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Merge branch 'master' of https://gitlab.com/openflexure/openflexure-microscope-server

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This commit is contained in:
Joel Collins 2020-05-22 10:35:30 +01:00
commit 877b2210ed
8 changed files with 68 additions and 64 deletions
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54
openflexure_microscope/api/app.py
View file

@ -9,7 +9,7 @@ import logging, logging.handlers
import os import os
import pkg_resources import pkg_resources
from flask import Flask, send_file from flask import Flask, send_file, abort
from datetime import datetime from datetime import datetime
@ -33,31 +33,42 @@ from openflexure_microscope.api.microscope import default_microscope as api_micr
from openflexure_microscope.api.v2 import views from openflexure_microscope.api.v2 import views
# Handle logging # Handle logging
DEFAULT_LOGFILE = logs_file_path("openflexure_microscope.log") ROOT_LOGFILE = logs_file_path("openflexure_microscope.log")
ACCESS_LOGFILE = logs_file_path("openflexure_microscope.access.log")
logger = logging.getLogger() # Basic log format
formatter = logging.Formatter(
error_formatter = logging.Formatter(
"[%(asctime)s] [%(threadName)s] [%(levelname)s] %(message)s" "[%(asctime)s] [%(threadName)s] [%(levelname)s] %(message)s"
) )
rotating_logfile = logging.handlers.RotatingFileHandler(
DEFAULT_LOGFILE, maxBytes=1_000_000, backupCount=7
)
error_handlers = [rotating_logfile, logging.StreamHandler()]
for handler in error_handlers:
handler.setFormatter(error_formatter)
logger.addHandler(handler)
# Get root logger
logger = logging.getLogger()
logger.setLevel(logging.INFO) logger.setLevel(logging.INFO)
# Create file handler
fh = logging.handlers.RotatingFileHandler(
ROOT_LOGFILE, maxBytes=1_000_000, backupCount=5
)
fh.setFormatter(formatter)
fh.setLevel(logging.INFO)
fh.propagate = False
# Create access log file handler
afh = logging.handlers.RotatingFileHandler(
ACCESS_LOGFILE, maxBytes=1_000_000, backupCount=5
)
afh.setFormatter(formatter)
afh.setLevel(logging.INFO)
afh.propagate = False
# Add file handler to root logger
logger.addHandler(fh)
# Log server paths being used # Log server paths being used
logging.info(f"Running with data path {OPENFLEXURE_VAR_PATH}") logging.info(f"Running with data path {OPENFLEXURE_VAR_PATH}")
print("Creating app") logging.info("Creating app")
# Create flask app # Create flask app
app, labthing = create_app( app, labthing = create_app(
__name__, __name__,
@ -141,11 +152,15 @@ def err_log():
""" """
timestamp = datetime.now().strftime("%Y-%m-%d_%H-%M-%S") timestamp = datetime.now().strftime("%Y-%m-%d_%H-%M-%S")
return send_file( return send_file(
DEFAULT_LOGFILE, ROOT_LOGFILE,
as_attachment=True, as_attachment=True,
attachment_filename="openflexure_microscope_{}.log".format(timestamp), attachment_filename="openflexure_microscope_{}.log".format(timestamp),
) )
@app.route('/api/v1/', defaults={'path': ''})
@app.route('/api/v1/<path:path>')
def api_v1_catch_all(path):
abort(410, 'API v1 is no longer in use. Please upgrade your client.')
# Automatically clean up microscope at exit # Automatically clean up microscope at exit
def cleanup(): def cleanup():
@ -176,6 +191,9 @@ atexit.register(cleanup)
if __name__ == "__main__": if __name__ == "__main__":
from labthings.server.wsgi import Server from labthings.server.wsgi import Server
print("Starting OpenFlexure Microscope Server...") # Block the access logs from propagating up to the root logger
server = Server(app, log=logger, error_log=logger) logging.getLogger("labthings.server.wsgi.handler").propagate = False
logging.info("Starting OpenFlexure Microscope Server...")
server = Server(app, log=afh, error_log=None)
server.run(host="::", port=5000, debug=False, zeroconf=True) server.run(host="::", port=5000, debug=False, zeroconf=True)

4
openflexure_microscope/api/default_extensions/autofocus.py
View file

@ -62,7 +62,7 @@ class JPEGSharpnessMonitor:
def stop(self): def stop(self):
"Stop the background thread" "Stop the background thread"
self.stop_event.set() self.stop_event.set()
print("Joining JPEG thread") logging.info("Joining JPEG thread")
self.background_thread.join() self.background_thread.join()
def _measure_jpegs(self): def _measure_jpegs(self):
@ -75,7 +75,7 @@ class JPEGSharpnessMonitor:
time_now = time.time() time_now = time.time()
self.jpeg_sizes.append(size_now) self.jpeg_sizes.append(size_now)
self.jpeg_times.append(time_now) self.jpeg_times.append(time_now)
print("Exited JPEG measure loop") logging.info("Exited JPEG measure loop")
if self.stop_event.is_set(): if self.stop_event.is_set():
logging.debug("Cleanly stopped sharpness measurement in background thread") logging.debug("Cleanly stopped sharpness measurement in background thread")
if self.should_stop(): if self.should_stop():

6
openflexure_microscope/api/default_extensions/camera_stage_mapping/camera_stage_calibration_2d.py
View file

@ -73,13 +73,13 @@ def calibrate_xy_grid(tracker, move, step=100, n_steps=4, backlash_compensation=
transformed_image_positions = np.dot(image_positions, A) transformed_image_positions = np.dot(image_positions, A)
residuals = transformed_image_positions - stage_positions residuals = transformed_image_positions - stage_positions
fractional_error = norm(residuals) / stage_positions.shape[0] fractional_error = norm(residuals) / stage_positions.shape[0]
print(f"Ratio of residuals to displacement is {fractional_error})") logging.debug(f"Ratio of residuals to displacement is {fractional_error})")
if fractional_error > 0.05: # Check it was a reasonably good fit if fractional_error > 0.05: # Check it was a reasonably good fit
print( logging.warning(
"Warning: the error fitting measured displacements was %.1f%%" "Warning: the error fitting measured displacements was %.1f%%"
% (fractional_error * 100) % (fractional_error * 100)
) )
print( logging.info(
f"Calibrated the pixel-location matrix.\nResiduals were {fractional_error*100:.1f}% of the shift." f"Calibrated the pixel-location matrix.\nResiduals were {fractional_error*100:.1f}% of the shift."
) )

26
openflexure_microscope/api/default_extensions/picamera_autocalibrate/recalibrate_utils.py
View file

@ -28,19 +28,19 @@ def flat_lens_shading_table(camera):
def adjust_exposure_to_setpoint(camera, setpoint): def adjust_exposure_to_setpoint(camera, setpoint):
"""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>."""
print("Adjusting shutter speed to hit setpoint {}".format(setpoint), end="") logging.info("Adjusting shutter speed to hit setpoint {}".format(setpoint), end="")
for i in range(3): for i in range(3):
print(".", end="") print(".", end="")
camera.shutter_speed = int( camera.shutter_speed = int(
camera.shutter_speed * setpoint / np.max(rgb_image(camera)) camera.shutter_speed * setpoint / np.max(rgb_image(camera))
) )
time.sleep(1) time.sleep(1)
print("done") logging.info("done")
def auto_expose_and_freeze_settings(camera): def auto_expose_and_freeze_settings(camera):
"""Freeze the settings after auto-exposing to white illumination""" """Freeze the settings after auto-exposing to white illumination"""
print("Allowing the camera to auto-expose") logging.info("Allowing the camera to auto-expose")
camera.awb_mode = "auto" camera.awb_mode = "auto"
camera.exposure_mode = "auto" camera.exposure_mode = "auto"
camera.iso = ( camera.iso = (
@ -49,18 +49,18 @@ def auto_expose_and_freeze_settings(camera):
for i in range(6): for i in range(6):
print(".", end="") print(".", end="")
time.sleep(0.5) time.sleep(0.5)
print("done") logging.info("done")
print("Freezing the camera settings...") logging.info("Freezing the camera settings...")
camera.shutter_speed = camera.exposure_speed camera.shutter_speed = camera.exposure_speed
print("Shutter speed = {}".format(camera.shutter_speed)) logging.info("Shutter speed = {}".format(camera.shutter_speed))
camera.exposure_mode = "off" camera.exposure_mode = "off"
print("Auto exposure disabled") logging.info("Auto exposure disabled")
g = camera.awb_gains g = camera.awb_gains
camera.awb_mode = "off" camera.awb_mode = "off"
camera.awb_gains = g camera.awb_gains = g
print("Auto white balance disabled, gains are {}".format(g)) logging.info("Auto white balance disabled, gains are {}".format(g))
print( logging.info(
"Analogue gain: {}, Digital gain: {}".format( "Analogue gain: {}, Digital gain: {}".format(
camera.analog_gain, camera.digital_gain camera.analog_gain, camera.digital_gain
) )
@ -90,7 +90,7 @@ def lst_from_channels(channels):
# lst_resolution = list(np.ceil(full_resolution / 64.0).astype(int)) # lst_resolution = list(np.ceil(full_resolution / 64.0).astype(int))
lst_resolution = [(r // 64) + 1 for r in full_resolution] lst_resolution = [(r // 64) + 1 for r in full_resolution]
# NB the size of the LST is 1/64th of the image, but rounded UP. # NB the size of the LST is 1/64th of the image, but rounded UP.
print("Generating a lens shading table at {}x{}".format(*lst_resolution)) logging.info("Generating a lens shading table at {}x{}".format(*lst_resolution))
lens_shading = np.zeros([channels.shape[0]] + lst_resolution, dtype=np.float) lens_shading = np.zeros([channels.shape[0]] + lst_resolution, dtype=np.float)
for i in range(lens_shading.shape[0]): for i in range(lens_shading.shape[0]):
image_channel = channels[i, :, :] image_channel = channels[i, :, :]
@ -107,7 +107,7 @@ def lst_from_channels(channels):
padded_image_channel = np.pad( padded_image_channel = np.pad(
image_channel, [(0, lw * 32 - iw), (0, lh * 32 - ih)], mode="edge" image_channel, [(0, lw * 32 - iw), (0, lh * 32 - ih)], mode="edge"
) # Pad image to the right and bottom ) # Pad image to the right and bottom
print( logging.info(
"Channel shape: {}x{}, shading table shape: {}x{}, after padding {}".format( "Channel shape: {}x{}, shading table shape: {}x{}, after padding {}".format(
iw, ih, lw * 32, lh * 32, padded_image_channel.shape iw, ih, lw * 32, lh * 32, padded_image_channel.shape
) )
@ -185,7 +185,7 @@ if __name__ == "__main__":
with PiCamera() as camera: with PiCamera() as camera:
camera.start_preview() camera.start_preview()
time.sleep(3) time.sleep(3)
print("Recalibrating...") logging.info("Recalibrating...")
recalibrate_camera(camera) recalibrate_camera(camera)
print("Done.") logging.info("Done.")
time.sleep(2) time.sleep(2)

5
openflexure_microscope/api/utilities/gui.py
View file

@ -13,9 +13,8 @@ def build_gui_from_dict(gui_description, extension_object):
# Make a working copy of GUI description # Make a working copy of GUI description
api_gui = copy.deepcopy(gui_description) api_gui = copy.deepcopy(gui_description)
print("") logging.debug(extension_object)
print(extension_object) logging.debug(extension_object._rules)
print(extension_object._rules)
# Expand shorthand routes into full relative URLs # Expand shorthand routes into full relative URLs
if "forms" in gui_description and isinstance(api_gui["forms"], list): if "forms" in gui_description and isinstance(api_gui["forms"], list):

8
openflexure_microscope/microscope.py
View file

@ -83,7 +83,7 @@ class Microscope:
""" """
### Detector ### Detector
print("Creating camera") logging.info("Creating camera")
if configuration.get("camera"): if configuration.get("camera"):
camera_type = configuration["camera"].get("type") camera_type = configuration["camera"].get("type")
if camera_type in ("PiCamera", "PiCameraStreamer"): if camera_type in ("PiCamera", "PiCameraStreamer"):
@ -94,7 +94,7 @@ class Microscope:
logging.warning("No compatible camera hardware found.") logging.warning("No compatible camera hardware found.")
### Stage ### Stage
print("Creating stage") logging.info("Creating stage")
if configuration.get("stage"): if configuration.get("stage"):
stage_type = configuration["stage"].get("type") stage_type = configuration["stage"].get("type")
stage_port = configuration["stage"].get("port") stage_port = configuration["stage"].get("port")
@ -105,7 +105,7 @@ class Microscope:
logging.error(e) logging.error(e)
logging.warning("No compatible Sangaboard hardware found.") logging.warning("No compatible Sangaboard hardware found.")
print("Handling fallbacks") logging.info("Handling fallbacks")
### Fallbacks ### Fallbacks
if not self.camera: if not self.camera:
self.camera = MissingCamera() self.camera = MissingCamera()
@ -113,7 +113,7 @@ class Microscope:
self.stage = MissingStage() self.stage = MissingStage()
### Locks ### Locks
print("Creating locks") logging.info("Creating locks")
if hasattr(self.camera, "lock"): if hasattr(self.camera, "lock"):
self.lock.locks.append(self.camera.lock) self.lock.locks.append(self.camera.lock)
if hasattr(self.stage, "lock"): if hasattr(self.stage, "lock"):

27
poetry.lock generated
View file

@ -290,7 +290,7 @@ description = "Python implementation of LabThings, based on the Flask microframe
name = "labthings" name = "labthings"
optional = false optional = false
python-versions = ">=3.6,<4.0" python-versions = ">=3.6,<4.0"
version = "0.6.2" version = "0.6.3"
[package.dependencies] [package.dependencies]
Flask = ">=1.1.1,<2.0.0" Flask = ">=1.1.1,<2.0.0"
@ -379,7 +379,7 @@ description = "Core utilities for Python packages"
name = "packaging" name = "packaging"
optional = false optional = false
python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
version = "20.3" version = "20.4"
[package.dependencies] [package.dependencies]
pyparsing = ">=2.0.2" pyparsing = ">=2.0.2"
@ -466,19 +466,6 @@ all = ["Sphinx (>=1.5.1)", "check-manifest (>=0.25)", "coverage (>=4.0)", "isort
docs = ["Sphinx (>=1.5.1)"] docs = ["Sphinx (>=1.5.1)"]
tests = ["check-manifest (>=0.25)", "coverage (>=4.0)", "isort (>=4.2.2)", "pydocstyle (>=1.0.0)", "pytest-cache (>=1.0)", "pytest-cov (>=1.8.0)", "pytest-pep8 (>=1.0.6)", "pytest (>=2.8.0)"] tests = ["check-manifest (>=0.25)", "coverage (>=4.0)", "isort (>=4.2.2)", "pydocstyle (>=1.0.0)", "pytest-cache (>=1.0)", "pytest-cov (>=1.8.0)", "pytest-pep8 (>=1.0.6)", "pytest (>=2.8.0)"]
[[package]]
category = "dev"
description = "Python interface to your NPM and package.json."
name = "pynpm"
optional = false
python-versions = "*"
version = "0.1.2"
[package.extras]
all = ["Sphinx (>=1.5.1)", "check-manifest (>=0.25)", "coverage (>=4.0)", "isort (>=4.2.2)", "pydocstyle (>=1.0.0)", "pytest-cache (>=1.0)", "pytest-cov (>=1.8.0)", "pytest-pep8 (>=1.0.6)", "pytest (>=2.8.0)"]
docs = ["Sphinx (>=1.5.1)"]
tests = ["check-manifest (>=0.25)", "coverage (>=4.0)", "isort (>=4.2.2)", "pydocstyle (>=1.0.0)", "pytest-cache (>=1.0)", "pytest-cov (>=1.8.0)", "pytest-pep8 (>=1.0.6)", "pytest (>=2.8.0)"]
[[package]] [[package]]
category = "dev" category = "dev"
description = "Python parsing module" description = "Python parsing module"
@ -773,7 +760,7 @@ ifaddr = "*"
rpi = ["RPi.GPIO"] rpi = ["RPi.GPIO"]
[metadata] [metadata]
content-hash = "4fbf4240ac033cff8c0879b570792626e29a5aa2c5ffa2ec08b825ef8c2b700c" content-hash = "1c923fc71ff343293798e1bd187df98791716e15e4d970fef1a8d77bf25de1e2"
python-versions = "^3.6" python-versions = "^3.6"
[metadata.files] [metadata.files]
@ -942,8 +929,8 @@ jinja2 = [
{file = "Jinja2-2.11.2.tar.gz", hash = "sha256:89aab215427ef59c34ad58735269eb58b1a5808103067f7bb9d5836c651b3bb0"}, {file = "Jinja2-2.11.2.tar.gz", hash = "sha256:89aab215427ef59c34ad58735269eb58b1a5808103067f7bb9d5836c651b3bb0"},
] ]
labthings = [ labthings = [
{file = "labthings-0.6.2-py3-none-any.whl", hash = "sha256:b83997a7dd115e0bfe20c2d5c52741c0b747fe8044e12db7bf82a433f8493d8e"}, {file = "labthings-0.6.3-py3-none-any.whl", hash = "sha256:63ef2a575d008b8e260dc5b64e7691b99d74a9dcdbea4263fb7975aeb50ce74b"},
{file = "labthings-0.6.2.tar.gz", hash = "sha256:6373e2d0fdd731752a6fabd09708adeaf233b67f0cdcabee669642f647e9d95d"}, {file = "labthings-0.6.3.tar.gz", hash = "sha256:f5756ad4622210923511b690a8deb378bddc7d1e300ebd9e42cca8bc562ef032"},
] ]
lazy-object-proxy = [ lazy-object-proxy = [
{file = "lazy-object-proxy-1.4.3.tar.gz", hash = "sha256:f3900e8a5de27447acbf900b4750b0ddfd7ec1ea7fbaf11dfa911141bc522af0"}, {file = "lazy-object-proxy-1.4.3.tar.gz", hash = "sha256:f3900e8a5de27447acbf900b4750b0ddfd7ec1ea7fbaf11dfa911141bc522af0"},
@ -1084,8 +1071,8 @@ opencv-python-headless = [
{file = "opencv_python_headless-4.2.0.34-cp38-cp38-win_amd64.whl", hash = "sha256:20c450943acebd9aa04566fdef4a658b94eec80a0c39a8f480c9aa1696034fcb"}, {file = "opencv_python_headless-4.2.0.34-cp38-cp38-win_amd64.whl", hash = "sha256:20c450943acebd9aa04566fdef4a658b94eec80a0c39a8f480c9aa1696034fcb"},
] ]
packaging = [ packaging = [
{file = "packaging-20.3-py2.py3-none-any.whl", hash = "sha256:82f77b9bee21c1bafbf35a84905d604d5d1223801d639cf3ed140bd651c08752"}, {file = "packaging-20.4-py2.py3-none-any.whl", hash = "sha256:998416ba6962ae7fbd6596850b80e17859a5753ba17c32284f67bfff33784181"},
{file = "packaging-20.3.tar.gz", hash = "sha256:3c292b474fda1671ec57d46d739d072bfd495a4f51ad01a055121d81e952b7a3"}, {file = "packaging-20.4.tar.gz", hash = "sha256:4357f74f47b9c12db93624a82154e9b120fa8293699949152b22065d556079f8"},
] ]
picamera = [] picamera = []
pillow = [ pillow = [

2
pyproject.toml
View file

@ -46,7 +46,7 @@ opencv-python-headless = [
{version = "4.1.0.25", python = "~3.7"}, # PiWheels build for RPi running Py37 {version = "4.1.0.25", python = "~3.7"}, # PiWheels build for RPi running Py37
{version = "4.2.0.34", python = "^3.8"} # Latest for Py38 systems {version = "4.2.0.34", python = "^3.8"} # Latest for Py38 systems
] ]
labthings = "0.6.2" labthings = "0.6.3"
pynpm = "^0.1.2" pynpm = "^0.1.2"
[tool.poetry.extras] [tool.poetry.extras]