# -*- coding: utf-8 -*- # Copyright 2007-2022 The HyperSpy developers # # This file is part of HyperSpy. # # HyperSpy is free software: you can redistribute it and/or modify # it under the terms of the GNU General Public License as published by # the Free Software Foundation, either version 3 of the License, or # (at your option) any later version. # # HyperSpy is distributed in the hope that it will be useful, # but WITHOUT ANY WARRANTY; without even the implied warranty of # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the # GNU General Public License for more details. # # You should have received a copy of the GNU General Public License # along with HyperSpy. If not, see . import gc import importlib import shutil from copy import deepcopy from pathlib import Path import numpy as np import pytest from rsciio.tests.generate_renishaw_test_file import WDFFileGenerator, WDFFileHandler hs = pytest.importorskip("hyperspy.api", reason="hyperspy not installed") testfile_dir = Path(__file__).parent / "data" / "renishaw" testfile_spec = (testfile_dir / "renishaw_test_spectrum.wdf").resolve() testfile_linescan = (testfile_dir / "renishaw_test_linescan.wdf").resolve() testfile_map = (testfile_dir / "renishaw_test_map.wdf").resolve() testfile_zscan = (testfile_dir / "renishaw_test_zscan.wdf").resolve() testfile_undefined = (testfile_dir / "renishaw_test_undefined.wdf").resolve() testfile_streamline = (testfile_dir / "renishaw_test_streamline.wdf").resolve() testfile_map_block = (testfile_dir / "renishaw_test_map2.wdf").resolve() testfile_timeseries = (testfile_dir / "renishaw_test_timeseries.wdf").resolve() testfile_focustrack = (testfile_dir / "renishaw_test_focustrack.wdf").resolve() testfile_focustrack_invariant = ( testfile_dir / "renishaw_test_focustrack_invariant.wdf" ).resolve() testfile_acc1_exptime1 = (testfile_dir / "renishaw_test_exptime1_acc1.wdf").resolve() testfile_acc1_exptime10 = (testfile_dir / "renishaw_test_exptime10_acc1.wdf").resolve() testfile_acc2_exptime1 = (testfile_dir / "renishaw_test_exptime1_acc2.wdf").resolve() class TestSpec: @classmethod def setup_class(cls): cls.s = hs.load( testfile_spec, reader="Renishaw", use_uniform_signal_axis=True, ) cls.s_non_uniform = hs.load( testfile_spec, reader="Renishaw", use_uniform_signal_axis=False, ) @classmethod def teardown_class(cls): del cls.s del cls.s_non_uniform gc.collect() def test_data(self): expected_data_start = [ 65.36617, 67.51018, 60.00703, 62.75381, 64.59786, 61.309525, ] expected_data_end = [ 63.337173, 64.90067, 61.871353, 59.75822, 67.45442, 68.10285, ] np.testing.assert_allclose(expected_data_start, self.s.isig[:6].data) np.testing.assert_allclose(expected_data_end, self.s.isig[-6:].data) np.testing.assert_allclose(self.s.data, self.s_non_uniform.data) assert len(self.s.data) == 36 def test_axes(self): expected_axis = { "axis-0": { "name": "Wavelength", "units": "nm", "navigate": False, "size": 36, } } axes_manager = self.s.axes_manager.as_dictionary() axes_manager["axis-0"].pop("_type", None) axes_manager["axis-0"].pop("is_binned", None) np.testing.assert_allclose( axes_manager["axis-0"].pop("scale"), 0.0847, rtol=0.0003 ) np.testing.assert_allclose(axes_manager["axis-0"].pop("offset"), 326.01, 0.01) assert axes_manager == expected_axis expected_non_uniform_axis_values = [ 326.01633, 326.101, 326.18573, 326.27042, 326.35513, 326.43985, ] non_uniform_axes_manager = self.s_non_uniform.axes_manager.as_dictionary() non_uniform_axes_manager["axis-0"].pop("_type", None) non_uniform_axes_manager["axis-0"].pop("is_binned", None) assert len(non_uniform_axes_manager["axis-0"]["axis"]) == 36 np.testing.assert_allclose( non_uniform_axes_manager["axis-0"].pop("axis")[:6], expected_non_uniform_axis_values, ) axes_manager["axis-0"].pop("size") assert axes_manager == non_uniform_axes_manager def test_original_metadata_WDF1(self): original_metadata = deepcopy(self.s.original_metadata.as_dictionary()) original_metadata_non_uniform = deepcopy( self.s_non_uniform.original_metadata.as_dictionary() ) np.testing.assert_allclose( original_metadata["WDF1_1"].pop("laser_wavenumber"), 30769.2 ) np.testing.assert_allclose( original_metadata_non_uniform["WDF1_1"].pop("laser_wavenumber"), 30769.2 ) assert original_metadata_non_uniform == original_metadata expected_metadata = { "flags": 0, "uuid": "3846669335-1129807005-716570026-4266516655", "ntracks": 0, "file_status_error_code": 0, "capacity": 1, "app_name": "WiRE", "app_version": "5-5-0-22400", "scan_type": "Static", "time_start": "2022-02-16#13:01:31", "time_end": "2022-02-16#13:13:31", "quantity_unit": "counts", "username": "optik", "title": "Single scan measurement 7", "points_per_spectrum": 36, "num_spectra": 1, "accumulations_per_spectrum": 4, "YLST_length": 1, "XLST_length": 36, "num_ORGN": 3, "measurement_type": "Single", } assert expected_metadata == original_metadata["WDF1_1"] def test_original_metadata_YLST(self): expected_YLST = {"name": "Unknown", "units": "px", "size": 1, "data": 25.0} assert self.s.original_metadata.YLST_0.as_dictionary() == expected_YLST def test_original_metadata_WXIS(self): expected_WXIS = { "Instrument type": "InVia", "logicalMotorPositions": { "Beam Expander": 0.0, "CCD lensfocus": 12.1875, "Entrance Filter 1": 7500.0, "Entrance Filter 2": 7500.0, "Grating Motor": 11.859422492401215, "Holographic Notch Filter": -0.7598784194528876, "Laser Shutter": 1.0, "ND Set Flag 1": 0.0, "ND Set Flag 2": -0.0, "ND Set Flag 3": -0.0, "ND Set Flag 4": 0.0, "Pinhole": -0.0, "Podule AStop": -5000.0, "Podule FStop": -5000.0, "Podule Lower Selector Wheel": 3.0, "Podule Silicon Ref tilt": 7500.0, "Podule Upper Selector Wheel": 1.0, "Post Beam Expander Axis 1": 738.0, "Post Beam Expander Axis 2": 572.0, "Post slit lensfocus": 12.1875, "Pre Beam Expander Axis 1": 461.0, "Pre Beam Expander Axis 2": 776.0, "Pre slit lensfocus": 5.96875, "Slit Master": 1698.2421875, "Slit Slave": 1754.0690104166667, "Waveplate Motor": 0.0, "XYZ Stage X Motor": 25219.8, "XYZ Stage Y Motor": -41827.5, "XYZ Stage Z Motor": -19023.2, }, "Microscope": {"Field of view X": 9096.0, "Field of view Y": 5761.0}, "Motor Positions": { "Beam Expander": "0 Percent", "CCD lensfocus": "12.1875 mm", "Entrance Filter 1": "7500 Steps", "Entrance Filter 2": "7500 Steps", "Grating Motor": "11.8594 Degrees", "Holographic Notch Filter": "-0.759878 Degrees", "Laser Shutter": "Open", "ND Set Flag 1": "100", "ND Set Flag 2": "100", "ND Set Flag 3": "100", "ND Set Flag 4": "100", "Pinhole": "Out", "Podule AStop": "-5000 Steps", "Podule FStop": "-5000 Steps", "Podule Lower Selector Wheel": "Sample", "Podule Silicon Ref tilt": "7500 Steps", "Podule Upper Selector Wheel": "Laser", "Post Beam Expander Axis 1": "738 Steps", "Post Beam Expander Axis 2": "572 Steps", "Post slit lensfocus": "12.1875 mm", "Pre Beam Expander Axis 1": "461 Steps", "Pre Beam Expander Axis 2": "776 Steps", "Pre slit lensfocus": "5.96875 mm", "Slit Master": "1698.24 microns", "Slit Slave": "1754.07 microns", "Waveplate Motor": "Normal", "XYZ Stage X Motor": "25219.8 microns", "XYZ Stage Y Motor": "-41827.5 microns", "XYZ Stage Z Motor": "-19023.2 microns", }, "ND Transmission %": "100", "Podule": { "Calibration lamp": "Off", "Calibration lamp intensity": 0, "Illumination lamp": "Off", "Illumination lamp intensity": 0, "Neon lamp": "Off", "Podule name": "Main podule", "Podule Temperature": "23°C", "podule type": 3, "Podule type": "Podule mk2", }, "Serial Numbers": {}, "Slits": {"Bias": "0µm", "Opening": "66µm", "SlitBeamCentre": "1731µm"}, "Stage": {"X": 25219.8, "Y": -41827.5, "Z": -19023.2}, "System Configuration": { "beamPath": 2, "detectorID": 1, "focusMode": 1, "FocusMode": "Regular", "Grating": "1200 l/mm (325nm PL / 532nm )", "key_Grating": "grating0", "key_Laser": "laser0", }, } assert expected_WXIS == self.s.original_metadata.WXIS_0.as_dictionary() def test_original_metadata_WXCS(self): expected_WXCS = { "AreakeyDependants": { "Microscope imaging factor": { "532 nm edge, Renishaw Centrus 2URV61": "800", "Default": "800", "mask": 5, "Mask": "laser detector ", "Use default": "true", }, "Response calibration target level (raw counts)": { "Default": "30000", "mask": 4, "Mask": "detector ", "Use default": "true", }, "Zero level & dark current": { "mask": 4, "Mask": "detector ", "Renishaw Centrus 2URV61": "", "Use default": "false", }, }, "CCD": { "Areas": { "Laser0, grating0, mode: Regular, path: Grating, det 1.": { "Area bottom": 55, "Area left": 18, "Area right": 1032, "Area top": 25, "Centre pixel": 517, "X binning": 1, "Y binning": 108, } }, "CCD": "Renishaw Centrus 2URV61", "Centrus": { "Channel 0": { "ChannelGain": 0.83, "ChannelGainName": "high", "ChannelIndex": 0, "ChannelName": "High sensitivity mode", "ChannelSpeed": 33.0, "ChannelSpeedName": "low", }, "Channel 1": { "ChannelGain": 2.4, "ChannelGainName": "medium", "ChannelIndex": 1, "ChannelName": "Standard mode", "ChannelSpeed": 33.0, "ChannelSpeedName": "low", }, "Channel 2": { "ChannelGain": 9.54, "ChannelGainName": "low", "ChannelIndex": 2, "ChannelName": "High range mode", "ChannelSpeed": 33.0, "ChannelSpeedName": "low", }, "Channel 3": { "ChannelGain": 0.84, "ChannelGainName": "high", "ChannelIndex": 3, "ChannelName": "High sensitivity fast readout mode", "ChannelSpeed": 200.0, "ChannelSpeedName": "medium", }, "Channel 4": { "ChannelGain": 2.44, "ChannelGainName": "medium", "ChannelIndex": 4, "ChannelName": "Standard fast readout mode", "ChannelSpeed": 200.0, "ChannelSpeedName": "medium", }, "Channel 5": { "ChannelGain": 9.77, "ChannelGainName": "low", "ChannelIndex": 5, "ChannelName": "High range fast readout mode ", "ChannelSpeed": 200.0, "ChannelSpeedName": "medium", }, "Channel 6": { "ChannelGain": 0.69, "ChannelGainName": "high", "ChannelIndex": 6, "ChannelName": "High sensitivity fastest readout mode", "ChannelSpeed": 2000.0, "ChannelSpeedName": "high", }, "Channel 7": { "ChannelGain": 2.47, "ChannelGainName": "medium", "ChannelIndex": 7, "ChannelName": "Standard fastest readout mode", "ChannelSpeed": 2000.0, "ChannelSpeedName": "high", }, "Channel 8": { "ChannelGain": 6.81, "ChannelGainName": "low", "ChannelIndex": 8, "ChannelName": "High range fastest readout mode", "ChannelSpeed": 2000.0, "ChannelSpeedName": "high", }, "DisplayName": "Renishaw Centrus 2URV61", "EMGainSupport": "false", "Identifier": "2URV61", "Type": "{D42848CA-072A-4ABA-B9CA-1D1AB50EFFA2}", }, "Charge clear mode": "once per exposure", "Gain factor (high)": 2.5, "Gain factor (low)": 10.0, "Height (pixels)": 256, "Pixel height (mm)": -0.026, "Pixel width (mm)": -0.026, "Preread": 18, "Preread_Ext": 3, "Readout axis": "X", "Readout dirn": "positive", "Readout from X1": "false", "Shutter always open": "false", "Shutter present": "false", "Target temperature": -70, "Use pixel intensity": "true", "Width (pixels)": 1040, }, "Gratings": { "1200 l/mm (325nm PL / 532nm )": { "325nm_PL": { "CalibrationType": "RM Standard", "Focal Length 0": 255.052664563221, "Focal Length 1": 2.82660353662461e-05, "Grating Order": 1, "Grating Status": "calibrated", "Groove Density (lines/mm)": 1200, "Include Angle (Rads)": 0.515767, "Lens Distortion 0": 0.0, "Lens Distortion 1": 1.0, "Lens Distortion 2": 2.88731884159059e-06, "Lens Distortion 3": 2.06664681416031e-08, "Lens Distortion 4": -5.75777927691806e-12, "Lens Distortion 5": -8.62270489788888e-16, "Polynomial 0": 0.0, "Polynomial 1": 1.0, "Polynomial 2": 0.0, "Polynomial 3": 0.0, "Zero Offset (Rads)": 0.0003818160379531949, }, "Grating key": "grating0", } }, "Lasers": { "325nm_PL": { "Laser key": "laser0", "Laser path": 2, "Wavenumber": 30769.2, } }, "Motor Calibration": { "Beam Expander": { "boardType": "Serial", "motor Address": 60, "Reference Position (steps)": -1250, "Steps Per Unit": 10.0, }, "CCD lensfocus": { "boardType": "Serial", "motor Address": 84, "Reference Position (steps)": -64000, "Steps Per Unit": -3200.0, }, "Entrance Filter 1": { "boardType": "Serial", "motor Address": 51, "Reference Position (steps)": 0, "Steps Per Unit": 1.0, }, "Entrance Filter 2": { "boardType": "Serial", "motor Address": 52, "Reference Position (steps)": 0, "Steps Per Unit": 1.0, }, "Grating Motor": { "boardType": "Serial", "motor Address": 61, "Reference Position (steps)": -4091971, "Steps Per Unit": 1316.0, }, "Holographic Notch Filter": { "boardType": "Serial", "motor Address": 62, "Reference Position (steps)": -4000000, "Steps Per Unit": 1316.0, }, "Laser Shutter": { "boardType": "Serial", "motor Address": 7, "Reference Position (steps)": -4475, "Steps Per Unit": -2544.0, }, "ND Set Flag 1": { "boardType": "Serial", "motor Address": 31, "Reference Position (steps)": -5000, "Steps Per Unit": 3891.0, }, "ND Set Flag 2": { "boardType": "Serial", "motor Address": 32, "Reference Position (steps)": -10000, "Steps Per Unit": -3954.0, }, "ND Set Flag 3": { "boardType": "Serial", "motor Address": 33, "Reference Position (steps)": -10000, "Steps Per Unit": -4182.0, }, "ND Set Flag 4": { "boardType": "Serial", "motor Address": 34, "Reference Position (steps)": -5000, "Steps Per Unit": 3979.0, }, "Pinhole": { "boardType": "Serial", "motor Address": 27, "Reference Position (steps)": -7650, "Steps Per Unit": -2700.0, }, "Podule AStop": { "boardType": "Serial", "motor Address": 37, "Reference Position (steps)": 0, "Steps Per Unit": -1.0, }, "Podule FStop": { "boardType": "Serial", "motor Address": 39, "Reference Position (steps)": 0, "Steps Per Unit": -1.0, }, "Podule Lower Selector Wheel": { "boardType": "Serial", "motor Address": 44, "Reference Position (steps)": 0, "Steps Per Unit": 1.0, }, "Podule Silicon Ref tilt": { "boardType": "Serial", "motor Address": 35, "Reference Position (steps)": 0, "Steps Per Unit": 1.0, }, "Podule Upper Selector Wheel": { "boardType": "Serial", "motor Address": 43, "Reference Position (steps)": 0, "Steps Per Unit": 1.0, }, "Post Beam Expander Axis 1": { "boardType": "Serial", "motor Address": 19, "Reference Position (steps)": 0, "Steps Per Unit": 1.0, }, "Post Beam Expander Axis 2": { "boardType": "Serial", "motor Address": 20, "Reference Position (steps)": 0, "Steps Per Unit": 1.0, }, "Post slit lensfocus": { "boardType": "Serial", "motor Address": 83, "Reference Position (steps)": -64000, "Steps Per Unit": -3200.0, }, "Pre Beam Expander Axis 1": { "boardType": "Serial", "motor Address": 21, "Reference Position (steps)": 0, "Steps Per Unit": 1.0, }, "Pre Beam Expander Axis 2": { "boardType": "Serial", "motor Address": 22, "Reference Position (steps)": 0, "Steps Per Unit": 1.0, }, "Pre slit lensfocus": { "boardType": "Serial", "motor Address": 82, "Reference Position (steps)": -64000, "Steps Per Unit": -3200.0, }, "Slit Master": { "boardType": "Serial", "motor Address": 2, "Reference Position (steps)": 0, "Steps Per Unit": 6.144, }, "Slit Slave": { "boardType": "Serial", "motor Address": 3, "Reference Position (steps)": 0, "Steps Per Unit": 6.144, }, "Waveplate Motor": { "boardType": "Serial", "motor Address": 50, "Reference Position (steps)": -6880, "Steps Per Unit": 932.0, }, "XYZ Stage X Motor": { "boardType": "Serial", "motor Address": 12, "Reference Position (steps)": -3867487, "Steps Per Unit": 10.0, }, "XYZ Stage Y Motor": { "boardType": "Serial", "motor Address": 13, "Reference Position (steps)": -3376226, "Steps Per Unit": -10.0, }, "XYZ Stage Z Motor": { "boardType": "Serial", "motor Address": 14, "Reference Position (steps)": -3802311, "Steps Per Unit": -10.0, }, }, "Slits": { "325nm_PL": { "Regular beam centre": "1730.7µm", "Regular opening": "65.0µm", } }, } assert expected_WXCS == self.s.original_metadata.WXCS_0.as_dictionary() def test_original_metadata_WXDM(self): expected_WXDM = { "ExportToSPC": 1, "ExportToTXT": 1, "extra_matches": { "sub0": { "subdicts": { "sub0": { "subdicts": { "sub0": { "сlsid": "{F22A2AF6-94E0-4814-B38B-68C824427192}", "LensSetID": 2, "id": 0, "detID": 1, } }, "сlsid": "{9E341908-F390-4472-82EA-F7EC3CD5E020}", "slitBias": 0.0, "slitOpening": 10.0, "NDPercent": 100.0, "BeamDefocus": 0.0, "PoduleUpper": 1, "PoduleLower": 3, "ShutterOpen": 1, "Pinhole_In": 0, "CalLamp_On": 0, "CalLamp_Intensity": 100, "IllumLamp_On": 0, "IllumLamp_Intensity": 100, "NeonLamp_On": 0, "linefocus_In": 0, "WaveplatePos": 0.0, "PodulePath": 2, "RunSilent": 0, "FOPMirrorPos": 1, "Lightpath": "", "LT_Filter_ND_IN": 0, "LT_Filter_Position": 1, }, "sub1": { "subdicts": { "sub0": { "сlsid": "{F22A2AF6-94E0-4814-B38B-68C824427192}", "LensSetID": 2, "id": 0, "detID": 1, }, "sub1": { "сlsid": "{6493207B-3132-46CC-BBE3-C915C277E83B}", "_nitems": 0, "ReadOnlyFlag": 0, }, }, "сlsid": "{065E4E4C-46D7-495D-A42B-02776B9B1EB7}", "Centre Wavenumber": 330.5873, "First Wavenumber": 286.826903499603, "Last Wavenumber": 373.035963708188, "DefaultRangeIsOverriden": 0, "scan Area Key": {}, "X Binning": 1, "y Binning": 31, "Accumulations": 2, "Exposure Time": 180000, "Units": 3, "monitoring": 1, "use MultiTrack": 0, "Use Cosmic Ray Remove": 1, "Camera Gain High": 1, "Camera Speed High": 0, "using WiRE2 Diagnostics": 1, "save Data As Single Spectrum": 0, "use Area Binning": 0, "Use Pixel intensity": 1, "nMapScans": 1, "useResponse": 0, "ignoreZelDac": 0, "SoftTriggers": 0, "track": 1, "useFullArea": 0, "mtrSteps": {}, "CloseLSForRead": 0, "MatchOverlap": 0, "MatchOverlapMultiplicative": 1, "DisableLiveTrackDuringStepAndRepeat": 0, "UseEMGain": 0, "EMGainValue": 0, "StreamSpotChargeClearThreshold": 1000, "detectorChannelIndex": 1, "SaturationProtectionLimit": 0, "use fast time series": 0, "time series count": 0, "Discard rows": 0, "time series delay": 0, "do infinite time series": 0, }, }, "сlsid": "{EA41D175-63DA-11D5-84E9-009027FE0FB4}", "_nitems": 2, "_key0": "InstrumentState", "_key1": "Scan", "Scan": {}, }, "sub1": { "subdicts": { "sub0": { "сlsid": "{D9303A2E-17E8-416C-AA67-9B0B4B2D8A19}", "Count": 0, "ReadOnly": 0, } }, "сlsid": "{C0795962-BCD1-4C1E-9A6D-D22CC237B73C}", "_nitems": 18, "_key0": "AcquisitionCount", "_key1": "closeLaserShutter", "_key2": "CreationTime", "_key3": "cycling", "cycling": 0, "_key4": "DepthSeriesStartPos", "_key5": "ETA", "_key6": "HWND", "HWND": 1707512, "_key7": "LUT_Auto", "LUT_Auto": -1, "_key8": "MeasurementType", "_key9": "minimizeLaserExposure", "minimizeLaserExposure": 0, "_key10": "Operator", "_key11": "PlugIns", "PlugIns": {}, "_key12": "queueHandle", "queueHandle": 214, "_key13": "responseCalibration", "_key14": "restoreInstrumentState", "_key15": "useExternalSignalMapping", "useExternalSignalMapping": 0, "_key16": "usePerformanceQualification", "usePerformanceQualification": 0, "_key17": "wizardclsid", }, }, } assert expected_WXDM == self.s.original_metadata.WXDM_0.as_dictionary() def test_original_metadata_WXDA(self): expected_WXDA = { "ScanDuration(ms)": 720530, "CCD Status 1": 1, "CCD Status 2": 1, "lastScanCompletionStatus": "Incomplete", "AutoExportErrorCode": 0, "AutoExportTxtError": "No Error", "AutoExportSpcError": "No Error", "Use CV mode": 0, "CentrusMapIndex": 1, "abortState": 0, "CCD firmware version": "4.99", "CCD not emulating": 1, "CCD serial number": "2URV61", "CCD SYSID": 17051001, "cycling": 0, "InterlockChainAtEnd": 221, "InterlockOKEnd": 0, "InterlockOKStart": 1, "InterlockPeripheralsAtEnd": 0, "InterlockRelaysEnd": -1, "InterlockRelaysStart": 3, "LUT_Auto": -1, "minimizeLaserExposure": 0, "PlugIns": {}, "SaturationProtectionUsed": 0, "SequenceDurationMS": 2098, "UnsaturatedExposureTime": 0, "UnsaturatedNDPercent": 0, "useExternalSignalMapping": 0, "usePerformanceQualification": 0, "ErrorSource": "No error", "ErrorDescription": "No error", "ErrorLine": 0, "MultiMeasurementAbort": 0, "ScanRangeOverridden": 0, } assert expected_WXDA == self.s.original_metadata.WXDA_0.as_dictionary() def test_original_metadata_ZLDC(self): expected_ZLDC = { "Type": "ZeroLevelAndDarkCurrent", "ProcessingOperation": -1, "ReadOnly": -1, } assert expected_ZLDC == self.s.original_metadata.ZLDC_0.as_dictionary() def test_original_metadata_WARP(self): expected_WARP0 = {"ProcessingOperation": 1, "SpectrumIndex": -1} expected_WARP1 = {"ProcessingOperation": 1, "SpectrumIndex": -1} assert expected_WARP0 == self.s.original_metadata.WARP_0.as_dictionary() assert expected_WARP1 == self.s.original_metadata.WARP_1.as_dictionary() def test_original_metadata_TEXT(self): expected_TEXT = ( "A single scan measurement generated by the " "WiRE spectral acquisition wizard." ) assert expected_TEXT == self.s.original_metadata.TEXT_0 def test_original_metadata_ORGN(self): expected_ORGN = { "Time": { "units": "ns", "annotation": "Time", "data": np.array([0], dtype=np.int64), }, "BitFlags": { "units": "", "annotation": "Flags", "data": np.array([0.0]), }, "SpectrumDataChecksum": { "units": "", "annotation": "Checksum", "data": np.array([0.0]), }, } assert expected_ORGN == self.s.original_metadata.ORGN_0.as_dictionary() def test_metadata(self): metadata = deepcopy(self.s.metadata.as_dictionary()) metadata_non_uniform = deepcopy(self.s_non_uniform.metadata.as_dictionary()) assert metadata["General"]["date"] == "2022-02-16" assert metadata["General"]["time"] == "13:01:31" assert metadata["General"]["original_filename"] == "renishaw_test_spectrum.wdf" assert metadata["General"]["title"] == "Single scan measurement 7" assert metadata["Signal"]["quantity"] == "Intensity (Counts)" if importlib.util.find_spec("lumispy") is None: signal_type = "" else: signal_type = "Luminescence" assert metadata["Signal"]["signal_type"] == signal_type assert metadata["Acquisition_instrument"]["Detector"]["detector_type"] == "CCD" assert metadata["Acquisition_instrument"]["Detector"]["frames"] == 2 assert ( metadata["Acquisition_instrument"]["Detector"]["processing"][ "cosmic_ray_removal" ] == 1 ) np.testing.assert_allclose( metadata["Acquisition_instrument"]["Detector"]["integration_time"], 360 ) assert ( metadata["Acquisition_instrument"]["Detector"]["model"] == "Renishaw Centrus 2URV61" ) assert np.isclose( metadata["Acquisition_instrument"]["Detector"]["temperature"], -70 ) assert np.isclose( metadata["Acquisition_instrument"]["Laser"]["wavelength"], 325, atol=1e-3 ) assert np.isclose( metadata["Acquisition_instrument"]["Spectrometer"]["Grating"][ "groove_density" ], 1200, ) del metadata["General"]["FileIO"] del metadata_non_uniform["General"]["FileIO"] assert metadata_non_uniform == metadata class TestLinescan: @classmethod def setup_class(cls): cls.s = hs.load( testfile_linescan, reader="Renishaw", use_uniform_signal_axis=True, )[0] @classmethod def teardown_class(cls): del cls.s gc.collect() def test_data(self): expected_column0_end = [ 1.4914633, 1.8651184, 0.74636304, 1.120018, -0.7469943, 0.0, ] expected_column0_start = [0.0, 1.1029433, 1.1034185, 0.0] expected_column4_end = [ 0.74573165, 1.4920948, 0.37318152, 1.4933574, 0.7469943, 1.1209648, ] expected_column4_start = [ 0.7349788, 1.4705911, 0.36780614, -0.73592895, ] np.testing.assert_allclose(expected_column0_start, self.s.inav[0].isig[:4]) np.testing.assert_allclose(expected_column0_end, self.s.inav[0].isig[-6:]) np.testing.assert_allclose(expected_column4_start, self.s.inav[-1].isig[:4]) np.testing.assert_allclose(expected_column4_end, self.s.inav[-1].isig[-6:]) assert self.s.data.shape == (5, 40) def test_axes(self): expected_axis = { "axis-0": { "name": "Abs. Distance", "units": "µm", "navigate": True, "size": 5, }, "axis-1": { "name": "Wavelength", "units": "nm", "navigate": False, "size": 40, }, } axes_manager = self.s.axes_manager.as_dictionary() np.testing.assert_allclose(axes_manager["axis-0"].pop("offset"), 0) np.testing.assert_allclose(axes_manager["axis-0"].pop("scale"), 30) np.testing.assert_allclose( axes_manager["axis-1"].pop("offset"), 361.3127556405415 ) np.testing.assert_allclose( axes_manager["axis-1"].pop("scale"), 0.08534686462516697 ) for key in axes_manager.keys(): axes_manager[key].pop("_type", None) axes_manager[key].pop("is_binned", None) assert axes_manager == expected_axis class TestMap: @classmethod def setup_class(cls): cls.s = hs.load( testfile_map, reader="Renishaw", use_uniform_signal_axis=True, )[0] @classmethod def teardown_class(cls): del cls.s gc.collect() def test_data(self): expected_data_00_end = [ 1.3878582, 1.3884968, 2.0837028, 1.3897737, 2.0856183, ] expected_data_00_start = [ 2.722048, 2.3829105, ] np.testing.assert_allclose( expected_data_00_start, self.s.inav[0, 0].isig[:2].data ) np.testing.assert_allclose( expected_data_00_end, self.s.inav[0, 0].isig[-5:].data ) expected_data_10_end = [ 0.34696454, 2.082745, 1.3891352, 2.7795475, 0.6952061, ] expected_data_10_start = [ 1.361024, 2.0424948, ] np.testing.assert_allclose( expected_data_10_start, self.s.inav[1, 0].isig[:2].data ) np.testing.assert_allclose( expected_data_10_end, self.s.inav[1, 0].isig[-5:].data ) expected_data_01_end = [ 1.3878582, 2.7769935, 1.3891352, 2.0846605, 2.0856183, ] expected_data_01_start = [ 0.680512, 1.702079, ] np.testing.assert_allclose( expected_data_01_start, self.s.inav[0, 1].isig[:2].data ) np.testing.assert_allclose( expected_data_01_end, self.s.inav[0, 1].isig[-5:].data ) expected_data_22_end = [ 1.3878582, 0.6942484, 0.6945676, 0.0, 1.0428091, ] expected_data_22_start = [ 0.680512, 1.3616632, ] np.testing.assert_allclose( expected_data_22_start, self.s.inav[2, 2].isig[:2].data ) np.testing.assert_allclose( expected_data_22_end, self.s.inav[2, 2].isig[-5:].data ) assert self.s.data.shape == (3, 3, 47) def test_axes(self): expected_axis = { "axis-0": { "name": "Y", "units": "µm", "navigate": True, "size": 3, }, "axis-1": { "name": "X", "units": "µm", "navigate": True, "size": 3, }, "axis-2": { "name": "Wavelength", "units": "nm", "navigate": False, "size": 47, }, } axes_manager = self.s.axes_manager.as_dictionary() np.testing.assert_allclose(axes_manager["axis-0"].pop("offset"), -100) np.testing.assert_allclose(axes_manager["axis-0"].pop("scale"), 100) np.testing.assert_allclose(axes_manager["axis-1"].pop("offset"), -100) np.testing.assert_allclose(axes_manager["axis-1"].pop("scale"), 100) np.testing.assert_allclose( axes_manager["axis-2"].pop("offset"), 346.7724758716342 ) np.testing.assert_allclose(axes_manager["axis-2"].pop("scale"), 0.0848807) for key in axes_manager.keys(): axes_manager[key].pop("_type", None) axes_manager[key].pop("is_binned", None) assert expected_axis == axes_manager class TestZscan: @classmethod def setup_class(cls): cls.s = hs.load( testfile_zscan, reader="Renishaw", use_uniform_signal_axis=True, ) @classmethod def teardown_class(cls): del cls.s gc.collect() def test_axes(self): axes_manager = self.s.axes_manager.as_dictionary() assert len(axes_manager) == 2 z_axis = axes_manager.pop("axis-0") expected_axis = { "_type": "UniformDataAxis", "name": "Z", "units": "µm", "navigate": True, "is_binned": False, "size": 40, } np.testing.assert_allclose(z_axis.pop("scale"), 0.5) np.testing.assert_allclose(z_axis.pop("offset"), -10) assert z_axis == expected_axis assert axes_manager["axis-1"]["units"] == "1/cm" assert axes_manager["axis-1"]["name"] == "Raman Shift" def test_data(self): np.testing.assert_allclose(self.s.inav[0].isig[:3].data, [0, 0, 0]) np.testing.assert_allclose(self.s.inav[0].isig[-3:].data, [0, 0, 0]) np.testing.assert_allclose( self.s.inav[-1].isig[-3:].data, [1.8109605, -1.8113279, 9.05664] ) np.testing.assert_allclose( self.s.inav[-1].isig[:3].data, [1.454424, -1.4547517, 4.365239] ) def test_measurement_type(self): assert self.s.original_metadata.WDF1_1.measurement_type == "Series" class TestUndefined: @classmethod def setup_class(cls): cls.s = hs.load( testfile_undefined, reader="Renishaw", use_uniform_signal_axis=True, ) @classmethod def teardown_class(cls): del cls.s gc.collect() def test_data(self): np.testing.assert_allclose( self.s.isig[-3:].data, [262.90552, 262.82877, 262.752] ) np.testing.assert_allclose( self.s.isig[:3].data, [349.54773, 349.45215, 349.3566] ) def test_measurement_type(self): assert self.s.original_metadata.WDF1_1.measurement_type == "Unspecified" class TestStreamline: @classmethod def setup_class(cls): cls.s = hs.load( testfile_streamline, reader="Renishaw", use_uniform_signal_axis=True, )[0] @classmethod def teardown_class(cls): del cls.s gc.collect() def test_data(self): np.testing.assert_allclose( self.s.inav[0, 0].isig[:3].data, [418.35907, 424.54782, 409.82785] ) np.testing.assert_allclose( self.s.inav[44, 48].isig[-3:].data, [587.48083, 570.73505, 583.5814] ) def test_WHTL(self): s = hs.load( testfile_streamline, reader="Renishaw", )[1] expected_WTHL = { "FocalPlaneResolutionUnit": 5, "FocalPlaneXResolution": 445.75, "FocalPlaneYResolution": 270.85, "FocalPlaneXYOrigins": (-8325.176, -1334.639), "ExifOffset": 114, "ImageDescription": "white-light image", "Make": "Renishaw", "Unknown": 20.0, "FieldOfViewXY": (8915.0, 5417.0), } for i, (axis, scale) in enumerate( zip(s.axes_manager._axes, (1.1285417, 1.1855053)) ): assert axis.units == "µm" np.testing.assert_allclose(axis.scale, scale) np.testing.assert_allclose( axis.offset, expected_WTHL["FocalPlaneXYOrigins"][::-1][i] ) metadata_WHTL = s.original_metadata.as_dictionary()["exif_tags"] assert metadata_WHTL == expected_WTHL md = s.metadata.Markers.as_dictionary() np.testing.assert_allclose( md["Map"]["kwargs"]["offsets"], [-8041.7998, -1137.6001], ) np.testing.assert_allclose(md["Map"]["kwargs"]["widths"], 116.99999) np.testing.assert_allclose(md["Map"]["kwargs"]["heights"], 127.39999) def test_original_metadata_WMAP(self): expected_WMAP = { "linefocus_size": 0, "flag": "column_major", } metadata_WMAP = deepcopy(self.s.original_metadata.WMAP_0.as_dictionary()) np.testing.assert_allclose( metadata_WMAP.pop("offset_xyz"), [-8100.3, -1201.3, 0.0] ) np.testing.assert_allclose(metadata_WMAP.pop("scale_xyz"), [2.6, 2.6, 1.0]) np.testing.assert_allclose(metadata_WMAP.pop("size_xyz"), [45, 49, 1]) assert expected_WMAP == metadata_WMAP def test_original_metadata_WDF1(self): expected_WDF1 = { "flags": 0, "uuid": "1899852918-1261200088-3066841267-2010995264", "ntracks": 0, "file_status_error_code": 0, "capacity": 2205, "accumulations_per_spectrum": 1, "XLST_length": 394, "app_name": "WiRE", "app_version": "4-2-0-5037", "scan_type": "StreamLine", "time_start": "2017-10-05#11:17:33", "time_end": "2017-10-05#11:21:24", "quantity_unit": "counts", "username": "Raman", "title": "StreamLine image acquisition 5", "points_per_spectrum": 394, "num_spectra": 2205, "YLST_length": 1, "num_ORGN": 5, "measurement_type": "Mapping", } metadata_WDF1 = deepcopy(self.s.original_metadata.WDF1_1.as_dictionary()) np.testing.assert_allclose(metadata_WDF1.pop("laser_wavenumber"), 12738.9) assert metadata_WDF1 == expected_WDF1 class TestMapBlock: @classmethod def setup_class(cls): cls.s = hs.load( testfile_map_block, reader="Renishaw", use_uniform_signal_axis=True, )[0] @classmethod def teardown_class(cls): del cls.s gc.collect() def test_original_metadata_MAP(self): metadata_MAP0 = self.s.original_metadata.MAP_0 assert metadata_MAP0.npoints == 400 assert metadata_MAP0.guid == "{57AAA72E-55A7-4F79-9FE3-EB4603813AB9}" np.testing.assert_allclose(metadata_MAP0.dataRange, [45.172123, 719.9313]) np.testing.assert_allclose( metadata_MAP0.data[:3], [66.674965, 62.949856, 107.18564] ) np.testing.assert_allclose( metadata_MAP0.data[-3:], [381.15073, 593.5397, 431.03043] ) assert len(metadata_MAP0.data) == 400 metadata_MAP1 = self.s.original_metadata.MAP_1 assert metadata_MAP1.npoints == 400 assert metadata_MAP1.guid == "{6cf9115b-c452-404f-b0f2-e654d9a05aea}" np.testing.assert_allclose(metadata_MAP1.dataRange, [42.882656, 518.5028]) np.testing.assert_allclose( metadata_MAP1.data[:3], [53.033577, 54.36599, 81.270424] ) np.testing.assert_allclose( metadata_MAP1.data[-3:], [224.7265, 380.83423, 261.48608] ) assert len(metadata_MAP1.data) == 400 class TestTimeseries: @classmethod def setup_class(cls): cls.s = hs.load( testfile_timeseries, reader="Renishaw", use_uniform_signal_axis=True, ) @classmethod def teardown_class(cls): del cls.s gc.collect() def test_axes(self): axes_manager = self.s.axes_manager.as_dictionary() assert len(axes_manager) == 2 time_axis = axes_manager.pop("axis-0") np.testing.assert_allclose(time_axis["scale"], 3.1e7, atol=1e6) np.testing.assert_allclose(time_axis["offset"], 0) def test_data(self): np.testing.assert_allclose( self.s.inav[0].isig[:3].data, [3714.725, 3475.6548, 3458.7114] ) np.testing.assert_allclose( self.s.inav[-1].isig[-3:].data, [5167.7383, 5379.82, 5174.1406] ) class TestFocusTrack: @classmethod def setup_class(cls): cls.s = hs.load( testfile_focustrack, reader="Renishaw", use_uniform_signal_axis=True, ) @classmethod def teardown_class(cls): del cls.s gc.collect() def test_axes(self): axes_manager = self.s.axes_manager.as_dictionary() assert len(axes_manager) == 2 z_axis = axes_manager.pop("axis-0") # As hyperspy doesn't support non-ordered axis, default axis are used np.testing.assert_allclose(z_axis["scale"], 1, atol=0.1) np.testing.assert_allclose(z_axis["offset"], 0, atol=0.5) def test_data(self): np.testing.assert_allclose( self.s.inav[0].isig[:3].data, [1.4015186, 1.402039, -0.7012797] ) np.testing.assert_allclose( self.s.inav[-1].isig[-3:].data, [4.8724666, 5.8486896, 3.8991265] ) def test_focus_track_invariant(): s = hs.load(testfile_focustrack_invariant) assert s.data.shape == (10, 1010) z_axis = s.axes_manager[0] assert z_axis.scale == 1 assert z_axis.offset == 0 assert str(z_axis.units) == "" class TestPSETMetadata: data_directory = ( Path(__file__).parent / "data" / "renishaw" / "generated_files" ).resolve() def get_filepath(self, filename): return (self.data_directory / filename).resolve() @classmethod def setup_class(cls): pass @classmethod def teardown_class(cls): shutil.rmtree(cls.data_directory) gc.collect() def test_pset_flat_normal(self): filepath = self.get_filepath("test_renishaw_pset_flat_normal.bin") wdf = WDFFileHandler(filepath) wdf.write_file(WDFFileGenerator.generate_flat_normal_testfile) data = wdf.read_file() expected_result = { "TEST_0": { "single->key": -12, "key->single": 46, "order1": 72, "order3": 347, "order2": 379, "order5": "1601-01-01#00:00:00", "key for test string": "test string 123", "key for binary": "binary: 62696E61727920737472696E6720313233", } } np.testing.assert_allclose(data["TEST_0"].pop("order4"), 74.7843) np.testing.assert_allclose(data["TEST_0"].pop("order6"), -378.36) assert data == expected_result def test_pset_nested_normal(self): filepath = self.get_filepath("test_renishaw_pset_nested_normal.bin") wdf = WDFFileHandler(filepath) wdf.write_file(WDFFileGenerator.generate_nested_normal_testfile) data = wdf.read_file() expected_result = { "TEST_0": { "pair_before_nested": -10, "key_before_nested": 87, "nested1": { "pair_in_nested": 40891, "pair_in_nested_doubled_key": -8279, }, "val_before_nested": 17, "nested2": { "pair_in_nested_doubled_key": 43, "nested3": {"pair_in_double_nested": -123}, "nested4": {}, }, } } assert expected_result == data def test_pset_flat_array_compressed(self): filepath = self.get_filepath("test_renishaw_pset_flat_array_compressed.bin") wdf = WDFFileHandler(filepath) wdf.write_file(WDFFileGenerator.generate_flat_array_compressed) data = wdf.read_file() expected_result = { "TEST_0": { "compressed": None, } } np.testing.assert_allclose(data["TEST_0"].pop("array"), np.arange(1, 11, 1)) assert expected_result == data class TestIntegrationtime: @classmethod def setup_class(cls): cls.s_11 = hs.load( testfile_acc1_exptime1, reader="Renishaw", use_uniform_signal_axis=False, ) cls.s_21 = hs.load( testfile_acc2_exptime1, reader="Renishaw", use_uniform_signal_axis=False, ) cls.s_110 = hs.load( testfile_acc1_exptime10, reader="Renishaw", use_uniform_signal_axis=False, ) @classmethod def teardown_class(cls): del cls.s_11 del cls.s_21 del cls.s_110 gc.collect() def test_frames(self): assert self.s_11.metadata.Acquisition_instrument.Detector.frames == 1 assert self.s_110.metadata.Acquisition_instrument.Detector.frames == 1 assert self.s_21.metadata.Acquisition_instrument.Detector.frames == 2 def test_integration_time(self): np.testing.assert_allclose( self.s_11.metadata.Acquisition_instrument.Detector.integration_time, 1 ) np.testing.assert_allclose( self.s_110.metadata.Acquisition_instrument.Detector.integration_time, 10 ) np.testing.assert_allclose( self.s_21.metadata.Acquisition_instrument.Detector.integration_time, 2 )