[ui/structure] updating repros to tab bar with individual plots and nix blocks

[ui/plots] fixing error if nothing has been plotted, the gui could not close
[repro/class] provides with repros with args and kwargs
2024-10-23 11:09:44 +02:00 · 2024-10-23 11:08:54 +02:00 · 2024-10-23 11:07:55 +02:00 · 2024-10-23 11:07:19 +02:00 · 2024-10-23 11:06:51 +02:00 · 2024-10-23 11:06:26 +02:00
17 changed files with 956 additions and 373 deletions
--- a/poetry.lock
+++ b/poetry.lock
@@ -142,6 +142,19 @@ files = [
 docs = ["ipython", "matplotlib", "numpydoc", "sphinx"]
 tests = ["pytest", "pytest-cov", "pytest-xdist"]

+[[package]]
+name = "dacite"
+version = "1.8.1"
+description = "Simple creation of data classes from dictionaries."
+optional = false
+python-versions = ">=3.6"
+files = [
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+]
+
+[package.extras]
+dev = ["black", "coveralls", "mypy", "pre-commit", "pylint", "pytest (>=5)", "pytest-benchmark", "pytest-cov"]
+
 [[package]]
 name = "decorator"
 version = "5.1.1"
@@ -153,20 +166,6 @@ files = [
    {file = "decorator-5.1.1.tar.gz", hash = "sha256:637996211036b6385ef91435e4fae22989472f9d571faba8927ba8253acbc330"},
 ]

-[[package]]
-name = "exceptiongroup"
-version = "1.2.2"
-description = "Backport of PEP 654 (exception groups)"
-optional = false
-python-versions = ">=3.7"
-files = [
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-]
-
-[package.extras]
-test = ["pytest (>=6)"]
-
 [[package]]
 name = "executing"
 version = "2.1.0"
@@ -183,53 +182,59 @@ tests = ["asttokens (>=2.1.0)", "coverage", "coverage-enable-subprocess", "ipyth

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 name = "fonttools"
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 [package.extras]
@@ -297,19 +302,18 @@ files = [

 [[package]]
 name = "ipython"
-version = "8.27.0"
+version = "8.28.0"
 description = "IPython: Productive Interactive Computing"
 optional = false
 python-versions = ">=3.10"
 files = [
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 jedi = ">=0.16"
 matplotlib-inline = "*"
 pexpect = {version = ">4.3", markers = "sys_platform != \"win32\" and sys_platform != \"emscripten\""}
@@ -904,16 +908,16 @@ PyQt6-sip = ">=13.8,<14"

 [[package]]
 name = "pyqt6-qt6"
-version = "6.7.2"
+version = "6.7.3"
 description = "The subset of a Qt installation needed by PyQt6."
 optional = false
 python-versions = "*"
 files = [
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 [[package]]
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 [package.dependencies]
 colorama = {version = "*", markers = "sys_platform == \"win32\""}
-exceptiongroup = {version = ">=1.0.0rc8", markers = "python_version < \"3.11\""}
 iniconfig = "*"
 packaging = "*"
 pluggy = ">=1.5,<2"
-tomli = {version = ">=1", markers = "python_version < \"3.11\""}

 [package.extras]
 dev = ["argcomplete", "attrs (>=19.2)", "hypothesis (>=3.56)", "mock", "pygments (>=2.7.2)", "requests", "setuptools", "xmlschema"]
@@ -996,15 +998,95 @@ files = [
 [package.dependencies]
 six = ">=1.5"

+[[package]]
+name = "pyyaml"
+version = "6.0.2"
+description = "YAML parser and emitter for Python"
+optional = false
+python-versions = ">=3.8"
+files = [
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+]
+
+[[package]]
+name = "quantities"
+version = "0.16.0"
+description = "Support for physical quantities with units, based on numpy"
+optional = false
+python-versions = ">=3.8"
+files = [
+    {file = "quantities-0.16.0-py3-none-any.whl", hash = "sha256:189e573953e7864d8c303a3472f6ad39fbe0698c3d75c17059b70bc457c7c66d"},
+    {file = "quantities-0.16.0.tar.gz", hash = "sha256:211cce2d268da7e202abab5c2533ce3200ff619dd8ac2a3cd98f861b8a57c6eb"},
+]
+
+[package.dependencies]
+numpy = ">=1.20"
+
+[package.extras]
+doc = ["sphinx"]
+test = ["pytest", "wheel"]
+
 [[package]]
 name = "rich"
-version = "13.8.1"
+version = "13.9.2"
 description = "Render rich text, tables, progress bars, syntax highlighting, markdown and more to the terminal"
 optional = false
-python-versions = ">=3.7.0"
+python-versions = ">=3.8.0"
 files = [
-    {file = "rich-13.8.1-py3-none-any.whl", hash = "sha256:1760a3c0848469b97b558fc61c85233e3dafb69c7a071b4d60c38099d3cd4c06"},
-    {file = "rich-13.8.1.tar.gz", hash = "sha256:8260cda28e3db6bf04d2d1ef4dbc03ba80a824c88b0e7668a0f23126a424844a"},
+    {file = "rich-13.9.2-py3-none-any.whl", hash = "sha256:8c82a3d3f8dcfe9e734771313e606b39d8247bb6b826e196f4914b333b743cf1"},
+    {file = "rich-13.9.2.tar.gz", hash = "sha256:51a2c62057461aaf7152b4d611168f93a9fc73068f8ded2790f29fe2b5366d0c"},
 ]

 [package.dependencies]
@@ -1105,17 +1187,6 @@ pure-eval = "*"
 [package.extras]
 tests = ["cython", "littleutils", "pygments", "pytest", "typeguard"]

-[[package]]
-name = "tomli"
-version = "2.0.1"
-description = "A lil' TOML parser"
-optional = false
-python-versions = ">=3.7"
-files = [
-    {file = "tomli-2.0.1-py3-none-any.whl", hash = "sha256:939de3e7a6161af0c887ef91b7d41a53e7c5a1ca976325f429cb46ea9bc30ecc"},
-    {file = "tomli-2.0.1.tar.gz", hash = "sha256:de526c12914f0c550d15924c62d72abc48d6fe7364aa87328337a31007fe8a4f"},
-]
-
 [[package]]
 name = "tomlkit"
 version = "0.13.2"
@@ -1194,5 +1265,5 @@ files = [

 [metadata]
 lock-version = "2.0"
-python-versions = ">=3.10, <3.13"
-content-hash = "e5e345e3e4d28ac0e7de7727be130454201be1949be08158e744cdc6089a3f66"
+python-versions = ">=3.11, <3.13"
+content-hash = "31433ed1dc0cc83dd7e781546dad5b8f068d59eaf692b4d3c12e07c604b1a6dd"
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -21,7 +21,7 @@ include = [
 ]

 [tool.poetry.dependencies]
-python = ">=3.10, <3.13"
+python = ">=3.11, <3.13"
 uldaq = "^1.2.3"
 typer = "^0.12.5"
 matplotlib = "^3.9.2"
@@ -33,6 +33,9 @@ nixio = "^1.5.3"
 pyqtgraph = "^0.13.7"
 pytest = "^8.3.3"
 pglive = "^0.7.6"
+pyyaml = "^6.0.2"
+dacite = "^1.8.1"
+quantities = "^0.16.0"

 [tool.poetry.scripts]
 pyrelacs = "pyrelacs.app:main"
--- a/pyrelacs/app.py
+++ b/pyrelacs/app.py
@@ -2,12 +2,11 @@ import sys

 from PyQt6.QtCore import QSettings
 from PyQt6.QtWidgets import QApplication
+from IPython import embed

 from pyrelacs import info
+from pyrelacs.config.config_loader import load_config
 from pyrelacs.ui.mainwindow import PyRelacs
-from pyrelacs.util.logging import config_logging
-
-log = config_logging()

 from pyrelacs import (
    resources,
@@ -28,7 +27,11 @@ def main():
    x = int(settings.value("app/pos_x", 100))
    y = int(settings.value("app/pos_y", 100))

-    window = PyRelacs()
+    # load the config
+
+    config = load_config()
+    # start the app
+    window = PyRelacs(config)
    window.setMinimumWidth(200)
    window.setMinimumHeight(200)
    window.resize(width, height)
--- a/pyrelacs/config.yaml
+++ b/pyrelacs/config.yaml
@@ -0,0 +1,76 @@
+settings:
+  # If true daq should be used, else starts without daq
+  daq: False
+  # class names of the repros to run
+  repros: [Calibration, Sinus]
+  path: ~/projects/pyrelacs/test/
+
+metadata:
+  SetupName        : Setup1
+  Maintainer       : Your name
+  Creator          : Whoever
+  SetupLocation    : virtual
+  Lab              : XYZ-Lab
+  Institute        : Your institute
+  University       : Your university
+  Address          : Your institute's address
+
+pyrelacs:
+  data:
+    input:
+        inputsamplerate        : 20
+        # Unit is rescaled to Hz
+        inputsamplerateunit    : kHz
+        # BufferSize
+        inputtracecapacity     : 600
+        # Unit is rescaled to s
+        inputtracecapacityunit : s
+        inputunipolar          : false
+        inputtraceid           : [ V-1, EOD, LocalEOD-1, GlobalEFieldStimulus ]
+        inputtracescale        : [ 100, 1, 10, 1 ]
+        inputtraceunit         : [ mV, mV, mV, mV ]
+        inputtracedevice       : [ ai-1, ai-1, ai-1, ai-1 ]
+        inputtracechannel      : [ 0, 2, 4, 6 ]
+        inputtracereference    : [ ground, ground, ground, ground ]
+        inputtracemaxvalue     : [ 100, 2, 2, 10 ]
+        inputtracecenter       : [ true, false, false, false ]
+    output:
+        outputtraceid          : [ GlobalEField, GlobalEFieldAM, LocalEField, I ]
+        outputtracedevice      : [ ao-1, ao-1, ao-1, ao-1 ]
+        outputtracechannel     : [ 0, 1, 2, 3 ]
+        outputtracescale       : [ 1, 1, 1, 1 ]
+        outputtraceunit        : [ V, V, V, V ]
+        outputtracemaxrate     : [ 40, 40, 40, 40]
+        outputtracemaxrateunit : [kHz, kHz, kHz, kHz]
+        outputtracemodality    : [ electric, electric, electric, current ]
+
+  sinus:
+      inputsamplerate         : 20
+      inputsamplerateunit     : kHz
+      # BufferSize
+      inputtracecapacity      : 600
+      inputtracecapacityunit  : s
+      outputtraceid           : [ Sinus ]
+      outputtracedevice       : [ ao-0 ]
+      outputtracechannel      : [ 0 ]
+      outputtracescale        : [ 1 ]
+      outputtraceunit         : [ V ] 
+      outputtracemaxrate      : [ 40 ]
+      outputtracemaxrateunit  : [kHz]
+      outputtracemodality     : [ electric ]
+
+  devices:
+    DAQFlexCore:
+      analogoutputpins    : [0, 1]
+      analoginputpinshigh : [0, 1, 2, 3,4,5,6,7]
+      analoginputpinslow  : [1,2]
+      digitalpins         : [0,1,2,3]
+
+    CS3310DIO:
+      ident      : attdev-1
+      strobepin  : 6
+      datainpin  : 5
+      dataoutpin : -1
+      cspin      : 4
+      mutepin    : 7
+      zcenpin    : -1
--- a/pyrelacs/config/config_loader.py
+++ b/pyrelacs/config/config_loader.py
@@ -0,0 +1,132 @@
+from typing import TypedDict, Union
+from dataclasses import dataclass
+import pathlib
+
+
+import dacite
+import yaml
+from dacite import from_dict
+from IPython import embed
+
+from pyrelacs.util.logging import config_logging
+
+log = config_logging()
+
+
+@dataclass
+class ValueUnit:
+    value: int
+    unit: str
+
+
+@dataclass
+class Settings:
+    daq: bool
+    repros: list[str]
+    path: str
+
+
+@dataclass
+class Metadata:
+    SetupName: str
+    Maintainer: str
+    Creator: str
+    SetupLocation: str
+    Lab: str
+    Institute: str
+    University: str
+    Address: str
+
+
+@dataclass
+class Input:
+    inputsamplerate: int
+    inputsamplerateunit: str
+    # BufferSize
+    inputtracecapacity: int
+    inputtracecapacityunit: str
+    inputunipolar: bool
+    inputtraceid: list[str]
+    inputtracescale: list[int]
+    inputtraceunit: list[str]
+    inputtracedevice: list[str]
+    inputtracechannel: list[int]
+    inputtracereference: list[str]
+    inputtracemaxvalue: list[int]
+    inputtracecenter: list[bool]
+
+
+@dataclass
+class Output:
+    outputtraceid: list[str]
+    outputtracedevice: list[str]
+    outputtracechannel: list[int]
+    outputtracescale: list[int]
+    outputtraceunit: list[str]
+    outputtracemaxrate: list[int]
+    outputtracemaxrateunit: list[str]
+    outputtracemodality: list[str]
+
+
+@dataclass
+class Data:
+    input: Input
+    output: Output
+
+
+@dataclass
+class Sinus:
+    inputsamplerate: int
+    inputsamplerateunit: str
+    # BufferSize
+    inputtracecapacity: int
+    inputtracecapacityunit: str
+    outputtraceid: list[str]
+    outputtracedevice: list[str]
+    outputtracechannel: list[int]
+    outputtracescale: list[int]
+    outputtraceunit: list[str]
+    outputtracemaxrate: list[int]
+    outputtracemaxrateunit: list[str]
+    outputtracemodality: list[str]
+
+
+@dataclass
+class PyRelacs:
+    data: Data
+    sinus: Sinus
+
+
+@dataclass
+class Config:
+    settings: Settings
+    metadata: Metadata
+    pyrelacs: PyRelacs
+
+
+def load_config():
+    pyrelacs_config_path = pathlib.Path(__file__).parent.parent / "config.yaml"
+    log.debug(pyrelacs_config_path)
+    if not pyrelacs_config_path.is_file():
+        log.error("Config File was not found")
+    with open(pyrelacs_config_path, "r") as config_file:
+        try:
+            data = yaml.full_load(config_file)
+            try:
+                config = from_dict(data_class=Config, data=data)
+                return config
+            except dacite.DaciteError as e:
+                log.error(f"Invalid Config, {e}")
+        except yaml.YAMLError as e:
+            raise yaml.YAMLError(f"Error parsing YAML file: {e}")
+
+
+if __name__ == "__main__":
+    pyrelacs_config_path = pathlib.Path(__file__).parent.parent / "config.yaml"
+    log.debug(pyrelacs_config_path)
+    if not pyrelacs_config_path.is_file():
+        log.error("Config File was not found")
+    with open(pyrelacs_config_path, "r") as config_file:
+        data = yaml.full_load(config_file)
+        embed()
+        exit()
--- a/pyrelacs/dataio/circbuffer.py
+++ b/pyrelacs/dataio/circbuffer.py
@@ -1,21 +1,29 @@
 from typing import Tuple
 import numpy as np
 from IPython import embed
+from pyqtgraph.Qt.QtCore import QMutex


 class CircBuffer:
-    def __init__(self, size: int, channels: int = 1, samplerate: int = 40_000):
+    def __init__(
+        self,
+        size: int,
+        channels: int = 1,
+        samplerate: float = 40_000.0,
+        mutex: QMutex = QMutex(),
+    ):
        self.__size = size
        self.__channels = channels
        self.__samplereate = samplerate
        self.__buffer = np.zeros(
            (channels, size), dtype=np.double
        )  # or dtype of your choice
-        self.__time = np.zeros(size, dtype=np.double)
+        self.__time = np.zeros((channels, size), dtype=np.double)
        self.__index = [0 for i in range(channels)]
        self.__is_full = [False for i in range(channels)]
        self.__totalcount = [0 for i in range(channels)]
        self.__overflows = [0 for i in range(channels)]
+        self.mutex = mutex

    @property
    def size(self):
@@ -39,15 +47,17 @@ class CircBuffer:
        return self.__index[channel]

    def append(self, item, channel: int = 0):
+        self.mutex.lock()
        self.__buffer[channel, self.write_index(channel)] = item
        self.__index[channel] = (self.write_index(channel) + 1) % self.__size
        self.__totalcount[channel] += 1
-        self.__time[self.write_index(channel=0)] = (
-            self.__time[self.write_index(channel=0) - 1] + 1 / self.__samplereate
+        self.__time[channel, self.write_index(channel)] = (
+            self.__time[channel, self.write_index(channel) - 1] + 1 / self.__samplereate
        )
        if self.__index[channel] == 0:
            self.__is_full[channel] = True
            self.__overflows[channel] += 1
+        self.mutex.unlock()

    def get_all(self, channel: int = 0):
        """
@@ -113,7 +123,7 @@ class CircBuffer:
        # easy case first, we can spare the effort of further checking
        if index >= 0 and index <= self.write_index(channel):
            if self.has_value(index, channel):
-                return (self.__buffer[channel, index], self.__time[index])
+                return (self.__buffer[channel, index], self.__time[channel, index])
            else:
                raise IndexError(
                    f"Invalid index {index} on ring buffer for channel{channel}"
@@ -122,20 +132,24 @@ class CircBuffer:
        if index < 0:
            index = self.write_index() - 1
        if self.has_value(index, channel):
-            return (self.__buffer[channel, index], self.__time[index])
+            return (self.__buffer[channel, index], self.__time[channel, index])
        else:
            raise IndexError(
                f"Invalid index {index} on ring buffer for channel{channel}"
            )

-    def read(self, start, count=1, channel=0):
+    def read(self, start, extend=1, channel=0):
        """Reads a numpy array from buffer"""
-        if start < 0 or count < 0:
-            raise IndexError(
-                f"Invalid start ({start}) or count ({count}) for channel{channel}"
-            )
+        if extend < 0:
+            raise IndexError(f"Invalid  extend ({extend}) for channel {channel}")
+        if not self.is_full(channel):
+            if start < 0:
+                raise IndexError(f"Invalid  start ({start}) for channel {channel}")
+        else:
+            if start < 0:
+                start = start + self.size

-        if count == 1:
+        if extend == 1:
            return np.array(self.get(start, channel))

        vs, vc = self.valid_range(channel)
@@ -147,17 +161,32 @@ class CircBuffer:
            raise IndexError(
                f"Invalid start index {start} for buffer with size {self.size}"
            )
-        if count > self.size:
-            count = self.size
-        if count > vc:
-            count = vc

-        if (start + count) < self.size:
-            return self.__buffer[channel, start : start + count]
-        else:
-            return np.concatenate(
-                (
-                    self.__buffer[channel, start:],
-                    self.__buffer[channel, : count - self.size + start],
-                )
+        if extend > vc:
+            extend = vc
+
+        if (start + extend) > self.__totalcount[channel]:
+            raise IndexError(
+                f" Invalid range, extended over the totalcount of the buffer {self.__totalcount[channel]}"
+            )
+
+        if (start + extend) < self.size:
+            return (
+                self.__time[channel, start : start + extend],
+                self.__buffer[channel, start : start + extend],
+            )
+        else:
+            return (
+                np.concatenate(
+                    (
+                        self.__time[channel, start:],
+                        self.__time[channel, : extend - self.size + start],
+                    )
+                ),
+                np.concatenate(
+                    (
+                        self.__buffer[channel, start:],
+                        self.__buffer[channel, : extend - self.size + start],
+                    )
+                ),
            )
--- a/pyrelacs/dataio/daq_producer.py
+++ b/pyrelacs/dataio/daq_producer.py
@@ -22,6 +22,8 @@ class DaqProducer:
        self.ai_device = self.device.get_ai_device()
        self.channels = channels

+        self.stop = False
+
    def read_analog_continously(
        self,
        *args,
@@ -39,7 +41,7 @@ class DaqProducer:
        )

        # let the buffer for the daq device hold 5 seconds of data
-        daq_buffer_size = self.buffer.samplerate * 5
+        daq_buffer_size = int(self.buffer.samplerate * 5)

        data_in = uldaq.create_float_buffer(channel_range.size, daq_buffer_size)
        log.debug(f"Buffersize for daq {len(data_in)}")
@@ -67,7 +69,7 @@ class DaqProducer:
            while daq_status != uldaq.ScanStatus.IDLE:
                prev_count = 0
                prev_index = 0
-                while time.time() - start_time < 10:
+                while not self.stop:
                    daq_status, transfer_status = self.ai_device.get_scan_status()
                    # The index into the data buffer immediately following the last sample transferred.
                    current_index = transfer_status.current_index
@@ -154,17 +156,20 @@ class DaqProducer:
            break
        return "Done. "

+    def stop_aquisition(self):
+        self.stop = True

-if __name__ == "__main__":
-    devices = uldaq.get_daq_device_inventory(uldaq.InterfaceType.USB)
-    log.debug(f"Found daq devices {len(devices)}, connecting to the first one")
-    try:
-        daq_device = uldaq.DaqDevice(devices[0])
-    except uldaq.ul_exception.ULException as e:
-        log.error("Did not found daq devices, please connect one")
-        raise e
-    daq_device.connect()

-    buf = CircBuffer(size=1_000_000, samplerate=100)
-    producer = DaqProducer(buf, daq_device, [1, 1])
-    producer.read_analog_continously()
+# if __name__ == "__main__":
+#     devices = uldaq.get_daq_device_inventory(uldaq.InterfaceType.USB)
+#     log.debug(f"Found daq devices {len(devices)}, connecting to the first one")
+#     try:
+#         daq_device = uldaq.DaqDevice(devices[0])
+#     except uldaq.ul_exception.ULException as e:
+#         log.error("Did not found daq devices, please connect one")
+#         raise e
+#     daq_device.connect()
+#
+#     buf = CircBuffer(size=1_000_000, samplerate=100)
+#     producer = DaqProducer(buf, daq_device, [1, 1])
+#     producer.read_analog_continously()
--- a/pyrelacs/dataio/nix_writer.py
+++ b/pyrelacs/dataio/nix_writer.py
@@ -0,0 +1,72 @@
+import time
+from IPython import embed
+from PyQt6.QtCore import QMutex
+import nixio
+
+from pyrelacs.dataio.circbuffer import CircBuffer
+from pyrelacs.util.logging import config_logging
+
+log = config_logging()
+
+
+class NixWriter:
+    def __init__(self, buffer: CircBuffer) -> None:
+        self.buffer = buffer
+
+    def write_nix(
+        self,
+        data_array: nixio.DataArray,
+        mutex: QMutex,
+        channel: int = 0,
+        chunk_size=1000,
+        *args,
+        **kwargs,
+    ):
+        index = 0
+        log.debug("Starting the writing")
+        self.write = True
+        while self.write:
+            total_count = self.buffer.totalcount(channel=channel)
+            if total_count - index >= chunk_size:
+                mutex.lock()
+                log.debug(index)
+                try:
+                    _, data = self.buffer.read(
+                        index, extend=chunk_size, channel=channel
+                    )
+                    if index == 0:
+                        data_array.write_direct(data)
+                    else:
+                        data_array.append(data)
+                    index += chunk_size
+                except IndexError as e:
+                    time.sleep(0.001)
+                    log.debug(f"{e}")
+                mutex.unlock()
+            else:
+                time.sleep(0.001)
+                continue
+        total_count = self.buffer.totalcount(channel=channel)
+        try:
+            mutex.lock()
+            _, data = self.buffer.read(
+                index, extend=total_count - index, channel=channel
+            )
+            data_array.append(data)
+            mutex.unlock()
+            index += total_count - index
+        except IndexError as e:
+            log.error(f"Could not read the last samples, {e}")
+
+        log.debug("Stoppint the writing")
+        log.debug(f"Samples written {index}")
+
+    def _write_header(self):
+        self.nix_file = nixio.File.open(path="data.nix", mode=nixio.FileMode.Overwrite)
+        self.block = self.nix_file.create_block("recording", "testfile")
+        self.data_array = self.block.create_data_array(
+            "Analog1", "ndarray", shape=(1000,), dtype=nixio.DataType.Double
+        )
+
+    def stop_writing(self):
+        self.write = False
--- a/pyrelacs/dataio/sin_producer.py
+++ b/pyrelacs/dataio/sin_producer.py
@@ -1,8 +1,5 @@
-from math import sin
 import time
-from PyQt6.QtGui import QAction
 import numpy as np
-import matplotlib.pyplot as plt
 from IPython import embed
 from pyrelacs.dataio.circbuffer import CircBuffer
 from pyrelacs.util.logging import config_logging
@@ -11,7 +8,6 @@ from pyrelacs.util.logging import config_logging
 log = config_logging()


-# stopbutton: QAction
 class SinProducer:
    def __init__(
        self,
@@ -28,6 +24,7 @@ class SinProducer:
        AMPLITUDE = 2
        FREQUENCY = 10

+        self.stop = False
        log.debug("producing Sin")
        start_time = time.time()
        t = 0
@@ -39,13 +36,9 @@ class SinProducer:

        end_time = time.time()

-        data = self.buffer.get_all()
        log.debug(f"duration sinus {end_time-start_time}")
        log.debug(f"Stimulation time {t}")
-        # log.debug(data.shape[0])
-        # log.debug(data.shape[0] / self.buffer.samplerate)
-        # plt.plot(np.arange(data.size) / self.buffer.samplerate, data)
-        # plt.show()
+        log.debug(f"Total samples produced {self.buffer.totalcount()}")

    def stop_request(self):
        self.stop = True
--- a/pyrelacs/devices/mccdaq.py
+++ b/pyrelacs/devices/mccdaq.py
@@ -41,13 +41,16 @@ class MccDaq:
        try:
            self.daq_device.connect()
        except uldaq.ul_exception.ULException:
-            self.disconnect_dac()
+            self.disconnect_daq()
            self.connect_dac()

        self.ai_device = self.daq_device.get_ai_device()
        self.ao_device = self.daq_device.get_ao_device()
        self.dio_device = self.daq_device.get_dio_device()
-        log.debug("Connected")
+
+        log.debug("Connected to MccDaq")
+        log.debug("Activating the Attenuator")
+        self.activate_attenuator()

    def connect_dac(self):
        """
@@ -194,7 +197,7 @@ class MccDaq:
        except Exception as e:
            print(f"{e}")
            self.set_analog_to_zero()
-            self.disconnect_dac()
+            self.disconnect_daq()

        return data_analog_output

@@ -221,10 +224,10 @@ class MccDaq:
                uldaq.AOutListFlag.DEFAULT,
                [0, 0],
            )
-        except Exception as e:
-            log.error("f{e}")
+        except Exception as er:
+            log.error(f"{er}")
            log.error("disconnection dac")
-            self.disconnect_dac()
+            # self.disconnect_daq()

    def digital_trigger(self, ch: int = 0) -> None:
        """
@@ -281,7 +284,9 @@ class MccDaq:
        bit = self.dio_device.d_bit_in(uldaq.DigitalPortType.AUXPORT, channel)
        return bit

-    def disconnect_dac(self):
+    def disconnect_daq(self):
+        log.debug("Disconnecting DAQ")
+        self.deactivate_attenuator()
        self.daq_device.disconnect()
        self.daq_device.release()

@@ -329,12 +334,12 @@ class MccDaq:
            except uldaq.ul_exception.ULException:
                log.debug("Operation timed out")
                self.write_bit(channel=0, bit=0)
-                self.disconnect_dac()
+                self.disconnect_daq()
                self.connect_dac()
                self.set_analog_to_zero()
            finally:
                self.write_bit(channel=0, bit=0)
-                self.disconnect_dac()
+                self.disconnect_daq()
                self.connect_dac()
                self.set_analog_to_zero()

--- a/pyrelacs/info.py
+++ b/pyrelacs/info.py
@@ -1,29 +1,26 @@
-import tomlkit
+import tomllib
 import pathlib


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

-    # Parse the toml content
-    pyproject = tomlkit.parse(pyproject_content)
-
-    # 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["project"]["organization"],
-        "classifiers": pyproject["tool"]["poetry"]["classifiers"],
-        "copyright": pyproject["project"]["copyright"],
-        "repository": pyproject["tool"]["poetry"]["repository"],
+    info_dict = {
+        "name": pyproject_content["tool"]["poetry"]["name"],
+        "version": pyproject_content["tool"]["poetry"]["version"],
+        "description": pyproject_content["tool"]["poetry"]["description"],
+        "authors": pyproject_content["tool"]["poetry"]["authors"],
+        "readme": pyproject_content["tool"]["poetry"]["authors"],
+        "licence": pyproject_content["tool"]["poetry"]["license"],
+        "organization": pyproject_content["project"]["organization"],
+        "classifiers": pyproject_content["tool"]["poetry"]["classifiers"],
+        "copyright": pyproject_content["project"]["copyright"],
+        "repository": pyproject_content["tool"]["poetry"]["repository"],
    }
+    return info_dict


 _root = pathlib.Path(__file__).parent.parent
--- a/pyrelacs/repros/calibration/calibration.py
+++ b/pyrelacs/repros/calibration/calibration.py
@@ -6,6 +6,8 @@ import uldaq
 from IPython import embed
 import numpy as np
 import matplotlib.pyplot as plt
+from scipy.signal import welch, find_peaks
+import pyqtgraph as pg

 from pyrelacs.devices.mccdaq import MccDaq
 from pyrelacs.util.logging import config_logging
@@ -15,40 +17,50 @@ log = config_logging()
 faulthandler.enable()


-class Calibration(MccDaq):
-    def __init__(self) -> None:
-        super().__init__()
+class Calibration:
+    def __init__(self, config, mccdaq: MccDaq) -> None:
+        self.config = config
+        self.mccdaq = mccdaq
        self.SAMPLERATE = 40_000.0
        self.DURATION = 5
        self.AMPLITUDE = 1
        self.SINFREQ = 750

    @staticmethod
-    def run(nix_file: nix.File):
-        calb = Calibration()
-        calb.check_beat(nix_file)
+    def run(*args, **kwargs):
+        nix_block = args[0]
+        figure = args[1]
+        mccdaq = args[2]
+        config = args[3]
+        calb = Calibration(config, mccdaq)
+        calb.check_beat(nix_block)
+        calb.plot(figure, nix_block)
+
+        return "finished"

    def check_amplitude(self):
        db_values = [0.0, -5.0, -10.0, -20.0, -50.0]
        colors = ["red", "green", "blue", "black", "yellow"]
-        self.set_attenuation_level(db_channel1=0.0, db_channel2=0.0)
+        self.mccdaq.set_attenuation_level(db_channel1=0.0, db_channel2=0.0)
        # write to ananlog 1
        t = np.arange(0, self.DURATION, 1 / self.SAMPLERATE)
        data = self.AMPLITUDE * np.sin(2 * np.pi * self.SINFREQ * t)
        fig, ax = plt.subplots()

        for i, db_value in enumerate(db_values):
-            self.set_attenuation_level(db_channel1=db_value, db_channel2=db_value)
+            self.mccdaq.set_attenuation_level(
+                db_channel1=db_value, db_channel2=db_value
+            )
            log.debug(f"{db_value}")

-            stim = self.write_analog(
+            stim = self.mccdaq.write_analog(
                data,
                [0, 0],
                self.SAMPLERATE,
                ScanOption=uldaq.ScanOption.EXTTRIGGER,
            )

-            data_channel_one = self.read_analog(
+            data_channel_one = self.mccdaq.read_analog(
                [0, 0],
                self.DURATION,
                self.SAMPLERATE,
@@ -57,21 +69,21 @@ class Calibration(MccDaq):
            time.sleep(1)

            log.debug("Starting the Scan")
-            self.digital_trigger()
+            self.mccdaq.digital_trigger()

            try:
-                self.ao_device.scan_wait(uldaq.WaitType.WAIT_UNTIL_DONE, 15)
+                self.mccdaq.ao_device.scan_wait(uldaq.WaitType.WAIT_UNTIL_DONE, 15)
                log.debug("Scan finished")
-                self.write_bit(channel=0, bit=0)
+                self.mccdaq.write_bit(channel=0, bit=0)
                time.sleep(1)
-                self.set_analog_to_zero()
+                self.mccdaq.set_analog_to_zero()
            except uldaq.ul_exception.ULException:
                log.debug("Operation timed out")
                # reset the diggital trigger
-                self.write_bit(channel=0, bit=0)
+                self.mccdaq.write_bit(channel=0, bit=0)
                time.sleep(1)
-                self.set_analog_to_zero()
-                self.disconnect_dac()
+                self.mccdaq.set_analog_to_zero()
+                # self.mccdaq.disconnect_daq()

            if i == 0:
                ax.plot(t, stim, label=f"Input_{db_value}", color=colors[i])
@@ -80,34 +92,33 @@ class Calibration(MccDaq):
        ax.legend()
        plt.show()

-        self.disconnect_dac()
+        # self.mccdaq.disconnect_daq()

-    def check_beat(self, nix_file: nix.File):
-        self.set_attenuation_level(db_channel1=-10.0, db_channel2=0.0)
+    def check_beat(self, nix_block: nix.Block):
+        self.mccdaq.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)
        # data = np.concatenate((data, data))
        db_values = [0.0, -5.0, -8.5, -10.0]
        colors = ["red", "blue", "black", "green"]
        colors_in = ["lightcoral", "lightblue", "grey", "lightgreen"]
-        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(
+            self.mccdaq.set_attenuation_level(db_channel1=db_value)
+            stim = self.mccdaq.write_analog(
                data,
                [0, 0],
                self.SAMPLERATE,
                ScanOption=uldaq.ScanOption.EXTTRIGGER,
            )
-            readout = self.read_analog(
+            readout = self.mccdaq.read_analog(
                [0, 1],
                self.DURATION,
                self.SAMPLERATE,
                ScanOption=uldaq.ScanOption.EXTTRIGGER,
            )
-            self.digital_trigger()
-            log.info(self.ao_device)
+            self.mccdaq.digital_trigger()
+            log.info(self.mccdaq.ao_device)
            ai_status = uldaq.ScanStatus.RUNNING
            ao_status = uldaq.ScanStatus.RUNNING

@@ -119,10 +130,10 @@ class Calibration(MccDaq):
            ):
                # log.debug("Scanning")
                time.time_ns()
-                ai_status = self.ai_device.get_scan_status()[0]
-                ao_status = self.ao_device.get_scan_status()[0]
+                ai_status = self.mccdaq.ai_device.get_scan_status()[0]
+                ao_status = self.mccdaq.ao_device.get_scan_status()[0]

-            self.write_bit(channel=0, bit=0)
+            self.mccdaq.write_bit(channel=0, bit=0)
            log.debug(
                f"Status Analog_output {ao_status}\n, Status Analog_input {ai_status}"
            )
@@ -130,7 +141,7 @@ class Calibration(MccDaq):
            channel1 = np.array(readout[::2])
            channel2 = np.array(readout[1::2])

-            stim_data = block.create_data_array(
+            stim_data = nix_block.create_data_array(
                f"stimulus_{db_value}",
                "nix.regular_sampled",
                shape=data.shape,
@@ -143,7 +154,7 @@ class Calibration(MccDaq):
                label="time",
                unit="s",
            )
-            fish_data = block.create_data_array(
+            fish_data = nix_block.create_data_array(
                f"fish_{db_value}",
                "Array",
                shape=data.shape,
@@ -157,7 +168,72 @@ class Calibration(MccDaq):
                unit="s",
            )

-        self.set_analog_to_zero()
+        time.time_ns()
+        self.mccdaq.set_analog_to_zero()
+
+    def plot(self, figure, block):
+        self.figure = figure
+        self.figure.setBackground("w")
+        self.beat_plot = self.figure.addPlot(row=0, col=0)
+        self.power_plot = self.figure.addPlot(row=1, col=0)
+        self.beat_plot.addLegend()
+        self.power_plot.addLegend()
+        # self.power_plot.setLogMode(x=False, y=True)
+
+        colors = ["red", "green", "blue", "black", "yellow"]
+        for i, (stim, fish) in enumerate(
+            zip(list(block.data_arrays)[::2], list(block.data_arrays)[1::2])
+        ):
+            f_stim, stim_power = welch(
+                stim[:],
+                fs=40_000.0,
+                window="flattop",
+                nperseg=100_000,
+            )
+            stim_power = decibel(stim_power)
+            stim_max_power_index = np.argmax(stim_power)
+            freq_stim = f_stim[stim_max_power_index]
+
+            f_fish, fish_power = welch(
+                fish[:],
+                fs=40_000.0,
+                window="flattop",
+                nperseg=100_000,
+            )
+            fish_power = decibel(fish_power)
+            fish_max_power_index = np.argmax(fish_power)
+            freq_fish = f_fish[fish_max_power_index]
+
+            beat_frequency = np.abs(freq_fish - freq_stim)
+
+            beat = stim[:] + fish[:]
+            beat_squared = beat**2
+
+            f, powerspec = welch(
+                beat_squared,
+                window="flattop",
+                fs=40_000.0,
+                nperseg=100_000,
+            )
+            powerspec = decibel(powerspec)
+
+            padding = 20
+            integration_window = powerspec[
+                (f > beat_frequency - padding) & (f < beat_frequency + padding)
+            ]
+
+            peaks = find_peaks(powerspec, prominence=40)[0]
+
+            pen = pg.mkPen(colors[i])
+
+            self.beat_plot.plot(
+                np.arange(0, len(beat)) / 40_000.0,
+                beat,
+                pen=pen,
+                name=stim.name,
+            )
+            self.power_plot.plot(f, powerspec, pen=pen, name=stim.name)
+            self.power_plot.plot(f[peaks], powerspec[peaks], pen=None, symbol="x")


 def decibel(power, ref_power=1.0, min_power=1e-20):
--- a/pyrelacs/repros/calibration/config.yaml
+++ b/pyrelacs/repros/calibration/config.yaml
--- a/pyrelacs/repros/repros.py
+++ b/pyrelacs/repros/repros.py
@@ -22,9 +22,7 @@ class Repro:
    def __init__(self) -> None:
        pass

-    def run_repro(
-        self, nix_file: nix.File, name: str, file: pathlib.Path, *args, **kwargs
-    ) -> None:
+    def run_repro(self, 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")
@@ -40,14 +38,19 @@ class Repro:
                    log.error(f"{spec.loader} is None")
                if hasattr(module, name):
                    rep_class = getattr(module, name)
-                    rep_class.run(nix_file)
+                    rep_class.run(*args, **kwargs)
                else:
                    raise AttributeError(f"{file.name} has no {name} class")

-    def names_of_repros(self) -> Tuple[list, list]:
+    def names_of_repros(self, include_repros: list[str]) -> Tuple[list, list]:
        """
        Searches for class names in the repro folder in all python files

+        Parameters
+        ----------
+        include_repros : list[str]
+            List of repros to include in the pyrelacs instance
+
        Returns
        -------
        Tuple[list, list]
@@ -73,4 +76,7 @@ class Repro:
                repro_names.extend(class_name)
                file_names.append(python_file)
            file.close()
+
+        repro_names = [r for r in repro_names if r in include_repros]
+        file_names = [f for r, f in zip(repro_names, file_names) if r in include_repros]
        return repro_names, file_names
--- a/pyrelacs/repros/sinus/sinus.py
+++ b/pyrelacs/repros/sinus/sinus.py
@@ -0,0 +1,17 @@
+import nixio
+from pyrelacs.util.logging import config_logging
+
+
+log = config_logging()
+
+
+class Sinus:
+    def __init__(self) -> None:
+        pass
+
+    @staticmethod
+    def run(config, mccdaq, nix_block: nixio.Block, figure) -> None:
+        log.debug(config)
+        log.debug(mccdaq)
+        log.debug(nix_block)
+        log.debug(figure)
--- a/pyrelacs/ui/mainwindow.py
+++ b/pyrelacs/ui/mainwindow.py
@@ -1,11 +1,16 @@
 import time
 from pathlib import Path as path
+from datetime import datetime
+from dataclasses import asdict

 from PyQt6.QtGui import QAction, QIcon, QKeySequence
-from PyQt6.QtCore import Qt, QSize, QThreadPool
+from PyQt6.QtCore import Qt, QSize, QThreadPool, QMutex
 from PyQt6.QtWidgets import (
    QGridLayout,
+    QPushButton,
+    QTabWidget,
    QToolBar,
+    QVBoxLayout,
    QWidget,
    QMainWindow,
    QPlainTextEdit,
@@ -13,21 +18,20 @@ from PyQt6.QtWidgets import (
    QStatusBar,
 )

-from pglive.sources.data_connector import DataConnector
-from pglive.sources.live_plot import LiveLinePlot
-from pglive.sources.live_plot_widget import LivePlotWidget

-import uldaq
-import nixio as nix
+import nixio
 import pyqtgraph as pg
-import numpy as np
+import quantities as pq

+from pyrelacs.devices.mccdaq import MccDaq

+from pyrelacs.dataio.circbuffer import CircBuffer
 from pyrelacs.dataio.daq_producer import DaqProducer
+from pyrelacs.dataio.nix_writer import NixWriter
 from pyrelacs.dataio.sin_producer import SinProducer
+
 from pyrelacs.worker import Worker
 from pyrelacs.repros.repros import Repro
-from pyrelacs.dataio.circbuffer import CircBuffer

 from pyrelacs.ui.about import AboutDialog
 from pyrelacs.ui.plots.calibration import CalibrationPlot
@@ -42,25 +46,32 @@ from IPython import embed


 class PyRelacs(QMainWindow):
-    def __init__(self):
+    def __init__(self, config):
        super().__init__()
+        # loaded config
+        self.config = config
+        if self.config.settings.daq:
+            start = time.time()
+            self.mccdaq = MccDaq()
+            end = time.time()
+            log.debug(f"Connection to DAQ took {end - start}")
+        else:
+            self.mccdaq = None
+
+        self.repros = Repro()
+
        self.setToolButtonStyle(
            Qt.ToolButtonStyle.ToolButtonTextBesideIcon
        )  # Ensure icons are displayed with text
        self.setWindowTitle("PyRelacs")

+        self.create_nix_file(f"{_root}/test.nix", self.config.metadata)
+
+        self.mutex = QMutex()
+
        self.figure = pg.GraphicsLayoutWidget()

-        filename = path.joinpath(path.cwd(), "data.nix")
-        if filename.exists():
-            self.nix_file = nix.File.open(str(filename), nix.FileMode.ReadOnly)
-        filename = path.joinpath(path.cwd(), "calibration.nix")
-        self.nix_file = nix.File.open(str(filename), nix.FileMode.Overwrite)
-
-        self.calibration_plot = CalibrationPlot(self.figure, self.nix_file)
-
        self.threadpool = QThreadPool()
-        self.repros = Repro()

        self.text = QPlainTextEdit()
        self.text.setReadOnly(True)
@@ -69,24 +80,47 @@ class PyRelacs(QMainWindow):
        self.setStatusBar(QStatusBar(self))
        self.create_actions()
        self.create_toolbars()
+        self.repro_tabs = QTabWidget()
+        self.create_repros_tabs()

        layout = QGridLayout()
        layout.addWidget(self.figure, 0, 0, 2, 2)
-        layout.addWidget(self.text, 2, 0, 1, 2)
+        layout.addWidget(self.repro_tabs, 2, 0, 2, 2)
+        layout.addWidget(self.text, 4, 0, 1, 1)

        widget = QWidget()
        widget.setLayout(layout)
        self.setCentralWidget(widget)

-        SAMPLERATE = 1_000
-        BUFFERSIZE = 1_0000
-        self.buffer = CircBuffer(size=BUFFERSIZE, samplerate=SAMPLERATE)
-        # self.connect_dac()
+        SAMPLERATE = pq.Quantity(
+            self.config.pyrelacs.data.input.inputsamplerate,
+            self.config.pyrelacs.data.input.inputsamplerateunit,
+        ).rescale("Hz")

-        # self.daq_producer = DaqProducer(self.buffer, self.daq_device, [1, 1])
-        self.sin_producer = SinProducer(self.buffer)
+        INPUTTRACECAPACITY = pq.Quantity(
+            self.config.pyrelacs.data.input.inputtracecapacity,
+            self.config.pyrelacs.data.input.inputtracecapacityunit,
+        ).rescale("s")
+        start = time.time()
+        BUFFERSIZE = (SAMPLERATE * INPUTTRACECAPACITY).simplified
+        end = time.time()
+        log.debug(f"Buffer allocation took {end - start}")
+
+        self.buffer = CircBuffer(
+            size=int(BUFFERSIZE.base),
+            samplerate=float(SAMPLERATE.base),
+            mutex=self.mutex,
+        )
        self.continously_plot = Continously(self.figure, self.buffer)
-        self.continously_plot.plot_daq()
+        # self.continously_plot.plot()
+
+        if self.mccdaq:
+            log.debug("Creating Daq Generator")
+            self.daq_producer = DaqProducer(self.buffer, self.mccdaq.daq_device, [1, 1])
+        log.debug("Creating Sinus Generator")
+        self.sinus_producer = SinProducer(self.buffer)
+
+        self.nix_writer = NixWriter(self.buffer)

    def create_actions(self):
        self._rlx_exitaction = QAction(QIcon(":/icons/exit.png"), "Exit", self)
@@ -102,25 +136,26 @@ class PyRelacs(QMainWindow):
        self._daq_connectaction = QAction(
            QIcon(":icons/connect.png"), "Connect DAQ", self
        )
-        self._daq_connectaction.setStatusTip("Connect to daq device")
-        # self._daq_connectaction.setShortcut(QKeySequence("Alt+d"))
-        self._daq_connectaction.triggered.connect(self.connect_dac)
+        if self.mccdaq:
+            self._daq_connectaction.setStatusTip("Connect to daq device")
+            # self._daq_connectaction.setShortcut(QKeySequence("Alt+d"))
+            self._daq_connectaction.triggered.connect(self.mccdaq.connect_dac)

-        self._daq_disconnectaction = QAction(
-            QIcon(":/icons/disconnect.png"), "Disconnect DAQ", self
-        )
-        self._daq_disconnectaction.setStatusTip("Disconnect the DAQ device")
-        # self._daq_connectaction.setShortcut(QKeySequence("Alt+d"))
-        self._daq_disconnectaction.triggered.connect(self.disconnect_dac)
+            self._daq_disconnectaction = QAction(
+                QIcon(":/icons/disconnect.png"), "Disconnect DAQ", self
+            )
+            self._daq_disconnectaction.setStatusTip("Disconnect the DAQ device")
+            # self._daq_connectaction.setShortcut(QKeySequence("Alt+d"))
+            self._daq_disconnectaction.triggered.connect(self.mccdaq.disconnect_daq)

-        self._daq_calibaction = QAction(
-            QIcon(":/icons/calibration.png"), "Plot calibration", self
-        )
-        self._daq_calibaction.setStatusTip("Calibrate the attenuator device")
-        # self._daq_calibaction.setShortcut(QKeySequence("Alt+d"))
-        self._daq_calibaction.triggered.connect(self.calibration_plot.plot)
+        # self._daq_calibaction = QAction(
+        #     QIcon(":/icons/calibration.png"), "Plot calibration", self
+        # )
+        # self._daq_calibaction.setStatusTip("Calibrate the attenuator device")
+        # # self._daq_calibaction.setShortcut(QKeySequence("Alt+d"))
+        # self._daq_calibaction.triggered.connect(self.calibration_plot.plot)

-        self._run_action = QAction(QIcon(":/icons/record.png"), "Run", self)
+        self._run_action = QAction(QIcon(":/icons/record.png"), "RunDAQ", self)
        self._run_action.triggered.connect(self.run_daq)

        self._run_sinus_action = QAction(QIcon(":/icons/record.png"), "Sinus", self)
@@ -129,6 +164,13 @@ class PyRelacs(QMainWindow):
        self._stop_recording = QAction(QIcon(":/icons/stop.png"), "Stop", self)
        self._stop_recording.triggered.connect(self.stop_recording)

+        self._recenter_plot = QAction("Recenter", self)
+        self._recenter_plot.triggered.connect(self.recenter_continously_plot)
+        self._recenter_plot.setShortcut(QKeySequence("Alt+r"))
+
+        self._record = QAction(QIcon(":/icons/record.png"), "Record", self)
+        self._record.triggered.connect(self.record)
+
        self.create_menu()

    def create_menu(self):
@@ -143,10 +185,11 @@ class PyRelacs(QMainWindow):
                file_menu.addAction(self._rlx_aboutaction)

            if device_menu is not None:
-                device_menu.addAction(self._daq_connectaction)
-                device_menu.addAction(self._daq_disconnectaction)
+                if self.config.settings.daq:
+                    device_menu.addAction(self._daq_connectaction)
+                    device_menu.addAction(self._daq_disconnectaction)
                device_menu.addSeparator()
-                device_menu.addAction(self._daq_calibaction)
+                # device_menu.addAction(self._daq_calibaction)
                device_menu.addAction(self._run_action)

            if help_menu is not None:
@@ -165,100 +208,160 @@ class PyRelacs(QMainWindow):

        self.addToolBar(Qt.ToolBarArea.TopToolBarArea, rlx_toolbar)
        daq_toolbar = QToolBar("DAQ")
-        daq_toolbar.addAction(self._daq_connectaction)
-        daq_toolbar.addAction(self._daq_disconnectaction)
-        daq_toolbar.addAction(self._daq_calibaction)
+        if self.config.settings.daq:
+            daq_toolbar.addAction(self._daq_connectaction)
+            daq_toolbar.addAction(self._daq_disconnectaction)
+        # daq_toolbar.addAction(self._daq_calibaction)
        daq_toolbar.addAction(self._run_action)
        daq_toolbar.addAction(self._run_sinus_action)
        daq_toolbar.addAction(self._stop_recording)
+        daq_toolbar.addAction(self._recenter_plot)
+        daq_toolbar.addSeparator()
+        daq_toolbar.addAction(self._record)
        self.addToolBar(Qt.ToolBarArea.TopToolBarArea, daq_toolbar)

-        repro_toolbar = QToolBar("Repros")
-        repro_names, file_names = self.repros.names_of_repros()
+    def create_repros_tabs(self):
+        repro_names, file_names = self.repros.names_of_repros(
+            include_repros=self.config.settings.repros
+        )
+        nix_blocks = {
+            rep: self.nix_file.create_block(f"{rep}", "Data Repro")
+            for rep in repro_names
+        }
+        figures_repros = {rep: pg.GraphicsLayoutWidget() for rep in repro_names}
        for rep, fn in zip(repro_names, file_names):
-            repro_action = QAction(rep, self)
-            repro_action.setStatusTip(rep)
-            repro_action.triggered.connect(
-                lambda checked, n=rep, f=fn: self.run_repro(n, f)
+            tab = QWidget()
+            tab_layout = QGridLayout()
+
+            run_repro_button = QPushButton(f"Run {rep}")
+            run_repro_button.setCheckable(True)
+            run_repro_button.clicked.connect(
+                lambda checked, n=rep, f=fn: self.run_repro(
+                    n,
+                    f,
+                    nix_blocks,
+                    figures_repros,
+                    self.mccdaq,
+                    self.config,
+                )
            )
-            repro_toolbar.addAction(repro_action)
-        self.addToolBar(Qt.ToolBarArea.BottomToolBarArea, repro_toolbar)
+            tab_layout.addWidget(run_repro_button, 0, 0, 1, 0)
+            tab_layout.addWidget(figures_repros[rep], 1, 0, 1, 1)
+            tab.setLayout(tab_layout)
+            self.repro_tabs.addTab(tab, f"{rep}")
+
+    def run_repro(
+        self,
+        name_of_repro: str,
+        file_of_repro: str,
+        nix_block,
+        figures,
+        *args,
+    ):
+        self.text.appendPlainText(f"started Repro {name_of_repro}, {file_of_repro}")
+        nix_block_repro = nix_block[name_of_repro]
+        figure_repro = figures[name_of_repro]
+        worker = Worker(
+            self.repros.run_repro,
+            name_of_repro,
+            file_of_repro,
+            nix_block_repro,
+            figure_repro,
+            *args[-2:],
+        )
+        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 create_nix_file(self, file_path, metadata):
+        self.nix_file = nixio.File.open(
+            path=f"{file_path}", mode=nixio.FileMode.Overwrite
+        )
+        self.block = self.nix_file.create_block("recording", "testfile")
+        self.section = self.nix_file.create_section("metadata", "config.yaml")
+        for key, value in asdict(metadata).items():
+            self.section[key] = value
+
+        self.data_array_analog1 = self.block.create_data_array(
+            "Analog1", "ndarray", shape=(1000,), dtype=nixio.DataType.Double
+        )
+        self.data_array_analog2 = self.block.create_data_array(
+            "Analog2", "ndarray", shape=(1000,), dtype=nixio.DataType.Double
+        )
+
+    def recenter_continously_plot(self):
+        self.continously_plot.refresh()

    def plot_continously(self):
-        plot_daq = Worker(self.continously_plot.plot_daq)
-        plot_daq.signals.result.connect(self.print_output)
-        plot_daq.signals.finished.connect(self.thread_complete)
-        plot_daq.signals.progress.connect(self.progress_fn)
-        self.threadpool.start(plot_daq)
+        plot_con = Worker(self.continously_plot.plot)
+        plot_con.signals.result.connect(self.print_output)
+        plot_con.signals.finished.connect(self.thread_complete)
+        plot_con.signals.progress.connect(self.progress_fn)
+        self.threadpool.start(plot_con)

    def run_daq(self):
        read_daq = Worker(self.daq_producer.read_analog_continously)
        read_daq.signals.result.connect(self.print_output)
        read_daq.signals.finished.connect(self.thread_complete)
        read_daq.signals.progress.connect(self.progress_fn)
-        # plot_daq = Worker(self.continously_plot.plot_daq)
-        # plot_daq.signals.result.connect(self.print_output)
-        # plot_daq.signals.finished.connect(self.thread_complete)
-        # plot_daq.signals.progress.connect(self.progress_fn)
        self.threadpool.start(read_daq)
-        time.sleep(0.5)
-        self.continously_plot.plot_daq()
-        # self.threadpool.start(plot_daq)
+
+        self.continously_plot.plot()

    def run_sinus(self):
-        sinus_pro = Worker(self.sin_producer.produce_sin)
+        sinus_pro = Worker(self.sinus_producer.produce_sin)
        sinus_pro.signals.result.connect(self.print_output)
        sinus_pro.signals.finished.connect(self.thread_complete)
        sinus_pro.signals.progress.connect(self.progress_fn)
        self.threadpool.start(sinus_pro)

-        # plot_daq = Worker(self.continously_plot.plot_daq)
-        # plot_daq.signals.result.connect(self.print_output)
-        # plot_daq.signals.finished.connect(self.thread_complete)
-        # plot_daq.signals.progress.connect(self.progress_fn)
-        # self.threadpool.start(plot_daq)
+        self.continously_plot.plot()

-        # self.continously_plot.plot_daq()
+    def record(self):
+        self.create_nix_file("test.nix", self.config.metadata)
+        log.debug("Created nix file")
+
+        nix_writer = Worker(
+            self.nix_writer.write_nix,
+            data_array=self.data_array_analog1,
+            mutex=self.mutex,
+            channel=0,
+            chunk_size=1000,
+        )
+        nix_writer.signals.result.connect(self.print_output)
+        nix_writer.signals.finished.connect(self.thread_complete)
+        nix_writer.signals.progress.connect(self.progress_fn)
+        self.threadpool.start(nix_writer)
+
+        nix_writer2 = Worker(
+            self.nix_writer.write_nix,
+            data_array=self.data_array_analog2,
+            mutex=self.mutex,
+            channel=0,
+            chunk_size=1000,
+        )
+        nix_writer2.signals.result.connect(self.print_output)
+        nix_writer2.signals.finished.connect(self.thread_complete)
+        nix_writer2.signals.progress.connect(self.progress_fn)
+        self.threadpool.start(nix_writer2)

    def stop_recording(self):
-        self.add_to_textfield("pressed")
-        self._stop_recording.setEnabled(False)
-        self.sin_producer.stop_request()
+        self.add_to_textfield("Stopping the recording")
        self.continously_plot.stop_plotting()
+        self.nix_writer.stop_writing()

-    def connect_dac(self):
-        devices = uldaq.get_daq_device_inventory(uldaq.InterfaceType.USB)
+        log.debug("Stopping acquisiton")
        try:
-            self.daq_device = uldaq.DaqDevice(devices[0])
-            log.debug(f"Found daq devices {len(devices)}, connecting to the first one")
-            self.daq_device.connect()
-            log.debug("connected")
-        except IndexError:
-            log.error("DAQ is not connected")
-            log.error("Please connect a DAQ device to the system")
+            self.sinus_producer.stop_request()
+            log.debug("Stopping Sinus")
+        except AttributeError:
+            log.debug("Did not generate Sinus")

        if hasattr(PyRelacs, "daq_device"):
-            try:
-                self.daq_device.connect()
-                log.debug("Connected")
-            except uldaq.ul_exception.ULException as e:
-                log.error(f"Could not Connect to DAQ: {e}")
-
-    def disconnect_dac(self):
-        try:
-            self.daq_device.disconnect()
-            self.daq_device.release()
-        except AttributeError:
-            log.debug("DAQ was not connected")
-
-    def run_repro(self, n, fn):
-        self.text.appendPlainText(f"started Repro {n}, {fn}")
-        worker = Worker(self.repros.run_repro, self.nix_calibration, 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)
+            log.debug("Stopping DAQ")
+            self.daq_producer.stop_aquisition()

    def add_to_textfield(self, s: str):
        self.text.appendPlainText(s)
@@ -267,7 +370,9 @@ class PyRelacs(QMainWindow):
        log.info("exit button!")
        self.stop_recording()
        self.add_to_textfield("exiting")
-        self.disconnect_dac()
+        if self.mccdaq:
+            self.mccdaq.disconnect_daq()
+        log.info("closing GUI")
        self.close()

    def on_about(self, e):
--- a/pyrelacs/ui/plots/continously.py
+++ b/pyrelacs/ui/plots/continously.py
@@ -1,9 +1,10 @@
 import time
+
 import pyqtgraph as pg
 from IPython import embed
 import numpy as np
+from pyqtgraph.Qt.QtCore import QTimer

-from PyQt6.QtCore import QTimer
 from pyrelacs.dataio.circbuffer import CircBuffer
 from pyrelacs.util.logging import config_logging

@@ -14,82 +15,74 @@ class Continously:
    def __init__(self, figure: pg.GraphicsLayoutWidget, buffer: CircBuffer):
        self.figure = figure
        self.buffer = buffer
+        self.last_plotted_index = 0
+        self.timer = QTimer()

-    def plot_daq(self, *args, **kwargs):
+    def plot(self, *args, **kwargs):
        self.figure.setBackground("w")
-        self.daq_plot = self.figure.addPlot(row=0, col=0)
+
+        prev_plot = self.figure.getItem(row=0, col=0)
+        if prev_plot:
+            self.figure.removeItem(prev_plot)
+        self.continous_ax = self.figure.addPlot(row=0, col=0)
+
        pen = pg.mkPen("red")
-        # self.time = np.zeros(self.buffer.size)
-        # self.data = np.zeros(self.buffer.size)
-        self.line = self.daq_plot.plot(
-            # self.time,
-            [0],
+        self.time = np.zeros(self.buffer.size)
+        self.data = np.empty(self.buffer.size)
+        self.line = self.continous_ax.plot(
+            self.time,
+            self.data,
            pen=pen,
-            setCliptoView=True,
-            symbol="o",
+            # symbol="o",
        )

-        # self.item = 0
-        # while self.buffer.totalcount() < 3_000_000:
-        #     log.debug(self.buffer.totalcount())
-        #     self.time = np.roll(self.time, -1)
-        #     self.data = np.roll(self.data, -1)
-        #     try:
-        #         item, time_index = self.buffer.get(self.item)
-        #     except IndexError:
-        #         item = 0
-        #         time_index = 0
-        #     self.time[-1] = time_index
-        #     self.data[-1] = item
-        #     self.line.setData(self.time, self.data)
-        #     self.item += 1
-
-        self.plot_index = 0
-        self.CHUNK_PLOT = 1000
-        self.timer = QTimer()
-        self.timer.setInterval(200)
+        # self.plot_index = 0
+        self.CHUNK_PLOT = int(self.buffer.samplerate / 6)
+        self.PLOT_HISTORY = 500_000  # The amount of data you want to keep on screen
+        self.timer.setInterval(150)
        self.timer.timeout.connect(self.update_plot)
        self.timer.start()

-        # self.update_plot()
-
    def update_plot(self):
-        log.debug(self.buffer.totalcount())
+        current_index = self.buffer.write_index()
+        total_count = self.buffer.totalcount()

-        if self.buffer.totalcount() > self.CHUNK_PLOT:
-
-            log.debug(self.buffer.totalcount())
+        start_time = time.time()
+        if total_count - self.last_plotted_index >= self.CHUNK_PLOT:
            try:
-                # item, time_index = self.buffer.get(self.buffer.write_index() - 1)
-                items = self.buffer.read(
-                    self.buffer.write_index() - self.CHUNK_PLOT, count=self.CHUNK_PLOT
+                times, items = self.buffer.read(
+                    self.last_plotted_index,
+                    extend=self.CHUNK_PLOT,
                )
-                # times = (np.arange(len(items)) / self.buffer.samplerate) + self.time[-1]
-
+                self.time = np.concatenate((self.time, times))[-self.PLOT_HISTORY :]
+                self.data = np.concatenate((self.data, items))[-self.PLOT_HISTORY :]
+                self.line.setData(
+                    self.time,
+                    self.data,
+                )
+                self.last_plotted_index += self.CHUNK_PLOT
            except IndexError:
-                item = 0
-                items = np.zeros(self.CHUNK_PLOT)
-                times = np.zeros(self.CHUNK_PLOT)
-                # log.debug("Stopping the timer")
-                # self.timer.stop()
-                time_index = 0
-                log.debug("No Data Available")
-            # self.time = np.roll(self.time, -len(items))
-            # self.data = np.roll(self.data, -len(items))
-            #
-            # # self.time[-len(times) :] = times
-            # self.data[-len(items) :] = items
-
-            self.line.setData(
-                # self.time,
-                items,
-            )
-            self.plot_index += len(items)
+                log.error("Could not acces the data from the buffer for plotting")
+            end_time = time.time()
+            log.debug(f"total time for plotting {end_time - start_time}")
        else:
-            # self.timer.stop()
-            # embed()
-            # exit()
            pass

    def stop_plotting(self):
        self.timer.stop()
+        if self.last_plotted_index > 0:
+            total_count = self.buffer.totalcount()
+            times, items = self.buffer.read(
+                self.last_plotted_index,
+                extend=total_count - self.last_plotted_index,
+            )
+            self.time = np.concatenate((self.time, times))[-self.PLOT_HISTORY :]
+            self.data = np.concatenate((self.data, items))[-self.PLOT_HISTORY :]
+            self.line.setData(
+                self.time,
+                self.data,
+            )
+            self.last_plotted_index += total_count - self.last_plotted_index
+
+    def refresh(self):
+        self.continous_ax.enableAutoRange()
Author	SHA1	Message	Date
wendtalexander	8f6c9b1e5e	[ui/structure] updating repros to tab bar with individual plots and nix blocks	2024-10-23 11:09:44 +02:00
wendtalexander	574e9a8110	[ui/plots] fixing error if nothing has been plotted, the gui could not close	2024-10-23 11:08:54 +02:00
wendtalexander	75619cf1c8	[repro/class] provides with repros with args and kwargs	2024-10-23 11:07:55 +02:00
wendtalexander	02911e57f8	[repros] moving to sperate folders	2024-10-23 11:07:19 +02:00
wendtalexander	557535ffa4	[repros] moving to sperate folder, writing run method	2024-10-23 11:06:51 +02:00
wendtalexander	110629dae0	[calibration] moving calibration to own folder, rewriting run method	2024-10-23 11:06:26 +02:00
wendtalexander	7c4b5098c1	[mccdaq] printing exception error	2024-10-23 11:05:41 +02:00
wendtalexander	e2b7ed3a61	[ui] creates a nix file with pressing the record button	2024-10-22 10:11:07 +02:00
wendtalexander	038327bfeb	[ui/continously] updating plot to plot the last chunk	2024-10-22 10:10:40 +02:00
wendtalexander	4f7ebbe8c3	[dataio/nix] adding mutex, writing data_array, and the last chunk	2024-10-22 10:10:09 +02:00
wendtalexander	12e82dceee	[dataio] adding time sleep for performance	2024-10-21 17:44:02 +02:00
wendtalexander	e4e86cbc49	[ui/plot] updating plot	2024-10-21 10:29:38 +02:00
wendtalexander	e36db5e7b0	[dataio/producer] removing comments	2024-10-21 10:28:46 +02:00
wendtalexander	33f046c072	[dataio/nix] adding sleep while writing	2024-10-21 10:28:25 +02:00
wendtalexander	6d2eb09c65	[ui/plot] changing chunk size of the plot depending on the sampling rate	2024-10-18 16:46:33 +02:00
wendtalexander	4029034174	[config] adding bool daq, hints	2024-10-18 16:32:05 +02:00
wendtalexander	9fd4892325	[ui/mainwindow] organising file	2024-10-18 16:31:45 +02:00
wendtalexander	85b5a71ccb	[ui/plots] updating plot	2024-10-18 16:31:22 +02:00
wendtalexander	5d62cb0384	[repros] adding example sinuns	2024-10-18 16:31:03 +02:00
wendtalexander	64cd1b00ad	[repros] updating names of repros	2024-10-18 16:30:46 +02:00
wendtalexander	f703687ed7	[repros] renaming file	2024-10-18 16:30:27 +02:00
wendtalexander	4e0a1f0ac5	[devices] spelling	2024-10-18 16:30:09 +02:00
wendtalexander	4864538213	[dataio/sinus] removing code	2024-10-18 16:29:27 +02:00
wendtalexander	28dd0b7080	[dataio/nix] removing log messages	2024-10-18 16:28:53 +02:00
wendtalexander	b94078634d	[dataio/daq] fixing daq_buffer to int	2024-10-18 16:28:24 +02:00
wendtalexander	e3c867f4fd	[dataio] changing samplerate from int to float	2024-10-18 16:27:55 +02:00
wendtalexander	13897f29e3	[config] adding bool for daq	2024-10-18 16:27:32 +02:00
wendtalexander	afc37adb1a	[project] adding quantities for unit conversion	2024-10-16 08:52:49 +02:00
wendtalexander	b87e7f1ffa	[app] adding config	2024-10-16 08:52:27 +02:00
wendtalexander	f576f33cc5	[ui/mainwindow] adding unitconversion	2024-10-16 08:52:16 +02:00
wendtalexander	e16211b988	[config] adding config loading function	2024-10-16 08:51:59 +02:00
wendtalexander	b22ef04317	[project] adding dacite for config loading	2024-10-16 07:57:09 +02:00
wendtalexander	d2f7d0e966	[config] fixing config	2024-10-16 07:56:46 +02:00
wendtalexander	cc9089f503	[config] fixing config loader	2024-10-16 07:56:32 +02:00
wendtalexander	351850e05c	[config] remaping values into dict of value and unit	2024-10-15 07:58:02 +02:00
wendtalexander	e44e021982	[config] converting config into dataclasses	2024-10-15 07:57:33 +02:00
wendtalexander	93fe2951cd	[project] adding pyyaml as dependecy	2024-10-14 08:41:57 +02:00
wendtalexander	452c3dcecb	[config] adding more fields from relacs	2024-10-14 08:41:33 +02:00
wendtalexander	e999d25951	[app] adding config	2024-10-14 08:41:12 +02:00
wendtalexander	30bd705e1a	[dataio/nix] removing embed	2024-10-14 08:41:03 +02:00
wendtalexander	38123cdff3	[config] adding dataclass for config	2024-10-14 08:40:52 +02:00
wendtalexander	0e0aaf9f04	[project] setting python to 3.11 for tomllib	2024-10-11 14:11:15 +02:00
wendtalexander	1332e067c6	[info] using python internal tomllib	2024-10-11 14:10:43 +02:00
wendtalexander	f7cfc96dde	[config] adding simple config	2024-10-11 14:10:07 +02:00
wendtalexander	71837dffc9	[app] removing logging	2024-10-11 14:09:47 +02:00
wendtalexander	1b889312ce	[ui] adding recording button, which writes to a nix file	2024-10-11 14:09:31 +02:00
wendtalexander	042826721b	[dataio/sinus] refactoring	2024-10-11 14:08:58 +02:00
wendtalexander	7510d04f8d	[dataio/nix] adding a simple nix writer	2024-10-11 14:08:35 +02:00
wendtalexander	0f09c948ec	[dataio/buffer] fixing bug in time buffer	2024-10-11 14:08:20 +02:00
wendtalexander	ff2d8ebb50	[ui] adding checks, refactoring	2024-10-10 15:11:40 +02:00
wendtalexander	57d3a83243	[ui/plot] refactoring	2024-10-10 15:11:15 +02:00
wendtalexander	2539fa7e25	[dataio/daq] adding stop signal from gui, commentin out	2024-10-10 15:10:50 +02:00
wendtalexander	b5f8d7663d	[ui] updating autorang button	2024-10-10 14:25:50 +02:00
wendtalexander	fe3e142452	[ui/plots] removing plotitem if the function gets called again, setting autorang	2024-10-10 14:22:03 +02:00
wendtalexander	bbc8def460	[dataio/buffer] setting mutex lock while appending	2024-10-10 14:19:41 +02:00
wendtalexander	25d16cc5fd	[ui] removing unessassery stuff	2024-10-10 09:59:42 +02:00
wendtalexander	523f5dc346	[ui/plot] rewriting continous plot, plotting chucks of the buffer	2024-10-10 09:58:54 +02:00
wendtalexander	b6bd9e23a0	[dataio/sinus] commenting debugging	2024-10-10 09:57:46 +02:00
wendtalexander	e100dac5ea	[dataio/buffer] adding time for both channels, reading range alows for overflows reads	2024-10-10 09:57:03 +02:00