pymagnetos 0.1.0__py3-none-any.whl

pymagnetos/pytdo/assets/config_default.toml

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+# This configuration file specifies the default values if they are not filled in the
+# per-experiment config.toml file.
+
+expid = ""
+data_directory = "."  # path or "."
+
+[files]
+[files.pickup]
+# Pickup coil binary file
+ext = ".pu"
+header = 2
+precision = 4       # number of bytes/element
+endian = "<"        # endian, ">" for big-endian, "<" for little-endian
+order = "F"         # order style in the binary file, "F" for Fortran, "C" for C
+[files.oscillo]
+# Oscilloscope binary file
+ext = ".tdo"
+header = 2
+precision = 4 # number of bytes/element
+endian = "<"  # endian, ">" for big-endian, "<" for little-endian
+order = "F"   # order style in the binary file, "F" for Fortran, "C" for C
+
+[measurements]
+# Measurements settings
+# Link a physical measurement to a channel of the oscilloscope
+# For oscillo data saved with LabVIEW, they correspond to the columns in the file (0-based)
+signal = 0
+
+# Parameters are values that should be fixed once and for all for a given experiment
+[parameters]
+pickup_surface = 1  # surface of the pickup coil (m²)
+
+pickup_number = 1  # number of pickup(s) used and save in the pickup bin file
+pickup_index = 0  # index of the pickup to use for analysis, 0-based
+
+# Settings are analysis-specific and can be changed afterwards
+[settings]
+# Settings for TDO signal extraction from raw data
+max_time = 1                # crop signals until this time in seconds
+
+spectro_nperseg = 1024      # spectrogram : number of points per segment
+spectro_win_size = 4096     # spectrogram : fft window size
+spectro_noverlap = -1       # size of windows overlap, set to -1 to be nperseg / 2
+
+barycenters_fwindow = 732421.875  # half size of the window to use around frequency maxima in spectrogram
+barycenters_fast = true     # use fast algo to find barycenters or not
+
+time_offset = 0
+
+# Settings for TDO signal analysis
+poly_window = [60, 84]              # field-range in which to do the polynomial fit
+poly_deg = 3                        # polynomial degree
+npoints_interp_inverse = 100000     # number of points for interpolation in 1/B
+fft_window = [64, 80]               # field-range in which to interpolate in 1/B
+fft_pad_mult = 100                  # multiplier of signal size to adjust 0-padding size for FFT
+max_bfreq = 70000                   # maximum B-frequency (in T) to plot and save
+
+# Settings for display/plotting
+offset = 1000                       # offset B up/down curves to see them better
+
+[metadata]
+# Parameters on how to handle binary files headers
+[metadata.index_map]
+# map a metadata to its index in the header (0-based)
+samplerate = 0
+temperature = 1
+[metadata.conversion_map]
+# determine whether conversion to numeric is required
+samplerate = true
+temperature = true
+
+[nx]
+# NeXus file consolidation
+
+[nexus]
+[nexus.groups]
+# NeXus groups attributes
+root = {name = ""}
+# processed/analysis
+analysis = {}
+# data
+data = {}
+[nexus.datasets]
+# NeXus datasets attributes

pymagnetos/pytdo/gui/__init__.py

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+"""Application for TDO experiments during high-magnetic field."""
+
+from PyQt6 import QtWidgets
+
+from .main import MainWindow
+
+
+def run(exec: bool = True) -> None | MainWindow:
+    """
+    Build and run the app.
+
+    Set `exec=False` in an interactive prompt to interact with the GUI from the shell.
+
+    Parameters
+    ----------
+    exec : bool, optional
+        Execute the process thread. Set to False in an interactive prompt. Default is
+        True.
+    """
+    app = QtWidgets.QApplication([])
+    win = MainWindow()
+    win.show()
+    if exec:
+        app.exec()
+    else:
+        return win

pymagnetos/pytdo/gui/_worker.py

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+"""Worker that connects to an TDOProcessor object."""
+
+from pathlib import Path
+
+from PyQt6.QtCore import QObject, pyqtSignal, pyqtSlot
+
+from pymagnetos.pytdo import TDOProcessor
+
+
+class DataWorker(QObject):
+    """
+    Wrapper around the TDOProcessor class.
+
+    It exposes the EchoProcessor methods as slots and emits a signal when the task is
+    finished.
+
+    Signals
+    -------
+    sig_load_finished : emits when loading data is finished.
+    sig_extract_finished : emits when extracting the TDO signal is finished.
+    sig_offset_finished : emits when the adjusting the pickup/signal offset is finished.
+    sig_align_finished : emits when the magnetic field is aligned on the TDO signal.
+    sig_analyse_finished : emits when the TDO signal is analysed (detrended and FFT in
+        1/B).
+    sig_tdocsv_finished : emits when the TDO signal is saved as CSV.
+    sig_rescsv_finished : emits when the analysis is saved as CSV.
+    sig_save_nexus_finished : emits when saving the NeXus file is finished.
+    sig_load_csv_finished : emits when loading a CSV file is finished.
+    """
+
+    sig_load_finished = pyqtSignal()
+    sig_extract_finished = pyqtSignal()
+    sig_offset_finished = pyqtSignal()
+    sig_align_finished = pyqtSignal()
+    sig_analyse_finished = pyqtSignal()
+    sig_batch_progress = pyqtSignal(int)  # required by upstream core.gui lib
+    sig_batch_finished = pyqtSignal()  # required by upstream core.gui lib
+    sig_tdocsv_finished = pyqtSignal()
+    sig_rescsv_finished = pyqtSignal()
+    sig_save_nexus_finished = pyqtSignal()
+    sig_load_csv_finished = pyqtSignal()
+
+    def __init__(self, *args, **kwargs) -> None:
+        super().__init__()
+
+        self.proc = TDOProcessor(*args, **kwargs)
+        if self.proc.is_nexus_file:
+            self.is_dataloaded = True
+        else:
+            self.is_dataloaded = False
+
+    @pyqtSlot()
+    def load_data(self):
+        """Load data."""
+        self.proc.load_oscillo()
+        self.is_dataloaded = True
+        self.sig_load_finished.emit()
+
+    @pyqtSlot()
+    def extract_tdo(self):
+        """Extract TDO signal."""
+        self.proc.extract_tdo()
+        self.sig_extract_finished.emit()
+
+    @pyqtSlot()
+    def time_offset(self):
+        """Apply time offset on experiment time vector."""
+        self.proc.apply_time_offset()
+        self.sig_offset_finished.emit()
+
+    def align_field(self):
+        self.proc.align_field()
+        self.sig_align_finished.emit()
+
+    @pyqtSlot()
+    def analyse(self):
+        """Remove background and oversample in 1/B."""
+        self.proc.analyse()
+        self.sig_analyse_finished.emit()
+
+    @pyqtSlot()
+    def batch_process(self):
+        return
+
+    @pyqtSlot(str)
+    def save_tdo_csv(self, fname: str | Path):
+        """Save TDO signal as CSV."""
+        self.proc.save_tdo_csv(filename=fname)
+        self.sig_tdocsv_finished.emit()
+
+    @pyqtSlot(str)
+    def save_results_csv(self, fname: str | Path):
+        """Save results as CSV."""
+        self.proc.save_results_csv(filename_prefix=fname)
+        self.sig_rescsv_finished.emit()
+
+    @pyqtSlot(str)
+    def save_as_nexus(self, fname: str | Path):
+        """Save data as NeXus."""
+        self.proc.save(filename=fname)
+        self.sig_save_nexus_finished.emit()
+
+    @pyqtSlot(str)
+    def load_csv_file(self, fname: str):
+        self.proc.load_csv(fname)
+        self.sig_load_csv_finished.emit()