Ulm-IQO /
qudi
| Total Complexity | 120 |
| Total Lines | 1122 |
| Duplicated Lines | 10.52 % |
| Changes | 4 | ||
| Bugs | 1 | 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_requested = 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_image_ranges_changed = QtCore.Signal() |
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| 281 | signal_image_resolution_changed = QtCore.Signal() |
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| 282 | |||
| 283 | sigImageXYInitialized = QtCore.Signal() |
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| 284 | sigImageDepthInitialized = QtCore.Signal() |
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| 285 | |||
| 286 | signal_history_event = QtCore.Signal() |
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| 287 | |||
| 288 | def __init__(self, config, **kwargs): |
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| 289 | super().__init__(config=config, **kwargs) |
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| 290 | |||
| 291 | #locking for thread safety |
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| 292 | self.threadlock = Mutex() |
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| 293 | |||
| 294 | # counter for scan_image |
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| 295 | self._scan_counter = 0 |
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| 296 | self._zscan = False |
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| 297 | self.stopRequested = False |
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| 298 | self.depth_scan_dir_is_xz = True |
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| 299 | self.depth_img_is_xz = True |
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| 300 | self.permanent_scan = False |
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| 301 | |||
| 302 | def on_activate(self): |
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| 303 | """ Initialisation performed during activation of the module. |
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| 304 | """ |
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| 305 | self._scanning_device = self.confocalscanner1() |
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| 306 | self._save_logic = self.savelogic() |
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| 307 | |||
| 308 | # Reads in the maximal scanning range. The unit of that scan range is micrometer! |
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| 309 | self.x_range = self._scanning_device.get_position_range()[0] |
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| 310 | self.y_range = self._scanning_device.get_position_range()[1] |
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| 311 | self.z_range = self._scanning_device.get_position_range()[2] |
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| 312 | |||
| 313 | # restore here ... |
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| 314 | self.history = [] |
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| 315 | for i in reversed(range(1, self.max_history_length)): |
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| 316 | try: |
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| 317 | new_history_item = ConfocalHistoryEntry(self) |
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| 318 | new_history_item.deserialize( |
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| 319 | self._statusVariables['history_{0}'.format(i)]) |
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| 320 | self.history.append(new_history_item) |
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| 321 | except KeyError: |
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| 322 | pass |
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| 323 | except OldConfigFileError: |
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| 324 | self.log.warning( |
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| 325 | 'Old style config file detected. History {0} ignored.'.format(i)) |
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| 326 | except: |
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| 327 | self.log.warning( |
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| 328 | 'Restoring history {0} failed.'.format(i)) |
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| 329 | try: |
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| 330 | new_state = ConfocalHistoryEntry(self) |
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| 331 | new_state.deserialize(self._statusVariables['history_0']) |
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| 332 | new_state.restore(self) |
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| 333 | except: |
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| 334 | new_state = ConfocalHistoryEntry(self) |
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| 335 | new_state.restore(self) |
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| 336 | finally: |
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| 337 | self.history.append(new_state) |
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| 338 | |||
| 339 | self.history_index = len(self.history) - 1 |
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| 340 | |||
| 341 | # Sets connections between signals and functions |
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| 342 | self.signal_scan_lines_next.connect(self._scan_line, QtCore.Qt.QueuedConnection) |
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| 343 | self.signal_start_scanning.connect(self.start_scanner, QtCore.Qt.QueuedConnection) |
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| 344 | self.signal_continue_scanning.connect(self.continue_scanner, QtCore.Qt.QueuedConnection) |
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| 345 | |||
| 346 | self._change_position('activation') |
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| 347 | |||
| 348 | def on_deactivate(self): |
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| 349 | """ Reverse steps of activation |
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| 350 | |||
| 351 | @return int: error code (0:OK, -1:error) |
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| 352 | """ |
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| 353 | closing_state = ConfocalHistoryEntry(self) |
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| 354 | closing_state.snapshot(self) |
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| 355 | self.history.append(closing_state) |
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| 356 | histindex = 0 |
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| 357 | for state in reversed(self.history): |
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| 358 | self._statusVariables['history_{0}'.format(histindex)] = state.serialize() |
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| 359 | histindex += 1 |
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| 360 | return 0 |
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| 361 | |||
| 362 | @property |
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| 363 | def image_x_range(self): |
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| 364 | """ Get image_x_range """ |
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| 365 | return self._image_x_range |
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| 366 | |||
| 367 | @image_x_range.setter |
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| 368 | def image_x_range(self, range): |
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| 369 | """ Set the new x-range of the region to be scanned. |
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| 370 | |||
| 371 | @param list range: 2-element list of floats giving new range |
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| 372 | """ |
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| 373 | if not self._image_range_ok(range, axis='x'): |
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| 374 | return -1 |
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| 375 | |||
| 376 | self._image_x_range = range |
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| 377 | |||
| 378 | # Tell the GUI or anything else that might need to update display. |
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| 379 | self.signal_image_ranges_changed.emit() |
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| 380 | |||
| 381 | @property |
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| 382 | def image_y_range(self): |
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| 383 | """ Get image_y_range """ |
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| 384 | return self._image_y_range |
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| 385 | |||
| 386 | @image_y_range.setter |
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| 387 | def image_y_range(self, range): |
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| 388 | """ Set the new y-range of the region to be scanned. |
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| 389 | |||
| 390 | @param list range: 2-element list of floats giving new range |
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| 391 | """ |
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| 392 | if not self._image_range_ok(range, axis='y'): |
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| 393 | return -1 |
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| 394 | |||
| 395 | self._image_y_range = range |
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| 396 | |||
| 397 | # Tell the GUI or anything else that might need to update display. |
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| 398 | self.signal_image_ranges_changed.emit() |
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| 399 | |||
| 400 | @property |
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| 401 | def image_z_range(self): |
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| 402 | """ Get image_z_range """ |
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| 403 | return self._image_z_range |
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| 404 | |||
| 405 | @image_z_range.setter |
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| 406 | def image_z_range(self, range): |
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| 407 | """ Set the new z-range of the region to be scanned. |
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| 408 | |||
| 409 | @param list range: 2-element list of floats giving new range |
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| 410 | """ |
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| 411 | if not self._image_range_ok(range, axis='z'): |
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| 412 | return -1 |
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| 413 | |||
| 414 | self._image_z_range = range |
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| 415 | |||
| 416 | # Tell the GUI or anything else that might need to update display. |
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| 417 | self.signal_image_ranges_changed.emit() |
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| 418 | |||
| 419 | def _image_range_ok(self, range, axis=''): |
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| 420 | """ Sanity check any image_range before setting it. |
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| 421 | |||
| 422 | @param list range: the desired image range. |
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| 423 | |||
| 424 | @param str axis: Axis label to give better error messages. |
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| 425 | """ |
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| 426 | if len(range) != 2: |
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| 427 | self.log.error( |
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| 428 | 'image_{ax}_range must be a 2-element list, [min, max].' |
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| 429 | 'It is not possible to set it to {0}'.format(range, ax=axis) |
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| 430 | ) |
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| 431 | return False |
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| 432 | if range[1] < range[0]: |
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| 433 | self.log.error( |
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| 434 | '{ax}_min must be smaller than {ax}_max, but they are ' |
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| 435 | '({0:.3f},{1:.3f}).'.format(range[0], range[1], ax=axis) |
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| 436 | ) |
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| 437 | return False |
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| 438 | |||
| 439 | return True |
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| 440 | |||
| 441 | @property |
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| 442 | def xy_resolution(self): |
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| 443 | """ Get image xy resolution.""" |
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| 444 | return self._xy_resolution |
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| 445 | |||
| 446 | @xy_resolution.setter |
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| 447 | def xy_resolution(self, new_res): |
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| 448 | """ Set the xy scan resolution. |
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| 449 | |||
| 450 | @param int new_res: new resolution |
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| 451 | """ |
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| 452 | if not self.image_resolution_ok(new_res, axis='xy'): |
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| 453 | return -1 |
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| 454 | |||
| 455 | self._xy_resolution = new_res |
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| 456 | |||
| 457 | # Tell the GUI or anything else that might need to update display. |
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| 458 | self.signal_image_resolution_changed.emit() |
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| 459 | |||
| 460 | |||
| 461 | @property |
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| 462 | def z_resolution(self): |
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| 463 | """ Get image z resolution.""" |
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| 464 | return self._z_resolution |
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| 465 | |||
| 466 | @z_resolution.setter |
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| 467 | def z_resolution(self, new_res): |
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| 468 | """ Set the z scan resolution. |
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| 469 | |||
| 470 | @param int new_res: new resolution |
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| 471 | """ |
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| 472 | if not self.image_resolution_ok(new_res, axis='z'): |
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| 473 | return -1 |
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| 474 | |||
| 475 | self._z_resolution = new_res |
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| 476 | |||
| 477 | # Tell the GUI or anything else that might need to update display. |
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| 478 | self.signal_image_resolution_changed.emit() |
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| 479 | |||
| 480 | def image_resolution_ok(self, resolution, axis=''): |
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| 481 | """ Check input resolution satisfies requirements. |
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| 482 | |||
| 483 | @param int resolution: requested resolution. |
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| 484 | |||
| 485 | @param string axis: name of axis to make error messages more readable. |
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| 486 | |||
| 487 | @return Boolean True means the resolution is ok. |
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| 488 | """ |
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| 489 | if isinstance(resolution, int): |
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| 490 | return True |
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| 491 | else: |
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| 492 | self.log.error( |
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| 493 | 'Resolution is number of pixels, and must be integer' |
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| 494 | 'instead of type {0} (requested for {1} image).' |
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| 495 | .format(type(resolution), axis) |
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| 496 | ) |
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| 497 | return False |
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| 498 | |||
| 499 | def switch_hardware(self, to_on=False): |
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| 500 | """ Switches the Hardware off or on. |
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| 501 | |||
| 502 | @param to_on: True switches on, False switched off |
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| 503 | |||
| 504 | @return int: error code (0:OK, -1:error) |
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| 505 | """ |
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| 506 | if to_on: |
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| 507 | return self._scanning_device.activation() |
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| 508 | else: |
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| 509 | return self._scanning_device.reset_hardware() |
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| 510 | |||
| 511 | def set_clock_frequency(self, clock_frequency): |
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| 512 | """Sets the frequency of the clock |
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| 513 | |||
| 514 | @param int clock_frequency: desired frequency of the clock |
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| 515 | |||
| 516 | @return int: error code (0:OK, -1:error) |
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| 517 | """ |
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| 518 | self._clock_frequency = int(clock_frequency) |
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| 519 | #checks if scanner is still running |
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| 520 | if self.module_state() == 'locked': |
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| 521 | return -1 |
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| 522 | else: |
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| 523 | return 0 |
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| 524 | |||
| 525 | def start_scanning(self, zscan = False, tag='logic'): |
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| 526 | """Starts scanning |
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| 527 | |||
| 528 | @param bool zscan: zscan if true, xyscan if false |
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| 529 | |||
| 530 | @return int: error code (0:OK, -1:error) |
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| 531 | """ |
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| 532 | # TODO: this is dirty, but it works for now |
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| 533 | # while self.module_state() == 'locked': |
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| 534 | # time.sleep(0.01) |
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| 535 | self._scan_counter = 0 |
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| 536 | self._zscan = zscan |
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| 537 | if self._zscan: |
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| 538 | self._zscan_continuable = True |
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| 539 | else: |
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| 540 | self._xyscan_continuable = True |
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| 541 | |||
| 542 | self.signal_start_scanning.emit(tag) |
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| 543 | return 0 |
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| 544 | |||
| 545 | def continue_scanning(self,zscan,tag='logic'): |
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| 546 | """Continue scanning |
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| 547 | |||
| 548 | @return int: error code (0:OK, -1:error) |
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| 549 | """ |
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| 550 | self._zscan = zscan |
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| 551 | if zscan: |
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| 552 | self._scan_counter = self._depth_line_pos |
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| 553 | else: |
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| 554 | self._scan_counter = self._xy_line_pos |
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| 555 | self.signal_continue_scanning.emit(tag) |
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| 556 | return 0 |
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| 557 | |||
| 558 | def stop_scanning(self): |
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| 559 | """Stops the scan |
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| 560 | |||
| 561 | @return int: error code (0:OK, -1:error) |
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| 562 | """ |
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| 563 | with self.threadlock: |
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| 564 | if self.module_state() == 'locked': |
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| 565 | self.stopRequested = True |
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| 566 | self.signal_stop_requested.emit() |
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| 567 | return 0 |
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| 568 | |||
| 569 | def initialize_image(self): |
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| 570 | """Initalization of the image. |
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| 571 | |||
| 572 | @return int: error code (0:OK, -1:error) |
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| 573 | """ |
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| 574 | # x1: x-start-value, x2: x-end-value |
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| 575 | x1, x2 = self.image_x_range[0], self.image_x_range[1] |
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| 576 | # y1: x-start-value, y2: x-end-value |
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| 577 | y1, y2 = self.image_y_range[0], self.image_y_range[1] |
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| 578 | # z1: x-start-value, z2: x-end-value |
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| 579 | z1, z2 = self.image_z_range[0], self.image_z_range[1] |
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| 580 | |||
| 581 | # Checks if the x-start and x-end value are ok |
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| 582 | if x2 < x1: |
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| 583 | self.log.error( |
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| 584 | 'x1 must be smaller than x2, but they are ' |
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| 585 | '({0:.3f},{1:.3f}).'.format(x1, x2)) |
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| 586 | return -1 |
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| 587 | |||
| 588 | if self._zscan: |
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| 589 | # creates an array of evenly spaced numbers over the interval |
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| 590 | # x1, x2 and the spacing is equal to xy_resolution |
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| 591 | self._X = np.linspace(x1, x2, self.xy_resolution) |
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| 592 | View Code Duplication | # Checks if the z-start and z-end value are ok |
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|
Duplication
introduced
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| 593 | if z2 < z1: |
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| 594 | self.log.error( |
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| 595 | 'z1 must be smaller than z2, but they are ' |
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| 596 | '({0:.3f},{1:.3f}).'.format(z1, z2)) |
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| 597 | return -1 |
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| 598 | # creates an array of evenly spaced numbers over the interval |
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| 599 | # z1, z2 and the spacing is equal to z_resolution |
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| 600 | self._Z = np.linspace(z1, z2, max(self.z_resolution, 2)) |
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| 601 | else: |
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| 602 | # Checks if the y-start and y-end value are ok |
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| 603 | if y2 < y1: |
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| 604 | self.log.error( |
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| 605 | 'y1 must be smaller than y2, but they are ' |
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| 606 | '({0:.3f},{1:.3f}).'.format(y1, y2)) |
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| 607 | return -1 |
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| 608 | |||
| 609 | # prevents distorion of the image |
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| 610 | if (x2 - x1) >= (y2 - y1): |
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| 611 | self._X = np.linspace(x1, x2, max(self.xy_resolution, 2)) |
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| 612 | self._Y = np.linspace(y1, y2, max(int(self.xy_resolution*(y2-y1)/(x2-x1)), 2)) |
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| 613 | else: |
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| 614 | self._Y = np.linspace(y1, y2, max(self.xy_resolution, 2)) |
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| 615 | self._X = np.linspace(x1, x2, max(int(self.xy_resolution*(x2-x1)/(y2-y1)), 2)) |
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| 616 | |||
| 617 | self._XL = self._X |
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| 618 | self._YL = self._Y |
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| 619 | self._AL = np.zeros(self._XL.shape) |
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| 620 | |||
| 621 | View Code Duplication | # Arrays for retrace line |
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| 622 | self._return_XL = np.linspace(self._XL[-1], self._XL[0], self.return_slowness) |
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| 623 | self._return_AL = np.zeros(self._return_XL.shape) |
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| 624 | |||
| 625 | if self._zscan: |
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| 626 | self._image_vert_axis = self._Z |
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| 627 | # update image scan direction from setting |
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| 628 | self.depth_img_is_xz = self.depth_scan_dir_is_xz |
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| 629 | # depth scan is in xz plane |
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| 630 | if self.depth_img_is_xz: |
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| 631 | #self._image_horz_axis = self._X |
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| 632 | # creates an image where each pixel will be [x,y,z,counts] |
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| 633 | self.depth_image = np.zeros(( |
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| 634 | len(self._image_vert_axis), |
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| 635 | len(self._X), |
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| 636 | 3 + len(self.get_scanner_count_channels()) |
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| 637 | )) |
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| 638 | |||
| 639 | self.depth_image[:, :, 0] = np.full( |
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| 640 | (len(self._image_vert_axis), len(self._X)), self._XL) |
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| 641 | |||
| 642 | self.depth_image[:, :, 1] = self._current_y * np.ones( |
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| 643 | (len(self._image_vert_axis), len(self._X))) |
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| 644 | |||
| 645 | z_value_matrix = np.full((len(self._X), len(self._image_vert_axis)), self._Z) |
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| 646 | self.depth_image[:, :, 2] = z_value_matrix.transpose() |
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| 647 | |||
| 648 | # depth scan is yz plane instead of xz plane |
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| 649 | else: |
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| 650 | #self._image_horz_axis = self._Y |
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| 651 | # creats an image where each pixel will be [x,y,z,counts] |
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| 652 | self.depth_image = np.zeros(( |
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| 653 | len(self._image_vert_axis), |
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| 654 | len(self._Y), |
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| 655 | 3 + len(self.get_scanner_count_channels()) |
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| 656 | )) |
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| 657 | |||
| 658 | self.depth_image[:, :, 0] = self._current_x * np.ones( |
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| 659 | (len(self._image_vert_axis), len(self._Y))) |
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| 660 | |||
| 661 | self.depth_image[:, :, 1] = np.full( |
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| 662 | (len(self._image_vert_axis), len(self._Y)), self._YL) |
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| 663 | |||
| 664 | z_value_matrix = np.full((len(self._Y), len(self._image_vert_axis)), self._Z) |
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| 665 | self.depth_image[:, :, 2] = z_value_matrix.transpose() |
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| 666 | |||
| 667 | # now we are scanning along the y-axis, so we need a new return line along Y: |
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| 668 | self._return_YL = np.linspace(self._YL[-1], self._YL[0], self.return_slowness) |
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| 669 | self._return_AL = np.zeros(self._return_YL.shape) |
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| 670 | |||
| 671 | self.sigImageDepthInitialized.emit() |
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| 672 | |||
| 673 | # xy scan is in xy plane |
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| 674 | else: |
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| 675 | #self._image_horz_axis = self._X |
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| 676 | self._image_vert_axis = self._Y |
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| 677 | # creats an image where each pixel will be [x,y,z,counts] |
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| 678 | self.xy_image = np.zeros(( |
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| 679 | len(self._image_vert_axis), |
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| 680 | len(self._X), |
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| 681 | 3 + len(self.get_scanner_count_channels()) |
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| 682 | )) |
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| 683 | |||
| 684 | self.xy_image[:, :, 0] = np.full( |
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| 685 | (len(self._image_vert_axis), len(self._X)), self._XL) |
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| 686 | |||
| 687 | y_value_matrix = np.full((len(self._X), len(self._image_vert_axis)), self._Y) |
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| 688 | self.xy_image[:, :, 1] = y_value_matrix.transpose() |
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| 689 | |||
| 690 | self.xy_image[:, :, 2] = self._current_z * np.ones( |
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| 691 | (len(self._image_vert_axis), len(self._X))) |
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| 692 | |||
| 693 | self.sigImageXYInitialized.emit() |
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| 694 | return 0 |
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| 695 | |||
| 696 | def start_scanner(self): |
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| 697 | """Setting up the scanner device and starts the scanning procedure |
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| 698 | |||
| 699 | @return int: error code (0:OK, -1:error) |
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| 700 | """ |
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| 701 | self.module_state.lock() |
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| 702 | |||
| 703 | self._scanning_device.module_state.lock() |
||
| 704 | if self.initialize_image() < 0: |
||
| 705 | self._scanning_device.module_state.unlock() |
||
| 706 | self.module_state.unlock() |
||
| 707 | return -1 |
||
| 708 | |||
| 709 | clock_status = self._scanning_device.set_up_scanner_clock( |
||
| 710 | clock_frequency=self._clock_frequency) |
||
| 711 | |||
| 712 | if clock_status < 0: |
||
| 713 | self._scanning_device.module_state.unlock() |
||
| 714 | self.module_state.unlock() |
||
| 715 | self.set_position('scanner') |
||
| 716 | return -1 |
||
| 717 | |||
| 718 | scanner_status = self._scanning_device.set_up_scanner() |
||
| 719 | |||
| 720 | if scanner_status < 0: |
||
| 721 | self._scanning_device.close_scanner_clock() |
||
| 722 | self._scanning_device.module_state.unlock() |
||
| 723 | self.module_state.unlock() |
||
| 724 | self.set_position('scanner') |
||
| 725 | return -1 |
||
| 726 | |||
| 727 | self.signal_scan_lines_next.emit() |
||
| 728 | return 0 |
||
| 729 | |||
| 730 | def continue_scanner(self): |
||
| 731 | """Continue the scanning procedure |
||
| 732 | |||
| 733 | @return int: error code (0:OK, -1:error) |
||
| 734 | """ |
||
| 735 | self.module_state.lock() |
||
| 736 | self._scanning_device.module_state.lock() |
||
| 737 | |||
| 738 | clock_status = self._scanning_device.set_up_scanner_clock( |
||
| 739 | clock_frequency=self._clock_frequency) |
||
| 740 | |||
| 741 | if clock_status < 0: |
||
| 742 | self._scanning_device.module_state.unlock() |
||
| 743 | self.module_state.unlock() |
||
| 744 | self.set_position('scanner') |
||
| 745 | return -1 |
||
| 746 | |||
| 747 | scanner_status = self._scanning_device.set_up_scanner() |
||
| 748 | |||
| 749 | View Code Duplication | if scanner_status < 0: |
|
| 750 | self._scanning_device.close_scanner_clock() |
||
| 751 | self._scanning_device.module_state.unlock() |
||
| 752 | self.module_state.unlock() |
||
| 753 | self.set_position('scanner') |
||
| 754 | return -1 |
||
| 755 | |||
| 756 | self.signal_scan_lines_next.emit() |
||
| 757 | return 0 |
||
| 758 | |||
| 759 | def kill_scanner(self): |
||
| 760 | """Closing the scanner device. |
||
| 761 | |||
| 762 | @return int: error code (0:OK, -1:error) |
||
| 763 | View Code Duplication | """ |
|
| 764 | try: |
||
| 765 | self._scanning_device.close_scanner() |
||
| 766 | except Exception as e: |
||
| 767 | self.log.exception('Could not close the scanner.') |
||
| 768 | try: |
||
| 769 | self._scanning_device.close_scanner_clock() |
||
| 770 | except Exception as e: |
||
| 771 | self.log.exception('Could not close the scanner clock.') |
||
| 772 | try: |
||
| 773 | self._scanning_device.module_state.unlock() |
||
| 774 | except Exception as e: |
||
| 775 | self.log.exception('Could not unlock scanning device.') |
||
| 776 | |||
| 777 | return 0 |
||
| 778 | |||
| 779 | def set_position(self, tag, x=None, y=None, z=None, a=None): |
||
| 780 | """Forwarding the desired new position from the GUI to the scanning device. |
||
| 781 | |||
| 782 | @param string tag: TODO |
||
| 783 | |||
| 784 | @param float x: if defined, changes to postion in x-direction (microns) |
||
| 785 | @param float y: if defined, changes to postion in y-direction (microns) |
||
| 786 | @param float z: if defined, changes to postion in z-direction (microns) |
||
| 787 | @param float a: if defined, changes to postion in a-direction (microns) |
||
| 788 | |||
| 789 | @return int: error code (0:OK, -1:error) |
||
| 790 | """ |
||
| 791 | # Changes the respective value |
||
| 792 | if x is not None: |
||
| 793 | self._current_x = x |
||
| 794 | if y is not None: |
||
| 795 | self._current_y = y |
||
| 796 | if z is not None: |
||
| 797 | self._current_z = z |
||
| 798 | if a is not None: |
||
| 799 | self._current_a = a |
||
| 800 | |||
| 801 | # Checks if the scanner is still running |
||
| 802 | if self.module_state() == 'locked' or self._scanning_device.module_state() == 'locked': |
||
| 803 | return -1 |
||
| 804 | else: |
||
| 805 | self._change_position(tag) |
||
| 806 | self.signal_change_position.emit(tag) |
||
| 807 | return 0 |
||
| 808 | |||
| 809 | def _change_position(self, tag): |
||
| 810 | """ Threaded method to change the hardware position. |
||
| 811 | |||
| 812 | @return int: error code (0:OK, -1:error) |
||
| 813 | """ |
||
| 814 | ch_array = ['x', 'y', 'z', 'a'] |
||
| 815 | pos_array = [self._current_x, self._current_y, self._current_z, self._current_a] |
||
| 816 | pos_dict = {} |
||
| 817 | |||
| 818 | for i, ch in enumerate(self.get_scanner_axes()): |
||
| 819 | pos_dict[ch_array[i]] = pos_array[i] |
||
| 820 | |||
| 821 | self._scanning_device.scanner_set_position(**pos_dict) |
||
| 822 | return 0 |
||
| 823 | |||
| 824 | def get_position(self): |
||
| 825 | """ Get position from scanning device. |
||
| 826 | |||
| 827 | @return list: with three entries x, y and z denoting the current |
||
| 828 | position in meters |
||
| 829 | """ |
||
| 830 | return self._scanning_device.get_scanner_position() |
||
| 831 | |||
| 832 | def get_scanner_axes(self): |
||
| 833 | """ Get axes from scanning device. |
||
| 834 | @return list(str): names of scanner axes |
||
| 835 | """ |
||
| 836 | return self._scanning_device.get_scanner_axes() |
||
| 837 | |||
| 838 | def get_scanner_count_channels(self): |
||
| 839 | """ Get lis of counting channels from scanning device. |
||
| 840 | @return list(str): names of counter channels |
||
| 841 | """ |
||
| 842 | return self._scanning_device.get_scanner_count_channels() |
||
| 843 | |||
| 844 | def _scan_line(self): |
||
| 845 | """scanning an image in either depth or xy |
||
| 846 | |||
| 847 | """ |
||
| 848 | # stops scanning |
||
| 849 | if self.stopRequested: |
||
| 850 | with self.threadlock: |
||
| 851 | self.kill_scanner() |
||
| 852 | self.stopRequested = False |
||
| 853 | self.module_state.unlock() |
||
| 854 | self.signal_xy_image_updated.emit() |
||
| 855 | self.signal_depth_image_updated.emit() |
||
| 856 | self.set_position('scanner') |
||
| 857 | if self._zscan: |
||
| 858 | self._depth_line_pos = self._scan_counter |
||
| 859 | else: |
||
| 860 | self._xy_line_pos = self._scan_counter |
||
| 861 | # add new history entry |
||
| 862 | new_history = ConfocalHistoryEntry(self) |
||
| 863 | new_history.snapshot(self) |
||
| 864 | self.history.append(new_history) |
||
| 865 | if len(self.history) > self.max_history_length: |
||
| 866 | self.history.pop(0) |
||
| 867 | self.history_index = len(self.history) - 1 |
||
| 868 | return |
||
| 869 | |||
| 870 | image = self.depth_image if self._zscan else self.xy_image |
||
| 871 | n_ch = len(self.get_scanner_axes()) |
||
| 872 | s_ch = len(self.get_scanner_count_channels()) |
||
| 873 | |||
| 874 | try: |
||
| 875 | if self._scan_counter == 0: |
||
| 876 | # make a line from the current cursor position to |
||
| 877 | # the starting position of the first scan line of the scan |
||
| 878 | rs = self.return_slowness |
||
| 879 | lsx = np.linspace(self._current_x, image[self._scan_counter, 0, 0], rs) |
||
| 880 | lsy = np.linspace(self._current_y, image[self._scan_counter, 0, 1], rs) |
||
| 881 | lsz = np.linspace(self._current_z, image[self._scan_counter, 0, 2], rs) |
||
| 882 | if n_ch <= 3: |
||
| 883 | start_line = np.vstack([lsx, lsy, lsz][0:n_ch]) |
||
| 884 | else: |
||
| 885 | start_line = np.vstack( |
||
| 886 | [lsx, lsy, lsz, np.ones(lsx.shape) * self._current_a]) |
||
| 887 | # move to the start position of the scan, counts are thrown away |
||
| 888 | start_line_counts = self._scanning_device.scan_line(start_line) |
||
| 889 | if np.any(start_line_counts == -1): |
||
| 890 | self.stopRequested = True |
||
| 891 | self.signal_scan_lines_next.emit() |
||
| 892 | return |
||
| 893 | |||
| 894 | # adjust z of line in image to current z before building the line |
||
| 895 | if not self._zscan: |
||
| 896 | z_shape = image[self._scan_counter, :, 2].shape |
||
| 897 | image[self._scan_counter, :, 2] = self._current_z * np.ones(z_shape) |
||
| 898 | |||
| 899 | # make a line in the scan, _scan_counter says which one it is |
||
| 900 | lsx = image[self._scan_counter, :, 0] |
||
| 901 | lsy = image[self._scan_counter, :, 1] |
||
| 902 | lsz = image[self._scan_counter, :, 2] |
||
| 903 | if n_ch <= 3: |
||
| 904 | line = np.vstack([lsx, lsy, lsz][0:n_ch]) |
||
| 905 | else: |
||
| 906 | line = np.vstack( |
||
| 907 | [lsx, lsy, lsz, np.ones(lsx.shape) * self._current_a]) |
||
| 908 | |||
| 909 | # scan the line in the scan |
||
| 910 | line_counts = self._scanning_device.scan_line(line, pixel_clock=True) |
||
| 911 | if np.any(line_counts == -1): |
||
| 912 | self.stopRequested = True |
||
| 913 | self.signal_scan_lines_next.emit() |
||
| 914 | return |
||
| 915 | |||
| 916 | # make a line to go to the starting position of the next scan line |
||
| 917 | if self.depth_img_is_xz or not self._zscan: |
||
| 918 | if n_ch <= 3: |
||
| 919 | return_line = np.vstack([ |
||
| 920 | self._return_XL, |
||
| 921 | image[self._scan_counter, 0, 1] * np.ones(self._return_XL.shape), |
||
| 922 | image[self._scan_counter, 0, 2] * np.ones(self._return_XL.shape) |
||
| 923 | ][0:n_ch]) |
||
| 924 | else: |
||
| 925 | return_line = np.vstack([ |
||
| 926 | self._return_XL, |
||
| 927 | image[self._scan_counter, 0, 1] * np.ones(self._return_XL.shape), |
||
| 928 | image[self._scan_counter, 0, 2] * np.ones(self._return_XL.shape), |
||
| 929 | np.ones(self._return_XL.shape) * self._current_a |
||
| 930 | ]) |
||
| 931 | else: |
||
| 932 | if n_ch <= 3: |
||
| 933 | return_line = np.vstack([ |
||
| 934 | image[self._scan_counter, 0, 1] * np.ones(self._return_YL.shape), |
||
| 935 | self._return_YL, |
||
| 936 | image[self._scan_counter, 0, 2] * np.ones(self._return_YL.shape) |
||
| 937 | ][0:n_ch]) |
||
| 938 | else: |
||
| 939 | return_line = np.vstack([ |
||
| 940 | image[self._scan_counter, 0, 1] * np.ones(self._return_YL.shape), |
||
| 941 | self._return_YL, |
||
| 942 | image[self._scan_counter, 0, 2] * np.ones(self._return_YL.shape), |
||
| 943 | np.ones(self._return_YL.shape) * self._current_a |
||
| 944 | ]) |
||
| 945 | |||
| 946 | # return the scanner to the start of next line, counts are thrown away |
||
| 947 | return_line_counts = self._scanning_device.scan_line(return_line) |
||
| 948 | if np.any(return_line_counts == -1): |
||
| 949 | self.stopRequested = True |
||
| 950 | self.signal_scan_lines_next.emit() |
||
| 951 | return |
||
| 952 | |||
| 953 | # update image with counts from the line we just scanned |
||
| 954 | if self._zscan: |
||
| 955 | if self.depth_img_is_xz: |
||
| 956 | self.depth_image[self._scan_counter, :, 3:3 + s_ch] = line_counts |
||
| 957 | else: |
||
| 958 | self.depth_image[self._scan_counter, :, 3:3 + s_ch] = line_counts |
||
| 959 | self.signal_depth_image_updated.emit() |
||
| 960 | else: |
||
| 961 | self.xy_image[self._scan_counter, :, 3:3 + s_ch] = line_counts |
||
| 962 | self.signal_xy_image_updated.emit() |
||
| 963 | |||
| 964 | # next line in scan |
||
| 965 | self._scan_counter += 1 |
||
| 966 | |||
| 967 | # stop scanning when last line scan was performed and makes scan not continuable |
||
| 968 | if self._scan_counter >= np.size(self._image_vert_axis): |
||
| 969 | if not self.permanent_scan: |
||
| 970 | self.stop_scanning() |
||
| 971 | if self._zscan: |
||
| 972 | self._zscan_continuable = False |
||
| 973 | else: |
||
| 974 | self._xyscan_continuable = False |
||
| 975 | else: |
||
| 976 | self._scan_counter = 0 |
||
| 977 | |||
| 978 | self.signal_scan_lines_next.emit() |
||
| 979 | except: |
||
| 980 | self.log.exception('The scan went wrong, killing the scanner.') |
||
| 981 | self.stop_scanning() |
||
| 982 | self.signal_scan_lines_next.emit() |
||
| 983 | |||
| 984 | def save_xy_data(self, colorscale_range=None, percentile_range=None): |
||
| 985 | """ Save the current confocal xy data to file. |
||
| 986 | |||
| 987 | Two files are created. The first is the imagedata, which has a text-matrix of count values |
||
| 988 | corresponding to the pixel matrix of the image. Only count-values are saved here. |
||
| 989 | |||
| 990 | The second file saves the full raw data with x, y, z, and counts at every pixel. |
||
| 991 | |||
| 992 | A figure is also saved. |
||
| 993 | |||
| 994 | @param: list colorscale_range (optional) The range [min, max] of the display colour scale (for the figure) |
||
| 995 | |||
| 996 | @param: list percentile_range (optional) The percentile range [min, max] of the color scale |
||
| 997 | """ |
||
| 998 | filepath = self._save_logic.get_path_for_module('Confocal') |
||
| 999 | timestamp = datetime.datetime.now() |
||
| 1000 | # Prepare the metadata parameters (common to both saved files): |
||
| 1001 | parameters = OrderedDict() |
||
| 1002 | |||
| 1003 | parameters['X image min (m)'] = self.image_x_range[0] |
||
| 1004 | parameters['X image max (m)'] = self.image_x_range[1] |
||
| 1005 | parameters['X image range (m)'] = self.image_x_range[1] - self.image_x_range[0] |
||
| 1006 | |||
| 1007 | parameters['Y image min'] = self.image_y_range[0] |
||
| 1008 | parameters['Y image max'] = self.image_y_range[1] |
||
| 1009 | parameters['Y image range'] = self.image_y_range[1] - self.image_y_range[0] |
||
| 1010 | |||
| 1011 | parameters['XY resolution (samples per range)'] = self.xy_resolution |
||
| 1012 | parameters['XY Image at z position (m)'] = self._current_z |
||
| 1013 | |||
| 1014 | parameters['Clock frequency of scanner (Hz)'] = self._clock_frequency |
||
| 1015 | parameters['Return Slowness (Steps during retrace line)'] = self.return_slowness |
||
| 1016 | |||
| 1017 | # Prepare a figure to be saved |
||
| 1018 | figure_data = self.xy_image[:, :, 3] |
||
| 1019 | image_extent = [self.image_x_range[0], |
||
| 1020 | self.image_x_range[1], |
||
| 1021 | self.image_y_range[0], |
||
| 1022 | self.image_y_range[1]] |
||
| 1023 | axes = ['X', 'Y'] |
||
| 1024 | crosshair_pos = [self.get_position()[0], self.get_position()[1]] |
||
| 1025 | |||
| 1026 | figs = {ch: self.draw_figure(data=self.xy_image[:, :, 3 + n], |
||
| 1027 | image_extent=image_extent, |
||
| 1028 | scan_axis=axes, |
||
| 1029 | cbar_range=colorscale_range, |
||
| 1030 | percentile_range=percentile_range, |
||
| 1031 | crosshair_pos=crosshair_pos) |
||
| 1032 | for n, ch in enumerate(self.get_scanner_count_channels())} |
||
| 1033 | |||
| 1034 | # Save the image data and figure |
||
| 1035 | for n, ch in enumerate(self.get_scanner_count_channels()): |
||
| 1036 | # data for the text-array "image": |
||
| 1037 | image_data = OrderedDict() |
||
| 1038 | image_data['Confocal pure XY scan image data without axis.\n' |
||
| 1039 | 'The upper left entry represents the signal at the upper left pixel position.\n' |
||
| 1040 | 'A pixel-line in the image corresponds to a row ' |
||
| 1041 | 'of entries where the Signal is in counts/s:'] = self.xy_image[:, :, 3 + n] |
||
| 1042 | |||
| 1043 | filelabel = 'confocal_xy_image_{0}'.format(ch.replace('/', '')) |
||
| 1044 | self._save_logic.save_data(image_data, |
||
| 1045 | filepath=filepath, |
||
| 1046 | timestamp=timestamp, |
||
| 1047 | parameters=parameters, |
||
| 1048 | filelabel=filelabel, |
||
| 1049 | fmt='%.6e', |
||
| 1050 | delimiter='\t', |
||
| 1051 | plotfig=figs[ch]) |
||
| 1052 | |||
| 1053 | # prepare the full raw data in an OrderedDict: |
||
| 1054 | data = OrderedDict() |
||
| 1055 | data['x position (m)'] = self.xy_image[:, :, 0].flatten() |
||
| 1056 | data['y position (m)'] = self.xy_image[:, :, 1].flatten() |
||
| 1057 | data['z position (m)'] = self.xy_image[:, :, 2].flatten() |
||
| 1058 | |||
| 1059 | for n, ch in enumerate(self.get_scanner_count_channels()): |
||
| 1060 | data['count rate {0} (Hz)'.format(ch)] = self.xy_image[:, :, 3 + n].flatten() |
||
| 1061 | |||
| 1062 | # Save the raw data to file |
||
| 1063 | filelabel = 'confocal_xy_data' |
||
| 1064 | self._save_logic.save_data(data, |
||
| 1065 | filepath=filepath, |
||
| 1066 | timestamp=timestamp, |
||
| 1067 | parameters=parameters, |
||
| 1068 | filelabel=filelabel, |
||
| 1069 | fmt='%.6e', |
||
| 1070 | delimiter='\t') |
||
| 1071 | |||
| 1072 | self.log.debug('Confocal Image saved.') |
||
| 1073 | self.signal_xy_data_saved.emit() |
||
| 1074 | return |
||
| 1075 | |||
| 1076 | def save_depth_data(self, colorscale_range=None, percentile_range=None): |
||
| 1077 | """ Save the current confocal depth data to file. |
||
| 1078 | |||
| 1079 | Two files are created. The first is the imagedata, which has a text-matrix of count values |
||
| 1080 | corresponding to the pixel matrix of the image. Only count-values are saved here. |
||
| 1081 | |||
| 1082 | The second file saves the full raw data with x, y, z, and counts at every pixel. |
||
| 1083 | """ |
||
| 1084 | filepath = self._save_logic.get_path_for_module('Confocal') |
||
| 1085 | timestamp = datetime.datetime.now() |
||
| 1086 | # Prepare the metadata parameters (common to both saved files): |
||
| 1087 | parameters = OrderedDict() |
||
| 1088 | |||
| 1089 | # TODO: This needs to check whether the scan was XZ or YZ direction |
||
| 1090 | parameters['X image min (m)'] = self.image_x_range[0] |
||
| 1091 | parameters['X image max (m)'] = self.image_x_range[1] |
||
| 1092 | parameters['X image range (m)'] = self.image_x_range[1] - self.image_x_range[0] |
||
| 1093 | |||
| 1094 | parameters['Z image min'] = self.image_z_range[0] |
||
| 1095 | parameters['Z image max'] = self.image_z_range[1] |
||
| 1096 | parameters['Z image range'] = self.image_z_range[1] - self.image_z_range[0] |
||
| 1097 | |||
| 1098 | parameters['XY resolution (samples per range)'] = self.xy_resolution |
||
| 1099 | parameters['Z resolution (samples per range)'] = self.z_resolution |
||
| 1100 | parameters['Depth Image at y position (m)'] = self._current_y |
||
| 1101 | |||
| 1102 | parameters['Clock frequency of scanner (Hz)'] = self._clock_frequency |
||
| 1103 | parameters['Return Slowness (Steps during retrace line)'] = self.return_slowness |
||
| 1104 | |||
| 1105 | if self.depth_img_is_xz: |
||
| 1106 | horizontal_range = [self.image_x_range[0], self.image_x_range[1]] |
||
| 1107 | axes = ['X', 'Z'] |
||
| 1108 | crosshair_pos = [self.get_position()[0], self.get_position()[2]] |
||
| 1109 | else: |
||
| 1110 | horizontal_range = [self.image_y_range[0], self.image_y_range[1]] |
||
| 1111 | axes = ['Y', 'Z'] |
||
| 1112 | crosshair_pos = [self.get_position()[1], self.get_position()[2]] |
||
| 1113 | |||
| 1114 | image_extent = [horizontal_range[0], |
||
| 1115 | horizontal_range[1], |
||
| 1116 | self.image_z_range[0], |
||
| 1117 | self.image_z_range[1]] |
||
| 1118 | |||
| 1119 | figs = {ch: self.draw_figure(data=self.depth_image[:, :, 3 + n], |
||
| 1120 | image_extent=image_extent, |
||
| 1121 | scan_axis=axes, |
||
| 1122 | cbar_range=colorscale_range, |
||
| 1123 | percentile_range=percentile_range, |
||
| 1124 | crosshair_pos=crosshair_pos) |
||
| 1125 | for n, ch in enumerate(self.get_scanner_count_channels())} |
||
| 1126 | |||
| 1127 | # Save the image data and figure |
||
| 1128 | for n, ch in enumerate(self.get_scanner_count_channels()): |
||
| 1129 | # data for the text-array "image": |
||
| 1130 | image_data = OrderedDict() |
||
| 1131 | image_data['Confocal pure depth scan image data without axis.\n' |
||
| 1132 | 'The upper left entry represents the signal at the upper left pixel position.\n' |
||
| 1133 | 'A pixel-line in the image corresponds to a row in ' |
||
| 1134 | 'of entries where the Signal is in counts/s:'] = self.depth_image[:, :, 3 + n] |
||
| 1135 | |||
| 1136 | filelabel = 'confocal_depth_image_{0}'.format(ch.replace('/', '')) |
||
| 1137 | self._save_logic.save_data(image_data, |
||
| 1138 | filepath=filepath, |
||
| 1139 | timestamp=timestamp, |
||
| 1140 | parameters=parameters, |
||
| 1141 | filelabel=filelabel, |
||
| 1142 | fmt='%.6e', |
||
| 1143 | View Code Duplication | delimiter='\t', |
|
| 1144 | plotfig=figs[ch]) |
||
| 1145 | |||
| 1146 | # prepare the full raw data in an OrderedDict: |
||
| 1147 | data = OrderedDict() |
||
| 1148 | data['x position (m)'] = self.depth_image[:, :, 0].flatten() |
||
| 1149 | data['y position (m)'] = self.depth_image[:, :, 1].flatten() |
||
| 1150 | data['z position (m)'] = self.depth_image[:, :, 2].flatten() |
||
| 1151 | |||
| 1152 | for n, ch in enumerate(self.get_scanner_count_channels()): |
||
| 1153 | data['count rate {0} (Hz)'.format(ch)] = self.depth_image[:, :, 3 + n].flatten() |
||
| 1154 | |||
| 1155 | # Save the raw data to file |
||
| 1156 | filelabel = 'confocal_depth_data' |
||
| 1157 | self._save_logic.save_data(data, |
||
| 1158 | filepath=filepath, |
||
| 1159 | timestamp=timestamp, |
||
| 1160 | parameters=parameters, |
||
| 1161 | filelabel=filelabel, |
||
| 1162 | fmt='%.6e', |
||
| 1163 | delimiter='\t') |
||
| 1164 | |||
| 1165 | self.log.debug('Confocal Image saved.') |
||
| 1166 | self.signal_depth_data_saved.emit() |
||
| 1167 | return |
||
| 1168 | |||
| 1169 | def draw_figure(self, data, image_extent, scan_axis=None, cbar_range=None, percentile_range=None, crosshair_pos=None): |
||
| 1170 | """ Create a 2-D color map figure of the scan image. |
||
| 1171 | |||
| 1172 | @param: array data: The NxM array of count values from a scan with NxM pixels. |
||
| 1173 | |||
| 1174 | @param: list image_extent: The scan range in the form [hor_min, hor_max, ver_min, ver_max] |
||
| 1175 | |||
| 1176 | @param: list axes: Names of the horizontal and vertical axes in the image |
||
| 1177 | |||
| 1178 | @param: list cbar_range: (optional) [color_scale_min, color_scale_max]. If not supplied then a default of |
||
| 1179 | data_min to data_max will be used. |
||
| 1180 | |||
| 1181 | @param: list percentile_range: (optional) Percentile range of the chosen cbar_range. |
||
| 1182 | |||
| 1183 | @param: list crosshair_pos: (optional) crosshair position as [hor, vert] in the chosen image axes. |
||
| 1184 | |||
| 1185 | @return: fig fig: a matplotlib figure object to be saved to file. |
||
| 1186 | """ |
||
| 1187 | if scan_axis is None: |
||
| 1188 | scan_axis = ['X', 'Y'] |
||
| 1189 | |||
| 1190 | # If no colorbar range was given, take full range of data |
||
| 1191 | if cbar_range is None: |
||
| 1192 | cbar_range = [np.min(data), np.max(data)] |
||
| 1193 | |||
| 1194 | # Scale color values using SI prefix |
||
| 1195 | prefix = ['', 'k', 'M', 'G'] |
||
| 1196 | prefix_count = 0 |
||
| 1197 | image_data = data |
||
| 1198 | draw_cb_range = np.array(cbar_range) |
||
| 1199 | image_dimension = image_extent.copy() |
||
| 1200 | |||
| 1201 | while draw_cb_range[1] > 1000: |
||
| 1202 | image_data = image_data/1000 |
||
| 1203 | draw_cb_range = draw_cb_range/1000 |
||
| 1204 | prefix_count = prefix_count + 1 |
||
| 1205 | |||
| 1206 | c_prefix = prefix[prefix_count] |
||
| 1207 | |||
| 1208 | |||
| 1209 | # Scale axes values using SI prefix |
||
| 1210 | axes_prefix = ['', 'm', r'$\mathrm{\mu}$', 'n'] |
||
| 1211 | x_prefix_count = 0 |
||
| 1212 | y_prefix_count = 0 |
||
| 1213 | |||
| 1214 | while np.abs(image_dimension[1]-image_dimension[0]) < 1: |
||
| 1215 | image_dimension[0] = image_dimension[0] * 1000. |
||
| 1216 | image_dimension[1] = image_dimension[1] * 1000. |
||
| 1217 | x_prefix_count = x_prefix_count + 1 |
||
| 1218 | |||
| 1219 | while np.abs(image_dimension[3] - image_dimension[2]) < 1: |
||
| 1220 | image_dimension[2] = image_dimension[2] * 1000. |
||
| 1221 | image_dimension[3] = image_dimension[3] * 1000. |
||
| 1222 | y_prefix_count = y_prefix_count + 1 |
||
| 1223 | |||
| 1224 | x_prefix = axes_prefix[x_prefix_count] |
||
| 1225 | y_prefix = axes_prefix[y_prefix_count] |
||
| 1226 | |||
| 1227 | # Use qudi style |
||
| 1228 | plt.style.use(self._save_logic.mpl_qd_style) |
||
| 1229 | |||
| 1230 | # Create figure |
||
| 1231 | fig, ax = plt.subplots() |
||
| 1232 | |||
| 1233 | # Create image plot |
||
| 1234 | cfimage = ax.imshow(image_data, |
||
| 1235 | cmap=plt.get_cmap('inferno'), # reference the right place in qd |
||
| 1236 | origin="lower", |
||
| 1237 | vmin=draw_cb_range[0], |
||
| 1238 | vmax=draw_cb_range[1], |
||
| 1239 | interpolation='none', |
||
| 1240 | extent=image_dimension |
||
| 1241 | ) |
||
| 1242 | |||
| 1243 | ax.set_aspect(1) |
||
| 1244 | ax.set_xlabel(scan_axis[0] + ' position (' + x_prefix + 'm)') |
||
| 1245 | ax.set_ylabel(scan_axis[1] + ' position (' + y_prefix + 'm)') |
||
| 1246 | ax.spines['bottom'].set_position(('outward', 10)) |
||
| 1247 | ax.spines['left'].set_position(('outward', 10)) |
||
| 1248 | ax.spines['top'].set_visible(False) |
||
| 1249 | ax.spines['right'].set_visible(False) |
||
| 1250 | ax.get_xaxis().tick_bottom() |
||
| 1251 | ax.get_yaxis().tick_left() |
||
| 1252 | |||
| 1253 | # draw the crosshair position if defined |
||
| 1254 | if crosshair_pos is not None: |
||
| 1255 | trans_xmark = mpl.transforms.blended_transform_factory( |
||
| 1256 | ax.transData, |
||
| 1257 | ax.transAxes) |
||
| 1258 | |||
| 1259 | trans_ymark = mpl.transforms.blended_transform_factory( |
||
| 1260 | ax.transAxes, |
||
| 1261 | ax.transData) |
||
| 1262 | |||
| 1263 | ax.annotate('', xy=(crosshair_pos[0]*np.power(1000,x_prefix_count), 0), |
||
| 1264 | xytext=(crosshair_pos[0]*np.power(1000,x_prefix_count), -0.01), xycoords=trans_xmark, |
||
| 1265 | arrowprops=dict(facecolor='#17becf', shrink=0.05), |
||
| 1266 | ) |
||
| 1267 | |||
| 1268 | ax.annotate('', xy=(0, crosshair_pos[1]*np.power(1000,y_prefix_count)), |
||
| 1269 | xytext=(-0.01, crosshair_pos[1]*np.power(1000,y_prefix_count)), xycoords=trans_ymark, |
||
| 1270 | arrowprops=dict(facecolor='#17becf', shrink=0.05), |
||
| 1271 | ) |
||
| 1272 | |||
| 1273 | # Draw the colorbar |
||
| 1274 | cbar = plt.colorbar(cfimage, shrink=0.8)#, fraction=0.046, pad=0.08, shrink=0.75) |
||
| 1275 | cbar.set_label('Fluorescence (' + c_prefix + 'c/s)') |
||
| 1276 | |||
| 1277 | # remove ticks from colorbar for cleaner image |
||
| 1278 | cbar.ax.tick_params(which=u'both', length=0) |
||
| 1279 | |||
| 1280 | # If we have percentile information, draw that to the figure |
||
| 1281 | if percentile_range is not None: |
||
| 1282 | cbar.ax.annotate(str(percentile_range[0]), |
||
| 1283 | xy=(-0.3, 0.0), |
||
| 1284 | xycoords='axes fraction', |
||
| 1285 | horizontalalignment='right', |
||
| 1286 | verticalalignment='center', |
||
| 1287 | rotation=90 |
||
| 1288 | ) |
||
| 1289 | cbar.ax.annotate(str(percentile_range[1]), |
||
| 1290 | xy=(-0.3, 1.0), |
||
| 1291 | xycoords='axes fraction', |
||
| 1292 | horizontalalignment='right', |
||
| 1293 | verticalalignment='center', |
||
| 1294 | rotation=90 |
||
| 1295 | ) |
||
| 1296 | cbar.ax.annotate('(percentile)', |
||
| 1297 | xy=(-0.3, 0.5), |
||
| 1298 | xycoords='axes fraction', |
||
| 1299 | horizontalalignment='right', |
||
| 1300 | verticalalignment='center', |
||
| 1301 | rotation=90 |
||
| 1302 | ) |
||
| 1303 | self.signal_draw_figure_completed.emit() |
||
| 1304 | return fig |
||
| 1305 | |||
| 1306 | ##################################### Tilt correction ######################################## |
||
| 1307 | |||
| 1308 | @QtCore.Slot() |
||
| 1309 | def set_tilt_point1(self): |
||
| 1310 | """ Gets the first reference point for tilt correction.""" |
||
| 1311 | self.point1 = np.array(self._scanning_device.get_scanner_position()[:3]) |
||
| 1312 | self.signal_tilt_correction_update.emit() |
||
| 1313 | |||
| 1314 | @QtCore.Slot() |
||
| 1315 | def set_tilt_point2(self): |
||
| 1316 | """ Gets the second reference point for tilt correction.""" |
||
| 1317 | self.point2 = np.array(self._scanning_device.get_scanner_position()[:3]) |
||
| 1318 | self.signal_tilt_correction_update.emit() |
||
| 1319 | |||
| 1320 | @QtCore.Slot() |
||
| 1321 | def set_tilt_point3(self): |
||
| 1322 | """Gets the third reference point for tilt correction.""" |
||
| 1323 | self.point3 = np.array(self._scanning_device.get_scanner_position()[:3]) |
||
| 1324 | self.signal_tilt_correction_update.emit() |
||
| 1325 | |||
| 1326 | @QtCore.Slot() |
||
| 1327 | def calc_tilt_correction(self): |
||
| 1328 | """ Calculates the values for the tilt correction. """ |
||
| 1329 | a = self.point2 - self.point1 |
||
| 1330 | b = self.point3 - self.point1 |
||
| 1331 | n = np.cross(a, b) |
||
| 1332 | self._scanning_device.tilt_variable_ax = n[0] / n[2] |
||
| 1333 | self._scanning_device.tilt_variable_ay = n[1] / n[2] |
||
| 1334 | |||
| 1335 | @QtCore.Slot(bool) |
||
| 1336 | def set_tilt_correction(self, enabled): |
||
| 1337 | """ Set tilt correction in tilt interfuse. |
||
| 1338 | |||
| 1339 | @param bool enabled: whether we want to use tilt correction |
||
| 1340 | """ |
||
| 1341 | self._scanning_device.tiltcorrection = enabled |
||
| 1342 | self._scanning_device.tilt_reference_x = self._scanning_device.get_scanner_position()[0] |
||
| 1343 | self._scanning_device.tilt_reference_y = self._scanning_device.get_scanner_position()[1] |
||
| 1344 | self.signal_tilt_correction_active.emit(enabled) |
||
| 1345 | |||
| 1346 | View Code Duplication | def history_forward(self): |
|
| 1347 | """ Move forward in confocal image history. |
||
| 1348 | """ |
||
| 1349 | if self.history_index < len(self.history) - 1: |
||
| 1350 | self.history_index += 1 |
||
| 1351 | self.history[self.history_index].restore(self) |
||
| 1352 | self.signal_xy_image_updated.emit() |
||
| 1353 | self.signal_depth_image_updated.emit() |
||
| 1354 | self.signal_tilt_correction_update.emit() |
||
| 1355 | self.signal_tilt_correction_active.emit(self._scanning_device.tiltcorrection) |
||
| 1356 | self._change_position('history') |
||
| 1357 | self.signal_change_position.emit('history') |
||
| 1358 | self.signal_history_event.emit() |
||
| 1359 | |||
| 1360 | View Code Duplication | def history_back(self): |
|
| 1361 | """ Move backwards in confocal image history. |
||
| 1362 | """ |
||
| 1363 | if self.history_index > 0: |
||
| 1364 | self.history_index -= 1 |
||
| 1365 | self.history[self.history_index].restore(self) |
||
| 1366 | self.signal_xy_image_updated.emit() |
||
| 1367 | self.signal_depth_image_updated.emit() |
||
| 1368 | self.signal_tilt_correction_update.emit() |
||
| 1369 | self.signal_tilt_correction_active.emit(self._scanning_device.tiltcorrection) |
||
| 1370 | self._change_position('history') |
||
| 1371 | self.signal_change_position.emit('history') |
||
| 1372 | self.signal_history_event.emit() |
||
| 1373 |
Loading history...
