Reverted logging style
This commit is contained in:
Joel Collins
parent
e25c23cf1c
commit
6fb61e1e3f
24 changed files with 100 additions and 106 deletions
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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 {}: \n{}",
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"Exception loading builtin extension %s: \n%s",
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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 {}", (stop))
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logging.debug("changing stop to %s", (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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@ -258,13 +258,12 @@ def fast_up_down_up_autofocus(
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# Ensure the MJPEG stream has started
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microscope.camera.start_stream_recording()
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df = dz # TODO: refactor so I actually use dz in the code below!
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logging.debug("Initial move")
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if initial_move_up:
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m.focus_rel(df / 2)
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m.focus_rel(dz / 2)
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# move down
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logging.debug("Move down")
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i, z = m.focus_rel(-df)
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i, z = m.focus_rel(-dz)
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# now inspect where the sharpest point is, and estimate the sharpness
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# (JPEG size) that we should find at the start of the Z stack
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_, jz, js = m.move_data(i)
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@ -285,14 +284,13 @@ def fast_up_down_up_autofocus(
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inow = np.argmax(
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js < current_js
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) # use the curve we recorded to estimate our position
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# TODO: fancy interpolation stuff
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# So, the Z position corresponding to our current sharpness value is zs[inow]
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# That means we should move forwards, by best_z - zs[inow]
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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",
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"Fast autofocus scan: correcting backlash by moving %s steps",
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(correction_move),
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)
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m.focus_rel(correction_move)
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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 {}", microscope_obj)
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logging.debug("Autostorage extension found microscope %s", 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 {}", self.capture_manager
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"Autostorage extension bound to CaptureManager %s", 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 {} is missing or cannot be written to. Restoring defaults.",
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"Preferred capture path %s 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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@ -63,15 +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 = {}", (camera.shutter_speed))
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logging.info("Shutter speed = %s", (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 {}", (g))
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logging.info("Auto white balance disabled, gains are %s", (g))
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logging.info(
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"Analogue gain: {}, Digital gain: {}", camera.analog_gain, camera.digital_gain
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"Analogue gain: %s, Digital gain: %s", camera.analog_gain, camera.digital_gain
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)
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adjust_exposure_to_setpoint(camera, 215)
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@ -98,7 +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{}", *lst_resolution)
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logging.info("Generating a lens shading table at %sx%s", *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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@ -116,7 +116,7 @@ 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 {}",
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"Channel shape: %sx%s, shading table shape: %sx%s, after padding %s",
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iw,
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ih,
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lw * 32,
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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 {}", ([x_y[0], x_y[1], next_z]))
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logging.debug("Moving to step %s", ([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 {}", (initial_position))
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logging.debug("Returning to %s", (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 {} seconds", end - start)
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logging.info("Scan took %s 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 {}", microscope.stage.position)
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logging.debug("Starting z-stack from position %s", 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 {}", microscope.stage.position)
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logging.debug("Starting scan from position %s", 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 {}", microscope.stage.position)
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logging.debug("Capturing from position %s", 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 {}", (step_size))
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logging.debug("Moving z by %s", (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 {}", (initial_position))
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logging.debug("Returning to %s", (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: {}", session_id)
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logging.info("Session ID: %s", 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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