Merge branch 'old-fast-autofocus' into 'master'
Old fast autofocus See merge request openflexure/openflexure-microscope-server!77
This commit is contained in:
Joel Collins
commit
b9bed71272
2 changed files with 96 additions and 59 deletions
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@ -80,13 +80,19 @@ class JPEGSharpnessMonitor:
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def focus_rel(self, dz, backlash=False, **kwargs):
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self.keep_alive()
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# Start time and position
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self.stage_times.append(time.time())
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self.stage_positions.append(self.stage.position)
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# Main move
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self.stage.move_rel([0, 0, dz], backlash=backlash, **kwargs)
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# End time and position
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self.stage_times.append(time.time())
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self.stage_positions.append(self.stage.position)
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i = len(self.stage_positions) - 2
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return i, self.stage_positions[-1][2]
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# Index of the data for this movement
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data_index = len(self.stage_positions) - 2
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# Final z position after move
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final_z_position = self.stage_positions[-1][2]
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return data_index, final_z_position
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def move_data(self, istart, istop=None):
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"Extract sharpness as a function of (interpolated) z"
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@ -218,20 +224,26 @@ def move_and_measure(microscope, dz):
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return m.data_dict()
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def fast_autofocus(microscope, dz=2000, backlash=None):
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def fast_autofocus(microscope, dz=2000):
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"""Perform a down-up-down-up autofocus"""
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with monitor_sharpness(
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microscope
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) as m, microscope.camera.lock as _, microscope.stage.lock as _:
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i, z = m.focus_rel(-dz / 2)
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i, z = m.focus_rel(dz)
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fz = m.sharpest_z_on_move(i)
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if backlash is None:
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i, z = m.focus_rel(-dz) # move all the way to the start so it's consistent
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else:
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i, z = m.focus_rel(fz - z - backlash)
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m.focus_rel(fz - z)
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return m.data_dict()
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with microscope.camera.lock, microscope.stage.lock:
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with monitor_sharpness(microscope) as m:
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# Move to (-dz / 2)
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m.focus_rel(-dz / 2)
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# Move to dz while monitoring sharpness
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# i: Sharpness monitor index for this move
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# z: Final z position after move
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i, z = m.focus_rel(dz)
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# Get the z position with highest sharpness from the previous move (index i)
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fz = m.sharpest_z_on_move(i)
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# Move all the way to the start so it's consistent
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# Store final absolute z position from this return move
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i, z = m.focus_rel(-dz)
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# Move to the target position fz
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# Can't do absolute move here yet so move by (fz - z)
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m.focus_rel(fz - z)
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# Return all focus data
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return m.data_dict()
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def fast_up_down_up_autofocus(
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@ -272,52 +284,51 @@ def fast_up_down_up_autofocus(
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might slightly hurt accuracy, but is unlikely to be a big issue. Too big
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may cause you to overshoot, which is a problem.
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"""
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with monitor_sharpness(
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microscope
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) as m, microscope.camera.lock as _, microscope.stage.lock as _:
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# Ensure the MJPEG stream has started
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microscope.camera.start_stream_recording()
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with microscope.camera.lock, microscope.stage.lock:
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with monitor_sharpness(microscope) as m:
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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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# move down
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logging.debug("Move down")
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i, z = m.focus_rel(-df)
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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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best_z = jz[np.argmax(js)]
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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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# move down
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logging.debug("Move down")
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i, z = m.focus_rel(-df)
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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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best_z = jz[np.argmax(js)]
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# now move to the start of the z stack
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logging.debug("Move to the start of the z stack")
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i, z = m.focus_rel(
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best_z + target_z - z + mini_backlash
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) # takes us to the start of the stack
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# now move to the start of the z stack
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logging.debug("Move to the start of the z stack")
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i, z = m.focus_rel(
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best_z + target_z - z + mini_backlash
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) # takes us to the start of the stack
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# We've deliberately undershot - figure out how much further we should move based on the curve
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logging.debug("Calculate remining movement")
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current_js = m.jpeg_size()
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imax = np.argmax(js) # we want to crop out just the bit below the peak
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js = js[imax:] # NB z is in DECREASING order
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jz = jz[imax:]
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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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# We've deliberately undershot - figure out how much further we should move based on the curve
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logging.debug("Calculate remining movement")
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current_js = m.jpeg_size()
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imax = np.argmax(js) # we want to crop out just the bit below the peak
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js = js[imax:] # NB z is in DECREASING order
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jz = jz[imax:]
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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".format(
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correction_move
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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".format(
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correction_move
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)
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)
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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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m.focus_rel(correction_move)
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return m.data_dict()
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class MeasureSharpnessAPI(View):
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@ -346,7 +357,6 @@ class MoveAndMeasureAPI(ActionView):
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if microscope.has_real_stage():
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# Acquire microscope lock with 1s timeout
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with microscope.lock(timeout=1):
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# Run fast_up_down_up_autofocus
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return move_and_measure(microscope, dz=args.get("dz"))
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else:
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@ -384,8 +394,32 @@ class FastAutofocusAPI(ActionView):
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Run a fast autofocus
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"""
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args = {"dz": fields.Int(missing=2000, example=2000)}
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def post(self, args):
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microscope = find_component("org.openflexure.microscope")
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if not microscope:
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abort(503, "No microscope connected. Unable to autofocus.")
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if microscope.has_real_stage():
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logging.debug("Running autofocus...")
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# Acquire microscope lock with 1s timeout
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with microscope.lock(timeout=1):
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# Run fast_autofocus
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return fast_autofocus(microscope, dz=args.get("dz"))
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else:
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abort(503, "No stage connected. Unable to autofocus.")
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class UpDownUpAutofocusAPI(ActionView):
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"""
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Run a fast up-down-up autofocus
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"""
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args = {
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"dz": fields.Int(missing=2000),
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"dz": fields.Int(missing=2000, example=2000),
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"backlash": fields.Int(missing=25, minimum=0),
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}
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@ -433,6 +467,9 @@ autofocus_extension_v2.add_view(AutofocusAPI, "/autofocus", endpoint="autofocus"
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autofocus_extension_v2.add_view(
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FastAutofocusAPI, "/fast_autofocus", endpoint="fast_autofocus"
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)
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autofocus_extension_v2.add_view(
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UpDownUpAutofocusAPI, "/updownup_autofocus", endpoint="updownup_autofocus"
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)
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autofocus_extension_v2.add_view(
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MoveAndMeasureAPI, "/move_and_measure", endpoint="move_and_measure"
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@ -203,7 +203,7 @@ class ScanExtension(BaseExtension):
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if autofocus_enabled:
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if fast_autofocus:
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# Run fast autofocus. Client should provide dz ~ 2000
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autofocus_extension.fast_up_down_up_autofocus(
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autofocus_extension.fast_autofocus(
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microscope, dz=autofocus_dz
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)
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else:
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