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Merge pull request #37 from ngergihun/fixes
[FIX][ENH] - NeaSpectrum
2 parents 310f977 + 0bb72cf commit a5569b1

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‎pySNOM/datasets/testspectrum_multipoint.txt‎

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# www.neaspec.com
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# Scan:   Fourier Scan
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# Project:   nanoFTIR-QualityControl
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# Description:   NeaSpec-Slow-Arrowhead-Clean-REV2-45avg
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# Date:   05/19/2024 16:59:10
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# Scanner Center Position (X, Y): [µm] 46.77 49.79  
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# Rotation: [°] 0    
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# Scan Area (X, Y, Z): [µm] 1.000 0.000 0.000
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# Pixel Area (X, Y, Z): [px] 2 1 2
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# Interferometer Center/Distance: [µm] 470.000 490.000  
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# Averaging:   45    
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# Integration time: [ms] 20    
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# Wavenumber Scaling:   1.003656    
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# Laser Source:  
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# Detector:   R
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# Target Wavelength: [µm]    
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# Demodulation Mode:   Fourier
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# Tip Frequency: [Hz] 68,263.500    
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# Tip Amplitude: [mV] 339.702    
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# Tapping Amplitude: [nm] 76.233    
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# Modulation Frequency: [Hz] 0.000    
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# Modulation Amplitude: [mV] 0.000    
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# Modulation Offset: [mV] 0.000    
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# Setpoint: [%] 80.49    
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# Regulator (P, I, D):   3.767854 6.228756 1.000000
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# Tip Potential: [mV] 0.000    
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# M1A Scaling: [nm/V] 1.520    
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# M1A Cantilever Factor:   2.066    
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# Q-Factor:   221.1    
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# Version:   2.1.11508.0
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Row Column Omega Wavenumber O0A O0P O1A O1P O2A O2P O3A O3P O4A O4P O5A O5P
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0 0 0 0 37.119324 3.1415927 1.738142 -3.1415913 0.1600194 8.742275E-08 0.12289047 -2.6534444E-10 0.03433025 -3.1415925 0.044003725 -3.1415925
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0 0 1 2.560346956632653 35.434025 2.681263 4.94985 0.9037826 0.43971792 -2.300659 0.16032808 -0.58963114 0.053768463 1.7078916 0.08377697 1.4515767
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0 0 2 5.120693913265306 32.58373 2.3122003 8.926398 -0.2935503 0.8658856 2.7100954 0.26857227 -1.3153769 0.09340307 0.8722349 0.14734396 0.52470887
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0 0 3 7.681040869897961 33.03119 2.0073247 12.101863 -1.3972439 1.3369256 1.5798267 0.43721926 -2.1214292 0.15267329 0.18834925 0.21037804 -0.2551048
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0 1 0 0 37.119324 3.1415927 1.738142 -3.1415913 0.1600194 8.742275E-08 0.12289047 -2.6534444E-10 0.03433025 -3.1415925 0.044003725 -3.1415925
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0 1 1 2.560346956632653 35.434025 2.681263 4.94985 0.9037826 0.43971792 -2.300659 0.16032808 -0.58963114 0.053768463 1.7078916 0.08377697 1.4515767
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0 1 2 5.120693913265306 32.58373 2.3122003 8.926398 -0.2935503 0.8658856 2.7100954 0.26857227 -1.3153769 0.09340307 0.8722349 0.14734396 0.52470887
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0 1 3 7.681040869897961 33.03119 2.0073247 12.101863 -1.3972439 1.3369256 1.5798267 0.43721926 -2.1214292 0.15267329 0.18834925 0.21037804 -0.2551048

‎pySNOM/datasets/testspectrum_nanoraman.txt‎

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# www.neaspec.com
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# Scan:   AFM-Raman/PL Scan (Tapping Mode)
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# Project:   KJK - Wiegner RCP - SM007
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# Description:   Area2
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# Date:   05/14/2025 17:07:02
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# Scanner Center Position (X, Y): [µm] 52.83 53.80  
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# Rotation: [°] 0    
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# Scan Area (X, Y, Z): [µm] 5.000 5.000 0.000
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# Pixel Area (X, Y, Z): [px] 2 1 1
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# Averaging:   1    
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# Integration time: [ms] 10    
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# Laser Source:   532 nm visible laser
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# Detector:   VIS
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# Target Wavelength: [µm]    
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# Demodulation Mode:   Fourier
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# Tip Frequency: [Hz] 56,332.262    
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# Tip Amplitude: [mV] 10.000    
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# Tapping Amplitude: [nm] 44.401    
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# Modulation Frequency: [Hz] 0.000    
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# Modulation Amplitude: [mV] 0.000    
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# Modulation Offset: [mV] 0.000    
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# Setpoint: [%] 80.28    
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# Regulator (P, I, D):   6.394934 13.411389 1.000000
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# Tip Potential: [mV] 0.000    
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# M1A Scaling: [nm/V] 1.800    
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# M1A Cantilever Factor:   2.449    
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# Q-Factor:   157.5    
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# Version:   2.3.13115.0
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# CCD Pixels: [px] 1340    
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# Spectral Range: [nm] 533.186 792.054  
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# Exposure Time: [s] 0.100    
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# Input slit:   Direct Input    
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# Output slit:   Direct    
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# Shutter:   Open    
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# Grating Offset:   0    
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# Focus Mirror: [nm] 0    
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# Camera:   CCD    
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# Temperature: [°C] -75.0    
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# Grating: [l/mm] 300.000 750nm  
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Row Column Wavelength Index Data Z
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0 0 533186.4014 0 11.0000 0.0000
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0 0 533383.8501 1 -5.0000 0.0000
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0 0 533581.2988 2 -2.0000 0.0000
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0 0 533778.7476 3 7.0000 0.0000
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0 1 533186.4014 0 5.0000 0.0000
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0 1 533383.8501 1 -4.0000 0.0000
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0 1 533581.2988 2 3.0000 0.0000
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0 1 533778.7476 3 -1.0000 0.0000

‎pySNOM/defaults.py‎

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@@ -17,6 +17,7 @@ def __init__(self) -> None:
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self.spectral_mode_defs = {
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"Fourier Scan": "nanoFTIR",
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"Pointspectroscopy PTE+": "PTE",
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"AFM-Raman/PL Scan (Tapping Mode)": "nanoRaman",
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}
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‎pySNOM/spectra.py‎

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from pySNOM.images import type_from_channelname
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from pySNOM.defaults import Defaults
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MeasurementModes = Enum("MeasurementModes", ["None", "nanoFTIR", "PsHet", "PTE"])
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MeasurementModes = Enum(
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"MeasurementModes", ["None", "nanoFTIR", "PsHet", "PTE", "nanoRaman"]
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)
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DataTypes = Enum("DataTypes", ["Amplitude", "Phase", "Complex", "Topography"])
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ChannelTypes = Enum("ChannelTypes", ["None", "Optical", "Mechanical"])
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ScanTypes = Enum("ScanTypes", ["Point", "LineScan", "HyperScan"])
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if params["Scan"] == "Fourier Scan":
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n = 2
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for channel in list(data.keys()):
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allchannels = list(data.keys())
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if "Depth" in allchannels:
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spectral_depth = len(np.unique(data["Depth"]))
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elif "Index" in allchannels:
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spectral_depth = len(np.unique(data["Index"]))
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elif "Omega" in allchannels:
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spectral_depth = len(np.unique(data["Omega"]))
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else:
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spectral_depth = params["PixelArea"][2] * n
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for channel in allchannels:
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# Point spectrum
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if params["PixelArea"][1] == 1 and params["PixelArea"][0] == 1:
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data[channel] = np.reshape(data[channel], (params["PixelArea"][2] * n))
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data[channel] = np.reshape(data[channel], (spectral_depth))
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# Linescan and HyperScan
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else:
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data[data[channel]] = np.reshape(
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data[channel] = np.reshape(
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data[channel],
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(
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params["PixelArea"][0],
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params["PixelArea"][1],
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params["PixelArea"][2] * n,
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spectral_depth,
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),
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)
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‎pySNOM/tests/test_readers.py‎

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np.testing.assert_almost_equal(data["O2A"][0], 0.1600194)
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np.testing.assert_string_equal(params["Scan"], "Fourier Scan")
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def test_general_reader_nanoraman(self):
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f = "datasets/testspectrum_nanoraman.txt"
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file_reader = readers.NeaSpectralReader(os.path.join(pySNOM.__path__[0], f))
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data, params = file_reader.read()
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np.testing.assert_almost_equal(data["Data"][0], 11.0)
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np.testing.assert_string_equal(
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params["Scan"], "AFM-Raman/PL Scan (Tapping Mode)"
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)
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def test_legacy_nea_reader(self):
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f = "datasets/neafile_test_ifg.nea"
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file_reader = readers.NeaFileLegacyReader(os.path.join(pySNOM.__path__[0], f))

‎pySNOM/tests/test_spectra.py‎

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@@ -20,6 +20,18 @@ def test_pointspectrum_object(self):
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np.testing.assert_string_equal(s.scantype, "Point")
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np.testing.assert_equal(np.shape(s.data["O2A"])[0], 2048)
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def test_multipointspectrum_object(self):
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f = "datasets/testspectrum_multipoint.txt"
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file_reader = readers.NeaSpectralReader(os.path.join(pySNOM.__path__[0], f))
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data, params = file_reader.read()
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s = spectra.NeaSpectrum(data, params)
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np.testing.assert_almost_equal(s.data["O2A"][1, 0, 0], 0.1600194)
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np.testing.assert_string_equal(s.parameters["Scan"], "Fourier Scan")
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np.testing.assert_string_equal(s.scantype, "LineScan")
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np.testing.assert_equal(np.shape(s.data["O2A"])[2], 4)
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def test_transfromations(self):
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f = "datasets/testspectrum_singlepoint.txt"
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file_reader = readers.NeaSpectralReader(os.path.join(pySNOM.__path__[0], f))

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