Loading openflexure_microscope/stage/sanga.py +44 −4 Original line number Diff line number Diff line Loading @@ -21,6 +21,7 @@ class SangaStage(BaseStage): self.board = Sangaboard(port, **kwargs) self._backlash = None self.axis_names = ['x', 'y', 'z'] @property def state(self): Loading Loading @@ -61,7 +62,10 @@ class SangaStage(BaseStage): back by ``backlash[i]``. This is computed per-axis, so if some axes are moving in the same direction as ``backlash``, they won't do two moves. """ return self._backlash if self._backlash else np.array([0]*self.n_axes) if self._backlash is not None: return self._backlash else: return np.array([0] * self.n_axes) @backlash.setter def backlash(self, blsh): Loading Loading @@ -114,6 +118,42 @@ 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""" self.board.close() Loading Loading @@ -141,8 +181,8 @@ class SangaStage(BaseStage): need to worry about that here. """ if type is not None: print("An exception occurred inside a with block, resetting " + "position to its value at the start of the with block") print("An exception occurred inside a with block, resetting position \ to its value at the start of the with block") try: time.sleep(0.5) self.move_abs(self._position_on_enter) Loading Loading
openflexure_microscope/stage/sanga.py +44 −4 Original line number Diff line number Diff line Loading @@ -21,6 +21,7 @@ class SangaStage(BaseStage): self.board = Sangaboard(port, **kwargs) self._backlash = None self.axis_names = ['x', 'y', 'z'] @property def state(self): Loading Loading @@ -61,7 +62,10 @@ class SangaStage(BaseStage): back by ``backlash[i]``. This is computed per-axis, so if some axes are moving in the same direction as ``backlash``, they won't do two moves. """ return self._backlash if self._backlash else np.array([0]*self.n_axes) if self._backlash is not None: return self._backlash else: return np.array([0] * self.n_axes) @backlash.setter def backlash(self, blsh): Loading Loading @@ -114,6 +118,42 @@ 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""" self.board.close() Loading Loading @@ -141,8 +181,8 @@ class SangaStage(BaseStage): need to worry about that here. """ if type is not None: print("An exception occurred inside a with block, resetting " + "position to its value at the start of the with block") print("An exception occurred inside a with block, resetting position \ to its value at the start of the with block") try: time.sleep(0.5) self.move_abs(self._position_on_enter) Loading