def test_sync_sem_ccd(self): """ try acquisition with fairly complex SEM/CCD stream """ # Create the streams and streamTree semsur = stream.SEMStream("test sem", self.sed, self.sed.data, self.ebeam) sems = stream.SEMStream("test sem cl", self.sed, self.sed.data, self.ebeam) ars = stream.ARSettingsStream("test ar", self.ccd, self.ccd.data, self.ebeam) semars = stream.SEMARMDStream("test SEM/AR", [sems, ars]) st = stream.StreamTree(streams=[semsur, semars]) # SEM survey settings are via the current hardware settings self.ebeam.dwellTime.value = self.ebeam.dwellTime.range[0] # SEM/AR settings are via the AR stream ars.roi.value = (0.1, 0.1, 0.8, 0.8) mx_brng = self.ccd.binning.range[1] binning = tuple(min(4, mx) for mx in mx_brng) # try binning 4x4 self.ccd.binning.value = binning self.ccd.exposureTime.value = 1 # s ars.repetition.value = (2, 3) num_ar = numpy.prod(ars.repetition.value) est_time = acqmng.estimateTime(st.getProjections()) # prepare callbacks self.start = None self.end = None self.updates = 0 self.done = 0 # Run acquisition start = time.time() f = acqmng.acquire(st.getProjections()) f.add_update_callback(self.on_progress_update) f.add_done_callback(self.on_done) data, e = f.result() dur = time.time() - start self.assertGreaterEqual(dur, est_time / 2) # Estimated time shouldn't be too small self.assertIsInstance(data[0], model.DataArray) self.assertIsNone(e) self.assertEqual(len(data), num_ar + 2) thumb = acqmng.computeThumbnail(st, f) self.assertIsInstance(thumb, model.DataArray) self.assertGreaterEqual(self.updates, 1) # at least one update at end self.assertLessEqual(self.end, time.time()) self.assertTrue(not f.cancelled()) time.sleep(0.1) self.assertEqual(self.done, 1)
def test_simple(self): # create a simple streamTree st = stream.StreamTree(streams=[self.streams[0]]) f = acqmng.acquire(st.getProjections()) data, e = f.result() self.assertIsInstance(data[0], model.DataArray) self.assertIsNone(e) thumb = acqmng.computeThumbnail(st, f) self.assertIsInstance(thumb, model.DataArray) # let's do it a second time, "just for fun" f = acqmng.acquire(st.getProjections()) data, e = f.result() self.assertIsInstance(data[0], model.DataArray) self.assertIsNone(e) thumb = acqmng.computeThumbnail(st, f) self.assertIsInstance(thumb, model.DataArray)
def _export_to_file(self, acq_future): """ return (list of DataArray, filename): data exported and filename """ streams = list(self._tab_data_model.acquisitionStreams) st = stream.StreamTree(streams=streams) thumb = acqmng.computeThumbnail(st, acq_future) data, exp = acq_future.result() filename = self.filename.value if data: exporter = dataio.get_converter(self.conf.last_format) exporter.export(filename, data, thumb) logging.info(u"Acquisition saved as file '%s'.", filename) else: logging.debug("Not saving into file '%s' as there is no data", filename) return data, exp, filename
def on_acquisition_done(self, future): """ Callback called when the acquisition is finished (either successfully or cancelled) """ if self._main_data_model.opm: self._main_data_model.opm.setAcqQuality(path.ACQ_QUALITY_FAST) # bind button back to direct closure self.btn_cancel.Bind(wx.EVT_BUTTON, self.on_close) self._resume_settings() self.acquiring = False # re-enable estimation time updates self._view.lastUpdate.subscribe(self.on_streams_changed) self.acq_future = None # To avoid holding the ref in memory self._acq_future_connector = None try: data, exp = future.result(1) # timeout is just for safety self.conf.fn_count = update_counter(self.conf.fn_count) except CancelledError: # put back to original state: # re-enable the acquire button self.btn_secom_acquire.Enable() # hide progress bar (+ put pack estimated time) self.update_acquisition_time() self.gauge_acq.Hide() self.Layout() return except Exception: # We cannot do much: just warn the user and pretend it was cancelled logging.exception("Acquisition failed") self.btn_secom_acquire.Enable() self.lbl_acqestimate.SetLabel("Acquisition failed.") self.lbl_acqestimate.Parent.Layout() # leave the gauge, to give a hint on what went wrong. return # Handle the case acquisition failed "a bit" if exp: logging.warning("Acquisition failed (after %d streams): %s", len(data), exp) # save result to file self.lbl_acqestimate.SetLabel("Saving file...") self.lbl_acqestimate.Parent.Layout() try: thumb = acqmng.computeThumbnail(self._view.stream_tree, future) filename = self.filename.value exporter = dataio.get_converter(self.conf.last_format) exporter.export(filename, data, thumb) logging.info("Acquisition saved as file '%s'.", filename) # Allow to see the acquisition self.btn_secom_acquire.SetLabel("VIEW") self.last_saved_file = filename except Exception: logging.exception("Saving acquisition failed") self.btn_secom_acquire.Enable() self.lbl_acqestimate.SetLabel("Saving acquisition file failed.") self.lbl_acqestimate.Parent.Layout() return if exp: self.lbl_acqestimate.SetLabel("Acquisition failed (partially).") else: self.lbl_acqestimate.SetLabel("Acquisition completed.") # As the action is complete, rename "Cancel" to "Close" self.btn_cancel.SetLabel("Close") self.lbl_acqestimate.Parent.Layout() # Make sure the file is not overridden self.btn_secom_acquire.Enable()
def test_leech(self): """ try acquisition with leech """ # Create the streams and streamTree semsur = stream.SEMStream("test sem", self.sed, self.sed.data, self.ebeam) sems = stream.SEMStream("test sem cl", self.sed, self.sed.data, self.ebeam) ars = stream.ARSettingsStream("test ar", self.ccd, self.ccd.data, self.ebeam) semars = stream.SEMARMDStream("test SEM/AR", [sems, ars]) st = stream.StreamTree(streams=[semsur, semars]) pcd = Fake0DDetector("test") pca = ProbeCurrentAcquirer(pcd) sems.leeches.append(pca) semsur.leeches.append(pca) # SEM survey settings are via the current hardware settings self.ebeam.dwellTime.value = self.ebeam.dwellTime.range[0] # SEM/AR settings are via the AR stream ars.roi.value = (0.1, 0.1, 0.8, 0.8) mx_brng = self.ccd.binning.range[1] binning = tuple(min(4, mx) for mx in mx_brng) # try binning 4x4 self.ccd.binning.value = binning self.ccd.exposureTime.value = 1 # s ars.repetition.value = (2, 3) num_ar = numpy.prod(ars.repetition.value) pca.period.value = 10 # Only at beginning and end est_time = acqmng.estimateTime(st.getProjections()) # prepare callbacks self.start = None self.end = None self.updates = 0 self.done = 0 # Run acquisition start = time.time() f = acqmng.acquire(st.getProjections()) f.add_update_callback(self.on_progress_update) f.add_done_callback(self.on_done) data, e = f.result() dur = time.time() - start self.assertGreaterEqual(dur, est_time / 2) # Estimated time shouldn't be too small self.assertIsInstance(data[0], model.DataArray) self.assertIsNone(e) self.assertEqual(len(data), num_ar + 2) thumb = acqmng.computeThumbnail(st, f) self.assertIsInstance(thumb, model.DataArray) self.assertGreaterEqual(self.updates, 1) # at least one update at end self.assertLessEqual(self.end, time.time()) self.assertTrue(not f.cancelled()) time.sleep(0.1) self.assertEqual(self.done, 1) for da in data: pcmd = da.metadata[model.MD_EBEAM_CURRENT_TIME] self.assertEqual(len(pcmd), 2)
def test_sync_path_guess(self): """ try synchronized acquisition using the Optical Path Manager """ # Create the streams and streamTree opmngr = path.OpticalPathManager(self.microscope) semsur = stream.SEMStream("test sem", self.sed, self.sed.data, self.ebeam) sems = stream.SEMStream("test sem cl", self.sed, self.sed.data, self.ebeam) ars = stream.ARSettingsStream("test ar", self.ccd, self.ccd.data, self.ebeam, opm=opmngr) semars = stream.SEMARMDStream("test SEM/AR", [sems, ars]) specs = stream.SpectrumSettingsStream("test spec", self.spec, self.spec.data, self.ebeam, opm=opmngr) sps = stream.SEMSpectrumMDStream("test sem-spec", [sems, specs]) st = stream.StreamTree(streams=[semsur, semars, sps]) # SEM survey settings are via the current hardware settings self.ebeam.dwellTime.value = self.ebeam.dwellTime.range[0] # SEM/AR/SPEC settings are via the AR stream ars.roi.value = (0.1, 0.1, 0.8, 0.8) specs.roi.value = (0.2, 0.2, 0.7, 0.7) mx_brng = self.ccd.binning.range[1] binning = tuple(min(4, mx) for mx in mx_brng) # try binning 4x4 self.ccd.binning.value = binning self.ccd.exposureTime.value = 1 # s ars.repetition.value = (2, 3) specs.repetition.value = (3, 2) num_ar = numpy.prod(ars.repetition.value) est_time = acqmng.estimateTime(st.getProjections()) # prepare callbacks self.start = None self.end = None self.updates = 0 self.done = 0 # Run acquisition start = time.time() f = acqmng.acquire(st.getProjections()) f.add_update_callback(self.on_progress_update) f.add_done_callback(self.on_done) data, e = f.result() dur = time.time() - start self.assertGreaterEqual(dur, est_time / 2) # Estimated time shouldn't be too small self.assertIsInstance(data[0], model.DataArray) self.assertIsNone(e) self.assertEqual(len(data), num_ar + 4) thumb = acqmng.computeThumbnail(st, f) self.assertIsInstance(thumb, model.DataArray) self.assertGreaterEqual(self.updates, 1) # at least one update at end self.assertLessEqual(self.end, time.time()) self.assertTrue(not f.cancelled()) # assert optical path configuration exp_pos = path.SPARC_MODES["spectral"][1] self.assertEqual(self.lenswitch.position.value, exp_pos["lens-switch"]) self.assertEqual(self.spec_det_sel.position.value, exp_pos["spec-det-selector"]) self.assertEqual(self.ar_spec_sel.position.value, exp_pos["ar-spec-selector"]) time.sleep(0.1) self.assertEqual(self.done, 1)