Docs, linting

docs/api/bit_operation.md

@@ -0,0 +1,7 @@
+# bit operation
+
+```{eval-rst}
+.. automodule:: miniscope_io.bit_operation
+    :members:
+    :undoc-members:
+```

docs/api/stream_daq.md

@@ -5,6 +5,8 @@ This module is a data acquisition module that captures video streams from Minisc
 After [installation](../guide/installation.md) and customizing [configurations](stream-daq-config) if necessary, run the following command in this Git repository to start the data acquisition process:
 ```bash
 >>> mio sdaq -c path/to/config.yml -o output_filename
+[24-06-25T04:19:46] INFO     [miniscope_io.okDev] Connected to           opalkelly.py:34
+                             XEM7310-A75
 Connected to XEM7310-A75
 Successfully uploaded /miniscope-io/miniscope_io/devices/selected_bitfile.bit
 FrontPanel is supported

docs/index.md

@@ -23,6 +23,7 @@ api/exceptions
 api/plots/index
 api/utils
 api/stream_daq
+api/bit_operation
 api/vendor/index
 ```
 

miniscope_io/formats/stream.py

@@ -12,14 +12,3 @@
     timestamp=6,
     pixel_count=7,
 )
-
-""" keeping for ref
-StreamBufferHeader = StreamBufferHeaderFormat(
-    linked_list=(0, 32),
-    frame_num=(32, 64),
-    buffer_count=(64, 96),
-    frame_buffer_count=(96, 128),
-    timestamp=(192, 224),
-    pixel_count=(224, 256),
-)
-"""

miniscope_io/stream_daq.py

@@ -526,7 +526,7 @@ def capture(
             p_recv = multiprocessing.Process(
                 target=self._fpga_recv,
                 args=(serial_buffer_queue, read_length, True, binary),
-                name="_fpga_recv"
+                name="_fpga_recv",
             )
         else:
             raise ValueError(f"source can be one of uart or fpga. Got {source}")
@@ -546,20 +546,17 @@ def capture(
                 serial_buffer_queue,
                 frame_buffer_queue,
             ),
-            name="_buffer_to_frame"
+            name="_buffer_to_frame",
         )
         p_format_frame = multiprocessing.Process(
             target=self._format_frame,
             args=(
                 frame_buffer_queue,
                 imagearray,
             ),
-            name="_format_frame"
+            name="_format_frame",
         )
-        """
-        p_terminate = multiprocessing.Process(
-            target=check_termination_flag, args=(self.terminate,))
-        """
+
         p_recv.start()
         p_buffer_to_frame.start()
         p_format_frame.start()
@@ -568,7 +565,7 @@ def capture(
             for image in exact_iter(imagearray.get, None):
                 if self.config.show_video is True:
                     cv2.imshow("image", image)
-                    if cv2.waitKey(1) == 27: # get out with ESC key
+                    if cv2.waitKey(1) == 27:  # get out with ESC key
                         self.terminate.set()
                         break
                 if writer:
@@ -586,19 +583,17 @@ def capture(
             if self.config.show_video:
                 cv2.destroyAllWindows()
                 cv2.waitKey(100)
-
-            # Give some time for processes to clean up
-            time.sleep(1)
 
             # Join child processes with a timeout
             for p in [p_recv, p_buffer_to_frame, p_format_frame]:
                 p.join(timeout=2)
                 if p.is_alive():
-                    self.logger.warning(f"Process {p.name} did not terminate in time and will be terminated forcefully.")
+                    self.logger.warning(f"Termination timeout: force terminating process {p.name}.")
                     p.terminate()
                     p.join()
             self.logger.info("Child processes joined. End capture.")
 
+
 def main() -> None:  # noqa: D103
     args = daqParser.parse_args()