# -*- coding: utf-8 -*- # Copyright 2007-2023 The HyperSpy developers # # This file is part of RosettaSciIO. # # RosettaSciIO 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. # # RosettaSciIO 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 RosettaSciIO. If not, see . import gc import importlib.util from copy import deepcopy from pathlib import Path import numpy as np import pytest hs = pytest.importorskip("hyperspy.api", reason="hyperspy not installed") TEST_DATA_PATH = Path(__file__).parent / "data" / "trivista" testfile_spec_path = TEST_DATA_PATH / "spec_1s_1acc_1frame_average.tvf" testfile_spec_2frames_path = TEST_DATA_PATH / "spec_3s_1acc_2frames_average.tvf" testfile_spec_2acc_path = TEST_DATA_PATH / "spec_3s_2acc_1frame_average.tvf" testfile_spec_2acc_no_average_path = ( TEST_DATA_PATH / "spec_3s_2acc_1frame_no_average.tvf" ) testfile_spec_timeseries_path = TEST_DATA_PATH / "spec_timeseries_2x1s_delta3s.tvf" testfile_map_path = TEST_DATA_PATH / "map.tvf" testfile_step_and_glue_path = TEST_DATA_PATH / "spec_step_and_glue.tvf" testfile_triple_add_path = TEST_DATA_PATH / "spec_multiple_spectrometers.tvf" testfile_linescan_path = TEST_DATA_PATH / "linescan.tvf" if importlib.util.find_spec("lumispy") is None: lumispy_installed = False else: lumispy_installed = True class TestSpec: @classmethod def setup_class(cls): cls.s = hs.load( testfile_spec_path, reader="TriVista", use_uniform_signal_axis=True, filter_original_metadata=True, ) cls.s_non_uniform_unfiltered = hs.load( testfile_spec_path, reader="TriVista", use_uniform_signal_axis=False, filter_original_metadata=False, ) @classmethod def teardown_class(cls): del cls.s del cls.s_non_uniform_unfiltered gc.collect() def test_data(self): expected_data = np.array([27732, 39135, 35343, -420, 32464]) np.testing.assert_allclose(expected_data, self.s.isig[:5].data) np.testing.assert_allclose( expected_data, self.s_non_uniform_unfiltered.isig[:5].data ) def test_axes(self): expected_axis = { "axis-0": { "_type": "UniformDataAxis", "name": "Wavelength", "units": "nm", "navigate": False, "is_binned": False, "size": 1024, } } expected_axis_non_uniform = { "axis-0": { "_type": "DataAxis", "name": "Wavelength", "units": "nm", "navigate": False, "is_binned": False, } } expected_values_non_uniform_axis = np.array( [794.220731002166, 794.261531331698, 794.302331149879] ) uniform_axes_manager = deepcopy(self.s.axes_manager.as_dictionary()) non_uniform_axis_manager = deepcopy( self.s_non_uniform_unfiltered.axes_manager.as_dictionary() ) np.testing.assert_allclose( uniform_axes_manager["axis-0"].pop("scale"), 0.040515, atol=0.000005 ) np.testing.assert_allclose( uniform_axes_manager["axis-0"].pop("offset"), 794.22, atol=0.1 ) np.testing.assert_allclose( expected_values_non_uniform_axis, non_uniform_axis_manager["axis-0"].pop("axis")[:3], ) assert expected_axis == uniform_axes_manager assert expected_axis_non_uniform == non_uniform_axis_manager def test_metadata(self): metadata = deepcopy(self.s.metadata.as_dictionary()) metadata_non_uniform = deepcopy( self.s_non_uniform_unfiltered.metadata.as_dictionary() ) assert metadata["General"]["FileIO"]["0"]["io_plugin"] == "rsciio.trivista" assert ( metadata_non_uniform["General"]["FileIO"]["0"]["io_plugin"] == "rsciio.trivista" ) assert metadata["General"]["date"] == "2022-06-14" assert ( metadata["General"]["original_filename"] == "spec_1s_1acc_1frame_average.tvf" ) assert metadata["General"]["time"] == "13:34:27" assert ( metadata["General"]["title"] == metadata["General"]["original_filename"][:-4] ) assert metadata["Signal"]["quantity"] == "Intensity (Counts)" if lumispy_installed: assert metadata["Signal"]["signal_type"] == "Luminescence" else: assert metadata["Signal"]["signal_type"] == "" assert metadata["Acquisition_instrument"]["Detector"]["glued_spectrum"] is False assert ( metadata["Acquisition_instrument"]["Detector"]["processing"]["calc_average"] == "True" ) np.testing.assert_allclose( metadata["Acquisition_instrument"]["Detector"]["exposure_per_frame"], 1 ) np.testing.assert_allclose( metadata["Acquisition_instrument"]["Detector"]["frames"], 1 ) np.testing.assert_allclose( metadata["Acquisition_instrument"]["Detector"]["integration_time"], 1 ) np.testing.assert_allclose( metadata["Acquisition_instrument"]["Detector"]["temperature"], -25 ) np.testing.assert_allclose( metadata["Acquisition_instrument"]["Laser"]["objective_magnification"], 100 ) assert ( metadata["Acquisition_instrument"]["Spectrometer"]["Grating"][ "blazing_wavelength" ] == "H-NIR" ) np.testing.assert_allclose( metadata["Acquisition_instrument"]["Spectrometer"]["Grating"][ "groove_density" ], 750, ) np.testing.assert_allclose( metadata["Acquisition_instrument"]["Spectrometer"]["central_wavelength"], 815, ) np.testing.assert_allclose( metadata["Acquisition_instrument"]["Spectrometer"]["entrance_slit_width"], 0.2, ) np.testing.assert_allclose( metadata["Acquisition_instrument"]["Spectrometer"]["exit_slit_width"], 0 ) assert ( metadata["Acquisition_instrument"]["Spectrometer"]["model"] == "SP-2-750i" ) del metadata["General"]["FileIO"] del metadata_non_uniform["General"]["FileIO"] assert metadata == metadata_non_uniform def test_original_metadata(self): expected_metadata = { "XmlMain": { "Version": "1.0.1", "Filename": "C:\\Users\\optik\\Desktop\\Testspectrum.tvf", "DateTime": "06/14/2022 13:35:01", "PlugInName": "", "PlugInData": "", "FileInfoSerialized": {"Info": {"Groups": None}}, }, "Document": { "Version": "2", "Label": "Intensity", "DataLabel": "Counts", "DocType": "Spectra", "RecordTime": "06/14/2022 13:34:27.453", "ModeName": "", "DataSource": "nothing", "Encoding": "Ascii", "ColorMode": "Grayscale", "ViewDisplayMode": "Graph", "ViewImageColorMode": "False", "InfoSerialized": { "Document": {"Record Time": "6/14/2022 1:34 PM"}, "Experiment": {"Used Setup": "PL_Stage3_750g"}, "Spectrometers": { "Spectrometer": { "Serialnumber": "27580185", "Model": "SP-2-750i", "Stage_Number": "1", "Focallength": "749", "Inclusion_Angle": "6.5", "Detector_Angle": "0.68", "Groove_Density": "750 g/mm", "Order": "1", "Slit_Entrance-Front": "200", "Slit_Entrance-Side": "0", "Slit_Exit-Front": "0", "Slit_Exit-Side": "0", } }, "Detector": { "Name": "Camera1", "Serialnumber": None, "Detector_Size": "1024;1", "Detector_Temperature": "-25", "Exposure_Time_(ms)": "1000", "Exposure_Mode": None, "No_of_Accumulations": "1", "Calc_Average": "True", "No_of_Frames": "1", "ADC__Readout_Port": "Normal", "ADC__Rate_Resolution": "1 MHz", "ADC__Gain": "2", "Clearing__Mode": None, "Clearing__No_of_Cleans": "1", "Region_of_Interests": "1|1;1024;1;1;1;1", }, "Calibration": { "Center_Wavelength": "815.000", "Laser_Wavelength": "0.000", }, }, }, "Hardware": { "Spectrometers": { "Spectrometer": { "Gratings": { "Grating": { "Offsets": {"Count": "0"}, "GrooveDensity": "750 g/mm", "Blaze": "H-NIR", "Turret": "1", }, "Count": "3", }, "MirrorEntrance": { "Name": "M1", "State": "isMotorized", "Position": "front", }, "MirrorExit": { "Name": "M2", "State": "isMotorized", "Position": "side", }, "SlitEntranceSide": { "Name": "S1", "State": "isMotorized", "MaxWidth": "12000", "Position": "0", }, "SlitEntranceFront": { "Name": "S2", "State": "isMotorized", "MaxWidth": "12000", "Position": "500", }, "SlitExitFront": { "Name": "S3", "State": "disabled", "MaxWidth": "12000", "Position": "0", }, "SlitExitSide": { "Name": "S4", "State": "disabled", "MaxWidth": "12000", "Position": "0", }, "FilterWheel": { "Name": "", "State": "disabled", "Position": "0", "FilterStrings": "6|#1|#2|#3|#4|#5|#6", }, "Shutter": { "Name": "", "State": "disabled", "Position": "open", "ShutterMode": "OpenForExperiment", "ShutterClosedForFilterwheel": "True", "ShutterClosedForSetupChange": "True", "ShutterClosedForLaserCrossing": "True", "ShutterClosedForLaserCrossingValue": "0.000", "ShutterClosedForLaserCrossingUnit": "Nanometer", }, "GUID": "37a2855b-db41-4268-970b-bb75d96e5654", "Model": "SP-2-750i", "Serialnumber": "27580185", "FocalLength": "749", "InclusionAngle": "6.500", "InclusionAngleAdditive": "39.000", "DetectorAngle": "0.680", "PixelWidthExitFront": "25.000", "PixelWidthExitSide": "-1.000", "Backlash": "ScanUp", "DriveDirection": "Normal", "ComPortSpec": "COM5", "ComPortEntrance": "", "ComPortExit": "", "DemoMode": "False", "UsedAsLightsource": "False", "UseBackwards": "False", "Wavelength": "850.184", "Grating": "2", "ReadTimeout": "35000", "Activated": "False", "IsFixedCalibration": "False", "FixedCalibrationPoints": "0", }, "Count": "3", }, "Detectors": { "Detector": { "GUID": "c1bc9fd2-135e-4098-b681-d30f6ea8be82", "Driver": "PvCam32 Driver", "Name": "Camera1", "DisplayName": "Camera1", "SerialNumber": "", "DetectorType": "None", "Size": "1024;1", "OpenAtStartup": "False", "Usage": "Default", }, "Count": "3", }, "SinglePointDetectors": {"Count": "0"}, "LightSources": { "LightSource": [ { "Wavelengths": {"Count": "1", "Value_0": "0.000"}, "GUID": "a57ac71a-c667-4501-a24a-596bc54b2c8c", "Name": "Calibration Lamp", "Serialnumber": "", "FixedWavelength": "True", "CanChange": "False", "Type": "CalibrationLamp", "ConnectionString": "None", "IsMirrorPositionValid": "False", "MirrorsAlignmentPositionTop": "0;0", "MirrorsAlignmentPositionBottom": "0;0", }, { "Wavelengths": {"Count": "0"}, "GUID": "cac03351-735e-4592-9bb2-c17f64b3649f", "Name": "Calibration Lamp2", "Serialnumber": "", "FixedWavelength": "True", "CanChange": "False", "Type": "CalibrationLamp", "ConnectionString": "None", "IsMirrorPositionValid": "False", "MirrorsAlignmentPositionTop": "0;0", "MirrorsAlignmentPositionBottom": "0;0", }, { "Wavelengths": {"Count": "0"}, "GUID": "84a08bee-227a-46f0-b1e1-0f171808a155", "Name": "Calibration Lamp3", "Serialnumber": "", "FixedWavelength": "True", "CanChange": "False", "Type": "CalibrationLamp", "ConnectionString": "None", "IsMirrorPositionValid": "False", "MirrorsAlignmentPositionTop": "0;0", "MirrorsAlignmentPositionBottom": "0;0", }, { "Wavelengths": {"Count": "1", "Value_0": "0.000"}, "GUID": "a0601d22-23a0-4587-bb79-35d5823916c4", "Name": "Laser", "Serialnumber": "", "FixedWavelength": "False", "CanChange": "False", "Type": "Laser", "ConnectionString": "None", "IsMirrorPositionValid": "False", "MirrorsAlignmentPositionTop": "0;0", "MirrorsAlignmentPositionBottom": "0;0", }, { "Wavelengths": {"Count": "1", "Value_0": "790.000"}, "GUID": "a36b29da-0d54-4ab7-860c-967269f76217", "Name": "tisa", "Serialnumber": "", "FixedWavelength": "True", "CanChange": "True", "Type": "Laser", "ConnectionString": "None", "IsMirrorPositionValid": "False", "MirrorsAlignmentPositionTop": "0;0", "MirrorsAlignmentPositionBottom": "0;0", }, ], "Count": "5", }, "ArduinoHardware": {"Count": "0"}, "Additionals": {"Count": "0"}, "MotorizedStages": { "MotorizedStage": { "GUID": "c551372e-56af-4686-b7c1-48ca00dfdf27", "DriverName": "Tango Driver", "Name": "XY-Stage", "ConnectionString": "COM15", "Serialnumber": "144012056", "IsTriggerModeAvailable": "False", }, "Count": "1", }, "Microscopes": { "Microscope": { "Objectives": { "Objective": { "IsEnabled": "True", "Name": "100x", "Magnification": "100.000", "FactorMeasuredWithResolution": "1280", "Factor": "34.700", "LaserOffsetX": "0.000", "LaserOffsetY": "0.000", "OffsetX": "0.000", "OffsetY": "0.000", "LineLaserOffsetX": "0.000", "LineLaserOffsetY": "0.000", "LineOffsetX": "0.000", "LineOffsetY": "0.000", "LineFocusFactor": "1.130", }, "Count": "10", }, "GUID": "841bfef9-b969-43f0-9ca3-2522c223a31f", "Name": "Microscope", "StageID": "c551372e-56af-4686-b7c1-48ca00dfdf27", "ImagingCameraID": "", "RamanBoxAvailable": "True", "RamanBoxLinearStage.Available": "False", "RamanBoxLinearStage.ConnectedHarwareID": "", "RamanBoxFilterWheel.Available": "False", "RamanBoxFilterWheel.ConnectedHarwareID": "", "RamanBoxBeamSplitter.Available": "False", "RamanBoxBeamSplitter.ConnectedHarwareID": "", "RamanBoxNotchFilter.Available": "False", "RamanBoxNotchFilter.ConnectedHarwareID": "", "ActiveObjectiveIndex": "0", }, "Count": "2", }, "Cryostats": {"Count": "0"}, "Version": "2", }, } assert expected_metadata == self.s.original_metadata.as_dictionary() def test_unfiltered_original_metadata(self): expected_metadata = { "XmlMain": { "Version": "1.0.1", "Filename": "C:\\Users\\optik\\Desktop\\Testspectrum.tvf", "DateTime": "06/14/2022 13:35:01", "PlugInName": "", "PlugInData": "", "FileInfoSerialized": {"Info": {"Groups": None}}, }, "Document": { "Version": "2", "Label": "Intensity", "DataLabel": "Counts", "DocType": "Spectra", "RecordTime": "06/14/2022 13:34:27.453", "ModeName": "", "DataSource": "nothing", "Encoding": "Ascii", "ColorMode": "Grayscale", "ViewDisplayMode": "Graph", "ViewImageColorMode": "False", "InfoSerialized": { "Info": { "Groups": { "Group": [ { "Name": "Document", "Items": { "Item": { "Name": "Record Time", "Value": "6/14/2022 1:34 PM", "IsVisible": "true", } }, "Groups": None, "IsVisible": "true", }, { "Name": "Experiment", "Items": { "Item": { "Name": "Used Setup", "Value": "PL_Stage3_750g", "IsVisible": "true", } }, "Groups": None, "IsVisible": "true", }, { "Name": "Spectrometers", "Items": None, "Groups": { "Group": { "Name": "Spectrometer", "Items": { "Item": [ { "Name": "Serialnumber", "Value": "27580185", "IsVisible": "true", }, { "Name": "Model", "Value": "SP-2-750i", "IsVisible": "true", }, { "Name": "Stage_Number", "Value": "1", "IsVisible": "true", }, { "Name": "Focallength", "Value": "749", "IsVisible": "true", }, { "Name": "Inclusion_Angle", "Value": "6.5", "IsVisible": "true", }, { "Name": "Detector_Angle", "Value": "0.68", "IsVisible": "true", }, { "Name": "Groove_Density", "Value": "750 g/mm", "IsVisible": "true", }, { "Name": "Order", "Value": "1", "IsVisible": "true", }, { "Name": "Slit_Entrance-Front", "Value": "200", "IsVisible": "true", }, { "Name": "Slit_Entrance-Side", "Value": "0", "IsVisible": "true", }, { "Name": "Slit_Exit-Front", "Value": "0", "IsVisible": "true", }, { "Name": "Slit_Exit-Side", "Value": "0", "IsVisible": "true", }, ] }, "Groups": None, "IsVisible": "true", } }, "IsVisible": "true", }, { "Name": "Detector", "Items": { "Item": [ { "Name": "Name", "Value": "Camera1", "IsVisible": "true", }, { "Name": "Serialnumber", "Value": None, "IsVisible": "true", }, { "Name": "Detector_Size", "Value": "1024;1", "IsVisible": "true", }, { "Name": "Detector_Temperature", "Value": "-25", "IsVisible": "true", }, { "Name": "Exposure_Time_(ms)", "Value": "1000", "IsVisible": "true", }, { "Name": "Exposure_Mode", "Value": None, "IsVisible": "true", }, { "Name": "No_of_Accumulations", "Value": "1", "IsVisible": "true", }, { "Name": "Calc_Average", "Value": "True", "IsVisible": "true", }, { "Name": "No_of_Frames", "Value": "1", "IsVisible": "true", }, { "Name": "ADC__Readout_Port", "Value": "Normal", "IsVisible": "true", }, { "Name": "ADC__Rate_Resolution", "Value": "1 MHz", "IsVisible": "true", }, { "Name": "ADC__Gain", "Value": "2", "IsVisible": "true", }, { "Name": "Clearing__Mode", "Value": None, "IsVisible": "true", }, { "Name": "Clearing__No_of_Cleans", "Value": "1", "IsVisible": "true", }, { "Name": "Region_of_Interests", "Value": "1|1;1024;1;1;1;1", "IsVisible": "true", }, ] }, "Groups": None, "IsVisible": "true", }, { "Name": "Calibration", "Items": { "Item": [ { "Name": "Center_Wavelength", "Value": "815.000", "IsVisible": "true", }, { "Name": "Laser_Wavelength", "Value": "0.000", "IsVisible": "true", }, ] }, "Groups": None, "IsVisible": "true", }, ] } } }, }, "Hardware": { "Spectrometers": { "Spectrometer": [ { "Gratings": { "Grating": [ { "Offsets": {"Count": "0"}, "GrooveDensity": "1800 g/mm", "Blaze": "H-VIS", "Turret": "1", }, { "Offsets": {"Count": "0"}, "GrooveDensity": "900 g/mm", "Blaze": "550NM", "Turret": "1", }, { "Offsets": {"Count": "0"}, "GrooveDensity": "750 g/mm", "Blaze": "H-NIR", "Turret": "1", }, ], "Count": "3", }, "MirrorEntrance": { "Name": "M1", "State": "isMotorized", "Position": "front", }, "MirrorExit": { "Name": "M2", "State": "isMotorized", "Position": "side", }, "SlitEntranceSide": { "Name": "S1", "State": "isMotorized", "MaxWidth": "12000", "Position": "0", }, "SlitEntranceFront": { "Name": "S2", "State": "isMotorized", "MaxWidth": "12000", "Position": "200", }, "SlitExitFront": { "Name": "S3", "State": "isMotorized", "MaxWidth": "12000", "Position": "0", }, "SlitExitSide": { "Name": "S4", "State": "disabled", "MaxWidth": "12000", "Position": "0", }, "FilterWheel": { "Name": "", "State": "disabled", "Position": "0", "FilterStrings": "6|#1|#2|#3|#4|#5|#6", }, "Shutter": { "Name": "", "State": "disabled", "Position": "open", "ShutterMode": "OpenForExperiment", "ShutterClosedForFilterwheel": "True", "ShutterClosedForSetupChange": "True", "ShutterClosedForLaserCrossing": "True", "ShutterClosedForLaserCrossingValue": "0.000", "ShutterClosedForLaserCrossingUnit": "Nanometer", }, "GUID": "c05fbec6-7cc0-4546-a009-06850868f43d", "Model": "SP-2-500i", "Serialnumber": "25580419", "FocalLength": "500", "InclusionAngle": "8.600", "InclusionAngleAdditive": "51.600", "DetectorAngle": "0.000", "PixelWidthExitFront": "-1.000", "PixelWidthExitSide": "-1.000", "Backlash": "ScanUp", "DriveDirection": "Normal", "ComPortSpec": "COM3", "ComPortEntrance": "", "ComPortExit": "", "DemoMode": "False", "UsedAsLightsource": "False", "UseBackwards": "False", "Wavelength": "925.010", "Grating": "2", "ReadTimeout": "35000", "Activated": "False", "IsFixedCalibration": "False", "FixedCalibrationPoints": "0", }, { "Gratings": { "Grating": [ { "Offsets": {"Count": "0"}, "GrooveDensity": "1800 g/mm", "Blaze": "H-VIS", "Turret": "1", }, { "Offsets": {"Count": "0"}, "GrooveDensity": "900 g/mm", "Blaze": "550NM", "Turret": "1", }, { "Offsets": {"Count": "0"}, "GrooveDensity": "750 g/mm", "Blaze": "H-NIR", "Turret": "1", }, ], "Count": "3", }, "MirrorEntrance": { "Name": "M1", "State": "isMotorized", "Position": "side", }, "MirrorExit": { "Name": "M2", "State": "isMotorized", "Position": "side", }, "SlitEntranceSide": { "Name": "S1", "State": "isMotorized", "MaxWidth": "12000", "Position": "10000", }, "SlitEntranceFront": { "Name": "S2", "State": "isMotorized", "MaxWidth": "12000", "Position": "0", }, "SlitExitFront": { "Name": "S3", "State": "isMotorized", "MaxWidth": "12000", "Position": "0", }, "SlitExitSide": { "Name": "S4", "State": "disabled", "MaxWidth": "12000", "Position": "0", }, "FilterWheel": { "Name": "", "State": "disabled", "Position": "0", "FilterStrings": "6|#1|#2|#3|#4|#5|#6", }, "Shutter": { "Name": "", "State": "disabled", "Position": "open", "ShutterMode": "OpenForExperiment", "ShutterClosedForFilterwheel": "True", "ShutterClosedForSetupChange": "True", "ShutterClosedForLaserCrossing": "True", "ShutterClosedForLaserCrossingValue": "0.000", "ShutterClosedForLaserCrossingUnit": "Nanometer", }, "GUID": "39ade9ad-caa8-48c2-a3d0-4f79cc44bda7", "Model": "SP-2-500i", "Serialnumber": "25580420", "FocalLength": "500", "InclusionAngle": "8.600", "InclusionAngleAdditive": "51.600", "DetectorAngle": "0.000", "PixelWidthExitFront": "1.000", "PixelWidthExitSide": "-1.000", "Backlash": "ScanUp", "DriveDirection": "Normal", "ComPortSpec": "COM4", "ComPortEntrance": "", "ComPortExit": "", "DemoMode": "False", "UsedAsLightsource": "False", "UseBackwards": "False", "Wavelength": "-924.910", "Grating": "2", "ReadTimeout": "35000", "Activated": "False", "IsFixedCalibration": "False", "FixedCalibrationPoints": "0", }, { "Gratings": { "Grating": [ { "Offsets": {"Count": "0"}, "GrooveDensity": "1800 g/mm", "Blaze": "H-VIS", "Turret": "1", }, { "Offsets": {"Count": "0"}, "GrooveDensity": "900 g/mm", "Blaze": "550NM", "Turret": "1", }, { "Offsets": {"Count": "0"}, "GrooveDensity": "750 g/mm", "Blaze": "H-NIR", "Turret": "1", }, ], "Count": "3", }, "MirrorEntrance": { "Name": "M1", "State": "isMotorized", "Position": "front", }, "MirrorExit": { "Name": "M2", "State": "isMotorized", "Position": "side", }, "SlitEntranceSide": { "Name": "S1", "State": "isMotorized", "MaxWidth": "12000", "Position": "0", }, "SlitEntranceFront": { "Name": "S2", "State": "isMotorized", "MaxWidth": "12000", "Position": "500", }, "SlitExitFront": { "Name": "S3", "State": "disabled", "MaxWidth": "12000", "Position": "0", }, "SlitExitSide": { "Name": "S4", "State": "disabled", "MaxWidth": "12000", "Position": "0", }, "FilterWheel": { "Name": "", "State": "disabled", "Position": "0", "FilterStrings": "6|#1|#2|#3|#4|#5|#6", }, "Shutter": { "Name": "", "State": "disabled", "Position": "open", "ShutterMode": "OpenForExperiment", "ShutterClosedForFilterwheel": "True", "ShutterClosedForSetupChange": "True", "ShutterClosedForLaserCrossing": "True", "ShutterClosedForLaserCrossingValue": "0.000", "ShutterClosedForLaserCrossingUnit": "Nanometer", }, "GUID": "37a2855b-db41-4268-970b-bb75d96e5654", "Model": "SP-2-750i", "Serialnumber": "27580185", "FocalLength": "749", "InclusionAngle": "6.500", "InclusionAngleAdditive": "39.000", "DetectorAngle": "0.680", "PixelWidthExitFront": "25.000", "PixelWidthExitSide": "-1.000", "Backlash": "ScanUp", "DriveDirection": "Normal", "ComPortSpec": "COM5", "ComPortEntrance": "", "ComPortExit": "", "DemoMode": "False", "UsedAsLightsource": "False", "UseBackwards": "False", "Wavelength": "850.184", "Grating": "2", "ReadTimeout": "35000", "Activated": "False", "IsFixedCalibration": "False", "FixedCalibrationPoints": "0", }, ], "Count": "3", }, "Detectors": { "Detector": [ { "GUID": "c1bc9fd2-135e-4098-b681-d30f6ea8be82", "Driver": "PvCam32 Driver", "Name": "Camera1", "DisplayName": "Camera1", "SerialNumber": "", "DetectorType": "None", "Size": "1024;1", "OpenAtStartup": "False", "Usage": "Default", }, { "GUID": "bbfbd5b4-6ea8-43de-8760-3b91c5867333", "Driver": "SpectraHub-Driver", "Name": "Spectra-Hub_COM7", "DisplayName": "Name", "SerialNumber": "210367", "DetectorType": "SinglePointDetector", "Size": "1;1", "OpenAtStartup": "False", "Usage": "Default", }, { "GUID": "98abd847-6843-4c4c-b88c-7340de27ce13", "Driver": "SpectraHub-Driver", "Name": "Spectra-Hub_COM8", "DisplayName": "Name", "SerialNumber": "210238", "DetectorType": "SinglePointDetector", "Size": "1;1", "OpenAtStartup": "False", "Usage": "Default", }, ], "Count": "3", }, "SinglePointDetectors": {"Count": "0"}, "LightSources": { "LightSource": [ { "Wavelengths": {"Count": "1", "Value_0": "0.000"}, "GUID": "a57ac71a-c667-4501-a24a-596bc54b2c8c", "Name": "Calibration Lamp", "Serialnumber": "", "FixedWavelength": "True", "CanChange": "False", "Type": "CalibrationLamp", "ConnectionString": "None", "IsMirrorPositionValid": "False", "MirrorsAlignmentPositionTop": "0;0", "MirrorsAlignmentPositionBottom": "0;0", }, { "Wavelengths": {"Count": "0"}, "GUID": "cac03351-735e-4592-9bb2-c17f64b3649f", "Name": "Calibration Lamp2", "Serialnumber": "", "FixedWavelength": "True", "CanChange": "False", "Type": "CalibrationLamp", "ConnectionString": "None", "IsMirrorPositionValid": "False", "MirrorsAlignmentPositionTop": "0;0", "MirrorsAlignmentPositionBottom": "0;0", }, { "Wavelengths": {"Count": "0"}, "GUID": "84a08bee-227a-46f0-b1e1-0f171808a155", "Name": "Calibration Lamp3", "Serialnumber": "", "FixedWavelength": "True", "CanChange": "False", "Type": "CalibrationLamp", "ConnectionString": "None", "IsMirrorPositionValid": "False", "MirrorsAlignmentPositionTop": "0;0", "MirrorsAlignmentPositionBottom": "0;0", }, { "Wavelengths": {"Count": "1", "Value_0": "0.000"}, "GUID": "a0601d22-23a0-4587-bb79-35d5823916c4", "Name": "Laser", "Serialnumber": "", "FixedWavelength": "False", "CanChange": "False", "Type": "Laser", "ConnectionString": "None", "IsMirrorPositionValid": "False", "MirrorsAlignmentPositionTop": "0;0", "MirrorsAlignmentPositionBottom": "0;0", }, { "Wavelengths": {"Count": "1", "Value_0": "790.000"}, "GUID": "a36b29da-0d54-4ab7-860c-967269f76217", "Name": "tisa", "Serialnumber": "", "FixedWavelength": "True", "CanChange": "True", "Type": "Laser", "ConnectionString": "None", "IsMirrorPositionValid": "False", "MirrorsAlignmentPositionTop": "0;0", "MirrorsAlignmentPositionBottom": "0;0", }, ], "Count": "5", }, "ArduinoHardware": {"Count": "0"}, "Additionals": {"Count": "0"}, "MotorizedStages": { "MotorizedStage": { "GUID": "c551372e-56af-4686-b7c1-48ca00dfdf27", "DriverName": "Tango Driver", "Name": "XY-Stage", "ConnectionString": "COM15", "Serialnumber": "144012056", "IsTriggerModeAvailable": "False", }, "Count": "1", }, "Microscopes": { "Microscope": [ { "Objectives": { "Objective": [ { "IsEnabled": "True", "Name": "100x", "Magnification": "100.000", "FactorMeasuredWithResolution": "1280", "Factor": "34.700", "LaserOffsetX": "0.000", "LaserOffsetY": "0.000", "OffsetX": "0.000", "OffsetY": "0.000", "LineLaserOffsetX": "0.000", "LineLaserOffsetY": "0.000", "LineOffsetX": "0.000", "LineOffsetY": "0.000", "LineFocusFactor": "1.130", }, { "IsEnabled": "False", "Name": "", "Magnification": "100.000", "FactorMeasuredWithResolution": "1280", "Factor": "34.700", "LaserOffsetX": "0.000", "LaserOffsetY": "0.000", "OffsetX": "0.000", "OffsetY": "0.000", "LineLaserOffsetX": "0.000", "LineLaserOffsetY": "0.000", "LineOffsetX": "0.000", "LineOffsetY": "0.000", "LineFocusFactor": "1.130", }, { "IsEnabled": "False", "Name": "", "Magnification": "100.000", "FactorMeasuredWithResolution": "1280", "Factor": "34.700", "LaserOffsetX": "0.000", "LaserOffsetY": "0.000", "OffsetX": "0.000", "OffsetY": "0.000", "LineLaserOffsetX": "0.000", "LineLaserOffsetY": "0.000", "LineOffsetX": "0.000", "LineOffsetY": "0.000", "LineFocusFactor": "1.130", }, { "IsEnabled": "False", "Name": "", "Magnification": "100.000", "FactorMeasuredWithResolution": "1280", "Factor": "34.700", "LaserOffsetX": "0.000", "LaserOffsetY": "0.000", "OffsetX": "0.000", "OffsetY": "0.000", "LineLaserOffsetX": "0.000", "LineLaserOffsetY": "0.000", "LineOffsetX": "0.000", "LineOffsetY": "0.000", "LineFocusFactor": "1.130", }, { "IsEnabled": "False", "Name": "", "Magnification": "100.000", "FactorMeasuredWithResolution": "1280", "Factor": "34.700", "LaserOffsetX": "0.000", "LaserOffsetY": "0.000", "OffsetX": "0.000", "OffsetY": "0.000", "LineLaserOffsetX": "0.000", "LineLaserOffsetY": "0.000", "LineOffsetX": "0.000", "LineOffsetY": "0.000", "LineFocusFactor": "1.130", }, { "IsEnabled": "False", "Name": "", "Magnification": "100.000", "FactorMeasuredWithResolution": "1280", "Factor": "34.700", "LaserOffsetX": "0.000", "LaserOffsetY": "0.000", "OffsetX": "0.000", "OffsetY": "0.000", "LineLaserOffsetX": "0.000", "LineLaserOffsetY": "0.000", "LineOffsetX": "0.000", "LineOffsetY": "0.000", "LineFocusFactor": "1.130", }, { "IsEnabled": "False", "Name": "", "Magnification": "100.000", "FactorMeasuredWithResolution": "1280", "Factor": "34.700", "LaserOffsetX": "0.000", "LaserOffsetY": "0.000", "OffsetX": "0.000", "OffsetY": "0.000", "LineLaserOffsetX": "0.000", "LineLaserOffsetY": "0.000", "LineOffsetX": "0.000", "LineOffsetY": "0.000", "LineFocusFactor": "1.130", }, { "IsEnabled": "False", "Name": "", "Magnification": "100.000", "FactorMeasuredWithResolution": "1280", "Factor": "34.700", "LaserOffsetX": "0.000", "LaserOffsetY": "0.000", "OffsetX": "0.000", "OffsetY": "0.000", "LineLaserOffsetX": "0.000", "LineLaserOffsetY": "0.000", "LineOffsetX": "0.000", "LineOffsetY": "0.000", "LineFocusFactor": "1.130", }, { "IsEnabled": "False", "Name": "", "Magnification": "100.000", "FactorMeasuredWithResolution": "1280", "Factor": "34.700", "LaserOffsetX": "0.000", "LaserOffsetY": "0.000", "OffsetX": "0.000", "OffsetY": "0.000", "LineLaserOffsetX": "0.000", "LineLaserOffsetY": "0.000", "LineOffsetX": "0.000", "LineOffsetY": "0.000", "LineFocusFactor": "1.130", }, { "IsEnabled": "False", "Name": "", "Magnification": "100.000", "FactorMeasuredWithResolution": "1280", "Factor": "34.700", "LaserOffsetX": "0.000", "LaserOffsetY": "0.000", "OffsetX": "0.000", "OffsetY": "0.000", "LineLaserOffsetX": "0.000", "LineLaserOffsetY": "0.000", "LineOffsetX": "0.000", "LineOffsetY": "0.000", "LineFocusFactor": "1.130", }, ], "Count": "10", }, "GUID": "841bfef9-b969-43f0-9ca3-2522c223a31f", "Name": "Microscope", "StageID": "c551372e-56af-4686-b7c1-48ca00dfdf27", "ImagingCameraID": "", "RamanBoxAvailable": "True", "RamanBoxLinearStage.Available": "False", "RamanBoxLinearStage.ConnectedHarwareID": "", "RamanBoxFilterWheel.Available": "False", "RamanBoxFilterWheel.ConnectedHarwareID": "", "RamanBoxBeamSplitter.Available": "False", "RamanBoxBeamSplitter.ConnectedHarwareID": "", "RamanBoxNotchFilter.Available": "False", "RamanBoxNotchFilter.ConnectedHarwareID": "", "ActiveObjectiveIndex": "0", }, { "Objectives": { "Objective": [ { "IsEnabled": "False", "Name": "", "Magnification": "100.000", "FactorMeasuredWithResolution": "1280", "Factor": "34.700", "LaserOffsetX": "0.000", "LaserOffsetY": "0.000", "OffsetX": "0.000", "OffsetY": "0.000", "LineLaserOffsetX": "0.000", "LineLaserOffsetY": "0.000", "LineOffsetX": "0.000", "LineOffsetY": "0.000", "LineFocusFactor": "1.130", }, { "IsEnabled": "False", "Name": "", "Magnification": "100.000", "FactorMeasuredWithResolution": "1280", "Factor": "34.700", "LaserOffsetX": "0.000", "LaserOffsetY": "0.000", "OffsetX": "0.000", "OffsetY": "0.000", "LineLaserOffsetX": "0.000", "LineLaserOffsetY": "0.000", "LineOffsetX": "0.000", "LineOffsetY": "0.000", "LineFocusFactor": "1.130", }, { "IsEnabled": "False", "Name": "", "Magnification": "100.000", "FactorMeasuredWithResolution": "1280", "Factor": "34.700", "LaserOffsetX": "0.000", "LaserOffsetY": "0.000", "OffsetX": "0.000", "OffsetY": "0.000", "LineLaserOffsetX": "0.000", "LineLaserOffsetY": "0.000", "LineOffsetX": "0.000", "LineOffsetY": "0.000", "LineFocusFactor": "1.130", }, { "IsEnabled": "False", "Name": "", "Magnification": "100.000", "FactorMeasuredWithResolution": "1280", "Factor": "34.700", "LaserOffsetX": "0.000", "LaserOffsetY": "0.000", "OffsetX": "0.000", "OffsetY": "0.000", "LineLaserOffsetX": "0.000", "LineLaserOffsetY": "0.000", "LineOffsetX": "0.000", "LineOffsetY": "0.000", "LineFocusFactor": "1.130", }, { "IsEnabled": "False", "Name": "", "Magnification": "100.000", "FactorMeasuredWithResolution": "1280", "Factor": "34.700", "LaserOffsetX": "0.000", "LaserOffsetY": "0.000", "OffsetX": "0.000", "OffsetY": "0.000", "LineLaserOffsetX": "0.000", "LineLaserOffsetY": "0.000", "LineOffsetX": "0.000", "LineOffsetY": "0.000", "LineFocusFactor": "1.130", }, { "IsEnabled": "False", "Name": "", "Magnification": "100.000", "FactorMeasuredWithResolution": "1280", "Factor": "34.700", "LaserOffsetX": "0.000", "LaserOffsetY": "0.000", "OffsetX": "0.000", "OffsetY": "0.000", "LineLaserOffsetX": "0.000", "LineLaserOffsetY": "0.000", "LineOffsetX": "0.000", "LineOffsetY": "0.000", "LineFocusFactor": "1.130", }, { "IsEnabled": "False", "Name": "", "Magnification": "100.000", "FactorMeasuredWithResolution": "1280", "Factor": "34.700", "LaserOffsetX": "0.000", "LaserOffsetY": "0.000", "OffsetX": "0.000", "OffsetY": "0.000", "LineLaserOffsetX": "0.000", "LineLaserOffsetY": "0.000", "LineOffsetX": "0.000", "LineOffsetY": "0.000", "LineFocusFactor": "1.130", }, { "IsEnabled": "False", "Name": "", "Magnification": "100.000", "FactorMeasuredWithResolution": "1280", "Factor": "34.700", "LaserOffsetX": "0.000", "LaserOffsetY": "0.000", "OffsetX": "0.000", "OffsetY": "0.000", "LineLaserOffsetX": "0.000", "LineLaserOffsetY": "0.000", "LineOffsetX": "0.000", "LineOffsetY": "0.000", "LineFocusFactor": "1.130", }, { "IsEnabled": "False", "Name": "", "Magnification": "100.000", "FactorMeasuredWithResolution": "1280", "Factor": "34.700", "LaserOffsetX": "0.000", "LaserOffsetY": "0.000", "OffsetX": "0.000", "OffsetY": "0.000", "LineLaserOffsetX": "0.000", "LineLaserOffsetY": "0.000", "LineOffsetX": "0.000", "LineOffsetY": "0.000", "LineFocusFactor": "1.130", }, { "IsEnabled": "False", "Name": "", "Magnification": "100.000", "FactorMeasuredWithResolution": "1280", "Factor": "34.700", "LaserOffsetX": "0.000", "LaserOffsetY": "0.000", "OffsetX": "0.000", "OffsetY": "0.000", "LineLaserOffsetX": "0.000", "LineLaserOffsetY": "0.000", "LineOffsetX": "0.000", "LineOffsetY": "0.000", "LineFocusFactor": "1.130", }, ], "Count": "10", }, "GUID": "ee496960-089d-4040-a5ca-cde5f9d1b0f8", "Name": "Microscope", "StageID": "", "ImagingCameraID": "", "RamanBoxAvailable": "False", "RamanBoxLinearStage.Available": "False", "RamanBoxLinearStage.ConnectedHarwareID": "", "RamanBoxFilterWheel.Available": "False", "RamanBoxFilterWheel.ConnectedHarwareID": "", "RamanBoxBeamSplitter.Available": "False", "RamanBoxBeamSplitter.ConnectedHarwareID": "", "RamanBoxNotchFilter.Available": "False", "RamanBoxNotchFilter.ConnectedHarwareID": "", "ActiveObjectiveIndex": "0", }, ], "Count": "2", }, "Cryostats": {"Count": "0"}, "Version": "2", }, } assert ( expected_metadata == self.s_non_uniform_unfiltered.original_metadata.as_dictionary() ) class TestLinescan: @classmethod def setup_class(cls): cls.s = hs.load( testfile_linescan_path, reader="TriVista", use_uniform_signal_axis=True ) cls.s_non_uniform = hs.load( testfile_linescan_path, reader="TriVista", 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_line1 = np.array([448, 482, 433, 407, 379]) np.testing.assert_allclose(expected_data_line1, self.s.inav[0].isig[:5].data) np.testing.assert_allclose( expected_data_line1, self.s_non_uniform.inav[0].isig[:5].data ) expected_data_last_line = np.array([430, 437, 378, 408, 488]) np.testing.assert_allclose( expected_data_last_line, self.s.inav[-1].isig[-5:].data ) np.testing.assert_allclose( expected_data_last_line, self.s_non_uniform.inav[-1].isig[-5:].data ) def test_axes(self): expected_axis = { "axis-0": { "_type": "UniformDataAxis", "name": "X", "units": "µm", "navigate": True, "is_binned": False, "size": 21, "scale": 0.001, "offset": -0.01, }, "axis-1": { "_type": "UniformDataAxis", "name": "Wavelength", "units": "nm", "navigate": False, "is_binned": False, "size": 97, }, } expected_axis_non_uniform = { "axis-0": { "_type": "UniformDataAxis", "name": "X", "units": "µm", "navigate": True, "is_binned": False, "size": 21, "scale": 0.001, "offset": -0.01, }, "axis-1": { "_type": "DataAxis", "name": "Wavelength", "units": "nm", "navigate": False, "is_binned": False, }, } expected_values_non_uniform_axis = np.array( [910.310424804688, 910.350219726563, 910.390014648438] ) uniform_axes_manager = deepcopy(self.s.axes_manager.as_dictionary()) non_uniform_axis_manager = deepcopy( self.s_non_uniform.axes_manager.as_dictionary() ) np.testing.assert_allclose( uniform_axes_manager["axis-1"].pop("scale"), 0.0397771, atol=0.0000005 ) np.testing.assert_allclose( uniform_axes_manager["axis-1"].pop("offset"), 910.3104, atol=0.005 ) np.testing.assert_allclose( expected_values_non_uniform_axis, non_uniform_axis_manager["axis-1"].pop("axis")[:3], ) assert expected_axis == uniform_axes_manager assert expected_axis_non_uniform == non_uniform_axis_manager def test_original_metadata(self): assert ( self.s.original_metadata.as_dictionary() == self.s_non_uniform.original_metadata.as_dictionary() ) metadata_experiment = ( self.s.original_metadata.Document.InfoSerialized.Experiment.as_dictionary() ) assert metadata_experiment["Mode"] == "Point by Point" assert metadata_experiment["Stage Mode"] == "LineScanX" assert metadata_experiment["Used Time"] == "00:00:21" class TestMap: @classmethod def setup_class(cls): cls.s = hs.load( testfile_map_path, reader="TriVista", use_uniform_signal_axis=True ) cls.s_non_uniform = hs.load( testfile_map_path, reader="TriVista", 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_00 = np.array([531, 499, 442, 446, 460]) np.testing.assert_allclose(expected_data_00, self.s.inav[0, 0].isig[:5].data) np.testing.assert_allclose( expected_data_00, self.s_non_uniform.inav[0, 0].isig[:5].data ) expected_data_10 = np.array([532, 516, 425, 438, 433]) np.testing.assert_allclose(expected_data_10, self.s.inav[1, 0].isig[:5].data) np.testing.assert_allclose( expected_data_10, self.s_non_uniform.inav[1, 0].isig[:5].data ) expected_data_01 = np.array([525, 498, 447, 433, 452]) np.testing.assert_allclose(expected_data_01, self.s.inav[0, 1].isig[:5].data) np.testing.assert_allclose( expected_data_01, self.s_non_uniform.inav[0, 1].isig[:5].data ) expected_data_99 = np.array([452, 478, 687, 1320, 1145]) np.testing.assert_allclose(expected_data_99, self.s.inav[-1, -1].isig[-5:].data) np.testing.assert_allclose( expected_data_99, self.s_non_uniform.inav[-1, -1].isig[-5:].data ) def test_axes(self): expected_axis = { "axis-0": { "_type": "UniformDataAxis", "name": "Y", "units": "µm", "navigate": True, "is_binned": False, "size": 9, "scale": 0.025, "offset": -0.1, }, "axis-1": { "_type": "UniformDataAxis", "name": "X", "units": "µm", "navigate": True, "is_binned": False, "size": 9, "scale": 0.025, "offset": -0.1, }, "axis-2": { "_type": "UniformDataAxis", "name": "Wavelength", "units": "nm", "navigate": False, "is_binned": False, "size": 1024, }, } expected_axis_non_uniform = { "axis-0": { "_type": "UniformDataAxis", "name": "Y", "units": "µm", "navigate": True, "is_binned": False, "size": 9, "scale": 0.025, "offset": -0.1, }, "axis-1": { "_type": "UniformDataAxis", "name": "X", "units": "µm", "navigate": True, "is_binned": False, "size": 9, "scale": 0.025, "offset": -0.1, }, "axis-2": { "_type": "DataAxis", "name": "Wavelength", "units": "nm", "navigate": False, "is_binned": False, }, } expected_values_non_uniform_axis = np.array( [891.894470214844, 891.9345703125, 891.974670410156] ) uniform_axes_manager = deepcopy(self.s.axes_manager.as_dictionary()) non_uniform_axis_manager = deepcopy( self.s_non_uniform.axes_manager.as_dictionary() ) np.testing.assert_allclose( uniform_axes_manager["axis-2"].pop("scale"), 0.039770, atol=0.000005 ) np.testing.assert_allclose( uniform_axes_manager["axis-2"].pop("offset"), 891.9, atol=0.05 ) np.testing.assert_allclose( expected_values_non_uniform_axis, non_uniform_axis_manager["axis-2"].pop("axis")[:3], ) assert expected_axis == uniform_axes_manager assert expected_axis_non_uniform == non_uniform_axis_manager def test_original_metadata(self): assert ( self.s.original_metadata.as_dictionary() == self.s_non_uniform.original_metadata.as_dictionary() ) metadata_experiment = ( self.s.original_metadata.Document.InfoSerialized.Experiment.as_dictionary() ) assert metadata_experiment["Mode"] == "Point by Point" assert metadata_experiment["Stage Mode"] == "MappingXY" assert metadata_experiment["Used Time"] == "00:01:27" class Test3Spectrometers: @classmethod def setup_class(cls): cls.s = hs.load( testfile_triple_add_path, reader="TriVista", use_uniform_signal_axis=True, filter_original_metadata=True, ) @classmethod def teardown_class(cls): del cls.s gc.collect() def test_original_metadata(self): expected_metadata = { "XmlMain": { "Version": "1.0.1", "Filename": "D:\\Data\\test-spectra\\spec_triple-add.tvf", "DateTime": "06/27/2022 17:56:15", "PlugInName": "", "PlugInData": "", "FileInfoSerialized": {"Info": {"Groups": None}}, }, "Document": { "Version": "2", "Label": "Intensity", "DataLabel": "Counts", "DocType": "Spectra", "RecordTime": "06/27/2022 17:55:55.294", "ModeName": "", "DataSource": "nothing", "Encoding": "Ascii", "ColorMode": "Grayscale", "ViewDisplayMode": "Graph", "ViewImageColorMode": "False", "InfoSerialized": { "Document": {"Record Time": "6/27/2022 5:55 PM"}, "Experiment": {"Used Setup": "PL_add777"}, "Spectrometers": { "Spectrometer2": { "Serialnumber": "25580420", "Model": "SP-2-500i", "Stage_Number": "2", "Focallength": "500", "Inclusion_Angle": "8.6", "Detector_Angle": "0", "Groove_Density": "750 g/mm", "Order": "1", "Slit_Entrance-Front": "0", "Slit_Entrance-Side": "6000", "Slit_Exit-Front": "0", "Slit_Exit-Side": "0", }, "Spectrometer3": { "Serialnumber": "27580185", "Model": "SP-2-750i", "Stage_Number": "3", "Focallength": "749", "Inclusion_Angle": "6.5", "Detector_Angle": "0.68", "Groove_Density": "750 g/mm", "Order": "1", "Slit_Entrance-Front": "0", "Slit_Entrance-Side": "12000", "Slit_Exit-Front": "0", "Slit_Exit-Side": "0", }, "Spectrometer1": { "Serialnumber": "25580419", "Model": "SP-2-500i", "Stage_Number": "1", "Focallength": "500", "Inclusion_Angle": "8.6", "Detector_Angle": "0", "Groove_Density": "750 g/mm", "Order": "1", "Slit_Entrance-Front": "300", "Slit_Entrance-Side": "0", "Slit_Exit-Front": "0", "Slit_Exit-Side": "0", }, }, "Detector": { "Name": "Camera1", "Serialnumber": None, "Detector_Size": "1024;1", "Detector_Temperature": "-25", "Exposure_Time_(ms)": "1000", "Exposure_Mode": None, "No_of_Accumulations": "1", "Calc_Average": "True", "No_of_Frames": "1", "ADC__Readout_Port": "Normal", "ADC__Rate_Resolution": "1 MHz", "ADC__Gain": "2", "Clearing__Mode": None, "Clearing__No_of_Cleans": "1", "Region_of_Interests": "1|1;1024;1;1;1;1", }, "Calibration": { "Center_Wavelength": "820.000", "Laser_Wavelength": "0.000", }, }, }, "Hardware": { "Spectrometers": { "Count": "3", "Spectrometer1": { "Gratings": { "Grating": { "Offsets": {"Count": "0"}, "GrooveDensity": "750 g/mm", "Blaze": "H-NIR", "Turret": "1", }, "Count": "3", }, "MirrorEntrance": { "Name": "M1", "State": "isMotorized", "Position": "front", }, "MirrorExit": { "Name": "M2", "State": "isMotorized", "Position": "side", }, "SlitEntranceSide": { "Name": "S1", "State": "isMotorized", "MaxWidth": "12000", "Position": "0", }, "SlitEntranceFront": { "Name": "S2", "State": "isMotorized", "MaxWidth": "12000", "Position": "200", }, "SlitExitFront": { "Name": "S3", "State": "isMotorized", "MaxWidth": "12000", "Position": "0", }, "SlitExitSide": { "Name": "S4", "State": "disabled", "MaxWidth": "12000", "Position": "0", }, "FilterWheel": { "Name": "", "State": "disabled", "Position": "0", "FilterStrings": "6|#1|#2|#3|#4|#5|#6", }, "Shutter": { "Name": "", "State": "disabled", "Position": "open", "ShutterMode": "OpenForExperiment", "ShutterClosedForFilterwheel": "True", "ShutterClosedForSetupChange": "True", "ShutterClosedForLaserCrossing": "True", "ShutterClosedForLaserCrossingValue": "0.000", "ShutterClosedForLaserCrossingUnit": "Nanometer", }, "GUID": "c05fbec6-7cc0-4546-a009-06850868f43d", "Model": "SP-2-500i", "Serialnumber": "25580419", "FocalLength": "500", "InclusionAngle": "8.600", "InclusionAngleAdditive": "51.600", "DetectorAngle": "0.000", "PixelWidthExitFront": "-1.000", "PixelWidthExitSide": "-1.000", "Backlash": "ScanUp", "DriveDirection": "Normal", "ComPortSpec": "COM3", "ComPortEntrance": "", "ComPortExit": "", "DemoMode": "False", "UsedAsLightsource": "False", "UseBackwards": "False", "Wavelength": "925.010", "Grating": "2", "ReadTimeout": "35000", "Activated": "False", "IsFixedCalibration": "False", "FixedCalibrationPoints": "0", }, "Spectrometer2": { "Gratings": { "Grating": { "Offsets": {"Count": "0"}, "GrooveDensity": "750 g/mm", "Blaze": "H-NIR", "Turret": "1", }, "Count": "3", }, "MirrorEntrance": { "Name": "M1", "State": "isMotorized", "Position": "side", }, "MirrorExit": { "Name": "M2", "State": "isMotorized", "Position": "side", }, "SlitEntranceSide": { "Name": "S1", "State": "isMotorized", "MaxWidth": "12000", "Position": "10000", }, "SlitEntranceFront": { "Name": "S2", "State": "isMotorized", "MaxWidth": "12000", "Position": "0", }, "SlitExitFront": { "Name": "S3", "State": "isMotorized", "MaxWidth": "12000", "Position": "0", }, "SlitExitSide": { "Name": "S4", "State": "disabled", "MaxWidth": "12000", "Position": "0", }, "FilterWheel": { "Name": "", "State": "disabled", "Position": "0", "FilterStrings": "6|#1|#2|#3|#4|#5|#6", }, "Shutter": { "Name": "", "State": "disabled", "Position": "open", "ShutterMode": "OpenForExperiment", "ShutterClosedForFilterwheel": "True", "ShutterClosedForSetupChange": "True", "ShutterClosedForLaserCrossing": "True", "ShutterClosedForLaserCrossingValue": "0.000", "ShutterClosedForLaserCrossingUnit": "Nanometer", }, "GUID": "39ade9ad-caa8-48c2-a3d0-4f79cc44bda7", "Model": "SP-2-500i", "Serialnumber": "25580420", "FocalLength": "500", "InclusionAngle": "8.600", "InclusionAngleAdditive": "51.600", "DetectorAngle": "0.000", "PixelWidthExitFront": "1.000", "PixelWidthExitSide": "-1.000", "Backlash": "ScanUp", "DriveDirection": "Normal", "ComPortSpec": "COM4", "ComPortEntrance": "", "ComPortExit": "", "DemoMode": "False", "UsedAsLightsource": "False", "UseBackwards": "False", "Wavelength": "-924.910", "Grating": "2", "ReadTimeout": "35000", "Activated": "False", "IsFixedCalibration": "False", "FixedCalibrationPoints": "0", }, "Spectrometer3": { "Gratings": { "Grating": { "Offsets": {"Count": "0"}, "GrooveDensity": "750 g/mm", "Blaze": "H-NIR", "Turret": "1", }, "Count": "3", }, "MirrorEntrance": { "Name": "M1", "State": "isMotorized", "Position": "front", }, "MirrorExit": { "Name": "M2", "State": "isMotorized", "Position": "side", }, "SlitEntranceSide": { "Name": "S1", "State": "isMotorized", "MaxWidth": "12000", "Position": "0", }, "SlitEntranceFront": { "Name": "S2", "State": "isMotorized", "MaxWidth": "12000", "Position": "500", }, "SlitExitFront": { "Name": "S3", "State": "disabled", "MaxWidth": "12000", "Position": "0", }, "SlitExitSide": { "Name": "S4", "State": "disabled", "MaxWidth": "12000", "Position": "0", }, "FilterWheel": { "Name": "", "State": "disabled", "Position": "0", "FilterStrings": "6|#1|#2|#3|#4|#5|#6", }, "Shutter": { "Name": "", "State": "disabled", "Position": "open", "ShutterMode": "OpenForExperiment", "ShutterClosedForFilterwheel": "True", "ShutterClosedForSetupChange": "True", "ShutterClosedForLaserCrossing": "True", "ShutterClosedForLaserCrossingValue": "0.000", "ShutterClosedForLaserCrossingUnit": "Nanometer", }, "GUID": "37a2855b-db41-4268-970b-bb75d96e5654", "Model": "SP-2-750i", "Serialnumber": "27580185", "FocalLength": "749", "InclusionAngle": "6.500", "InclusionAngleAdditive": "39.000", "DetectorAngle": "0.680", "PixelWidthExitFront": "25.000", "PixelWidthExitSide": "-1.000", "Backlash": "ScanUp", "DriveDirection": "Normal", "ComPortSpec": "COM5", "ComPortEntrance": "", "ComPortExit": "", "DemoMode": "False", "UsedAsLightsource": "False", "UseBackwards": "False", "Wavelength": "850.184", "Grating": "2", "ReadTimeout": "35000", "Activated": "False", "IsFixedCalibration": "False", "FixedCalibrationPoints": "0", }, }, "Detectors": { "Detector": { "GUID": "c1bc9fd2-135e-4098-b681-d30f6ea8be82", "Driver": "PvCam32 Driver", "Name": "Camera1", "DisplayName": "Camera1", "SerialNumber": "", "DetectorType": "None", "Size": "1024;1", "OpenAtStartup": "False", "Usage": "Default", }, "Count": "3", }, "SinglePointDetectors": {"Count": "0"}, "LightSources": { "LightSource": [ { "Wavelengths": {"Count": "1", "Value_0": "0.000"}, "GUID": "a57ac71a-c667-4501-a24a-596bc54b2c8c", "Name": "Calibration Lamp", "Serialnumber": "", "FixedWavelength": "True", "CanChange": "False", "Type": "CalibrationLamp", "ConnectionString": "None", "IsMirrorPositionValid": "False", "MirrorsAlignmentPositionTop": "0;0", "MirrorsAlignmentPositionBottom": "0;0", }, { "Wavelengths": {"Count": "0"}, "GUID": "cac03351-735e-4592-9bb2-c17f64b3649f", "Name": "Calibration Lamp2", "Serialnumber": "", "FixedWavelength": "True", "CanChange": "False", "Type": "CalibrationLamp", "ConnectionString": "None", "IsMirrorPositionValid": "False", "MirrorsAlignmentPositionTop": "0;0", "MirrorsAlignmentPositionBottom": "0;0", }, { "Wavelengths": {"Count": "0"}, "GUID": "84a08bee-227a-46f0-b1e1-0f171808a155", "Name": "Calibration Lamp3", "Serialnumber": "", "FixedWavelength": "True", "CanChange": "False", "Type": "CalibrationLamp", "ConnectionString": "None", "IsMirrorPositionValid": "False", "MirrorsAlignmentPositionTop": "0;0", "MirrorsAlignmentPositionBottom": "0;0", }, { "Wavelengths": {"Count": "1", "Value_0": "0.000"}, "GUID": "a0601d22-23a0-4587-bb79-35d5823916c4", "Name": "Laser", "Serialnumber": "", "FixedWavelength": "False", "CanChange": "False", "Type": "Laser", "ConnectionString": "None", "IsMirrorPositionValid": "False", "MirrorsAlignmentPositionTop": "0;0", "MirrorsAlignmentPositionBottom": "0;0", }, { "Wavelengths": {"Count": "1", "Value_0": "790.000"}, "GUID": "a36b29da-0d54-4ab7-860c-967269f76217", "Name": "tisa", "Serialnumber": "", "FixedWavelength": "True", "CanChange": "True", "Type": "Laser", "ConnectionString": "None", "IsMirrorPositionValid": "False", "MirrorsAlignmentPositionTop": "0;0", "MirrorsAlignmentPositionBottom": "0;0", }, ], "Count": "5", }, "ArduinoHardware": {"Count": "0"}, "Additionals": {"Count": "0"}, "MotorizedStages": { "MotorizedStage": { "GUID": "c551372e-56af-4686-b7c1-48ca00dfdf27", "DriverName": "Tango Driver", "Name": "XY-Stage", "ConnectionString": "COM15", "Serialnumber": "144012056", "IsTriggerModeAvailable": "False", }, "Count": "1", }, "Microscopes": { "Microscope": { "Objectives": { "Objective": { "IsEnabled": "True", "Name": "100x", "Magnification": "100.000", "FactorMeasuredWithResolution": "1280", "Factor": "34.700", "LaserOffsetX": "0.000", "LaserOffsetY": "0.000", "OffsetX": "0.000", "OffsetY": "0.000", "LineLaserOffsetX": "0.000", "LineLaserOffsetY": "0.000", "LineOffsetX": "0.000", "LineOffsetY": "0.000", "LineFocusFactor": "1.130", }, "Count": "10", }, "GUID": "841bfef9-b969-43f0-9ca3-2522c223a31f", "Name": "Microscope", "StageID": "c551372e-56af-4686-b7c1-48ca00dfdf27", "ImagingCameraID": "", "RamanBoxAvailable": "True", "RamanBoxLinearStage.Available": "False", "RamanBoxLinearStage.ConnectedHarwareID": "", "RamanBoxFilterWheel.Available": "False", "RamanBoxFilterWheel.ConnectedHarwareID": "", "RamanBoxBeamSplitter.Available": "False", "RamanBoxBeamSplitter.ConnectedHarwareID": "", "RamanBoxNotchFilter.Available": "False", "RamanBoxNotchFilter.ConnectedHarwareID": "", "ActiveObjectiveIndex": "0", }, "Count": "2", }, "Cryostats": {"Count": "0"}, "Version": "2", }, } assert self.s.original_metadata.as_dictionary() == expected_metadata def test_metadata_acquisition_instrument(self): expected_metadata = { "Detector": { "processing": {"calc_average": "True"}, "temperature": -25.0, "exposure_per_frame": 1.0, "frames": 1.0, "glued_spectrum": False, "integration_time": 1.0, }, "Laser": {"objective_magnification": 100.0}, "Spectrometer1": { "Grating": {"blazing_wavelength": "H-NIR", "groove_density": 750.0}, "central_wavelength": 820.0, "model": "SP-2-500i", "entrance_slit_width": 0.3, "exit_slit_width": 0.0, }, "Spectrometer2": { "Grating": {"blazing_wavelength": "H-NIR", "groove_density": 750.0}, "central_wavelength": 820.0, "model": "SP-2-500i", "entrance_slit_width": 6.0, "exit_slit_width": 0.0, }, "Spectrometer3": { "Grating": {"blazing_wavelength": "H-NIR", "groove_density": 750.0}, "central_wavelength": 820.0, "model": "SP-2-750i", "entrance_slit_width": 12.0, "exit_slit_width": 0.0, }, } assert ( self.s.metadata.Acquisition_instrument.as_dictionary() == expected_metadata ) class TestStepAndGlue: @classmethod def setup_class(cls): cls.glued = hs.load( testfile_step_and_glue_path, reader="TriVista", use_uniform_signal_axis=True, filter_original_metadata=True, glued_data_as_stack=False, ) cls.stack = hs.load( testfile_step_and_glue_path, reader="TriVista", use_uniform_signal_axis=False, filter_original_metadata=True, glued_data_as_stack=True, ) @classmethod def teardown_class(cls): del cls.glued del cls.stack gc.collect() def test_data_glued(self): assert np.isclose(self.glued.isig[0].data, 1071) assert np.isclose(self.glued.isig[17999].data, 978) def test_data_stack(self): data_stack1 = np.array([1071, 1134, 1092]) data_stack19 = np.array([1064, 1150, 1111]) np.testing.assert_allclose(self.stack[0].isig[:3].data, data_stack1) np.testing.assert_allclose(self.stack[18].isig[:3].data, data_stack19) def test_axes_stack(self): expected_axis = { "axis-0": { "_type": "DataAxis", "name": "Wavelength", "units": "nm", "navigate": False, "is_binned": False, } } for frame in self.stack: axes_manager = frame.axes_manager.as_dictionary() data_axis = axes_manager["axis-0"].pop("axis") assert data_axis.size == 1024 assert axes_manager == expected_axis assert np.isclose( self.stack[0].axes_manager.as_dictionary()["axis-0"]["axis"][0], 900.027, atol=0.001, ) def test_metadata(self): original_metadata_glued = self.glued.original_metadata.Document.InfoSerialized.Experiment.as_dictionary() # noqa: E501 metadata_detector = self.glued.metadata.Acquisition_instrument.Detector assert original_metadata_glued["From"] == "900.000 nm" assert original_metadata_glued["To"] == "1500.000 nm" assert original_metadata_glued["Mode:"] == "Step & Glue" assert original_metadata_glued["Overlap (%)"] == "15" assert original_metadata_glued["Skipped Pixel Left"] == "0" assert original_metadata_glued["Skipped Pixel Right"] == "0" assert metadata_detector.glued_spectrum is True assert np.isclose(metadata_detector.glued_spectrum_overlap, 15) assert np.isclose(metadata_detector.glued_spectrum_windows, 19) metadata_glued = deepcopy(self.glued.metadata.as_dictionary()) del metadata_glued["General"]["FileIO"] for frame in self.stack: assert ( self.glued.original_metadata.as_dictionary() == frame.original_metadata.as_dictionary() ) metadata_frame = deepcopy(frame.metadata.as_dictionary()) del metadata_frame["General"]["FileIO"] assert metadata_frame == metadata_glued class TestTimeSeries: @classmethod def setup_class(cls): cls.timeseries = hs.load( testfile_spec_timeseries_path, reader="TriVista", use_uniform_signal_axis=True, filter_original_metadata=True, ) cls.frames = hs.load( testfile_spec_2frames_path, reader="TriVista", use_uniform_signal_axis=True, filter_original_metadata=True, ) @classmethod def teardown_class(cls): del cls.timeseries del cls.frames gc.collect() def test_data_timeseries(self): data_ts_1 = np.array([27381, 39153, 35022, -425, 32430]) data_ts_2 = np.array([27449.5, 38971.5, 35168.5, -425, 32484.5]) np.testing.assert_allclose(self.timeseries.isig[:5, 0].data, data_ts_1) np.testing.assert_allclose(self.timeseries.isig[:5, 1].data, data_ts_2) def test_data_frames(self): data_frame_1 = np.array([49868, 65074, 60325, 10241, 52539]) data_frame_2 = np.array([49909, 65074, 60017, 10022, 52639]) np.testing.assert_allclose(self.frames.isig[:5, 0].data, data_frame_1) np.testing.assert_allclose(self.frames.isig[:5, 1].data, data_frame_2) def test_axes_timeseries(self): expected_axis = { "axis-0": { "_type": "UniformDataAxis", "name": "time", "units": "s", "navigate": False, "is_binned": False, "size": 2, "offset": 0.0, }, "axis-1": { "_type": "UniformDataAxis", "name": "Wavelength", "units": "nm", "navigate": False, "is_binned": False, "size": 1024, }, } axes_manager = deepcopy(self.timeseries.axes_manager.as_dictionary()) np.testing.assert_allclose(axes_manager["axis-0"].pop("scale"), 4.04, atol=0.01) np.testing.assert_allclose(axes_manager["axis-1"].pop("scale"), 0.03, atol=0.01) np.testing.assert_allclose(axes_manager["axis-1"].pop("offset"), 934, atol=1) assert expected_axis == axes_manager def test_axes_frames(self): expected_axis = { "axis-0": { "_type": "UniformDataAxis", "name": "time", "units": "s", "navigate": False, "is_binned": False, "size": 2, "offset": 0.0, }, "axis-1": { "_type": "UniformDataAxis", "name": "Wavelength", "units": "nm", "navigate": False, "is_binned": False, "size": 1024, }, } axes_manager = deepcopy(self.frames.axes_manager.as_dictionary()) np.testing.assert_allclose(axes_manager["axis-1"].pop("scale"), 0.03, atol=0.01) np.testing.assert_allclose(axes_manager["axis-1"].pop("offset"), 934, atol=1) np.testing.assert_allclose(axes_manager["axis-0"].pop("scale"), 6, atol=0.01) assert expected_axis == axes_manager class TestSpecIntegrationTime: @classmethod def setup_class(cls): cls.s_2acc = hs.load( testfile_spec_2acc_path, reader="TriVista", use_uniform_signal_axis=True, filter_original_metadata=True, glued_data_as_stack=True, ) ## glued_data_as_stack set to True here ## to ensure that this setting doesn't affect ## non-glued datasets cls.s_2acc_no_average = hs.load( testfile_spec_2acc_no_average_path, reader="TriVista", use_uniform_signal_axis=True, filter_original_metadata=True, glued_data_as_stack=True, ) @classmethod def teardown_class(cls): del cls.s_2acc del cls.s_2acc_no_average gc.collect() def test_metadata_2acc(self): metadata_detector = self.s_2acc.metadata.Acquisition_instrument.Detector assert np.isclose(metadata_detector.exposure_per_frame, 3) assert np.isclose(metadata_detector.frames, 2) assert np.isclose(metadata_detector.integration_time, 3) assert metadata_detector.processing.calc_average == "True" def test_metadata_2acc_no_average(self): metadata_detector = ( self.s_2acc_no_average.metadata.Acquisition_instrument.Detector ) assert np.isclose(metadata_detector.exposure_per_frame, 3) assert np.isclose(metadata_detector.frames, 2) assert np.isclose(metadata_detector.integration_time, 6) assert metadata_detector.processing.calc_average == "False"