension(BaseExtension):
             "/delete_lens_shading_table",
             endpoint="delete_lens_shading_table",
         )
+        self.add_view(
+            GetRawChannelPercentilesView,
+            "/get_raw_channel_percentiles",
+            endpoint="get_raw_channel_percentiles",
+        )
+        self.add_view(
+            AutoExposureFromRawView,
+            "/auto_exposure_from_raw",
+            endpoint="auto_exposure_from_raw",
+        )
+        self.add_view(
+            AutoWhiteBalanceFromRawView,
+            "/auto_white_balance_from_raw",
+            endpoint="auto_white_balance_from_raw",
+        )
+        
+                
 
-    def recalibrate(self, microscope: Microscope):
+
+def find_microscope():
+    """Locate the microscope and raise a sensible error if it's missing."""
+    microscope = find_component("org.openflexure.microscope")
+
+    if not microscope:
+        abort(
+            503, "No microscope connected. Unable to use camera calibration functions."
+        )
+
+    if not hasattr(microscope.camera, "picamera"):
+        abort(
+            503, "The PiCamera calibration plugin requires a Raspberry Pi camera."
+        )
+
+    return microscope
+
+
+class RecalibrateView(ActionView):
+    args = {
+        "skip_auto_exposure": fields.Bool(
+            missing=False, 
+            description="Whether to "
+        )
+    }
+    def post(self, args):
         """Reset the camera's settings.
 
         This generates new gains, exposure time, and lens shading
         table such that the background is as uniform as possible
         with a gray level of 230.  It takes a little while to run.
         """
-        with pause_stream(microscope.camera) as scamera:
-            if hasattr(scamera, "picamera"):
-                picamera_obj: picamerax.PiCamera = getattr(scamera, "picamera")
-                auto_expose_and_freeze_settings(picamera_obj)
-                recalibrate_camera(picamera_obj)
-                microscope.save_settings()
-            else:
-                raise RuntimeError(
-                    "Recalibrate can only be used with a Raspberry Pi camera"
-                )
-
-
-class RecalibrateView(ActionView):
-    def post(self):
-        microscope = find_component("org.openflexure.microscope")
-
-        if not microscope:
-            abort(503, "No microscope connected. Unable to recalibrate.")
-
+        microscope = find_microscope()
         logging.info("Starting microscope recalibration...")
-
-        return self.extension.recalibrate(microscope)
+        picamera = microscope.camera.picamera
+        if not args.get("skip_auto_exposure"):
+            adjust_shutter_and_gain_from_raw(picamera)
+            adjust_white_balance_from_raw(picamera)
+        lst = lst_from_camera(picamera)
+        with pause_stream(microscope.camera) as scamera:
+            scamera.picamera.lens_shading_table = lst
+        microscope.save_settings()
 
 
 class FlattenLSTView(ActionView):
     def post(self):
-        microscope = find_component("org.openflexure.microscope")
-
-        if not microscope:
-            abort(
-                503,
-                "No microscope connected. Unable to flatten the lens shading table.",
-            )
-
+        microscope = find_microscope()
         with pause_stream(microscope.camera) as scamera:
             flat_lst = flat_lens_shading_table(scamera.camera)
             scamera.camera.lens_shading_table = flat_lst
@@ -111,14 +140,86 @@ class FlattenLSTView(ActionView):
 
 class DeleteLSTView(ActionView):
     def post(self):
-        microscope = find_component("org.openflexure.microscope")
-
-        if not microscope:
-            abort(
-                503,
-                "No microscope connected. Unable to flatten the lens shading table.",
-            )
-
+        microscope = find_microscope()
         with pause_stream(microscope.camera) as scamera:
             scamera.camera.lens_shading_table = None
         microscope.save_settings()
+
+
+class AutoExposureFromRawView(ActionView):
+    args = {
+        "target_white_level": fields.Int(
+            missing=700,
+            example=700,
+            description=(
+                "The pixel value (10-bit format) that we aim for when adjusting shutter/gain."
+            ),
+        ),
+        "max_iterations": fields.Int(
+            missing=20,
+            description=(
+                "The number of adjustments to the camera's settings to make before giving up."
+            ),
+        ),
+        "tolerance": fields.Float(
+            missing=0.05,
+            example=0.05,
+            description=(
+                "We stop adjusting when we get within this fraction of the target "
+                "value.  It is a number between 0 and 1, usually 0.01--0.1."
+            ),
+        ),
+        "percentile": fields.Float(
+            missing=99.9,
+            example=99.9,
+            description=(
+                "A float between 0 and 100 setting the centile to use "
+                "to measure the white point of the image.  A value "
+                "of 99.9 allows 0.1% of the pixels to be erroneously "
+                "bright - this helps stability in low light."
+            ),
+        ),
+    }
+
+    def post(self, args):
+        camera = find_component("org.openflexure.microscope").camera.picamera
+        adjust_shutter_and_gain_from_raw(
+            camera,
+            **args  # I'm relying on the schema to fill in missing values
+        )
+
+
+class AutoWhiteBalanceFromRawView(ActionView):
+    args = {
+        "percentile": fields.Float(
+            missing=99.9,
+            example=99.9,
+            description=(
+                "A float between 0 and 100 setting the centile to use "
+                "to measure the white point of the image.  A value "
+                "of 99.9 allows 0.1% of the pixels to be erroneously "
+                "bright - this helps stability in low light."
+            ),
+        )
+    }
+
+    def post(self, args):
+        camera = find_component("org.openflexure.microscope").camera.picamera
+        adjust_white_balance_from_raw(
+            camera,
+            **args  # I'm relying on the schema to fill in missing values
+        )
+
+
+class GetRawChannelPercentilesView(ActionView):
+    args = {
+        "percentile": fields.Float(
+            example=99.9,
+            description="A float between 0 and 100 setting the centile to calculate",
+        )
+    }
+    schema = fields.List(fields.Integer)
+
+    def post(self, args):
+        camera = find_component("org.openflexure.microscope").camera.picamera
+        return get_channel_percentiles(camera, args["percentile"])
diff --git a/openflexure_microscope/api/default_extensions/picamera_autocalibrate/recalibrate_utils.py b/openflexure_microscope/api/default_extensions/picamera_autocalibrate/recalibrate_utils.py
index 0392720e..b8b46044 100644
--- a/openflexure_microscope/api/default_extensions/picamera_autocalibrate/recalibrate_utils.py
+++ b/openflexure_microscope/api/default_extensions/picamera_autocalibrate/recalibrate_utils.py
@@ -44,14 +44,66 @@ def adjust_exposure_to_setpoint(camera: PiCamera, setpoint: int):
     print("done")
 
 
+def adjust_exposure_and_gain(
+    camera: PiCamera, target_white_level: int = 700, max_iterations: int = 99
+):
+    """Adjust exposure and analog gain based on raw images.
+    
+    This routine is slow but effective.  It uses raw images, so we
+    are not affected by white balance or digital gain.
+    """
+    # Start by setting fully manual exposure.
+    camera.exposure_mode = "off"
+    camera.iso = 0  # We must set ISO=0 (auto) or we can't set gain
+    camera.analog_gain = 1
+    camera.digital_gain = 1
+    camera.shutter_speed = 1  # This is not valid - we'll get the minimum
+    time.sleep(0.5)
+
+    # We start with very low exposure settings and work up in coarse steps
+    # until either the brightness is high enough, or we can't increase the
+    # shutter speed any more.
+    iterations = 0
+    while True:
+        iterations += 1
+
+        with PiBayerArray(camera) as a:
+            camera.capture(a, format="jpeg", bayer=True)
+            max_brightness = np.max(a.array)
+
+        if max_brightness > target_white_level:
+            break
+
+        previous_shutter_speed = camera.shutter_speed
+        camera.shutter_speed = previous_shutter_speed * 2
+        time.sleep(0.5)
+        current_shutter_speed = camera.shutter_speed
+        # NB we save this in a variable in case it changes between
+        # here and the next loop
+        logging.info(
+            f"Max brightness {max_brightness} < {target_white_level}. "
+            f"Attempting to double exposure from "
+            f"{previous_shutter_speed} to {current_shutter_speed}"
+        )
+        if current_shutter_speed == previous_shutter_speed:
+            logging.info(f"Shutter speed has saturated, stopping.")
+            break
+
+    if max_brightness > target_white_level:
+        logging.info("Brightness is high enough, fine-tuning")
+        camera.shutter_speed = int(
+            current_shutter_speed * target_white_level / max_brightness
+        )
+
+
 def auto_expose_and_freeze_settings(camera: PiCamera):
     """Freeze the settings after auto-exposing to white illumination"""
     logging.info("Allowing the camera to auto-expose")
     if "greyworld" in camera.AWB_MODES:
-        print("Calibrating with greyworld AWB")
+        logging.info("Calibrating with greyworld AWB")
         camera.awb_mode = "greyworld"
     else:
-        print("Calibrating with auto AWB")
+        logging.warning("Calibrating with auto AWB as greyworld is missing")
         camera.awb_mode = "auto"
     camera.exposure_mode = "auto"
     camera.iso = (
@@ -77,6 +129,112 @@ def auto_expose_and_freeze_settings(camera: PiCamera):
     adjust_exposure_to_setpoint(camera, 215)
 
 
+def adjust_shutter_and_gain_from_raw(
+    camera: PiCamera,
+    target_white_level: int = 700,
+    max_iterations: int = 20,
+    tolerance: float = 0.05,
+    percentile: float = 99.9,
+) -> float:
+    """Adjust exposure and analog gain based on raw images.
+    
+    This routine is slow but effective.  It uses raw images, so we
+    are not affected by white balance or digital gain.
+    """
+    # Start by setting fully manual exposure.
+    camera.exposure_mode = "off"
+    camera.iso = 0  # We must set ISO=0 (auto) or we can't set gain
+    camera.analog_gain = 1
+    camera.digital_gain = 1
+    camera.shutter_speed = 1  # This is not valid - we'll get the minimum
+    time.sleep(0.5)
+
+    # We start with very low exposure settings and work up in coarse steps
+    # until either the brightness is high enough, or we can't increase the
+    # shutter speed any more.
+    iterations = 0
+    shutter_speed_maximised = False
+    shutter_speed_increments = [10, 2, None]
+    shutter_speed_increment = shutter_speed_increments.pop(0)
+    while iterations < max_iterations:
+        iterations += 1
+        max_brightness = np.max(get_channel_percentiles(camera, percentile))
+        tested_shutter_speed = camera.shutter_speed
+        tested_analog_gain = camera.analog_gain
+        logging.info(
+            f"Brightness: {max_brightness: >5.0f}, "
+            f"Target: {target_white_level: >5.0f}, "
+            f"Gain: {float(tested_analog_gain): >4.1f}, "
+            f"Shutter: {float(tested_shutter_speed): >7.0f}"
+        )
+
+        if abs(max_brightness - target_white_level) < target_white_level * tolerance:
+            logging.info(
+                f"Brightness has converged to within {tolerance * 100 :.0f}% "
+                f"after {iterations} iterations."
+            )
+            break
+
+        # if not shutter_speed_maximised:  # Start by adjusting shutter speed
+        if max_brightness > target_white_level // 2:
+            shutter_speed_increment = (
+                None
+            )  # If we're within a factor of 2, trigger fine-tuning
+        if shutter_speed_increment is None:
+            logging.info("Fine-tuning shutter speed")
+            new_shutter_speed = int(
+                tested_shutter_speed * target_white_level / max_brightness
+            )
+            camera.shutter_speed = new_shutter_speed
+        else:
+            if max_brightness > target_white_level:
+                logging.info("Reducing shutter speed")
+                camera.shutter_speed = int(
+                    tested_shutter_speed / shutter_speed_increment
+                )
+            else:
+                logging.info("Increasing shutter speed")
+                camera.shutter_speed = tested_shutter_speed * shutter_speed_increment
+        time.sleep(0.5)
+
+        # Check whether the shutter speed is still going up - if not, we've hit a maximum
+        current_shutter_speed = camera.shutter_speed
+        if current_shutter_speed == tested_shutter_speed:
+            camera.analog_gain *= 2
+            if camera.analog_gain == tested_analog_gain:
+                logging.info(f"Shutter speed and gain are both maxed out.  Giving up!")
+                break
+            logging.info(
+                f"Shutter speed has maxed out at {current_shutter_speed}, doubled gain."
+            )
+
+    max_brightness = np.max(get_channel_percentiles(camera, percentile))
+    logging.info(f"Brightness {max_brightness} after {iterations} tries.")
+    return max_brightness
+
+
+def adjust_white_balance_from_raw(
+    camera: PiCamera, percentile: float = 99
+) -> (float, float):
+    """Adjust the white balance in a single shot, based on the raw image.
+    
+    NB if ``channels_from_raw_image`` is broken, this will go haywire.
+    We should probably have better logic to verify the channels really
+    are BGGR...
+    """
+    blue, g1, g2, red = get_channel_percentiles(camera, percentile)
+    green = (g1 + g2) / 2.0
+    new_awb_gains = (green / red, green / blue)
+    logging.info(
+        f"Raw white point is R: {red} G: {green} B: {blue}, "
+        f"setting AWB gains to ({new_awb_gains[0]:.2f}, "
+        f"{new_awb_gains[1]:.2f})."
+    )
+    camera.awb_mode = "off"
+    camera.awb_gains = new_awb_gains
+    return new_awb_gains
+
+
 def channels_from_bayer_array(bayer_array: np.ndarray) -> np.ndarray:
     """Given the 'array' from a PiBayerArray, return the 4 channels."""
     bayer_pattern: List[Tuple[int, int]] = [(0, 0), (0, 1), (1, 0), (1, 1)]
@@ -95,6 +253,14 @@ def channels_from_bayer_array(bayer_array: np.ndarray) -> np.ndarray:
     return channels
 
 
+def get_channel_percentiles(camera: PiCamera, percentile: float) -> np.ndarray:
+    """Calculate the brightness percentile of the pixels in each channel"""
+    with PiBayerArray(camera) as output:
+        camera.capture(output, format="jpeg", bayer=True)
+        channels = channels_from_bayer_array(output.array)
+        return np.percentile(channels, percentile, axis=(1, 2))
+
+
 def lst_from_channels(channels: np.ndarray) -> np.ndarray:
     """Given the 4 Bayer colour channels from a white image, generate a LST."""
     full_resolution: np.ndarray = np.array(
@@ -164,6 +330,18 @@ def lst_from_channels(channels: np.ndarray) -> np.ndarray:
     lens_shading_table: np.ndarray = gains.astype(np.uint8)
     return lens_shading_table[::-1, :, :].copy()
 
+def lst_from_camera(camera: PiCamera) -> np.ndarray:
+    """Acquire a raw image and use it to calculate a lens shading table."""
+    with PiBayerArray(camera) as a:
+        camera.capture(a, format="jpeg", bayer=True)
+        raw_image = a.array.copy()
+
+    # Now we need to calculate a lens shading table that would make this flat.
+    # raw_image is a 3D array, with full resolution and 3 colour channels.  No
+    # de-mosaicing has been done, so 2/3 of the values are zero (3/4 for R and B
+    # channels, 1/2 for green because there's twice as many green pixels).
+    channels = channels_from_bayer_array(raw_image)
+    return lst_from_channels(channels)
 
 def recalibrate_camera(camera: PiCamera):
     """Reset the lens shading table and exposure settings.
@@ -178,16 +356,7 @@ def recalibrate_camera(camera: PiCamera):
     camera.lens_shading_table = flat_lens_shading_table(camera)
     _ = rgb_image(camera)  # for some reason the camera won't work unless I do this!
 
-    with PiBayerArray(camera) as a:
-        camera.capture(a, format="jpeg", bayer=True)
-        raw_image = a.array.copy()
-
-    # Now we need to calculate a lens shading table that would make this flat.
-    # raw_image is a 3D array, with full resolution and 3 colour channels.  No
-    # de-mosaicing has been done, so 2/3 of the values are zero (3/4 for R and B
-    # channels, 1/2 for green because there's twice as many green pixels).
-    channels = channels_from_bayer_array(raw_image)
-    lens_shading_table = lst_from_channels(channels)
+    lens_shading_table = lst_from_camera(camera)
 
     camera.lens_shading_table = lens_shading_table
     _ = rgb_image(camera)

From 4c27d88b37ffd20ca212399422954e943703db2a Mon Sep 17 00:00:00 2001
From: Richard Bowman <richard.bowman@cantab.net>
Date: Thu, 11 Feb 2021 15:54:58 +0000
Subject: [PATCH 05/41] Fixed description and linted

---
 .../picamera_autocalibrate/extension.py       | 31 ++++++++-----------
 .../recalibrate_utils.py                      | 26 ++++++++++------
 2 files changed, 30 insertions(+), 27 deletions(-)

diff --git a/openflexure_microscope/api/default_extensions/picamera_autocalibrate/extension.py b/openflexure_microscope/api/default_extensions/picamera_autocalibrate/extension.py
index 5a0f56dc..1f8caf88 100644
--- a/openflexure_microscope/api/default_extensions/picamera_autocalibrate/extension.py
+++ b/openflexure_microscope/api/default_extensions/picamera_autocalibrate/extension.py
@@ -2,8 +2,6 @@ import logging
 from contextlib import contextmanager
 
 import labthings.fields as fields
-import numpy as np
-import picamerax
 from flask import abort
 from labthings import find_component
 from labthings.extensions import BaseExtension
@@ -13,12 +11,10 @@ from openflexure_microscope.camera.base import BaseCamera
 from openflexure_microscope.microscope import Microscope
 
 from .recalibrate_utils import (
-    auto_expose_and_freeze_settings,
-    flat_lens_shading_table,
-    get_channel_percentiles,
-    recalibrate_camera,
     adjust_shutter_and_gain_from_raw,
     adjust_white_balance_from_raw,
+    flat_lens_shading_table,
+    get_channel_percentiles,
     lst_from_camera,
 )
 
@@ -82,11 +78,9 @@ class LSTExtension(BaseExtension):
             "/auto_white_balance_from_raw",
             endpoint="auto_white_balance_from_raw",
         )
-        
-                
 
 
-def find_microscope():
+def find_microscope() -> Microscope:
     """Locate the microscope and raise a sensible error if it's missing."""
     microscope = find_component("org.openflexure.microscope")
 
@@ -96,9 +90,7 @@ def find_microscope():
         )
 
     if not hasattr(microscope.camera, "picamera"):
-        abort(
-            503, "The PiCamera calibration plugin requires a Raspberry Pi camera."
-        )
+        abort(503, "The PiCamera calibration plugin requires a Raspberry Pi camera.")
 
     return microscope
 
@@ -106,10 +98,15 @@ def find_microscope():
 class RecalibrateView(ActionView):
     args = {
         "skip_auto_exposure": fields.Bool(
-            missing=False, 
-            description="Whether to "
+            missing=False,
+            description=(
+                "By default we perform an auto-exposure and AWB "
+                "step before updating the lens shading table.  Set "
+                "this argument to True to disable those steps."
+            ),
         )
     }
+
     def post(self, args):
         """Reset the camera's settings.
 
@@ -184,8 +181,7 @@ class AutoExposureFromRawView(ActionView):
     def post(self, args):
         camera = find_component("org.openflexure.microscope").camera.picamera
         adjust_shutter_and_gain_from_raw(
-            camera,
-            **args  # I'm relying on the schema to fill in missing values
+            camera, **args  # I'm relying on the schema to fill in missing values
         )
 
 
@@ -206,8 +202,7 @@ class AutoWhiteBalanceFromRawView(ActionView):
     def post(self, args):
         camera = find_component("org.openflexure.microscope").camera.picamera
         adjust_white_balance_from_raw(
-            camera,
-            **args  # I'm relying on the schema to fill in missing values
+            camera, **args  # I'm relying on the schema to fill in missing values
         )
 
 
diff --git a/openflexure_microscope/api/default_extensions/picamera_autocalibrate/recalibrate_utils.py b/openflexure_microscope/api/default_extensions/picamera_autocalibrate/recalibrate_utils.py
index b8b46044..788d856d 100644
--- a/openflexure_microscope/api/default_extensions/picamera_autocalibrate/recalibrate_utils.py
+++ b/openflexure_microscope/api/default_extensions/picamera_autocalibrate/recalibrate_utils.py
@@ -7,6 +7,12 @@ import numpy as np
 from picamerax import PiCamera
 from picamerax.array import PiBayerArray, PiRGBArray
 
+# I have used f strings throughout, for readability.
+# The performance implication of using them in logging statements
+# really doesn't matter here - also, loglevel is usually set to
+# INFO to report progress via the LabThings action API
+# pylint: disable=logging-fstring-interpolation
+
 
 def rgb_image(
     camera: PiCamera, resize: Optional[Tuple[int, int]] = None, **kwargs
@@ -66,6 +72,12 @@ def adjust_exposure_and_gain(
     iterations = 0
     while True:
         iterations += 1
+        if iterations > max_iterations:
+            logging.warning(
+                f"Auto exposure is stopping after {max_iterations} "
+                "but it has not converged."
+            )
+            break
 
         with PiBayerArray(camera) as a:
             camera.capture(a, format="jpeg", bayer=True)
@@ -86,7 +98,7 @@ def adjust_exposure_and_gain(
             f"{previous_shutter_speed} to {current_shutter_speed}"
         )
         if current_shutter_speed == previous_shutter_speed:
-            logging.info(f"Shutter speed has saturated, stopping.")
+            logging.info("Shutter speed has saturated, stopping.")
             break
 
     if max_brightness > target_white_level:
@@ -153,7 +165,6 @@ def adjust_shutter_and_gain_from_raw(
     # until either the brightness is high enough, or we can't increase the
     # shutter speed any more.
     iterations = 0
-    shutter_speed_maximised = False
     shutter_speed_increments = [10, 2, None]
     shutter_speed_increment = shutter_speed_increments.pop(0)
     while iterations < max_iterations:
@@ -202,14 +213,9 @@ def adjust_shutter_and_gain_from_raw(
         if current_shutter_speed == tested_shutter_speed:
             camera.analog_gain *= 2
             if camera.analog_gain == tested_analog_gain:
-                logging.info(f"Shutter speed and gain are both maxed out.  Giving up!")
+                logging.info("Shutter speed and gain are both maxed out.  Giving up!")
                 break
-            logging.info(
-                f"Shutter speed has maxed out at {current_shutter_speed}, doubled gain."
-            )
-
-    max_brightness = np.max(get_channel_percentiles(camera, percentile))
-    logging.info(f"Brightness {max_brightness} after {iterations} tries.")
+            logging.info("Shutter speed has maxed out, doubled gain to compensate.")
     return max_brightness
 
 
@@ -330,6 +336,7 @@ def lst_from_channels(channels: np.ndarray) -> np.ndarray:
     lens_shading_table: np.ndarray = gains.astype(np.uint8)
     return lens_shading_table[::-1, :, :].copy()
 
+
 def lst_from_camera(camera: PiCamera) -> np.ndarray:
     """Acquire a raw image and use it to calculate a lens shading table."""
     with PiBayerArray(camera) as a:
@@ -343,6 +350,7 @@ def lst_from_camera(camera: PiCamera) -> np.ndarray:
     channels = channels_from_bayer_array(raw_image)
     return lst_from_channels(channels)
 
+
 def recalibrate_camera(camera: PiCamera):
     """Reset the lens shading table and exposure settings.
 

From ff322decfca35bbf361b29ec5f642aa079ab20b7 Mon Sep 17 00:00:00 2001
From: Richard Bowman <richard.bowman@cantab.net>
Date: Thu, 11 Feb 2021 19:37:40 +0000
Subject: [PATCH 06/41] updated poetry lockfile

---
 poetry.lock | 352 ++++++++++++++++++++++++++++------------------------
 1 file changed, 189 insertions(+), 163 deletions(-)

diff --git a/poetry.lock b/poetry.lock
index 2e5f3cbe..5588bca5 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -8,7 +8,7 @@ python-versions = "*"
 
 [[package]]
 name = "apispec"
-version = "4.0.0"
+version = "4.3.0"
 description = "A pluggable API specification generator. Currently supports the OpenAPI Specification (f.k.a. the Swagger specification)."
 category = "main"
 optional = false
@@ -18,12 +18,12 @@ python-versions = ">=3.6"
 PyYAML = {version = ">=3.10", optional = true, markers = "extra == \"yaml\""}
 
 [package.extras]
-dev = ["PyYAML (>=3.10)", "prance[osv] (>=0.11)", "marshmallow (>=3.0.0)", "pytest", "mock", "flake8 (==3.8.3)", "flake8-bugbear (==20.1.4)", "pre-commit (>=2.4,<3.0)", "tox"]
-docs = ["marshmallow (>=3.0.0)", "pyyaml (==5.3.1)", "sphinx (==3.2.1)", "sphinx-issues (==1.2.0)", "sphinx-rtd-theme (==0.5.0)"]
-lint = ["flake8 (==3.8.3)", "flake8-bugbear (==20.1.4)", "pre-commit (>=2.4,<3.0)"]
 tests = ["PyYAML (>=3.10)", "prance[osv] (>=0.11)", "marshmallow (>=3.0.0)", "pytest", "mock"]
-validation = ["prance[osv] (>=0.11)"]
+docs = ["marshmallow (>=3.0.0)", "pyyaml (==5.4.1)", "sphinx (==3.4.3)", "sphinx-issues (==1.2.0)", "sphinx-rtd-theme (==0.5.1)"]
+lint = ["flake8 (==3.8.4)", "flake8-bugbear (==20.11.1)", "pre-commit (>=2.4,<3.0)"]
+dev = ["PyYAML (>=3.10)", "prance[osv] (>=0.11)", "marshmallow (>=3.0.0)", "pytest", "mock", "flake8 (==3.8.4)", "flake8-bugbear (==20.11.1)", "pre-commit (>=2.4,<3.0)", "tox"]
 yaml = ["PyYAML (>=3.10)"]
+validation = ["prance[osv] (>=0.11)"]
 
 [[package]]
 name = "apispec-webframeworks"
@@ -37,9 +37,9 @@ python-versions = ">=3.6"
 apispec = {version = ">=2.0.0", extras = ["yaml"]}
 
 [package.extras]
-dev = ["pytest", "mock", "Flask (==1.1.1)", "tornado", "bottle (==0.12.17)", "flake8 (==3.7.9)", "flake8-bugbear (==19.8.0)", "pre-commit (>=1.18,<2.0)", "tox"]
-lint = ["flake8 (==3.7.9)", "flake8-bugbear (==19.8.0)", "pre-commit (>=1.18,<2.0)"]
 tests = ["pytest", "mock", "Flask (==1.1.1)", "tornado", "bottle (==0.12.17)"]
+lint = ["flake8 (==3.7.9)", "flake8-bugbear (==19.8.0)", "pre-commit (>=1.18,<2.0)"]
+dev = ["pytest", "mock", "Flask (==1.1.1)", "tornado", "bottle (==0.12.17)", "flake8 (==3.7.9)", "flake8-bugbear (==19.8.0)", "pre-commit (>=1.18,<2.0)", "tox"]
 
 [[package]]
 name = "appdirs"
@@ -59,8 +59,8 @@ python-versions = ">=3.5"
 
 [package.dependencies]
 lazy-object-proxy = ">=1.4.0,<1.5.0"
-six = ">=1.12,<2.0"
 typed-ast = {version = ">=1.4.0,<1.5", markers = "implementation_name == \"cpython\" and python_version < \"3.8\""}
+six = ">=1.12,<2.0"
 wrapt = ">=1.11,<2.0"
 
 [[package]]
@@ -80,10 +80,10 @@ optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
 
 [package.extras]
-dev = ["coverage[toml] (>=5.0.2)", "hypothesis", "pympler", "pytest (>=4.3.0)", "six", "zope.interface", "furo", "sphinx", "pre-commit"]
 docs = ["furo", "sphinx", "zope.interface"]
 tests = ["coverage[toml] (>=5.0.2)", "hypothesis", "pympler", "pytest (>=4.3.0)", "six", "zope.interface"]
 tests_no_zope = ["coverage[toml] (>=5.0.2)", "hypothesis", "pympler", "pytest (>=4.3.0)", "six"]
+dev = ["coverage[toml] (>=5.0.2)", "hypothesis", "pympler", "pytest (>=4.3.0)", "six", "zope.interface", "furo", "sphinx", "pre-commit"]
 
 [[package]]
 name = "babel"
@@ -105,10 +105,10 @@ optional = false
 python-versions = ">=3.6"
 
 [package.dependencies]
-appdirs = "*"
-attrs = ">=17.4.0"
-click = ">=6.5"
 toml = ">=0.9.4"
+attrs = ">=17.4.0"
+appdirs = "*"
+click = ">=6.5"
 
 [package.extras]
 d = ["aiohttp (>=3.3.2)"]
@@ -125,8 +125,8 @@ python-versions = ">=3.6,<4.0"
 numpy = ">=1.17,<2.0"
 
 [package.extras]
-correlation = ["opencv-python-headless (>=4.1,<5.0)", "scipy (>=1.4,<2.0)"]
 all = ["opencv-python-headless (>=4.1,<5.0)", "scipy (>=1.4,<2.0)"]
+correlation = ["opencv-python-headless (>=4.1,<5.0)", "scipy (>=1.4,<2.0)"]
 
 [[package]]
 name = "certifi"
@@ -169,12 +169,12 @@ optional = false
 python-versions = "*"
 
 [package.extras]
-doc = ["sphinx"]
 test = ["pytest", "coverage", "mock"]
+doc = ["sphinx"]
 
 [[package]]
 name = "coverage"
-version = "5.3.1"
+version = "5.4"
 description = "Code coverage measurement for Python"
 category = "main"
 optional = false
@@ -211,15 +211,15 @@ optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*"
 
 [package.dependencies]
-click = ">=5.1"
 itsdangerous = ">=0.24"
 Jinja2 = ">=2.10.1"
+click = ">=5.1"
 Werkzeug = ">=0.15"
 
 [package.extras]
-dev = ["pytest", "coverage", "tox", "sphinx", "pallets-sphinx-themes", "sphinxcontrib-log-cabinet", "sphinx-issues"]
-docs = ["sphinx", "pallets-sphinx-themes", "sphinxcontrib-log-cabinet", "sphinx-issues"]
 dotenv = ["python-dotenv"]
+docs = ["sphinx", "pallets-sphinx-themes", "sphinxcontrib-log-cabinet", "sphinx-issues"]
+dev = ["pytest", "coverage", "tox", "sphinx", "pallets-sphinx-themes", "sphinxcontrib-log-cabinet", "sphinx-issues"]
 
 [[package]]
 name = "flask-cors"
@@ -235,7 +235,7 @@ Six = "*"
 
 [[package]]
 name = "freezegun"
-version = "1.0.0"
+version = "1.1.0"
 description = "Let your Python tests travel through time"
 category = "dev"
 optional = false
@@ -278,7 +278,7 @@ python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
 
 [[package]]
 name = "importlib-metadata"
-version = "3.3.0"
+version = "3.4.0"
 description = "Read metadata from Python packages"
 category = "main"
 optional = false
@@ -289,8 +289,8 @@ typing-extensions = {version = ">=3.6.4", markers = "python_version < \"3.8\""}
 zipp = ">=0.5"
 
 [package.extras]
-docs = ["sphinx", "jaraco.packaging (>=3.2)", "rst.linker (>=1.9)"]
-testing = ["pytest (>=3.5,!=3.7.3)", "pytest-checkdocs (>=1.2.3)", "pytest-flake8", "pytest-cov", "jaraco.test (>=3.2.0)", "packaging", "pep517", "pyfakefs", "flufl.flake8", "pytest-black (>=0.3.7)", "pytest-mypy", "importlib-resources (>=1.3)"]
+docs = ["sphinx", "jaraco.packaging (>=8.2)", "rst.linker (>=1.9)"]
+testing = ["pytest (>=3.5,!=3.7.3)", "pytest-checkdocs (>=1.2.3)", "pytest-flake8", "pytest-cov", "pytest-enabler", "packaging", "pep517", "pyfakefs", "flufl.flake8", "pytest-black (>=0.3.7)", "pytest-mypy", "importlib-resources (>=1.3)"]
 
 [[package]]
 name = "iniconfig"
@@ -309,9 +309,9 @@ optional = false
 python-versions = ">=3.6,<4.0"
 
 [package.extras]
+colors = ["colorama (>=0.4.3,<0.5.0)"]
 pipfile_deprecated_finder = ["pipreqs", "requirementslib"]
 requirements_deprecated_finder = ["pipreqs", "pip-api"]
-colors = ["colorama (>=0.4.3,<0.5.0)"]
 
 [[package]]
 name = "itsdangerous"
@@ -323,7 +323,7 @@ python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
 
 [[package]]
 name = "jinja2"
-version = "2.11.2"
+version = "2.11.3"
 description = "A very fast and expressive template engine."
 category = "main"
 optional = false
@@ -344,13 +344,13 @@ optional = false
 python-versions = ">=3.6,<4.0"
 
 [package.dependencies]
-apispec = ">=3.2,<5.0"
 apispec_webframeworks = ">=0.5.2,<0.6.0"
-Flask = ">=1.1.1,<2.0.0"
-flask-cors = ">=3.0.8,<4.0.0"
-marshmallow = ">=3.4.0,<4.0.0"
 webargs = ">=6,<8"
+marshmallow = ">=3.4.0,<4.0.0"
+Flask = ">=1.1.1,<2.0.0"
+apispec = ">=3.2,<5.0"
 zeroconf = ">=0.24.5,<0.29.0"
+flask-cors = ">=3.0.8,<4.0.0"
 
 [[package]]
 name = "lazy-object-proxy"
@@ -369,10 +369,10 @@ optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, != 3.4.*"
 
 [package.extras]
+source = ["Cython (>=0.29.7)"]
 cssselect = ["cssselect (>=0.7)"]
 html5 = ["html5lib"]
 htmlsoup = ["beautifulsoup4"]
-source = ["Cython (>=0.29.7)"]
 
 [[package]]
 name = "markupsafe"
@@ -391,10 +391,10 @@ optional = false
 python-versions = ">=3.5"
 
 [package.extras]
-dev = ["pytest", "pytz", "simplejson", "mypy (==0.790)", "flake8 (==3.8.4)", "flake8-bugbear (==20.11.1)", "pre-commit (>=2.4,<3.0)", "tox"]
 docs = ["sphinx (==3.3.1)", "sphinx-issues (==1.2.0)", "alabaster (==0.7.12)", "sphinx-version-warning (==1.1.2)", "autodocsumm (==0.2.2)"]
-lint = ["mypy (==0.790)", "flake8 (==3.8.4)", "flake8-bugbear (==20.11.1)", "pre-commit (>=2.4,<3.0)"]
 tests = ["pytest", "pytz", "simplejson"]
+lint = ["mypy (==0.790)", "flake8 (==3.8.4)", "flake8-bugbear (==20.11.1)", "pre-commit (>=2.4,<3.0)"]
+dev = ["pytest", "pytz", "simplejson", "mypy (==0.790)", "flake8 (==3.8.4)", "flake8-bugbear (==20.11.1)", "pre-commit (>=2.4,<3.0)", "tox"]
 
 [[package]]
 name = "mccabe"
@@ -439,15 +439,15 @@ python-versions = ">=3.6"
 [[package]]
 name = "numpy-stubs"
 version = "0.0.1"
-description = ""
+description = "PEP 561 type stubs for numpy"
 category = "main"
 optional = false
 python-versions = "*"
 develop = false
 
 [package.dependencies]
+typing-extensions = {version = ">=3.7.4", markers = "python_version < \"3.8\""}
 numpy = ">=1.16.0"
-typing_extensions = {version = ">=3.7.4", markers = "python_version < \"3.8\""}
 
 [package.source]
 type = "git"
@@ -463,12 +463,9 @@ category = "main"
 optional = false
 python-versions = ">=3.6"
 
-[package.dependencies]
-numpy = ">=1.17.3"
-
 [[package]]
 name = "packaging"
-version = "20.8"
+version = "20.9"
 description = "Core utilities for Python packages"
 category = "main"
 optional = false
@@ -497,9 +494,9 @@ python-versions = "*"
 colorzero = "*"
 
 [package.extras]
-array = ["numpy"]
-doc = ["sphinx"]
 test = ["coverage", "pytest", "mock", "pillow", "numpy"]
+doc = ["sphinx"]
+array = ["numpy"]
 
 [[package]]
 name = "piexif"
@@ -564,7 +561,7 @@ python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
 
 [[package]]
 name = "pygments"
-version = "2.7.3"
+version = "2.7.4"
 description = "Pygments is a syntax highlighting package written in Python."
 category = "dev"
 optional = false
@@ -580,10 +577,10 @@ python-versions = ">=3.5.*"
 
 [package.dependencies]
 astroid = ">=2.4.0,<=2.5"
-colorama = {version = "*", markers = "sys_platform == \"win32\""}
-isort = ">=4.2.5,<6"
 mccabe = ">=0.6,<0.7"
+colorama = {version = "*", markers = "sys_platform == \"win32\""}
 toml = ">=0.7.1"
+isort = ">=4.2.5,<6"
 
 [[package]]
 name = "pyparsing"
@@ -606,37 +603,37 @@ cp2110 = ["hidapi"]
 
 [[package]]
 name = "pytest"
-version = "6.2.1"
+version = "6.2.2"
 description = "pytest: simple powerful testing with Python"
 category = "main"
 optional = false
 python-versions = ">=3.6"
 
 [package.dependencies]
-atomicwrites = {version = ">=1.0", markers = "sys_platform == \"win32\""}
-attrs = ">=19.2.0"
-colorama = {version = "*", markers = "sys_platform == \"win32\""}
-importlib-metadata = {version = ">=0.12", markers = "python_version < \"3.8\""}
-iniconfig = "*"
 packaging = "*"
-pluggy = ">=0.12,<1.0.0a1"
 py = ">=1.8.2"
+iniconfig = "*"
+importlib-metadata = {version = ">=0.12", markers = "python_version < \"3.8\""}
+colorama = {version = "*", markers = "sys_platform == \"win32\""}
+attrs = ">=19.2.0"
 toml = "*"
+pluggy = ">=0.12,<1.0.0a1"
+atomicwrites = {version = ">=1.0", markers = "sys_platform == \"win32\""}
 
 [package.extras]
 testing = ["argcomplete", "hypothesis (>=3.56)", "mock", "nose", "requests", "xmlschema"]
 
 [[package]]
 name = "pytest-cov"
-version = "2.10.1"
+version = "2.11.1"
 description = "Pytest plugin for measuring coverage."
 category = "main"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*"
 
 [package.dependencies]
-coverage = ">=4.4"
 pytest = ">=4.6"
+coverage = ">=5.2.1"
 
 [package.extras]
 testing = ["fields", "hunter", "process-tests (==2.0.2)", "six", "pytest-xdist", "virtualenv"]
@@ -654,7 +651,7 @@ six = ">=1.5"
 
 [[package]]
 name = "pytz"
-version = "2020.5"
+version = "2021.1"
 description = "World timezone definitions, modern and historical"
 category = "dev"
 optional = false
@@ -662,11 +659,11 @@ python-versions = "*"
 
 [[package]]
 name = "pyyaml"
-version = "5.3.1"
+version = "5.4.1"
 description = "YAML parser and emitter for Python"
 category = "main"
 optional = false
-python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*"
+python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, !=3.5.*"
 
 [[package]]
 name = "requests"
@@ -677,9 +674,9 @@ optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*"
 
 [package.dependencies]
+idna = ">=2.5,<3"
 certifi = ">=2017.4.17"
 chardet = ">=3.0.2,<5"
-idna = ">=2.5,<3"
 urllib3 = ">=1.21.1,<1.27"
 
 [package.extras]
@@ -736,8 +733,8 @@ python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*"
 
 [[package]]
 name = "snowballstemmer"
-version = "2.0.0"
-description = "This package provides 26 stemmers for 25 languages generated from Snowball algorithms."
+version = "2.1.0"
+description = "This package provides 29 stemmers for 28 languages generated from Snowball algorithms."
 category = "dev"
 optional = false
 python-versions = "*"
@@ -751,27 +748,27 @@ optional = false
 python-versions = ">=3.5"
 
 [package.dependencies]
-alabaster = ">=0.7,<0.8"
-babel = ">=1.3"
-colorama = {version = ">=0.3.5", markers = "sys_platform == \"win32\""}
-docutils = ">=0.12"
+sphinxcontrib-qthelp = "*"
 imagesize = "*"
-Jinja2 = ">=2.3"
-packaging = "*"
-Pygments = ">=2.0"
-requests = ">=2.5.0"
-snowballstemmer = ">=1.1"
-sphinxcontrib-applehelp = "*"
 sphinxcontrib-devhelp = "*"
+snowballstemmer = ">=1.1"
+babel = ">=1.3"
+alabaster = ">=0.7,<0.8"
+sphinxcontrib-serializinghtml = "*"
+packaging = "*"
+docutils = ">=0.12"
+Pygments = ">=2.0"
+Jinja2 = ">=2.3"
+colorama = {version = ">=0.3.5", markers = "sys_platform == \"win32\""}
+requests = ">=2.5.0"
+sphinxcontrib-applehelp = "*"
 sphinxcontrib-htmlhelp = "*"
 sphinxcontrib-jsmath = "*"
-sphinxcontrib-qthelp = "*"
-sphinxcontrib-serializinghtml = "*"
 
 [package.extras]
+test = ["pytest", "pytest-cov", "html5lib", "cython", "typed-ast"]
 docs = ["sphinxcontrib-websupport"]
 lint = ["flake8 (>=3.5.0)", "isort", "mypy (>=0.790)", "docutils-stubs"]
-test = ["pytest", "pytest-cov", "html5lib", "cython", "typed-ast"]
 
 [[package]]
 name = "sphinxcontrib-applehelp"
@@ -782,8 +779,8 @@ optional = false
 python-versions = ">=3.5"
 
 [package.extras]
-lint = ["flake8", "mypy", "docutils-stubs"]
 test = ["pytest"]
+lint = ["flake8", "mypy", "docutils-stubs"]
 
 [[package]]
 name = "sphinxcontrib-devhelp"
@@ -794,8 +791,8 @@ optional = false
 python-versions = ">=3.5"
 
 [package.extras]
-lint = ["flake8", "mypy", "docutils-stubs"]
 test = ["pytest"]
+lint = ["flake8", "mypy", "docutils-stubs"]
 
 [[package]]
 name = "sphinxcontrib-htmlhelp"
@@ -806,8 +803,8 @@ optional = false
 python-versions = ">=3.5"
 
 [package.extras]
-lint = ["flake8", "mypy", "docutils-stubs"]
 test = ["pytest", "html5lib"]
+lint = ["flake8", "mypy", "docutils-stubs"]
 
 [[package]]
 name = "sphinxcontrib-httpdomain"
@@ -841,8 +838,8 @@ optional = false
 python-versions = ">=3.5"
 
 [package.extras]
-lint = ["flake8", "mypy", "docutils-stubs"]
 test = ["pytest"]
+lint = ["flake8", "mypy", "docutils-stubs"]
 
 [[package]]
 name = "sphinxcontrib-serializinghtml"
@@ -853,8 +850,8 @@ optional = false
 python-versions = ">=3.5"
 
 [package.extras]
-lint = ["flake8", "mypy", "docutils-stubs"]
 test = ["pytest"]
+lint = ["flake8", "mypy", "docutils-stubs"]
 
 [[package]]
 name = "toml"
@@ -890,7 +887,7 @@ python-versions = "*"
 
 [[package]]
 name = "urllib3"
-version = "1.26.2"
+version = "1.26.3"
 description = "HTTP library with thread-safe connection pooling, file post, and more."
 category = "dev"
 optional = false
@@ -913,11 +910,11 @@ python-versions = ">=3.6"
 marshmallow = ">=3.0.0"
 
 [package.extras]
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+lint = ["mypy (==0.790)", "flake8 (==3.8.4)", "flake8-bugbear (==20.11.1)", "pre-commit (>=2.4,<3.0)"]
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 [[package]]
 name = "werkzeug"
@@ -928,8 +925,8 @@ optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*"
 
 [package.extras]
-dev = ["pytest", "pytest-timeout", "coverage", "tox", "sphinx", "pallets-sphinx-themes", "sphinx-issues"]
 watchdog = ["watchdog"]
+dev = ["pytest", "pytest-timeout", "coverage", "tox", "sphinx", "pallets-sphinx-themes", "sphinx-issues"]
 
 [[package]]
 name = "wrapt"
@@ -968,7 +965,7 @@ rpi = ["RPi.GPIO"]
 [metadata]
 lock-version = "1.1"
 python-versions = "^3.7.3"
-content-hash = "57a3c3fcab4e72f4ff6f37b461967e9c60903baa9f879842c93305069165513c"
+content-hash = "701b37eec89567411e3263227a4f23a3372c09feb511cfe491fb0e1cbe14b555"
 
 [metadata.files]
 alabaster = [
@@ -976,8 +973,8 @@ alabaster = [
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+    {file = "Pygments-2.7.4.tar.gz", hash = "sha256:df49d09b498e83c1a73128295860250b0b7edd4c723a32e9bc0d295c7c2ec337"},
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@@ -1417,33 +1433,43 @@ pyserial = [
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 ]
 pytest = [
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+    {file = "pytest-6.2.2-py3-none-any.whl", hash = "sha256:b574b57423e818210672e07ca1fa90aaf194a4f63f3ab909a2c67ebb22913839"},
+    {file = "pytest-6.2.2.tar.gz", hash = "sha256:9d1edf9e7d0b84d72ea3dbcdfd22b35fb543a5e8f2a60092dd578936bf63d7f9"},
 ]
 pytest-cov = [
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+    {file = "pytest-cov-2.11.1.tar.gz", hash = "sha256:359952d9d39b9f822d9d29324483e7ba04a3a17dd7d05aa6beb7ea01e359e5f7"},
+    {file = "pytest_cov-2.11.1-py2.py3-none-any.whl", hash = "sha256:bdb9fdb0b85a7cc825269a4c56b48ccaa5c7e365054b6038772c32ddcdc969da"},
 ]
 python-dateutil = [
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 ]
 pytz = [
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-    {file = "pytz-2020.5.tar.gz", hash = "sha256:180befebb1927b16f6b57101720075a984c019ac16b1b7575673bea42c6c3da5"},
+    {file = "pytz-2021.1-py2.py3-none-any.whl", hash = "sha256:eb10ce3e7736052ed3623d49975ce333bcd712c7bb19a58b9e2089d4057d0798"},
+    {file = "pytz-2021.1.tar.gz", hash = "sha256:83a4a90894bf38e243cf052c8b58f381bfe9a7a483f6a9cab140bc7f702ac4da"},
 ]
 pyyaml = [
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-    {file = "PyYAML-5.3.1.tar.gz", hash = "sha256:b8eac752c5e14d3eca0e6dd9199cd627518cb5ec06add0de9d32baeee6fe645d"},
+    {file = "PyYAML-5.4.1-cp27-cp27m-macosx_10_9_x86_64.whl", hash = "sha256:3b2b1824fe7112845700f815ff6a489360226a5609b96ec2190a45e62a9fc922"},
+    {file = "PyYAML-5.4.1-cp27-cp27m-win32.whl", hash = "sha256:129def1b7c1bf22faffd67b8f3724645203b79d8f4cc81f674654d9902cb4393"},
+    {file = "PyYAML-5.4.1-cp27-cp27m-win_amd64.whl", hash = "sha256:4465124ef1b18d9ace298060f4eccc64b0850899ac4ac53294547536533800c8"},
+    {file = "PyYAML-5.4.1-cp27-cp27mu-manylinux1_x86_64.whl", hash = "sha256:bb4191dfc9306777bc594117aee052446b3fa88737cd13b7188d0e7aa8162185"},
+    {file = "PyYAML-5.4.1-cp36-cp36m-macosx_10_9_x86_64.whl", hash = "sha256:6c78645d400265a062508ae399b60b8c167bf003db364ecb26dcab2bda048253"},
+    {file = "PyYAML-5.4.1-cp36-cp36m-manylinux1_x86_64.whl", hash = "sha256:4e0583d24c881e14342eaf4ec5fbc97f934b999a6828693a99157fde912540cc"},
+    {file = "PyYAML-5.4.1-cp36-cp36m-win32.whl", hash = "sha256:3bd0e463264cf257d1ffd2e40223b197271046d09dadf73a0fe82b9c1fc385a5"},
+    {file = "PyYAML-5.4.1-cp36-cp36m-win_amd64.whl", hash = "sha256:e4fac90784481d221a8e4b1162afa7c47ed953be40d31ab4629ae917510051df"},
+    {file = "PyYAML-5.4.1-cp37-cp37m-macosx_10_9_x86_64.whl", hash = "sha256:5accb17103e43963b80e6f837831f38d314a0495500067cb25afab2e8d7a4018"},
+    {file = "PyYAML-5.4.1-cp37-cp37m-manylinux1_x86_64.whl", hash = "sha256:e1d4970ea66be07ae37a3c2e48b5ec63f7ba6804bdddfdbd3cfd954d25a82e63"},
+    {file = "PyYAML-5.4.1-cp37-cp37m-win32.whl", hash = "sha256:dd5de0646207f053eb0d6c74ae45ba98c3395a571a2891858e87df7c9b9bd51b"},
+    {file = "PyYAML-5.4.1-cp37-cp37m-win_amd64.whl", hash = "sha256:08682f6b72c722394747bddaf0aa62277e02557c0fd1c42cb853016a38f8dedf"},
+    {file = "PyYAML-5.4.1-cp38-cp38-macosx_10_9_x86_64.whl", hash = "sha256:d2d9808ea7b4af864f35ea216be506ecec180628aced0704e34aca0b040ffe46"},
+    {file = "PyYAML-5.4.1-cp38-cp38-manylinux1_x86_64.whl", hash = "sha256:8c1be557ee92a20f184922c7b6424e8ab6691788e6d86137c5d93c1a6ec1b8fb"},
+    {file = "PyYAML-5.4.1-cp38-cp38-win32.whl", hash = "sha256:fa5ae20527d8e831e8230cbffd9f8fe952815b2b7dae6ffec25318803a7528fc"},
+    {file = "PyYAML-5.4.1-cp38-cp38-win_amd64.whl", hash = "sha256:0f5f5786c0e09baddcd8b4b45f20a7b5d61a7e7e99846e3c799b05c7c53fa696"},
+    {file = "PyYAML-5.4.1-cp39-cp39-macosx_10_9_x86_64.whl", hash = "sha256:294db365efa064d00b8d1ef65d8ea2c3426ac366c0c4368d930bf1c5fb497f77"},
+    {file = "PyYAML-5.4.1-cp39-cp39-manylinux1_x86_64.whl", hash = "sha256:74c1485f7707cf707a7aef42ef6322b8f97921bd89be2ab6317fd782c2d53183"},
+    {file = "PyYAML-5.4.1-cp39-cp39-win32.whl", hash = "sha256:49d4cdd9065b9b6e206d0595fee27a96b5dd22618e7520c33204a4a3239d5b10"},
+    {file = "PyYAML-5.4.1-cp39-cp39-win_amd64.whl", hash = "sha256:c20cfa2d49991c8b4147af39859b167664f2ad4561704ee74c1de03318e898db"},
+    {file = "PyYAML-5.4.1.tar.gz", hash = "sha256:607774cbba28732bfa802b54baa7484215f530991055bb562efbed5b2f20a45e"},
 ]
 requests = [
     {file = "requests-2.25.1-py2.py3-none-any.whl", hash = "sha256:c210084e36a42ae6b9219e00e48287def368a26d03a048ddad7bfee44f75871e"},
@@ -1487,8 +1513,8 @@ six = [
     {file = "six-1.15.0.tar.gz", hash = "sha256:30639c035cdb23534cd4aa2dd52c3bf48f06e5f4a941509c8bafd8ce11080259"},
 ]
 snowballstemmer = [
-    {file = "snowballstemmer-2.0.0-py2.py3-none-any.whl", hash = "sha256:209f257d7533fdb3cb73bdbd24f436239ca3b2fa67d56f6ff88e86be08cc5ef0"},
-    {file = "snowballstemmer-2.0.0.tar.gz", hash = "sha256:df3bac3df4c2c01363f3dd2cfa78cce2840a79b9f1c2d2de9ce8d31683992f52"},
+    {file = "snowballstemmer-2.1.0-py2.py3-none-any.whl", hash = "sha256:b51b447bea85f9968c13b650126a888aabd4cb4463fca868ec596826325dedc2"},
+    {file = "snowballstemmer-2.1.0.tar.gz", hash = "sha256:e997baa4f2e9139951b6f4c631bad912dfd3c792467e2f03d7239464af90e914"},
 ]
 sphinx = [
     {file = "Sphinx-3.4.3-py3-none-any.whl", hash = "sha256:c314c857e7cd47c856d2c5adff514ac2e6495f8b8e0f886a8a37e9305dfea0d8"},
@@ -1568,8 +1594,8 @@ typing-extensions = [
     {file = "typing_extensions-3.7.4.3.tar.gz", hash = "sha256:99d4073b617d30288f569d3f13d2bd7548c3a7e4c8de87db09a9d29bb3a4a60c"},
 ]
 urllib3 = [
-    {file = "urllib3-1.26.2-py2.py3-none-any.whl", hash = "sha256:d8ff90d979214d7b4f8ce956e80f4028fc6860e4431f731ea4a8c08f23f99473"},
-    {file = "urllib3-1.26.2.tar.gz", hash = "sha256:19188f96923873c92ccb987120ec4acaa12f0461fa9ce5d3d0772bc965a39e08"},
+    {file = "urllib3-1.26.3-py2.py3-none-any.whl", hash = "sha256:1b465e494e3e0d8939b50680403e3aedaa2bc434b7d5af64dfd3c958d7f5ae80"},
+    {file = "urllib3-1.26.3.tar.gz", hash = "sha256:de3eedaad74a2683334e282005cd8d7f22f4d55fa690a2a1020a416cb0a47e73"},
 ]
 webargs = [
     {file = "webargs-7.0.1-py2.py3-none-any.whl", hash = "sha256:ce8c565789ece1584be7edba41617319eb75de59b2987958bee3f3fdb3669e60"},

From 0f1a4009795b9b56d86ee9d0a244c0ebac41ba0b Mon Sep 17 00:00:00 2001
From: Richard Bowman <richard.bowman@cantab.net>
Date: Mon, 15 Feb 2021 17:04:44 +0000
Subject: [PATCH 07/41] Fixed type hint

---
 .../picamera_autocalibrate/recalibrate_utils.py                 | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/openflexure_microscope/api/default_extensions/picamera_autocalibrate/recalibrate_utils.py b/openflexure_microscope/api/default_extensions/picamera_autocalibrate/recalibrate_utils.py
index 788d856d..1f804b2c 100644
--- a/openflexure_microscope/api/default_extensions/picamera_autocalibrate/recalibrate_utils.py
+++ b/openflexure_microscope/api/default_extensions/picamera_autocalibrate/recalibrate_utils.py
@@ -221,7 +221,7 @@ def adjust_shutter_and_gain_from_raw(
 
 def adjust_white_balance_from_raw(
     camera: PiCamera, percentile: float = 99
-) -> (float, float):
+) -> Tuple[float, float]:
     """Adjust the white balance in a single shot, based on the raw image.
     
     NB if ``channels_from_raw_image`` is broken, this will go haywire.

From 2f6049610f3c5152c3cd2dd6af5101f7f31c2568 Mon Sep 17 00:00:00 2001
From: Richard Bowman <richard.bowman@cantab.net>
Date: Mon, 15 Feb 2021 17:50:39 +0000
Subject: [PATCH 08/41] Added controls for AWB gains,

I also increased the precision of the numbers, which makes the step
buttons annoyingly useless but allows floating point
values without validation errors.
---
 .../settingsComponents/cameraSettings.vue     | 38 ++++++++++++++++---
 1 file changed, 33 insertions(+), 5 deletions(-)

diff --git a/openflexure_microscope/api/static/src/components/tabContentComponents/settingsComponents/cameraSettings.vue b/openflexure_microscope/api/static/src/components/tabContentComponents/settingsComponents/cameraSettings.vue
index 8e37a0b9..67c1fdda 100644
--- a/openflexure_microscope/api/static/src/components/tabContentComponents/settingsComponents/cameraSettings.vue
+++ b/openflexure_microscope/api/static/src/components/tabContentComponents/settingsComponents/cameraSettings.vue
@@ -3,7 +3,7 @@
     <div class="uk-grid uk-grid-divider uk-child-width-expand" uk-grid>
       <div class="uk-width-large">
         <h3>Manual camera settings</h3>
-        <form @submit.prevent="applySettingsRequest">
+        <form @submit.prevent="applySettingsRequest" >
           <div class="uk-margin-small-bottom">
             <ul uk-accordion="multiple: true">
               <li class="uk-open">
@@ -31,7 +31,7 @@
                         v-model="picamera.analog_gain"
                         class="uk-input uk-form-small"
                         type="number"
-                        step="0.000001"
+                        step="0.0000000000000001"
                       />
                     </div>
                   </div>
@@ -45,7 +45,29 @@
                         v-model="picamera.digital_gain"
                         class="uk-input uk-form-small"
                         type="number"
-                        step="0.000001"
+                        step="0.0000000000000001"
+                      />
+                    </div>
+                  </div>
+
+                  <div v-if="picamera.awb_gains !== undefined">
+                    <label class="uk-form-label" for="form-stacked-text" >
+                      White Balance gains
+                    </label>
+                    <div class="uk-form-controls">
+                      <label class="uk-form-label" >R:</label>
+                      <input
+                        v-model="picamera.awb_gains[0]"
+                        class="uk-input uk-form-small"
+                        type="number"
+                        step="0.0000000000000001"
+                      />
+                      <label class="uk-form-label" >B:</label>
+                      <input
+                        v-model="picamera.awb_gains[1]"
+                        class="uk-input uk-form-small"
+                        type="number"
+                        step="0.0000000000000001"
                       />
                     </div>
                   </div>
@@ -194,7 +216,8 @@ export default {
         shutter_speed: undefined,
         analog_gain: undefined,
         digital_gain: undefined,
-        framerate: undefined
+        framerate: undefined,
+        awb_gains: undefined
       },
       mjpeg_bitrate: undefined,
       stream_resolution: undefined,
@@ -244,6 +267,7 @@ export default {
             this.picamera.digital_gain = cameraSettings.picamera.digital_gain;
             this.picamera.shutter_speed = cameraSettings.picamera.shutter_speed;
             this.picamera.framerate = cameraSettings.picamera.framerate;
+            this.picamera.awb_gains = cameraSettings.picamera.awb_gains;
           }
         })
         .catch(error => {
@@ -263,7 +287,11 @@ export default {
             shutter_speed: parseFloat(this.picamera.shutter_speed),
             analog_gain: parseFloat(this.picamera.analog_gain),
             digital_gain: parseFloat(this.picamera.digital_gain),
-            framerate: parseInt(this.picamera.framerate)
+            framerate: parseInt(this.picamera.framerate),
+            awb_gains: [
+              parseFloat(this.picamera.awb_gains[0]),
+              parseFloat(this.picamera.awb_gains[1]),
+            ],
           }
         }
       };

From 36284c10bebc2576a1c3e7bb5897035fc0dc97c1 Mon Sep 17 00:00:00 2001
From: Richard Bowman <richard.bowman@cantab.net>
Date: Mon, 15 Feb 2021 19:17:20 +0000
Subject: [PATCH 09/41] UI Improvements

I've added buttons to perform the separate calibrations (gain, AWB)
under the full recalibrate link.
It would be really nice to have a modal dialog though.
---
 .../cameraCalibrationSettings.vue             | 32 +++++++++++++------
 1 file changed, 23 insertions(+), 9 deletions(-)

diff --git a/openflexure_microscope/api/static/src/components/tabContentComponents/settingsComponents/cameraSettingsComponents/cameraCalibrationSettings.vue b/openflexure_microscope/api/static/src/components/tabContentComponents/settingsComponents/cameraSettingsComponents/cameraCalibrationSettings.vue
index e6f3c8d8..09e38e15 100644
--- a/openflexure_microscope/api/static/src/components/tabContentComponents/settingsComponents/cameraSettingsComponents/cameraCalibrationSettings.vue
+++ b/openflexure_microscope/api/static/src/components/tabContentComponents/settingsComponents/cameraSettingsComponents/cameraCalibrationSettings.vue
@@ -9,7 +9,29 @@
           'Start recalibration? This may take a while, and the microscope will be locked during this time.'
         "
         :submit-url="recalibrationLinks.recalibrate.href"
-        :submit-label="'Auto-Calibrate'"
+        :submit-label="'Full Auto-Calibrate'"
+        @response="onRecalibrateResponse"
+        @error="modalError"
+      >
+      </taskSubmitter>
+    </div>
+    <div v-if="'auto_exposure_from_raw' in recalibrationLinks" class="uk-margin-small">
+      <taskSubmitter
+        :can-terminate="false"
+        :requires-confirmation="false"
+        :submit-url="recalibrationLinks.auto_exposure_from_raw.href"
+        :submit-label="'Auto gain &amp; shutter speed'"
+        @response="onRecalibrateResponse"
+        @error="modalError"
+      >
+      </taskSubmitter>
+    </div>
+    <div v-if="'auto_white_balance_from_raw' in recalibrationLinks" class="uk-margin-small">
+      <taskSubmitter
+        :can-terminate="false"
+        :requires-confirmation="false"
+        :submit-url="recalibrationLinks.auto_white_balance_from_raw.href"
+        :submit-label="'Auto white balance'"
         @response="onRecalibrateResponse"
         @error="modalError"
       >
@@ -24,14 +46,6 @@
       >
         Disable flat-field correction
       </button>
-
-      <button
-        v-if="'delete_lens_shading_table' in recalibrationLinks"
-        class="uk-button uk-button-danger uk-margin-small-top uk-width-1-1"
-        @click="deleteLensShadingTableRequest"
-      >
-        Adaptive flat-field correction
-      </button>
     </div>
 
     <div v-if="LstDownloadEnabled">

From a9709b14eaacfd1c947ce359071bf39234145643 Mon Sep 17 00:00:00 2001
From: Richard Bowman <richard.bowman@cantab.net>
Date: Mon, 15 Feb 2021 19:21:27 +0000
Subject: [PATCH 10/41] Added locking to recalibrate functions

When testing the UI I noticed that the different recalibrate routines
don't use locks properly, so they try to run
concurrently.

This commit isn't tested yet...
---
 .../picamera_autocalibrate/extension.py       | 25 +++++++++++--------
 1 file changed, 14 insertions(+), 11 deletions(-)

diff --git a/openflexure_microscope/api/default_extensions/picamera_autocalibrate/extension.py b/openflexure_microscope/api/default_extensions/picamera_autocalibrate/extension.py
index 1f8caf88..5ff1a4dc 100644
--- a/openflexure_microscope/api/default_extensions/picamera_autocalibrate/extension.py
+++ b/openflexure_microscope/api/default_extensions/picamera_autocalibrate/extension.py
@@ -117,13 +117,14 @@ class RecalibrateView(ActionView):
         microscope = find_microscope()
         logging.info("Starting microscope recalibration...")
         picamera = microscope.camera.picamera
-        if not args.get("skip_auto_exposure"):
-            adjust_shutter_and_gain_from_raw(picamera)
-            adjust_white_balance_from_raw(picamera)
-        lst = lst_from_camera(picamera)
-        with pause_stream(microscope.camera) as scamera:
-            scamera.picamera.lens_shading_table = lst
-        microscope.save_settings()
+        with microscope.camera.lock:
+            if not args.get("skip_auto_exposure"):
+                adjust_shutter_and_gain_from_raw(picamera)
+                adjust_white_balance_from_raw(picamera)
+            lst = lst_from_camera(picamera)
+            with pause_stream(microscope.camera) as scamera:
+                scamera.picamera.lens_shading_table = lst
+            microscope.save_settings()
 
 
 class FlattenLSTView(ActionView):
@@ -179,10 +180,12 @@ class AutoExposureFromRawView(ActionView):
     }
 
     def post(self, args):
-        camera = find_component("org.openflexure.microscope").camera.picamera
-        adjust_shutter_and_gain_from_raw(
-            camera, **args  # I'm relying on the schema to fill in missing values
-        )
+        camera = find_component("org.openflexure.microscope").camera
+
+        with camera.lock:
+            adjust_shutter_and_gain_from_raw(
+                camera.picamera, **args  # I'm relying on the schema to fill in missing values
+            )
 
 
 class AutoWhiteBalanceFromRawView(ActionView):

From 069d27bf153779cdc7ffd73006af1e1063285ce4 Mon Sep 17 00:00:00 2001
From: Richard Bowman <richard.bowman@cantab.net>
Date: Mon, 15 Feb 2021 20:15:55 +0000
Subject: [PATCH 11/41] Lock access to picamera

The picamera object isn't thread safe; I have now wrapped all access
in context managers that acquire the BaseCamera.lock

I also added an endpoint to reset the LST without auto-gain.
---
 .../picamera_autocalibrate/extension.py       | 108 +++++++++++-------
 1 file changed, 64 insertions(+), 44 deletions(-)

diff --git a/openflexure_microscope/api/default_extensions/picamera_autocalibrate/extension.py b/openflexure_microscope/api/default_extensions/picamera_autocalibrate/extension.py
index 5ff1a4dc..bdb0022b 100644
--- a/openflexure_microscope/api/default_extensions/picamera_autocalibrate/extension.py
+++ b/openflexure_microscope/api/default_extensions/picamera_autocalibrate/extension.py
@@ -6,6 +6,8 @@ from flask import abort
 from labthings import find_component
 from labthings.extensions import BaseExtension
 from labthings.views import ActionView
+from picamerax import PiCamera
+from typing import Tuple
 
 from openflexure_microscope.camera.base import BaseCamera
 from openflexure_microscope.microscope import Microscope
@@ -78,9 +80,14 @@ class LSTExtension(BaseExtension):
             "/auto_white_balance_from_raw",
             endpoint="auto_white_balance_from_raw",
         )
+        self.add_view(
+            AutoLensShadingTableView,
+            "/auto_lens_shading_table",
+            endpoint="auto_lens_shading_table",
+        )
 
-
-def find_microscope() -> Microscope:
+@contextmanager
+def find_picamera() -> Tuple[PiCamera, BaseCamera, Microscope]:
     """Locate the microscope and raise a sensible error if it's missing."""
     microscope = find_component("org.openflexure.microscope")
 
@@ -89,23 +96,17 @@ def find_microscope() -> Microscope:
             503, "No microscope connected. Unable to use camera calibration functions."
         )
 
-    if not hasattr(microscope.camera, "picamera"):
+    scamera = microscope.camera
+
+    if not hasattr(scamera, "picamera"):
         abort(503, "The PiCamera calibration plugin requires a Raspberry Pi camera.")
 
-    return microscope
+    with scamera.lock:
+        yield scamera.picamera, scamera, microscope
 
 
 class RecalibrateView(ActionView):
-    args = {
-        "skip_auto_exposure": fields.Bool(
-            missing=False,
-            description=(
-                "By default we perform an auto-exposure and AWB "
-                "step before updating the lens shading table.  Set "
-                "this argument to True to disable those steps."
-            ),
-        )
-    }
+    args = {}
 
     def post(self, args):
         """Reset the camera's settings.
@@ -113,35 +114,60 @@ class RecalibrateView(ActionView):
         This generates new gains, exposure time, and lens shading
         table such that the background is as uniform as possible
         with a gray level of 230.  It takes a little while to run.
+
+        This consists of three steps:
+
+        * Reset gain and exposure time, then increase them until
+          we have a suitably bright image
+        * Set the auto white balance based on a raw image
+        * Set the lens shading table based on a raw image
+
+        Each of these steps has its own endpoint if you want to
+        perform them separately.
         """
-        microscope = find_microscope()
-        logging.info("Starting microscope recalibration...")
-        picamera = microscope.camera.picamera
-        with microscope.camera.lock:
-            if not args.get("skip_auto_exposure"):
-                adjust_shutter_and_gain_from_raw(picamera)
-                adjust_white_balance_from_raw(picamera)
+        with find_picamera() as (picamera, scamera, microscope):
+            logging.info("Starting microscope recalibration...")
+            adjust_shutter_and_gain_from_raw(picamera)
+            adjust_white_balance_from_raw(picamera)
             lst = lst_from_camera(picamera)
-            with pause_stream(microscope.camera) as scamera:
-                scamera.picamera.lens_shading_table = lst
+            with pause_stream(scamera):
+                picamera.lens_shading_table = lst
             microscope.save_settings()
 
+class AutoLensShadingTableView(ActionView):
+    args = {}
+
+    def post(self, args):
+        """Perform flat-field correction
+
+        This routine acquires a new image (which should be an
+        empty field of view, i.e. a perfect microscope would
+        record a uniform white image), and then uses it to set
+        the "lens shading table" such that future images will
+        be corrected for vignetting.
+        """
+        with find_picamera() as (picamera, scamera, microscope):
+            logging.info("Generating lens shading table")
+            lst = lst_from_camera(picamera)
+            with pause_stream(scamera):
+                picamera.lens_shading_table = lst
+            microscope.save_settings()
 
 class FlattenLSTView(ActionView):
     def post(self):
-        microscope = find_microscope()
-        with pause_stream(microscope.camera) as scamera:
-            flat_lst = flat_lens_shading_table(scamera.camera)
-            scamera.camera.lens_shading_table = flat_lst
-        microscope.save_settings()
+        with find_picamera() as (picamera, scamera, microscope):
+            with pause_stream(scamera):
+                flat_lst = flat_lens_shading_table(picamera)
+                picamera.lens_shading_table = flat_lst
+            microscope.save_settings()
 
 
 class DeleteLSTView(ActionView):
     def post(self):
-        microscope = find_microscope()
-        with pause_stream(microscope.camera) as scamera:
-            scamera.camera.lens_shading_table = None
-        microscope.save_settings()
+        with find_picamera() as (picamera, scamera, microscope):
+            with pause_stream(scamera):
+                picamera.lens_shading_table = None
+            microscope.save_settings()
 
 
 class AutoExposureFromRawView(ActionView):
@@ -180,12 +206,8 @@ class AutoExposureFromRawView(ActionView):
     }
 
     def post(self, args):
-        camera = find_component("org.openflexure.microscope").camera
-
-        with camera.lock:
-            adjust_shutter_and_gain_from_raw(
-                camera.picamera, **args  # I'm relying on the schema to fill in missing values
-            )
+        with find_picamera() as (picamera, scamera, microscope):
+            adjust_shutter_and_gain_from_raw(picamera, **args)
 
 
 class AutoWhiteBalanceFromRawView(ActionView):
@@ -203,10 +225,8 @@ class AutoWhiteBalanceFromRawView(ActionView):
     }
 
     def post(self, args):
-        camera = find_component("org.openflexure.microscope").camera.picamera
-        adjust_white_balance_from_raw(
-            camera, **args  # I'm relying on the schema to fill in missing values
-        )
+        with find_picamera() as (picamera, scamera, microscope):
+            adjust_white_balance_from_raw(picamera, **args)
 
 
 class GetRawChannelPercentilesView(ActionView):
@@ -219,5 +239,5 @@ class GetRawChannelPercentilesView(ActionView):
     schema = fields.List(fields.Integer)
 
     def post(self, args):
-        camera = find_component("org.openflexure.microscope").camera.picamera
-        return get_channel_percentiles(camera, args["percentile"])
+        with find_picamera() as (picamera, scamera, microscope):
+            return get_channel_percentiles(picamera, args["percentile"])

From b06dd187ec52f3b2ff05c624095cfb142ddb3602 Mon Sep 17 00:00:00 2001
From: Richard Bowman <richard.bowman@cantab.net>
Date: Mon, 15 Feb 2021 20:18:34 +0000
Subject: [PATCH 12/41] Fixed args in endpoints

---
 .../picamera_autocalibrate/extension.py                   | 8 ++------
 1 file changed, 2 insertions(+), 6 deletions(-)

diff --git a/openflexure_microscope/api/default_extensions/picamera_autocalibrate/extension.py b/openflexure_microscope/api/default_extensions/picamera_autocalibrate/extension.py
index bdb0022b..28f51352 100644
--- a/openflexure_microscope/api/default_extensions/picamera_autocalibrate/extension.py
+++ b/openflexure_microscope/api/default_extensions/picamera_autocalibrate/extension.py
@@ -106,9 +106,7 @@ def find_picamera() -> Tuple[PiCamera, BaseCamera, Microscope]:
 
 
 class RecalibrateView(ActionView):
-    args = {}
-
-    def post(self, args):
+    def post(self):
         """Reset the camera's settings.
 
         This generates new gains, exposure time, and lens shading
@@ -135,9 +133,7 @@ class RecalibrateView(ActionView):
             microscope.save_settings()
 
 class AutoLensShadingTableView(ActionView):
-    args = {}
-
-    def post(self, args):
+    def post(self):
         """Perform flat-field correction
 
         This routine acquires a new image (which should be an

From 1e45640195524968092f9b32f04dd58c1ae9f69e Mon Sep 17 00:00:00 2001
From: Richard Bowman <richard.bowman@cantab.net>
Date: Mon, 15 Feb 2021 20:19:39 +0000
Subject: [PATCH 13/41] Added control to reset LST

You can now recalibrate the LST without running auto-gain.
---
 .../cameraCalibrationSettings.vue               | 17 ++++++++++++++++-
 1 file changed, 16 insertions(+), 1 deletion(-)

diff --git a/openflexure_microscope/api/static/src/components/tabContentComponents/settingsComponents/cameraSettingsComponents/cameraCalibrationSettings.vue b/openflexure_microscope/api/static/src/components/tabContentComponents/settingsComponents/cameraSettingsComponents/cameraCalibrationSettings.vue
index 09e38e15..c306e87b 100644
--- a/openflexure_microscope/api/static/src/components/tabContentComponents/settingsComponents/cameraSettingsComponents/cameraCalibrationSettings.vue
+++ b/openflexure_microscope/api/static/src/components/tabContentComponents/settingsComponents/cameraSettingsComponents/cameraCalibrationSettings.vue
@@ -37,6 +37,21 @@
       >
       </taskSubmitter>
     </div>
+    <div v-if="'auto_lens_shading_table' in recalibrationLinks" class="uk-margin-small">
+      <taskSubmitter
+        :can-terminate="false"
+        :requires-confirmation="true"
+        :confirmation-message="
+          'Is the microscope looking at an evenly illuminated, empty field of view? ' +
+          'If not, the current image will show through in any images captured afterwards.'
+        "
+        :submit-url="recalibrationLinks.auto_lens_shading_table.href"
+        :submit-label="'Auto flat field correction'"
+        @response="onRecalibrateResponse"
+        @error="modalError"
+      >
+      </taskSubmitter>
+    </div>
 
     <div v-show="showExtraSettings" class="uk-child-width-expand">
       <button
@@ -44,7 +59,7 @@
         class="uk-button uk-button-danger uk-width-1-1"
         @click="flattenLensShadingTableRequest"
       >
-        Disable flat-field correction
+        Disable flat field correction
       </button>
     </div>
 

From 20001e49465e0292192a9618695aa65e561e39b2 Mon Sep 17 00:00:00 2001
From: Richard Bowman <richard.bowman@cantab.net>
Date: Thu, 18 Feb 2021 13:29:02 +0000
Subject: [PATCH 14/41] Force installation only from piwheels

Forcing the use of piwheels avoids trying
to install numpy/scipy from source,
which is the Right Answer.

Unfortunately, sometimes packages fail on piwheels, but poetry still
tries to install them.  I've had to fix
pyyaml at 5.4.0 for that reason.
---
 poetry.lock    | 1039 +++++++++++++++++++++++++-----------------------
 pyproject.toml |   18 +-
 2 files changed, 562 insertions(+), 495 deletions(-)

diff --git a/poetry.lock b/poetry.lock
index 5588bca5..a900e866 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -6,6 +6,11 @@ category = "dev"
 optional = false
 python-versions = "*"
 
+[package.source]
+type = "legacy"
+url = "https://www.piwheels.org/simple"
+reference = "piwheels"
+
 [[package]]
 name = "apispec"
 version = "4.3.0"
@@ -18,12 +23,17 @@ python-versions = ">=3.6"
 PyYAML = {version = ">=3.10", optional = true, markers = "extra == \"yaml\""}
 
 [package.extras]
-tests = ["PyYAML (>=3.10)", "prance[osv] (>=0.11)", "marshmallow (>=3.0.0)", "pytest", "mock"]
+dev = ["PyYAML (>=3.10)", "prance[osv] (>=0.11)", "marshmallow (>=3.0.0)", "pytest", "mock", "flake8 (==3.8.4)", "flake8-bugbear (==20.11.1)", "pre-commit (>=2.4,<3.0)", "tox"]
 docs = ["marshmallow (>=3.0.0)", "pyyaml (==5.4.1)", "sphinx (==3.4.3)", "sphinx-issues (==1.2.0)", "sphinx-rtd-theme (==0.5.1)"]
 lint = ["flake8 (==3.8.4)", "flake8-bugbear (==20.11.1)", "pre-commit (>=2.4,<3.0)"]
-dev = ["PyYAML (>=3.10)", "prance[osv] (>=0.11)", "marshmallow (>=3.0.0)", "pytest", "mock", "flake8 (==3.8.4)", "flake8-bugbear (==20.11.1)", "pre-commit (>=2.4,<3.0)", "tox"]
-yaml = ["PyYAML (>=3.10)"]
+tests = ["PyYAML (>=3.10)", "prance[osv] (>=0.11)", "marshmallow (>=3.0.0)", "pytest", "mock"]
 validation = ["prance[osv] (>=0.11)"]
+yaml = ["PyYAML (>=3.10)"]
+
+[package.source]
+type = "legacy"
+url = "https://www.piwheels.org/simple"
+reference = "piwheels"
 
 [[package]]
 name = "apispec-webframeworks"
@@ -37,9 +47,14 @@ python-versions = ">=3.6"
 apispec = {version = ">=2.0.0", extras = ["yaml"]}
 
 [package.extras]
-tests = ["pytest", "mock", "Flask (==1.1.1)", "tornado", "bottle (==0.12.17)"]
-lint = ["flake8 (==3.7.9)", "flake8-bugbear (==19.8.0)", "pre-commit (>=1.18,<2.0)"]
 dev = ["pytest", "mock", "Flask (==1.1.1)", "tornado", "bottle (==0.12.17)", "flake8 (==3.7.9)", "flake8-bugbear (==19.8.0)", "pre-commit (>=1.18,<2.0)", "tox"]
+lint = ["flake8 (==3.7.9)", "flake8-bugbear (==19.8.0)", "pre-commit (>=1.18,<2.0)"]
+tests = ["pytest", "mock", "Flask (==1.1.1)", "tornado", "bottle (==0.12.17)"]
+
+[package.source]
+type = "legacy"
+url = "https://www.piwheels.org/simple"
+reference = "piwheels"
 
 [[package]]
 name = "appdirs"
@@ -49,6 +64,11 @@ category = "dev"
 optional = false
 python-versions = "*"
 
+[package.source]
+type = "legacy"
+url = "https://www.piwheels.org/simple"
+reference = "piwheels"
+
 [[package]]
 name = "astroid"
 version = "2.4.2"
@@ -59,10 +79,15 @@ python-versions = ">=3.5"
 
 [package.dependencies]
 lazy-object-proxy = ">=1.4.0,<1.5.0"
-typed-ast = {version = ">=1.4.0,<1.5", markers = "implementation_name == \"cpython\" and python_version < \"3.8\""}
 six = ">=1.12,<2.0"
+typed-ast = {version = ">=1.4.0,<1.5", markers = "implementation_name == \"cpython\" and python_version < \"3.8\""}
 wrapt = ">=1.11,<2.0"
 
+[package.source]
+type = "legacy"
+url = "https://www.piwheels.org/simple"
+reference = "piwheels"
+
 [[package]]
 name = "atomicwrites"
 version = "1.4.0"
@@ -71,6 +96,11 @@ category = "main"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
 
+[package.source]
+type = "legacy"
+url = "https://www.piwheels.org/simple"
+reference = "piwheels"
+
 [[package]]
 name = "attrs"
 version = "20.3.0"
@@ -80,10 +110,15 @@ optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
 
 [package.extras]
+dev = ["coverage[toml] (>=5.0.2)", "hypothesis", "pympler", "pytest (>=4.3.0)", "six", "zope.interface", "furo", "sphinx", "pre-commit"]
 docs = ["furo", "sphinx", "zope.interface"]
 tests = ["coverage[toml] (>=5.0.2)", "hypothesis", "pympler", "pytest (>=4.3.0)", "six", "zope.interface"]
 tests_no_zope = ["coverage[toml] (>=5.0.2)", "hypothesis", "pympler", "pytest (>=4.3.0)", "six"]
-dev = ["coverage[toml] (>=5.0.2)", "hypothesis", "pympler", "pytest (>=4.3.0)", "six", "zope.interface", "furo", "sphinx", "pre-commit"]
+
+[package.source]
+type = "legacy"
+url = "https://www.piwheels.org/simple"
+reference = "piwheels"
 
 [[package]]
 name = "babel"
@@ -96,6 +131,11 @@ python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
 [package.dependencies]
 pytz = ">=2015.7"
 
+[package.source]
+type = "legacy"
+url = "https://www.piwheels.org/simple"
+reference = "piwheels"
+
 [[package]]
 name = "black"
 version = "18.9b0"
@@ -105,14 +145,19 @@ optional = false
 python-versions = ">=3.6"
 
 [package.dependencies]
-toml = ">=0.9.4"
-attrs = ">=17.4.0"
 appdirs = "*"
+attrs = ">=17.4.0"
 click = ">=6.5"
+toml = ">=0.9.4"
 
 [package.extras]
 d = ["aiohttp (>=3.3.2)"]
 
+[package.source]
+type = "legacy"
+url = "https://www.piwheels.org/simple"
+reference = "piwheels"
+
 [[package]]
 name = "camera-stage-mapping"
 version = "0.1.4"
@@ -125,8 +170,13 @@ python-versions = ">=3.6,<4.0"
 numpy = ">=1.17,<2.0"
 
 [package.extras]
-all = ["opencv-python-headless (>=4.1,<5.0)", "scipy (>=1.4,<2.0)"]
 correlation = ["opencv-python-headless (>=4.1,<5.0)", "scipy (>=1.4,<2.0)"]
+all = ["opencv-python-headless (>=4.1,<5.0)", "scipy (>=1.4,<2.0)"]
+
+[package.source]
+type = "legacy"
+url = "https://www.piwheels.org/simple"
+reference = "piwheels"
 
 [[package]]
 name = "certifi"
@@ -136,6 +186,11 @@ category = "dev"
 optional = false
 python-versions = "*"
 
+[package.source]
+type = "legacy"
+url = "https://www.piwheels.org/simple"
+reference = "piwheels"
+
 [[package]]
 name = "chardet"
 version = "4.0.0"
@@ -144,6 +199,11 @@ category = "dev"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*"
 
+[package.source]
+type = "legacy"
+url = "https://www.piwheels.org/simple"
+reference = "piwheels"
+
 [[package]]
 name = "click"
 version = "7.1.2"
@@ -152,6 +212,11 @@ category = "main"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*"
 
+[package.source]
+type = "legacy"
+url = "https://www.piwheels.org/simple"
+reference = "piwheels"
+
 [[package]]
 name = "colorama"
 version = "0.4.4"
@@ -160,6 +225,11 @@ category = "main"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*"
 
+[package.source]
+type = "legacy"
+url = "https://www.piwheels.org/simple"
+reference = "piwheels"
+
 [[package]]
 name = "colorzero"
 version = "1.1"
@@ -169,8 +239,13 @@ optional = false
 python-versions = "*"
 
 [package.extras]
-test = ["pytest", "coverage", "mock"]
 doc = ["sphinx"]
+test = ["pytest", "coverage", "mock"]
+
+[package.source]
+type = "legacy"
+url = "https://www.piwheels.org/simple"
+reference = "piwheels"
 
 [[package]]
 name = "coverage"
@@ -183,6 +258,11 @@ python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, <4"
 [package.extras]
 toml = ["toml"]
 
+[package.source]
+type = "legacy"
+url = "https://www.piwheels.org/simple"
+reference = "piwheels"
+
 [[package]]
 name = "docutils"
 version = "0.16"
@@ -191,6 +271,11 @@ category = "dev"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*"
 
+[package.source]
+type = "legacy"
+url = "https://www.piwheels.org/simple"
+reference = "piwheels"
+
 [[package]]
 name = "expiringdict"
 version = "1.2.1"
@@ -202,6 +287,11 @@ python-versions = "*"
 [package.extras]
 tests = ["dill", "coverage", "coveralls", "mock", "nose"]
 
+[package.source]
+type = "legacy"
+url = "https://www.piwheels.org/simple"
+reference = "piwheels"
+
 [[package]]
 name = "flask"
 version = "1.1.2"
@@ -211,15 +301,20 @@ optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*"
 
 [package.dependencies]
+click = ">=5.1"
 itsdangerous = ">=0.24"
 Jinja2 = ">=2.10.1"
-click = ">=5.1"
 Werkzeug = ">=0.15"
 
 [package.extras]
-dotenv = ["python-dotenv"]
-docs = ["sphinx", "pallets-sphinx-themes", "sphinxcontrib-log-cabinet", "sphinx-issues"]
 dev = ["pytest", "coverage", "tox", "sphinx", "pallets-sphinx-themes", "sphinxcontrib-log-cabinet", "sphinx-issues"]
+docs = ["sphinx", "pallets-sphinx-themes", "sphinxcontrib-log-cabinet", "sphinx-issues"]
+dotenv = ["python-dotenv"]
+
+[package.source]
+type = "legacy"
+url = "https://www.piwheels.org/simple"
+reference = "piwheels"
 
 [[package]]
 name = "flask-cors"
@@ -233,6 +328,11 @@ python-versions = "*"
 Flask = ">=0.9"
 Six = "*"
 
+[package.source]
+type = "legacy"
+url = "https://www.piwheels.org/simple"
+reference = "piwheels"
+
 [[package]]
 name = "freezegun"
 version = "1.1.0"
@@ -244,6 +344,11 @@ python-versions = ">=3.5"
 [package.dependencies]
 python-dateutil = ">=2.7"
 
+[package.source]
+type = "legacy"
+url = "https://www.piwheels.org/simple"
+reference = "piwheels"
+
 [[package]]
 name = "future"
 version = "0.18.2"
@@ -252,6 +357,11 @@ category = "main"
 optional = false
 python-versions = ">=2.6, !=3.0.*, !=3.1.*, !=3.2.*"
 
+[package.source]
+type = "legacy"
+url = "https://www.piwheels.org/simple"
+reference = "piwheels"
+
 [[package]]
 name = "idna"
 version = "2.10"
@@ -260,6 +370,11 @@ category = "dev"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
 
+[package.source]
+type = "legacy"
+url = "https://www.piwheels.org/simple"
+reference = "piwheels"
+
 [[package]]
 name = "ifaddr"
 version = "0.1.7"
@@ -268,6 +383,11 @@ category = "main"
 optional = false
 python-versions = "*"
 
+[package.source]
+type = "legacy"
+url = "https://www.piwheels.org/simple"
+reference = "piwheels"
+
 [[package]]
 name = "imagesize"
 version = "1.2.0"
@@ -276,6 +396,11 @@ category = "dev"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
 
+[package.source]
+type = "legacy"
+url = "https://www.piwheels.org/simple"
+reference = "piwheels"
+
 [[package]]
 name = "importlib-metadata"
 version = "3.4.0"
@@ -292,6 +417,11 @@ zipp = ">=0.5"
 docs = ["sphinx", "jaraco.packaging (>=8.2)", "rst.linker (>=1.9)"]
 testing = ["pytest (>=3.5,!=3.7.3)", "pytest-checkdocs (>=1.2.3)", "pytest-flake8", "pytest-cov", "pytest-enabler", "packaging", "pep517", "pyfakefs", "flufl.flake8", "pytest-black (>=0.3.7)", "pytest-mypy", "importlib-resources (>=1.3)"]
 
+[package.source]
+type = "legacy"
+url = "https://www.piwheels.org/simple"
+reference = "piwheels"
+
 [[package]]
 name = "iniconfig"
 version = "1.1.1"
@@ -300,6 +430,11 @@ category = "main"
 optional = false
 python-versions = "*"
 
+[package.source]
+type = "legacy"
+url = "https://www.piwheels.org/simple"
+reference = "piwheels"
+
 [[package]]
 name = "isort"
 version = "5.7.0"
@@ -310,8 +445,13 @@ python-versions = ">=3.6,<4.0"
 
 [package.extras]
 colors = ["colorama (>=0.4.3,<0.5.0)"]
+requirements_deprecated_finder = ["pip-api", "pipreqs"]
 pipfile_deprecated_finder = ["pipreqs", "requirementslib"]
-requirements_deprecated_finder = ["pipreqs", "pip-api"]
+
+[package.source]
+type = "legacy"
+url = "https://www.piwheels.org/simple"
+reference = "piwheels"
 
 [[package]]
 name = "itsdangerous"
@@ -321,6 +461,11 @@ category = "main"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
 
+[package.source]
+type = "legacy"
+url = "https://www.piwheels.org/simple"
+reference = "piwheels"
+
 [[package]]
 name = "jinja2"
 version = "2.11.3"
@@ -335,6 +480,11 @@ MarkupSafe = ">=0.23"
 [package.extras]
 i18n = ["Babel (>=0.8)"]
 
+[package.source]
+type = "legacy"
+url = "https://www.piwheels.org/simple"
+reference = "piwheels"
+
 [[package]]
 name = "labthings"
 version = "1.2.3"
@@ -344,13 +494,18 @@ optional = false
 python-versions = ">=3.6,<4.0"
 
 [package.dependencies]
-apispec_webframeworks = ">=0.5.2,<0.6.0"
-webargs = ">=6,<8"
-marshmallow = ">=3.4.0,<4.0.0"
-Flask = ">=1.1.1,<2.0.0"
 apispec = ">=3.2,<5.0"
-zeroconf = ">=0.24.5,<0.29.0"
+apispec_webframeworks = ">=0.5.2,<0.6.0"
+Flask = ">=1.1.1,<2.0.0"
 flask-cors = ">=3.0.8,<4.0.0"
+marshmallow = ">=3.4.0,<4.0.0"
+webargs = ">=6,<8"
+zeroconf = ">=0.24.5,<0.29.0"
+
+[package.source]
+type = "legacy"
+url = "https://www.piwheels.org/simple"
+reference = "piwheels"
 
 [[package]]
 name = "lazy-object-proxy"
@@ -360,6 +515,11 @@ category = "dev"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
 
+[package.source]
+type = "legacy"
+url = "https://www.piwheels.org/simple"
+reference = "piwheels"
+
 [[package]]
 name = "lxml"
 version = "4.6.2"
@@ -369,10 +529,15 @@ optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, != 3.4.*"
 
 [package.extras]
-source = ["Cython (>=0.29.7)"]
 cssselect = ["cssselect (>=0.7)"]
 html5 = ["html5lib"]
 htmlsoup = ["beautifulsoup4"]
+source = ["Cython (>=0.29.7)"]
+
+[package.source]
+type = "legacy"
+url = "https://www.piwheels.org/simple"
+reference = "piwheels"
 
 [[package]]
 name = "markupsafe"
@@ -382,6 +547,11 @@ category = "main"
 optional = false
 python-versions = ">=2.7,!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*"
 
+[package.source]
+type = "legacy"
+url = "https://www.piwheels.org/simple"
+reference = "piwheels"
+
 [[package]]
 name = "marshmallow"
 version = "3.10.0"
@@ -391,10 +561,15 @@ optional = false
 python-versions = ">=3.5"
 
 [package.extras]
-docs = ["sphinx (==3.3.1)", "sphinx-issues (==1.2.0)", "alabaster (==0.7.12)", "sphinx-version-warning (==1.1.2)", "autodocsumm (==0.2.2)"]
-tests = ["pytest", "pytz", "simplejson"]
-lint = ["mypy (==0.790)", "flake8 (==3.8.4)", "flake8-bugbear (==20.11.1)", "pre-commit (>=2.4,<3.0)"]
 dev = ["pytest", "pytz", "simplejson", "mypy (==0.790)", "flake8 (==3.8.4)", "flake8-bugbear (==20.11.1)", "pre-commit (>=2.4,<3.0)", "tox"]
+docs = ["sphinx (==3.3.1)", "sphinx-issues (==1.2.0)", "alabaster (==0.7.12)", "sphinx-version-warning (==1.1.2)", "autodocsumm (==0.2.2)"]
+lint = ["mypy (==0.790)", "flake8 (==3.8.4)", "flake8-bugbear (==20.11.1)", "pre-commit (>=2.4,<3.0)"]
+tests = ["pytest", "pytz", "simplejson"]
+
+[package.source]
+type = "legacy"
+url = "https://www.piwheels.org/simple"
+reference = "piwheels"
 
 [[package]]
 name = "mccabe"
@@ -404,6 +579,11 @@ category = "dev"
 optional = false
 python-versions = "*"
 
+[package.source]
+type = "legacy"
+url = "https://www.piwheels.org/simple"
+reference = "piwheels"
+
 [[package]]
 name = "mypy"
 version = "0.790"
@@ -420,6 +600,11 @@ typing-extensions = ">=3.7.4"
 [package.extras]
 dmypy = ["psutil (>=4.0)"]
 
+[package.source]
+type = "legacy"
+url = "https://www.piwheels.org/simple"
+reference = "piwheels"
+
 [[package]]
 name = "mypy-extensions"
 version = "0.4.3"
@@ -428,6 +613,11 @@ category = "dev"
 optional = false
 python-versions = "*"
 
+[package.source]
+type = "legacy"
+url = "https://www.piwheels.org/simple"
+reference = "piwheels"
+
 [[package]]
 name = "numpy"
 version = "1.19.2"
@@ -436,18 +626,23 @@ category = "main"
 optional = false
 python-versions = ">=3.6"
 
+[package.source]
+type = "legacy"
+url = "https://www.piwheels.org/simple"
+reference = "piwheels"
+
 [[package]]
 name = "numpy-stubs"
 version = "0.0.1"
-description = "PEP 561 type stubs for numpy"
+description = ""
 category = "main"
 optional = false
 python-versions = "*"
 develop = false
 
 [package.dependencies]
-typing-extensions = {version = ">=3.7.4", markers = "python_version < \"3.8\""}
 numpy = ">=1.16.0"
+typing_extensions = {version = ">=3.7.4", markers = "python_version < \"3.8\""}
 
 [package.source]
 type = "git"
@@ -457,12 +652,20 @@ resolved_reference = "c49d2d6875971a669a166ea93ef998911af283a1"
 
 [[package]]
 name = "opencv-python-headless"
-version = "4.4.0.44"
+version = "4.5.1.48"
 description = "Wrapper package for OpenCV python bindings."
 category = "main"
 optional = false
 python-versions = ">=3.6"
 
+[package.dependencies]
+numpy = ">=1.14.5"
+
+[package.source]
+type = "legacy"
+url = "https://www.piwheels.org/simple"
+reference = "piwheels"
+
 [[package]]
 name = "packaging"
 version = "20.9"
@@ -474,6 +677,11 @@ python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
 [package.dependencies]
 pyparsing = ">=2.0.2"
 
+[package.source]
+type = "legacy"
+url = "https://www.piwheels.org/simple"
+reference = "piwheels"
+
 [[package]]
 name = "pastel"
 version = "0.2.1"
@@ -482,6 +690,11 @@ category = "dev"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
 
+[package.source]
+type = "legacy"
+url = "https://www.piwheels.org/simple"
+reference = "piwheels"
+
 [[package]]
 name = "picamerax"
 version = "20.9.1"
@@ -494,9 +707,14 @@ python-versions = "*"
 colorzero = "*"
 
 [package.extras]
-test = ["coverage", "pytest", "mock", "pillow", "numpy"]
-doc = ["sphinx"]
 array = ["numpy"]
+doc = ["sphinx"]
+test = ["coverage", "pytest", "mock", "pillow", "numpy"]
+
+[package.source]
+type = "legacy"
+url = "https://www.piwheels.org/simple"
+reference = "piwheels"
 
 [[package]]
 name = "piexif"
@@ -506,6 +724,11 @@ category = "main"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*"
 
+[package.source]
+type = "legacy"
+url = "https://www.piwheels.org/simple"
+reference = "piwheels"
+
 [[package]]
 name = "pillow"
 version = "7.2.0"
@@ -514,6 +737,11 @@ category = "main"
 optional = false
 python-versions = ">=3.5"
 
+[package.source]
+type = "legacy"
+url = "https://www.piwheels.org/simple"
+reference = "piwheels"
+
 [[package]]
 name = "pluggy"
 version = "0.13.1"
@@ -528,6 +756,11 @@ importlib-metadata = {version = ">=0.12", markers = "python_version < \"3.8\""}
 [package.extras]
 dev = ["pre-commit", "tox"]
 
+[package.source]
+type = "legacy"
+url = "https://www.piwheels.org/simple"
+reference = "piwheels"
+
 [[package]]
 name = "poethepoet"
 version = "0.9.0"
@@ -540,6 +773,11 @@ python-versions = ">=3.6,<4.0"
 pastel = ">=0.2.0,<0.3.0"
 tomlkit = ">=0.6.0,<1.0.0"
 
+[package.source]
+type = "legacy"
+url = "https://www.piwheels.org/simple"
+reference = "piwheels"
+
 [[package]]
 name = "psutil"
 version = "5.8.0"
@@ -551,6 +789,11 @@ python-versions = ">=2.6, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
 [package.extras]
 test = ["ipaddress", "mock", "unittest2", "enum34", "pywin32", "wmi"]
 
+[package.source]
+type = "legacy"
+url = "https://www.piwheels.org/simple"
+reference = "piwheels"
+
 [[package]]
 name = "py"
 version = "1.10.0"
@@ -559,28 +802,43 @@ category = "main"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
 
+[package.source]
+type = "legacy"
+url = "https://www.piwheels.org/simple"
+reference = "piwheels"
+
 [[package]]
 name = "pygments"
-version = "2.7.4"
+version = "2.8.0"
 description = "Pygments is a syntax highlighting package written in Python."
 category = "dev"
 optional = false
 python-versions = ">=3.5"
 
+[package.source]
+type = "legacy"
+url = "https://www.piwheels.org/simple"
+reference = "piwheels"
+
 [[package]]
 name = "pylint"
-version = "2.6.0"
+version = "2.6.2"
 description = "python code static checker"
 category = "dev"
 optional = false
 python-versions = ">=3.5.*"
 
 [package.dependencies]
-astroid = ">=2.4.0,<=2.5"
-mccabe = ">=0.6,<0.7"
+astroid = ">=2.4.0,<2.5"
 colorama = {version = "*", markers = "sys_platform == \"win32\""}
-toml = ">=0.7.1"
 isort = ">=4.2.5,<6"
+mccabe = ">=0.6,<0.7"
+toml = ">=0.7.1"
+
+[package.source]
+type = "legacy"
+url = "https://www.piwheels.org/simple"
+reference = "piwheels"
 
 [[package]]
 name = "pyparsing"
@@ -590,6 +848,11 @@ category = "main"
 optional = false
 python-versions = ">=2.6, !=3.0.*, !=3.1.*, !=3.2.*"
 
+[package.source]
+type = "legacy"
+url = "https://www.piwheels.org/simple"
+reference = "piwheels"
+
 [[package]]
 name = "pyserial"
 version = "3.5"
@@ -601,6 +864,11 @@ python-versions = "*"
 [package.extras]
 cp2110 = ["hidapi"]
 
+[package.source]
+type = "legacy"
+url = "https://www.piwheels.org/simple"
+reference = "piwheels"
+
 [[package]]
 name = "pytest"
 version = "6.2.2"
@@ -610,19 +878,24 @@ optional = false
 python-versions = ">=3.6"
 
 [package.dependencies]
-packaging = "*"
-py = ">=1.8.2"
-iniconfig = "*"
-importlib-metadata = {version = ">=0.12", markers = "python_version < \"3.8\""}
-colorama = {version = "*", markers = "sys_platform == \"win32\""}
-attrs = ">=19.2.0"
-toml = "*"
-pluggy = ">=0.12,<1.0.0a1"
 atomicwrites = {version = ">=1.0", markers = "sys_platform == \"win32\""}
+attrs = ">=19.2.0"
+colorama = {version = "*", markers = "sys_platform == \"win32\""}
+importlib-metadata = {version = ">=0.12", markers = "python_version < \"3.8\""}
+iniconfig = "*"
+packaging = "*"
+pluggy = ">=0.12,<1.0.0a1"
+py = ">=1.8.2"
+toml = "*"
 
 [package.extras]
 testing = ["argcomplete", "hypothesis (>=3.56)", "mock", "nose", "requests", "xmlschema"]
 
+[package.source]
+type = "legacy"
+url = "https://www.piwheels.org/simple"
+reference = "piwheels"
+
 [[package]]
 name = "pytest-cov"
 version = "2.11.1"
@@ -632,12 +905,17 @@ optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*"
 
 [package.dependencies]
-pytest = ">=4.6"
 coverage = ">=5.2.1"
+pytest = ">=4.6"
 
 [package.extras]
 testing = ["fields", "hunter", "process-tests (==2.0.2)", "six", "pytest-xdist", "virtualenv"]
 
+[package.source]
+type = "legacy"
+url = "https://www.piwheels.org/simple"
+reference = "piwheels"
+
 [[package]]
 name = "python-dateutil"
 version = "2.8.1"
@@ -649,6 +927,11 @@ python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,>=2.7"
 [package.dependencies]
 six = ">=1.5"
 
+[package.source]
+type = "legacy"
+url = "https://www.piwheels.org/simple"
+reference = "piwheels"
+
 [[package]]
 name = "pytz"
 version = "2021.1"
@@ -657,14 +940,24 @@ category = "dev"
 optional = false
 python-versions = "*"
 
+[package.source]
+type = "legacy"
+url = "https://www.piwheels.org/simple"
+reference = "piwheels"
+
 [[package]]
 name = "pyyaml"
-version = "5.4.1"
+version = "5.4"
 description = "YAML parser and emitter for Python"
 category = "main"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, !=3.5.*"
 
+[package.source]
+type = "legacy"
+url = "https://www.piwheels.org/simple"
+reference = "piwheels"
+
 [[package]]
 name = "requests"
 version = "2.25.1"
@@ -674,15 +967,20 @@ optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*"
 
 [package.dependencies]
-idna = ">=2.5,<3"
 certifi = ">=2017.4.17"
 chardet = ">=3.0.2,<5"
+idna = ">=2.5,<3"
 urllib3 = ">=1.21.1,<1.27"
 
 [package.extras]
 security = ["pyOpenSSL (>=0.14)", "cryptography (>=1.3.4)"]
 socks = ["PySocks (>=1.5.6,!=1.5.7)", "win-inet-pton"]
 
+[package.source]
+type = "legacy"
+url = "https://www.piwheels.org/simple"
+reference = "piwheels"
+
 [[package]]
 name = "rope"
 version = "0.14.0"
@@ -691,6 +989,11 @@ category = "dev"
 optional = false
 python-versions = "*"
 
+[package.source]
+type = "legacy"
+url = "https://www.piwheels.org/simple"
+reference = "piwheels"
+
 [[package]]
 name = "rpi.gpio"
 version = "0.7.0"
@@ -699,6 +1002,11 @@ category = "main"
 optional = true
 python-versions = "*"
 
+[package.source]
+type = "legacy"
+url = "https://www.piwheels.org/simple"
+reference = "piwheels"
+
 [[package]]
 name = "sangaboard"
 version = "0.2.3"
@@ -712,16 +1020,26 @@ future = "*"
 numpy = "*"
 pyserial = "*"
 
+[package.source]
+type = "legacy"
+url = "https://www.piwheels.org/simple"
+reference = "piwheels"
+
 [[package]]
 name = "scipy"
-version = "1.5.3"
+version = "1.6.1"
 description = "SciPy: Scientific Library for Python"
 category = "main"
 optional = false
-python-versions = ">=3.6"
+python-versions = ">=3.7"
 
 [package.dependencies]
-numpy = ">=1.14.5"
+numpy = ">=1.16.5"
+
+[package.source]
+type = "legacy"
+url = "https://www.piwheels.org/simple"
+reference = "piwheels"
 
 [[package]]
 name = "six"
@@ -731,6 +1049,11 @@ category = "main"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*"
 
+[package.source]
+type = "legacy"
+url = "https://www.piwheels.org/simple"
+reference = "piwheels"
+
 [[package]]
 name = "snowballstemmer"
 version = "2.1.0"
@@ -739,36 +1062,46 @@ category = "dev"
 optional = false
 python-versions = "*"
 
+[package.source]
+type = "legacy"
+url = "https://www.piwheels.org/simple"
+reference = "piwheels"
+
 [[package]]
 name = "sphinx"
-version = "3.4.3"
+version = "3.5.1"
 description = "Python documentation generator"
 category = "dev"
 optional = false
 python-versions = ">=3.5"
 
 [package.dependencies]
-sphinxcontrib-qthelp = "*"
-imagesize = "*"
-sphinxcontrib-devhelp = "*"
-snowballstemmer = ">=1.1"
-babel = ">=1.3"
 alabaster = ">=0.7,<0.8"
-sphinxcontrib-serializinghtml = "*"
-packaging = "*"
-docutils = ">=0.12"
-Pygments = ">=2.0"
-Jinja2 = ">=2.3"
+babel = ">=1.3"
 colorama = {version = ">=0.3.5", markers = "sys_platform == \"win32\""}
+docutils = ">=0.12"
+imagesize = "*"
+Jinja2 = ">=2.3"
+packaging = "*"
+Pygments = ">=2.0"
 requests = ">=2.5.0"
+snowballstemmer = ">=1.1"
 sphinxcontrib-applehelp = "*"
+sphinxcontrib-devhelp = "*"
 sphinxcontrib-htmlhelp = "*"
 sphinxcontrib-jsmath = "*"
+sphinxcontrib-qthelp = "*"
+sphinxcontrib-serializinghtml = "*"
 
 [package.extras]
-test = ["pytest", "pytest-cov", "html5lib", "cython", "typed-ast"]
 docs = ["sphinxcontrib-websupport"]
-lint = ["flake8 (>=3.5.0)", "isort", "mypy (>=0.790)", "docutils-stubs"]
+lint = ["flake8 (>=3.5.0)", "isort", "mypy (>=0.800)", "docutils-stubs"]
+test = ["pytest", "pytest-cov", "html5lib", "cython", "typed-ast"]
+
+[package.source]
+type = "legacy"
+url = "https://www.piwheels.org/simple"
+reference = "piwheels"
 
 [[package]]
 name = "sphinxcontrib-applehelp"
@@ -779,8 +1112,13 @@ optional = false
 python-versions = ">=3.5"
 
 [package.extras]
-test = ["pytest"]
 lint = ["flake8", "mypy", "docutils-stubs"]
+test = ["pytest"]
+
+[package.source]
+type = "legacy"
+url = "https://www.piwheels.org/simple"
+reference = "piwheels"
 
 [[package]]
 name = "sphinxcontrib-devhelp"
@@ -791,8 +1129,13 @@ optional = false
 python-versions = ">=3.5"
 
 [package.extras]
-test = ["pytest"]
 lint = ["flake8", "mypy", "docutils-stubs"]
+test = ["pytest"]
+
+[package.source]
+type = "legacy"
+url = "https://www.piwheels.org/simple"
+reference = "piwheels"
 
 [[package]]
 name = "sphinxcontrib-htmlhelp"
@@ -803,8 +1146,13 @@ optional = false
 python-versions = ">=3.5"
 
 [package.extras]
-test = ["pytest", "html5lib"]
 lint = ["flake8", "mypy", "docutils-stubs"]
+test = ["pytest", "html5lib"]
+
+[package.source]
+type = "legacy"
+url = "https://www.piwheels.org/simple"
+reference = "piwheels"
 
 [[package]]
 name = "sphinxcontrib-httpdomain"
@@ -818,6 +1166,11 @@ python-versions = "*"
 six = "*"
 Sphinx = ">=1.5"
 
+[package.source]
+type = "legacy"
+url = "https://www.piwheels.org/simple"
+reference = "piwheels"
+
 [[package]]
 name = "sphinxcontrib-jsmath"
 version = "1.0.1"
@@ -829,6 +1182,11 @@ python-versions = ">=3.5"
 [package.extras]
 test = ["pytest", "flake8", "mypy"]
 
+[package.source]
+type = "legacy"
+url = "https://www.piwheels.org/simple"
+reference = "piwheels"
+
 [[package]]
 name = "sphinxcontrib-qthelp"
 version = "1.0.3"
@@ -838,8 +1196,13 @@ optional = false
 python-versions = ">=3.5"
 
 [package.extras]
-test = ["pytest"]
 lint = ["flake8", "mypy", "docutils-stubs"]
+test = ["pytest"]
+
+[package.source]
+type = "legacy"
+url = "https://www.piwheels.org/simple"
+reference = "piwheels"
 
 [[package]]
 name = "sphinxcontrib-serializinghtml"
@@ -850,8 +1213,13 @@ optional = false
 python-versions = ">=3.5"
 
 [package.extras]
-test = ["pytest"]
 lint = ["flake8", "mypy", "docutils-stubs"]
+test = ["pytest"]
+
+[package.source]
+type = "legacy"
+url = "https://www.piwheels.org/simple"
+reference = "piwheels"
 
 [[package]]
 name = "toml"
@@ -861,6 +1229,11 @@ category = "main"
 optional = false
 python-versions = ">=2.6, !=3.0.*, !=3.1.*, !=3.2.*"
 
+[package.source]
+type = "legacy"
+url = "https://www.piwheels.org/simple"
+reference = "piwheels"
+
 [[package]]
 name = "tomlkit"
 version = "0.7.0"
@@ -869,6 +1242,11 @@ category = "dev"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*"
 
+[package.source]
+type = "legacy"
+url = "https://www.piwheels.org/simple"
+reference = "piwheels"
+
 [[package]]
 name = "typed-ast"
 version = "1.4.2"
@@ -877,6 +1255,11 @@ category = "dev"
 optional = false
 python-versions = "*"
 
+[package.source]
+type = "legacy"
+url = "https://www.piwheels.org/simple"
+reference = "piwheels"
+
 [[package]]
 name = "typing-extensions"
 version = "3.7.4.3"
@@ -885,6 +1268,11 @@ category = "main"
 optional = false
 python-versions = "*"
 
+[package.source]
+type = "legacy"
+url = "https://www.piwheels.org/simple"
+reference = "piwheels"
+
 [[package]]
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 version = "1.26.3"
@@ -898,6 +1286,11 @@ brotli = ["brotlipy (>=0.6.0)"]
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 socks = ["PySocks (>=1.5.6,!=1.5.7,<2.0)"]
 
+[package.source]
+type = "legacy"
+url = "https://www.piwheels.org/simple"
+reference = "piwheels"
+
 [[package]]
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 version = "7.0.1"
@@ -910,11 +1303,16 @@ python-versions = ">=3.6"
 marshmallow = ">=3.0.0"
 
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+
+[package.source]
+type = "legacy"
+url = "https://www.piwheels.org/simple"
+reference = "piwheels"
 
 [[package]]
 name = "werkzeug"
@@ -925,8 +1323,13 @@ optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*"
 
 [package.extras]
-watchdog = ["watchdog"]
 dev = ["pytest", "pytest-timeout", "coverage", "tox", "sphinx", "pallets-sphinx-themes", "sphinx-issues"]
+watchdog = ["watchdog"]
+
+[package.source]
+type = "legacy"
+url = "https://www.piwheels.org/simple"
+reference = "piwheels"
 
 [[package]]
 name = "wrapt"
@@ -936,6 +1339,11 @@ category = "dev"
 optional = false
 python-versions = "*"
 
+[package.source]
+type = "legacy"
+url = "https://www.piwheels.org/simple"
+reference = "piwheels"
+
 [[package]]
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 version = "0.28.8"
@@ -947,6 +1355,11 @@ python-versions = "*"
 [package.dependencies]
 ifaddr = ">=0.1.7"
 
+[package.source]
+type = "legacy"
+url = "https://www.piwheels.org/simple"
+reference = "piwheels"
+
 [[package]]
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@@ -959,660 +1372,304 @@ python-versions = ">=3.6"
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+[package.source]
+type = "legacy"
+url = "https://www.piwheels.org/simple"
+reference = "piwheels"
+
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 zeroconf = [
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 zipp = [
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-    {file = "zipp-3.4.0.tar.gz", hash = "sha256:ed5eee1974372595f9e416cc7bbeeb12335201d8081ca8a0743c954d4446e5cb"},
 ]
diff --git a/pyproject.toml b/pyproject.toml
index d7bccc65..81609ef2 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -28,21 +28,31 @@ packages = [
     { include = "openflexure_microscope" },
 ]
 
+# Installing numpy/scipy/etc. from source is unlikely to work.
+# The block below forces Poetry to use piwheels.
+# We can add other repositories if we need them.
+# Setting default=true disables fallback to PyPI.
+
+[[tool.poetry.source]]
+name = "piwheels"
+url = "https://www.piwheels.org/simple"
+default = true
+
 [tool.poetry.dependencies]
 python = "^3.7.3"
 Flask = "^1.0"
 numpy = "1.19.2" # Exact version so we can guarantee a wheel
 Pillow = "^7.2.0"
-scipy = "1.5.3" # Exact version so we can guarantee a wheel
+scipy = "1.6.1" # Exact version so we can guarantee a wheel
 "RPi.GPIO" = { version = "^0.7.0", optional = true }
 python-dateutil = "^2.8"
 psutil = "^5.6.7" # Autostorage extension
-opencv-python-headless = "4.4.0.44"
+opencv-python-headless = "4.5.1.48"
 sangaboard = "^0.2"
 expiringdict = "^1.2.1"
 camera-stage-mapping = "0.1.4"
 picamerax = ">=20.9.1"
-pyyaml = "^5.3.1"
+pyyaml = "5.4.0" # pyyaml 5.4.1 is broken in piwheels
 pytest-cov = "^2.10.1"
 piexif = "^1.1.3"
 labthings = "^1.2.2"
@@ -64,7 +74,7 @@ pytest = "^6.1.2"
 mypy = "^0.790"
 poethepoet = "^0.9.0"
 freezegun = "^1.0.0"
-lxml = "^4.6.2"
+lxml = "^4.6.2" # Fix version so piwheels works
 
 [tool.black]
 exclude = '(\.eggs|\.git|\.venv|\venv|node_modules/)'

From 414fd55c5be92e6e023a53f7832194884580f4b4 Mon Sep 17 00:00:00 2001
From: Richard Bowman <richard.bowman@cantab.net>
Date: Thu, 18 Feb 2021 14:33:07 +0000
Subject: [PATCH 15/41] Upgrade numpy

numpy/scipy were mismatched in version, which led to a confusing
import error.  I've removed the numpy version specification entirely
and left it to scipy to ensure numpy
is installed.  This could do with
review in the future...
---
 poetry.lock    | 40 +++++++++++++++++++++++++++-------------
 pyproject.toml | 11 ++++++-----
 2 files changed, 33 insertions(+), 18 deletions(-)

diff --git a/poetry.lock b/poetry.lock
index a900e866..5c309797 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -620,11 +620,11 @@ reference = "piwheels"
 
 [[package]]
 name = "numpy"
-version = "1.19.2"
+version = "1.20.1"
 description = "NumPy is the fundamental package for array computing with Python."
 category = "main"
 optional = false
-python-versions = ">=3.6"
+python-versions = ">=3.7"
 
 [package.source]
 type = "legacy"
@@ -947,17 +947,12 @@ reference = "piwheels"
 
 [[package]]
 name = "pyyaml"
-version = "5.4"
+version = "5.4.1"
 description = "YAML parser and emitter for Python"
 category = "main"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, !=3.5.*"
 
-[package.source]
-type = "legacy"
-url = "https://www.piwheels.org/simple"
-reference = "piwheels"
-
 [[package]]
 name = "requests"
 version = "2.25.1"
@@ -1383,7 +1378,7 @@ rpi = ["RPi.GPIO"]
 [metadata]
 lock-version = "1.1"
 python-versions = "^3.7.3"
-content-hash = "7144f1f0652692911988bfc402489aa1d693d818e4152c57dca592d1c4f65fe1"
+content-hash = "26a514da40cebddf91dd6020cb4a8f130e8684063d3aaf6a984e548b16338575"
 
 [metadata.files]
 alabaster = [
@@ -1515,8 +1510,8 @@ mypy-extensions = [
     {file = "mypy_extensions-0.4.3-py2.py3-none-any.whl", hash = "sha256:090fedd75945a69ae91ce1303b5824f428daf5a028d2f6ab8a299250a846f15d"},
 ]
 numpy = [
-    {file = "numpy-1.19.2-cp37-cp37m-linux_armv6l.whl", hash = "sha256:bff0719af5134d472546e601f83e5335ec8919464084b34d602541fc80a33698"},
-    {file = "numpy-1.19.2-cp37-cp37m-linux_armv7l.whl", hash = "sha256:bff0719af5134d472546e601f83e5335ec8919464084b34d602541fc80a33698"},
+    {file = "numpy-1.20.1-cp37-cp37m-linux_armv6l.whl", hash = "sha256:23d6802e7f2ceb9a1572f375470478251e821bdb4babbbbf3f2420c858d5dbde"},
+    {file = "numpy-1.20.1-cp37-cp37m-linux_armv7l.whl", hash = "sha256:23d6802e7f2ceb9a1572f375470478251e821bdb4babbbbf3f2420c858d5dbde"},
 ]
 numpy-stubs = []
 opencv-python-headless = [
@@ -1581,8 +1576,27 @@ pytz = [
     {file = "pytz-2021.1-py2.py3-none-any.whl", hash = "sha256:eb10ce3e7736052ed3623d49975ce333bcd712c7bb19a58b9e2089d4057d0798"},
 ]
 pyyaml = [
-    {file = "PyYAML-5.4-cp37-cp37m-linux_armv6l.whl", hash = "sha256:64a89e4ab1e56c6bd2dcb4578df6a29b480abffcc78eba175fba87eb140da5d0"},
-    {file = "PyYAML-5.4-cp37-cp37m-linux_armv7l.whl", hash = "sha256:64a89e4ab1e56c6bd2dcb4578df6a29b480abffcc78eba175fba87eb140da5d0"},
+    {file = "PyYAML-5.4.1-cp27-cp27m-macosx_10_9_x86_64.whl", hash = "sha256:3b2b1824fe7112845700f815ff6a489360226a5609b96ec2190a45e62a9fc922"},
+    {file = "PyYAML-5.4.1-cp27-cp27m-win32.whl", hash = "sha256:129def1b7c1bf22faffd67b8f3724645203b79d8f4cc81f674654d9902cb4393"},
+    {file = "PyYAML-5.4.1-cp27-cp27m-win_amd64.whl", hash = "sha256:4465124ef1b18d9ace298060f4eccc64b0850899ac4ac53294547536533800c8"},
+    {file = "PyYAML-5.4.1-cp27-cp27mu-manylinux1_x86_64.whl", hash = "sha256:bb4191dfc9306777bc594117aee052446b3fa88737cd13b7188d0e7aa8162185"},
+    {file = "PyYAML-5.4.1-cp36-cp36m-macosx_10_9_x86_64.whl", hash = "sha256:6c78645d400265a062508ae399b60b8c167bf003db364ecb26dcab2bda048253"},
+    {file = "PyYAML-5.4.1-cp36-cp36m-manylinux1_x86_64.whl", hash = "sha256:4e0583d24c881e14342eaf4ec5fbc97f934b999a6828693a99157fde912540cc"},
+    {file = "PyYAML-5.4.1-cp36-cp36m-win32.whl", hash = "sha256:3bd0e463264cf257d1ffd2e40223b197271046d09dadf73a0fe82b9c1fc385a5"},
+    {file = "PyYAML-5.4.1-cp36-cp36m-win_amd64.whl", hash = "sha256:e4fac90784481d221a8e4b1162afa7c47ed953be40d31ab4629ae917510051df"},
+    {file = "PyYAML-5.4.1-cp37-cp37m-macosx_10_9_x86_64.whl", hash = "sha256:5accb17103e43963b80e6f837831f38d314a0495500067cb25afab2e8d7a4018"},
+    {file = "PyYAML-5.4.1-cp37-cp37m-manylinux1_x86_64.whl", hash = "sha256:e1d4970ea66be07ae37a3c2e48b5ec63f7ba6804bdddfdbd3cfd954d25a82e63"},
+    {file = "PyYAML-5.4.1-cp37-cp37m-win32.whl", hash = "sha256:dd5de0646207f053eb0d6c74ae45ba98c3395a571a2891858e87df7c9b9bd51b"},
+    {file = "PyYAML-5.4.1-cp37-cp37m-win_amd64.whl", hash = "sha256:08682f6b72c722394747bddaf0aa62277e02557c0fd1c42cb853016a38f8dedf"},
+    {file = "PyYAML-5.4.1-cp38-cp38-macosx_10_9_x86_64.whl", hash = "sha256:d2d9808ea7b4af864f35ea216be506ecec180628aced0704e34aca0b040ffe46"},
+    {file = "PyYAML-5.4.1-cp38-cp38-manylinux1_x86_64.whl", hash = "sha256:8c1be557ee92a20f184922c7b6424e8ab6691788e6d86137c5d93c1a6ec1b8fb"},
+    {file = "PyYAML-5.4.1-cp38-cp38-win32.whl", hash = "sha256:fa5ae20527d8e831e8230cbffd9f8fe952815b2b7dae6ffec25318803a7528fc"},
+    {file = "PyYAML-5.4.1-cp38-cp38-win_amd64.whl", hash = "sha256:0f5f5786c0e09baddcd8b4b45f20a7b5d61a7e7e99846e3c799b05c7c53fa696"},
+    {file = "PyYAML-5.4.1-cp39-cp39-macosx_10_9_x86_64.whl", hash = "sha256:294db365efa064d00b8d1ef65d8ea2c3426ac366c0c4368d930bf1c5fb497f77"},
+    {file = "PyYAML-5.4.1-cp39-cp39-manylinux1_x86_64.whl", hash = "sha256:74c1485f7707cf707a7aef42ef6322b8f97921bd89be2ab6317fd782c2d53183"},
+    {file = "PyYAML-5.4.1-cp39-cp39-win32.whl", hash = "sha256:49d4cdd9065b9b6e206d0595fee27a96b5dd22618e7520c33204a4a3239d5b10"},
+    {file = "PyYAML-5.4.1-cp39-cp39-win_amd64.whl", hash = "sha256:c20cfa2d49991c8b4147af39859b167664f2ad4561704ee74c1de03318e898db"},
+    {file = "PyYAML-5.4.1.tar.gz", hash = "sha256:607774cbba28732bfa802b54baa7484215f530991055bb562efbed5b2f20a45e"},
 ]
 requests = [
     {file = "requests-2.25.1-py2.py3-none-any.whl", hash = "sha256:c210084e36a42ae6b9219e00e48287def368a26d03a048ddad7bfee44f75871e"},
diff --git a/pyproject.toml b/pyproject.toml
index 81609ef2..5124bbb5 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -31,19 +31,20 @@ packages = [
 # Installing numpy/scipy/etc. from source is unlikely to work.
 # The block below forces Poetry to use piwheels.
 # We can add other repositories if we need them.
-# Setting default=true disables fallback to PyPI.
+# Setting default=true disables fallback to PyPI. I have removed
+# this for now, because it will prevent installation on non-Pi 
+# platforms.
 
 [[tool.poetry.source]]
 name = "piwheels"
 url = "https://www.piwheels.org/simple"
-default = true
 
 [tool.poetry.dependencies]
 python = "^3.7.3"
 Flask = "^1.0"
-numpy = "1.19.2" # Exact version so we can guarantee a wheel
+# let scipy specify numpy?? numpy = "1.19.2" # Exact version so we can guarantee a wheel
 Pillow = "^7.2.0"
-scipy = "1.6.1" # Exact version so we can guarantee a wheel
+scipy = "^1.6.1" # Exact version so we can guarantee a wheel
 "RPi.GPIO" = { version = "^0.7.0", optional = true }
 python-dateutil = "^2.8"
 psutil = "^5.6.7" # Autostorage extension
@@ -52,7 +53,7 @@ sangaboard = "^0.2"
 expiringdict = "^1.2.1"
 camera-stage-mapping = "0.1.4"
 picamerax = ">=20.9.1"
-pyyaml = "5.4.0" # pyyaml 5.4.1 is broken in piwheels
+pyyaml = "^5.4.0" # pyyaml 5.4.1 is broken in piwheels
 pytest-cov = "^2.10.1"
 piexif = "^1.1.3"
 labthings = "^1.2.2"

From 3b435ab2ee0cf0140aa8d80fd1d5be582c8099ad Mon Sep 17 00:00:00 2001
From: Richard Bowman <richard.bowman@cantab.net>
Date: Thu, 18 Feb 2021 15:56:11 +0000
Subject: [PATCH 16/41] Deleted obsolete functions

---
 .../recalibrate_utils.py                      | 111 ++++--------------
 1 file changed, 20 insertions(+), 91 deletions(-)

diff --git a/openflexure_microscope/api/default_extensions/picamera_autocalibrate/recalibrate_utils.py b/openflexure_microscope/api/default_extensions/picamera_autocalibrate/recalibrate_utils.py
index 1f804b2c..50eb3905 100644
--- a/openflexure_microscope/api/default_extensions/picamera_autocalibrate/recalibrate_utils.py
+++ b/openflexure_microscope/api/default_extensions/picamera_autocalibrate/recalibrate_utils.py
@@ -50,97 +50,6 @@ def adjust_exposure_to_setpoint(camera: PiCamera, setpoint: int):
     print("done")
 
 
-def adjust_exposure_and_gain(
-    camera: PiCamera, target_white_level: int = 700, max_iterations: int = 99
-):
-    """Adjust exposure and analog gain based on raw images.
-    
-    This routine is slow but effective.  It uses raw images, so we
-    are not affected by white balance or digital gain.
-    """
-    # Start by setting fully manual exposure.
-    camera.exposure_mode = "off"
-    camera.iso = 0  # We must set ISO=0 (auto) or we can't set gain
-    camera.analog_gain = 1
-    camera.digital_gain = 1
-    camera.shutter_speed = 1  # This is not valid - we'll get the minimum
-    time.sleep(0.5)
-
-    # We start with very low exposure settings and work up in coarse steps
-    # until either the brightness is high enough, or we can't increase the
-    # shutter speed any more.
-    iterations = 0
-    while True:
-        iterations += 1
-        if iterations > max_iterations:
-            logging.warning(
-                f"Auto exposure is stopping after {max_iterations} "
-                "but it has not converged."
-            )
-            break
-
-        with PiBayerArray(camera) as a:
-            camera.capture(a, format="jpeg", bayer=True)
-            max_brightness = np.max(a.array)
-
-        if max_brightness > target_white_level:
-            break
-
-        previous_shutter_speed = camera.shutter_speed
-        camera.shutter_speed = previous_shutter_speed * 2
-        time.sleep(0.5)
-        current_shutter_speed = camera.shutter_speed
-        # NB we save this in a variable in case it changes between
-        # here and the next loop
-        logging.info(
-            f"Max brightness {max_brightness} < {target_white_level}. "
-            f"Attempting to double exposure from "
-            f"{previous_shutter_speed} to {current_shutter_speed}"
-        )
-        if current_shutter_speed == previous_shutter_speed:
-            logging.info("Shutter speed has saturated, stopping.")
-            break
-
-    if max_brightness > target_white_level:
-        logging.info("Brightness is high enough, fine-tuning")
-        camera.shutter_speed = int(
-            current_shutter_speed * target_white_level / max_brightness
-        )
-
-
-def auto_expose_and_freeze_settings(camera: PiCamera):
-    """Freeze the settings after auto-exposing to white illumination"""
-    logging.info("Allowing the camera to auto-expose")
-    if "greyworld" in camera.AWB_MODES:
-        logging.info("Calibrating with greyworld AWB")
-        camera.awb_mode = "greyworld"
-    else:
-        logging.warning("Calibrating with auto AWB as greyworld is missing")
-        camera.awb_mode = "auto"
-    camera.exposure_mode = "auto"
-    camera.iso = (
-        0  # This is important, if it's on a fixed ISO, gain might not set properly.
-    )
-    for _ in range(6):
-        print(".", end="")
-        time.sleep(0.5)
-    logging.info("done")
-
-    logging.info("Freezing the camera settings...")
-    camera.shutter_speed = camera.exposure_speed
-    logging.info("Shutter speed = %s", (camera.shutter_speed))
-    camera.exposure_mode = "off"
-    logging.info("Auto exposure disabled")
-    g: Tuple[Fraction, Fraction] = camera.awb_gains
-    camera.awb_mode = "off"
-    camera.awb_gains = g
-    logging.info("Auto white balance disabled, gains are %s", (g))
-    logging.info(
-        "Analogue gain: %s, Digital gain: %s", camera.analog_gain, camera.digital_gain
-    )
-    adjust_exposure_to_setpoint(camera, 215)
-
-
 def adjust_shutter_and_gain_from_raw(
     camera: PiCamera,
     target_white_level: int = 700,
@@ -152,6 +61,26 @@ def adjust_shutter_and_gain_from_raw(
     
     This routine is slow but effective.  It uses raw images, so we
     are not affected by white balance or digital gain.
+
+    
+    Arguments:
+        target_white_level: 
+            The raw, 10-bit value we aim for.  The brightest pixels 
+            should be approximately this bright.  Maximum possible 
+            is 1023, 700 is reasonable.
+        max_iterations:
+            We will terminate once we perform this many iterations,
+            whether or not we converge.  More than 10 shouldn't happen.
+        tolerance: 
+            How close to the target value we consider "done".  Expressed
+            as a fraction of the ``target_white_level`` so 0.05 means
+            +/- 5%
+        percentile:
+            Rather then use the maximum value for each channel, we
+            calculate a percentile.  This makes us robust to single
+            pixels that are bright/noisy.  99.9% still picks the top
+            of the brightness range, but seems much more reliable
+            than just ``np.max()``.
     """
     # Start by setting fully manual exposure.
     camera.exposure_mode = "off"

From bc0995d0cf9bdbc849dd694be1dde1e33ba42df1 Mon Sep 17 00:00:00 2001
From: Richard Bowman <richard.bowman@cantab.net>
Date: Thu, 18 Feb 2021 18:03:42 +0000
Subject: [PATCH 17/41] Added poe serve

To save some typing ``poe serve`` now runs a debug server.
---
 pyproject.toml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/pyproject.toml b/pyproject.toml
index 5124bbb5..3476e253 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -99,6 +99,7 @@ isort = "isort ."
 pylint = "pylint openflexure_microscope"
 mypy = "mypy --cobertura-xml-report openflexure_microscope openflexure_microscope"
 test = "pytest ."
+serve = "python -m openflexure_microscope.api.app"
 
 format = ["black", "isort"]
 lint = ["pylint", "mypy"]

From 1f3ba2bff10e0228bbf4c8163d48dd5fd6083f1f Mon Sep 17 00:00:00 2001
From: Richard Bowman <richard.bowman@cantab.net>
Date: Tue, 23 Feb 2021 15:54:28 +0000
Subject: [PATCH 18/41] Allow origin to be overridden by query

Specifying overrideOrigin in the URL now
sets up the store with the modified origin.
This is intended for development, and makes it
much less annoying to develop with a Vue dev server.
---
 openflexure_microscope/api/static/src/store.js | 15 ++++++++++++++-
 1 file changed, 14 insertions(+), 1 deletion(-)

diff --git a/openflexure_microscope/api/static/src/store.js b/openflexure_microscope/api/static/src/store.js
index 8b92ca38..31f1fd0a 100644
--- a/openflexure_microscope/api/static/src/store.js
+++ b/openflexure_microscope/api/static/src/store.js
@@ -3,9 +3,22 @@ import Vuex from "vuex";
 
 Vue.use(Vuex);
 
+function getOriginFromLocation(){
+  // This will default to the same origin that's serving
+  // the web app - but can be overridden by the URL.
+  // See also devTools.vue which can change the origin.
+  let url = new URL(window.location.href);
+  let origin = url.searchParams.get("overrideOrigin");
+  if(origin){
+    return origin;
+  }else{
+    return url.origin;
+  }
+}
+
 export default new Vuex.Store({
   state: {
-    origin: window.location.origin,
+    origin: getOriginFromLocation(),
     available: false,
     waiting: false,
     error: "",

From a7bb0f9423956a39ea5493d8b688cebb3f3c0ed3 Mon Sep 17 00:00:00 2001
From: Richard Bowman <richard.bowman@cantab.net>
Date: Tue, 23 Feb 2021 15:56:15 +0000
Subject: [PATCH 19/41] Reset tour button and URL origin

Reset tour button resets the local storage used to mark the tour
as done.

Overriding the origin can now be done with a query string.
This will load the store with the new origin from the start,
so might be better for testing some things.
I'm not worried about unexpected bugs, as it is quite obvious
from the URL what's going on.
---
 .../aboutComponents/devTools.vue              | 37 ++++++++++++++++---
 1 file changed, 32 insertions(+), 5 deletions(-)

diff --git a/openflexure_microscope/api/static/src/components/tabContentComponents/aboutComponents/devTools.vue b/openflexure_microscope/api/static/src/components/tabContentComponents/aboutComponents/devTools.vue
index fecf56de..08f47e9b 100644
--- a/openflexure_microscope/api/static/src/components/tabContentComponents/aboutComponents/devTools.vue
+++ b/openflexure_microscope/api/static/src/components/tabContentComponents/aboutComponents/devTools.vue
@@ -1,12 +1,26 @@
 <template>
   <div>
-    <form class="uk-form-stacked" @submit.prevent="overrideAPIHost">
+    <form 
+      class="uk-form-stacked" 
+      @submit="overrideAPIHost"
+      action=""
+      method="GET">
       <label class="uk-form-label">Override API origin</label>
-      <input v-model="newOrigin" class="uk-input" type="text" />
+      <input v-model="newOrigin" name="overrideOrigin" class="uk-input" type="text" />
+      <label class="uk-form-label" >
+        <input v-model="reloadWhenOverridingOrigin" class="uk-input uk-checkbox" type="checkbox" />
+        Reload web app with new origin
+      </label>
       <button class="uk-button uk-button-default uk-margin-small">
         Apply
       </button>
     </form>
+    <form class="uk-form-stacked" @submit.prevent="resetTour">
+      <label class="uk-form-label">Re-run tour on next load</label>
+      <button class="uk-button uk-button-default uk-margin-small">
+        Reset
+      </button>
+    </form>
   </div>
 </template>
 
@@ -19,7 +33,8 @@ export default {
 
   data: function() {
     return {
-      newOrigin: this.$store.state.origin
+      newOrigin: this.$store.state.origin,
+      reloadWhenOverridingOrigin: true
     };
   },
 
@@ -32,9 +47,21 @@ export default {
   },
 
   methods: {
-    overrideAPIHost: function() {
-      this.$store.commit("changeOrigin", this.newOrigin);
+    overrideAPIHost: function(event) {
+      // Save the origin override, so that if we reload the web app, you can easily
       localStorage.overrideOrigin = this.newOrigin;
+      
+      // If we have elected not to reload the interface, just update the origin
+      // in the store.  Otherwise, the form's default action will do the job for us.
+      // TODO: preserve other query parameters when reloading
+      if(!this.reloadWhenOverridingOrigin){
+        this.$store.commit("changeOrigin", this.newOrigin);
+        event.preventDefault();
+      }
+    },
+    resetTour: function() {
+      // Make the introduction tour run next time the app loads
+      this.setLocalStorageObj("completedTour", false);
     }
   }
 };

From 8624e45df49fedd8ec9224080c2bd0452fb7b048 Mon Sep 17 00:00:00 2001
From: Richard Bowman <richard.bowman@cantab.net>
Date: Tue, 23 Feb 2021 17:36:58 +0000
Subject: [PATCH 20/41] Axios version bump and vuex-map-fields

vuex-map-fields cleans up code when mapping
store state to local computed properties.
---
 .../api/static/package-lock.json              | 235 ++++++++----------
 .../api/static/package.json                   |   5 +-
 2 files changed, 110 insertions(+), 130 deletions(-)

diff --git a/openflexure_microscope/api/static/package-lock.json b/openflexure_microscope/api/static/package-lock.json
index f8a024be..1a855c5a 100644
--- a/openflexure_microscope/api/static/package-lock.json
+++ b/openflexure_microscope/api/static/package-lock.json
@@ -2917,16 +2917,6 @@
           "integrity": "sha512-bY6fj56OUQ0hU1KjFNDQuJFezqKdrAyFdIevADiqrWHwSlbmBNMHp5ak2f40Pm8JTFyM2mqxkG6ngkHO11f/lg==",
           "dev": true
         },
-        "ansi-styles": {
-          "version": "4.3.0",
-          "resolved": "https://registry.npmjs.org/ansi-styles/-/ansi-styles-4.3.0.tgz",
-          "integrity": "sha512-zbB9rCJAT1rbjiVDb2hqKFHNYLxgtk8NURxZ3IZwD3F6NtxbXZQCnnSi1Lkx+IDohdPlFp222wVALIheZJQSEg==",
-          "dev": true,
-          "optional": true,
-          "requires": {
-            "color-convert": "^2.0.1"
-          }
-        },
         "browserslist": {
           "version": "4.15.0",
           "resolved": "https://registry.npmjs.org/browserslist/-/browserslist-4.15.0.tgz",
@@ -2972,36 +2962,12 @@
           "integrity": "sha512-8cEsSMwXfx7lWSUMA2s08z9dIgsnR5NAqjXP23stdsU3AUWkCr/rr4s4OFtHXn5XXr6+7kam3QFVoYyXNPdJPA==",
           "dev": true
         },
-        "color-convert": {
-          "version": "2.0.1",
-          "resolved": "https://registry.npmjs.org/color-convert/-/color-convert-2.0.1.tgz",
-          "integrity": "sha512-RRECPsj7iu/xb5oKYcsFHSppFNnsj/52OVTRKb4zP5onXwVF3zVmmToNcOfGC+CRDpfK/U584fMg38ZHCaElKQ==",
-          "dev": true,
-          "optional": true,
-          "requires": {
-            "color-name": "~1.1.4"
-          }
-        },
-        "color-name": {
-          "version": "1.1.4",
-          "resolved": "https://registry.npmjs.org/color-name/-/color-name-1.1.4.tgz",
-          "integrity": "sha512-dOy+3AuW3a2wNbZHIuMZpTcgjGuLU/uBL/ubcZF9OXbDo8ff4O8yVp5Bf0efS8uEoYo5q4Fx7dY9OgQGXgAsQA==",
-          "dev": true,
-          "optional": true
-        },
         "electron-to-chromium": {
           "version": "1.3.615",
           "resolved": "https://registry.npmjs.org/electron-to-chromium/-/electron-to-chromium-1.3.615.tgz",
           "integrity": "sha512-fNYTQXoUhNc6RmHDlGN4dgcLURSBIqQCN7ls6MuQ741+NJyLNRz8DxAC+pZpOKfRs6cfY0lv2kWdy8Oxf9j4+A==",
           "dev": true
         },
-        "emojis-list": {
-          "version": "3.0.0",
-          "resolved": "https://registry.npmjs.org/emojis-list/-/emojis-list-3.0.0.tgz",
-          "integrity": "sha512-/kyM18EfinwXZbno9FyUGeFh87KC8HRQBQGildHZbEuRyWFOmv1U10o9BBp8XVZDVNNuQKyIGIu5ZYAAXJ0V2Q==",
-          "dev": true,
-          "optional": true
-        },
         "fast-deep-equal": {
           "version": "3.1.3",
           "resolved": "https://registry.npmjs.org/fast-deep-equal/-/fast-deep-equal-3.1.3.tgz",
@@ -3035,35 +3001,6 @@
           "integrity": "sha512-WjKPNJF79dtJAVniUlGGWHYGz2jWxT6VhN/4m1NdkbZ2nOsEF+cI1Edgql5zCRhs/VsQYRvrXctxktVXZUkixw==",
           "dev": true
         },
-        "has-flag": {
-          "version": "4.0.0",
-          "resolved": "https://registry.npmjs.org/has-flag/-/has-flag-4.0.0.tgz",
-          "integrity": "sha512-EykJT/Q1KjTWctppgIAgfSO0tKVuZUjhgMr17kqTumMl6Afv3EISleU7qZUzoXDFTAHTDC4NOoG/ZxU3EvlMPQ==",
-          "dev": true,
-          "optional": true
-        },
-        "json5": {
-          "version": "2.1.3",
-          "resolved": "https://registry.npmjs.org/json5/-/json5-2.1.3.tgz",
-          "integrity": "sha512-KXPvOm8K9IJKFM0bmdn8QXh7udDh1g/giieX0NLCaMnb4hEiVFqnop2ImTXCc5e0/oHz3LTqmHGtExn5hfMkOA==",
-          "dev": true,
-          "optional": true,
-          "requires": {
-            "minimist": "^1.2.5"
-          }
-        },
-        "loader-utils": {
-          "version": "2.0.0",
-          "resolved": "https://registry.npmjs.org/loader-utils/-/loader-utils-2.0.0.tgz",
-          "integrity": "sha512-rP4F0h2RaWSvPEkD7BLDFQnvSf+nK+wr3ESUjNTyAGobqrijmW92zc+SO6d4p4B1wh7+B/Jg1mkQe5NYUEHtHQ==",
-          "dev": true,
-          "optional": true,
-          "requires": {
-            "big.js": "^5.2.2",
-            "emojis-list": "^3.0.0",
-            "json5": "^2.1.2"
-          }
-        },
         "locate-path": {
           "version": "5.0.0",
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@@ -3197,16 +3134,6 @@
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@@ -3233,31 +3160,6 @@
             "psl": "^1.1.28",
             "punycode": "^2.1.1"
           }
-        },
-        "vue-loader-v16": {
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-          "resolved": "https://registry.npmjs.org/vue-loader/-/vue-loader-16.1.1.tgz",
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-          "optional": true,
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-            "hash-sum": "^2.0.0",
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-          },
-          "dependencies": {
-            "chalk": {
-              "version": "4.1.0",
-              "resolved": "https://registry.npmjs.org/chalk/-/chalk-4.1.0.tgz",
-              "integrity": "sha512-qwx12AxXe2Q5xQ43Ac//I6v5aXTipYrSESdOgzrN+9XjgEpyjpKuvSGaN4qE93f7TQTlerQQ8S+EQ0EyDoVL1A==",
-              "dev": true,
-              "optional": true,
-              "requires": {
-                "ansi-styles": "^4.1.0",
-                "supports-color": "^7.1.0"
-              }
-            }
-          }
         }
       }
     },
@@ -3917,38 +3819,12 @@
       "dev": true
     },
     "axios": {
-      "version": "0.19.2",
-      "resolved": "https://registry.npmjs.org/axios/-/axios-0.19.2.tgz",
-      "integrity": "sha512-fjgm5MvRHLhx+osE2xoekY70AhARk3a6hkN+3Io1jc00jtquGvxYlKlsFUhmUET0V5te6CcZI7lcv2Ym61mjHA==",
+      "version": "0.21.1",
+      "resolved": "https://registry.npmjs.org/axios/-/axios-0.21.1.tgz",
+      "integrity": "sha512-dKQiRHxGD9PPRIUNIWvZhPTPpl1rf/OxTYKsqKUDjBwYylTvV7SjSHJb9ratfyzM6wCdLCOYLzs73qpg5c4iGA==",
       "dev": true,
       "requires": {
-        "follow-redirects": "1.5.10"
-      },
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-          "integrity": "sha512-OX8XqP7/1a9cqkxYw2yXss15f26NKWBpDXQd0/uK/KPqdQhxbPa994hnzjcE2VqQpDslf55723cKPUOGSmMY3g==",
-          "dev": true,
-          "requires": {
-            "ms": "2.0.0"
-          }
-        },
-        "follow-redirects": {
-          "version": "1.5.10",
-          "resolved": "https://registry.npmjs.org/follow-redirects/-/follow-redirects-1.5.10.tgz",
-          "integrity": "sha512-0V5l4Cizzvqt5D44aTXbFZz+FtyXV1vrDN6qrelxtfYQKW0KO0W2T/hkE8xvGa/540LkZlkaUjO4ailYTFtHVQ==",
-          "dev": true,
-          "requires": {
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-          "integrity": "sha1-VgiurfwAvmwpAd9fmGF4jeDVl8g=",
-          "dev": true
-        }
+        "follow-redirects": "^1.10.0"
       }
     },
     "babel-eslint": {
@@ -13811,6 +13687,104 @@
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       }
     },
+    "vue-loader-v16": {
+      "version": "npm:vue-loader@16.1.2",
+      "resolved": "https://registry.npmjs.org/vue-loader/-/vue-loader-16.1.2.tgz",
+      "integrity": "sha512-8QTxh+Fd+HB6fiL52iEVLKqE9N1JSlMXLR92Ijm6g8PZrwIxckgpqjPDWRP5TWxdiPaHR+alUWsnu1ShQOwt+Q==",
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+      "optional": true,
+      "requires": {
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+        "hash-sum": "^2.0.0",
+        "loader-utils": "^2.0.0"
+      },
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+        "ansi-styles": {
+          "version": "4.3.0",
+          "resolved": "https://registry.npmjs.org/ansi-styles/-/ansi-styles-4.3.0.tgz",
+          "integrity": "sha512-zbB9rCJAT1rbjiVDb2hqKFHNYLxgtk8NURxZ3IZwD3F6NtxbXZQCnnSi1Lkx+IDohdPlFp222wVALIheZJQSEg==",
+          "dev": true,
+          "optional": true,
+          "requires": {
+            "color-convert": "^2.0.1"
+          }
+        },
+        "chalk": {
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+          "resolved": "https://registry.npmjs.org/chalk/-/chalk-4.1.0.tgz",
+          "integrity": "sha512-qwx12AxXe2Q5xQ43Ac//I6v5aXTipYrSESdOgzrN+9XjgEpyjpKuvSGaN4qE93f7TQTlerQQ8S+EQ0EyDoVL1A==",
+          "dev": true,
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+          "requires": {
+            "ansi-styles": "^4.1.0",
+            "supports-color": "^7.1.0"
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+          "integrity": "sha512-rP4F0h2RaWSvPEkD7BLDFQnvSf+nK+wr3ESUjNTyAGobqrijmW92zc+SO6d4p4B1wh7+B/Jg1mkQe5NYUEHtHQ==",
+          "dev": true,
+          "optional": true,
+          "requires": {
+            "big.js": "^5.2.2",
+            "emojis-list": "^3.0.0",
+            "json5": "^2.1.2"
+          }
+        },
+        "supports-color": {
+          "version": "7.2.0",
+          "resolved": "https://registry.npmjs.org/supports-color/-/supports-color-7.2.0.tgz",
+          "integrity": "sha512-qpCAvRl9stuOHveKsn7HncJRvv501qIacKzQlO/+Lwxc9+0q2wLyv4Dfvt80/DPn2pqOBsJdDiogXGR9+OvwRw==",
+          "dev": true,
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+          "requires": {
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+          }
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+    },
     "vue-observe-visibility": {
       "version": "0.4.6",
       "resolved": "https://registry.npmjs.org/vue-observe-visibility/-/vue-observe-visibility-0.4.6.tgz",
@@ -13874,6 +13848,11 @@
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       "dev": true
     },
+    "vuex-map-fields": {
+      "version": "1.4.1",
+      "resolved": "https://registry.npmjs.org/vuex-map-fields/-/vuex-map-fields-1.4.1.tgz",
+      "integrity": "sha512-jvIcpvoIPqwvJCOfRkPU9Rj0EbjWuk7GlNC5LXU9mCXVGZph6bWGHZssnoUzpLMxJtXQEHoVyZkKf7YQV+/bnQ=="
+    },
     "watchpack": {
       "version": "1.7.4",
       "resolved": "https://registry.npmjs.org/watchpack/-/watchpack-1.7.4.tgz",
diff --git a/openflexure_microscope/api/static/package.json b/openflexure_microscope/api/static/package.json
index a0d8b116..c05324b1 100644
--- a/openflexure_microscope/api/static/package.json
+++ b/openflexure_microscope/api/static/package.json
@@ -13,14 +13,15 @@
   "dependencies": {
     "material-design-icons": "^3.0.1",
     "mousetrap": "^1.6.5",
-    "vue-observe-visibility": "^0.4.6"
+    "vue-observe-visibility": "^0.4.6",
+    "vuex-map-fields": "^1.4.1"
   },
   "devDependencies": {
     "@vue/cli-plugin-babel": "^3.12.1",
     "@vue/cli-plugin-eslint": "^4.5.9",
     "@vue/cli-service": "^4.5.9",
     "@vue/eslint-config-prettier": "^6.0.0",
-    "axios": "^0.19.2",
+    "axios": "^0.21.1",
     "babel-eslint": "^10.1.0",
     "css-loader": "^3.6.0",
     "eslint": "^6.8.0",

From 03a4f36556814cecde20ab7e822446fc5e095ca7 Mon Sep 17 00:00:00 2001
From: Richard Bowman <richard.bowman@cantab.net>
Date: Mon, 1 Mar 2021 12:20:04 +0000
Subject: [PATCH 21/41] Remove spurious GPU preview event

---
 .../tabContentComponents/settingsComponents/featuresSettings.vue | 1 -
 1 file changed, 1 deletion(-)

diff --git a/openflexure_microscope/api/static/src/components/tabContentComponents/settingsComponents/featuresSettings.vue b/openflexure_microscope/api/static/src/components/tabContentComponents/settingsComponents/featuresSettings.vue
index 8d2fbde2..581d7c0f 100644
--- a/openflexure_microscope/api/static/src/components/tabContentComponents/settingsComponents/featuresSettings.vue
+++ b/openflexure_microscope/api/static/src/components/tabContentComponents/settingsComponents/featuresSettings.vue
@@ -33,7 +33,6 @@ export default {
       },
       set(value) {
         this.$store.commit("changeIHIEnabled", value);
-        this.$root.$emit("globalSafeTogglePreview", value);
       }
     }
   },

From a373afd955cadca3ffdf22ac1a9e313ed46df1b0 Mon Sep 17 00:00:00 2001
From: Richard Bowman <r.w.bowman@bath.ac.uk>
Date: Tue, 16 Mar 2021 11:01:57 +0000
Subject: [PATCH 22/41] swap print for logging in old function

---
 .../picamera_autocalibrate/recalibrate_utils.py               | 4 +---
 1 file changed, 1 insertion(+), 3 deletions(-)

diff --git a/openflexure_microscope/api/default_extensions/picamera_autocalibrate/recalibrate_utils.py b/openflexure_microscope/api/default_extensions/picamera_autocalibrate/recalibrate_utils.py
index 50eb3905..58a340a1 100644
--- a/openflexure_microscope/api/default_extensions/picamera_autocalibrate/recalibrate_utils.py
+++ b/openflexure_microscope/api/default_extensions/picamera_autocalibrate/recalibrate_utils.py
@@ -40,14 +40,12 @@ def flat_lens_shading_table(camera: PiCamera) -> np.ndarray:
 
 def adjust_exposure_to_setpoint(camera: PiCamera, setpoint: int):
     """Adjust the camera's exposure time until the maximum pixel value is <setpoint>."""
-    print("Adjusting shutter speed to hit setpoint {}".format(setpoint), end="")
+    logging.info("Adjusting shutter speed to hit setpoint {}".format(setpoint))
     for _ in range(3):
-        print(".", end="")
         camera.shutter_speed = int(
             camera.shutter_speed * setpoint / np.max(rgb_image(camera))
         )
         time.sleep(1)
-    print("done")
 
 
 def adjust_shutter_and_gain_from_raw(

From 64f2263e81899c4f3065dd359d5a977179c02b9c Mon Sep 17 00:00:00 2001
From: Richard Bowman <r.w.bowman@bath.ac.uk>
Date: Wed, 21 Apr 2021 12:35:49 +0100
Subject: [PATCH 23/41] Remove poetry.lock

We've switched to pipenv, poetry.lock is now superfluous
---
 poetry.lock | 1689 ---------------------------------------------------
 1 file changed, 1689 deletions(-)
 delete mode 100644 poetry.lock

diff --git a/poetry.lock b/poetry.lock
deleted file mode 100644
index 5c309797..00000000
--- a/poetry.lock
+++ /dev/null
@@ -1,1689 +0,0 @@
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-version = "0.7.12"
-description = "A configurable sidebar-enabled Sphinx theme"
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-[package.source]
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-description = "A pluggable API specification generator. Currently supports the OpenAPI Specification (f.k.a. the Swagger specification)."
-category = "main"
-optional = false
-python-versions = ">=3.6"
-
-[package.dependencies]
-PyYAML = {version = ">=3.10", optional = true, markers = "extra == \"yaml\""}
-
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-dev = ["PyYAML (>=3.10)", "prance[osv] (>=0.11)", "marshmallow (>=3.0.0)", "pytest", "mock", "flake8 (==3.8.4)", "flake8-bugbear (==20.11.1)", "pre-commit (>=2.4,<3.0)", "tox"]
-docs = ["marshmallow (>=3.0.0)", "pyyaml (==5.4.1)", "sphinx (==3.4.3)", "sphinx-issues (==1.2.0)", "sphinx-rtd-theme (==0.5.1)"]
-lint = ["flake8 (==3.8.4)", "flake8-bugbear (==20.11.1)", "pre-commit (>=2.4,<3.0)"]
-tests = ["PyYAML (>=3.10)", "prance[osv] (>=0.11)", "marshmallow (>=3.0.0)", "pytest", "mock"]
-validation = ["prance[osv] (>=0.11)"]
-yaml = ["PyYAML (>=3.10)"]
-
-[package.source]
-type = "legacy"
-url = "https://www.piwheels.org/simple"
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-
-[[package]]
-name = "apispec-webframeworks"
-version = "0.5.2"
-description = "Web framework plugins for apispec."
-category = "main"
-optional = false
-python-versions = ">=3.6"
-
-[package.dependencies]
-apispec = {version = ">=2.0.0", extras = ["yaml"]}
-
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-    {file = "webargs-7.0.1-py2.py3-none-any.whl", hash = "sha256:ce8c565789ece1584be7edba41617319eb75de59b2987958bee3f3fdb3669e60"},
-]
-werkzeug = [
-    {file = "Werkzeug-1.0.1-py2.py3-none-any.whl", hash = "sha256:2de2a5db0baeae7b2d2664949077c2ac63fbd16d98da0ff71837f7d1dea3fd43"},
-]
-wrapt = [
-    {file = "wrapt-1.12.1-cp34-cp34m-linux_armv6l.whl", hash = "sha256:c16fd7cad3d27a5db392ae0e6215533a912a7d3d83a40b8cf275744276989780"},
-    {file = "wrapt-1.12.1-cp34-cp34m-linux_armv7l.whl", hash = "sha256:c16fd7cad3d27a5db392ae0e6215533a912a7d3d83a40b8cf275744276989780"},
-    {file = "wrapt-1.12.1-cp35-cp35m-linux_armv6l.whl", hash = "sha256:1ba3a6bcb5014ed4d9c98afe8aa47b5ed320f84292b4f1b9f6afa0f4b2b91351"},
-    {file = "wrapt-1.12.1-cp35-cp35m-linux_armv7l.whl", hash = "sha256:1ba3a6bcb5014ed4d9c98afe8aa47b5ed320f84292b4f1b9f6afa0f4b2b91351"},
-    {file = "wrapt-1.12.1-cp37-cp37m-linux_armv6l.whl", hash = "sha256:d3294c918c5529e50b5454d39b589648d9baf6152e380067606d5566d71369a0"},
-    {file = "wrapt-1.12.1-cp37-cp37m-linux_armv7l.whl", hash = "sha256:d3294c918c5529e50b5454d39b589648d9baf6152e380067606d5566d71369a0"},
-]
-zeroconf = [
-    {file = "zeroconf-0.28.8-py3-none-any.whl", hash = "sha256:3608be2db58f6f0dc70665e02ab420fb8bf428016f2c78403d879e066ecc9bff"},
-]
-zipp = [
-    {file = "zipp-3.4.0-py3-none-any.whl", hash = "sha256:102c24ef8f171fd729d46599845e95c7ab894a4cf45f5de11a44cc7444fb1108"},
-]

From fd32c22e30846660e2015032cd9b99a356f500e7 Mon Sep 17 00:00:00 2001
From: Richard Bowman <r.w.bowman@bath.ac.uk>
Date: Wed, 21 Apr 2021 12:40:10 +0100
Subject: [PATCH 24/41] Fixed formatting

---
 .../default_extensions/picamera_autocalibrate/extension.py   | 5 ++++-
 setup.py                                                     | 5 +++--
 2 files changed, 7 insertions(+), 3 deletions(-)

diff --git a/openflexure_microscope/api/default_extensions/picamera_autocalibrate/extension.py b/openflexure_microscope/api/default_extensions/picamera_autocalibrate/extension.py
index 28f51352..146bc8d7 100644
--- a/openflexure_microscope/api/default_extensions/picamera_autocalibrate/extension.py
+++ b/openflexure_microscope/api/default_extensions/picamera_autocalibrate/extension.py
@@ -1,5 +1,6 @@
 import logging
 from contextlib import contextmanager
+from typing import Tuple
 
 import labthings.fields as fields
 from flask import abort
@@ -7,7 +8,6 @@ from labthings import find_component
 from labthings.extensions import BaseExtension
 from labthings.views import ActionView
 from picamerax import PiCamera
-from typing import Tuple
 
 from openflexure_microscope.camera.base import BaseCamera
 from openflexure_microscope.microscope import Microscope
@@ -86,6 +86,7 @@ class LSTExtension(BaseExtension):
             endpoint="auto_lens_shading_table",
         )
 
+
 @contextmanager
 def find_picamera() -> Tuple[PiCamera, BaseCamera, Microscope]:
     """Locate the microscope and raise a sensible error if it's missing."""
@@ -132,6 +133,7 @@ class RecalibrateView(ActionView):
                 picamera.lens_shading_table = lst
             microscope.save_settings()
 
+
 class AutoLensShadingTableView(ActionView):
     def post(self):
         """Perform flat-field correction
@@ -149,6 +151,7 @@ class AutoLensShadingTableView(ActionView):
                 picamera.lens_shading_table = lst
             microscope.save_settings()
 
+
 class FlattenLSTView(ActionView):
     def post(self):
         with find_picamera() as (picamera, scamera, microscope):
diff --git a/setup.py b/setup.py
index 73269b1a..adf729ff 100644
--- a/setup.py
+++ b/setup.py
@@ -6,10 +6,11 @@ https://packaging.python.org/guides/distributing-packages-using-setuptools/
 
 """
 
-# the following imports, from the guide above, prefer `setuptools` to `distutils`
-from setuptools import setup, find_packages
 from os import path
 
+# the following imports, from the guide above, prefer `setuptools` to `distutils`
+from setuptools import find_packages, setup
+
 here = path.abspath(path.dirname(__file__))
 
 # Get the long description from the README file

From 8c50f73b347815902195c280012618244d38d71a Mon Sep 17 00:00:00 2001
From: Richard Bowman <r.w.bowman@bath.ac.uk>
Date: Wed, 21 Apr 2021 12:54:53 +0100
Subject: [PATCH 25/41] Fixed type of context manager

---
 .../default_extensions/picamera_autocalibrate/extension.py    | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/openflexure_microscope/api/default_extensions/picamera_autocalibrate/extension.py b/openflexure_microscope/api/default_extensions/picamera_autocalibrate/extension.py
index 146bc8d7..e8dc726e 100644
--- a/openflexure_microscope/api/default_extensions/picamera_autocalibrate/extension.py
+++ b/openflexure_microscope/api/default_extensions/picamera_autocalibrate/extension.py
@@ -1,6 +1,6 @@
 import logging
 from contextlib import contextmanager
-from typing import Tuple
+from typing import Tuple, Generator
 
 import labthings.fields as fields
 from flask import abort
@@ -88,7 +88,7 @@ class LSTExtension(BaseExtension):
 
 
 @contextmanager
-def find_picamera() -> Tuple[PiCamera, BaseCamera, Microscope]:
+def find_picamera() -> Generator[Tuple[PiCamera, BaseCamera, Microscope], None, None]:
     """Locate the microscope and raise a sensible error if it's missing."""
     microscope = find_component("org.openflexure.microscope")
 

From 88de3089eabc1aaf5880488ceb7fa9d8474697d5 Mon Sep 17 00:00:00 2001
From: Richard Bowman <r.w.bowman@bath.ac.uk>
Date: Wed, 21 Apr 2021 13:38:14 +0100
Subject: [PATCH 26/41] Fixed linter errors

---
 .../default_extensions/picamera_autocalibrate/extension.py  | 6 +++---
 .../picamera_autocalibrate/recalibrate_utils.py             | 3 +--
 2 files changed, 4 insertions(+), 5 deletions(-)

diff --git a/openflexure_microscope/api/default_extensions/picamera_autocalibrate/extension.py b/openflexure_microscope/api/default_extensions/picamera_autocalibrate/extension.py
index e8dc726e..5f0d9c7e 100644
--- a/openflexure_microscope/api/default_extensions/picamera_autocalibrate/extension.py
+++ b/openflexure_microscope/api/default_extensions/picamera_autocalibrate/extension.py
@@ -205,7 +205,7 @@ class AutoExposureFromRawView(ActionView):
     }
 
     def post(self, args):
-        with find_picamera() as (picamera, scamera, microscope):
+        with find_picamera() as (picamera, _, _):
             adjust_shutter_and_gain_from_raw(picamera, **args)
 
 
@@ -224,7 +224,7 @@ class AutoWhiteBalanceFromRawView(ActionView):
     }
 
     def post(self, args):
-        with find_picamera() as (picamera, scamera, microscope):
+        with find_picamera() as (picamera, _, _):
             adjust_white_balance_from_raw(picamera, **args)
 
 
@@ -238,5 +238,5 @@ class GetRawChannelPercentilesView(ActionView):
     schema = fields.List(fields.Integer)
 
     def post(self, args):
-        with find_picamera() as (picamera, scamera, microscope):
+        with find_picamera() as (picamera, _, _):
             return get_channel_percentiles(picamera, args["percentile"])
diff --git a/openflexure_microscope/api/default_extensions/picamera_autocalibrate/recalibrate_utils.py b/openflexure_microscope/api/default_extensions/picamera_autocalibrate/recalibrate_utils.py
index e6c6b5fe..352d2354 100644
--- a/openflexure_microscope/api/default_extensions/picamera_autocalibrate/recalibrate_utils.py
+++ b/openflexure_microscope/api/default_extensions/picamera_autocalibrate/recalibrate_utils.py
@@ -1,6 +1,5 @@
 import logging
 import time
-from fractions import Fraction
 from typing import List, Optional, Tuple
 
 import numpy as np
@@ -40,7 +39,7 @@ def flat_lens_shading_table(camera: PiCamera) -> np.ndarray:
 
 def adjust_exposure_to_setpoint(camera: PiCamera, setpoint: int):
     """Adjust the camera's exposure time until the maximum pixel value is <setpoint>."""
-    logging.info("Adjusting shutter speed to hit setpoint {}".format(setpoint))
+    logging.info(f"Adjusting shutter speed to hit setpoint {setpoint}")
     for _ in range(3):
         camera.shutter_speed = int(
             camera.shutter_speed * setpoint / np.max(rgb_image(camera))

From e14800b549040463c75a0989133b7d1670333816 Mon Sep 17 00:00:00 2001
From: Richard <richard.bowman@cantab.net>
Date: Tue, 27 Apr 2021 14:28:08 +0100
Subject: [PATCH 27/41] linter fixes

---
 .../aboutComponents/devTools.vue              | 28 +++++++++++++------
 .../api/static/src/store.js                   |  6 ++--
 2 files changed, 22 insertions(+), 12 deletions(-)

diff --git a/openflexure_microscope/api/static/src/components/tabContentComponents/aboutComponents/devTools.vue b/openflexure_microscope/api/static/src/components/tabContentComponents/aboutComponents/devTools.vue
index 08f47e9b..0bcc9cb5 100644
--- a/openflexure_microscope/api/static/src/components/tabContentComponents/aboutComponents/devTools.vue
+++ b/openflexure_microscope/api/static/src/components/tabContentComponents/aboutComponents/devTools.vue
@@ -1,14 +1,24 @@
 <template>
   <div>
-    <form 
-      class="uk-form-stacked" 
-      @submit="overrideAPIHost"
+    <form
+      class="uk-form-stacked"
       action=""
-      method="GET">
+      method="GET"
+      @submit="overrideAPIHost"
+    >
       <label class="uk-form-label">Override API origin</label>
-      <input v-model="newOrigin" name="overrideOrigin" class="uk-input" type="text" />
-      <label class="uk-form-label" >
-        <input v-model="reloadWhenOverridingOrigin" class="uk-input uk-checkbox" type="checkbox" />
+      <input
+        v-model="newOrigin"
+        name="overrideOrigin"
+        class="uk-input"
+        type="text"
+      />
+      <label class="uk-form-label">
+        <input
+          v-model="reloadWhenOverridingOrigin"
+          class="uk-input uk-checkbox"
+          type="checkbox"
+        />
         Reload web app with new origin
       </label>
       <button class="uk-button uk-button-default uk-margin-small">
@@ -50,11 +60,11 @@ export default {
     overrideAPIHost: function(event) {
       // Save the origin override, so that if we reload the web app, you can easily
       localStorage.overrideOrigin = this.newOrigin;
-      
+
       // If we have elected not to reload the interface, just update the origin
       // in the store.  Otherwise, the form's default action will do the job for us.
       // TODO: preserve other query parameters when reloading
-      if(!this.reloadWhenOverridingOrigin){
+      if (!this.reloadWhenOverridingOrigin) {
         this.$store.commit("changeOrigin", this.newOrigin);
         event.preventDefault();
       }
diff --git a/openflexure_microscope/api/static/src/store.js b/openflexure_microscope/api/static/src/store.js
index 31f1fd0a..f8255fdc 100644
--- a/openflexure_microscope/api/static/src/store.js
+++ b/openflexure_microscope/api/static/src/store.js
@@ -3,15 +3,15 @@ import Vuex from "vuex";
 
 Vue.use(Vuex);
 
-function getOriginFromLocation(){
+function getOriginFromLocation() {
   // This will default to the same origin that's serving
   // the web app - but can be overridden by the URL.
   // See also devTools.vue which can change the origin.
   let url = new URL(window.location.href);
   let origin = url.searchParams.get("overrideOrigin");
-  if(origin){
+  if (origin) {
     return origin;
-  }else{
+  } else {
     return url.origin;
   }
 }

From 82a277b04c925ea5886836870140bb7a7eb9665b Mon Sep 17 00:00:00 2001
From: Richard <richard.bowman@cantab.net>
Date: Tue, 27 Apr 2021 16:36:55 +0100
Subject: [PATCH 28/41] Cache stream settings in local storage

GPU preview and MJPEG stream settings are now persisted
using localStorage.  The old code that disabled
the stream for local connections now
just sets the initial/default value.

The initialisation of stream settings is now done
in the created() method of streamContent.vue.

I've eliminated the "globalsafetogglepreview" event
in favour of watching the store.
---
 .../api/static/src/components/appContent.vue  | 40 ++++++------------
 .../settingsComponents/streamSettings.vue     | 41 ++++++++++++++++++-
 .../tabContentComponents/streamContent.vue    | 15 +++++--
 3 files changed, 63 insertions(+), 33 deletions(-)

diff --git a/openflexure_microscope/api/static/src/components/appContent.vue b/openflexure_microscope/api/static/src/components/appContent.vue
index 60713801..fbc12e8d 100644
--- a/openflexure_microscope/api/static/src/components/appContent.vue
+++ b/openflexure_microscope/api/static/src/components/appContent.vue
@@ -140,6 +140,8 @@ import loggingContent from "./tabContentComponents/loggingContent.vue";
 // Import modal components for device initialisation
 import calibrationModal from "./modalComponents/calibrationModal.vue";
 
+import { mapState } from "vuex";
+
 // Export main app
 export default {
   name: "AppContent",
@@ -241,21 +243,21 @@ export default {
 
     currentTabIndex: function() {
       return this.tabOrder.indexOf(this.currentTab);
+    },
+
+    // Map the setting for IHI's interface so we can watch it
+    ...mapState(["IHIEnabled"])
+  },
+
+  watch: {
+    // Update the interface when the IHI interface is enabled/disabled
+    IHIEnabled: function(newValue) {
+      this.updateTopTabs(newValue);
     }
   },
 
   created: function() {
     if (this.$store.getters.ready) {
-      // Detect local connection
-      if (
-        ["localhost", "0.0.0.0", "127.0.0.1", "[::1]"].includes(
-          window.location.hostname
-        )
-      ) {
-        this.$store.commit("changeDisableStream", true);
-        this.$store.commit("changeAutoGpuPreview", true);
-        this.$store.commit("changeTrackWindow", true);
-      }
       // Update top tabs
       this.updateTopTabs(this.$store.state.IHIEnabled);
       // Update plugins
@@ -264,16 +266,6 @@ export default {
         this.startModals();
       });
     }
-
-    // Watch for host 'ready', then update status
-    this.unwatchStoreFunction = this.$store.watch(
-      state => {
-        return state.IHIEnabled;
-      },
-      IHIEnabled => {
-        this.updateTopTabs(IHIEnabled);
-      }
-    );
   },
 
   mounted() {
@@ -291,14 +283,6 @@ export default {
     });
   },
 
-  beforeDestroy() {
-    // Then we call that function here to unwatch
-    if (this.unwatchStoreFunction) {
-      this.unwatchStoreFunction();
-      this.unwatchStoreFunction = null;
-    }
-  },
-
   methods: {
     updateTopTabs: function(IHIEnabled) {
       if (IHIEnabled) {
diff --git a/openflexure_microscope/api/static/src/components/tabContentComponents/settingsComponents/streamSettings.vue b/openflexure_microscope/api/static/src/components/tabContentComponents/settingsComponents/streamSettings.vue
index b21627a6..2136ad5a 100644
--- a/openflexure_microscope/api/static/src/components/tabContentComponents/settingsComponents/streamSettings.vue
+++ b/openflexure_microscope/api/static/src/components/tabContentComponents/settingsComponents/streamSettings.vue
@@ -73,8 +73,11 @@ export default {
         return this.$store.state.autoGpuPreview;
       },
       set(value) {
+        // NB the stream viewer watches the store, and is
+        // responsible for making the request that switches
+        // GPU preview on/off
+        // see streamContent.vue
         this.$store.commit("changeAutoGpuPreview", value);
-        this.$root.$emit("globalSafeTogglePreview", value);
       }
     },
 
@@ -86,6 +89,42 @@ export default {
         this.$store.commit("changeTrackWindow", value);
       }
     }
+  },
+
+  watch: {
+    // Cache the stream settings to local storage for persistence
+    // (the next 3 functions all relate to this)
+    disableStream: function(newValue) {
+      console.log(`disableStream updated to ${newValue} and saved in local storage`);
+    },
+    autoGpuPreview: function(newValue) {
+      console.log(`GPU preview updated to ${newValue} and saved in local storage`);
+    },
+    trackWindow: function(newValue) {
+      console.log(`trackWindow updated to ${newValue} and saved in local storage`);
+    }
+  },
+
+  created() {
+    // Apply sensible defaults for stream settings, depending on
+    // whether we're connecting locally or remotely, respecting
+    // the settings that were cached previously.
+    const localMode = ["localhost", "0.0.0.0", "127.0.0.1", "[::1]"].includes(
+      window.location.hostname
+    );
+    const localDefaults = {
+      disableStream: true,
+      autoGpuPreview: true,
+      trackWindow: true
+    };
+    for (let k in localDefaults) {
+      if (localStorage.getItem(k) !== null) {
+        this[k] = this.getLocalStorageObj(k);
+      } else if (localMode) {
+        console.log(`${k} set to default value for a local connection`);
+        this[k] = localDefaults[k];
+      }
+    }
   }
 };
 </script>
diff --git a/openflexure_microscope/api/static/src/components/tabContentComponents/streamContent.vue b/openflexure_microscope/api/static/src/components/tabContentComponents/streamContent.vue
index 2554d621..16fde3e1 100644
--- a/openflexure_microscope/api/static/src/components/tabContentComponents/streamContent.vue
+++ b/openflexure_microscope/api/static/src/components/tabContentComponents/streamContent.vue
@@ -69,6 +69,16 @@ export default {
     },
     settingsUri: function() {
       return `${this.$store.getters.baseUri}/api/v2/instrument/settings`;
+    },
+    autoGpuPreview: function() {
+      return this.$store.state.autoGpuPreview;
+    }
+  },
+
+  watch: {
+    autoGpuPreview: function(newValue) {
+      // When the GPU preview setting in the store changes, update the server
+      this.safePreviewRequest(newValue);
     }
   },
 
@@ -77,9 +87,6 @@ export default {
     this.$root.$on("globalTogglePreview", state => {
       this.previewRequest(state);
     });
-    this.$root.$on("globalSafeTogglePreview", state => {
-      this.safePreviewRequest(state);
-    });
     // A global signal listener to flash the stream element
     this.$root.$on("globalFlashStream", () => {
       this.flashStream();
@@ -97,7 +104,7 @@ export default {
 
   created: function() {
     // Send a request to start/stop GPU preview based on global setting
-    this.safePreviewRequest(this.$store.state.autoGpuPreview);
+    this.safePreviewRequest(this.autoGpuPreview);
   },
 
   beforeDestroy: function() {

From 79b0d48cf4463fbdd0aecdb3a2bdfac159b2ab24 Mon Sep 17 00:00:00 2001
From: Richard Bowman <r.w.bowman@bath.ac.uk>
Date: Tue, 27 Apr 2021 17:13:40 +0100
Subject: [PATCH 29/41] Swap Generator annotation for Iterator

---
 .../default_extensions/picamera_autocalibrate/extension.py    | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/openflexure_microscope/api/default_extensions/picamera_autocalibrate/extension.py b/openflexure_microscope/api/default_extensions/picamera_autocalibrate/extension.py
index 5f0d9c7e..af31741e 100644
--- a/openflexure_microscope/api/default_extensions/picamera_autocalibrate/extension.py
+++ b/openflexure_microscope/api/default_extensions/picamera_autocalibrate/extension.py
@@ -1,6 +1,6 @@
 import logging
 from contextlib import contextmanager
-from typing import Tuple, Generator
+from typing import Tuple, Iterator
 
 import labthings.fields as fields
 from flask import abort
@@ -88,7 +88,7 @@ class LSTExtension(BaseExtension):
 
 
 @contextmanager
-def find_picamera() -> Generator[Tuple[PiCamera, BaseCamera, Microscope], None, None]:
+def find_picamera() -> Iterator[Tuple[PiCamera, BaseCamera, Microscope]]:
     """Locate the microscope and raise a sensible error if it's missing."""
     microscope = find_component("org.openflexure.microscope")
 

From bb303d4766392565cc9ae3dc0d63f4e77ddcb945 Mon Sep 17 00:00:00 2001
From: Richard Bowman <r.w.bowman@bath.ac.uk>
Date: Tue, 27 Apr 2021 18:54:21 +0100
Subject: [PATCH 30/41] Simplified auto gain/exposure algorithm

adjust_shutter_and_gain_from_raw now uses a simpler algorithm.
The code is longer overall but hides some details in fuctions.
I've also split the loop into one for shutter speed and one for gain.
This isn't the algorithm that I originally wrote, but it seems to
work and is more readable.
---
 .../recalibrate_utils.py                      | 219 +++++++++++++-----
 1 file changed, 155 insertions(+), 64 deletions(-)

diff --git a/openflexure_microscope/api/default_extensions/picamera_autocalibrate/recalibrate_utils.py b/openflexure_microscope/api/default_extensions/picamera_autocalibrate/recalibrate_utils.py
index 352d2354..a6112cfe 100644
--- a/openflexure_microscope/api/default_extensions/picamera_autocalibrate/recalibrate_utils.py
+++ b/openflexure_microscope/api/default_extensions/picamera_autocalibrate/recalibrate_utils.py
@@ -1,17 +1,44 @@
+"""
+Functions to set up a Raspberry Pi Camera v2 for scientific use
+
+This module provides slower, simpler functions to set the
+gain, exposure, and white balance of a Raspberry Pi camera, using
+`picamerax` (a fork of `picamera`) to get as-manual-as-possible
+control over the camera.  It's mostly used by the OpenFlexure
+Microscope, though it deliberately has no hard dependencies on
+said software, so that it's useful on its own.
+
+There are three main calibration steps:
+
+* Setting exposure time and gain to get a reasonably bright
+  image.
+* Fixing the white balance to get a neutral image
+* Taking a uniform white image and using it to calibrate
+  the Lens Shading Table
+
+The most reliable way to do this, avoiding any issues relating
+to "memory" or nonlinearities in the camera's image processing
+pipeline, is to use raw images.  This is quite slow, but very
+reliable.  The three steps above can be accomplished by:
+
+```
+picamera = picamerax.PiCamera()
+
+adjust_shutter_and_gain_from_raw(picamera)
+adjust_white_balance_from_raw(picamera)
+lst = lst_from_camera(picamera)
+picamera.lens_shading_table = lst
+```
+"""
+
 import logging
 import time
-from typing import List, Optional, Tuple
+from typing import List, Optional, Tuple, NamedTuple
 
 import numpy as np
 from picamerax import PiCamera
 from picamerax.array import PiBayerArray, PiRGBArray
 
-# I have used f strings throughout, for readability.
-# The performance implication of using them in logging statements
-# really doesn't matter here - also, loglevel is usually set to
-# INFO to report progress via the LabThings action API
-# pylint: disable=logging-fstring-interpolation
-
 
 def rgb_image(
     camera: PiCamera, resize: Optional[Tuple[int, int]] = None, **kwargs
@@ -38,7 +65,10 @@ def flat_lens_shading_table(camera: PiCamera) -> np.ndarray:
 
 
 def adjust_exposure_to_setpoint(camera: PiCamera, setpoint: int):
-    """Adjust the camera's exposure time until the maximum pixel value is <setpoint>."""
+    """Adjust the camera's exposure time until the maximum pixel value is <setpoint>.
+    
+    NB this method uses RGB images (i.e. processed ones) not raw images.
+    """
     logging.info(f"Adjusting shutter speed to hit setpoint {setpoint}")
     for _ in range(3):
         camera.shutter_speed = int(
@@ -47,6 +77,69 @@ def adjust_exposure_to_setpoint(camera: PiCamera, setpoint: int):
         time.sleep(1)
 
 
+def set_minimum_exposure(
+    camera: PiCamera
+):
+    """Enable manual exposure, with low gain and shutter speed
+    
+    We set exposure mode to manual, analog and digital gain
+    to 1, and shutter speed to the minimum (8us for Pi Camera v2)
+    NB ISO is left at auto, because this is needed for the gains
+    to be set correctly.
+    """
+    camera.exposure_mode = "off"
+    camera.iso = 0  # We must set ISO=0 (auto) or we can't set gain
+    camera.analog_gain = 1
+    camera.digital_gain = 1
+    # Setting the shutter speed to 1us will result in it being set
+    # to the minimum possible, which is probably 8us for PiCamera v2
+    camera.shutter_speed = 1
+    time.sleep(0.5)
+
+class ExposureTest(NamedTuple):
+    """Record the results of testing the camera's current exposure settings"""
+    level: int
+    shutter_speed: int
+    analog_gain: float
+
+
+def test_exposure_settings(
+    camera: PiCamera,
+    percentile: float
+) -> ExposureTest:
+    """Evaluate current exposure settings using a raw image
+
+    We will acquire a raw image and calculate the given percentile
+    of the pixel values.  We return a dictionary containing the
+    percentile (which will be compared to the target), as well as
+    the camera's shutter and gain values.
+    """
+    max_brightness = np.max(get_channel_percentiles(camera, percentile))
+    # The reported brightness can, theoretically, be negative or zero
+    # because of black level compensation.  The line below forces a
+    # minimum value of 1 which will keep things well-behaved!
+    if max_brightness < 1:
+        logging.warning(
+            f"Measured brightness of {max_brightness}. "
+            "This should normally be >= 1, and may indicate the "
+            "camera's black level compensation has gone wrong."
+        )
+        max_brightness = 1
+    shutter_speed = float(camera.shutter_speed)
+    analog_gain = float(camera.analog_gain)
+    logging.info(
+        f"Brightness: {max_brightness: >5.0f}, "
+        f"Gain: {analog_gain: >4.1f}, "
+        f"Shutter: {shutter_speed: >7.0f}"
+    )
+    return ExposureTest(max_brightness, shutter_speed, analog_gain)
+
+def check_convergence(test: ExposureTest, target: int, tolerance: float):
+    """Check whether the brightness is within the specified target range"""
+    converged = abs(test.level - target) < target * tolerance
+    return converged
+
+
 def adjust_shutter_and_gain_from_raw(
     camera: PiCamera,
     target_white_level: int = 700,
@@ -64,7 +157,7 @@ def adjust_shutter_and_gain_from_raw(
         target_white_level: 
             The raw, 10-bit value we aim for.  The brightest pixels 
             should be approximately this bright.  Maximum possible 
-            is 1023, 700 is reasonable.
+            is about 900, 700 is reasonable.
         max_iterations:
             We will terminate once we perform this many iterations,
             whether or not we converge.  More than 10 shouldn't happen.
@@ -79,70 +172,61 @@ def adjust_shutter_and_gain_from_raw(
             of the brightness range, but seems much more reliable
             than just ``np.max()``.
     """
-    # Start by setting fully manual exposure.
-    camera.exposure_mode = "off"
-    camera.iso = 0  # We must set ISO=0 (auto) or we can't set gain
-    camera.analog_gain = 1
-    camera.digital_gain = 1
-    camera.shutter_speed = 1  # This is not valid - we'll get the minimum
-    time.sleep(0.5)
+    if target_white_level * (tolerance + 1) >= 959:
+        raise ValueError("The target level is too high - a saturated image would be considered successful.  target_white_level * (tolerance + 1) must be less than 959.")
+    
+    set_minimum_exposure(camera)
 
-    # We start with very low exposure settings and work up in coarse steps
+    # We start with very low exposure settings and work up
     # until either the brightness is high enough, or we can't increase the
     # shutter speed any more.
     iterations = 0
-    shutter_speed_increments = [10, 2, None]
-    shutter_speed_increment = shutter_speed_increments.pop(0)
     while iterations < max_iterations:
-        iterations += 1
-        max_brightness = np.max(get_channel_percentiles(camera, percentile))
-        tested_shutter_speed = camera.shutter_speed
-        tested_analog_gain = camera.analog_gain
-        logging.info(
-            f"Brightness: {max_brightness: >5.0f}, "
-            f"Target: {target_white_level: >5.0f}, "
-            f"Gain: {float(tested_analog_gain): >4.1f}, "
-            f"Shutter: {float(tested_shutter_speed): >7.0f}"
-        )
+        test = test_exposure_settings(camera, percentile)
 
-        if abs(max_brightness - target_white_level) < target_white_level * tolerance:
-            logging.info(
-                f"Brightness has converged to within {tolerance * 100 :.0f}% "
-                f"after {iterations} iterations."
-            )
+        if check_convergence(test, target_white_level, tolerance):
             break
+        iterations += 1
 
-        # if not shutter_speed_maximised:  # Start by adjusting shutter speed
-        if max_brightness > target_white_level // 2:
-            shutter_speed_increment = (
-                None
-            )  # If we're within a factor of 2, trigger fine-tuning
-        if shutter_speed_increment is None:
-            logging.info("Fine-tuning shutter speed")
-            new_shutter_speed = int(
-                tested_shutter_speed * target_white_level / max_brightness
-            )
-            camera.shutter_speed = new_shutter_speed
-        else:
-            if max_brightness > target_white_level:
-                logging.info("Reducing shutter speed")
-                camera.shutter_speed = int(
-                    tested_shutter_speed / shutter_speed_increment
-                )
-            else:
-                logging.info("Increasing shutter speed")
-                camera.shutter_speed = tested_shutter_speed * shutter_speed_increment
+        # Adjust shutter speed so that the brightness approximates the target
+        # NB we put a maximum of 32 on this, to stop it increasing too quickly.
+        camera.shutter_speed = int(
+            test.shutter_speed * min(target_white_level / test.level, 32)
+        )
         time.sleep(0.5)
 
         # Check whether the shutter speed is still going up - if not, we've hit a maximum
-        current_shutter_speed = camera.shutter_speed
-        if current_shutter_speed == tested_shutter_speed:
-            camera.analog_gain *= 2
-            if camera.analog_gain == tested_analog_gain:
-                logging.info("Shutter speed and gain are both maxed out.  Giving up!")
-                break
-            logging.info("Shutter speed has maxed out, doubled gain to compensate.")
-    return max_brightness
+        if camera.shutter_speed == test.shutter_speed:
+            logging.info("Shutter speed has maxed out.")
+            break
+
+    # Now, if we've not converged, increase gain until we converge or run out of options.
+    while iterations < max_iterations:
+        test = test_exposure_settings(camera, percentile)
+        if check_convergence(test, target_white_level, tolerance):
+            break
+        iterations += 1
+
+        # Adjust gain to make the white level hit the target, again with a maximum
+        camera.analog_gain *= min(target_white_level / test.level, 2)
+        time.sleep(0.5)
+
+        # Check the gain is still changing - if not, we have probably hit the maximum
+        if camera.analog_gain == test.analog_gain:
+            logging.info("Gain has maxed out.")
+            break
+    
+    if check_convergence(test, target_white_level, tolerance):
+        logging.info(
+            f"Brightness has converged to within {tolerance * 100 :.0f}%."
+        )
+    else:
+        logging.warning(
+            f"Failed to reach target brightness of {target_white_level}."
+            f"Brightness reached {test.level} after {iterations} iterations."
+        )
+
+    return test.level
 
 
 def adjust_white_balance_from_raw(
@@ -186,11 +270,18 @@ def channels_from_bayer_array(bayer_array: np.ndarray) -> np.ndarray:
 
 
 def get_channel_percentiles(camera: PiCamera, percentile: float) -> np.ndarray:
-    """Calculate the brightness percentile of the pixels in each channel"""
+    """Calculate the brightness percentile of the pixels in each channel
+    
+    This is a number between -64 and 959 for each channel, because the
+    camera takes 10-bit images (maximum=1023) and its zero level is set
+    at 64 for denoising purposes (there's black level compensation built
+    in, and to avoid skewing the noise, the black level is set as 64 to
+    leave some room for negative values.
+    """
     with PiBayerArray(camera) as output:
         camera.capture(output, format="jpeg", bayer=True)
         channels = channels_from_bayer_array(output.array)
-        return np.percentile(channels, percentile, axis=(1, 2))
+        return np.percentile(channels, percentile, axis=(1, 2)) - 64
 
 
 def lst_from_channels(channels: np.ndarray) -> np.ndarray:

From 87f636ecc09d4bf90b336089a225e77a4e96a99e Mon Sep 17 00:00:00 2001
From: Richard Bowman <r.w.bowman@bath.ac.uk>
Date: Tue, 27 Apr 2021 19:56:54 +0100
Subject: [PATCH 31/41] Code format and linting

---
 .../picamera_autocalibrate/extension.py       |  2 +-
 .../recalibrate_utils.py                      | 28 +++++++++----------
 2 files changed, 15 insertions(+), 15 deletions(-)

diff --git a/openflexure_microscope/api/default_extensions/picamera_autocalibrate/extension.py b/openflexure_microscope/api/default_extensions/picamera_autocalibrate/extension.py
index af31741e..1a0bf539 100644
--- a/openflexure_microscope/api/default_extensions/picamera_autocalibrate/extension.py
+++ b/openflexure_microscope/api/default_extensions/picamera_autocalibrate/extension.py
@@ -1,6 +1,6 @@
 import logging
 from contextlib import contextmanager
-from typing import Tuple, Iterator
+from typing import Iterator, Tuple
 
 import labthings.fields as fields
 from flask import abort
diff --git a/openflexure_microscope/api/default_extensions/picamera_autocalibrate/recalibrate_utils.py b/openflexure_microscope/api/default_extensions/picamera_autocalibrate/recalibrate_utils.py
index a6112cfe..c1aba3c7 100644
--- a/openflexure_microscope/api/default_extensions/picamera_autocalibrate/recalibrate_utils.py
+++ b/openflexure_microscope/api/default_extensions/picamera_autocalibrate/recalibrate_utils.py
@@ -33,7 +33,7 @@ picamera.lens_shading_table = lst
 
 import logging
 import time
-from typing import List, Optional, Tuple, NamedTuple
+from typing import List, NamedTuple, Optional, Tuple
 
 import numpy as np
 from picamerax import PiCamera
@@ -77,9 +77,7 @@ def adjust_exposure_to_setpoint(camera: PiCamera, setpoint: int):
         time.sleep(1)
 
 
-def set_minimum_exposure(
-    camera: PiCamera
-):
+def set_minimum_exposure(camera: PiCamera):
     """Enable manual exposure, with low gain and shutter speed
     
     We set exposure mode to manual, analog and digital gain
@@ -96,17 +94,16 @@ def set_minimum_exposure(
     camera.shutter_speed = 1
     time.sleep(0.5)
 
+
 class ExposureTest(NamedTuple):
     """Record the results of testing the camera's current exposure settings"""
+
     level: int
     shutter_speed: int
     analog_gain: float
 
 
-def test_exposure_settings(
-    camera: PiCamera,
-    percentile: float
-) -> ExposureTest:
+def test_exposure_settings(camera: PiCamera, percentile: float) -> ExposureTest:
     """Evaluate current exposure settings using a raw image
 
     We will acquire a raw image and calculate the given percentile
@@ -134,6 +131,7 @@ def test_exposure_settings(
     )
     return ExposureTest(max_brightness, shutter_speed, analog_gain)
 
+
 def check_convergence(test: ExposureTest, target: int, tolerance: float):
     """Check whether the brightness is within the specified target range"""
     converged = abs(test.level - target) < target * tolerance
@@ -173,8 +171,12 @@ def adjust_shutter_and_gain_from_raw(
             than just ``np.max()``.
     """
     if target_white_level * (tolerance + 1) >= 959:
-        raise ValueError("The target level is too high - a saturated image would be considered successful.  target_white_level * (tolerance + 1) must be less than 959.")
-    
+        raise ValueError(
+            "The target level is too high - a saturated image would be "
+            "considered successful.  target_white_level * (tolerance + 1) "
+            "must be less than 959."
+        )
+
     set_minimum_exposure(camera)
 
     # We start with very low exposure settings and work up
@@ -215,11 +217,9 @@ def adjust_shutter_and_gain_from_raw(
         if camera.analog_gain == test.analog_gain:
             logging.info("Gain has maxed out.")
             break
-    
+
     if check_convergence(test, target_white_level, tolerance):
-        logging.info(
-            f"Brightness has converged to within {tolerance * 100 :.0f}%."
-        )
+        logging.info(f"Brightness has converged to within {tolerance * 100 :.0f}%.")
     else:
         logging.warning(
             f"Failed to reach target brightness of {target_white_level}."

From 82eba1e99a0948274b1971ffefa4728a1ca2a304 Mon Sep 17 00:00:00 2001
From: Richard Bowman <r.w.bowman@bath.ac.uk>
Date: Tue, 27 Apr 2021 20:17:07 +0100
Subject: [PATCH 32/41] fixed typing error

---
 .../picamera_autocalibrate/recalibrate_utils.py                 | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/openflexure_microscope/api/default_extensions/picamera_autocalibrate/recalibrate_utils.py b/openflexure_microscope/api/default_extensions/picamera_autocalibrate/recalibrate_utils.py
index c1aba3c7..450584ed 100644
--- a/openflexure_microscope/api/default_extensions/picamera_autocalibrate/recalibrate_utils.py
+++ b/openflexure_microscope/api/default_extensions/picamera_autocalibrate/recalibrate_utils.py
@@ -122,7 +122,7 @@ def test_exposure_settings(camera: PiCamera, percentile: float) -> ExposureTest:
             "camera's black level compensation has gone wrong."
         )
         max_brightness = 1
-    shutter_speed = float(camera.shutter_speed)
+    shutter_speed = int(camera.shutter_speed)
     analog_gain = float(camera.analog_gain)
     logging.info(
         f"Brightness: {max_brightness: >5.0f}, "

From 6e7adb66cd0c0ca34258426f8b159e6635942ebd Mon Sep 17 00:00:00 2001
From: Richard Bowman <r.w.bowman@bath.ac.uk>
Date: Wed, 28 Apr 2021 22:29:56 +0100
Subject: [PATCH 33/41] Fix handling of missing CSM matrix

The code checks for the camera-stage mapper matrix by looking at its truth value.
However, this is ambiguous because the matrix has many elements.  That means that
if it's missing, we get the expected result, but if it's present
we get an error.

I have avoided dict.get() and instead look it up with [] notation.
This will raise a KeyError if it's missing, which I
handle helpfully.
If the key is present but the value is not castable to an array, we'll
get an exception anyway.
---
 .../api/default_extensions/camera_stage_mapping.py         | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/openflexure_microscope/api/default_extensions/camera_stage_mapping.py b/openflexure_microscope/api/default_extensions/camera_stage_mapping.py
index ca479e97..6630d8a3 100644
--- a/openflexure_microscope/api/default_extensions/camera_stage_mapping.py
+++ b/openflexure_microscope/api/default_extensions/camera_stage_mapping.py
@@ -194,10 +194,11 @@ class CSMExtension(BaseExtension):
     @property
     def image_to_stage_displacement_matrix(self) -> np.ndarray:  # 2x2 integer array
         """A 2x2 matrix that converts displacement in image coordinates to stage coordinates."""
-        displacement_matrix = self.get_settings().get("image_to_stage_displacement")
-        if not displacement_matrix:
+        settings = self.get_settings()
+        try:
+            return np.array(settings["image_to_stage_displacement"])
+        except KeyError:
             raise ValueError("The microscope has not yet been calibrated.")
-        return np.array(displacement_matrix)
 
     def move_in_image_coordinates(self, displacement_in_pixels: XYCoordinateType):
         """Move by a given number of pixels on the camera"""

From 14c4908a9827a77eba371211dd299006990f1d9d Mon Sep 17 00:00:00 2001
From: Richard Bowman <r.w.bowman@bath.ac.uk>
Date: Tue, 4 May 2021 13:41:39 +0100
Subject: [PATCH 34/41] fix linter error

---
 .../api/default_extensions/camera_stage_mapping.py            | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/openflexure_microscope/api/default_extensions/camera_stage_mapping.py b/openflexure_microscope/api/default_extensions/camera_stage_mapping.py
index 6630d8a3..13716359 100644
--- a/openflexure_microscope/api/default_extensions/camera_stage_mapping.py
+++ b/openflexure_microscope/api/default_extensions/camera_stage_mapping.py
@@ -197,8 +197,8 @@ class CSMExtension(BaseExtension):
         settings = self.get_settings()
         try:
             return np.array(settings["image_to_stage_displacement"])
-        except KeyError:
-            raise ValueError("The microscope has not yet been calibrated.")
+        except KeyError as exc:
+            raise ValueError("The microscope has not yet been calibrated.") from exc
 
     def move_in_image_coordinates(self, displacement_in_pixels: XYCoordinateType):
         """Move by a given number of pixels on the camera"""

From 0c6e6caade9e5b097db89364c84d891619ca3eac Mon Sep 17 00:00:00 2001
From: Richard <richard.bowman@cantab.net>
Date: Wed, 5 May 2021 10:05:47 +0100
Subject: [PATCH 35/41] Improve errors with better exception

I've swapped the ValueError for a RuntimeError subclass to
make it clearer what's gone wrong.
---
 .../camera_stage_mapping.py                   | 20 +++++++++++++++++--
 1 file changed, 18 insertions(+), 2 deletions(-)

diff --git a/openflexure_microscope/api/default_extensions/camera_stage_mapping.py b/openflexure_microscope/api/default_extensions/camera_stage_mapping.py
index 13716359..032660ba 100644
--- a/openflexure_microscope/api/default_extensions/camera_stage_mapping.py
+++ b/openflexure_microscope/api/default_extensions/camera_stage_mapping.py
@@ -83,6 +83,15 @@ class LoggingMoveWrapper:
         self._history: List[Tuple[float, Optional[CoordinateType]]] = []
 
 
+class CSMUncalibratedError(RuntimeError):
+    """A calibrated camera stage mapper is required, but this one is not calibrated.
+
+    The camera stage mapper requires calibration information to relate image pixels
+    to stage coordinates.  If a method attempts to retrieve this calibration before
+    it exists, we raise this exception.
+    """
+
+
 class CSMExtension(BaseExtension):
     """
     Use the camera as an encoder, so we can relate camera and stage coordinates
@@ -133,7 +142,12 @@ class CSMExtension(BaseExtension):
     def get_settings(self) -> Dict[str, Any]:
         """Retrieve the settings for this extension"""
         keys: List[str] = ["extensions", self.name]
-        return get_by_path(self.microscope.read_settings(), keys)
+        try:
+            return get_by_path(self.microscope.read_settings(), keys)
+        except KeyError as exc:
+            raise CSMUncalibratedError(
+                "Camera stage mapping calibration data is missing"
+            ) from exc
 
     def camera_stage_functions(self) -> Tuple[Callable, Callable, Callable, Callable]:
         """Return functions that allow us to interface with the microscope"""
@@ -198,7 +212,9 @@ class CSMExtension(BaseExtension):
         try:
             return np.array(settings["image_to_stage_displacement"])
         except KeyError as exc:
-            raise ValueError("The microscope has not yet been calibrated.") from exc
+            raise CSMUncalibratedError(
+                "The microscope has not yet been calibrated."
+            ) from exc
 
     def move_in_image_coordinates(self, displacement_in_pixels: XYCoordinateType):
         """Move by a given number of pixels on the camera"""

From 0bdb5b4721b16c145871f177a8207a2734440475 Mon Sep 17 00:00:00 2001
From: Richard <richard.bowman@cantab.net>
Date: Wed, 5 May 2021 16:19:43 +0100
Subject: [PATCH 36/41] Actually save stream settings to local storage

After some refactoring, I lost the code that actually
saved stream settings to local storage.
This commit restores that functionality.
---
 .../settingsComponents/streamSettings.vue         | 15 ++++++++++++---
 1 file changed, 12 insertions(+), 3 deletions(-)

diff --git a/openflexure_microscope/api/static/src/components/tabContentComponents/settingsComponents/streamSettings.vue b/openflexure_microscope/api/static/src/components/tabContentComponents/settingsComponents/streamSettings.vue
index 2136ad5a..60b7cdb7 100644
--- a/openflexure_microscope/api/static/src/components/tabContentComponents/settingsComponents/streamSettings.vue
+++ b/openflexure_microscope/api/static/src/components/tabContentComponents/settingsComponents/streamSettings.vue
@@ -95,13 +95,22 @@ export default {
     // Cache the stream settings to local storage for persistence
     // (the next 3 functions all relate to this)
     disableStream: function(newValue) {
-      console.log(`disableStream updated to ${newValue} and saved in local storage`);
+      console.log(
+        `disableStream updated to ${newValue} and saved in local storage`
+      );
+      this.setLocalStorageObj("disableStream", newValue);
     },
     autoGpuPreview: function(newValue) {
-      console.log(`GPU preview updated to ${newValue} and saved in local storage`);
+      console.log(
+        `GPU preview updated to ${newValue} and saved in local storage`
+      );
+      this.setLocalStorageObj("autoGpuPreview", newValue);
     },
     trackWindow: function(newValue) {
-      console.log(`trackWindow updated to ${newValue} and saved in local storage`);
+      console.log(
+        `trackWindow updated to ${newValue} and saved in local storage`
+      );
+      this.setLocalStorageObj("trackWindow", newValue);
     }
   },
 

From 126766aa06f84e829012ad31efdccebc0b027612 Mon Sep 17 00:00:00 2001
From: Richard <richard.bowman@cantab.net>
Date: Wed, 5 May 2021 16:44:25 +0100
Subject: [PATCH 37/41] Removed unnecessary package

I'm not using vuex-map-fields, so have
removed it.
---
 .../api/static/package-lock.json              | 201 +++++++++---------
 .../api/static/package.json                   |   3 +-
 2 files changed, 99 insertions(+), 105 deletions(-)

diff --git a/openflexure_microscope/api/static/package-lock.json b/openflexure_microscope/api/static/package-lock.json
index 1a855c5a..364ee484 100644
--- a/openflexure_microscope/api/static/package-lock.json
+++ b/openflexure_microscope/api/static/package-lock.json
@@ -2917,6 +2917,16 @@
           "integrity": "sha512-bY6fj56OUQ0hU1KjFNDQuJFezqKdrAyFdIevADiqrWHwSlbmBNMHp5ak2f40Pm8JTFyM2mqxkG6ngkHO11f/lg==",
           "dev": true
         },
+        "ansi-styles": {
+          "version": "4.3.0",
+          "resolved": "https://registry.npmjs.org/ansi-styles/-/ansi-styles-4.3.0.tgz",
+          "integrity": "sha512-zbB9rCJAT1rbjiVDb2hqKFHNYLxgtk8NURxZ3IZwD3F6NtxbXZQCnnSi1Lkx+IDohdPlFp222wVALIheZJQSEg==",
+          "dev": true,
+          "optional": true,
+          "requires": {
+            "color-convert": "^2.0.1"
+          }
+        },
         "browserslist": {
           "version": "4.15.0",
           "resolved": "https://registry.npmjs.org/browserslist/-/browserslist-4.15.0.tgz",
@@ -2962,12 +2972,36 @@
           "integrity": "sha512-8cEsSMwXfx7lWSUMA2s08z9dIgsnR5NAqjXP23stdsU3AUWkCr/rr4s4OFtHXn5XXr6+7kam3QFVoYyXNPdJPA==",
           "dev": true
         },
+        "color-convert": {
+          "version": "2.0.1",
+          "resolved": "https://registry.npmjs.org/color-convert/-/color-convert-2.0.1.tgz",
+          "integrity": "sha512-RRECPsj7iu/xb5oKYcsFHSppFNnsj/52OVTRKb4zP5onXwVF3zVmmToNcOfGC+CRDpfK/U584fMg38ZHCaElKQ==",
+          "dev": true,
+          "optional": true,
+          "requires": {
+            "color-name": "~1.1.4"
+          }
+        },
+        "color-name": {
+          "version": "1.1.4",
+          "resolved": "https://registry.npmjs.org/color-name/-/color-name-1.1.4.tgz",
+          "integrity": "sha512-dOy+3AuW3a2wNbZHIuMZpTcgjGuLU/uBL/ubcZF9OXbDo8ff4O8yVp5Bf0efS8uEoYo5q4Fx7dY9OgQGXgAsQA==",
+          "dev": true,
+          "optional": true
+        },
         "electron-to-chromium": {
           "version": "1.3.615",
           "resolved": "https://registry.npmjs.org/electron-to-chromium/-/electron-to-chromium-1.3.615.tgz",
           "integrity": "sha512-fNYTQXoUhNc6RmHDlGN4dgcLURSBIqQCN7ls6MuQ741+NJyLNRz8DxAC+pZpOKfRs6cfY0lv2kWdy8Oxf9j4+A==",
           "dev": true
         },
+        "emojis-list": {
+          "version": "3.0.0",
+          "resolved": "https://registry.npmjs.org/emojis-list/-/emojis-list-3.0.0.tgz",
+          "integrity": "sha512-/kyM18EfinwXZbno9FyUGeFh87KC8HRQBQGildHZbEuRyWFOmv1U10o9BBp8XVZDVNNuQKyIGIu5ZYAAXJ0V2Q==",
+          "dev": true,
+          "optional": true
+        },
         "fast-deep-equal": {
           "version": "3.1.3",
           "resolved": "https://registry.npmjs.org/fast-deep-equal/-/fast-deep-equal-3.1.3.tgz",
@@ -3001,6 +3035,35 @@
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           "dev": true
         },
+        "has-flag": {
+          "version": "4.0.0",
+          "resolved": "https://registry.npmjs.org/has-flag/-/has-flag-4.0.0.tgz",
+          "integrity": "sha512-EykJT/Q1KjTWctppgIAgfSO0tKVuZUjhgMr17kqTumMl6Afv3EISleU7qZUzoXDFTAHTDC4NOoG/ZxU3EvlMPQ==",
+          "dev": true,
+          "optional": true
+        },
+        "json5": {
+          "version": "2.2.0",
+          "resolved": "https://registry.npmjs.org/json5/-/json5-2.2.0.tgz",
+          "integrity": "sha512-f+8cldu7X/y7RAJurMEJmdoKXGB/X550w2Nr3tTbezL6RwEE/iMcm+tZnXeoZtKuOq6ft8+CqzEkrIgx1fPoQA==",
+          "dev": true,
+          "optional": true,
+          "requires": {
+            "minimist": "^1.2.5"
+          }
+        },
+        "loader-utils": {
+          "version": "2.0.0",
+          "resolved": "https://registry.npmjs.org/loader-utils/-/loader-utils-2.0.0.tgz",
+          "integrity": "sha512-rP4F0h2RaWSvPEkD7BLDFQnvSf+nK+wr3ESUjNTyAGobqrijmW92zc+SO6d4p4B1wh7+B/Jg1mkQe5NYUEHtHQ==",
+          "dev": true,
+          "optional": true,
+          "requires": {
+            "big.js": "^5.2.2",
+            "emojis-list": "^3.0.0",
+            "json5": "^2.1.2"
+          }
+        },
         "locate-path": {
           "version": "5.0.0",
           "resolved": "https://registry.npmjs.org/locate-path/-/locate-path-5.0.0.tgz",
@@ -3134,6 +3197,16 @@
             "ansi-regex": "^5.0.0"
           }
         },
+        "supports-color": {
+          "version": "7.2.0",
+          "resolved": "https://registry.npmjs.org/supports-color/-/supports-color-7.2.0.tgz",
+          "integrity": "sha512-qpCAvRl9stuOHveKsn7HncJRvv501qIacKzQlO/+Lwxc9+0q2wLyv4Dfvt80/DPn2pqOBsJdDiogXGR9+OvwRw==",
+          "dev": true,
+          "optional": true,
+          "requires": {
+            "has-flag": "^4.0.0"
+          }
+        },
         "terser-webpack-plugin": {
           "version": "2.3.8",
           "resolved": "https://registry.npmjs.org/terser-webpack-plugin/-/terser-webpack-plugin-2.3.8.tgz",
@@ -3160,6 +3233,31 @@
             "psl": "^1.1.28",
             "punycode": "^2.1.1"
           }
+        },
+        "vue-loader-v16": {
+          "version": "npm:vue-loader@16.2.0",
+          "resolved": "https://registry.npmjs.org/vue-loader/-/vue-loader-16.2.0.tgz",
+          "integrity": "sha512-TitGhqSQ61RJljMmhIGvfWzJ2zk9m1Qug049Ugml6QP3t0e95o0XJjk29roNEiPKJQBEi8Ord5hFuSuELzSp8Q==",
+          "dev": true,
+          "optional": true,
+          "requires": {
+            "chalk": "^4.1.0",
+            "hash-sum": "^2.0.0",
+            "loader-utils": "^2.0.0"
+          },
+          "dependencies": {
+            "chalk": {
+              "version": "4.1.1",
+              "resolved": "https://registry.npmjs.org/chalk/-/chalk-4.1.1.tgz",
+              "integrity": "sha512-diHzdDKxcU+bAsUboHLPEDQiw0qEe0qd7SYUn3HgcFlWgbDcfLGswOHYeGrHKzG9z6UYf01d9VFMfZxPM1xZSg==",
+              "dev": true,
+              "optional": true,
+              "requires": {
+                "ansi-styles": "^4.1.0",
+                "supports-color": "^7.1.0"
+              }
+            }
+          }
         }
       }
     },
@@ -13687,104 +13785,6 @@
         }
       }
     },
-    "vue-loader-v16": {
-      "version": "npm:vue-loader@16.1.2",
-      "resolved": "https://registry.npmjs.org/vue-loader/-/vue-loader-16.1.2.tgz",
-      "integrity": "sha512-8QTxh+Fd+HB6fiL52iEVLKqE9N1JSlMXLR92Ijm6g8PZrwIxckgpqjPDWRP5TWxdiPaHR+alUWsnu1ShQOwt+Q==",
-      "dev": true,
-      "optional": true,
-      "requires": {
-        "chalk": "^4.1.0",
-        "hash-sum": "^2.0.0",
-        "loader-utils": "^2.0.0"
-      },
-      "dependencies": {
-        "ansi-styles": {
-          "version": "4.3.0",
-          "resolved": "https://registry.npmjs.org/ansi-styles/-/ansi-styles-4.3.0.tgz",
-          "integrity": "sha512-zbB9rCJAT1rbjiVDb2hqKFHNYLxgtk8NURxZ3IZwD3F6NtxbXZQCnnSi1Lkx+IDohdPlFp222wVALIheZJQSEg==",
-          "dev": true,
-          "optional": true,
-          "requires": {
-            "color-convert": "^2.0.1"
-          }
-        },
-        "chalk": {
-          "version": "4.1.0",
-          "resolved": "https://registry.npmjs.org/chalk/-/chalk-4.1.0.tgz",
-          "integrity": "sha512-qwx12AxXe2Q5xQ43Ac//I6v5aXTipYrSESdOgzrN+9XjgEpyjpKuvSGaN4qE93f7TQTlerQQ8S+EQ0EyDoVL1A==",
-          "dev": true,
-          "optional": true,
-          "requires": {
-            "ansi-styles": "^4.1.0",
-            "supports-color": "^7.1.0"
-          }
-        },
-        "color-convert": {
-          "version": "2.0.1",
-          "resolved": "https://registry.npmjs.org/color-convert/-/color-convert-2.0.1.tgz",
-          "integrity": "sha512-RRECPsj7iu/xb5oKYcsFHSppFNnsj/52OVTRKb4zP5onXwVF3zVmmToNcOfGC+CRDpfK/U584fMg38ZHCaElKQ==",
-          "dev": true,
-          "optional": true,
-          "requires": {
-            "color-name": "~1.1.4"
-          }
-        },
-        "color-name": {
-          "version": "1.1.4",
-          "resolved": "https://registry.npmjs.org/color-name/-/color-name-1.1.4.tgz",
-          "integrity": "sha512-dOy+3AuW3a2wNbZHIuMZpTcgjGuLU/uBL/ubcZF9OXbDo8ff4O8yVp5Bf0efS8uEoYo5q4Fx7dY9OgQGXgAsQA==",
-          "dev": true,
-          "optional": true
-        },
-        "emojis-list": {
-          "version": "3.0.0",
-          "resolved": "https://registry.npmjs.org/emojis-list/-/emojis-list-3.0.0.tgz",
-          "integrity": "sha512-/kyM18EfinwXZbno9FyUGeFh87KC8HRQBQGildHZbEuRyWFOmv1U10o9BBp8XVZDVNNuQKyIGIu5ZYAAXJ0V2Q==",
-          "dev": true,
-          "optional": true
-        },
-        "has-flag": {
-          "version": "4.0.0",
-          "resolved": "https://registry.npmjs.org/has-flag/-/has-flag-4.0.0.tgz",
-          "integrity": "sha512-EykJT/Q1KjTWctppgIAgfSO0tKVuZUjhgMr17kqTumMl6Afv3EISleU7qZUzoXDFTAHTDC4NOoG/ZxU3EvlMPQ==",
-          "dev": true,
-          "optional": true
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-        "json5": {
-          "version": "2.2.0",
-          "resolved": "https://registry.npmjs.org/json5/-/json5-2.2.0.tgz",
-          "integrity": "sha512-f+8cldu7X/y7RAJurMEJmdoKXGB/X550w2Nr3tTbezL6RwEE/iMcm+tZnXeoZtKuOq6ft8+CqzEkrIgx1fPoQA==",
-          "dev": true,
-          "optional": true,
-          "requires": {
-            "minimist": "^1.2.5"
-          }
-        },
-        "loader-utils": {
-          "version": "2.0.0",
-          "resolved": "https://registry.npmjs.org/loader-utils/-/loader-utils-2.0.0.tgz",
-          "integrity": "sha512-rP4F0h2RaWSvPEkD7BLDFQnvSf+nK+wr3ESUjNTyAGobqrijmW92zc+SO6d4p4B1wh7+B/Jg1mkQe5NYUEHtHQ==",
-          "dev": true,
-          "optional": true,
-          "requires": {
-            "big.js": "^5.2.2",
-            "emojis-list": "^3.0.0",
-            "json5": "^2.1.2"
-          }
-        },
-        "supports-color": {
-          "version": "7.2.0",
-          "resolved": "https://registry.npmjs.org/supports-color/-/supports-color-7.2.0.tgz",
-          "integrity": "sha512-qpCAvRl9stuOHveKsn7HncJRvv501qIacKzQlO/+Lwxc9+0q2wLyv4Dfvt80/DPn2pqOBsJdDiogXGR9+OvwRw==",
-          "dev": true,
-          "optional": true,
-          "requires": {
-            "has-flag": "^4.0.0"
-          }
-        }
-      }
-    },
     "vue-observe-visibility": {
       "version": "0.4.6",
       "resolved": "https://registry.npmjs.org/vue-observe-visibility/-/vue-observe-visibility-0.4.6.tgz",
@@ -13848,11 +13848,6 @@
       "integrity": "sha512-W74OO2vCJPs9/YjNjW8lLbj+jzT24waTo2KShI8jLvJW8OaIkgb3wuAMA7D+ZiUxDOx3ubwSZTaJBip9G8a3aQ==",
       "dev": true
     },
-    "vuex-map-fields": {
-      "version": "1.4.1",
-      "resolved": "https://registry.npmjs.org/vuex-map-fields/-/vuex-map-fields-1.4.1.tgz",
-      "integrity": "sha512-jvIcpvoIPqwvJCOfRkPU9Rj0EbjWuk7GlNC5LXU9mCXVGZph6bWGHZssnoUzpLMxJtXQEHoVyZkKf7YQV+/bnQ=="
-    },
     "watchpack": {
       "version": "1.7.4",
       "resolved": "https://registry.npmjs.org/watchpack/-/watchpack-1.7.4.tgz",
diff --git a/openflexure_microscope/api/static/package.json b/openflexure_microscope/api/static/package.json
index c05324b1..af3524c4 100644
--- a/openflexure_microscope/api/static/package.json
+++ b/openflexure_microscope/api/static/package.json
@@ -13,8 +13,7 @@
   "dependencies": {
     "material-design-icons": "^3.0.1",
     "mousetrap": "^1.6.5",
-    "vue-observe-visibility": "^0.4.6",
-    "vuex-map-fields": "^1.4.1"
+    "vue-observe-visibility": "^0.4.6"
   },
   "devDependencies": {
     "@vue/cli-plugin-babel": "^3.12.1",

From f2a4b976b9a93dca8a639e8694e6643fb3cfe121 Mon Sep 17 00:00:00 2001
From: Richard <richard.bowman@cantab.net>
Date: Thu, 13 May 2021 10:43:50 +0100
Subject: [PATCH 38/41] Fix whitespace

---
 openflexure_microscope/api/app.py                     | 3 ++-
 openflexure_microscope/api/default_extensions/scan.py | 6 +++++-
 2 files changed, 7 insertions(+), 2 deletions(-)

diff --git a/openflexure_microscope/api/app.py b/openflexure_microscope/api/app.py
index 205e9333..c27bc90d 100644
--- a/openflexure_microscope/api/app.py
+++ b/openflexure_microscope/api/app.py
@@ -106,7 +106,7 @@ app, labthing = create_app(
 cors: CORS = CORS(app)
 
 # Enable correct handling of Marshmallow/Webargs validation errors
-# Return validation errors as JSON 
+# Return validation errors as JSON
 # (see  https://webargs.readthedocs.io/en/latest/framework_support.html)
 @app.errorhandler(422)
 @app.errorhandler(400)
@@ -118,6 +118,7 @@ def handle_error(err):
     else:
         return jsonify({"errors": messages}), err.code
 
+
 # Use custom JSON encoder
 labthing.json_encoder = JSONEncoder
 app.json_encoder = JSONEncoder
diff --git a/openflexure_microscope/api/default_extensions/scan.py b/openflexure_microscope/api/default_extensions/scan.py
index e05f7352..782ad8f4 100644
--- a/openflexure_microscope/api/default_extensions/scan.py
+++ b/openflexure_microscope/api/default_extensions/scan.py
@@ -362,7 +362,11 @@ class ScanExtension(BaseExtension):
 
 class TileScanArgs(FullCaptureArgs):
     namemode = fields.String(missing="coordinates", example="coordinates")
-    grid = fields.List(fields.Integer(validate=marshmallow.validate.Range(min=1)), missing=[3, 3, 3], example=[3, 3, 3], )
+    grid = fields.List(
+        fields.Integer(validate=marshmallow.validate.Range(min=1)),
+        missing=[3, 3, 3],
+        example=[3, 3, 3],
+    )
     style = fields.String(missing="raster")
     autofocus_dz = fields.Integer(missing=50)
     fast_autofocus = fields.Boolean(missing=False)

From ba95b25800226c5c6731e1da1dbabdeaa44c5839 Mon Sep 17 00:00:00 2001
From: Richard Bowman <richard.bowman@cantab.net>
Date: Tue, 25 May 2021 10:20:40 +0000
Subject: [PATCH 39/41] Updated changelog for beta release

---
 CHANGELOG.md | 33 +++++++++++++++++++++++++++++++++
 1 file changed, 33 insertions(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 0e4bbe63..685a09c3 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,3 +1,36 @@
+# [v2.10.0b0](https://gitlab.com/openflexure/openflexure-microscope-server/compare/v2.9.3...v2.10.0b0) (2021-05-18)
+
+## New features
+* Improved auto gain, white balance, and lens shading table correction (!119).  Fixes #191.
+  The old auto calibration code has been replaced by a slower, more manual method that is more reliable.
+  Individual parts of the calibration can be run independently (auto gain/exposure, auto white balance, lens shading).
+  This should also improve the experience when using e.g. fluorescence imaging modes.
+
+## Developer changes
+* Build instructions were updated (!115)
+* We've switched from `poetry` to `pipenv` to solve dependency management issues on the Raspberry Pi (!124).  See the updated 
+  repository README for a full breakdown of what configuration information goes where.  Closes #218.
+* Improved handling of stream settings and origin override (!125, !116, !117)
+  This fixes a longstanding irritation when developing on localhost using `npm run serve`, where it was necessary to
+  enter the API origin address every time the page was refreshed, and then manually re-enable the web stream.  Both
+  these issues are now fixed.
+  * The API origin override field in the "dev tools" pane now remembers its value
+  * The API origin can be overridden using the URL
+  * Stream settings are now remembered in local storage
+
+## Minor bug fixes and improvements
+* Better error handling for picamerax (!86)
+* Add coverage report to mypy (!110)
+* `MissingStage` can now be explicitly selected in microscope configuration (!112)
+* The first-run "tour" placement is improved and shouldn't block the interface any more (!114)
+  * Fix placement of tour messages for icons ([afbb716](https://gitlab.com/openflexure/openflexure-microscope-server/commit/afbb716))
+  * This closes #199 and helps with #193
+* The IHI interface now explicitly states scan style should be raster (!113)
+* Absolute moves are now fixed (!126), closing #220, #221, and #222.
+* Fixed a typing error with the camera stage mapping matrix and `numpy` 1.20 (!127).
+* Scans now have a minimum dimension of 1 in each axis, which avoids dividing by zero (!123)
+
+
 # [v2.9.3](https://gitlab.com/openflexure/openflexure-microscope-server/compare/v2.9.2...v2.9.3) (2020-12-14)
 
 - Fix #194 ([0592d31](https://gitlab.com/openflexure/openflexure-microscope-server/commit/0592d31)), closes [#194](https://gitlab.com/openflexure/openflexure-microscope-server/issues/194)

From 9c5d040d821b32dc9a24cf349331692f4c4677db Mon Sep 17 00:00:00 2001
From: Richard Bowman <r.w.bowman@bath.ac.uk>
Date: Tue, 25 May 2021 11:28:46 +0100
Subject: [PATCH 40/41] Re-locked dependencies

---
 Pipfile.lock | 645 ++++++++++++++++++++++++---------------------------
 1 file changed, 302 insertions(+), 343 deletions(-)

diff --git a/Pipfile.lock b/Pipfile.lock
index b00fd3de..d3a660f7 100644
--- a/Pipfile.lock
+++ b/Pipfile.lock
@@ -26,11 +26,11 @@
                 "yaml"
             ],
             "hashes": [
-                "sha256:5ec0fe72f1422a1198973fcbb48d0eb5c7390f4b0fbe55474fce999ad6826a9b",
-                "sha256:83e4d30edce987f4791f950c847d2b8cbe91e55af3d1ac7e3a35011a5c6fdbdd"
+                "sha256:aaded4ae451752c58b70e579923d8db7daf0b71f62def8c8fe7a2a52bd7c06a2",
+                "sha256:f49c49e0dee3fa545462d4536856458aae61b972727b3c32eabc7d6db8c074f8"
             ],
             "markers": "python_version >= '3.6'",
-            "version": "==4.3.0"
+            "version": "==4.4.1"
         },
         "apispec-webframeworks": {
             "hashes": [
@@ -40,21 +40,13 @@
             "markers": "python_version >= '3.6'",
             "version": "==0.5.2"
         },
-        "atomicwrites": {
-            "hashes": [
-                "sha256:6d1784dea7c0c8d4a5172b6c620f40b6e4cbfdf96d783691f2e1302a7b88e197",
-                "sha256:ae70396ad1a434f9c7046fd2dd196fc04b12f9e91ffb859164193be8b6168a7a"
-            ],
-            "markers": "sys_platform == 'win32'",
-            "version": "==1.4.0"
-        },
         "attrs": {
             "hashes": [
-                "sha256:31b2eced602aa8423c2aea9c76a724617ed67cf9513173fd3a4f03e3a929c7e6",
-                "sha256:832aa3cde19744e49938b91fea06d69ecb9e649c93ba974535d08ad92164f700"
+                "sha256:149e90d6d8ac20db7a955ad60cf0e6881a3f20d37096140088356da6c716b0b1",
+                "sha256:ef6aaac3ca6cd92904cdd0d83f629a15f18053ec84e6432106f7a4d04ae4f5fb"
             ],
-            "markers": "python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'",
-            "version": "==20.3.0"
+            "markers": "python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4'",
+            "version": "==21.2.0"
         },
         "camera-stage-mapping": {
             "hashes": [
@@ -73,14 +65,6 @@
             "markers": "python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4'",
             "version": "==7.1.2"
         },
-        "colorama": {
-            "hashes": [
-                "sha256:5941b2b48a20143d2267e95b1c2a7603ce057ee39fd88e7329b0c292aa16869b",
-                "sha256:9f47eda37229f68eee03b24b9748937c7dc3868f906e8ba69fbcbdd3bc5dc3e2"
-            ],
-            "markers": "sys_platform == 'win32'",
-            "version": "==0.4.4"
-        },
         "colorzero": {
             "hashes": [
                 "sha256:0e60d743a6b8071498a56465f7719c96a5e92928f858bab1be2a0d606c9aa0f8",
@@ -155,11 +139,11 @@
         },
         "flask": {
             "hashes": [
-                "sha256:4efa1ae2d7c9865af48986de8aeb8504bf32c7f3d6fdc9353d34b21f4b127060",
-                "sha256:8a4fdd8936eba2512e9c85df320a37e694c93945b33ef33c89946a340a238557"
+                "sha256:0fbeb6180d383a9186d0d6ed954e0042ad9f18e0e8de088b2b419d526927d196",
+                "sha256:c34f04500f2cbbea882b1acb02002ad6fe6b7ffa64a6164577995657f50aed22"
             ],
             "markers": "python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4'",
-            "version": "==1.1.2"
+            "version": "==1.1.4"
         },
         "flask-cors": {
             "hashes": [
@@ -185,11 +169,11 @@
         },
         "importlib-metadata": {
             "hashes": [
-                "sha256:c9db46394197244adf2f0b08ec5bc3cf16757e9590b02af1fca085c16c0d600a",
-                "sha256:d2d46ef77ffc85cbf7dac7e81dd663fde71c45326131bea8033b9bad42268ebe"
+                "sha256:8c501196e49fb9df5df43833bdb1e4328f64847763ec8a50703148b73784d581",
+                "sha256:d7eb1dea6d6a6086f8be21784cc9e3bcfa55872b52309bc5fad53a8ea444465d"
             ],
             "markers": "python_version < '3.8'",
-            "version": "==3.10.0"
+            "version": "==4.0.1"
         },
         "iniconfig": {
             "hashes": [
@@ -225,103 +209,83 @@
         },
         "markupsafe": {
             "hashes": [
-                "sha256:00bc623926325b26bb9605ae9eae8a215691f33cae5df11ca5424f06f2d1f473",
-                "sha256:09027a7803a62ca78792ad89403b1b7a73a01c8cb65909cd876f7fcebd79b161",
-                "sha256:09c4b7f37d6c648cb13f9230d847adf22f8171b1ccc4d5682398e77f40309235",
-                "sha256:1027c282dad077d0bae18be6794e6b6b8c91d58ed8a8d89a89d59693b9131db5",
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@@ -470,11 +434,11 @@
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@@ -510,6 +474,7 @@
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@@ -526,6 +491,16 @@
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@@ -535,37 +510,37 @@
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-            "version": "==1.6.2"
+            "version": "==1.6.3"
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-            "version": "==1.15.0"
+            "version": "==1.16.0"
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         "toml": {
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@@ -629,11 +604,11 @@
                 "yaml"
             ],
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-            "version": "==4.3.0"
+            "version": "==4.4.1"
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         "apispec-webframeworks": {
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@@ -652,35 +627,27 @@
         },
         "astroid": {
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-            "markers": "sys_platform == 'win32'",
-            "version": "==1.4.0"
+            "markers": "python_version ~= '3.6'",
+            "version": "==2.5.6"
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         "attrs": {
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-                "sha256:832aa3cde19744e49938b91fea06d69ecb9e649c93ba974535d08ad92164f700"
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-            "markers": "python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'",
-            "version": "==20.3.0"
+            "markers": "python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4'",
+            "version": "==21.2.0"
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-            "version": "==2.9.0"
+            "version": "==2.9.1"
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@@ -722,14 +689,6 @@
             "markers": "python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4'",
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@@ -797,11 +756,11 @@
         },
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-            "version": "==0.16"
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@@ -812,11 +771,11 @@
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-            "version": "==1.1.2"
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@@ -867,11 +826,11 @@
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@@ -886,7 +845,7 @@
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+            "markers": "python_version >= '3.6' and python_version < '4'",
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@@ -948,18 +907,24 @@
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@@ -973,10 +938,14 @@
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@@ -988,72 +957,52 @@
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@@ -1244,7 +1193,7 @@
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@@ -1276,19 +1225,19 @@
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@@ -1307,11 +1256,11 @@
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@@ -1354,6 +1303,7 @@
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@@ -1386,6 +1336,16 @@
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@@ -1395,37 +1355,37 @@
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-                "sha256:e547f84cd52343ac2d56df0ab08d3e9cc202338e7d09fafe286d6c069ddacb31",
-                "sha256:e89091e6a8e211269e23f049473b2fde0c0e5ae0dd5bd276c3fc91b97da83480",
-                "sha256:e9da33e21c9bc1b92c20b5328adb13e5f193b924c9b969cd700c8908f315aa59",
-                "sha256:ffdfb09315896c6e9ac739bb6e13a19255b698c24e6b28314426fd40a1180822"
+                "sha256:01b38dec7e9f897d4db04f8de4e20f0f5be3feac98468188a0f47a991b796055",
+                "sha256:10dbcc7de03b8d635a1031cb18fd3eaa997969b64fdf78f99f19ac163a825445",
+                "sha256:19aeac1ad3e57338723f4657ac8520f41714804568f2e30bd547d684d72c392e",
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+                "sha256:1caade0ede6967cc675e235c41451f9fb89ae34319ddf4740194094ab736b88d",
+                "sha256:208fe23655561a95ede6bb3bb15342882f6a8f3867bf5564cafbdbcc401b1a5d",
+                "sha256:23995dfcf269ec3735e5a8c80cfceaf384369a47699df111a6246b83a55da582",
+                "sha256:2a799714bf1f791fb2650d73222b248d18d53fd40d6af2df2c898db048189606",
+                "sha256:3274ce145b5dc416c49c0cf8b6119f787f0965cd35e22058fe1932c09fe15d77",
+                "sha256:33d1677d46111cfa1c84b87472a0274dde9ef4a7ef2e1f155f012f5f1e995d8f",
+                "sha256:44d452850f77e65e25b1eb1ac01e25770323a782bfe3a1a3e43847ad4266d93d",
+                "sha256:9e3302149a369697c6aaea18b430b216e3c88f9a61b62869f6104881e5f9ef85",
+                "sha256:a75b014d3294fce26852a9d04ea27b5671d86736beb34acdfc05859246260707",
+                "sha256:ad7269254de06743fb4768f658753de47d8b54e4672c5ebe8612a007a088bd48",
+                "sha256:b30280fbc1fd8082ac822994a98632111810311a9ece71a0e48f739df3c555a2",
+                "sha256:b79104878003487e2b4639a20b9092b02e1bad07fc4cf924b495cf413748a777",
+                "sha256:d449d40e830366b4c612692ad19fbebb722b6b847f78a7b701b1e0d6cda3cc13",
+                "sha256:d647757373985207af3343301d89fe738d5a294435a4f2aafb04c13b4388c896",
+                "sha256:f68eb46b86b2c246af99fcaa6f6e37c7a7a413e1084a794990b877f2ff71f7b6",
+                "sha256:fdf606341cd798530b05705c87779606fcdfaf768a8129c348ea94441da15b04"
             ],
             "markers": "python_version < '3.10' and python_version >= '3.7'",
-            "version": "==1.6.2"
+            "version": "==1.6.3"
         },
         "six": {
             "hashes": [
-                "sha256:30639c035cdb23534cd4aa2dd52c3bf48f06e5f4a941509c8bafd8ce11080259",
-                "sha256:8b74bedcbbbaca38ff6d7491d76f2b06b3592611af620f8426e82dddb04a5ced"
+                "sha256:1e61c37477a1626458e36f7b1d82aa5c9b094fa4802892072e49de9c60c4c926",
+                "sha256:8abb2f1d86890a2dfb989f9a77cfcfd3e47c2a354b01111771326f8aa26e0254"
             ],
             "markers": "python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'",
-            "version": "==1.15.0"
+            "version": "==1.16.0"
         },
         "snowballstemmer": {
             "hashes": [
@@ -1436,11 +1396,11 @@
         },
         "sphinx": {
             "hashes": [
-                "sha256:3f01732296465648da43dec8fb40dc451ba79eb3e2cc5c6d79005fd98197107d",
-                "sha256:ce9c228456131bab09a3d7d10ae58474de562a6f79abb3dc811ae401cf8c1abc"
+                "sha256:b5c2ae4120bf00c799ba9b3699bc895816d272d120080fbc967292f29b52b48c",
+                "sha256:d1cb10bee9c4231f1700ec2e24a91be3f3a3aba066ea4ca9f3bbe47e59d5a1d4"
             ],
-            "markers": "python_version >= '3.5'",
-            "version": "==3.5.3"
+            "markers": "python_version >= '3.6'",
+            "version": "==4.0.2"
         },
         "sphinxcontrib-applehelp": {
             "hashes": [
@@ -1507,49 +1467,48 @@
         },
         "tomlkit": {
             "hashes": [
-                "sha256:6babbd33b17d5c9691896b0e68159215a9387ebfa938aa3ac42f4a4beeb2b831",
-                "sha256:ac57f29693fab3e309ea789252fcce3061e19110085aa31af5446ca749325618"
+                "sha256:173ad840fa5d2aac140528ca1933c29791b79a374a0861a80347f42ec9328117",
+                "sha256:d7a454f319a7e9bd2e249f239168729327e4dd2d27b17dc68be264ad1ce36754"
             ],
             "markers": "python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4'",
-            "version": "==0.7.0"
+            "version": "==0.7.2"
         },
         "typed-ast": {
             "hashes": [
-                "sha256:07d49388d5bf7e863f7fa2f124b1b1d89d8aa0e2f7812faff0a5658c01c59aa1",
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-                "sha256:36d829b31ab67d6fcb30e185ec996e1f72b892255a745d3a82138c97d21ed1cd",
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-                "sha256:4822449fb865605582a22d23997444ff3eaa3d0920b04b9902e37f8edbeadca6",
-                "sha256:4c790331247081ea7c632a76d5b2a265e6d325ecd3179d06e9cf8d46d90dd151",
-                "sha256:5dcfc2e264bd8a1db8b11a892bd1647154ce03eeba94b461effe68790d8b8e07",
-                "sha256:7147e2a76c75f0f64c4319886e7639e490fee87c9d25cb1d4faef1d8cf83a440",
-                "sha256:7703620125e4fb79b64aa52427ec192822e9f45d37d4b6625ab37ef403e1df70",
-                "sha256:8368f83e93c7156ccd40e49a783a6a6850ca25b556c0fa0240ed0f659d2fe496",
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-                "sha256:85f95aa97a35bdb2f2f7d10ec5bbdac0aeb9dafdaf88e17492da0504de2e6400",
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-                "sha256:9044ef2df88d7f33692ae3f18d3be63dec69c4fb1b5a4a9ac950f9b4ba571606",
-                "sha256:963c80b583b0661918718b095e02303d8078950b26cc00b5e5ea9ababe0de1fc",
-                "sha256:987f15737aba2ab5f3928c617ccf1ce412e2e321c77ab16ca5a293e7bbffd581",
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-                "sha256:9fc0b3cb5d1720e7141d103cf4819aea239f7d136acf9ee4a69b047b7986175a",
-                "sha256:a2c927c49f2029291fbabd673d51a2180038f8cd5a5b2f290f78c4516be48be2",
-                "sha256:a38878a223bdd37c9709d07cd357bb79f4c760b29210e14ad0fb395294583787",
-                "sha256:a93908d202f52ec64e24a41031f1336a14b66706be2c9e51949647f7ac4cbd22",
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-                "sha256:c0c74e5579af4b977c8b932f40a5464764b2f86681327410aa028a22d2f54937",
-                "sha256:c1c876fd795b36126f773db9cbb393f19808edd2637e00fd6caba0e25f2c7b64",
-                "sha256:c9aadc4924d4b5799112837b226160428524a9a45f830e0d0f184b19e4090487",
-                "sha256:cc7b98bf58167b7f2db91a4327da24fb93368838eb84a44c472283778fc2446b",
-                "sha256:cf54cfa843f297991b7388c281cb3855d911137223c6b6d2dd82a47ae5125a41",
-                "sha256:d003156bb6a59cda9050e983441b7fa2487f7800d76bdc065566b7d728b4581a",
-                "sha256:d175297e9533d8d37437abc14e8a83cbc68af93cc9c1c59c2c292ec59a0697a3",
-                "sha256:d746a437cdbca200622385305aedd9aef68e8a645e385cc483bdc5e488f07166",
-                "sha256:e683e409e5c45d5c9082dc1daf13f6374300806240719f95dc783d1fc942af10"
+                "sha256:01ae5f73431d21eead5015997ab41afa53aa1fbe252f9da060be5dad2c730ace",
+                "sha256:067a74454df670dcaa4e59349a2e5c81e567d8d65458d480a5b3dfecec08c5ff",
+                "sha256:0fb71b8c643187d7492c1f8352f2c15b4c4af3f6338f21681d3681b3dc31a266",
+                "sha256:1b3ead4a96c9101bef08f9f7d1217c096f31667617b58de957f690c92378b528",
+                "sha256:2068531575a125b87a41802130fa7e29f26c09a2833fea68d9a40cf33902eba6",
+                "sha256:209596a4ec71d990d71d5e0d312ac935d86930e6eecff6ccc7007fe54d703808",
+                "sha256:2c726c276d09fc5c414693a2de063f521052d9ea7c240ce553316f70656c84d4",
+                "sha256:398e44cd480f4d2b7ee8d98385ca104e35c81525dd98c519acff1b79bdaac363",
+                "sha256:52b1eb8c83f178ab787f3a4283f68258525f8d70f778a2f6dd54d3b5e5fb4341",
+                "sha256:5feca99c17af94057417d744607b82dd0a664fd5e4ca98061480fd8b14b18d04",
+                "sha256:6cd1c6665796c58380121c2dd3e6abef605a3ae1116b95cfc585370ebfefdd5c",
+                "sha256:7538e495704e2ccda9b234b82423a4038f324f3a10c43bc088a1636180f11a41",
+                "sha256:760ad187b1041a154f0e4d0f6aae3e40fdb51d6de16e5c99aedadd9246450e9e",
+                "sha256:777a26c84bea6cd934422ac2e3b78863a37017618b6e5c08f92ef69853e765d3",
+                "sha256:95431a26309a21874005845c21118c83991c63ea800dd44843e42a916aec5899",
+                "sha256:9ad2c92ec681e02baf81fdfa056fe0d818645efa9af1f1cd5fd6f1bd2bdfd805",
+                "sha256:9c6d1a54552b5330bc657b7ef0eae25d00ba7ffe85d9ea8ae6540d2197a3788c",
+                "sha256:aee0c1256be6c07bd3e1263ff920c325b59849dc95392a05f258bb9b259cf39c",
+                "sha256:af3d4a73793725138d6b334d9d247ce7e5f084d96284ed23f22ee626a7b88e39",
+                "sha256:b36b4f3920103a25e1d5d024d155c504080959582b928e91cb608a65c3a49e1a",
+                "sha256:b9574c6f03f685070d859e75c7f9eeca02d6933273b5e69572e5ff9d5e3931c3",
+                "sha256:bff6ad71c81b3bba8fa35f0f1921fb24ff4476235a6e94a26ada2e54370e6da7",
+                "sha256:c190f0899e9f9f8b6b7863debfb739abcb21a5c054f911ca3596d12b8a4c4c7f",
+                "sha256:c907f561b1e83e93fad565bac5ba9c22d96a54e7ea0267c708bffe863cbe4075",
+                "sha256:cae53c389825d3b46fb37538441f75d6aecc4174f615d048321b716df2757fb0",
+                "sha256:dd4a21253f42b8d2b48410cb31fe501d32f8b9fbeb1f55063ad102fe9c425e40",
+                "sha256:dde816ca9dac1d9c01dd504ea5967821606f02e510438120091b84e852367428",
+                "sha256:f2362f3cb0f3172c42938946dbc5b7843c2a28aec307c49100c8b38764eb6927",
+                "sha256:f328adcfebed9f11301eaedfa48e15bdece9b519fb27e6a8c01aa52a17ec31b3",
+                "sha256:f8afcf15cc511ada719a88e013cec87c11aff7b91f019295eb4530f96fe5ef2f",
+                "sha256:fb1bbeac803adea29cedd70781399c99138358c26d05fcbd23c13016b7f5ec65"
             ],
             "markers": "python_version < '3.8' and implementation_name == 'cpython'",
-            "version": "==1.4.2"
+            "version": "==1.4.3"
         },
         "typing-extensions": {
             "hashes": [
@@ -1565,7 +1524,7 @@
                 "sha256:2f4da4594db7e1e110a944bb1b551fdf4e6c136ad42e4234131391e21eb5b0df",
                 "sha256:e7b021f7241115872f92f43c6508082facffbd1c048e3c6e2bb9c2a157e28937"
             ],
-            "markers": "python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4' and python_version < '4.0'",
+            "markers": "python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4' and python_version < '4'",
             "version": "==1.26.4"
         },
         "webargs": {

From 4ca51d9ba91907b6d83ff02afc4dbf4c1ed1beb9 Mon Sep 17 00:00:00 2001
From: Richard <richard.bowman@cantab.net>
Date: Tue, 25 May 2021 17:03:02 +0100
Subject: [PATCH 41/41] Version bump

---
 setup.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/setup.py b/setup.py
index adf729ff..b6f552d8 100644
--- a/setup.py
+++ b/setup.py
@@ -22,7 +22,7 @@ with open(path.join(here, "README.md"), encoding="utf-8") as f:
 
 setup(
     name="openflexure-microscope-server",
-    version="2.10.0b0",
+    version="2.10.0b1",
     description="Python module, and Flask-based web API, to run the OpenFlexure Microscope.",
     long_description=long_description,
     long_description_content_type="text/markdown",