adding doc string

pyrelacs/app.py

@@ -126,10 +126,10 @@ class PyRelacs(QMainWindow):
                 np.arange(0, len(beat)) / 40_000.0,
                 beat_squared,
                 pen=pen,
-                name=stim.name,
+                # name=stim.name,
             )
             self.power_plot.plot(f_sq, powerspec_sq, pen=pen)
-            self.power_plot.scatter(f[peaks], powerspec_sq[peaks])
+            # self.power_plot.plotItem.scatterPlot(f[peaks], powerspec_sq[peaks])
 
     def connect_dac(self):
         devices = uldaq.get_daq_device_inventory(uldaq.InterfaceType.USB)
@@ -165,7 +165,7 @@ class PyRelacs(QMainWindow):
             self.toolbar.addAction(individual_repro_button)
 
     def run_repro(self, n, fn):
-        self.text.appendPlainText(f"started Repro {n}, {fn}")
+        log.debug(f"Running repro {n} in the file {fn}")
         worker = Worker(self.repros.run_repro, self.nix_file, n, fn)
         worker.signals.result.connect(self.print_output)
         worker.signals.finished.connect(self.thread_complete)

pyrelacs/devices/mccdac.py

@@ -12,13 +12,32 @@ log = config_logging()
 
 
 class MccDac:
+    """
+    Represents the Digital/Analog Converter from Meassuring Computing.
+    provides methods for writing and reading the Analog / Digital input and output.
+
+    Connects to the DAC device.
+
+    Attributes
+    ----------
+    daq_device : uldaq.DaqDevice
+        DaqDevice for handling connecting, releasing and disconnecting
+    ai_device : uldaq.AiDevice
+        The Analog input Device
+    ao_device :
+        Analog output Device
+    dio_device :
+        Digital Input Output
+    """
+
     def __init__(self) -> None:
         devices = uldaq.get_daq_device_inventory(uldaq.InterfaceType.USB)
         log.debug(f"Found daq devices {len(devices)}, connecting to the first one")
-        if len(devices) == 0:
+        try:
+            self.daq_device = uldaq.DaqDevice(devices[0])
+        except uldaq.ul_exception.ULException as e:
             log.error("Did not found daq devices, please connect one")
-            exit(1)
-        self.daq_device = uldaq.DaqDevice(devices[0])
+            raise e
         try:
             self.daq_device.connect()
         except uldaq.ul_exception.ULException:
@@ -30,6 +49,10 @@ class MccDac:
         log.debug("Connected")
 
     def connect_dac(self):
+        """
+        Connecting to the DAQ device
+
+        """
         devices = uldaq.get_daq_device_inventory(uldaq.InterfaceType.USB)
         log.debug(f"Found daq devices {len(devices)}, connecting to the first one")
         if len(devices) == 0:
@@ -52,6 +75,40 @@ class MccDac:
         ScanOption: uldaq.ScanOption = uldaq.ScanOption.DEFAULTIO,
         AInScanFlag: uldaq.AInScanFlag = uldaq.AInScanFlag.DEFAULT,
     ) -> Array[c_double]:
+        """
+        Reading the analog input of the DAC device
+        Creates a c_double Array for storing the acquired data
+
+        Parameters
+        ----------
+        channels : list[int]
+            channels to read from, provide only two int's in a list (ex [0, 1] or [0, 4])
+            for sampling from the range(channel0, channel4)
+
+        duration : int
+            duration of sampling period
+
+        samplerate : float
+            samplerate for the duration of sampling
+
+        AiInputMode : uldaq.AiInputMode = uldaq.AiInputMode.SINGLE_ENDED
+            Contains attributes indicating A/D channel input modes.
+            Compares to Ground
+
+        Range : uldaq.Range = uldaq.Range.BIP10VOLTS
+            Range of the output
+
+        ScanOption : uldaq.ScanOption = uldaq.ScanOption.DEFAULTIO
+            Specific Flags for acuiring the input
+
+        AInScanFlag : uldaq.AInScanFlag = uldaq.AInScanFlag.DEFAULT
+            Scaling of the data
+
+        Returns
+        -------
+        Array[c_double]
+
+        """
         assert len(channels) == 2, log.error("You can only provide two channels [0, 1]")
 
         if channels[0] != channels[1]:
@@ -85,6 +142,37 @@ class MccDac:
         ScanOption: uldaq.ScanOption = uldaq.ScanOption.DEFAULTIO,
         AOutScanFlag: uldaq.AOutScanFlag = uldaq.AOutScanFlag.DEFAULT,
     ) -> Array[c_double]:
+        """
+        Writes data to the DAC device.
+        Creates a c_double Array for writing the data
+
+        Parameters
+        ----------
+        data : Union[list, npt.NDArray]
+            data which should be written to the DAC
+
+        channels : list[int]
+            channels to read from, provide only two int's in a list (ex [0, 1])
+            for sampling from the range(channel0, channel1)
+            DAC 16 has only 2 output channels
+
+        samplerate : float
+            samplerate for the duration of sampling
+
+        Range : uldaq.Range = uldaq.Range.BIP10VOLTS
+            Range of the output
+
+        ScanOption : uldaq.ScanOption = uldaq.ScanOption.DEFAULTIO
+            Specific Flags for acuiring the input
+
+        AOutScanFlag : uldaq.AOutScanFlag = uldaq.AOutScanFlag.DEFAULT
+            For Scaling the data
+
+        Returns
+        -------
+        Array[c_double]
+        """
+
         assert len(channels) == 2, log.error("You can only provide two channels [0, 1]")
 
         buffer = c_double * len(data)
@@ -109,7 +197,18 @@ class MccDac:
 
         return data_analog_output
 
-    def set_analog_to_zero(self, channels: list[int] = [0, 1]):
+    def set_analog_to_zero(self, channels: list[int] = [0, 1]) -> None:
+        """
+        Sets all analog outputs to zero
+
+        Parameters
+        ----------
+        channels : list[int]
+            channels to read from, provide only two int's in a list (ex [0, 1])
+            for sampling from the range(channel0, channel1)
+            DAC 16 has only 2 output channels
+
+        """
         try:
             err = self.ao_device.a_out_list(
                 channels[0],
@@ -126,16 +225,37 @@ class MccDac:
             log.error("disconnection dac")
             self.disconnect_dac()
 
-    def diggital_trigger(self) -> None:
-        data = self.read_bit(channel=0)
+    def digital_trigger(self, ch: int = 0) -> None:
+        """
+        Writes a 1 to a specified digital channel, if the channel is already on 1 switches it to
+        0 and after Nanosekond it writes a 1 to the specified digital channel
+
+        Parameters
+        ----------
+        ch : int
+            Channel to trigger
+        """
+        data = self.read_bit(channel=ch)
         if data:
-            self.write_bit(channel=0, bit=0)
+            self.write_bit(channel=ch, bit=0)
             time.time_ns()
-            self.write_bit(channel=0, bit=1)
+            self.write_bit(channel=ch, bit=1)
         else:
-            self.write_bit(channel=0, bit=1)
+            self.write_bit(channel=ch, bit=1)
 
     def write_bit(self, channel: int = 0, bit: int = 1) -> None:
+        """
+        Writes a 0 / 1 to a specified digitial channel
+
+        Parameters
+        ----------
+        channel : int
+            Digital channel to write
+
+        bit : int
+            0 / 1 for writing to the digital channel
+
+        """
         self.dio_device.d_config_bit(
             uldaq.DigitalPortType.AUXPORT, channel, uldaq.DigitalDirection.OUTPUT
         )
@@ -143,55 +263,36 @@ class MccDac:
             uldaq.DigitalPortType.AUXPORT, bit_number=channel, data=bit
         )
 
-    def read_bit(self, channel: int = 0):
-        bit = self.dio_device.d_bit_in(uldaq.DigitalPortType.AUXPORT, channel)
-        return bit
-
-    def read_digitalio(
-        self,
-        channels: list[int],
-        duration,
-        samplerate,
-        ScanOptions: uldaq.ScanOption = uldaq.ScanOption.DEFAULTIO,
-        DInScanFlag: uldaq.DInScanFlag = uldaq.DInScanFlag.DEFAULT,
-    ):
-        if channels[0] == channels[1]:
-            channel_len = 1
-        else:
-            channel_len = len(channels)
+    def read_bit(self, channel: int = 0) -> int:
+        """
+        Reads a 0 / 1 from the specified digital channel
 
-        buffer_len = np.shape(np.arange(0, duration, 1 / samplerate))[0]
-        data_digital_input = uldaq.create_int_buffer(channel_len, buffer_len)
+        Parameters
+        ----------
+        channel : int
+            Digital channel to read from
 
-        self.dio_device.d_config_port(
-            uldaq.DigitalPortType.AUXPORT, uldaq.DigitalDirection.INPUT
-        )
-        scan_rate = self.dio_device.d_in_scan(
-            uldaq.DigitalPortType.AUXPORT0,
-            uldaq.DigitalPortType.AUXPORT0,
-            len(data_digital_input),
-            samplerate,
-            ScanOptions,
-            DInScanFlag,
-            data_digital_input,
-        )
-        return data_digital_input
+        Returns
+        -------
+        bit : int
+            0 or 1 from the digital channel
+        """
+        bit = self.dio_device.d_bit_in(uldaq.DigitalPortType.AUXPORT, channel)
+        return bit
 
     def disconnect_dac(self):
         self.daq_device.disconnect()
         self.daq_device.release()
 
-    def check_attenuator(self):
-        """
-        ident     : attdev-1
-        strobepin : 6
-        datainpin : 5
-        dataoutpin: -1
-        cspin     : 4
-        mutepin   : 7
-        zcenpin   : -1
+    def check_attenuator(self) -> None:
         """
+        For checking the attenuator in the DAC device that was implemented to attenuate the
+        analog signal to mV.
+
+        Writes to Channel 0 of the analog output with different attenuation levels
+        0, 0, -2, -5, -10, -20, -50 dB and the second 0 has a software mute
 
+        """
         SAMPLERATE = 40_000.0
         DURATION = 5
         AMPLITUDE = 1
@@ -201,7 +302,6 @@ class MccDac:
         # data_channels = np.concatenate((data, data))
 
         db_values = [0, 0, -2, -5, -10, -20, -50]
-        db_values = [0, -10, -20]
         for i, db_value in enumerate(db_values):
             log.info(f"Attenuating the Channels, with {db_value}")
             if i == 1:
@@ -219,7 +319,7 @@ class MccDac:
                 ScanOption=uldaq.ScanOption.EXTTRIGGER,
                 Range=uldaq.Range.BIP10VOLTS,
             )
-            self.diggital_trigger()
+            self.digital_trigger()
 
             try:
                 self.ao_device.scan_wait(uldaq.WaitType.WAIT_UNTIL_DONE, 15)
@@ -248,6 +348,16 @@ class MccDac:
         mute_channel2: bool = False,
     ):
         """
+        Setting the attenuation level of the chip that is connected to the DAQ
+        The attenuation level is set by writing to the connected digital output pin 5
+        where the strobepin 6 is signaling the when the bit was send.
+        The cspin is set from 1 to 0 for the start and 0 to 1 for signaling the end
+        of the data write process.
+
+        The mute pin should be set to 1 for the device to be working.
+
+        More information in the AttCS3310.pdf in the doc
+
         ident     : attdev-1
         strobepin : 6
         datainpin : 5
@@ -255,8 +365,23 @@ class MccDac:
         cspin     : 4
         mutepin   : 7
         zcenpin   : -1
-        """
 
+        Parameters
+        ----------
+        db_channel1 : float
+            dB Attenuation level for the first channel
+
+        db_channel2 : float
+            dB Attenuation level for the second channel
+
+        mute_channel1 : bool
+            Software mute for the first channel
+
+        mute_channel2 : bool
+            Software mute for the second channel
+
+
+        """
         self.activate_attenuator()
         hardware_possible_db = np.arange(-95.5, 32.0, 0.5)
         byte_number = np.arange(1, 256)
@@ -283,9 +408,18 @@ class MccDac:
         self.write_bit(channel=4, bit=1)
 
     def activate_attenuator(self):
+        """
+        Activation of the attenuator, where the cspin and mute pin is set to 1,
+        and the datapin and strobpin to 0
+
+        """
         for ch, b in zip([4, 5, 6, 7], [1, 0, 0, 1]):
             self.write_bit(channel=ch, bit=b)
 
     def deactivate_attenuator(self):
+        """
+        Writes a 0 to the mute pin, which is deactivating the attenuator
+
+        """
         # mute should be enabled for starting calibration
         self.write_bit(channel=7, bit=0)

pyrelacs/repros/calbi.py

@@ -60,7 +60,7 @@ class Calibration(MccDac):
             time.sleep(1)
 
             log.debug("Starting the Scan")
-            self.diggital_trigger()
+            self.digital_trigger()
 
             try:
                 self.ao_device.scan_wait(uldaq.WaitType.WAIT_UNTIL_DONE, 15)
@@ -109,7 +109,7 @@ class Calibration(MccDac):
                 self.SAMPLERATE,
                 ScanOption=uldaq.ScanOption.EXTTRIGGER,
             )
-            self.diggital_trigger()
+            self.digital_trigger()
             log.info(self.ao_device)
             ai_status = uldaq.ScanStatus.RUNNING
             ao_status = uldaq.ScanStatus.RUNNING