odroseroc · odroseroc · Feb 27, 2026 · Mar 19, 2026 · Mar 19, 2026 · Mar 19, 2026
diff --git a/.gitignore b/.gitignore
@@ -3,6 +3,8 @@ data/*
 .ipynb_checkpoints/
 notebooks/root_tests
 visualization/SiphraReader/build
+__pycache__/
+*.pyc
 # Do not ignore the sample_data. Track only .dat and .json files
 !data/test_data
 data/test_data/*

diff --git a/Output.root b/Output.root
diff --git a/analysis/__init__.py b/analysis/__init__.py
@@ -1,3 +1,4 @@
 from .fit import *
+from .calibration import *
 
-__all__ = ['gauspeak', 'bg_exp', 'peak_and_bg', 'fit_peak_expbg']
+__all__ = ['gauspeak', 'bg_exp', 'peak_and_bg', 'fit_peak_expbg', 'calibration_fit', 'calibrated_histogram', 'calibrated_acquisition' ]
diff --git a/analysis/__pycache__/__init__.cpython-314.pyc b/analysis/__pycache__/__init__.cpython-314.pyc
diff --git a/analysis/__pycache__/fit.cpython-314.pyc b/analysis/__pycache__/fit.cpython-314.pyc
diff --git a/analysis/calibration.py b/analysis/calibration.py
@@ -0,0 +1,66 @@
+import ROOT
+import numpy as np
+
+def calibration_fit(histogram, energy_ranges, energies):
+    """Function to create a linear calibration fit based on a histogram. Returns slope and constant of linear fit. 
+    Inputs: Histogram to base calibration on.
+    Ranges within which the peaks of the histogram are located, input as a list if tuples. AT LEAST 2 points.
+    Known energies of these peaks, in MeV."""
+
+    channels = []
+    for i in range(len(energy_ranges)):
+        cal_fit=ROOT.TF1("cal_fit_" + str(i), "gaus", energy_ranges[i][0], energy_ranges[i][1])
+        histogram.Fit(cal_fit, "R+S")
+        channels.append(cal_fit.GetParameter('Mean'))
+
+    channels = np.array(channels, dtype='float64')
+    energies = np.array(energies, dtype='float64')
+
+    graph = ROOT.TGraph(len(channels), channels, energies)
+    fit = ROOT.TF1("calib", "pol1", min(channels), max(channels))
+    graph.Fit(fit)
+
+    a = fit.GetParameter(1)
+    b = fit.GetParameter(0)
+
+    return [a, b]
+
+
+def calibrated_histogram(linear_fit, acquisition, n_of_bins):
+    a = linear_fit[0]
+    b = linear_fit[1]
+    data_cal = a * (acquisition['s']/len(acquisition.active_chs)) + b
+
+    emax = a * n_of_bins + b
+    emin = b
+
+    hist_cal = ROOT.TH1F("h_cal", "Calibrated Spectrum", n_of_bins, emin, emax)
+    hist_cal.Fill(data_cal)
+
+    return(hist_cal)
+
+
+def calibrated_acquisition(linear_fit, acquisition, n_of_bins):
+    a = linear_fit[0]
+    b = linear_fit[1]
+    data_cal = a * (acquisition['s']/len(acquisition.active_chs)) + b
+
+    emax = a * n_of_bins + b
+    emin = b
+
+    return(data_cal, emin, emax)
+
+
+def energy_resolution(hist, peak_ranges, peak_energies):
+    """Calculates energy resolution. Input peak_ranges as a list of tuples. 
+    Outputs a list of resolutions for the different energies."""
+    resolutions = []
+    for i in range (len(peak_ranges)):
+        resolution_fit = ROOT.TF1("res_fit_" + str(i), "gaus", peak_ranges[i][0], peak_ranges[i][1])
+        hist.Fit(resolution_fit, "R+S")
+
+        std_dev = resolution_fit.GetParameter('Sigma')
+        resolution = (2.355 * std_dev)/peak_energies[i]
+        resolutions.append(resolution)
+
+    return resolutions
diff --git a/file_converters/__pycache__/d2a_decoder.cpython-314.pyc b/file_converters/__pycache__/d2a_decoder.cpython-314.pyc
diff --git a/noteboks/baseline_subtraction.ipynb b/noteboks/baseline_subtraction.ipynb
diff --git a/noteboks/energyResolution-Copy1.ipynb b/noteboks/energyResolution-Copy1.ipynb
diff --git a/noteboks/root_tests/hist010.ipynb b/noteboks/root_tests/hist010.ipynb
diff --git a/noteboks/root_tests/hist010_TH1_two_scales.py b/noteboks/root_tests/hist010_TH1_two_scales.py
diff --git a/...boks/22Na_60Co_bg-subtraction_calib.ipynb → ...ooks/22Na_60Co_bg-subtraction_calib.ipynb b/...boks/22Na_60Co_bg-subtraction_calib.ipynb → ...ooks/22Na_60Co_bg-subtraction_calib.ipynb
diff --git a/noteboks/260204_CC_BG_comparison.ipynb → notebooks/260204_CC_BG_comparison.ipynb b/noteboks/260204_CC_BG_comparison.ipynb → notebooks/260204_CC_BG_comparison.ipynb
diff --git a/noteboks/260205.ipynb → notebooks/260205.ipynb b/noteboks/260205.ipynb → notebooks/260205.ipynb
diff --git a/noteboks/260206_CMIS_voffset.ipynb → notebooks/260206_CMIS_voffset.ipynb b/noteboks/260206_CMIS_voffset.ipynb → notebooks/260206_CMIS_voffset.ipynb
diff --git a/noteboks/260209_Cs137_BGsubtraction.ipynb → notebooks/260209_Cs137_BGsubtraction.ipynb b/noteboks/260209_Cs137_BGsubtraction.ipynb → notebooks/260209_Cs137_BGsubtraction.ipynb
diff --git a/noteboks/260212.ipynb → notebooks/260212.ipynb b/noteboks/260212.ipynb → notebooks/260212.ipynb
diff --git a/noteboks/CT_Cs137_calib.ipynb → notebooks/CT_Cs137_calib.ipynb b/noteboks/CT_Cs137_calib.ipynb → notebooks/CT_Cs137_calib.ipynb
diff --git a/notebooks/Calibration_EnergyResolution.ipynb b/notebooks/Calibration_EnergyResolution.ipynb
diff --git a/noteboks/QT_compare_channels.ipynb → notebooks/QT_compare_channels.ipynb b/noteboks/QT_compare_channels.ipynb → notebooks/QT_compare_channels.ipynb
diff --git a/noteboks/Untitled.ipynb → notebooks/Untitled.ipynb b/noteboks/Untitled.ipynb → notebooks/Untitled.ipynb
diff --git a/notebooks/Voltage_dependency.ipynb b/notebooks/Voltage_dependency.ipynb
diff --git a/noteboks/banana.ipynb → notebooks/banana.ipynb b/noteboks/banana.ipynb → notebooks/banana.ipynb
diff --git a/notebooks/baseline_subtraction.ipynb b/notebooks/baseline_subtraction.ipynb
diff --git a/notebooks/energyResolution-Copy1.ipynb b/notebooks/energyResolution-Copy1.ipynb
diff --git a/notebooks/energyResolution-Copy2.ipynb b/notebooks/energyResolution-Copy2.ipynb
diff --git a/notebooks/energyResolution.ipynb b/notebooks/energyResolution.ipynb
diff --git a/noteboks/etcTests/converters_explore.ipynb → notebooks/etcTests/converters_explore.ipynb b/noteboks/etcTests/converters_explore.ipynb → notebooks/etcTests/converters_explore.ipynb
diff --git a/noteboks/etcTests/siphraAcq_test_json.ipynb → notebooks/etcTests/siphraAcq_test_json.ipynb b/noteboks/etcTests/siphraAcq_test_json.ipynb → notebooks/etcTests/siphraAcq_test_json.ipynb
diff --git a/notebooks/gainTesting.ipynb b/notebooks/gainTesting.ipynb
diff --git a/noteboks/histogram_summed.ipynb → notebooks/histogram_summed.ipynb b/noteboks/histogram_summed.ipynb → notebooks/histogram_summed.ipynb
diff --git a/noteboks/img/etc/CMIS_internal.png → notebooks/img/etc/CMIS_internal.png b/noteboks/img/etc/CMIS_internal.png → notebooks/img/etc/CMIS_internal.png
diff --git a/noteboks/img/etc/SIPHRA_arch.png → notebooks/img/etc/SIPHRA_arch.png b/noteboks/img/etc/SIPHRA_arch.png → notebooks/img/etc/SIPHRA_arch.png
diff --git a/noteboks/include_project_root.py → notebooks/include_project_root.py b/noteboks/include_project_root.py → notebooks/include_project_root.py
diff --git a/noteboks/spectra_current_thrsh.ipynb → notebooks/spectra_current_thrsh.ipynb b/noteboks/spectra_current_thrsh.ipynb → notebooks/spectra_current_thrsh.ipynb
diff --git a/noteboks/spectrum_plotter.ipynb → notebooks/spectrum_plotter.ipynb b/noteboks/spectrum_plotter.ipynb → notebooks/spectrum_plotter.ipynb
diff --git a/processing/__pycache__/__init__.cpython-314.pyc b/processing/__pycache__/__init__.cpython-314.pyc
diff --git a/processing/__pycache__/metadata.cpython-314.pyc b/processing/__pycache__/metadata.cpython-314.pyc
diff --git a/processing/__pycache__/siphraacquisition.cpython-314.pyc b/processing/__pycache__/siphraacquisition.cpython-314.pyc
diff --git a/processing/metadata.py b/processing/metadata.py
@@ -11,6 +11,7 @@ class Metadata:
     active_chs: list[int]
     sipm_chs: str | list[str]
     n_events: int
+    source: str | None
 
 class MetadataLoader:
 
@@ -29,10 +30,12 @@ def load(path: PathLike) -> Metadata:
     @staticmethod
     def _parse_v1(raw: dict) -> Metadata:
         acq = raw["acquisition"]
+        source = raw["source"]["type"]
 
         return Metadata(
             exposure_sec=acq["exposure_sec"],
             active_chs=[int(ch) for ch in acq["active_chs"]],
             sipm_chs=acq["sipm_chs"],
             n_events=acq["counts"],
+            source=source,
         )
diff --git a/siphractl/__pycache__/d2a_lib.cpython-314.pyc b/siphractl/__pycache__/d2a_lib.cpython-314.pyc
diff --git a/siphractl/siphra_controller.py b/siphractl/siphra_controller.py
diff --git a/...ractl/ComptonCam_DMA_To_RAW_File/Makefile → ...actrl/ComptonCam_DMA_To_RAW_File/Makefile b/...ractl/ComptonCam_DMA_To_RAW_File/Makefile → ...actrl/ComptonCam_DMA_To_RAW_File/Makefile
diff --git a/...Cam_DMA_To_RAW_File/src/dma_to_raw_file.c → ...Cam_DMA_To_RAW_File/src/dma_to_raw_file.c b/...Cam_DMA_To_RAW_File/src/dma_to_raw_file.c → ...Cam_DMA_To_RAW_File/src/dma_to_raw_file.c
diff --git a/siphractl/MK_WriteConfiguration_251210.py → siphractrl/MK_WriteConfiguration_251210.py b/siphractl/MK_WriteConfiguration_251210.py → siphractrl/MK_WriteConfiguration_251210.py
diff --git a/siphractl/acquire.py → siphractrl/acquire.py b/siphractl/acquire.py → siphractrl/acquire.py
@@ -30,13 +30,14 @@ def parse_args():
                         help="A single string containing \'Background\' or any radioactive source present")
     parser.add_argument("--source-description", type=str, default='[NOT SPECIFIED]',
                         help="A single string.")
-    parser.add_argument("--notes", type=str, default='[NONE]')
+    parser.add_argument("--notes", type=str, default='[NONE]',
+                        help="A single string.")
     parser.add_argument("--siphra-config-file", type=str, default='D2a/Ongoing.txt',
                         help="By default, it takes the \'Ongoing.txt\' file in the \'D2a\' directory and writes its contents to the metadata file. If any other configuration is used, the path to the text file containing it must be specified here.")
     parser.add_argument("-s", "--size", type=int, default=4095,
-                        help="([DO NOT CHANGE UNLESS CHANGING dma_to_raw_file SETTINGS]. Block size. Default is 4095.")
+                        help="[DO NOT CHANGE UNLESS CHANGING dma_to_raw_file SETTINGS]. Block size. Default is 4095.")
     parser.add_argument("--device", default="/dev/D2A_DMA",
-                        help = "([DO NOT CHANGE UNLESS CHANGING dma_to_raw_file SETTINGS].")
+                        help = "[DO NOT CHANGE UNLESS CHANGING dma_to_raw_file SETTINGS].")
 
 
     return parser.parse_args()

diff --git a/siphractl/d2a_lib.py → siphractrl/d2a_lib.py b/siphractl/d2a_lib.py → siphractrl/d2a_lib.py
@@ -65,7 +65,7 @@ def compareUpTo(a, b, len):
 
 class D2a:
     '''
-    Contains all fucntions required to interface with hardware devices through OS.
+    Contains all functions required to interface with hardware devices through OS.
     '''
     def __init__(self, uio='/dev/uio0', spi='/dev/spi'):
         try:

diff --git a/siphractl/regs_bit_structure.py → siphractrl/regs_bit_structure.py b/siphractl/regs_bit_structure.py → siphractrl/regs_bit_structure.py
@@ -16,7 +16,7 @@
 )
 
 # Register 0x10: Summing channel configuration registers
-SUMM_CHANNEL = BitStruct(
+SUM_CHANNEL = BitStruct(
     Padding(18),
     'cal_select_channel' / Flag,
     'qc_threshold' / BitsInteger(8),
@@ -88,4 +88,46 @@
     'pu_mb' / Flag,
 )
 
-#
+# Register 0x16
+CAL_CTRL = BitStruct(
+    Padding(26),
+    'cal_cv_range_low' / Flag,
+    'cal_cv_range_mid' / Flag,
+    'cal_cv_range_high' / Flag,
+    'cal_trigger_select' / Flag,
+    'cal_mode' / BitsInteger(2)
+)
+
+# Register 0x17
+ch_names = [f'CH_{n}_rofl' for n in range(16, 0, -1)]
+READOUT_FIXED_LIST = BitStruct(
+    Padding(13),
+    'ADC_IN_rofl' / Flag,
+    'SUM_CH_rofl' / Flag,
+    *[name / Flag for name in ch_names],
+    'ADC_PT100_SENSE_rofl' / Flag,
+)
+
+# Register 0x18
+READOUT_MODE = BitStruct(
+    Padding(17),
+    'int_hold_tune' / BitsInteger(5),
+    'int_hold_delay' / BitsInteger(4),
+    'int_hold_source' / BitsInteger(2),
+    'readout_list_mode' / BitsInteger(1),
+    'readout_en_spi_forced_start' / Flag,
+    'readout_en_ext_hold_start' / Flag,
+    'readout_en_int_hold_start' / Flag,
+)
+
+reg_str_lst = [*[CHANNEL]*16,
+               SUM_CHANNEL,
+               CHANNEL_CONFIG,
+               CHANNEL_CONTROL,
+               ADC_CONFIG,
+               CAL_DAC,
+               PD_MODULES,
+               CAL_CTRL,
+               READOUT_FIXED_LIST,
+               READOUT_MODE,
+               ]