# -*- 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 from pathlib import Path import numpy as np import pytest hs = pytest.importorskip("hyperspy.api", reason="hyperspy not installed") testfile_dir = (Path(__file__).parent / "data" / "hamamatsu").resolve() testfile_focus_mode_path = (testfile_dir / "focus_mode.img").resolve() testfile_operate_mode_path = (testfile_dir / "operate_mode.img").resolve() testfile_photon_count_path = (testfile_dir / "photon_counting.img").resolve() testfile_shading_path = (testfile_dir / "shading_file.img").resolve() class TestOperate: @classmethod def setup_class(cls): cls.s = hs.load(testfile_operate_mode_path, reader="Hamamatsu") @classmethod def teardown_class(cls): del cls.s gc.collect() def test_data_deflection(self): expected_data_start = [ [0, 0, 715], [246, 161, 475], [106, 899, 0], ] np.testing.assert_allclose(expected_data_start, self.s.isig[:3, :3].data) def test_axes_deflection(self): axes = self.s.axes_manager assert axes.signal_dimension == 2 assert axes.navigation_dimension == 0 ax0 = axes[0] ax1 = axes[1] assert ax0.name == "Wavelength" assert ax1.name == "Time" assert ax0.size == 672 assert ax1.size == 512 assert ax0.units == "nm" assert ax1.units == "µs" expected_data_start_X = [472.252, 472.33337, 472.41473, 472.4961, 472.57745] expected_data_start_Y = [0.0, 0.031080816, 0.062164314, 0.09325048, 0.12433932] np.testing.assert_allclose(ax0.axis[:5], expected_data_start_X) np.testing.assert_allclose(ax1.axis[:5], expected_data_start_Y) def test_original_metadata_no_comment(self): original_metadata_no_comment = { k: v for (k, v) in self.s.original_metadata.as_dictionary().items() if k != "Comment" } expected_metadata = { "character_im": "IM", "offset_x": 0, "offset_y": 0, "file_type": "bit32", "num_images_in_channel": 0, "num_additional_channels": 0, "channel_number": 0, "timestamp": 0.0, "marker": "", "additional_info": "", "image_width_px": 672, "image_height_lines": 512, "comment_length": 3311, } assert expected_metadata == original_metadata_no_comment def test_original_metadata_comment(self): original_metadata = self.s.original_metadata.Comment.as_dictionary() expected_metadata = { "Application": { "Enconding": "UTF-8", "Date": "20/01/2023", "Time": "11:34:55.147", "Software": "HPD-TA", "Application": "2", "ApplicationTitle": "High Performance Digital Temporal Analyzer", "SoftwareVersion": "9.5 pf10", "SoftwareDate": "15.12.2020", }, "Camera": { "CameraName": "Orca R2", "SerialNumber": "S/N: 891892", "Type": "37", "ScanMode": "1", "Subarray": "0", "Binning": "2", "BitsPerChannel": "0", "HighDynamicRangeMode": "0", "ScanSpeed": "0", "SubarrayHpos": "0", "SubarrayHsize": "0", "SubarrayVpos": "0", "SubarrayVsize": "0", "TriggerMode": "3", "TriggerModeKeyVal": "Internal", "TriggerPolarity": "1", "TriggerPolarityKeyVal": "neg.", "CoolerSwitch": "-1", "Gain": "0", "Prop_SensorMode": "1", "Prop_Colortype": "1", "Prop_TriggerTimes": "1", "Prop_ExposureTimeControl": "2", "Prop_TimingMinTriggerInterval": "0.500139", "Prop_TimingExposure": "2", "Prop_ImageTopOffsetBytes": "0", "Prop_ImagePixelType": "2", "Prop_BufferRowbytes": "1344", "Prop_BufferFramebytes": "688128", "Prop_BufferTopOffsetBytes": "0", "Prop_BufferPixelType": "2", "Prop_RecordFixedBytesPerFile": "256", "Prop_RecordFixedBytesPerSession": "784", "Prop_RecordFixedBytesPerFrame": "688176", "Prop_NumberOfOutputTriggerConnector": "1", "Prop_OutputTriggerPolarity": "1", "Prop_OutputTriggerActive": "1", "Prop_OutputTriggerDelay": "0", "Prop_OutputTriggerPeriod": "0.0001", "Prop_SystemAlive": "2", "Prop_ImageDetectorPixelWidth": "6.45", "Prop_ImageDetectorPixelHeight": "6.45", "Prop_TimeStampProducer": "2", "Prop_FrameStampProducer": "2", }, "Acquisition": { "NrExposure": "60", "NrTrigger": "0", "ExposureTime": "5 s", "AcqMode": "4", "DataType": "8", "DataTypeOfSingleImage": "7", "CurveCorr": "0", "DefectCorrection": "0", "areSource": "0,0,672,512", "areGRBScan": "0,0,672,512", "pntOrigCh": "0,0", "pntOrigFB": "0,0", "pntBinning": "2,2", "BytesPerPixel": "4", "IsLineData": "0", "BacksubCorr": "-1", "ShadingCorr": "0", "ZAxisLabel": "Intensity", "ZAxisUnit": "Count", "miMirrorRotate": "0", }, "Grabber": {"Type": "5", "SubType": "0"}, "DisplayLUT": { "EntrySize": "9", "LowerValue": "764", "UpperValue": "3562", "LowerValueEx": "0", "UpperValueEx": "32767", "BitRange": "16x bit", "Color": "2", "LUTType": "0", "LUTInverted": "0", "AutoLutInLiveMode": "0", "DisplayNegative": "0", "Gamma": "1", "First812OvlCol": "1", "Lut16xShift": "7", "Lut16xOvlVal": "3932100", }, "ExternalDevices": { "TriggerDelay": "150", "PostTriggerTime": "10", "ExposureTime": "10", "TDStatusCableConnected": "0", "ConnectMonitorOut": "0", "ConnectResetIn": "0", "TriggerMethod": "2", "UseDTBE": "0", "ExpTimeAddMultiple": "-1", "DontSendReset": "0", "MultipleOfSweep": "1", "A6538Connected": "0", "CounterBoardInstalled": "0", "MotorizedSlitInstalled": "0", "UseSpecAsMono": "0", "GPIBInstalled": "-1", "CounterBoardIOBase": "0", "MotorizedSlitPortID": "1", "GPIBIOBase": "0", }, "Streak camera": { "UseDevice": "-1", "DeviceName": "C5680", "PluginName": "M5677", "GPIBCableConnected": "-1", "GPIBBase": "8", "Time Range": "20 us", "Mode": "Operate", "Gate Mode": "Normal", "MCP Gain": "50", "Shutter": "Open", "Gate Time": "0", "Trig. Mode": "Cont", "Trigger status": "Ready", "Trig. level": "1", "Trig. slope": "Rising", "FocusTimeOver": "11", }, "Spectrograph": { "UseDevice": "-1", "DeviceName": "Andor SG", "PluginName": "Kymera 328i", "GPIBCableConnected": "0", "GPIBBase": "13", "Wavelength": "500", "Grating": "300 g/mm", "Blaze": "500", "Ruling": "300", "Exit Mirror": "Front", "Side Ent. Slitw.": "10", "Turret": "1", "Focus Mirror": "234", "Side Entry Iris": "26", }, "Delay box": { "UseDevice": "-1", "DeviceName": "C4792-01", "PluginName": "", "GPIBCableConnected": "0", "Trig. Mode": "Int. Trig.", "Repetition Rate": "1 Hz", "L-Pulsewidth": "300 ns", "Delay Int.Trig": "-999999999900", "Delay Ext.Trig": "0", "Dly Mode-Lock": "0", "Dly1 DmpMode": "0", "Dly2 DmpMode": "0", }, "Delay2 box": {"UseDevice": "0"}, "Filter wheel": {"UseDevice": "0"}, "Scaling": { "ScalingXType": "2", "ScalingXScale": "1", "ScalingXUnit": "nm", "ScalingXScalingFile": "#1379631,0672", "ScalingYType": "2", "ScalingYScale": "1", "ScalingYUnit": "us", "ScalingYScalingFile": "#1382319,0512", }, "Comment": {"UserComment": ""}, } assert expected_metadata == original_metadata def test_metadata(self): metadata = self.s.metadata detector = self.s.metadata.Acquisition_instrument.Detector spectrometer = self.s.metadata.Acquisition_instrument.Spectrometer assert metadata.General.date == "2023-01-20" assert metadata.General.time == "11:34:55" assert metadata.General.original_filename == "operate_mode.img" assert metadata.General.title == metadata.General.original_filename[:-4] 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 isinstance(detector.binning, tuple) assert len(detector.binning) == 2 assert detector.binning[0] == 2 assert detector.binning[1] == 2 assert detector.detector_type == "StreakCamera" assert detector.model == "C5680" assert detector.frames == 60 np.testing.assert_allclose(detector.integration_time, 300) assert detector.processing.background_correction is True assert detector.processing.curvature_correction is False assert detector.processing.defect_correction is False assert detector.processing.shading_correction is False np.testing.assert_allclose(detector.time_range, 20) assert detector.time_range_units == "µs" np.testing.assert_allclose(detector.mcp_gain, 50) assert detector.acquisition_mode == "analog_integration" np.testing.assert_allclose(spectrometer.entrance_slit_width, 10) assert spectrometer.model == "Andor SG" assert spectrometer.Grating.blazing_wavelength == 500 assert spectrometer.Grating.groove_density == 300 np.testing.assert_allclose(spectrometer.central_wavelength, 500) class TestFocus: @classmethod def setup_class(cls): cls.s_focus = hs.load(testfile_focus_mode_path, reader="Hamamatsu") @classmethod def teardown_class(cls): del cls.s_focus gc.collect() def test_data_focus(self): expected_data_end = [[0, 0, 36], [0, 0, 0], [21, 0, 0]] np.testing.assert_allclose(expected_data_end, self.s_focus.isig[-3:, -3:].data) def test_axes_focus(self): axes = self.s_focus.axes_manager assert axes.signal_dimension == 2 assert axes.navigation_dimension == 0 ax0 = axes[0] ax1 = axes[1] assert ax0.name == "Wavelength" assert ax1.name == "Vertical CCD Position" assert ax1.units == "px" assert ax0.units == "nm" assert ax0.size == 672 assert ax1.size == 512 np.testing.assert_allclose(ax1.scale, 1) np.testing.assert_allclose(ax1.offset, 0) expected_data_start_X = [472.252, 472.33337, 472.41473, 472.4961, 472.57745] np.testing.assert_allclose(ax0.axis[:5], expected_data_start_X) class TestPhotonCount: @classmethod def setup_class(cls): cls.s = hs.load(testfile_photon_count_path, reader="Hamamatsu") @classmethod def teardown_class(cls): del cls.s gc.collect() def test_data(self): expected_data = [0, 0, 0] np.testing.assert_allclose(self.s.isig[-3:, 0].data, expected_data) def test_metadata(self): metadata = self.s.metadata assert metadata.General.date == "2018-08-29" assert ( metadata.Acquisition_instrument.Detector.acquisition_mode == "photon_counting" ) assert "Grating" not in list( self.s.metadata.Acquisition_instrument.Spectrometer.as_dictionary() ) assert self.s.original_metadata.file_type == "bit16" class TestShading: @classmethod def setup_class(cls): cls.s = hs.load(testfile_shading_path, reader="Hamamatsu") @classmethod def teardown_class(cls): del cls.s gc.collect() def test_metadata(self): np.testing.assert_allclose( self.s.metadata.Acquisition_instrument.Detector.time_range, 4 ) def test_data(self): expected_data = [9385, 8354, 7658] np.testing.assert_allclose(self.s.isig[:3, 0].data, expected_data)