[dataio/nix] adding comments

pyrelacs/config.yaml

@@ -1,9 +1,11 @@
 settings:
   # If true daq should be used, else starts without daq
-  daq: False
+  daq: True
   # class names of the repros to run
   repros: [Calibration, Sinus]
   path: ~/projects/pyrelacs/test/
+  # string to append after the file name
+  postappend: ehpys
 
 metadata:
   SetupName        : Setup1

pyrelacs/dataio/daq_producer.py

@@ -21,7 +21,6 @@ class DaqProducer:
         self.device = device
         self.ai_device = self.device.get_ai_device()
         self.channels = channels
-
         self.stop = False
 
     def read_analog_continously(
@@ -41,7 +40,7 @@ class DaqProducer:
         )
 
         # let the buffer for the daq device hold 5 seconds of data
-        daq_buffer_size = int(self.buffer.samplerate * 5)
+        daq_buffer_size = int(self.buffer.samplerate * 30)
 
         data_in = uldaq.create_float_buffer(channel_range.size, daq_buffer_size)
         log.debug(f"Buffersize for daq {len(data_in)}")
@@ -70,7 +69,12 @@ class DaqProducer:
                 prev_count = 0
                 prev_index = 0
                 while not self.stop:
+                    try:
                         daq_status, transfer_status = self.ai_device.get_scan_status()
+                    except uldaq.ul_exception.ULException as e:
+                        log.error("Could not get the scan status")
+                        log.error("Stopping writting")
+                        break
                     # The index into the data buffer immediately following the last sample transferred.
                     current_index = transfer_status.current_index
                     # total samples since start of the scan
@@ -79,7 +83,7 @@ class DaqProducer:
                     channel_samples = transfer_status.current_scan_count
 
                     new_data_count = total_samples - prev_count
-                    # check if counts if new data is bigger than the buffer
+                    # check if new data is bigger than the buffer
                     # if that happends stop the acquisition
                     if new_data_count > len(data_in):
                         self.ai_device.scan_stop()
@@ -92,23 +96,54 @@ class DaqProducer:
                         if prev_index + chunk_size > len(data_in) - 1:
                             log.debug("Chunk wraps around buffersize")
                             first_chunk = len(data_in) - prev_index
+
+                            data_first_channel = data_in[
+                                prev_index : prev_index + first_chunk : 2
+                            ]
+                            data_second_channel = data_in[
+                                prev_index + 1 : prev_index + first_chunk : 2
+                            ]
+
                             [
-                                self.buffer.append(data_in[prev_index + i])
+                                self.buffer.append(data_first_channel[i], channel=0)
-                                for i in range(first_chunk)
+                                for i in range(int(first_chunk / 2))
+                            ]
+
+                            [
+                                self.buffer.append(data_second_channel[i], channel=1)
+                                for i in range(int(first_chunk / 2))
                             ]
                             second_chunk = chunk_size - first_chunk
+                            data_first_channel = data_in[0:second_chunk:2]
+                            data_second_channel = data_in[1:second_chunk:2]
+
                             [
-                                self.buffer.append(data_in[i])
+                                self.buffer.append(data_first_channel[i], channel=0)
-                                for i in range(second_chunk)
+                                for i in range(int(second_chunk / 2))
+                            ]
+                            [
+                                self.buffer.append(data_second_channel[i], channel=1)
+                                for i in range(int(second_chunk / 2))
                             ]
                         else:
                             log.debug("Writing chunk to buffer")
+                            # appending to the first channel
+
+                            data_first_channel = data_in[
+                                prev_index : prev_index + chunk_size : 2
+                            ]
+                            data_second_channel = data_in[
+                                prev_index + 1 : prev_index + chunk_size : 2
+                            ]
                             [
-                                self.buffer.append(data_in[prev_index + i])
+                                self.buffer.append(data_first_channel[i], channel=0)
-                                for i in range(chunk_size)
+                                for i in range(int(chunk_size / 2))
                             ]
 
-                            self.buffer.append(data_in[current_index])
+                            [
+                                self.buffer.append(data_second_channel[i], channel=1)
+                                for i in range(int(chunk_size / 2))
+                            ]
 
                         if total_samples - prev_count > len(data_in):
                             self.ai_device.scan_stop()
@@ -124,33 +159,70 @@ class DaqProducer:
 
                 self.ai_device.scan_stop()
                 daq_status, transfer_status = self.ai_device.get_scan_status()
-                current_index = transfer_status.current_index
                 log.debug(daq_status)
+                chunk_size = transfer_status.current_total_count - prev_count
 
-                log.debug(transfer_status.current_index)
+                log.debug(f"DAQ current index {transfer_status.current_index}")
-                log.debug(transfer_status.current_total_count)
+                log.debug(f"DAQ total count {transfer_status.current_total_count}")
-                log.debug(transfer_status.current_scan_count)
+                log.debug(
-                log.debug(self.buffer.totalcount())
+                    f"DAQ Samples per channel {transfer_status.current_scan_count}"
+                )
                 log.debug("Appending last chunk")
 
                 if prev_index + chunk_size > len(data_in) - 1:
                     log.debug("Chunk wraps around buffersize")
                     first_chunk = len(data_in) - prev_index
+
+                    data_first_channel = data_in[
+                        prev_index : prev_index + first_chunk : 2
+                    ]
+                    data_second_channel = data_in[
+                        prev_index + 1 : prev_index + first_chunk : 2
+                    ]
+
                     [
-                        self.buffer.append(data_in[prev_index + i])
+                        self.buffer.append(data_first_channel[i], channel=0)
-                        for i in range(first_chunk)
+                        for i in range(int(first_chunk / 2))
+                    ]
+
+                    [
+                        self.buffer.append(data_second_channel[i], channel=1)
+                        for i in range(int(first_chunk / 2))
                     ]
                     second_chunk = chunk_size - first_chunk
-                    [self.buffer.append(data_in[i]) for i in range(second_chunk)]
+                    data_first_channel = data_in[0:second_chunk:2]
+                    data_second_channel = data_in[1:second_chunk:2]
+
+                    [
+                        self.buffer.append(data_first_channel[i], channel=0)
+                        for i in range(int(second_chunk / 2))
+                    ]
+                    [
+                        self.buffer.append(data_second_channel[i], channel=1)
+                        for i in range(int(second_chunk / 2))
+                    ]
                 else:
                     log.debug("Writing chunk to buffer")
+                    # appending to the first channel
+
+                    data_first_channel = data_in[
+                        prev_index : prev_index + chunk_size : 2
+                    ]
+                    data_second_channel = data_in[
+                        prev_index + 1 : prev_index + chunk_size : 2
+                    ]
                     [
-                        self.buffer.append(data_in[prev_index + i])
+                        self.buffer.append(data_first_channel[i], channel=0)
-                        for i in range(chunk_size)
+                        for i in range(int(chunk_size / 2))
                     ]
 
-                    self.buffer.append(data_in[current_index])
+                    [
+                        self.buffer.append(data_second_channel[i], channel=1)
+                        for i in range(int(chunk_size / 2))
+                    ]
                 log.info("stopping")
+                log.debug(self.buffer.totalcount())
+                log.debug(self.ai_device.get_scan_status())
 
                 break
             break

pyrelacs/dataio/nix_writer.py

@@ -1,4 +1,9 @@
+from datetime import datetime
+import itertools
+import string
 import time
+from dataclasses import asdict
+
 from IPython import embed
 from PyQt6.QtCore import QMutex
 import nixio
@@ -10,8 +15,9 @@ log = config_logging()
 
 
 class NixWriter:
-    def __init__(self, buffer: CircBuffer) -> None:
+    def __init__(self, buffer: CircBuffer, config) -> None:
         self.buffer = buffer
+        self.config = config
 
     def write_nix(
         self,
@@ -62,11 +68,42 @@ class NixWriter:
         log.debug(f"Samples written {index}")
 
     def _write_header(self):
+        """
+        Writing the header of the nix file
+        """
         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 generate_letter_sequence(self):
+        alphabet = string.ascii_lowercase
+        for size in range(2, 3):
+            for combo in itertools.product(alphabet, repeat=size):
+                yield "".join(combo)
+
+    def create_nix_file(self, file_path, metadata):
+        data_time = datetime.now().strftime("%Y-%m-%t_%H-%M-%S")
+        sequence_generator = self.generate_letter_sequence()
+        sequence = next(sequence_generator)
+
+        self.nix_file = nixio.File.open(
+            path=f"{file_path}/{data_time}_{sequence}.nix",
+            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
+        )
+        return self.data_array_analog1, self.data_array_analog2
+
     def stop_writing(self):
         self.write = False

pyrelacs/ui/mainwindow.py

@@ -10,7 +10,6 @@ from PyQt6.QtWidgets import (
     QPushButton,
     QTabWidget,
     QToolBar,
-    QVBoxLayout,
     QWidget,
     QMainWindow,
     QPlainTextEdit,
@@ -50,6 +49,8 @@ class PyRelacs(QMainWindow):
         super().__init__()
         # loaded config
         self.config = config
+
+        # check if daq is connencted else None
         if self.config.settings.daq:
             start = time.time()
             self.mccdaq = MccDaq()
@@ -65,8 +66,6 @@ class PyRelacs(QMainWindow):
         )  # 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()
@@ -76,22 +75,6 @@ class PyRelacs(QMainWindow):
         self.text = QPlainTextEdit()
         self.text.setReadOnly(True)
 
-        self.setMenuBar(QMenuBar(self))
-        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.repro_tabs, 2, 0, 2, 2)
-        layout.addWidget(self.text, 4, 0, 1, 1)
-
-        widget = QWidget()
-        widget.setLayout(layout)
-        self.setCentralWidget(widget)
-
         SAMPLERATE = pq.Quantity(
             self.config.pyrelacs.data.input.inputsamplerate,
             self.config.pyrelacs.data.input.inputsamplerateunit,
@@ -109,6 +92,7 @@ class PyRelacs(QMainWindow):
         self.buffer = CircBuffer(
             size=int(BUFFERSIZE.base),
             samplerate=float(SAMPLERATE.base),
+            channels=2,
             mutex=self.mutex,
         )
         self.continously_plot = Continously(self.figure, self.buffer)
@@ -116,11 +100,26 @@ class PyRelacs(QMainWindow):
 
         if self.mccdaq:
             log.debug("Creating Daq Generator")
-            self.daq_producer = DaqProducer(self.buffer, self.mccdaq.daq_device, [1, 1])
+            self.daq_producer = DaqProducer(self.buffer, self.mccdaq.daq_device, [4, 5])
         log.debug("Creating Sinus Generator")
         self.sinus_producer = SinProducer(self.buffer)
 
-        self.nix_writer = NixWriter(self.buffer)
+        self.nix_writer = NixWriter(self.buffer, self.config)
+        self.setMenuBar(QMenuBar(self))
+        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.repro_tabs, 2, 0, 2, 2)
+        layout.addWidget(self.text, 4, 0, 1, 1)
+
+        widget = QWidget()
+        widget.setLayout(layout)
+        self.setCentralWidget(widget)
 
     def create_actions(self):
         self._rlx_exitaction = QAction(QIcon(":/icons/exit.png"), "Exit", self)
@@ -224,10 +223,6 @@ class PyRelacs(QMainWindow):
         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):
             tab = QWidget()
@@ -239,7 +234,6 @@ class PyRelacs(QMainWindow):
                 lambda checked, n=rep, f=fn: self.run_repro(
                     n,
                     f,
-                    nix_blocks,
                     figures_repros,
                     self.mccdaq,
                     self.config,
@@ -254,20 +248,18 @@ class PyRelacs(QMainWindow):
         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:],
+            *args[-1:],
         )
         worker.signals.result.connect(self.print_output)
         worker.signals.finished.connect(self.thread_complete)
@@ -275,22 +267,6 @@ class PyRelacs(QMainWindow):
 
         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()
 
@@ -320,7 +296,9 @@ class PyRelacs(QMainWindow):
         self.continously_plot.plot()
 
     def record(self):
-        self.create_nix_file("test.nix", self.config.metadata)
+        self.data_array_analog1, self.data_array_analog2 = (
+            self.nix_writer.create_nix_file(f"{_root}/test/", self.config.metadata)
+        )
         log.debug("Created nix file")
 
         nix_writer = Worker(
@@ -359,7 +337,7 @@ class PyRelacs(QMainWindow):
         except AttributeError:
             log.debug("Did not generate Sinus")
 
-        if hasattr(PyRelacs, "daq_device"):
+        if self.config.settings.daq:
             log.debug("Stopping DAQ")
             self.daq_producer.stop_aquisition()
 

pyrelacs/ui/plots/continously.py

@@ -15,7 +15,8 @@ class Continously:
     def __init__(self, figure: pg.GraphicsLayoutWidget, buffer: CircBuffer):
         self.figure = figure
         self.buffer = buffer
-        self.last_plotted_index = 0
+        self.last_plotted_index_analog_in_0 = 0
+        self.last_plotted_index_analog_in_1 = 0
         self.timer = QTimer()
 
     def plot(self, *args, **kwargs):
@@ -24,14 +25,25 @@ class Continously:
         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)
+        self.analog_in_0 = self.figure.addPlot(row=0, col=0)
+        self.analog_in_1 = self.figure.addPlot(row=1, col=0)
 
         pen = pg.mkPen("red")
-        self.time = np.zeros(self.buffer.size)
+        self.time_analog_in_0 = np.zeros(self.buffer.size)
-        self.data = np.empty(self.buffer.size)
+        self.data_analog_in_0 = np.empty(self.buffer.size)
-        self.line = self.continous_ax.plot(
+        self.line_analog_in_0 = self.analog_in_0.plot(
-            self.time,
+            self.time_analog_in_0,
-            self.data,
+            self.data_analog_in_0,
+            pen=pen,
+            # symbol="o",
+        )
+
+        pen = pg.mkPen("red")
+        self.time_analog_in_1 = np.zeros(self.buffer.size)
+        self.data_analog_in_1 = np.empty(self.buffer.size)
+        self.line_analog_in_1 = self.analog_in_1.plot(
+            self.time_analog_in_1,
+            self.data_analog_in_1,
             pen=pen,
             # symbol="o",
         )
@@ -41,26 +53,61 @@ class Continously:
         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.timeout.connect(self.update_plot_1)
         self.timer.start()
 
     def update_plot(self):
         current_index = self.buffer.write_index()
-        total_count = self.buffer.totalcount()
+        total_count = self.buffer.totalcount(channel=0)
 
         start_time = time.time()
-        if total_count - self.last_plotted_index >= self.CHUNK_PLOT:
+        if total_count - self.last_plotted_index_analog_in_0 >= self.CHUNK_PLOT:
             try:
                 times, items = self.buffer.read(
-                    self.last_plotted_index,
+                    self.last_plotted_index_analog_in_0,
                     extend=self.CHUNK_PLOT,
+                    channel=0,
                 )
-                self.time = np.concatenate((self.time, times))[-self.PLOT_HISTORY :]
+                self.time_analog_in_0 = np.concatenate((self.time_analog_in_0, times))[
-                self.data = np.concatenate((self.data, items))[-self.PLOT_HISTORY :]
+                    -self.PLOT_HISTORY :
-                self.line.setData(
+                ]
-                    self.time,
+                self.data_analog_in_0 = np.concatenate((self.data_analog_in_0, items))[
-                    self.data,
+                    -self.PLOT_HISTORY :
+                ]
+                self.line_analog_in_0.setData(
+                    self.time_analog_in_0,
+                    self.data_analog_in_0,
                 )
-                self.last_plotted_index += self.CHUNK_PLOT
+                self.last_plotted_index_analog_in_0 += self.CHUNK_PLOT
+            except IndexError:
+                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:
+            pass
+
+    def update_plot_1(self):
+        total_count = self.buffer.totalcount(channel=1)
+
+        start_time = time.time()
+        if total_count - self.last_plotted_index_analog_in_1 >= self.CHUNK_PLOT:
+            try:
+                times, items = self.buffer.read(
+                    self.last_plotted_index_analog_in_1,
+                    extend=self.CHUNK_PLOT,
+                    channel=1,
+                )
+                self.time_analog_in_1 = np.concatenate((self.time_analog_in_0, times))[
+                    -self.PLOT_HISTORY :
+                ]
+                self.data_analog_in_1 = np.concatenate((self.data_analog_in_0, items))[
+                    -self.PLOT_HISTORY :
+                ]
+                self.line_analog_in_1.setData(
+                    self.time_analog_in_1,
+                    self.data_analog_in_1,
+                )
+                self.last_plotted_index_analog_in_1 += self.CHUNK_PLOT
             except IndexError:
                 log.error("Could not acces the data from the buffer for plotting")
             end_time = time.time()
@@ -70,19 +117,26 @@ class Continously:
 
     def stop_plotting(self):
         self.timer.stop()
-        if self.last_plotted_index > 0:
+        if self.last_plotted_index_analog_in_0 > 0:
             total_count = self.buffer.totalcount()
             times, items = self.buffer.read(
-                self.last_plotted_index,
+                self.last_plotted_index_analog_in_0,
-                extend=total_count - self.last_plotted_index,
+                extend=total_count - self.last_plotted_index_analog_in_0,
+            )
+            self.time_analog_in_0 = np.concatenate((self.time_analog_in_0, times))[
+                -self.PLOT_HISTORY :
+            ]
+            self.data_analog_in_0 = np.concatenate((self.data_analog_in_0, items))[
+                -self.PLOT_HISTORY :
+            ]
+            self.line_analog_in_0.setData(
+                self.time_analog_in_0,
+                self.data_analog_in_0,
             )
-            self.time = np.concatenate((self.time, times))[-self.PLOT_HISTORY :]
+            self.last_plotted_index_analog_in_0 += (
-            self.data = np.concatenate((self.data, items))[-self.PLOT_HISTORY :]
+                total_count - self.last_plotted_index_analog_in_0
-            self.line.setData(
-                self.time,
-                self.data,
             )
-            self.last_plotted_index += total_count - self.last_plotted_index
 
     def refresh(self):
-        self.continous_ax.enableAutoRange()
+        self.analog_in_0.enableAutoRange()
+        self.analog_in_1.enableAutoRange()