Loading openflexure_microscope/stage/base.py +38 −0 Original line number Diff line number Diff line Loading @@ -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) No newline at end of file openflexure_microscope/stage/sanga.py +1 −39 Original line number Diff line number Diff line Loading @@ -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' Loading Loading @@ -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"): Loading Loading
openflexure_microscope/stage/base.py +38 −0 Original line number Diff line number Diff line Loading @@ -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) No newline at end of file
openflexure_microscope/stage/sanga.py +1 −39 Original line number Diff line number Diff line Loading @@ -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' Loading Loading @@ -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"): Loading
