Detector library examples

src/microsim/schema/detectors/Andor_iXon_Ultra_888_BVF_QE.csv

@@ -0,0 +1,80 @@
+310,12.482
+320,14.224
+330,16.11
+340,19.158
+350,21.916
+360,25.399
+370,31.06
+380,38.607
+390,45.957
+400,53.308
+410,60.051
+420,65.08
+430,70.827
+440,74.456
+450,78.52
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+570,96.907
+580,96.829
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+830,63.28
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+1000,11.466
+1010,9.434
+1020,7.692
+1030,5.951
+1040,4.499
+1050,3.193
+1060,2.177
+1070,1.306
+1080,0.653
+1090,0.218
+1100,0.145

src/microsim/schema/detectors/Andor_iXon_Ultra_888_EXF_QE.csv

@@ -0,0 +1,80 @@
+310,8.417
+320,11.412
+330,14.265
+340,18.545
+350,23.871
+360,29.957
+370,39.777
+380,50.839
+390,60.288
+400,69.126
+410,76.788
+420,80.171
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+570,89.539
+580,89.872
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+600,90.442
+610,90.68
+620,91.013
+630,91.298
+640,91.441
+650,91.441
+660,91.441
+670,91.369
+680,91.191
+690,91.013
+700,90.514
+710,89.872
+720,89.016
+730,88.16
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+750,85.877
+760,84.165
+770,82.596
+780,80.456
+790,78.459
+800,75.892
+810,73.039
+820,70.471
+830,67.19
+840,64.337
+850,60.77
+860,57.632
+870,53.78
+880,50.499
+890,46.648
+900,42.796
+910,39.515
+920,35.663
+930,32.382
+940,28.816
+950,25.82
+960,22.539
+970,19.686
+980,16.833
+990,14.408
+1000,11.84
+1010,9.558
+1020,7.846
+1030,5.991
+1040,4.565
+1050,3.138
+1060,2.14
+1070,1.284
+1080,0.713
+1090,0.285
+1100,0.143

src/microsim/schema/detectors/C15440_20UP_QE.csv

@@ -0,0 +1,99 @@
+308,4.73
+316,7.973
+324,16.757
+332,30.27
+340,41.622
+348,45.27
+356,48.649
+364,52.162
+372,57.432
+380,62.162
+388,66.351
+396,70.135
+404,72.703
+412,74.73
+420,76.757
+428,78.514
+436,80.405
+444,82.027
+452,83.784
+460,85.27
+468,86.351
+476,87.432
+484,88.649
+492,89.595
+500,90.405
+508,91.216
+516,92.027
+524,92.838
+532,93.514
+540,94.324
+548,94.595
+556,94.865
+564,94.865
+572,94.595
+580,94.459
+588,94.324
+596,94.054
+604,93.649
+612,93.108
+620,92.432
+628,91.892
+636,91.216
+644,90.541
+652,89.865
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+668,87.838
+676,86.622
+684,85.541
+692,84.189
+700,82.838
+708,81.351
+716,79.73
+724,78.108
+732,76.622
+740,74.459
+748,72.297
+756,70
+764,67.568
+772,65.27
+780,63.108
+788,60.811
+796,58.514
+804,56.216
+812,53.919
+820,51.892
+828,50.27
+836,48.784
+844,47.027
+852,45.27
+860,42.973
+868,40.676
+876,38.378
+884,35.946
+892,33.243
+900,31.216
+908,29.324
+916,27.568
+924,25.811
+932,23.784
+940,21.622
+948,20.27
+956,18.784
+964,17.432
+972,16.216
+980,14.865
+988,13.243
+996,11.486
+1004,10
+1012,8.784
+1020,7.432
+1028,6.351
+1036,5.27
+1044,4.189
+1052,3.243
+1060,2.568
+1068,2.027
+1076,1.514
+1084,1.081
+1092,0.811

src/microsim/schema/detectors/lib.py

@@ -1,10 +1,40 @@
 """Library of commercial detectors for the microsim schema."""
 
+import csv
+from pathlib import Path
+
 import numpy as np
 
-from microsim.schema.detectors._camera import CameraCCD
+from microsim.schema.detectors._camera import CameraCCD, CameraCMOS, CameraEMCCD
 from microsim.schema.spectrum import Spectrum
 
+
+def _load_qe_from_csv(csv_filename: str) -> tuple[np.ndarray, np.ndarray]:
+    """Load QE curve from CSV file.
+
+    Args:
+        csv_filename: Name of the CSV, first col should be wavelength in nm,
+         second col should be QE in %
+
+    Returns
+    -------
+        tuple: (wavelengths, qe_values) where qe_values are normalized to [0,1]
+    """
+    csv_path = Path(__file__).parent / csv_filename
+    wavelengths = []
+    qe_values = []
+
+    with open(csv_path) as f:
+        reader = csv.reader(f)
+        for row in reader:
+            if len(row) >= 2:
+                wavelengths.append(float(row[0]))
+                # Convert percentage
+                qe_values.append(float(row[1]) / 100.0)
+
+    return np.array(wavelengths), np.array(qe_values)
+
+
 # fmt: off
 r2qe = [0.5188,0.5219,0.5249,0.5279,0.5307,0.5335,0.5363,0.539,0.5418,0.5445,0.5473,0.5501,0.5531,0.5561,0.5593,0.5627,0.5662,0.57,0.5738,0.5778,0.5819,0.586,0.5902,0.5943,0.5984,0.6024,0.6064,0.6102,0.6138,0.6172,0.6204,0.6234,0.6261,0.6286,0.631,0.6333,0.6356,0.6378,0.6401,0.6425,0.6451,0.6478,0.6508,0.654,0.6573,0.6607,0.6641,0.6675,0.6708,0.6739,0.6769,0.6796,0.682,0.6841,0.6859,0.6876,0.6891,0.6905,0.6919,0.6933,0.6948,0.6964,0.698,0.6997,0.7013,0.7027,0.7041,0.7053,0.7062,0.7068,0.7072,0.7072,0.707,0.7065,0.7058,0.7049,0.7039,0.7027,0.7014,0.7001,0.6988,0.6976,0.6964,0.6954,0.6946,0.6939,0.6934,0.6931,0.693,0.693,0.6931,0.6932,0.6932,0.6931,0.6928,0.6923,0.6914,0.6902,0.6886,0.6864,0.6837,0.6805,0.6769,0.673,0.6689,0.6648,0.6608,0.657,0.6536,0.6506,0.6481,0.6459,0.6442,0.6426,0.6413,0.6401,0.639,0.6378,0.6365,0.6351,0.6334,0.6315,0.6294,0.6272,0.6249,0.6224,0.6199,0.6174,0.6148,0.6123,0.6099,0.6075,0.6052,0.603,0.6009,0.599,0.5971,0.5954,0.5938,0.5923,0.5908,0.5894,0.588,0.5866,0.5853,0.5839,0.5826,0.5811,0.5797,0.5781,0.5765,0.5748,0.573,0.571,0.5689,0.5667,0.5645,0.5624,0.5604,0.5586,0.557,0.5556,0.5543,0.553,0.5517,0.5505,0.5491,0.5476,0.546,0.5442,0.5422,0.5401,0.5379,0.5356,0.5335,0.5314,0.5294,0.5275,0.5257,0.5238,0.522,0.5202,0.5184,0.5165,0.5146,0.5127,0.5107,0.5086,0.5065,0.5043,0.5021,0.4998,0.4974,0.4949,0.4923,0.4897,0.487,0.4842,0.4813,0.4784,0.4754,0.4724,0.4694,0.4664,0.4634,0.4605,0.4576,0.4548,0.4521,0.4494,0.4469,0.4445,0.4421,0.4399,0.4377,0.4356,0.4335,0.4315,0.4296,0.4277,0.4259,0.424,0.4223,0.4205,0.4188,0.4171,0.4154,0.4137,0.4119,0.4101,0.4083,0.4065,0.4045,0.4025,0.4005,0.3983,0.3961,0.3938,0.3914,0.389,0.3865,0.3841,0.3816,0.3792,0.3767,0.3743,0.372,0.3697,0.3674,0.3653,0.3633,0.3614,0.3595,0.3578,0.3561,0.3545,0.3529,0.3513,0.3497,0.3481,0.3464,0.3446,0.3427,0.3408,0.3387,0.3366,0.3345,0.3324,0.3303,0.3282,0.3262,0.3243,0.3225,0.3208,0.3193,0.3178,0.3164,0.3149,0.3134,0.3118,0.3101,0.3082,0.3062,0.3041,0.3019,0.2996,0.2974,0.2951,0.293,0.2909,0.289,0.2873,0.2856,0.2842,0.2828,0.2815,0.2803,0.2792,0.2781,0.277,0.2759,0.2748,0.2737,0.2725,0.2712,0.2699,0.2684,0.267,0.2654,0.2638,0.2621,0.2604,0.2586,0.2569,0.255,0.2532,0.2514,0.2495,0.2477,0.2459,0.2441,0.2423,0.2405,0.2388,0.2371,0.2355,0.2339,0.2324,0.2309,0.2295,0.2281,0.2267,0.2254,0.2241,0.2228,0.2215,0.2202,0.2189,0.2176,0.2162,0.2149,0.2135,0.2121,0.2106,0.2092,0.2076,0.2061,0.2045,0.2029,0.2012,0.1996,0.198,0.1964,0.1948,0.1933,0.1918,0.1903,0.1889,0.1875,0.1862,0.185,0.1839,0.1828,0.1819,0.181,0.1803,0.1796,0.1789,0.1782,0.1775,0.1768,0.176,0.1752,0.1742,0.1731,0.1719,0.1704,0.1689,0.1672,0.1654,0.1635,0.1616,0.1596,0.1577,0.1558,0.154,0.1523,0.1507,0.1492,0.1478,0.1464,0.1452,0.144,0.1429,0.1418,0.1408,0.1399,0.139,0.1381,0.1372,0.1364,0.1355,0.1347,0.1339,0.133,0.1321,0.1312,0.1303,0.1293,0.1283,0.1273,0.1262,0.1252,0.1241,0.123,0.1218,0.1207,0.1195,0.1184,0.1172,0.1161,0.1149,0.1138,0.1126,0.1115,0.1104,0.1093,0.1082,0.1071,0.106,0.105,0.104,0.1029,0.1019,0.1009,0.0999,0.099,0.098,0.0971,0.0962,0.0952,0.0943,0.0935,0.0926,0.0917,0.0909,0.09,0.0892,0.0884,0.0876,0.0868,0.086,0.0852,0.0844,0.0837,0.0829,0.0822,0.0815,0.0807,0.08,0.0793,0.0786,0.0779,0.0772,0.0766,0.0759,0.0752,0.0746,0.0739,0.0732,0.0726,0.0719,0.0713,0.0707,0.07,0.0694,0.0688,0.0681,0.0675,0.0669,0.0663,0.0656,0.065,0.0644,0.0638,0.0632,0.0626,0.0619,0.0613,0.0607,0.0601,0.0595,0.0589,0.0583,0.0577,0.057,0.0564,0.0558,0.0552,0.0546,0.054,0.0534,0.0527,0.0521,0.0515,0.0509,0.0503,0.0496,0.049,0.0484,0.0477,0.0471,0.0465,0.0458,0.0452,0.0445,0.0439,0.0432,0.0426,0.0419,0.0413,0.0406,0.04,0.0393,0.0387,0.038,0.0374,0.0367,0.0361,0.0355,0.0349,0.0343,0.0337,0.0331,0.0325,0.0319,0.0314,0.0308,0.0303,0.0298,0.0293,0.0288,0.0283,0.0278,0.0274,0.027,0.0266,0.0262,0.0258,0.0254,0.025,0.0247,0.0243,0.024,0.0237,0.0233,0.023,0.0227,0.0224,0.0221,0.0218,0.0215,0.0213,0.021,0.0207,0.0204,0.0201,0.0198,0.0195,0.0193,0.019,0.0187,0.0184,0.0181,0.0178,0.0174,0.0171,0.0168,0.0165,0.0162,0.0159,0.0155,0.0152,0.0149,0.0146,0.0142,0.0139,0.0136,0.0133,0.013,0.0127,0.0124,0.0121,0.0118,0.0115,0.0112,0.0109,0.0106,0.0103,0.0101,0.0098]  # noqa
 # fmt: on
@@ -23,3 +53,46 @@
     # npixels_h=1344,
     # npixels_v=1024,
 )
+
+
+# Load quantum efficiency data from CSV files
+_bvf_wavelengths, _bvf_qe = _load_qe_from_csv("Andor_iXon_Ultra_888_BVF_QE.csv")
+_exf_wavelengths, _exf_qe = _load_qe_from_csv("Andor_iXon_Ultra_888_EXF_QE.csv")
+
+
+Andor_iXon_Ultra_888_BVF = CameraEMCCD(
+    # photodiode_size=13, #adding in case it's needed in the future
+    name="Andor iXon Ultra 888 BVF",
+    qe=Spectrum(wavelength=_bvf_wavelengths, intensity=_bvf_qe),
+    dark_current=0.0005,
+    full_well=80_000,
+    bit_depth=16,
+    em_gain=1000,  # up to 1000x
+    offset=100,
+    read_noise=40,  # Native read noise at 10MHz read speed. See https://www.biovis.com/resources/ccd/iXon_Ultra_888_EMCCD_Specifications.pdf
+)
+
+
+Andor_iXon_Ultra_888_EXF = CameraEMCCD(
+    # photodiode_size=13, #adding in case it's needed in the future
+    name="Andor iXon Ultra 888 EXF",
+    qe=Spectrum(wavelength=_exf_wavelengths, intensity=_exf_qe),
+    dark_current=0.0005,
+    full_well=80_000,
+    bit_depth=16,
+    em_gain=1000,  # up to 1000x
+    offset=100,
+    read_noise=40,  # Native read noise at 10MHz read speed. See https://www.biovis.com/resources/ccd/iXon_Ultra_888_EMCCD_Specifications.pdf
+)
+
+_orca_wavelengths, _orca_qe = _load_qe_from_csv("C15440_20UP_QE.csv")
+
+C15440_20UP = CameraCMOS(
+    name="C15440-20UP (Hamamatsu ORCA-Fusion BT)",
+    qe=Spectrum(wavelength=_orca_wavelengths, intensity=_orca_qe),
+    dark_current=1.0,  # (-8C , Ambient temperature: +25 ˚C) see https://www.hamamatsu.com/us/en/product/cameras/cmos-cameras/C15440-20UP.html
+    full_well=15_000,
+    bit_depth=16,
+    offset=100,
+    read_noise=1.0,
+)