[project] adding dev dependencies

[project] updating project structure
[app] adding pyqtplot for displaying the beat
2024-09-27 16:24:05 +02:00 · 2024-09-27 14:21:13 +02:00 · 2024-09-27 14:20:43 +02:00 · 2024-09-27 14:20:18 +02:00 · 2024-09-27 14:19:46 +02:00 · 2024-09-27 10:21:05 +02:00
8 changed files with 571 additions and 161 deletions
--- a/docs/0900766b804c9851.pdf
+++ b/docs/0900766b804c9851.pdf
--- a/poetry.lock
+++ b/poetry.lock
@@ -1,4 +1,22 @@
-# This file is automatically @generated by Poetry 1.8.3 and should not be changed by hand.
+# This file is automatically @generated by Poetry 1.8.2 and should not be changed by hand.
+
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+version = "2.4.1"
+description = "Annotate AST trees with source code positions"
+optional = false
+python-versions = "*"
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+
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+test = ["astroid (>=1,<2)", "astroid (>=2,<4)", "pytest"]

 [[package]]
 name = "click"
@@ -124,6 +142,31 @@ files = [
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 tests = ["pytest", "pytest-cov", "pytest-xdist"]

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+description = "Decorators for Humans"
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+
 [[package]]
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 version = "4.53.1"
@@ -189,6 +232,99 @@ ufo = ["fs (>=2.2.0,<3)"]
 unicode = ["unicodedata2 (>=15.1.0)"]
 woff = ["brotli (>=1.0.1)", "brotlicffi (>=0.8.0)", "zopfli (>=0.1.4)"]

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+
 [[package]]
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 version = "1.4.7"
@@ -399,6 +535,20 @@ python-dateutil = ">=2.7"
 [package.extras]
 dev = ["meson-python (>=0.13.1)", "numpy (>=1.25)", "pybind11 (>=2.6)", "setuptools (>=64)", "setuptools_scm (>=7)"]

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@@ -410,66 +560,65 @@ files = [
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+python-versions = "*"
+files = [
+    {file = "wcwidth-0.2.13-py2.py3-none-any.whl", hash = "sha256:3da69048e4540d84af32131829ff948f1e022c1c6bdb8d6102117aac784f6859"},
+    {file = "wcwidth-0.2.13.tar.gz", hash = "sha256:72ea0c06399eb286d978fdedb6923a9eb47e1c486ce63e9b4e64fc18303972b5"},
+]
+
 [metadata]
 lock-version = "2.0"
 python-versions = "^3.12"
-content-hash = "477748fbc18bde095d13dea548108541c1b584242099398155787361b1dc31fe"
+content-hash = "b1076b7f750e8f7e66542918ec746e74544fbfdb376875158f083fb573d18107"
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,3 +1,7 @@
+[project]
+organization = "de.uni-tuebingen.neuroetho"
+copyright = "(c) 2020, Neuroethology lab, Uni Tuebingen"
+
 [tool.poetry]
 name = "pyrelacs"
 version = "0.1.0"
@@ -6,14 +10,11 @@ authors = ["wendtalexander <wendtalexander@protonmail.com>"]
 repository = "https://whale.am28.uni-tuebingen.de/git/awendt/pyrelacs"
 readme = "README.md"
 license = "MIT"
-organization = "de.uni-tuebingen.neuroetho"
 classifiers = [
    "Topic :: Scientific/Engineering",
    "Intended Audience :: Science/Research",
    "Intended Audience :: End Users/Desktop",
 ]
-copyright = "(c) 2020, Neuroethology lab, Uni Tuebingen"
-
 include = [
    { path = "pyproject.toml" }
 ]
@@ -23,15 +24,19 @@ python = "^3.12"
 uldaq = "^1.2.3"
 typer = "^0.12.5"
 matplotlib = "^3.9.2"
-numpy = "^2.1.1"
+numpy = "^1.9"
 pyqt6 = "^6.7.1"
-tomli = "^2.0.1"
 tomlkit = "^0.13.2"
 scipy = "^1.14.1"
+nixio = "^1.5.3"
+pyqtgraph = "^0.13.7"

 [tool.poetry.scripts]
 pyrelacs = "pyrelacs.app:main"

+[tool.poetry.group.dev.dependencies]
+ipython = "^8.27.0"
+
 [build-system]
-requires = ["poetry-core"]
+requires = ["poetry-core>=1.0.0"]
 build-backend = "poetry.core.masonry.api"
--- a/pyrelacs/app.py
+++ b/pyrelacs/app.py
@@ -1,8 +1,8 @@
+import pathlib
 from PyQt6.QtGui import QAction
 import sys
-import pathlib

-from PyQt6.QtCore import QProcess, QSize, QThreadPool, Qt, QSettings
+from PyQt6.QtCore import QSize, QThreadPool, QSettings
 from PyQt6.QtWidgets import (
    QApplication,
    QGridLayout,
@@ -12,9 +12,12 @@ from PyQt6.QtWidgets import (
    QMainWindow,
    QPlainTextEdit,
 )
+import pyqtgraph as pg
 import uldaq
 from IPython import embed
+from scipy.signal import welch, find_peaks
 import numpy as np
+import nixio as nix

 from pyrelacs.util.logging import config_logging
 import pyrelacs.info as info
@@ -29,6 +32,7 @@ class PyRelacs(QMainWindow):
        super().__init__()
        self.setWindowTitle("PyRelacs")
        self.setMinimumSize(1000, 1000)
+        self.plot_graph = pg.PlotWidget()

        self.threadpool = QThreadPool()
        self.repros = Repro()
@@ -41,13 +45,18 @@ class PyRelacs(QMainWindow):
        self.daq_disconnect_button.setCheckable(True)
        self.daq_disconnect_button.clicked.connect(self.disconnect_dac)

+        self.plot_calibration_button = QPushButton("Plot Calibration")
+        self.plot_calibration_button.setCheckable(True)
+        self.plot_calibration_button.clicked.connect(self.plot_calibration)
+
        self.text = QPlainTextEdit()
        self.text.setReadOnly(True)

        layout = QGridLayout()
-        layout.addWidget(self.daq_connect_button, 0, 0)
+        layout.addWidget(self.plot_calibration_button, 0, 0)
        layout.addWidget(self.daq_disconnect_button, 0, 1)
-        layout.addWidget(self.text, 2, 0, 1, 2)
+        layout.addWidget(self.text, 3, 0, 1, 2)
+        layout.addWidget(self.plot_graph, 2, 0, 1, 2)

        self.toolbar = QToolBar("Repros")
        self.addToolBar(self.toolbar)
@@ -58,6 +67,67 @@ class PyRelacs(QMainWindow):
        widget.setLayout(layout)
        self.setCentralWidget(widget)

+        self.nix_file = nix.File.open(
+            str(pathlib.Path(__file__).parent / "data"), nix.FileMode.ReadOnly
+        )
+
+    def plot_calibration(self):
+        def decibel(power, ref_power=1.0, min_power=1e-20):
+            """Transform power to decibel relative to ref_power.
+
+            \\[ decibel = 10 \\cdot \\log_{10}(power/ref\\_power) \\]
+            Power values smaller than `min_power` are set to `-np.inf`.
+
+            Parameters
+            ----------
+            power: float or array
+                Power values, for example from a power spectrum or spectrogram.
+            ref_power: float or None or 'peak'
+                Reference power for computing decibel.
+                If set to `None` or 'peak', the maximum power is used.
+            min_power: float
+                Power values smaller than `min_power` are set to `-np.inf`.
+
+            Returns
+            -------
+            decibel_psd: array
+                Power values in decibel relative to `ref_power`.
+            """
+            if np.isscalar(power):
+                tmp_power = np.array([power])
+                decibel_psd = np.array([power])
+            else:
+                tmp_power = power
+                decibel_psd = power.copy()
+            if ref_power is None or ref_power == "peak":
+                ref_power = np.max(decibel_psd)
+            decibel_psd[tmp_power <= min_power] = float("-inf")
+            decibel_psd[tmp_power > min_power] = 10.0 * np.log10(
+                decibel_psd[tmp_power > min_power] / ref_power
+            )
+            if np.isscalar(power):
+                return decibel_psd[0]
+            else:
+                return decibel_psd
+
+        block = self.nix_file.blocks[0]
+        for stim, fish in zip(
+            list(block.data_arrays)[::2], list(block.data_arrays)[1::2]
+        ):
+            beat = stim[:] + fish[:]
+            beat_squared = beat**2
+
+            f, powerspec = welch(beat, fs=40_000.0)
+            powerspec = decibel(powerspec)
+
+            f_sq, powerspec_sq = welch(beat_squared, fs=40_000.0)
+            powerspec_sq = decibel(powerspec_sq)
+            peaks = find_peaks(powerspec_sq, prominence=20)[0]
+            pen = pg.mkPen()
+            self.plot_graph.plot(
+                np.arange(0, len(beat)) / 40_000.0, beat_squared, pen=pen
+            )
+
    def connect_dac(self):
        devices = uldaq.get_daq_device_inventory(uldaq.InterfaceType.USB)
        try:
@@ -93,6 +163,21 @@ class PyRelacs(QMainWindow):

    def run_repro(self, n, fn):
        self.text.appendPlainText(f"started Repro {n}, {fn}")
+        worker = Worker(self.repros.run_repro, self.nix_file, n, fn)
+        worker.signals.result.connect(self.print_output)
+        worker.signals.finished.connect(self.thread_complete)
+        worker.signals.progress.connect(self.progress_fn)
+
+        self.threadpool.start(worker)
+
+    def print_output(self, s):
+        print(s)
+
+    def thread_complete(self):
+        print("THREAD COMPLETE!")
+
+    def progress_fn(self, n):
+        print("%d%% done" % n)


 def main():
@@ -114,7 +199,7 @@ def main():
    window.resize(width, height)
    window.move(x, y)
    window.show()
-    app.exec()
+    exit_code = app.exec()

    # store window position and size
    pos = window.pos()
@@ -126,4 +211,4 @@ def main():


 if __name__ == "__main__":
-    main()
+    main()
--- a/pyrelacs/data
+++ b/pyrelacs/data
--- a/pyrelacs/info.py
+++ b/pyrelacs/info.py
@@ -1,9 +1,10 @@
 import tomlkit
 import pathlib

+
 def load_project_settings(project_root):
    # Read the pyproject.toml file
-    with open(pathlib.Path.joinpath(project_root, 'pyproject.toml'), 'r') as f:
+    with open(pathlib.Path.joinpath(project_root, "pyproject.toml"), "r") as f:
        pyproject_content = f.read()

    # Parse the toml content
@@ -11,16 +12,16 @@ def load_project_settings(project_root):

    # Access project settings
    return {
-        'name': pyproject['tool']['poetry']['name'],
-        'version': pyproject['tool']['poetry']['version'],
-        'description': pyproject['tool']['poetry']['description'],
-        'authors': pyproject['tool']['poetry']['authors'],
-        'readme': pyproject['tool']['poetry']['authors'],
-        'licence': pyproject['tool']['poetry']['license'],
-        'organization': pyproject['tool']['poetry']['organization'],
-        'classifiers': pyproject['tool']['poetry']['classifiers'],
-        'copyright': pyproject['tool']['poetry']['copyright'],
-        "repository": pyproject['tool']['poetry']['repository'],
+        "name": pyproject["tool"]["poetry"]["name"],
+        "version": pyproject["tool"]["poetry"]["version"],
+        "description": pyproject["tool"]["poetry"]["description"],
+        "authors": pyproject["tool"]["poetry"]["authors"],
+        "readme": pyproject["tool"]["poetry"]["authors"],
+        "licence": pyproject["tool"]["poetry"]["license"],
+        "organization": pyproject["project"]["organization"],
+        "classifiers": pyproject["tool"]["poetry"]["classifiers"],
+        "copyright": pyproject["project"]["copyright"],
+        "repository": pyproject["tool"]["poetry"]["repository"],
    }


--- a/pyrelacs/repros/calbi.py
+++ b/pyrelacs/repros/calbi.py
@@ -3,6 +3,7 @@ import sys
 import faulthandler
 import time

+import nixio as nix
 import uldaq
 from IPython import embed
 import numpy as np
@@ -25,12 +26,10 @@ class Calibration(MccDac):
        self.AMPLITUDE = 1
        self.SINFREQ = 750

-    def run(self):
-
-    def segfault_handler(self, signum, frame):
-        print(f"Segmentation fault caught! Signal number: {signum}")
-        self.disconnect_dac()
-        sys.exit(1)  # Gracefully exit the program
+    @staticmethod
+    def run(nix_file: nix.File):
+        calb = Calibration()
+        calb.check_beat(nix_file)

    def check_amplitude(self):
        db_values = [0.0, -5.0, -10.0, -20.0, -50.0]
@@ -53,7 +52,10 @@ class Calibration(MccDac):
            )

            data_channel_one = self.read_analog(
-                [0, 0], self.DURATION, self.SAMPLERATE, ScanOption=uldaq.ScanOption.EXTTRIGGER
+                [0, 0],
+                self.DURATION,
+                self.SAMPLERATE,
+                ScanOption=uldaq.ScanOption.EXTTRIGGER,
            )
            time.sleep(1)

@@ -83,7 +85,7 @@ class Calibration(MccDac):

        self.disconnect_dac()

-    def check_beat(self):
+    def check_beat(self, nix_file: nix.File):
        self.set_attenuation_level(db_channel1=-10.0, db_channel2=0.0)
        t = np.arange(0, self.DURATION, 1 / self.SAMPLERATE)
        data = self.AMPLITUDE * np.sin(2 * np.pi * self.SINFREQ * t)
@@ -91,7 +93,8 @@ class Calibration(MccDac):
        db_values = [0.0, -5.0, -8.5, -10.0]
        colors = ["red", "blue", "black", "green"]
        colors_in = ["lightcoral", "lightblue", "grey", "lightgreen"]
-        fig, axes = plt.subplots(2, 2, sharex="col")
+        block = nix_file.create_block("Calibration", "data")
+        # fig, axes = plt.subplots(2, 2, sharex="col")
        for i, db_value in enumerate(db_values):
            self.set_attenuation_level(db_channel1=db_value)
            stim = self.write_analog(
@@ -107,7 +110,6 @@ class Calibration(MccDac):
                ScanOption=uldaq.ScanOption.EXTTRIGGER,
            )
            self.diggital_trigger()
-            signal.signal(signal.SIGSEGV, self.segfault_handler)
            log.info(self.ao_device)
            ai_status = uldaq.ScanStatus.RUNNING
            ao_status = uldaq.ScanStatus.RUNNING
@@ -127,8 +129,27 @@ class Calibration(MccDac):
            log.debug(
                f"Status Analog_output {ao_status}\n, Status Analog_input {ai_status}"
            )
+
            channel1 = np.array(readout[::2])
            channel2 = np.array(readout[1::2])
+
+            block.create_data_array(
+                f"stimulus_{db_value}",
+                "Array",
+                shape=data.shape,
+                data=channel1,
+                label="Voltage",
+                unit="V",
+            )
+            block.create_data_array(
+                f"fish_{db_value}",
+                "Array",
+                shape=data.shape,
+                data=channel2,
+                label="Voltage",
+                unit="V",
+            )
+
            beat = channel1 + channel2
            beat_square = beat**2

@@ -145,69 +166,69 @@ class Calibration(MccDac):
            f_in, powerspec_in = welch(channel2, fs=self.SAMPLERATE)
            powerspec_in = decibel(powerspec_in)

-            axes[0, 0].plot(
-                t,
-                channel1,
-                label=f"{db_value} Readout Channel0",
-                color=colors[i],
-            )
-            axes[0, 0].plot(
-                t,
-                channel2,
-                label=f"{db_value} Readout Channel1",
-                color=colors_in[i],
-            )
-
-            axes[0, 1].plot(
-                f_stim,
-                powerspec_stim,
-                label=f"{db_value} powerspec Channel0",
-                color=colors[i],
-            )
-            axes[0, 1].plot(
-                f_in,
-                powerspec_in,
-                label=f"{db_value} powerspec Channel2",
-                color=colors_in[i],
-            )
-            axes[0, 1].set_xlabel("Freq [HZ]")
-            axes[0, 1].set_ylabel("dB")
-
-            axes[1, 0].plot(
-                t,
-                beat,
-                label="Beat",
-                color=colors[i],
-            )
-            axes[1, 0].plot(
-                t,
-                beat**2,
-                label="Beat squared",
-                color=colors_in[i],
-            )
-            axes[1, 0].legend()
-
-            axes[1, 1].plot(
-                f,
-                powerspec,
-                color=colors[i],
-            )
-            axes[1, 1].plot(
-                f_sq,
-                powerspec_sq,
-                color=colors_in[i],
-                label=f"dB {db_value}, first peak {np.min(f_sq[peaks])}",
-            )
-            axes[1, 1].scatter(
-                f_sq[peaks],
-                powerspec_sq[peaks],
-                color="maroon",
-            )
-            axes[1, 1].set_xlabel("Freq [HZ]")
-            axes[1, 1].set_ylabel("dB")
-            axes[0, 0].legend()
-            axes[1, 1].legend()
-        plt.show()
+        #     axes[0, 0].plot(
+        #         t,
+        #         channel1,
+        #         label=f"{db_value} Readout Channel0",
+        #         color=colors[i],
+        #     )
+        #     axes[0, 0].plot(
+        #         t,
+        #         channel2,
+        #         label=f"{db_value} Readout Channel1",
+        #         color=colors_in[i],
+        #     )
+        #
+        #     axes[0, 1].plot(
+        #         f_stim,
+        #         powerspec_stim,
+        #         label=f"{db_value} powerspec Channel0",
+        #         color=colors[i],
+        #     )
+        #     axes[0, 1].plot(
+        #         f_in,
+        #         powerspec_in,
+        #         label=f"{db_value} powerspec Channel2",
+        #         color=colors_in[i],
+        #     )
+        #     axes[0, 1].set_xlabel("Freq [HZ]")
+        #     axes[0, 1].set_ylabel("dB")
+        #
+        #     axes[1, 0].plot(
+        #         t,
+        #         beat,
+        #         label="Beat",
+        #         color=colors[i],
+        #     )
+        #     axes[1, 0].plot(
+        #         t,
+        #         beat**2,
+        #         label="Beat squared",
+        #         color=colors_in[i],
+        #     )
+        #     axes[1, 0].legend()
+        #
+        #     axes[1, 1].plot(
+        #         f,
+        #         powerspec,
+        #         color=colors[i],
+        #     )
+        #     axes[1, 1].plot(
+        #         f_sq,
+        #         powerspec_sq,
+        #         color=colors_in[i],
+        #         label=f"dB {db_value}, first peak {np.min(f_sq[peaks])}",
+        #     )
+        #     axes[1, 1].scatter(
+        #         f_sq[peaks],
+        #         powerspec_sq[peaks],
+        #         color="maroon",
+        #     )
+        #     axes[1, 1].set_xlabel("Freq [HZ]")
+        #     axes[1, 1].set_ylabel("dB")
+        #     axes[0, 0].legend()
+        #     axes[1, 1].legend()
+        # plt.show()
        self.set_analog_to_zero()
        self.disconnect_dac()

--- a/pyrelacs/repros/repros.py
+++ b/pyrelacs/repros/repros.py
@@ -1,15 +1,37 @@
+import sys
+import importlib.util
 import ast
 import pathlib

 from IPython import embed
+import nixio as nix
+from pyrelacs.util.logging import config_logging
+
+log = config_logging()


 class Repro:
    def __init__(self) -> None:
        pass

-    def run_repro(self, name: str, *args, **kwargs) -> None:
-        pass
+    def run_repro(
+        self, nix_file: nix.File, name: str, file: pathlib.Path, *args, **kwargs
+    ) -> None:
+        spec = importlib.util.spec_from_file_location("rep", file)
+        if not spec:
+            log.error("Could not load the file")
+        else:
+            module = importlib.util.module_from_spec(spec)
+            if not module:
+                log.error("Could not load the module of the repro")
+            else:
+                sys.modules[name] = module
+                spec.loader.exec_module(module)
+                if hasattr(module, name):
+                    rep_class = getattr(module, name)
+                    rep_class.run(nix_file)
+                else:
+                    raise AttributeError(f"{file.name} has no {name} class")

    def names_of_repros(self):
        file_path_cur = pathlib.Path(__file__).parent
Author	SHA1	Message	Date
wendtalexander	a16fe0b735	[project] adding dev dependencies	2024-09-27 16:24:05 +02:00
wendtalexander	5c3c2c407a	[project] updating project structure	2024-09-27 14:21:13 +02:00
wendtalexander	8ef8ac7506	[app] adding pyqtplot for displaying the beat	2024-09-27 14:20:43 +02:00
wendtalexander	7d3224f351	[app][repros] adding nix file and checks	2024-09-27 14:20:18 +02:00
wendtalexander	a748385335	[app] [calibration] adding writing to nix file	2024-09-27 14:19:46 +02:00
wendtalexander	cd6bc0dc04	[app] starting repos with as a thread	2024-09-27 10:21:05 +02:00
wendtalexander	cb5c08bc94	[doc] renaming spec sheet	2024-09-27 09:30:46 +02:00
Awendt	45a267c8c7	Merge pull request 'main' (#1 ) from jgrewe/minipyrelacs:main into main Reviewed-on: Awendt/pyrelacs#1	2024-09-27 07:29:03 +00:00