Merge pull request Quasars#37 from ngergihun/fixes

ngergihun · web-flow · commit a5569b19fe6f · 2025-06-30T13:45:34.000+02:00
[FIX][ENH] - NeaSpectrum
diff --git a/pySNOM/datasets/testspectrum_multipoint.txt b/pySNOM/datasets/testspectrum_multipoint.txt
@@ -0,0 +1,39 @@
+# www.neaspec.com
+# Scan:	 	Fourier Scan
+# Project:	 	nanoFTIR-QualityControl
+# Description:	 	NeaSpec-Slow-Arrowhead-Clean-REV2-45avg
+# Date:	 	05/19/2024 16:59:10
+# Scanner Center Position (X, Y):	[µm]	46.77	49.79	 
+# Rotation:	[°]	0	 	 
+# Scan Area (X, Y, Z):	[µm]	1.000	0.000	0.000
+# Pixel Area (X, Y, Z):	[px]	2	1	2
+# Interferometer Center/Distance:	[µm]	470.000	490.000	 
+# Averaging:	 	45	 	 
+# Integration time:	[ms]	20	 	 
+# Wavenumber Scaling:	 	1.003656	 	 
+# Laser Source:	 	
+# Detector:	 	R
+# Target Wavelength:	[µm]		 	 
+# Demodulation Mode:	 	Fourier
+# Tip Frequency:	[Hz]	68,263.500	 	 
+# Tip Amplitude:	[mV]	339.702	 	 
+# Tapping Amplitude:	[nm]	76.233	 	 
+# Modulation Frequency:	[Hz]	0.000	 	 
+# Modulation Amplitude:	[mV]	0.000	 	 
+# Modulation Offset:	[mV]	0.000	 	 
+# Setpoint:	[%]	80.49	 	 
+# Regulator (P, I, D):	 	3.767854	6.228756	1.000000
+# Tip Potential:	[mV]	0.000	 	 
+# M1A Scaling:	[nm/V]	1.520	 	 
+# M1A Cantilever Factor:	 	2.066	 	 
+# Q-Factor:	 	221.1	 	 
+# Version:	 	2.1.11508.0
+Row	Column	Omega	Wavenumber	O0A	O0P	O1A	O1P	O2A	O2P	O3A	O3P	O4A	O4P	O5A	O5P	
+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	
+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	
+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	
+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	
+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	
+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	
+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	
+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	
diff --git a/pySNOM/datasets/testspectrum_nanoraman.txt b/pySNOM/datasets/testspectrum_nanoraman.txt
@@ -0,0 +1,48 @@
+# www.neaspec.com
+# Scan:	 	AFM-Raman/PL Scan (Tapping Mode)
+# Project:	 	KJK - Wiegner RCP - SM007
+# Description:	 	Area2
+# Date:	 	05/14/2025 17:07:02
+# Scanner Center Position (X, Y):	[µm]	52.83	53.80	 
+# Rotation:	[°]	0	 	 
+# Scan Area (X, Y, Z):	[µm]	5.000	5.000	0.000
+# Pixel Area (X, Y, Z):	[px]	2	1	1
+# Averaging:	 	1	 	 
+# Integration time:	[ms]	10	 	 
+# Laser Source:	 	532 nm visible laser	
+# Detector:	 	VIS
+# Target Wavelength:	[µm]		 	 
+# Demodulation Mode:	 	Fourier
+# Tip Frequency:	[Hz]	56,332.262	 	 
+# Tip Amplitude:	[mV]	10.000	 	 
+# Tapping Amplitude:	[nm]	44.401	 	 
+# Modulation Frequency:	[Hz]	0.000	 	 
+# Modulation Amplitude:	[mV]	0.000	 	 
+# Modulation Offset:	[mV]	0.000	 	 
+# Setpoint:	[%]	80.28	 	 
+# Regulator (P, I, D):	 	6.394934	13.411389	1.000000
+# Tip Potential:	[mV]	0.000	 	 
+# M1A Scaling:	[nm/V]	1.800	 	 
+# M1A Cantilever Factor:	 	2.449	 	 
+# Q-Factor:	 	157.5	 	 
+# Version:	 	2.3.13115.0
+# CCD Pixels:	[px]	1340	 	 
+# Spectral Range:	[nm]	533.186	792.054	 
+# Exposure Time:	[s]	0.100	 	 
+# Input slit:	 	Direct Input	 	 
+# Output slit:	 	Direct	 	 
+# Shutter:	 	Open	 	 
+# Grating Offset:	 	0	 	 
+# Focus Mirror:	[nm]	0	 	 
+# Camera:	 	CCD	 	 
+# Temperature:	[°C]	-75.0	 	 
+# Grating:	[l/mm]	300.000	750nm	 
+Row	Column	Wavelength	Index	Data	Z
+0	0	533186.4014	0	11.0000	0.0000
+0	0	533383.8501	1	-5.0000	0.0000
+0	0	533581.2988	2	-2.0000	0.0000
+0	0	533778.7476	3	7.0000	0.0000
+0	1	533186.4014	0	5.0000	0.0000
+0	1	533383.8501	1	-4.0000	0.0000
+0	1	533581.2988	2	3.0000	0.0000
+0	1	533778.7476	3	-1.0000	0.0000
diff --git a/pySNOM/defaults.py b/pySNOM/defaults.py
@@ -17,6 +17,7 @@ def __init__(self) -> None:
         self.spectral_mode_defs = {
             "Fourier Scan": "nanoFTIR",
             "Pointspectroscopy PTE+": "PTE",
+            "AFM-Raman/PL Scan (Tapping Mode)": "nanoRaman",
         }
 
 
diff --git a/pySNOM/spectra.py b/pySNOM/spectra.py
@@ -3,7 +3,9 @@
 from pySNOM.images import type_from_channelname
 from pySNOM.defaults import Defaults
 
-MeasurementModes = Enum("MeasurementModes", ["None", "nanoFTIR", "PsHet", "PTE"])
+MeasurementModes = Enum(
+    "MeasurementModes", ["None", "nanoFTIR", "PsHet", "PTE", "nanoRaman"]
+)
 DataTypes = Enum("DataTypes", ["Amplitude", "Phase", "Complex", "Topography"])
 ChannelTypes = Enum("ChannelTypes", ["None", "Optical", "Mechanical"])
 ScanTypes = Enum("ScanTypes", ["Point", "LineScan", "HyperScan"])
@@ -219,19 +221,29 @@ def reshape_spectrum_data(data, params):
         if params["Scan"] == "Fourier Scan":
             n = 2
 
-        for channel in list(data.keys()):
+        allchannels = list(data.keys())
+        if "Depth" in allchannels:
+            spectral_depth = len(np.unique(data["Depth"]))
+        elif "Index" in allchannels:
+            spectral_depth = len(np.unique(data["Index"]))
+        elif "Omega" in allchannels:
+            spectral_depth = len(np.unique(data["Omega"]))
+        else:
+            spectral_depth = params["PixelArea"][2] * n
+
+        for channel in allchannels:
             # Point spectrum
             if params["PixelArea"][1] == 1 and params["PixelArea"][0] == 1:
-                data[channel] = np.reshape(data[channel], (params["PixelArea"][2] * n))
+                data[channel] = np.reshape(data[channel], (spectral_depth))
 
             # Linescan and HyperScan
             else:
-                data[data[channel]] = np.reshape(
+                data[channel] = np.reshape(
                     data[channel],
                     (
                         params["PixelArea"][0],
                         params["PixelArea"][1],
-                        params["PixelArea"][2] * n,
+                        spectral_depth,
                     ),
                 )
 
diff --git a/pySNOM/tests/test_readers.py b/pySNOM/tests/test_readers.py
@@ -54,6 +54,16 @@ def test_general_reader_spectrum(self):
         np.testing.assert_almost_equal(data["O2A"][0], 0.1600194)
         np.testing.assert_string_equal(params["Scan"], "Fourier Scan")
 
+    def test_general_reader_nanoraman(self):
+        f = "datasets/testspectrum_nanoraman.txt"
+        file_reader = readers.NeaSpectralReader(os.path.join(pySNOM.__path__[0], f))
+        data, params = file_reader.read()
+
+        np.testing.assert_almost_equal(data["Data"][0], 11.0)
+        np.testing.assert_string_equal(
+            params["Scan"], "AFM-Raman/PL Scan (Tapping Mode)"
+        )
+
     def test_legacy_nea_reader(self):
         f = "datasets/neafile_test_ifg.nea"
         file_reader = readers.NeaFileLegacyReader(os.path.join(pySNOM.__path__[0], f))
diff --git a/pySNOM/tests/test_spectra.py b/pySNOM/tests/test_spectra.py
@@ -20,6 +20,18 @@ def test_pointspectrum_object(self):
         np.testing.assert_string_equal(s.scantype, "Point")
         np.testing.assert_equal(np.shape(s.data["O2A"])[0], 2048)
 
+    def test_multipointspectrum_object(self):
+        f = "datasets/testspectrum_multipoint.txt"
+        file_reader = readers.NeaSpectralReader(os.path.join(pySNOM.__path__[0], f))
+        data, params = file_reader.read()
+
+        s = spectra.NeaSpectrum(data, params)
+
+        np.testing.assert_almost_equal(s.data["O2A"][1, 0, 0], 0.1600194)
+        np.testing.assert_string_equal(s.parameters["Scan"], "Fourier Scan")
+        np.testing.assert_string_equal(s.scantype, "LineScan")
+        np.testing.assert_equal(np.shape(s.data["O2A"])[2], 4)
+
     def test_transfromations(self):
         f = "datasets/testspectrum_singlepoint.txt"
         file_reader = readers.NeaSpectralReader(os.path.join(pySNOM.__path__[0], f))

Original file line number	Diff line number	Diff line change
`@@ -17,6 +17,7 @@ def __init__(self) -> None:`
`17`	`17`	`self.spectral_mode_defs = {`
`18`	`18`	`"Fourier Scan": "nanoFTIR",`
`19`	`19`	`"Pointspectroscopy PTE+": "PTE",`
	`20`	`+ "AFM-Raman/PL Scan (Tapping Mode)": "nanoRaman",`
`20`	`21`	`}`
`21`	`22`
`22`	`23`