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

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 = [
+    {file = "dacite-1.8.1-py3-none-any.whl", hash = "sha256:cc31ad6fdea1f49962ea42db9421772afe01ac5442380d9a99fcf3d188c61afe"},
+]
+
+[package.extras]
+dev = ["black", "coveralls", "mypy", "pre-commit", "pylint", "pytest (>=5)", "pytest-benchmark", "pytest-cov"]
+
 [[package]]
 name = "decorator"
 version = "5.1.1"
@@ -985,6 +998,86 @@ 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"
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+    {file = "pyyaml-6.0.2.tar.gz", hash = "sha256:d584d9ec91ad65861cc08d42e834324ef890a082e591037abe114850ff7bbc3e"},
+]
+
+[[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 = "13.9.2"
@@ -1173,4 +1266,4 @@ files = [
 [metadata]
 lock-version = "2.0"
 python-versions = ">=3.11, <3.13"
-content-hash = "869348ffb24d0a55aee308a54cae333d5029c5aa52bc4082b720d766c63c2f9c"
+content-hash = "31433ed1dc0cc83dd7e781546dad5b8f068d59eaf692b4d3c12e07c604b1a6dd"

pyproject.toml

@@ -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"

pyrelacs/app.py

@@ -2,8 +2,10 @@ 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 import (
@@ -25,8 +27,11 @@ def main():
     x = int(settings.value("app/pos_x", 100))
     y = int(settings.value("app/pos_y", 100))
 
-    # load config
+    # load the config
-    window = PyRelacs()
+
+    config = load_config()
+    # start the app
+    window = PyRelacs(config)
     window.setMinimumWidth(200)
     window.setMinimumHeight(200)
     window.resize(width, height)

pyrelacs/config.yaml

@@ -1,12 +1,76 @@
-Settings:
+settings:
-  Repros: [Calibration]
+  # If true daq should be used, else starts without daq
-  Path: ~/projects/pyrelacs/test/
+  daq: False
+  # class names of the repros to run
+  repros: [Calibration, Sinus]
+  path: ~/projects/pyrelacs/test/
 
-Metadata:
+metadata:
-  Lab: Neuroethology
+  SetupName        : Setup1
+  Maintainer       : Your name
+  Creator          : Whoever
+  SetupLocation    : virtual
+  Lab              : XYZ-Lab
+  Institute        : Your institute
+  University       : Your university
+  Address          : Your institute's address
 
-PyRelacs:
+pyrelacs:
-  Input:
+  data:
-    Name: DAQ
+    input:
-    Samplingrate: 40_000
+        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

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()

pyrelacs/dataio/circbuffer.py

@@ -9,7 +9,7 @@ class CircBuffer:
         self,
         size: int,
         channels: int = 1,
-        samplerate: int = 40_000,
+        samplerate: float = 40_000.0,
         mutex: QMutex = QMutex(),
     ):
         self.__size = size

pyrelacs/dataio/daq_producer.py

@@ -41,7 +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)}")

pyrelacs/dataio/nix_writer.py

@@ -1,4 +1,6 @@
+import time
 from IPython import embed
+from PyQt6.QtCore import QMutex
 import nixio
 
 from pyrelacs.dataio.circbuffer import CircBuffer
@@ -11,26 +13,53 @@ class NixWriter:
     def __init__(self, buffer: CircBuffer) -> None:
         self.buffer = buffer
 
-    def write_nix(self, *args, **kwargs):
+    def write_nix(
-        self._write_header()
+        self,
-        items = 0
+        data_array: nixio.DataArray,
-        chunk = 1000
+        mutex: QMutex,
+        channel: int = 0,
+        chunk_size=1000,
+        *args,
+        **kwargs,
+    ):
+        index = 0
         log.debug("Starting the writing")
         self.write = True
         while self.write:
-            log.debug(items)
+            total_count = self.buffer.totalcount(channel=channel)
-            try:
+            if total_count - index >= chunk_size:
-                data, _ = self.buffer.read(items, extend=chunk)
+                mutex.lock()
-                self.data_array.append(data)
+                log.debug(index)
-            except IndexError as e:
+                try:
-                log.debug(f"{e}")
+                    _, 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
-            items += chunk
+        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 {items}")
+        log.debug(f"Samples written {index}")
-        embed()
-        exit()
-        self.nix_file.close()
 
     def _write_header(self):
         self.nix_file = nixio.File.open(path="data.nix", mode=nixio.FileMode.Overwrite)

pyrelacs/dataio/sin_producer.py

@@ -8,7 +8,6 @@ from pyrelacs.util.logging import config_logging
 log = config_logging()
 
 
-# stopbutton: QAction
 class SinProducer:
     def __init__(
         self,
@@ -39,12 +38,7 @@ class SinProducer:
 
         log.debug(f"duration sinus {end_time-start_time}")
         log.debug(f"Stimulation time {t}")
-        log.debug(f"{self.buffer.totalcount()}")
+        log.debug(f"Total samples produced {self.buffer.totalcount()}")
-        # data = self.buffer.get_all()
-        # 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()
 
     def stop_request(self):
         self.stop = True

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:
+        except Exception as er:
-            log.error("f{e}")
+            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()
 

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):
+class Calibration:
-    def __init__(self) -> None:
+    def __init__(self, config, mccdaq: MccDaq) -> None:
-        super().__init__()
+        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):
+    def run(*args, **kwargs):
-        calb = Calibration()
+        nix_block = args[0]
-        calb.check_beat(nix_file)
+        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.mccdaq.set_analog_to_zero()
-                self.disconnect_dac()
+                # 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):
+    def check_beat(self, nix_block: nix.Block):
-        self.set_attenuation_level(db_channel1=-10.0, db_channel2=0.0)
+        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)
+            self.mccdaq.set_attenuation_level(db_channel1=db_value)
-            stim = self.write_analog(
+            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()
+            self.mccdaq.digital_trigger()
-            log.info(self.ao_device)
+            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]
+                ai_status = self.mccdaq.ai_device.get_scan_status()[0]
-                ao_status = self.ao_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):

pyrelacs/repros/repros.py

@@ -22,9 +22,7 @@ class Repro:
     def __init__(self) -> None:
         pass
 
-    def run_repro(
+    def run_repro(self, name: str, file: pathlib.Path, *args, **kwargs) -> None:
-        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")
@@ -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

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)

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, QMutex, QTimer
+from PyQt6.QtCore import Qt, QSize, QThreadPool, QMutex
 from PyQt6.QtWidgets import (
     QGridLayout,
+    QPushButton,
+    QTabWidget,
     QToolBar,
+    QVBoxLayout,
     QWidget,
     QMainWindow,
     QPlainTextEdit,
@@ -13,18 +18,20 @@ from PyQt6.QtWidgets import (
     QStatusBar,
 )
 
-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
@@ -39,29 +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.timer = QTimer(self)
-        self.timer.setInterval(200)
 
         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.nix_file.close()
-
         self.threadpool = QThreadPool()
-        self.repros = Repro()
 
         self.text = QPlainTextEdit()
         self.text.setReadOnly(True)
@@ -70,38 +80,45 @@ 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 = 40_000
+        SAMPLERATE = pq.Quantity(
+            self.config.pyrelacs.data.input.inputsamplerate,
+            self.config.pyrelacs.data.input.inputsamplerateunit,
+        ).rescale("Hz")
+
+        INPUTTRACECAPACITY = pq.Quantity(
+            self.config.pyrelacs.data.input.inputtracecapacity,
+            self.config.pyrelacs.data.input.inputtracecapacityunit,
+        ).rescale("s")
         start = time.time()
-        BUFFERSIZE = SAMPLERATE * 10 * 60
+        BUFFERSIZE = (SAMPLERATE * INPUTTRACECAPACITY).simplified
         end = time.time()
         log.debug(f"Buffer allocation took {end - start}")
 
         self.buffer = CircBuffer(
-            size=BUFFERSIZE, samplerate=SAMPLERATE, mutex=self.mutex
+            size=int(BUFFERSIZE.base),
+            samplerate=float(SAMPLERATE.base),
+            mutex=self.mutex,
         )
         self.continously_plot = Continously(self.figure, self.buffer)
-        self.continously_plot.plot()
+        # self.continously_plot.plot()
 
-        start = time.time()
+        if self.mccdaq:
-        self.connect_dac()
-        end = time.time()
-        log.debug(f"Connection to DAQ took {end - start}")
-
-        if hasattr(PyRelacs, "daq_device"):
             log.debug("Creating Daq Generator")
-            self.daq_producer = DaqProducer(self.buffer, self.daq_device, [1, 1])
+            self.daq_producer = DaqProducer(self.buffer, self.mccdaq.daq_device, [1, 1])
-        else:
+        log.debug("Creating Sinus Generator")
-            log.debug("Creating Sinus Generator")
+        self.sinus_producer = SinProducer(self.buffer)
-            self.sinus_producer = SinProducer(self.buffer)
 
         self.nix_writer = NixWriter(self.buffer)
 
@@ -119,16 +136,17 @@ class PyRelacs(QMainWindow):
         self._daq_connectaction = QAction(
             QIcon(":icons/connect.png"), "Connect DAQ", self
         )
-        self._daq_connectaction.setStatusTip("Connect to daq device")
+        if self.mccdaq:
-        # self._daq_connectaction.setShortcut(QKeySequence("Alt+d"))
+            self._daq_connectaction.setStatusTip("Connect to daq device")
-        self._daq_connectaction.triggered.connect(self.connect_dac)
+            # self._daq_connectaction.setShortcut(QKeySequence("Alt+d"))
+            self._daq_connectaction.triggered.connect(self.mccdaq.connect_dac)
 
-        self._daq_disconnectaction = QAction(
+            self._daq_disconnectaction = QAction(
-            QIcon(":/icons/disconnect.png"), "Disconnect DAQ", self
+                QIcon(":/icons/disconnect.png"), "Disconnect DAQ", self
-        )
+            )
-        self._daq_disconnectaction.setStatusTip("Disconnect the DAQ device")
+            self._daq_disconnectaction.setStatusTip("Disconnect the DAQ device")
-        # self._daq_connectaction.setShortcut(QKeySequence("Alt+d"))
+            # self._daq_connectaction.setShortcut(QKeySequence("Alt+d"))
-        self._daq_disconnectaction.triggered.connect(self.disconnect_dac)
+            self._daq_disconnectaction.triggered.connect(self.mccdaq.disconnect_daq)
 
         # self._daq_calibaction = QAction(
         #     QIcon(":/icons/calibration.png"), "Plot calibration", self
@@ -137,7 +155,7 @@ class PyRelacs(QMainWindow):
         # # 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)
@@ -167,8 +185,9 @@ class PyRelacs(QMainWindow):
                 file_menu.addAction(self._rlx_aboutaction)
 
             if device_menu is not None:
-                device_menu.addAction(self._daq_connectaction)
+                if self.config.settings.daq:
-                device_menu.addAction(self._daq_disconnectaction)
+                    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._run_action)
@@ -189,8 +208,9 @@ class PyRelacs(QMainWindow):
 
         self.addToolBar(Qt.ToolBarArea.TopToolBarArea, rlx_toolbar)
         daq_toolbar = QToolBar("DAQ")
-        daq_toolbar.addAction(self._daq_connectaction)
+        if self.config.settings.daq:
-        daq_toolbar.addAction(self._daq_disconnectaction)
+            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)
@@ -200,16 +220,76 @@ class PyRelacs(QMainWindow):
         daq_toolbar.addAction(self._record)
         self.addToolBar(Qt.ToolBarArea.TopToolBarArea, daq_toolbar)
 
-        repro_toolbar = QToolBar("Repros")
+    def create_repros_tabs(self):
-        repro_names, file_names = self.repros.names_of_repros()
+        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)
+            tab = QWidget()
-            repro_action.setStatusTip(rep)
+            tab_layout = QGridLayout()
-            repro_action.triggered.connect(
+
-                lambda checked, n=rep, f=fn: self.run_repro(n, f)
+            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)
+            tab_layout.addWidget(run_repro_button, 0, 0, 1, 0)
-        self.addToolBar(Qt.ToolBarArea.BottomToolBarArea, repro_toolbar)
+            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()
@@ -240,12 +320,33 @@ class PyRelacs(QMainWindow):
         self.continously_plot.plot()
 
     def record(self):
-        nix_writer = Worker(self.nix_writer.write_nix)
+        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("Stopping the recording")
         self.continously_plot.stop_plotting()
@@ -262,33 +363,6 @@ class PyRelacs(QMainWindow):
             log.debug("Stopping DAQ")
             self.daq_producer.stop_aquisition()
 
-    def connect_dac(self):
-        devices = uldaq.get_daq_device_inventory(uldaq.InterfaceType.USB)
-        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.info("DAQ is not connected")
-            log.info("Please connect a DAQ device to the system")
-
-    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)
-
     def add_to_textfield(self, s: str):
         self.text.appendPlainText(s)
 
@@ -296,7 +370,8 @@ 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()
 

pyrelacs/ui/plots/continously.py

@@ -1,3 +1,5 @@
+import time
+
 import pyqtgraph as pg
 from IPython import embed
 import numpy as np
@@ -13,6 +15,8 @@ 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(self, *args, **kwargs):
         self.figure.setBackground("w")
@@ -24,7 +28,7 @@ class Continously:
 
         pen = pg.mkPen("red")
         self.time = np.zeros(self.buffer.size)
-        self.data = np.zeros(self.buffer.size)
+        self.data = np.empty(self.buffer.size)
         self.line = self.continous_ax.plot(
             self.time,
             self.data,
@@ -33,43 +37,52 @@ class Continously:
         )
 
         # self.plot_index = 0
-        self.timer = QTimer()
+        self.CHUNK_PLOT = int(self.buffer.samplerate / 6)
-        self.CHUNK_PLOT = 10_000
+        self.PLOT_HISTORY = 500_000  # The amount of data you want to keep on screen
-        self.timer.setInterval(200)
+        self.timer.setInterval(150)
         self.timer.timeout.connect(self.update_plot)
         self.timer.start()
 
     def update_plot(self):
-        # log.debug(self.buffer.totalcount())
+        current_index = self.buffer.write_index()
-        if self.buffer.totalcount() > self.CHUNK_PLOT:
+        total_count = self.buffer.totalcount()
-            log.debug(self.buffer.totalcount())
+
+        start_time = time.time()
+        if total_count - self.last_plotted_index >= self.CHUNK_PLOT:
             try:
                 times, items = self.buffer.read(
-                    self.buffer.write_index() - self.CHUNK_PLOT - 1_000,
+                    self.last_plotted_index,
                     extend=self.CHUNK_PLOT,
                 )
-            except IndexError as e:
+                self.time = np.concatenate((self.time, times))[-self.PLOT_HISTORY :]
-                items = np.zeros(self.CHUNK_PLOT)
+                self.data = np.concatenate((self.data, items))[-self.PLOT_HISTORY :]
-                times = np.zeros(self.CHUNK_PLOT)
+                self.line.setData(
-                log.debug("No Data Available")
+                    self.time,
-                log.debug(f"Index Error {e}")
+                    self.data,
-
+                )
-            # self.time = np.roll(self.time, -len(items))
+                self.last_plotted_index += self.CHUNK_PLOT
-            # self.data = np.roll(self.data, -len(items))
+            except IndexError:
-            #
+                log.error("Could not acces the data from the buffer for plotting")
-            # self.time[-len(times) :] = times
+            end_time = time.time()
-            # self.data[-len(items) :] = items
+            log.debug(f"total time for plotting {end_time - start_time}")
-
-            self.line.setData(
-                times,
-                items,
-            )
-            # self.plot_index += len(items)
         else:
             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()