Commit 4a553040 authored by Joel Collins's avatar Joel Collins
Browse files

Fixed logging and split access and root file handlers

parent b8c0ca25

openflexure_microscope/api/app.py

+29 −15
Original line number Diff line number Diff line
@@ -33,31 +33,42 @@ from openflexure_microscope.api.microscope import default_microscope as api_micr 
from openflexure_microscope.api.v2 import views



# 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()



error_formatter = logging.Formatter(

# Basic log format

formatter = logging.Formatter(

    "[%(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()]

# Get root logger

logger = logging.getLogger()

logger.setLevel(logging.INFO)



for handler in error_handlers:

    handler.setFormatter(error_formatter)

    logger.addHandler(handler)

# 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



logger.setLevel(logging.INFO)

# 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

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



print("Creating app")

logging.info("Creating app")

# Create flask app

app, labthing = create_app(

    __name__,
@@ -176,6 +187,9 @@ atexit.register(cleanup) 
if __name__ == "__main__":

    from labthings.server.wsgi import Server



    print("Starting OpenFlexure Microscope Server...")

    server = Server(app, log=logger, error_log=logger)

    # Block the access logs from propagating up to the root 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)

openflexure_microscope/api/default_extensions/autofocus.py

+2 −2
Original line number Diff line number Diff line
@@ -62,7 +62,7 @@ class JPEGSharpnessMonitor: 
    def stop(self):

        "Stop the background thread"

        self.stop_event.set()

        print("Joining JPEG thread")

        logging.info("Joining JPEG thread")

        self.background_thread.join()



    def _measure_jpegs(self):
@@ -75,7 +75,7 @@ class JPEGSharpnessMonitor: 
            time_now = time.time()

            self.jpeg_sizes.append(size_now)

            self.jpeg_times.append(time_now)

        print("Exited JPEG measure loop")

        logging.info("Exited JPEG measure loop")

        if self.stop_event.is_set():

            logging.debug("Cleanly stopped sharpness measurement in background thread")

        if self.should_stop():

openflexure_microscope/api/default_extensions/camera_stage_mapping/camera_stage_calibration_2d.py

+3 −3
Original line number Diff line number Diff line
@@ -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)

    residuals = transformed_image_positions - stage_positions

    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

        print(

        logging.warning(

            "Warning: the error fitting measured displacements was %.1f%%"

            % (fractional_error * 100)

        )

    print(

    logging.info(

        f"Calibrated the pixel-location matrix.\nResiduals were {fractional_error*100:.1f}% of the shift."

    )

openflexure_microscope/api/default_extensions/picamera_autocalibrate/recalibrate_utils.py

+13 −13
Original line number Diff line number Diff line
@@ -28,19 +28,19 @@ def flat_lens_shading_table(camera): 


def adjust_exposure_to_setpoint(camera, 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):

        print(".", end="")

        camera.shutter_speed = int(

            camera.shutter_speed * setpoint / np.max(rgb_image(camera))

        )

        time.sleep(1)

    print("done")

    logging.info("done")





def auto_expose_and_freeze_settings(camera):

    """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.exposure_mode = "auto"

    camera.iso = (
@@ -49,18 +49,18 @@ def auto_expose_and_freeze_settings(camera): 
    for i in range(6):

        print(".", end="")

        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

    print("Shutter speed = {}".format(camera.shutter_speed))

    logging.info("Shutter speed = {}".format(camera.shutter_speed))

    camera.exposure_mode = "off"

    print("Auto exposure disabled")

    logging.info("Auto exposure disabled")

    g = camera.awb_gains

    camera.awb_mode = "off"

    camera.awb_gains = g

    print("Auto white balance disabled, gains are {}".format(g))

    print(

    logging.info("Auto white balance disabled, gains are {}".format(g))

    logging.info(

        "Analogue gain: {}, Digital gain: {}".format(

            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 = [(r // 64) + 1 for r in full_resolution]

    # 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)

    for i in range(lens_shading.shape[0]):

        image_channel = channels[i, :, :]
@@ -107,7 +107,7 @@ def lst_from_channels(channels): 
        padded_image_channel = np.pad(

            image_channel, [(0, lw * 32 - iw), (0, lh * 32 - ih)], mode="edge"

        )  # Pad image to the right and bottom

        print(

        logging.info(

            "Channel shape: {}x{}, shading table shape: {}x{}, after padding {}".format(

                iw, ih, lw * 32, lh * 32, padded_image_channel.shape

            )
@@ -185,7 +185,7 @@ if __name__ == "__main__": 
    with PiCamera() as camera:

        camera.start_preview()

        time.sleep(3)

        print("Recalibrating...")

        logging.info("Recalibrating...")

        recalibrate_camera(camera)

        print("Done.")

        logging.info("Done.")

        time.sleep(2)

openflexure_microscope/api/utilities/gui.py

+2 −3
Original line number Diff line number Diff line
@@ -13,9 +13,8 @@ def build_gui_from_dict(gui_description, extension_object): 
    # Make a working copy of GUI description

    api_gui = copy.deepcopy(gui_description)



    print("")

    print(extension_object)

    print(extension_object._rules)

    logging.debug(extension_object)

    logging.debug(extension_object._rules)



    # Expand shorthand routes into full relative URLs

    if "forms" in gui_description and isinstance(api_gui["forms"], list):