Ulm-IQO /
qudi
| Total Complexity | 101 |
| Total Lines | 988 |
| Duplicated Lines | 11.34 % |
| Changes | 1 | ||
| Bugs | 0 | Features | 0 |
Duplicate code is one of the most pungent code smells. A rule that is often used is to re-structure code once it is duplicated in three or more places.
Common duplication problems, and corresponding solutions are:
Complex classes like ConfocalLogic often do a lot of different things. To break such a class down, we need to identify a cohesive component within that class. A common approach to find such a component is to look for fields/methods that share the same prefixes, or suffixes.
Once you have determined the fields that belong together, you can apply the Extract Class refactoring. If the component makes sense as a sub-class, Extract Subclass is also a candidate, and is often faster.
| 1 | # -*- coding: utf-8 -*- |
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| 251 | class ConfocalLogic(GenericLogic): |
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| 252 | """ |
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| 253 | This is the Logic class for confocal scanning. |
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| 254 | """ |
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| 255 | _modclass = 'confocallogic' |
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| 256 | _modtype = 'logic' |
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| 257 | |||
| 258 | # declare connectors |
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| 259 | confocalscanner1 = Connector(interface='ConfocalScannerInterface') |
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| 260 | savelogic = Connector(interface='SaveLogic') |
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| 261 | |||
| 262 | # status vars |
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| 263 | _clock_frequency = StatusVar('clock_frequency', 500) |
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| 264 | return_slowness = StatusVar(default=50) |
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| 265 | max_history_length = StatusVar(default=10) |
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| 266 | |||
| 267 | # signals |
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| 268 | signal_start_scanning = QtCore.Signal(str) |
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| 269 | signal_continue_scanning = QtCore.Signal(str) |
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| 270 | signal_stop_scanning = QtCore.Signal() |
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| 271 | signal_scan_lines_next = QtCore.Signal() |
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| 272 | signal_xy_image_updated = QtCore.Signal() |
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| 273 | signal_depth_image_updated = QtCore.Signal() |
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| 274 | signal_change_position = QtCore.Signal(str) |
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| 275 | signal_xy_data_saved = QtCore.Signal() |
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| 276 | signal_depth_data_saved = QtCore.Signal() |
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| 277 | signal_tilt_correction_active = QtCore.Signal(bool) |
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| 278 | signal_tilt_correction_update = QtCore.Signal() |
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| 279 | signal_draw_figure_completed = QtCore.Signal() |
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| 280 | signal_position_changed = QtCore.Signal() |
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| 281 | |||
| 282 | sigImageXYInitialized = QtCore.Signal() |
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| 283 | sigImageDepthInitialized = QtCore.Signal() |
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| 284 | |||
| 285 | signal_history_event = QtCore.Signal() |
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| 286 | |||
| 287 | def __init__(self, config, **kwargs): |
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| 288 | super().__init__(config=config, **kwargs) |
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| 289 | |||
| 290 | #locking for thread safety |
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| 291 | self.threadlock = Mutex() |
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| 292 | |||
| 293 | # counter for scan_image |
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| 294 | self._scan_counter = 0 |
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| 295 | self._zscan = False |
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| 296 | self.stopRequested = False |
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| 297 | self.depth_scan_dir_is_xz = True |
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| 298 | self.depth_img_is_xz = True |
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| 299 | self.permanent_scan = False |
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| 300 | |||
| 301 | def on_activate(self): |
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| 302 | """ Initialisation performed during activation of the module. |
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| 303 | """ |
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| 304 | self._scanning_device = self.confocalscanner1() |
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| 305 | self._save_logic = self.savelogic() |
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| 306 | |||
| 307 | # Reads in the maximal scanning range. The unit of that scan range is micrometer! |
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| 308 | self.x_range = self._scanning_device.get_position_range()[0] |
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| 309 | self.y_range = self._scanning_device.get_position_range()[1] |
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| 310 | self.z_range = self._scanning_device.get_position_range()[2] |
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| 311 | |||
| 312 | # restore here ... |
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| 313 | self.history = [] |
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| 314 | for i in reversed(range(1, self.max_history_length)): |
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| 315 | try: |
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| 316 | new_history_item = ConfocalHistoryEntry(self) |
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| 317 | new_history_item.deserialize( |
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| 318 | self._statusVariables['history_{0}'.format(i)]) |
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| 319 | self.history.append(new_history_item) |
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| 320 | except KeyError: |
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| 321 | pass |
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| 322 | except OldConfigFileError: |
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| 323 | self.log.warning( |
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| 324 | 'Old style config file detected. History {0} ignored.'.format(i)) |
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| 325 | except: |
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| 326 | self.log.warning( |
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| 327 | 'Restoring history {0} failed.'.format(i)) |
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| 328 | try: |
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| 329 | new_state = ConfocalHistoryEntry(self) |
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| 330 | new_state.deserialize(self._statusVariables['history_0']) |
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| 331 | new_state.restore(self) |
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| 332 | except: |
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| 333 | new_state = ConfocalHistoryEntry(self) |
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| 334 | new_state.restore(self) |
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| 335 | finally: |
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| 336 | self.history.append(new_state) |
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| 337 | |||
| 338 | self.history_index = len(self.history) - 1 |
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| 339 | |||
| 340 | # Sets connections between signals and functions |
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| 341 | self.signal_scan_lines_next.connect(self._scan_line, QtCore.Qt.QueuedConnection) |
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| 342 | self.signal_start_scanning.connect(self.start_scanner, QtCore.Qt.QueuedConnection) |
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| 343 | self.signal_continue_scanning.connect(self.continue_scanner, QtCore.Qt.QueuedConnection) |
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| 344 | |||
| 345 | self._change_position('activation') |
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| 346 | |||
| 347 | def on_deactivate(self): |
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| 348 | """ Reverse steps of activation |
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| 349 | |||
| 350 | @return int: error code (0:OK, -1:error) |
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| 351 | """ |
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| 352 | closing_state = ConfocalHistoryEntry(self) |
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| 353 | closing_state.snapshot(self) |
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| 354 | self.history.append(closing_state) |
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| 355 | histindex = 0 |
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| 356 | for state in reversed(self.history): |
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| 357 | self._statusVariables['history_{0}'.format(histindex)] = state.serialize() |
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| 358 | histindex += 1 |
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| 359 | return 0 |
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| 360 | |||
| 361 | def switch_hardware(self, to_on=False): |
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| 362 | """ Switches the Hardware off or on. |
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| 363 | |||
| 364 | @param to_on: True switches on, False switched off |
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| 365 | |||
| 366 | @return int: error code (0:OK, -1:error) |
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| 367 | """ |
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| 368 | if to_on: |
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| 369 | return self._scanning_device.activation() |
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| 370 | else: |
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| 371 | return self._scanning_device.reset_hardware() |
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| 372 | |||
| 373 | def set_clock_frequency(self, clock_frequency): |
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| 374 | """Sets the frequency of the clock |
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| 375 | |||
| 376 | @param int clock_frequency: desired frequency of the clock |
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| 377 | |||
| 378 | @return int: error code (0:OK, -1:error) |
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| 379 | """ |
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| 380 | self._clock_frequency = int(clock_frequency) |
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| 381 | #checks if scanner is still running |
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| 382 | if self.module_state() == 'locked': |
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| 383 | return -1 |
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| 384 | else: |
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| 385 | return 0 |
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| 386 | |||
| 387 | def start_scanning(self, zscan = False, tag='logic'): |
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| 388 | """Starts scanning |
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| 389 | |||
| 390 | @param bool zscan: zscan if true, xyscan if false |
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| 391 | |||
| 392 | @return int: error code (0:OK, -1:error) |
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| 393 | """ |
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| 394 | # TODO: this is dirty, but it works for now |
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| 395 | # while self.module_state() == 'locked': |
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| 396 | # time.sleep(0.01) |
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| 397 | self._scan_counter = 0 |
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| 398 | self._zscan = zscan |
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| 399 | if self._zscan: |
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| 400 | self._zscan_continuable = True |
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| 401 | else: |
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| 402 | self._xyscan_continuable = True |
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| 403 | |||
| 404 | self.signal_start_scanning.emit(tag) |
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| 405 | return 0 |
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| 406 | |||
| 407 | def continue_scanning(self,zscan,tag='logic'): |
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| 408 | """Continue scanning |
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| 409 | |||
| 410 | @return int: error code (0:OK, -1:error) |
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| 411 | """ |
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| 412 | self._zscan = zscan |
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| 413 | if zscan: |
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| 414 | self._scan_counter = self._depth_line_pos |
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| 415 | else: |
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| 416 | self._scan_counter = self._xy_line_pos |
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| 417 | self.signal_continue_scanning.emit(tag) |
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| 418 | return 0 |
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| 419 | |||
| 420 | def stop_scanning(self): |
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| 421 | """Stops the scan |
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| 422 | |||
| 423 | @return int: error code (0:OK, -1:error) |
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| 424 | """ |
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| 425 | with self.threadlock: |
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| 426 | if self.module_state() == 'locked': |
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| 427 | self.stopRequested = True |
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| 428 | self.signal_stop_scanning.emit() |
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| 429 | return 0 |
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| 430 | |||
| 431 | def initialize_image(self): |
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| 432 | """Initalization of the image. |
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| 433 | |||
| 434 | @return int: error code (0:OK, -1:error) |
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| 435 | """ |
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| 436 | # x1: x-start-value, x2: x-end-value |
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| 437 | x1, x2 = self.image_x_range[0], self.image_x_range[1] |
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| 438 | # y1: x-start-value, y2: x-end-value |
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| 439 | y1, y2 = self.image_y_range[0], self.image_y_range[1] |
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| 440 | # z1: x-start-value, z2: x-end-value |
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| 441 | z1, z2 = self.image_z_range[0], self.image_z_range[1] |
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| 442 | |||
| 443 | # Checks if the x-start and x-end value are ok |
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| 444 | if x2 < x1: |
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| 445 | self.log.error( |
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| 446 | 'x1 must be smaller than x2, but they are ' |
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| 447 | '({0:.3f},{1:.3f}).'.format(x1, x2)) |
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| 448 | return -1 |
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| 449 | |||
| 450 | if self._zscan: |
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| 451 | if self.depth_img_is_xz: |
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| 452 | # creates an array of evenly spaced numbers over the interval |
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| 453 | # x1, x2 and the spacing is equal to xy_resolution |
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| 454 | self._X = np.linspace(x1, x2, self.xy_resolution) |
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| 455 | else: |
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| 456 | self._Y = np.linspace(y1, y2, self.xy_resolution) |
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| 457 | |||
| 458 | # Checks if the z-start and z-end value are ok |
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| 459 | if z2 < z1: |
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| 460 | self.log.error( |
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| 461 | 'z1 must be smaller than z2, but they are ' |
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| 462 | '({0:.3f},{1:.3f}).'.format(z1, z2)) |
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| 463 | return -1 |
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| 464 | # creates an array of evenly spaced numbers over the interval |
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| 465 | # z1, z2 and the spacing is equal to z_resolution |
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| 466 | self._Z = np.linspace(z1, z2, max(self.z_resolution, 2)) |
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| 467 | else: |
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| 468 | # Checks if the y-start and y-end value are ok |
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| 469 | if y2 < y1: |
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| 470 | self.log.error( |
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| 471 | 'y1 must be smaller than y2, but they are ' |
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| 472 | '({0:.3f},{1:.3f}).'.format(y1, y2)) |
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| 473 | return -1 |
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| 474 | |||
| 475 | # prevents distorion of the image |
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| 476 | if (x2 - x1) >= (y2 - y1): |
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| 477 | self._X = np.linspace(x1, x2, max(self.xy_resolution, 2)) |
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| 478 | self._Y = np.linspace(y1, y2, max(int(self.xy_resolution*(y2-y1)/(x2-x1)), 2)) |
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| 479 | else: |
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| 480 | self._Y = np.linspace(y1, y2, max(self.xy_resolution, 2)) |
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| 481 | self._X = np.linspace(x1, x2, max(int(self.xy_resolution*(x2-x1)/(y2-y1)), 2)) |
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| 482 | |||
| 483 | self._XL = self._X |
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| 484 | self._YL = self._Y |
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| 485 | self._AL = np.zeros(self._XL.shape) |
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| 486 | |||
| 487 | # Arrays for retrace line |
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| 488 | self._return_XL = np.linspace(self._XL[-1], self._XL[0], self.return_slowness) |
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| 489 | self._return_AL = np.zeros(self._return_XL.shape) |
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| 490 | |||
| 491 | if self._zscan: |
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| 492 | self._image_vert_axis = self._Z |
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| 493 | # update image scan direction from setting |
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| 494 | self.depth_img_is_xz = self.depth_scan_dir_is_xz |
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| 495 | # depth scan is in xz plane |
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| 496 | if self.depth_img_is_xz: |
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| 497 | #self._image_horz_axis = self._X |
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| 498 | # creates an image where each pixel will be [x,y,z,counts] |
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| 499 | self.depth_image = np.zeros(( |
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| 500 | len(self._image_vert_axis), |
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| 501 | len(self._X), |
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| 502 | 3 + len(self.get_scanner_count_channels()) |
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| 503 | )) |
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| 504 | |||
| 505 | self.depth_image[:, :, 0] = np.full( |
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| 506 | (len(self._image_vert_axis), len(self._X)), self._XL) |
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| 507 | |||
| 508 | self.depth_image[:, :, 1] = self._current_y * np.ones( |
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| 509 | (len(self._image_vert_axis), len(self._X))) |
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| 510 | |||
| 511 | z_value_matrix = np.full((len(self._X), len(self._image_vert_axis)), self._Z) |
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| 512 | self.depth_image[:, :, 2] = z_value_matrix.transpose() |
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| 513 | |||
| 514 | # depth scan is yz plane instead of xz plane |
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| 515 | else: |
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| 516 | #self._image_horz_axis = self._Y |
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| 517 | # creats an image where each pixel will be [x,y,z,counts] |
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| 518 | self.depth_image = np.zeros(( |
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| 519 | len(self._image_vert_axis), |
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| 520 | len(self._Y), |
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| 521 | 3 + len(self.get_scanner_count_channels()) |
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| 522 | )) |
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| 523 | |||
| 524 | self.depth_image[:, :, 0] = self._current_x * np.ones( |
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| 525 | (len(self._image_vert_axis), len(self._Y))) |
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| 526 | |||
| 527 | self.depth_image[:, :, 1] = np.full( |
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| 528 | (len(self._image_vert_axis), len(self._Y)), self._YL) |
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| 529 | |||
| 530 | z_value_matrix = np.full((len(self._Y), len(self._image_vert_axis)), self._Z) |
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| 531 | self.depth_image[:, :, 2] = z_value_matrix.transpose() |
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| 532 | |||
| 533 | # now we are scanning along the y-axis, so we need a new return line along Y: |
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| 534 | self._return_YL = np.linspace(self._YL[-1], self._YL[0], self.return_slowness) |
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| 535 | self._return_AL = np.zeros(self._return_YL.shape) |
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| 536 | |||
| 537 | self.sigImageDepthInitialized.emit() |
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| 538 | |||
| 539 | # xy scan is in xy plane |
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| 540 | else: |
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| 541 | #self._image_horz_axis = self._X |
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| 542 | self._image_vert_axis = self._Y |
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| 543 | # creats an image where each pixel will be [x,y,z,counts] |
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| 544 | self.xy_image = np.zeros(( |
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| 545 | len(self._image_vert_axis), |
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| 546 | len(self._X), |
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| 547 | 3 + len(self.get_scanner_count_channels()) |
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| 548 | )) |
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| 549 | |||
| 550 | self.xy_image[:, :, 0] = np.full( |
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| 551 | (len(self._image_vert_axis), len(self._X)), self._XL) |
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| 552 | |||
| 553 | y_value_matrix = np.full((len(self._X), len(self._image_vert_axis)), self._Y) |
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| 554 | self.xy_image[:, :, 1] = y_value_matrix.transpose() |
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| 555 | |||
| 556 | self.xy_image[:, :, 2] = self._current_z * np.ones( |
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| 557 | (len(self._image_vert_axis), len(self._X))) |
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| 558 | |||
| 559 | self.sigImageXYInitialized.emit() |
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| 560 | return 0 |
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| 561 | |||
| 562 | def start_scanner(self): |
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| 563 | """Setting up the scanner device and starts the scanning procedure |
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| 564 | |||
| 565 | @return int: error code (0:OK, -1:error) |
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| 566 | """ |
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| 567 | self.module_state.lock() |
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| 568 | |||
| 569 | self._scanning_device.module_state.lock() |
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| 570 | if self.initialize_image() < 0: |
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| 571 | self._scanning_device.module_state.unlock() |
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| 572 | self.module_state.unlock() |
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| 573 | return -1 |
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| 574 | |||
| 575 | clock_status = self._scanning_device.set_up_scanner_clock( |
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| 576 | clock_frequency=self._clock_frequency) |
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| 577 | |||
| 578 | if clock_status < 0: |
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| 579 | self._scanning_device.module_state.unlock() |
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| 580 | self.module_state.unlock() |
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| 581 | self.set_position('scanner') |
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| 582 | return -1 |
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| 583 | |||
| 584 | scanner_status = self._scanning_device.set_up_scanner() |
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| 585 | |||
| 586 | if scanner_status < 0: |
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| 587 | self._scanning_device.close_scanner_clock() |
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| 588 | self._scanning_device.module_state.unlock() |
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| 589 | self.module_state.unlock() |
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| 590 | self.set_position('scanner') |
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| 591 | return -1 |
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| 592 | View Code Duplication | ||
|
Duplication
introduced
by
|
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| 593 | self.signal_scan_lines_next.emit() |
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| 594 | return 0 |
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| 595 | |||
| 596 | def continue_scanner(self): |
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| 597 | """Continue the scanning procedure |
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| 598 | |||
| 599 | @return int: error code (0:OK, -1:error) |
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| 600 | """ |
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| 601 | self.module_state.lock() |
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| 602 | self._scanning_device.module_state.lock() |
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| 603 | |||
| 604 | clock_status = self._scanning_device.set_up_scanner_clock( |
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| 605 | clock_frequency=self._clock_frequency) |
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| 606 | |||
| 607 | if clock_status < 0: |
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| 608 | self._scanning_device.module_state.unlock() |
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| 609 | self.module_state.unlock() |
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| 610 | self.set_position('scanner') |
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| 611 | return -1 |
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| 612 | |||
| 613 | scanner_status = self._scanning_device.set_up_scanner() |
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| 614 | |||
| 615 | if scanner_status < 0: |
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| 616 | self._scanning_device.close_scanner_clock() |
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| 617 | self._scanning_device.module_state.unlock() |
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| 618 | self.module_state.unlock() |
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| 619 | self.set_position('scanner') |
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| 620 | return -1 |
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| 621 | View Code Duplication | ||
| 622 | self.signal_scan_lines_next.emit() |
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| 623 | return 0 |
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| 624 | |||
| 625 | def kill_scanner(self): |
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| 626 | """Closing the scanner device. |
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| 627 | |||
| 628 | @return int: error code (0:OK, -1:error) |
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| 629 | """ |
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| 630 | try: |
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| 631 | self._scanning_device.close_scanner() |
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| 632 | except Exception as e: |
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| 633 | self.log.exception('Could not close the scanner.') |
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| 634 | try: |
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| 635 | self._scanning_device.close_scanner_clock() |
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| 636 | except Exception as e: |
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| 637 | self.log.exception('Could not close the scanner clock.') |
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| 638 | try: |
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| 639 | self._scanning_device.module_state.unlock() |
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| 640 | except Exception as e: |
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| 641 | self.log.exception('Could not unlock scanning device.') |
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| 642 | |||
| 643 | return 0 |
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| 644 | |||
| 645 | def set_position(self, tag, x=None, y=None, z=None, a=None): |
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| 646 | """Forwarding the desired new position from the GUI to the scanning device. |
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| 647 | |||
| 648 | @param string tag: TODO |
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| 649 | |||
| 650 | @param float x: if defined, changes to postion in x-direction (microns) |
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| 651 | @param float y: if defined, changes to postion in y-direction (microns) |
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| 652 | @param float z: if defined, changes to postion in z-direction (microns) |
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| 653 | @param float a: if defined, changes to postion in a-direction (microns) |
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| 654 | |||
| 655 | @return int: error code (0:OK, -1:error) |
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| 656 | """ |
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| 657 | # Changes the respective value |
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| 658 | if x is not None: |
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| 659 | self._current_x = x |
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| 660 | if y is not None: |
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| 661 | self._current_y = y |
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| 662 | if z is not None: |
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| 663 | self._current_z = z |
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| 664 | if a is not None: |
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| 665 | self._current_a = a |
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| 666 | |||
| 667 | # Checks if the scanner is still running |
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| 668 | if self.module_state() == 'locked' or self._scanning_device.module_state() == 'locked': |
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| 669 | return -1 |
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| 670 | else: |
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| 671 | self._change_position(tag) |
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| 672 | self.signal_change_position.emit(tag) |
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| 673 | return 0 |
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| 674 | |||
| 675 | def _change_position(self, tag): |
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| 676 | """ Threaded method to change the hardware position. |
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| 677 | |||
| 678 | @return int: error code (0:OK, -1:error) |
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| 679 | """ |
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| 680 | ch_array = ['x', 'y', 'z', 'a'] |
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| 681 | pos_array = [self._current_x, self._current_y, self._current_z, self._current_a] |
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| 682 | pos_dict = {} |
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| 683 | |||
| 684 | for i, ch in enumerate(self.get_scanner_axes()): |
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| 685 | pos_dict[ch_array[i]] = pos_array[i] |
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| 686 | |||
| 687 | self._scanning_device.scanner_set_position(**pos_dict) |
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| 688 | return 0 |
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| 689 | |||
| 690 | def get_position(self): |
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| 691 | """ Get position from scanning device. |
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| 692 | |||
| 693 | @return list: with three entries x, y and z denoting the current |
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| 694 | position in meters |
||
| 695 | """ |
||
| 696 | return self._scanning_device.get_scanner_position() |
||
| 697 | |||
| 698 | def get_scanner_axes(self): |
||
| 699 | """ Get axes from scanning device. |
||
| 700 | @return list(str): names of scanner axes |
||
| 701 | """ |
||
| 702 | return self._scanning_device.get_scanner_axes() |
||
| 703 | |||
| 704 | def get_scanner_count_channels(self): |
||
| 705 | """ Get lis of counting channels from scanning device. |
||
| 706 | @return list(str): names of counter channels |
||
| 707 | """ |
||
| 708 | return self._scanning_device.get_scanner_count_channels() |
||
| 709 | |||
| 710 | def _scan_line(self): |
||
| 711 | """scanning an image in either depth or xy |
||
| 712 | |||
| 713 | """ |
||
| 714 | # stops scanning |
||
| 715 | if self.stopRequested: |
||
| 716 | with self.threadlock: |
||
| 717 | self.kill_scanner() |
||
| 718 | self.stopRequested = False |
||
| 719 | self.module_state.unlock() |
||
| 720 | self.signal_xy_image_updated.emit() |
||
| 721 | self.signal_depth_image_updated.emit() |
||
| 722 | self.set_position('scanner') |
||
| 723 | if self._zscan: |
||
| 724 | self._depth_line_pos = self._scan_counter |
||
| 725 | else: |
||
| 726 | self._xy_line_pos = self._scan_counter |
||
| 727 | # add new history entry |
||
| 728 | new_history = ConfocalHistoryEntry(self) |
||
| 729 | new_history.snapshot(self) |
||
| 730 | self.history.append(new_history) |
||
| 731 | if len(self.history) > self.max_history_length: |
||
| 732 | self.history.pop(0) |
||
| 733 | self.history_index = len(self.history) - 1 |
||
| 734 | return |
||
| 735 | |||
| 736 | image = self.depth_image if self._zscan else self.xy_image |
||
| 737 | n_ch = len(self.get_scanner_axes()) |
||
| 738 | s_ch = len(self.get_scanner_count_channels()) |
||
| 739 | |||
| 740 | try: |
||
| 741 | if self._scan_counter == 0: |
||
| 742 | # make a line from the current cursor position to |
||
| 743 | # the starting position of the first scan line of the scan |
||
| 744 | rs = self.return_slowness |
||
| 745 | lsx = np.linspace(self._current_x, image[self._scan_counter, 0, 0], rs) |
||
| 746 | lsy = np.linspace(self._current_y, image[self._scan_counter, 0, 1], rs) |
||
| 747 | lsz = np.linspace(self._current_z, image[self._scan_counter, 0, 2], rs) |
||
| 748 | if n_ch <= 3: |
||
| 749 | start_line = np.vstack([lsx, lsy, lsz][0:n_ch]) |
||
| 750 | else: |
||
| 751 | start_line = np.vstack( |
||
| 752 | [lsx, lsy, lsz, np.ones(lsx.shape) * self._current_a]) |
||
| 753 | # move to the start position of the scan, counts are thrown away |
||
| 754 | start_line_counts = self._scanning_device.scan_line(start_line) |
||
| 755 | if np.any(start_line_counts == -1): |
||
| 756 | self.stopRequested = True |
||
| 757 | self.signal_scan_lines_next.emit() |
||
| 758 | return |
||
| 759 | |||
| 760 | # adjust z of line in image to current z before building the line |
||
| 761 | if not self._zscan: |
||
| 762 | z_shape = image[self._scan_counter, :, 2].shape |
||
| 763 | image[self._scan_counter, :, 2] = self._current_z * np.ones(z_shape) |
||
| 764 | |||
| 765 | # make a line in the scan, _scan_counter says which one it is |
||
| 766 | lsx = image[self._scan_counter, :, 0] |
||
| 767 | lsy = image[self._scan_counter, :, 1] |
||
| 768 | lsz = image[self._scan_counter, :, 2] |
||
| 769 | if n_ch <= 3: |
||
| 770 | line = np.vstack([lsx, lsy, lsz][0:n_ch]) |
||
| 771 | else: |
||
| 772 | line = np.vstack( |
||
| 773 | [lsx, lsy, lsz, np.ones(lsx.shape) * self._current_a]) |
||
| 774 | |||
| 775 | # scan the line in the scan |
||
| 776 | line_counts = self._scanning_device.scan_line(line, pixel_clock=True) |
||
| 777 | if np.any(line_counts == -1): |
||
| 778 | self.stopRequested = True |
||
| 779 | self.signal_scan_lines_next.emit() |
||
| 780 | View Code Duplication | return |
|
| 781 | |||
| 782 | # make a line to go to the starting position of the next scan line |
||
| 783 | if self.depth_img_is_xz or not self._zscan: |
||
| 784 | if n_ch <= 3: |
||
| 785 | return_line = np.vstack([ |
||
| 786 | self._return_XL, |
||
| 787 | image[self._scan_counter, 0, 1] * np.ones(self._return_XL.shape), |
||
| 788 | image[self._scan_counter, 0, 2] * np.ones(self._return_XL.shape) |
||
| 789 | ][0:n_ch]) |
||
| 790 | else: |
||
| 791 | return_line = np.vstack([ |
||
| 792 | self._return_XL, |
||
| 793 | image[self._scan_counter, 0, 1] * np.ones(self._return_XL.shape), |
||
| 794 | View Code Duplication | image[self._scan_counter, 0, 2] * np.ones(self._return_XL.shape), |
|
| 795 | np.ones(self._return_XL.shape) * self._current_a |
||
| 796 | ]) |
||
| 797 | else: |
||
| 798 | if n_ch <= 3: |
||
| 799 | return_line = np.vstack([ |
||
| 800 | image[self._scan_counter, 0, 1] * np.ones(self._return_YL.shape), |
||
| 801 | self._return_YL, |
||
| 802 | image[self._scan_counter, 0, 2] * np.ones(self._return_YL.shape) |
||
| 803 | ][0:n_ch]) |
||
| 804 | else: |
||
| 805 | return_line = np.vstack([ |
||
| 806 | image[self._scan_counter, 0, 1] * np.ones(self._return_YL.shape), |
||
| 807 | self._return_YL, |
||
| 808 | image[self._scan_counter, 0, 2] * np.ones(self._return_YL.shape), |
||
| 809 | np.ones(self._return_YL.shape) * self._current_a |
||
| 810 | ]) |
||
| 811 | |||
| 812 | # return the scanner to the start of next line, counts are thrown away |
||
| 813 | return_line_counts = self._scanning_device.scan_line(return_line) |
||
| 814 | if np.any(return_line_counts == -1): |
||
| 815 | self.stopRequested = True |
||
| 816 | self.signal_scan_lines_next.emit() |
||
| 817 | return |
||
| 818 | |||
| 819 | # update image with counts from the line we just scanned |
||
| 820 | if self._zscan: |
||
| 821 | if self.depth_img_is_xz: |
||
| 822 | self.depth_image[self._scan_counter, :, 3:3 + s_ch] = line_counts |
||
| 823 | else: |
||
| 824 | self.depth_image[self._scan_counter, :, 3:3 + s_ch] = line_counts |
||
| 825 | self.signal_depth_image_updated.emit() |
||
| 826 | else: |
||
| 827 | self.xy_image[self._scan_counter, :, 3:3 + s_ch] = line_counts |
||
| 828 | self.signal_xy_image_updated.emit() |
||
| 829 | |||
| 830 | # next line in scan |
||
| 831 | self._scan_counter += 1 |
||
| 832 | |||
| 833 | # stop scanning when last line scan was performed and makes scan not continuable |
||
| 834 | if self._scan_counter >= np.size(self._image_vert_axis): |
||
| 835 | if not self.permanent_scan: |
||
| 836 | self.stop_scanning() |
||
| 837 | if self._zscan: |
||
| 838 | self._zscan_continuable = False |
||
| 839 | else: |
||
| 840 | self._xyscan_continuable = False |
||
| 841 | else: |
||
| 842 | self._scan_counter = 0 |
||
| 843 | |||
| 844 | self.signal_scan_lines_next.emit() |
||
| 845 | except: |
||
| 846 | self.log.exception('The scan went wrong, killing the scanner.') |
||
| 847 | self.stop_scanning() |
||
| 848 | self.signal_scan_lines_next.emit() |
||
| 849 | |||
| 850 | def save_xy_data(self, colorscale_range=None, percentile_range=None): |
||
| 851 | """ Save the current confocal xy data to file. |
||
| 852 | |||
| 853 | Two files are created. The first is the imagedata, which has a text-matrix of count values |
||
| 854 | corresponding to the pixel matrix of the image. Only count-values are saved here. |
||
| 855 | |||
| 856 | The second file saves the full raw data with x, y, z, and counts at every pixel. |
||
| 857 | |||
| 858 | A figure is also saved. |
||
| 859 | |||
| 860 | @param: list colorscale_range (optional) The range [min, max] of the display colour scale (for the figure) |
||
| 861 | |||
| 862 | @param: list percentile_range (optional) The percentile range [min, max] of the color scale |
||
| 863 | """ |
||
| 864 | filepath = self._save_logic.get_path_for_module('Confocal') |
||
| 865 | timestamp = datetime.datetime.now() |
||
| 866 | # Prepare the metadata parameters (common to both saved files): |
||
| 867 | parameters = OrderedDict() |
||
| 868 | |||
| 869 | parameters['X image min (m)'] = self.image_x_range[0] |
||
| 870 | parameters['X image max (m)'] = self.image_x_range[1] |
||
| 871 | parameters['X image range (m)'] = self.image_x_range[1] - self.image_x_range[0] |
||
| 872 | |||
| 873 | parameters['Y image min'] = self.image_y_range[0] |
||
| 874 | parameters['Y image max'] = self.image_y_range[1] |
||
| 875 | parameters['Y image range'] = self.image_y_range[1] - self.image_y_range[0] |
||
| 876 | |||
| 877 | parameters['XY resolution (samples per range)'] = self.xy_resolution |
||
| 878 | parameters['XY Image at z position (m)'] = self._current_z |
||
| 879 | |||
| 880 | parameters['Clock frequency of scanner (Hz)'] = self._clock_frequency |
||
| 881 | parameters['Return Slowness (Steps during retrace line)'] = self.return_slowness |
||
| 882 | |||
| 883 | # Prepare a figure to be saved |
||
| 884 | figure_data = self.xy_image[:, :, 3] |
||
| 885 | image_extent = [self.image_x_range[0], |
||
| 886 | self.image_x_range[1], |
||
| 887 | self.image_y_range[0], |
||
| 888 | self.image_y_range[1]] |
||
| 889 | axes = ['X', 'Y'] |
||
| 890 | crosshair_pos = [self.get_position()[0], self.get_position()[1]] |
||
| 891 | |||
| 892 | figs = {ch: self.draw_figure(data=self.xy_image[:, :, 3 + n], |
||
| 893 | image_extent=image_extent, |
||
| 894 | scan_axis=axes, |
||
| 895 | cbar_range=colorscale_range, |
||
| 896 | percentile_range=percentile_range, |
||
| 897 | crosshair_pos=crosshair_pos) |
||
| 898 | for n, ch in enumerate(self.get_scanner_count_channels())} |
||
| 899 | |||
| 900 | # Save the image data and figure |
||
| 901 | for n, ch in enumerate(self.get_scanner_count_channels()): |
||
| 902 | # data for the text-array "image": |
||
| 903 | image_data = OrderedDict() |
||
| 904 | image_data['Confocal pure XY scan image data without axis.\n' |
||
| 905 | 'The upper left entry represents the signal at the upper left pixel position.\n' |
||
| 906 | 'A pixel-line in the image corresponds to a row ' |
||
| 907 | 'of entries where the Signal is in counts/s:'] = self.xy_image[:, :, 3 + n] |
||
| 908 | |||
| 909 | filelabel = 'confocal_xy_image_{0}'.format(ch.replace('/', '')) |
||
| 910 | self._save_logic.save_data(image_data, |
||
| 911 | filepath=filepath, |
||
| 912 | timestamp=timestamp, |
||
| 913 | parameters=parameters, |
||
| 914 | filelabel=filelabel, |
||
| 915 | fmt='%.6e', |
||
| 916 | delimiter='\t', |
||
| 917 | plotfig=figs[ch]) |
||
| 918 | |||
| 919 | # prepare the full raw data in an OrderedDict: |
||
| 920 | data = OrderedDict() |
||
| 921 | data['x position (m)'] = self.xy_image[:, :, 0].flatten() |
||
| 922 | data['y position (m)'] = self.xy_image[:, :, 1].flatten() |
||
| 923 | data['z position (m)'] = self.xy_image[:, :, 2].flatten() |
||
| 924 | |||
| 925 | for n, ch in enumerate(self.get_scanner_count_channels()): |
||
| 926 | data['count rate {0} (Hz)'.format(ch)] = self.xy_image[:, :, 3 + n].flatten() |
||
| 927 | |||
| 928 | # Save the raw data to file |
||
| 929 | filelabel = 'confocal_xy_data' |
||
| 930 | self._save_logic.save_data(data, |
||
| 931 | filepath=filepath, |
||
| 932 | timestamp=timestamp, |
||
| 933 | parameters=parameters, |
||
| 934 | filelabel=filelabel, |
||
| 935 | fmt='%.6e', |
||
| 936 | delimiter='\t') |
||
| 937 | |||
| 938 | self.log.debug('Confocal Image saved.') |
||
| 939 | self.signal_xy_data_saved.emit() |
||
| 940 | return |
||
| 941 | |||
| 942 | def save_depth_data(self, colorscale_range=None, percentile_range=None): |
||
| 943 | """ Save the current confocal depth data to file. |
||
| 944 | |||
| 945 | Two files are created. The first is the imagedata, which has a text-matrix of count values |
||
| 946 | corresponding to the pixel matrix of the image. Only count-values are saved here. |
||
| 947 | |||
| 948 | The second file saves the full raw data with x, y, z, and counts at every pixel. |
||
| 949 | """ |
||
| 950 | filepath = self._save_logic.get_path_for_module('Confocal') |
||
| 951 | timestamp = datetime.datetime.now() |
||
| 952 | # Prepare the metadata parameters (common to both saved files): |
||
| 953 | parameters = OrderedDict() |
||
| 954 | |||
| 955 | # TODO: This needs to check whether the scan was XZ or YZ direction |
||
| 956 | parameters['X image min (m)'] = self.image_x_range[0] |
||
| 957 | parameters['X image max (m)'] = self.image_x_range[1] |
||
| 958 | parameters['X image range (m)'] = self.image_x_range[1] - self.image_x_range[0] |
||
| 959 | |||
| 960 | parameters['Z image min'] = self.image_z_range[0] |
||
| 961 | parameters['Z image max'] = self.image_z_range[1] |
||
| 962 | parameters['Z image range'] = self.image_z_range[1] - self.image_z_range[0] |
||
| 963 | |||
| 964 | parameters['XY resolution (samples per range)'] = self.xy_resolution |
||
| 965 | parameters['Z resolution (samples per range)'] = self.z_resolution |
||
| 966 | parameters['Depth Image at y position (m)'] = self._current_y |
||
| 967 | |||
| 968 | parameters['Clock frequency of scanner (Hz)'] = self._clock_frequency |
||
| 969 | parameters['Return Slowness (Steps during retrace line)'] = self.return_slowness |
||
| 970 | |||
| 971 | if self.depth_img_is_xz: |
||
| 972 | horizontal_range = [self.image_x_range[0], self.image_x_range[1]] |
||
| 973 | axes = ['X', 'Z'] |
||
| 974 | crosshair_pos = [self.get_position()[0], self.get_position()[2]] |
||
| 975 | else: |
||
| 976 | horizontal_range = [self.image_y_range[0], self.image_y_range[1]] |
||
| 977 | axes = ['Y', 'Z'] |
||
| 978 | crosshair_pos = [self.get_position()[1], self.get_position()[2]] |
||
| 979 | |||
| 980 | image_extent = [horizontal_range[0], |
||
| 981 | horizontal_range[1], |
||
| 982 | self.image_z_range[0], |
||
| 983 | self.image_z_range[1]] |
||
| 984 | |||
| 985 | figs = {ch: self.draw_figure(data=self.depth_image[:, :, 3 + n], |
||
| 986 | image_extent=image_extent, |
||
| 987 | scan_axis=axes, |
||
| 988 | cbar_range=colorscale_range, |
||
| 989 | percentile_range=percentile_range, |
||
| 990 | crosshair_pos=crosshair_pos) |
||
| 991 | for n, ch in enumerate(self.get_scanner_count_channels())} |
||
| 992 | |||
| 993 | # Save the image data and figure |
||
| 994 | for n, ch in enumerate(self.get_scanner_count_channels()): |
||
| 995 | # data for the text-array "image": |
||
| 996 | image_data = OrderedDict() |
||
| 997 | image_data['Confocal pure depth scan image data without axis.\n' |
||
| 998 | 'The upper left entry represents the signal at the upper left pixel position.\n' |
||
| 999 | 'A pixel-line in the image corresponds to a row in ' |
||
| 1000 | 'of entries where the Signal is in counts/s:'] = self.depth_image[:, :, 3 + n] |
||
| 1001 | |||
| 1002 | filelabel = 'confocal_depth_image_{0}'.format(ch.replace('/', '')) |
||
| 1003 | self._save_logic.save_data(image_data, |
||
| 1004 | filepath=filepath, |
||
| 1005 | timestamp=timestamp, |
||
| 1006 | parameters=parameters, |
||
| 1007 | filelabel=filelabel, |
||
| 1008 | fmt='%.6e', |
||
| 1009 | delimiter='\t', |
||
| 1010 | plotfig=figs[ch]) |
||
| 1011 | |||
| 1012 | # prepare the full raw data in an OrderedDict: |
||
| 1013 | data = OrderedDict() |
||
| 1014 | data['x position (m)'] = self.depth_image[:, :, 0].flatten() |
||
| 1015 | data['y position (m)'] = self.depth_image[:, :, 1].flatten() |
||
| 1016 | data['z position (m)'] = self.depth_image[:, :, 2].flatten() |
||
| 1017 | |||
| 1018 | for n, ch in enumerate(self.get_scanner_count_channels()): |
||
| 1019 | data['count rate {0} (Hz)'.format(ch)] = self.depth_image[:, :, 3 + n].flatten() |
||
| 1020 | |||
| 1021 | # Save the raw data to file |
||
| 1022 | filelabel = 'confocal_depth_data' |
||
| 1023 | self._save_logic.save_data(data, |
||
| 1024 | filepath=filepath, |
||
| 1025 | timestamp=timestamp, |
||
| 1026 | parameters=parameters, |
||
| 1027 | filelabel=filelabel, |
||
| 1028 | fmt='%.6e', |
||
| 1029 | delimiter='\t') |
||
| 1030 | |||
| 1031 | self.log.debug('Confocal Image saved.') |
||
| 1032 | self.signal_depth_data_saved.emit() |
||
| 1033 | return |
||
| 1034 | |||
| 1035 | def draw_figure(self, data, image_extent, scan_axis=None, cbar_range=None, percentile_range=None, crosshair_pos=None): |
||
| 1036 | """ Create a 2-D color map figure of the scan image. |
||
| 1037 | |||
| 1038 | @param: array data: The NxM array of count values from a scan with NxM pixels. |
||
| 1039 | |||
| 1040 | @param: list image_extent: The scan range in the form [hor_min, hor_max, ver_min, ver_max] |
||
| 1041 | |||
| 1042 | @param: list axes: Names of the horizontal and vertical axes in the image |
||
| 1043 | |||
| 1044 | @param: list cbar_range: (optional) [color_scale_min, color_scale_max]. If not supplied then a default of |
||
| 1045 | data_min to data_max will be used. |
||
| 1046 | |||
| 1047 | @param: list percentile_range: (optional) Percentile range of the chosen cbar_range. |
||
| 1048 | |||
| 1049 | @param: list crosshair_pos: (optional) crosshair position as [hor, vert] in the chosen image axes. |
||
| 1050 | |||
| 1051 | @return: fig fig: a matplotlib figure object to be saved to file. |
||
| 1052 | """ |
||
| 1053 | if scan_axis is None: |
||
| 1054 | scan_axis = ['X', 'Y'] |
||
| 1055 | |||
| 1056 | # If no colorbar range was given, take full range of data |
||
| 1057 | if cbar_range is None: |
||
| 1058 | cbar_range = [np.min(data), np.max(data)] |
||
| 1059 | |||
| 1060 | # Scale color values using SI prefix |
||
| 1061 | prefix = ['', 'k', 'M', 'G'] |
||
| 1062 | prefix_count = 0 |
||
| 1063 | image_data = data |
||
| 1064 | draw_cb_range = np.array(cbar_range) |
||
| 1065 | image_dimension = image_extent.copy() |
||
| 1066 | |||
| 1067 | while draw_cb_range[1] > 1000: |
||
| 1068 | image_data = image_data/1000 |
||
| 1069 | draw_cb_range = draw_cb_range/1000 |
||
| 1070 | prefix_count = prefix_count + 1 |
||
| 1071 | |||
| 1072 | c_prefix = prefix[prefix_count] |
||
| 1073 | |||
| 1074 | |||
| 1075 | # Scale axes values using SI prefix |
||
| 1076 | axes_prefix = ['', 'm', r'$\mathrm{\mu}$', 'n'] |
||
| 1077 | x_prefix_count = 0 |
||
| 1078 | y_prefix_count = 0 |
||
| 1079 | |||
| 1080 | while np.abs(image_dimension[1]-image_dimension[0]) < 1: |
||
| 1081 | image_dimension[0] = image_dimension[0] * 1000. |
||
| 1082 | image_dimension[1] = image_dimension[1] * 1000. |
||
| 1083 | x_prefix_count = x_prefix_count + 1 |
||
| 1084 | |||
| 1085 | while np.abs(image_dimension[3] - image_dimension[2]) < 1: |
||
| 1086 | image_dimension[2] = image_dimension[2] * 1000. |
||
| 1087 | image_dimension[3] = image_dimension[3] * 1000. |
||
| 1088 | y_prefix_count = y_prefix_count + 1 |
||
| 1089 | |||
| 1090 | x_prefix = axes_prefix[x_prefix_count] |
||
| 1091 | y_prefix = axes_prefix[y_prefix_count] |
||
| 1092 | |||
| 1093 | # Use qudi style |
||
| 1094 | plt.style.use(self._save_logic.mpl_qd_style) |
||
| 1095 | |||
| 1096 | # Create figure |
||
| 1097 | fig, ax = plt.subplots() |
||
| 1098 | |||
| 1099 | # Create image plot |
||
| 1100 | cfimage = ax.imshow(image_data, |
||
| 1101 | cmap=plt.get_cmap('inferno'), # reference the right place in qd |
||
| 1102 | origin="lower", |
||
| 1103 | vmin=draw_cb_range[0], |
||
| 1104 | vmax=draw_cb_range[1], |
||
| 1105 | interpolation='none', |
||
| 1106 | extent=image_dimension |
||
| 1107 | ) |
||
| 1108 | |||
| 1109 | ax.set_aspect(1) |
||
| 1110 | ax.set_xlabel(scan_axis[0] + ' position (' + x_prefix + 'm)') |
||
| 1111 | ax.set_ylabel(scan_axis[1] + ' position (' + y_prefix + 'm)') |
||
| 1112 | ax.spines['bottom'].set_position(('outward', 10)) |
||
| 1113 | ax.spines['left'].set_position(('outward', 10)) |
||
| 1114 | ax.spines['top'].set_visible(False) |
||
| 1115 | ax.spines['right'].set_visible(False) |
||
| 1116 | ax.get_xaxis().tick_bottom() |
||
| 1117 | ax.get_yaxis().tick_left() |
||
| 1118 | |||
| 1119 | # draw the crosshair position if defined |
||
| 1120 | if crosshair_pos is not None: |
||
| 1121 | trans_xmark = mpl.transforms.blended_transform_factory( |
||
| 1122 | ax.transData, |
||
| 1123 | ax.transAxes) |
||
| 1124 | |||
| 1125 | trans_ymark = mpl.transforms.blended_transform_factory( |
||
| 1126 | ax.transAxes, |
||
| 1127 | ax.transData) |
||
| 1128 | |||
| 1129 | ax.annotate('', xy=(crosshair_pos[0]*np.power(1000,x_prefix_count), 0), |
||
| 1130 | xytext=(crosshair_pos[0]*np.power(1000,x_prefix_count), -0.01), xycoords=trans_xmark, |
||
| 1131 | arrowprops=dict(facecolor='#17becf', shrink=0.05), |
||
| 1132 | ) |
||
| 1133 | |||
| 1134 | ax.annotate('', xy=(0, crosshair_pos[1]*np.power(1000,y_prefix_count)), |
||
| 1135 | xytext=(-0.01, crosshair_pos[1]*np.power(1000,y_prefix_count)), xycoords=trans_ymark, |
||
| 1136 | arrowprops=dict(facecolor='#17becf', shrink=0.05), |
||
| 1137 | ) |
||
| 1138 | |||
| 1139 | # Draw the colorbar |
||
| 1140 | cbar = plt.colorbar(cfimage, shrink=0.8)#, fraction=0.046, pad=0.08, shrink=0.75) |
||
| 1141 | cbar.set_label('Fluorescence (' + c_prefix + 'c/s)') |
||
| 1142 | |||
| 1143 | View Code Duplication | # remove ticks from colorbar for cleaner image |
|
| 1144 | cbar.ax.tick_params(which=u'both', length=0) |
||
| 1145 | |||
| 1146 | # If we have percentile information, draw that to the figure |
||
| 1147 | if percentile_range is not None: |
||
| 1148 | cbar.ax.annotate(str(percentile_range[0]), |
||
| 1149 | xy=(-0.3, 0.0), |
||
| 1150 | xycoords='axes fraction', |
||
| 1151 | horizontalalignment='right', |
||
| 1152 | verticalalignment='center', |
||
| 1153 | rotation=90 |
||
| 1154 | ) |
||
| 1155 | cbar.ax.annotate(str(percentile_range[1]), |
||
| 1156 | xy=(-0.3, 1.0), |
||
| 1157 | xycoords='axes fraction', |
||
| 1158 | horizontalalignment='right', |
||
| 1159 | verticalalignment='center', |
||
| 1160 | rotation=90 |
||
| 1161 | ) |
||
| 1162 | cbar.ax.annotate('(percentile)', |
||
| 1163 | xy=(-0.3, 0.5), |
||
| 1164 | xycoords='axes fraction', |
||
| 1165 | horizontalalignment='right', |
||
| 1166 | verticalalignment='center', |
||
| 1167 | rotation=90 |
||
| 1168 | ) |
||
| 1169 | self.signal_draw_figure_completed.emit() |
||
| 1170 | return fig |
||
| 1171 | |||
| 1172 | ##################################### Tilt correction ######################################## |
||
| 1173 | |||
| 1174 | @QtCore.Slot() |
||
| 1175 | def set_tilt_point1(self): |
||
| 1176 | """ Gets the first reference point for tilt correction.""" |
||
| 1177 | self.point1 = np.array(self._scanning_device.get_scanner_position()[:3]) |
||
| 1178 | self.signal_tilt_correction_update.emit() |
||
| 1179 | |||
| 1180 | @QtCore.Slot() |
||
| 1181 | def set_tilt_point2(self): |
||
| 1182 | """ Gets the second reference point for tilt correction.""" |
||
| 1183 | self.point2 = np.array(self._scanning_device.get_scanner_position()[:3]) |
||
| 1184 | self.signal_tilt_correction_update.emit() |
||
| 1185 | |||
| 1186 | @QtCore.Slot() |
||
| 1187 | def set_tilt_point3(self): |
||
| 1188 | """Gets the third reference point for tilt correction.""" |
||
| 1189 | self.point3 = np.array(self._scanning_device.get_scanner_position()[:3]) |
||
| 1190 | self.signal_tilt_correction_update.emit() |
||
| 1191 | |||
| 1192 | @QtCore.Slot() |
||
| 1193 | def calc_tilt_correction(self): |
||
| 1194 | """ Calculates the values for the tilt correction. """ |
||
| 1195 | a = self.point2 - self.point1 |
||
| 1196 | b = self.point3 - self.point1 |
||
| 1197 | n = np.cross(a, b) |
||
| 1198 | self._scanning_device.tilt_variable_ax = n[0] / n[2] |
||
| 1199 | self._scanning_device.tilt_variable_ay = n[1] / n[2] |
||
| 1200 | |||
| 1201 | @QtCore.Slot(bool) |
||
| 1202 | def set_tilt_correction(self, enabled): |
||
| 1203 | """ Set tilt correction in tilt interfuse. |
||
| 1204 | |||
| 1205 | @param bool enabled: whether we want to use tilt correction |
||
| 1206 | """ |
||
| 1207 | self._scanning_device.tiltcorrection = enabled |
||
| 1208 | self._scanning_device.tilt_reference_x = self._scanning_device.get_scanner_position()[0] |
||
| 1209 | self._scanning_device.tilt_reference_y = self._scanning_device.get_scanner_position()[1] |
||
| 1210 | self.signal_tilt_correction_active.emit(enabled) |
||
| 1211 | |||
| 1212 | def history_forward(self): |
||
| 1213 | """ Move forward in confocal image history. |
||
| 1214 | """ |
||
| 1215 | View Code Duplication | if self.history_index < len(self.history) - 1: |
|
| 1216 | self.history_index += 1 |
||
| 1217 | self.history[self.history_index].restore(self) |
||
| 1218 | self.signal_xy_image_updated.emit() |
||
| 1219 | self.signal_depth_image_updated.emit() |
||
| 1220 | self.signal_tilt_correction_update.emit() |
||
| 1221 | self.signal_tilt_correction_active.emit(self._scanning_device.tiltcorrection) |
||
| 1222 | self._change_position('history') |
||
| 1223 | self.signal_change_position.emit('history') |
||
| 1224 | self.signal_history_event.emit() |
||
| 1225 | |||
| 1226 | def history_back(self): |
||
| 1227 | """ Move backwards in confocal image history. |
||
| 1228 | """ |
||
| 1229 | View Code Duplication | if self.history_index > 0: |
|
| 1230 | self.history_index -= 1 |
||
| 1231 | self.history[self.history_index].restore(self) |
||
| 1232 | self.signal_xy_image_updated.emit() |
||
| 1233 | self.signal_depth_image_updated.emit() |
||
| 1234 | self.signal_tilt_correction_update.emit() |
||
| 1235 | self.signal_tilt_correction_active.emit(self._scanning_device.tiltcorrection) |
||
| 1236 | self._change_position('history') |
||
| 1237 | self.signal_change_position.emit('history') |
||
| 1238 | self.signal_history_event.emit() |
||
| 1239 |
Loading history...
