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# -*- 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 <https://www.gnu.org/licenses/#GPL>.
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)
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