Reverted logging style

.pylintrc

@@ -1,8 +1,4 @@
 [MESSAGES CONTROL]
 
 disable=fixme,C,R
-max-line-length = 88
+max-line-length = 88
-
-[LOGGING]
-
-logging-format-style=new

openflexure_microscope/api/app.py

@@ -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

openflexure_microscope/api/default_extensions/__init__.py

@@ -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(),
         )

openflexure_microscope/api/default_extensions/autofocus.py

@@ -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)

openflexure_microscope/api/default_extensions/autostorage.py

@@ -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

openflexure_microscope/api/default_extensions/picamera_autocalibrate/recalibrate_utils.py

@@ -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,

openflexure_microscope/api/default_extensions/scan.py

@@ -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)
 
 

openflexure_microscope/api/default_extensions/zip_builder.py

@@ -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,

openflexure_microscope/api/dev_extensions/tools.py

@@ -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()

openflexure_microscope/api/utilities/__init__.py

@@ -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)
 

openflexure_microscope/api/utilities/gui.py

@@ -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

openflexure_microscope/api/v2/views/actions/stage.py

@@ -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

openflexure_microscope/camera/base.py

@@ -113,10 +113,10 @@ class BaseCamera(metaclass=ABCMeta):
 
     def close(self):
         """Close the BaseCamera and all attached StreamObjects."""
-        logging.info("Closing {}", (self))
+        logging.info("Closing %s", (self))
         # Stop worker thread
         self.stop_worker()
-        logging.info("Closed {}", (self))
+        logging.info("Closed %s", (self))
 
     # START AND STOP WORKER THREAD
 

openflexure_microscope/camera/pi.py

@@ -156,10 +156,10 @@ class PiCameraStreamer(BaseCamera):
         for key in PiCameraStreamer.picamera_settings_keys:
             try:
                 value = getattr(self.camera, key)
-                logging.debug("Reading PiCamera().{}: {}", key, value)
+                logging.debug("Reading PiCamera().%s: %s", key, value)
                 conf_dict["picamera"][key] = value
             except AttributeError:
-                logging.debug("Unable to read PiCamera attribute {}", (key))
+                logging.debug("Unable to read PiCamera attribute %s", (key))
 
         # Include a serialised lens shading table
         if (
@@ -243,22 +243,22 @@ class PiCameraStreamer(BaseCamera):
         # Set exposure mode
         if "exposure_mode" in settings_dict:
             logging.debug(
-                "Applying exposure_mode: {}", (settings_dict["exposure_mode"])
+                "Applying exposure_mode: %s", (settings_dict["exposure_mode"])
             )
             self.camera.exposure_mode = settings_dict["exposure_mode"]
 
         # Apply gains and let them settle
         if "analog_gain" in settings_dict:
-            logging.debug("Applying analog_gain: {}", (settings_dict["analog_gain"]))
+            logging.debug("Applying analog_gain: %s", (settings_dict["analog_gain"]))
             set_analog_gain(self.camera, float(settings_dict["analog_gain"]))
         if "digital_gain" in settings_dict:
-            logging.debug("Applying digital_gain: {}", (settings_dict["digital_gain"]))
+            logging.debug("Applying digital_gain: %s", (settings_dict["digital_gain"]))
             set_digital_gain(self.camera, float(settings_dict["digital_gain"]))
 
         # Apply shutter speed
         if "shutter_speed" in settings_dict:
             logging.debug(
-                "Applying shutter_speed: {}", (settings_dict["shutter_speed"])
+                "Applying shutter_speed: %s", (settings_dict["shutter_speed"])
             )
             self.camera.shutter_speed = int(settings_dict["shutter_speed"])
 
@@ -268,17 +268,17 @@ class PiCameraStreamer(BaseCamera):
         if "awb_gains" in settings_dict:
             logging.debug("Applying awb_mode: off")
             self.camera.awb_mode = "off"
-            logging.debug("Applying awb_gains: {}", (settings_dict["awb_gains"]))
+            logging.debug("Applying awb_gains: %s", (settings_dict["awb_gains"]))
             self.camera.awb_gains = settings_dict["awb_gains"]
         elif "awb_mode" in settings_dict:
-            logging.debug("Applying awb_mode: {}", (settings_dict["awb_mode"]))
+            logging.debug("Applying awb_mode: %s", (settings_dict["awb_mode"]))
             self.camera.awb_mode = settings_dict["awb_mode"]
 
         # Handle some properties that can be quickly applied
         batched_keys = ["framerate", "saturation"]
         for key in batched_keys:
             if (key in settings_dict) and hasattr(self.camera, key):
-                logging.debug("Applying {}: {}", key, settings_dict[key])
+                logging.debug("Applying %s: %s", key, settings_dict[key])
                 setattr(self.camera, key, settings_dict[key])
 
         # Final optional pause to settle
@@ -303,7 +303,7 @@ class PiCameraStreamer(BaseCamera):
             for i in range(2):
                 if np.abs(centre[i] - 0.5) + size / 2 > 0.5:
                     centre[i] = 0.5 + (1.0 - size) / 2 * np.sign(centre[i] - 0.5)
-            logging.info("setting zoom, centre {}, size {}", centre, size)
+            logging.info("setting zoom, centre %s, size %s", centre, size)
             new_fov = (centre[0] - size / 2, centre[1] - size / 2, size, size)
             self.camera.zoom = new_fov
 
@@ -325,11 +325,11 @@ class PiCameraStreamer(BaseCamera):
                 self.preview_active = True
             except picamerax.exc.PiCameraMMALError as e:
                 logging.error(
-                    "Suppressed a MMALError in start_preview. Exception: {}", (e)
+                    "Suppressed a MMALError in start_preview. Exception: %s", (e)
                 )
             except picamerax.exc.PiCameraValueError as e:
                 logging.error(
-                    "Suppressed a ValueError exception in start_preview. Exception: {}",
+                    "Suppressed a ValueError exception in start_preview. Exception: %s",
                     (e),
                 )
 
@@ -359,7 +359,7 @@ class PiCameraStreamer(BaseCamera):
             if not self.record_active:
 
                 # Start the camera video recording on port 2
-                logging.info("Recording to {}", (output))
+                logging.info("Recording to %s", (output))
 
                 self.camera.start_recording(
                     output,
@@ -401,17 +401,17 @@ class PiCameraStreamer(BaseCamera):
         """
         for k in kwargs.keys():
             logging.warning(
-                "Warning, kwarg {} is invalid for stop_stream_recording.", k
+                "Warning, kwarg %s is invalid for stop_stream_recording.", k
             )
         with self.lock:
             # Stop the camera video recording on port 1
             try:
                 self.camera.stop_recording(splitter_port=splitter_port)
             except picamerax.exc.PiCameraNotRecording:
-                logging.info("Not recording on splitter_port {}", (splitter_port))
+                logging.info("Not recording on splitter_port %s", (splitter_port))
             else:
                 logging.info(
-                    "Stopped MJPEG stream on port {}. Switching to {}.",
+                    "Stopped MJPEG stream on port %s. Switching to %s.",
                     splitter_port,
                     self.image_resolution,
                 )
@@ -431,7 +431,7 @@ class PiCameraStreamer(BaseCamera):
         """
         for k in kwargs.keys():
             logging.warning(
-                "Warning, kwarg {} is invalid for stop_stream_recording.", k
+                "Warning, kwarg %s is invalid for stop_stream_recording.", k
             )
         with self.lock(timeout=None):
             # Reduce the resolution for video streaming
@@ -465,7 +465,7 @@ class PiCameraStreamer(BaseCamera):
                     )
                 else:
                     logging.debug(
-                        "Started MJPEG stream at {} on port {}",
+                        "Started MJPEG stream at %s on port %s",
                         self.stream_resolution,
                         splitter_port,
                     )
@@ -496,7 +496,7 @@ class PiCameraStreamer(BaseCamera):
             output_object (str/BytesIO): Target object.
         """
         with self.lock:
-            logging.info("Capturing to {}", (output))
+            logging.info("Capturing to %s", (output))
 
             # Set resolution and stop stream recording if necessary
             if not use_video_port:
@@ -532,7 +532,7 @@ class PiCameraStreamer(BaseCamera):
             logging.debug("Creating PiRGBArray")
             with picamerax.array.PiRGBArray(self.camera) as output:
 
-                logging.info("Capturing to {}", (output))
+                logging.info("Capturing to %s", (output))
 
                 self.camera.capture(output, format="rgb", use_video_port=True)
 

openflexure_microscope/camera/set_picamera_gain.py

@@ -55,7 +55,7 @@ if __name__ == "__main__":
         # fix the shutter speed
         cam.shutter_speed = cam.exposure_speed
 
-        logging.info("Current a/d gains: {}, {}", cam.analog_gain, cam.digital_gain)
+        logging.info("Current a/d gains: %s, %s", cam.analog_gain, cam.digital_gain)
 
         logging.info("Attempting to set analogue gain to 1")
         set_analog_gain(cam, 1)
@@ -65,7 +65,7 @@ if __name__ == "__main__":
         try:
             while True:
                 logging.info(
-                    "Current a/d gains: {}, {}", cam.analog_gain, cam.digital_gain
+                    "Current a/d gains: %s, %s", cam.analog_gain, cam.digital_gain
                 )
                 time.sleep(1)
         except KeyboardInterrupt:

openflexure_microscope/captures/capture.py

@@ -25,23 +25,23 @@ def make_file_list(directory, formats):
             glob.glob("{}/**/*.{}".format(directory, fmt.lower()), recursive=True)
         )
 
-    logging.info("{} capture files found on disk", (len(files)))
+    logging.info("%s capture files found on disk", (len(files)))
 
     return files
 
 
 def build_captures_from_exif(capture_path):
-    logging.debug("Reloading captures from {}...", (capture_path))
+    logging.debug("Reloading captures from %s...", (capture_path))
     files = make_file_list(capture_path, EXIF_FORMATS)
     captures = OrderedDict()
 
     for f in files:
-        logging.debug("Reloading capture {}...", (f))
+        logging.debug("Reloading capture %s...", (f))
         capture = capture_from_path(f)
         if capture:
             captures[capture.id] = capture
 
-    logging.info("{} capture files successfully reloaded", (len(captures)))
+    logging.info("%s capture files successfully reloaded", (len(captures)))
 
     return captures
 
@@ -58,7 +58,7 @@ def capture_from_path(path):
         capture.sync_basic_metadata()
         return capture
     except (InvalidImageDataError, json.decoder.JSONDecodeError):
-        logging.error("Invalid metadata at {}.", (path))
+        logging.error("Invalid metadata at %s.", (path))
         return None
 
 
@@ -75,7 +75,7 @@ class CaptureObject(object):
 
         # Store a nice ID
         self.id = uuid.uuid4()  #: str: Unique capture ID
-        logging.debug("Created CaptureObject {}", (self.id))
+        logging.debug("Created CaptureObject %s", (self.id))
 
         self.time = datetime.datetime.now()
 
@@ -97,17 +97,17 @@ class CaptureObject(object):
         self.tags = []
 
     def write(self, s):
-        logging.debug("Writing to {}", self)
+        logging.debug("Writing to %s", self)
         self.stream.write(s)
 
     def flush(self):
-        logging.info("Writing image data to disk {}", self.file)
+        logging.info("Writing image data to disk %s", self.file)
         with open(self.file, "wb") as outfile:
             outfile.write(self.stream.getbuffer())
         self.stream.close()
-        logging.info("Writing metadata to disk {}", self.file)
+        logging.info("Writing metadata to disk %s", self.file)
         self._init_metadata()
-        logging.info("Finished writing to disk {}", self.file)
+        logging.info("Finished writing to disk %s", self.file)
 
     def open(self, mode):
         return open(self.file, mode)
@@ -175,7 +175,7 @@ class CaptureObject(object):
             }
 
     def read_full_metadata(self):
-        logging.info("Reading full capture metadata from {}...", self.file)
+        logging.info("Reading full capture metadata from %s...", self.file)
         exif_dict = self._read_exif()
         return self._decode_usercomment(exif_dict)
 
@@ -271,7 +271,7 @@ class CaptureObject(object):
 
         # Write new data to file EXIF, if supported
         if self.format.upper() in EXIF_FORMATS and self.exists:
-            logging.info("Writing Exif data to {}", self.file)
+            logging.info("Writing Exif data to %s", self.file)
 
             # Extract current Exif data
             exif_dict = self._read_exif()
@@ -286,7 +286,7 @@ class CaptureObject(object):
 
             # Serialize metadata
             metadata_string = json.dumps(metadata_dict, cls=JSONEncoder)
-            logging.debug("Saving metadata string to file: {}", metadata_string)
+            logging.debug("Saving metadata string to file: %s", metadata_string)
 
             # Insert metadata into exif_dict
             exif_dict["Exif"][piexif.ExifIFD.UserComment] = metadata_string.encode()
@@ -296,7 +296,7 @@ class CaptureObject(object):
 
             # Insert exif into file
             piexif.insert(exif_bytes, self.file)
-            logging.info("Finished writing Exif data to {}", self.file)
+            logging.info("Finished writing Exif data to %s", self.file)
 
     # PROPERTIES
 
@@ -316,7 +316,7 @@ class CaptureObject(object):
         """
 
         if self.exists:  # If data file exists
-            logging.info("Opening from file {}", (self.file))
+            logging.info("Opening from file %s", (self.file))
             with open(self.file, "rb") as f:
                 d = io.BytesIO(f.read())  # Load bytes from file
             d.seek(0)  # Rewind loaded bytestream
@@ -364,7 +364,7 @@ class CaptureObject(object):
         """If the StreamObject has been saved, delete the file."""
 
         if os.path.isfile(self.file):
-            logging.info("Deleting file {}", (self.file))
+            logging.info("Deleting file %s", (self.file))
             os.remove(self.file)
 
             return True

openflexure_microscope/captures/capture_manager.py

@@ -61,7 +61,7 @@ class CaptureManager:
         self.close()
 
     def close(self):
-        logging.info("Closing {}", (self))
+        logging.info("Closing %s", (self))
         # Close all StreamObjects
         for capture_list in [self.images.values(), self.videos.values()]:
             for stream_object in capture_list:
@@ -75,9 +75,9 @@ class CaptureManager:
         """
 
         if os.path.isdir(self.paths["temp"]):
-            logging.info("Clearing {}...", (self.paths["temp"]))
+            logging.info("Clearing %s...", (self.paths["temp"]))
             shutil.rmtree(self.paths["temp"])
-            logging.debug("Cleared {}.", (self.paths["temp"]))
+            logging.debug("Cleared %s.", (self.paths["temp"]))
 
     def rebuild_captures(self):
         self.images = build_captures_from_exif(self.paths["default"])
@@ -158,7 +158,7 @@ class CaptureManager:
 
         # Update capture list
         capture_key = str(output.id)
-        logging.debug("Adding image {} with key {}", output, capture_key)
+        logging.debug("Adding image %s with key %s", output, capture_key)
 
         self.images[capture_key] = output
 
@@ -205,7 +205,7 @@ class CaptureManager:
 
         # Update capture list
         capture_key = str(output.id)
-        logging.debug("Adding video {} with key {}", output, capture_key)
+        logging.debug("Adding video %s with key %s", output, capture_key)
         self.videos[capture_key] = output
 
         return output

openflexure_microscope/config.py

@@ -86,7 +86,7 @@ def load_json_file(config_path) -> dict:
     """
     config_path = os.path.expanduser(config_path)
 
-    logging.info("Loading {}...", config_path)
+    logging.info("Loading %s...", config_path)
 
     with open(config_path) as config_file:
         try:
@@ -109,7 +109,7 @@ def save_json_file(config_path: str, config_dict: dict):
     """
     config_path = os.path.expanduser(config_path)
 
-    logging.info("Saving {}...", config_path)
+    logging.info("Saving %s...", config_path)
     logging.debug(config_dict)
 
     with open(config_path, "w") as outfile:
@@ -142,14 +142,14 @@ def initialise_file(config_path, populate: str = "{}\n"):
     """
     config_path = os.path.expanduser(config_path)
 
-    logging.debug("Initialising {}", (config_path))
+    logging.debug("Initialising %s", (config_path))
-    logging.debug("Exists: {}", (os.path.exists(config_path)))
+    logging.debug("Exists: %s", (os.path.exists(config_path)))
 
     if not os.path.exists(config_path):  # If user config file doesn't exist
-        logging.warning("No config file found at {}. Creating...", (config_path))
+        logging.warning("No config file found at %s. Creating...", (config_path))
         create_file(config_path)
 
-        logging.info("Populating {}...", (config_path))
+        logging.info("Populating %s...", (config_path))
         with open(config_path, "w") as outfile:
             outfile.write(populate)
 

openflexure_microscope/microscope.py

@@ -71,7 +71,7 @@ class Microscope:
 
     def close(self):
         """Shut down the microscope hardware."""
-        logging.info("Closing {}", (self))
+        logging.info("Closing %s", (self))
         if self.camera:
             try:
                 self.camera.close()
@@ -83,7 +83,7 @@ class Microscope:
             except TimeoutError as e:
                 logging.error(e)
         self.captures.close()
-        logging.info("Closed {}", (self))
+        logging.info("Closed %s", (self))
 
     def setup(self, configuration):
         """
@@ -196,7 +196,7 @@ class Microscope:
         Applies a settings dictionary to the microscope. Missing parameters will be left untouched.
         """
         with self.lock:
-            logging.debug("Microscope: Applying settings: {}", (settings))
+            logging.debug("Microscope: Applying settings: %s", (settings))
 
             # If attached to a camera
             if ("camera" in settings) and self.camera:
@@ -329,14 +329,14 @@ class Microscope:
 
         # Load cached bits of metadata
         if cache_key:
-            logging.debug("Reading cached microscope metadata: {}", cache_key)
+            logging.debug("Reading cached microscope metadata: %s", cache_key)
             metadata = self.metadata_cache.get(cache_key, None)
             if not metadata:
-                logging.debug("Building and caching microscope metadata: {}", cache_key)
+                logging.debug("Building and caching microscope metadata: %s", cache_key)
                 metadata = self.force_get_metadata()
                 self.metadata_cache[cache_key] = metadata
         else:
-            logging.debug("Building microscope metadata: {}", cache_key)
+            logging.debug("Building microscope metadata: %s", cache_key)
             metadata = self.force_get_metadata()
 
         # Keys that should never be cached
@@ -362,7 +362,7 @@ class Microscope:
         metadata: dict = None,
         cache_key: str = None,
     ):
-        logging.debug("Microscope capturing to {}", filename)
+        logging.debug("Microscope capturing to %s", filename)
         if not annotations:
             annotations = {}
         if not metadata:
@@ -384,7 +384,7 @@ class Microscope:
             extras = {}
             if fmt == "jpeg":
                 extras["thumbnail"] = (*THUMBNAIL_SIZE, 85)
-            logging.info("Starting microscope capture {}", output.file)
+            logging.info("Starting microscope capture %s", output.file)
             self.camera.capture(
                 output,
                 use_video_port=use_video_port,
@@ -395,6 +395,6 @@ class Microscope:
             )
 
         output.put_and_save(tags, annotations, full_metadata)
-        logging.debug("Finished capture to {}", output.file)
+        logging.debug("Finished capture to %s", output.file)
 
         return output

openflexure_microscope/rescue/check_capture_reload.py

@@ -27,7 +27,7 @@ def main():
     logging.info("Loading user settings...")
     settings = user_settings.load()
     cap_path = str(settings.get("captures", {}).get("paths", {}).get("default"))
-    logging.info("Capture path found: {}", cap_path)
+    logging.info("Capture path found: %s", cap_path)
 
     if not cap_path:
         logging.error(

openflexure_microscope/rescue/monitor_timeout.py

@@ -24,7 +24,7 @@ def launch_timeout_test_process(target, args=(), kwargs=None, timeout=10):
     # If thread is still active
     if p.is_alive():
         logging.error(
-            "Function {} reached timeout after {} seconds. Terminating.",
+            "Function %s reached timeout after %s seconds. Terminating.",
             target,
             timeout,
         )

openflexure_microscope/stage/mock.py

@@ -80,13 +80,13 @@ class MissingStage(BaseStage):
 
         self._position = list(np.array(self._position) + np.array(initial_move))
         logging.debug(np.array(self._position) + np.array(initial_move))
-        logging.debug("New position: {}", self._position)
+        logging.debug("New position: %s", self._position)
 
     def move_abs(self, final, **kwargs):
         time.sleep(0.5)
 
         self._position = list(final)
-        logging.debug("New position: {}", self._position)
+        logging.debug("New position: %s", self._position)
 
     def zero_position(self):
         """Set the current position to zero"""

openflexure_microscope/stage/sanga.py

@@ -81,7 +81,7 @@ class SangaStage(BaseStage):
 
     @backlash.setter
     def backlash(self, blsh):
-        logging.debug("Setting backlash to {}", (blsh))
+        logging.debug("Setting backlash to %s", (blsh))
         if blsh is None:
             self._backlash = None
         elif isinstance(blsh, Iterable):
@@ -118,7 +118,7 @@ class SangaStage(BaseStage):
         backlash: (default: True) whether to correct for backlash.
         """
         with self.lock:
-            logging.debug("Moving sangaboard by {}", displacement)
+            logging.debug("Moving sangaboard by %s", displacement)
             if not backlash or self.backlash is None:
                 return self.board.move_rel(displacement, axis=axis)
             if axis is not None:
@@ -158,7 +158,7 @@ class SangaStage(BaseStage):
         """Make an absolute move to a position
         """
         with self.lock:
-            logging.debug("Moving sangaboard to {}", final)
+            logging.debug("Moving sangaboard to %s", final)
             self.board.move_abs(final, **kwargs)
         # Settle outside of the stage lock so that another move request
         # can just take over before settling
@@ -262,7 +262,7 @@ class SangaDeltaStage(SangaStage):
         # Transform into delta coordinates
         displacement = np.dot(self.Tdv, displacement)
 
-        logging.debug("Delta displacement: {}", (displacement))
+        logging.debug("Delta displacement: %s", (displacement))
 
         # Do the move
         SangaStage.move_rel(self, displacement, axis=None, backlash=backlash)
@@ -274,7 +274,7 @@ class SangaDeltaStage(SangaStage):
         # Transform into delta coordinates
         final = np.dot(self.Tdv, final)
 
-        logging.debug("Delta final: {}", (final))
+        logging.debug("Delta final: %s", (final))
 
         # Do the move
         SangaStage.move_abs(self, final, **kwargs)

openflexure_microscope/utilities.py

@@ -22,7 +22,7 @@ class Timer(object):
 
     def __exit__(self, type_, value, traceback):
         self.end = time.time()
-        logging.debug("{} time: {}", self.name, self.end - self.start)
+        logging.debug("%s time: %s", self.name, self.end - self.start)
 
 
 def deserialise_array_b64(b64_string, dtype, shape):