Updated all log strings to new format
This commit is contained in:
Joel Collins
parent
36e837d374
commit
9f5252194a
35 changed files with 121 additions and 715 deletions
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@ -72,7 +72,7 @@ root_log.addHandler(fh)
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access_log.addHandler(afh)
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# Log server paths being used
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logging.info("Running with data path %s", OPENFLEXURE_VAR_PATH)
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logging.info("Running with data path {}", OPENFLEXURE_VAR_PATH)
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logging.info("Creating app")
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# Create flask app
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@ -10,7 +10,7 @@ def handle_extension_error(extension_name):
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yield
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except Exception: # pylint: disable=W0703
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logging.error(
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"Exception loading builtin extension %s: \n%s",
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"Exception loading builtin extension {}: \n{}",
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extension_name,
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traceback.format_exc(),
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)
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@ -83,7 +83,7 @@ class JPEGSharpnessMonitor:
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raise e
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if stop < 1:
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stop = len(jpeg_times)
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logging.debug("changing stop to {}".format(stop))
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logging.debug("changing stop to {}", (stop))
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jpeg_times = jpeg_times[start:stop]
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jpeg_zs = np.interp(jpeg_times, stage_times, stage_zs)
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return jpeg_times, jpeg_zs, jpeg_sizes[start:stop]
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@ -292,9 +292,8 @@ def fast_up_down_up_autofocus(
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logging.debug("Correction move")
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correction_move = best_z + target_z - jz[inow]
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logging.debug(
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"Fast autofocus scan: correcting backlash by moving {} steps".format(
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correction_move
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)
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"Fast autofocus scan: correcting backlash by moving {} steps",
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(correction_move),
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)
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m.focus_rel(correction_move)
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return m.data_dict()
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@ -95,10 +95,10 @@ class AutostorageExtension(BaseExtension):
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def on_microscope(self, microscope_obj):
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"""Function to automatically call when the parent LabThing has a microscope attached."""
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logging.debug("Autostorage extension found microscope %s", microscope_obj)
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logging.debug("Autostorage extension found microscope {}", microscope_obj)
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if hasattr(microscope_obj, "captures"):
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logging.debug(
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"Autostorage extension bound to CaptureManager %s", self.capture_manager
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"Autostorage extension bound to CaptureManager {}", self.capture_manager
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)
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# Store a reference to the CaptureManager
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@ -117,7 +117,7 @@ class AutostorageExtension(BaseExtension):
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# If preferred path does not exist, or cannot be written to
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if not (os.path.isdir(location) and check_rw(location)):
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logging.error(
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"Preferred capture path %s is missing or cannot be written to. Restoring defaults.",
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"Preferred capture path {} is missing or cannot be written to. Restoring defaults.",
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location,
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)
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# Reset the storage location to default
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@ -63,17 +63,15 @@ def auto_expose_and_freeze_settings(camera):
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logging.info("Freezing the camera settings...")
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camera.shutter_speed = camera.exposure_speed
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logging.info("Shutter speed = {}".format(camera.shutter_speed))
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logging.info("Shutter speed = {}", (camera.shutter_speed))
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camera.exposure_mode = "off"
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logging.info("Auto exposure disabled")
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g = camera.awb_gains
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camera.awb_mode = "off"
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camera.awb_gains = g
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logging.info("Auto white balance disabled, gains are {}".format(g))
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logging.info("Auto white balance disabled, gains are {}", (g))
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logging.info(
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"Analogue gain: {}, Digital gain: {}".format(
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camera.analog_gain, camera.digital_gain
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)
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"Analogue gain: {}, Digital gain: {}", camera.analog_gain, camera.digital_gain
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)
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adjust_exposure_to_setpoint(camera, 215)
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@ -100,7 +98,7 @@ def lst_from_channels(channels):
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# lst_resolution = list(np.ceil(full_resolution / 64.0).astype(int))
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lst_resolution = [(r // 64) + 1 for r in full_resolution]
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# NB the size of the LST is 1/64th of the image, but rounded UP.
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logging.info("Generating a lens shading table at {}x{}".format(*lst_resolution))
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logging.info("Generating a lens shading table at {}x{}", *lst_resolution)
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lens_shading = np.zeros([channels.shape[0]] + lst_resolution, dtype=np.float)
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for i in range(lens_shading.shape[0]):
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image_channel = channels[i, :, :]
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@ -118,9 +116,12 @@ def lst_from_channels(channels):
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image_channel, [(0, lw * 32 - iw), (0, lh * 32 - ih)], mode="edge"
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) # Pad image to the right and bottom
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logging.info(
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"Channel shape: {}x{}, shading table shape: {}x{}, after padding {}".format(
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iw, ih, lw * 32, lh * 32, padded_image_channel.shape
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)
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"Channel shape: {}x{}, shading table shape: {}x{}, after padding {}",
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iw,
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ih,
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lw * 32,
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lh * 32,
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padded_image_channel.shape,
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)
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# Next, fill the shading table (except edge pixels). Please excuse the
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# for loop - I know it's not fast but this code needn't be!
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@ -216,7 +216,7 @@ class ScanExtension(BaseExtension):
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for x_y in line:
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# Move to new grid position without changing z
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logging.debug("Moving to step {}".format([x_y[0], x_y[1], next_z]))
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logging.debug("Moving to step {}", ([x_y[0], x_y[1], next_z]))
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microscope.stage.move_abs([x_y[0], x_y[1], next_z])
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# Refocus
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if autofocus_enabled:
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@ -270,11 +270,11 @@ class ScanExtension(BaseExtension):
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# Make sure we use our current best estimate of focus (i.e. the current position) next point
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next_z = microscope.stage.position[2]
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logging.debug("Returning to {}".format(initial_position))
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logging.debug("Returning to {}", (initial_position))
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microscope.stage.move_abs(initial_position)
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end = time.time()
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logging.info("Scan took %s seconds", end - start)
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logging.info("Scan took {} seconds", end - start)
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def stack(
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self,
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@ -298,17 +298,17 @@ class ScanExtension(BaseExtension):
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# Store initial position
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initial_position = microscope.stage.position
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logging.debug("Starting z-stack from position %s", microscope.stage.position)
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logging.debug("Starting z-stack from position {}", microscope.stage.position)
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with microscope.lock:
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# Move to center scan
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logging.debug("Moving to z-stack starting position")
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microscope.stage.move_rel([0, 0, int((-step_size * steps) / 2)])
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logging.debug("Starting scan from position %s", microscope.stage.position)
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logging.debug("Starting scan from position {}", microscope.stage.position)
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for i in range(steps):
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time.sleep(0.1)
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logging.debug("Capturing from position %s", microscope.stage.position)
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logging.debug("Capturing from position {}", microscope.stage.position)
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self.capture(
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microscope,
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basename,
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@ -328,10 +328,10 @@ class ScanExtension(BaseExtension):
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return
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if i != steps - 1:
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logging.debug("Moving z by {}".format(step_size))
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logging.debug("Moving z by {}", (step_size))
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microscope.stage.move_rel([0, 0, step_size])
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if return_to_start:
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logging.debug("Returning to {}".format(initial_position))
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logging.debug("Returning to {}", (initial_position))
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microscope.stage.move_abs(initial_position)
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@ -156,7 +156,7 @@ class ZipGetterAPIView(View):
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if not session_id in default_zip_manager.session_zips:
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return abort(404) # 404 Not Found
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logging.info("Session ID: %s", session_id)
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logging.info("Session ID: {}", session_id)
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return send_file(
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default_zip_manager.zip_fp_from_id(session_id).name,
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@ -17,7 +17,7 @@ class SleepFor(ActionView):
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def post(self, args):
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sleep_time = args.get("time")
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logging.info("Going to sleep for %s...", sleep_time)
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logging.info("Going to sleep for {}...", sleep_time)
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start = time.time()
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time.sleep(sleep_time)
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end = time.time()
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@ -73,12 +73,10 @@ def init_default_extensions(extension_dir):
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default_ext_path = os.path.join(extension_dir, "defaults.py")
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if not os.path.isfile(default_ext_path): # If user extensions file doesn't exist
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logging.warning(
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"No extension file found at {}. Creating...".format(extension_dir)
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)
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logging.warning("No extension file found at {}. Creating...", (extension_dir))
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create_file(default_ext_path)
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logging.info("Populating {}...".format(default_ext_path))
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logging.info("Populating {}...", (default_ext_path))
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with open(default_ext_path, "w") as outfile:
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outfile.write(_DEFAULT_EXTENSION_INIT)
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@ -27,7 +27,7 @@ def build_gui_from_dict(gui_description, extension_object):
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if "route" in form and form["route"] in ext_rules.keys():
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form["route"] = ext_rules[form["route"]]["urls"][0]
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else:
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logging.warning("No valid expandable route found for %s", form["route"])
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logging.warning("No valid expandable route found for {}", form["route"])
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# Inject extension information
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api_gui["id"] = extension_object.name
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@ -25,11 +25,11 @@ class MoveStageAPI(ActionView):
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# Handle absolute positioning (calculate a relative move from current position and target)
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if (args.get("absolute")) and (microscope.stage): # Only if stage exists
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target_position = axes_to_array(args, ["x", "y", "z"])
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logging.debug("TARGET: {}".format(target_position))
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logging.debug("TARGET: {}", (target_position))
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position = [
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target_position[i] - microscope.stage.position[i] for i in range(3)
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]
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logging.debug("DELTA: {}".format(position))
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logging.debug("DELTA: {}", (position))
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else:
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# Get coordinates from payload
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