fix cython and tests

Author: tannermpeterson

controller/src/controller/constants.py

@@ -237,7 +237,6 @@ class SerialCommPacketTypes(IntEnum):
 
 NUM_INITIAL_MAG_PACKETS_TO_DROP = 2
 
-
 # Stimulation
 STIM_MAX_ABSOLUTE_CURRENT_MICROAMPS = int(100e3)
 STIM_MAX_ABSOLUTE_VOLTAGE_MILLIVOLTS = int(1.2e3)

controller/src/controller/subsystems/instrument_comm.py

@@ -633,8 +633,8 @@ def _log_dur_since_events(self) -> None:
 
 @dataclass
 class StimDataBuffers:
-    raw: dict[int, NDArray[(2, Any), int]] = {}
-    reduced: dict[int, NDArray[(2, Any), int]] = {}
+    raw: dict[int, NDArray[(2, Any), int]] = dataclasses.field(default_factory=dict)
+    reduced: dict[int, NDArray[(2, Any), int]] = dataclasses.field(default_factory=dict)
 
 
 class DataStreamManager:

controller/src/controller/utils/data_parsing_cy.pyx

@@ -8,6 +8,7 @@ from ..constants import SERIAL_COMM_PAYLOAD_INDEX
 from ..constants import SERIAL_COMM_CHECKSUM_LENGTH_BYTES
 from ..constants import SERIAL_COMM_DATA_SAMPLE_LENGTH_BYTES
 from ..constants import SERIAL_COMM_MAGIC_WORD_BYTES
+from ..constants import NUM_MAG_SENSORS_PER_WELL
 from ..constants import SERIAL_COMM_PACKET_METADATA_LENGTH_BYTES
 from ..constants import SERIAL_COMM_PACKET_REMAINDER_SIZE_LENGTH_BYTES
 from ..constants import SERIAL_COMM_TIME_OFFSET_LENGTH_BYTES
@@ -42,7 +43,7 @@ DEF NUM_CHANNELS_PER_SENSOR = 3
 
 # these values exist only for importing the constants defined above into the python test suite
 SERIAL_COMM_MAGIC_WORD_LENGTH_BYTES_CY = MAGIC_WORD_LEN
-SERIAL_COMM_NUM_CHANNELS_PER_SENSOR_CY = NUM_CHANNELS_PER_SENSOR
+NUM_CHANNELS_PER_MAG_SENSOR_CY = NUM_CHANNELS_PER_SENSOR
 
 # convert python constants to C types
 cdef char[MAGIC_WORD_LEN + 1] MAGIC_WORD = SERIAL_COMM_MAGIC_WORD_BYTES + bytes(1)
@@ -54,13 +55,15 @@ cdef int MIN_PACKET_SIZE = SERIAL_COMM_PACKET_METADATA_LENGTH_BYTES
 
 cdef int SERIAL_COMM_TIME_OFFSET_LENGTH_BYTES_C_INT = SERIAL_COMM_TIME_OFFSET_LENGTH_BYTES
 cdef int SERIAL_COMM_DATA_SAMPLE_LENGTH_BYTES_C_INT = SERIAL_COMM_DATA_SAMPLE_LENGTH_BYTES
-cdef int SERIAL_COMM_NUM_CHANNELS_PER_SENSOR_C_INT = NUM_CHANNELS_PER_SENSOR
+cdef int NUM_CHANNELS_PER_MAG_SENSOR_C_INT = NUM_CHANNELS_PER_SENSOR
+cdef int NUM_MAG_SENSORS_PER_WELL_C_INT = NUM_MAG_SENSORS_PER_WELL
 
 cdef int SERIAL_COMM_PAYLOAD_INDEX_C_INT = SERIAL_COMM_PAYLOAD_INDEX
 cdef int SERIAL_COMM_STIM_STATUS_PACKET_TYPE_C_INT = SerialCommPacketTypes.STIM_STATUS
 
 
 cdef int TOTAL_NUM_WELLS_C_INT = NUM_WELLS
+cdef int TOTAL_NUM_SENSORS_C_INT = TOTAL_NUM_WELLS_C_INT * NUM_MAG_SENSORS_PER_WELL_C_INT
 
 
 cdef packed struct Packet:
@@ -203,7 +206,7 @@ cpdef dict parse_magnetometer_data(
     cdef int magnetometer_data_packet_len = len(mag_data_packet_bytes) // num_mag_data_packets
 
     cdef int num_time_offsets = TOTAL_NUM_SENSORS_C_INT
-    cdef int num_data_channels = TOTAL_NUM_SENSORS_C_INT * SERIAL_COMM_NUM_CHANNELS_PER_SENSOR_C_INT
+    cdef int num_data_channels = TOTAL_NUM_SENSORS_C_INT * NUM_CHANNELS_PER_MAG_SENSOR_C_INT
 
     # arrays for storing parsed data
     time_indices = np.empty(num_mag_data_packets, dtype=np.uint64, order="C")
@@ -233,14 +236,14 @@ cpdef dict parse_magnetometer_data(
         for sensor in range(TOTAL_NUM_SENSORS_C_INT):
             time_offsets_view[time_offset_arr_idx, data_packet_idx] = sensor_data_ptr.time_offset
             time_offset_arr_idx += 1
-            for channel in range(SERIAL_COMM_NUM_CHANNELS_PER_SENSOR_C_INT):
+            for channel in range(NUM_CHANNELS_PER_MAG_SENSOR_C_INT):
                 data_view[channel_arr_idx, data_packet_idx] = sensor_data_ptr.data_points[channel]
                 channel_arr_idx += 1
             # shift SensorData ptr by appropriate amount
             sensor_data_ptr = <SensorData *> (
                 (<uint8_t *> sensor_data_ptr)
                 + SERIAL_COMM_TIME_OFFSET_LENGTH_BYTES_C_INT
-                + (SERIAL_COMM_NUM_CHANNELS_PER_SENSOR_C_INT * SERIAL_COMM_DATA_SAMPLE_LENGTH_BYTES_C_INT)
+                + (NUM_CHANNELS_PER_MAG_SENSOR_C_INT * SERIAL_COMM_DATA_SAMPLE_LENGTH_BYTES_C_INT)
             )
         # increment idxs
         bytes_idx += magnetometer_data_packet_len

controller/tests/subsystems/test_instrument_comm.py

@@ -22,7 +22,7 @@
 
 @pytest.fixture(scope="function", name="test_instrument_comm_obj")
 def fixture__test_instrument_comm_obj(mocker):
-    ic = InstrumentComm(asyncio.Queue(), asyncio.Queue())
+    ic = InstrumentComm(*[asyncio.Queue() for _ in range(4)])
     yield ic
     # TODO any teardown needed here?
 
@@ -69,7 +69,7 @@ async def test_InstrumentComm__creates_connection_to_real_instrument_correctly(
 
     assert test_instrument_comm_obj._instrument is mocked_aioserial.return_value
 
-    assert test_instrument_comm_obj._to_monitor_queue.get_nowait() == {
+    assert test_instrument_comm_obj._comm_to_monitor_queue.get_nowait() == {
         "command": "get_board_connection_status",
         "in_simulation_mode": False,
     }
@@ -100,7 +100,7 @@ async def test_InstrumentComm__creates_connection_to_virtual_instrument_correctl
     mocked_vic_init.assert_called_once_with(test_instrument_comm_obj._instrument)
     mocked_vic_connect.assert_awaited_once_with(test_instrument_comm_obj._instrument)
 
-    assert test_instrument_comm_obj._to_monitor_queue.get_nowait() == {
+    assert test_instrument_comm_obj._comm_to_monitor_queue.get_nowait() == {
         "command": "get_board_connection_status",
         "in_simulation_mode": True,
     }

controller/tests/test_main.py

@@ -276,14 +276,20 @@ async def test_main__creates_Server_and_runs_correctly(patch_run_tasks, patch_su
 async def test_main__creates_InstrumentComm_and_runs_correctly(
     patch_run_tasks, patch_subsystem_inits, mocker
 ):
-    spied_create_queues = mocker.spy(main, "create_system_comm_queues")
+    spied_create_comm_queues = mocker.spy(main, "create_system_comm_queues")
+    spied_create_data_queues = mocker.spy(main, "create_system_data_queues")
 
     await main.main([])
 
-    expected_queues = spied_create_queues.spy_return
+    expected_comm_queues = spied_create_comm_queues.spy_return
+    expected_data_queues = spied_create_data_queues.spy_return
 
     patch_subsystem_inits["instrument_comm"].assert_called_once_with(
-        mocker.ANY, expected_queues["to"]["instrument_comm"], expected_queues["from"]["instrument_comm"]
+        mocker.ANY,
+        expected_comm_queues["to"]["instrument_comm"],
+        expected_comm_queues["from"]["instrument_comm"],
+        expected_data_queues["main"],
+        expected_data_queues["file_writer"],
     )
 
 

virtual-instrument/src/virtual_instrument/constants.py

@@ -1,7 +1,2 @@
 # -*- coding: utf-8 -*-
-
-DEFAULT_SAMPLING_PERIOD = 10000  # valid as of 4/12/22
 MICROSECONDS_PER_CENTIMILLISECOND = 10
-
-SERIAL_COMM_NUM_CHANNELS_PER_SENSOR = 3
-SERIAL_COMM_NUM_SENSORS_PER_WELL = 3

virtual-instrument/src/virtual_instrument/virtual_instrument.py

@@ -15,10 +15,13 @@
 from uuid import UUID
 from zlib import crc32
 
+from controller.constants import DEFAULT_MAG_SAMPLING_PERIOD
 from controller.constants import GOING_DORMANT_HANDSHAKE_TIMEOUT_CODE
 from controller.constants import MAX_MC_REBOOT_DURATION_SECONDS
 from controller.constants import MICRO_TO_BASE_CONVERSION
 from controller.constants import MICROS_PER_MILLIS
+from controller.constants import NUM_CHANNELS_PER_MAG_SENSOR
+from controller.constants import NUM_MAG_SENSORS_PER_WELL
 from controller.constants import SERIAL_COMM_CHECKSUM_LENGTH_BYTES
 from controller.constants import SERIAL_COMM_HANDSHAKE_PERIOD_SECONDS
 from controller.constants import SERIAL_COMM_HANDSHAKE_TIMEOUT_SECONDS
@@ -57,10 +60,7 @@
 from stdlib_utils import InfiniteProcess
 from stdlib_utils import resource_path
 
-from .constants import DEFAULT_SAMPLING_PERIOD
 from .constants import MICROSECONDS_PER_CENTIMILLISECOND
-from .constants import SERIAL_COMM_NUM_CHANNELS_PER_SENSOR
-from .constants import SERIAL_COMM_NUM_SENSORS_PER_WELL
 from .exceptions import SerialCommInvalidSamplingPeriodError
 from .exceptions import SerialCommTooManyMissedHandshakesError
 from .exceptions import UnrecognizedSerialCommPacketTypeError
@@ -253,7 +253,7 @@ def _handle_boot_up_config(self, reboot: bool = False) -> None:
         self._reset_start_time()
         self._reboot_time_secs = None
         self._status_codes = [SERIAL_COMM_OKAY_CODE] * (self._num_wells + 2)
-        self._sampling_period_us = DEFAULT_SAMPLING_PERIOD
+        self._sampling_period_us = DEFAULT_MAG_SAMPLING_PERIOD
         self._adc_readings = [(self.default_adc_reading, self.default_adc_reading)] * self._num_wells
         self._stim_info = {}
         self._is_stimulating = False
@@ -620,8 +620,8 @@ def _create_magnetometer_data_payload(self) -> bytes:
                 SERIAL_COMM_MODULE_ID_TO_WELL_IDX[module_id] + 1
             )
             # add data points
-            well_sensor_data = time_offset + (data_value.tobytes() * SERIAL_COMM_NUM_CHANNELS_PER_SENSOR)
-            well_data = well_sensor_data * SERIAL_COMM_NUM_SENSORS_PER_WELL
+            well_sensor_data = time_offset + (data_value.tobytes() * NUM_CHANNELS_PER_MAG_SENSOR)
+            well_data = well_sensor_data * NUM_MAG_SENSORS_PER_WELL
             magnetometer_data_payload += well_data
         return magnetometer_data_payload