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Reverted logging style

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This commit is contained in:
Joel Collins 2020-11-12 15:45:58 +00:00
parent e25c23cf1c
commit 6fb61e1e3f
24 changed files with 100 additions and 106 deletions
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2
openflexure_microscope/api/app.py
View file

@ -72,7 +72,7 @@ root_log.addHandler(fh)
access_log.addHandler(afh)
# Log server paths being used
logging.info("Running with data path {}", OPENFLEXURE_VAR_PATH)
logging.info("Running with data path %s", OPENFLEXURE_VAR_PATH)
logging.info("Creating app")
# Create flask app

2
openflexure_microscope/api/default_extensions/__init__.py
View file

@ -10,7 +10,7 @@ def handle_extension_error(extension_name):
yield
except Exception: # pylint: disable=W0703
logging.error(
"Exception loading builtin extension {}: \n{}",
"Exception loading builtin extension %s: \n%s",
extension_name,
traceback.format_exc(),
)

10
openflexure_microscope/api/default_extensions/autofocus.py
View file

@ -83,7 +83,7 @@ class JPEGSharpnessMonitor:
raise e
if stop < 1:
stop = len(jpeg_times)
logging.debug("changing stop to {}", (stop))
logging.debug("changing stop to %s", (stop))
jpeg_times = jpeg_times[start:stop]
jpeg_zs = np.interp(jpeg_times, stage_times, stage_zs)
return jpeg_times, jpeg_zs, jpeg_sizes[start:stop]
@ -258,13 +258,12 @@ def fast_up_down_up_autofocus(
# Ensure the MJPEG stream has started
microscope.camera.start_stream_recording()
df = dz # TODO: refactor so I actually use dz in the code below!
logging.debug("Initial move")
if initial_move_up:
m.focus_rel(df / 2)
m.focus_rel(dz / 2)
# move down
logging.debug("Move down")
i, z = m.focus_rel(-df)
i, z = m.focus_rel(-dz)
# now inspect where the sharpest point is, and estimate the sharpness
# (JPEG size) that we should find at the start of the Z stack
_, jz, js = m.move_data(i)
@ -285,14 +284,13 @@ def fast_up_down_up_autofocus(
inow = np.argmax(
js < current_js
) # use the curve we recorded to estimate our position
# TODO: fancy interpolation stuff
# So, the Z position corresponding to our current sharpness value is zs[inow]
# That means we should move forwards, by best_z - zs[inow]
logging.debug("Correction move")
correction_move = best_z + target_z - jz[inow]
logging.debug(
"Fast autofocus scan: correcting backlash by moving {} steps",
"Fast autofocus scan: correcting backlash by moving %s steps",
(correction_move),
)
m.focus_rel(correction_move)

6
openflexure_microscope/api/default_extensions/autostorage.py
View file

@ -95,10 +95,10 @@ class AutostorageExtension(BaseExtension):
def on_microscope(self, microscope_obj):
"""Function to automatically call when the parent LabThing has a microscope attached."""
logging.debug("Autostorage extension found microscope {}", microscope_obj)
logging.debug("Autostorage extension found microscope %s", microscope_obj)
if hasattr(microscope_obj, "captures"):
logging.debug(
"Autostorage extension bound to CaptureManager {}", self.capture_manager
"Autostorage extension bound to CaptureManager %s", self.capture_manager
)
# Store a reference to the CaptureManager
@ -117,7 +117,7 @@ class AutostorageExtension(BaseExtension):
# If preferred path does not exist, or cannot be written to
if not (os.path.isdir(location) and check_rw(location)):
logging.error(
"Preferred capture path {} is missing or cannot be written to. Restoring defaults.",
"Preferred capture path %s is missing or cannot be written to. Restoring defaults.",
location,
)
# Reset the storage location to default

10
openflexure_microscope/api/default_extensions/picamera_autocalibrate/recalibrate_utils.py
View file

@ -63,15 +63,15 @@ def auto_expose_and_freeze_settings(camera):
logging.info("Freezing the camera settings...")
camera.shutter_speed = camera.exposure_speed
logging.info("Shutter speed = {}", (camera.shutter_speed))
logging.info("Shutter speed = %s", (camera.shutter_speed))
camera.exposure_mode = "off"
logging.info("Auto exposure disabled")
g = camera.awb_gains
camera.awb_mode = "off"
camera.awb_gains = g
logging.info("Auto white balance disabled, gains are {}", (g))
logging.info("Auto white balance disabled, gains are %s", (g))
logging.info(
"Analogue gain: {}, Digital gain: {}", camera.analog_gain, camera.digital_gain
"Analogue gain: %s, Digital gain: %s", camera.analog_gain, camera.digital_gain
)
adjust_exposure_to_setpoint(camera, 215)
@ -98,7 +98,7 @@ 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.
logging.info("Generating a lens shading table at {}x{}", *lst_resolution)
logging.info("Generating a lens shading table at %sx%s", *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, :, :]
@ -116,7 +116,7 @@ def lst_from_channels(channels):
image_channel, [(0, lw * 32 - iw), (0, lh * 32 - ih)], mode="edge"
) # Pad image to the right and bottom
logging.info(
"Channel shape: {}x{}, shading table shape: {}x{}, after padding {}",
"Channel shape: %sx%s, shading table shape: %sx%s, after padding %s",
iw,
ih,
lw * 32,

16
openflexure_microscope/api/default_extensions/scan.py
View file

@ -216,7 +216,7 @@ class ScanExtension(BaseExtension):
for x_y in line:
# Move to new grid position without changing z
logging.debug("Moving to step {}", ([x_y[0], x_y[1], next_z]))
logging.debug("Moving to step %s", ([x_y[0], x_y[1], next_z]))
microscope.stage.move_abs([x_y[0], x_y[1], next_z])
# Refocus
if autofocus_enabled:
@ -270,11 +270,11 @@ class ScanExtension(BaseExtension):
# Make sure we use our current best estimate of focus (i.e. the current position) next point
next_z = microscope.stage.position[2]
logging.debug("Returning to {}", (initial_position))
logging.debug("Returning to %s", (initial_position))
microscope.stage.move_abs(initial_position)
end = time.time()
logging.info("Scan took {} seconds", end - start)
logging.info("Scan took %s seconds", end - start)
def stack(
self,
@ -298,17 +298,17 @@ class ScanExtension(BaseExtension):
# Store initial position
initial_position = microscope.stage.position
logging.debug("Starting z-stack from position {}", microscope.stage.position)
logging.debug("Starting z-stack from position %s", microscope.stage.position)
with microscope.lock:
# Move to center scan
logging.debug("Moving to z-stack starting position")
microscope.stage.move_rel([0, 0, int((-step_size * steps) / 2)])
logging.debug("Starting scan from position {}", microscope.stage.position)
logging.debug("Starting scan from position %s", microscope.stage.position)
for i in range(steps):
time.sleep(0.1)
logging.debug("Capturing from position {}", microscope.stage.position)
logging.debug("Capturing from position %s", microscope.stage.position)
self.capture(
microscope,
basename,
@ -328,10 +328,10 @@ class ScanExtension(BaseExtension):
return
if i != steps - 1:
logging.debug("Moving z by {}", (step_size))
logging.debug("Moving z by %s", (step_size))
microscope.stage.move_rel([0, 0, step_size])
if return_to_start:
logging.debug("Returning to {}", (initial_position))
logging.debug("Returning to %s", (initial_position))
microscope.stage.move_abs(initial_position)

2
openflexure_microscope/api/default_extensions/zip_builder.py
View file

@ -156,7 +156,7 @@ class ZipGetterAPIView(View):
if not session_id in default_zip_manager.session_zips:
return abort(404) # 404 Not Found
logging.info("Session ID: {}", session_id)
logging.info("Session ID: %s", session_id)
return send_file(
default_zip_manager.zip_fp_from_id(session_id).name,

2
openflexure_microscope/api/dev_extensions/tools.py
View file

@ -17,7 +17,7 @@ class SleepFor(ActionView):
def post(self, args):
sleep_time = args.get("time")
logging.info("Going to sleep for {}...", sleep_time)
logging.info("Going to sleep for %s...", sleep_time)
start = time.time()
time.sleep(sleep_time)
end = time.time()

4
openflexure_microscope/api/utilities/__init__.py
View file

@ -73,10 +73,10 @@ def init_default_extensions(extension_dir):
default_ext_path = os.path.join(extension_dir, "defaults.py")
if not os.path.isfile(default_ext_path): # If user extensions file doesn't exist
logging.warning("No extension file found at {}. Creating...", (extension_dir))
logging.warning("No extension file found at %s. Creating...", (extension_dir))
create_file(default_ext_path)
logging.info("Populating {}...", (default_ext_path))
logging.info("Populating %s...", (default_ext_path))
with open(default_ext_path, "w") as outfile:
outfile.write(_DEFAULT_EXTENSION_INIT)

2
openflexure_microscope/api/utilities/gui.py
View file

@ -27,7 +27,7 @@ def build_gui_from_dict(gui_description, extension_object):
if "route" in form and form["route"] in ext_rules.keys():
form["route"] = ext_rules[form["route"]]["urls"][0]
else:
logging.warning("No valid expandable route found for {}", form["route"])
logging.warning("No valid expandable route found for %s", form["route"])
# Inject extension information
api_gui["id"] = extension_object.name

4
openflexure_microscope/api/v2/views/actions/stage.py
View file

@ -25,11 +25,11 @@ class MoveStageAPI(ActionView):
# Handle absolute positioning (calculate a relative move from current position and target)
if (args.get("absolute")) and (microscope.stage): # Only if stage exists
target_position = axes_to_array(args, ["x", "y", "z"])
logging.debug("TARGET: {}", (target_position))
logging.debug("TARGET: %s", (target_position))
position = [
target_position[i] - microscope.stage.position[i] for i in range(3)
]
logging.debug("DELTA: {}", (position))
logging.debug("DELTA: %s", (position))
else:
# Get coordinates from payload