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Moved scans into base class

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This commit is contained in:
Joel Collins 2019-11-04 12:09:23 +00:00
parent 0db0a89092
commit 0728b6fe08
2 changed files with 39 additions and 39 deletions
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38
openflexure_microscope/stage/base.py
View file

@ -73,3 +73,41 @@ class BaseStage(metaclass=ABCMeta):
def close(self):
"""Cleanly close communication with the stage"""
pass
def scan_linear(self, rel_positions, backlash=True, return_to_start=True):
"""
Scan through a list of (relative) positions (generator fn)
rel_positions should be an nx3-element array (or list of 3 element arrays).
Positions should be relative to the starting position - not a list of relative moves.
backlash argument is passed to move_rel
if return_to_start is True (default) we return to the starting position after a
successful scan. NB we always attempt to return to the starting position if an
exception occurs during the scan..
"""
starting_position = self.position
rel_positions = np.array(rel_positions)
assert rel_positions.shape[1] == 3, ValueError(
"Positions should be 3 elements long."
)
try:
self.move_rel(rel_positions[0], backlash=backlash)
yield 0
for i, step in enumerate(np.diff(rel_positions, axis=0)):
self.move_rel(step, backlash=backlash)
yield i + 1
except Exception as e:
return_to_start = True # always return to start if it went wrong.
raise e
finally:
if return_to_start:
self.move_abs(starting_position, backlash=backlash)
def scan_z(self, dz, **kwargs):
"""Scan through a list of (relative) z positions (generator fn)
This function takes a 1D numpy array of Z positions, relative to
the position at the start of the scan, and converts it into an
array of 3D positions with x=y=0. This, along with all the
keyword arguments, is then passed to ``scan_linear``.
"""
return self.scan_linear([[0, 0, z] for z in dz], **kwargs)

40
openflexure_microscope/stage/sanga.py
View file

@ -101,7 +101,7 @@ class SangaStage(BaseStage):
return config
def move_rel(self, displacement, axis=None, backlash=True):
def move_rel(self, displacement: list, axis=None, backlash=True):
"""Make a relative move, optionally correcting for backlash.
displacement: integer or array/list of 3 integers
axis: None (for 3-axis moves) or one of 'x','y','z'
@ -147,44 +147,6 @@ class SangaStage(BaseStage):
with self.lock:
self.board.move_abs(final, **kwargs)
def scan_linear(self, rel_positions, backlash=True, return_to_start=True):
"""
Scan through a list of (relative) positions (generator fn)
rel_positions should be an nx3-element array (or list of 3 element arrays).
Positions should be relative to the starting position - not a list of relative moves.
backlash argument is passed to move_rel
if return_to_start is True (default) we return to the starting position after a
successful scan. NB we always attempt to return to the starting position if an
exception occurs during the scan..
"""
starting_position = self.position
rel_positions = np.array(rel_positions)
assert rel_positions.shape[1] == 3, ValueError(
"Positions should be 3 elements long."
)
try:
self.move_rel(rel_positions[0], backlash=backlash)
yield 0
for i, step in enumerate(np.diff(rel_positions, axis=0)):
self.move_rel(step, backlash=backlash)
yield i + 1
except Exception as e:
return_to_start = True # always return to start if it went wrong.
raise e
finally:
if return_to_start:
self.move_abs(starting_position, backlash=backlash)
def scan_z(self, dz, **kwargs):
"""Scan through a list of (relative) z positions (generator fn)
This function takes a 1D numpy array of Z positions, relative to
the position at the start of the scan, and converts it into an
array of 3D positions with x=y=0. This, along with all the
keyword arguments, is then passed to ``scan_linear``.
"""
return self.scan_linear([[0, 0, z] for z in dz], **kwargs)
def close(self):
"""Cleanly close communication with the stage"""
if hasattr(self, "board"):