def test_FileWriterProcess__process_next_data_packet__does_not_write_tissue_data_if_data_chunk_is_all_before_the_timestamp_idx(
four_board_file_writer_process, ):
file_writer_process = four_board_file_writer_process["fw_process"]
board_queues = four_board_file_writer_process["board_queues"]
from_main_queue = four_board_file_writer_process["from_main_queue"]
file_dir = four_board_file_writer_process["file_dir"]
this_command = copy.deepcopy(GENERIC_BETA_1_START_RECORDING_COMMAND)
this_command["active_well_indices"] = [4]
put_object_into_queue_and_raise_error_if_eventually_still_empty(
this_command,
from_main_queue,
)
num_data_points = 5
data = np.zeros((2, num_data_points), dtype=np.int32)
for this_index in range(num_data_points):
data[0, this_index] = (
this_command["timepoint_to_begin_recording_at"] +
(this_index - 25) * CONSTRUCT_SENSOR_SAMPLING_PERIOD)
data[1, this_index] = this_index * 2
this_data_packet = copy.deepcopy(GENERIC_TISSUE_DATA_PACKET)
this_data_packet["data"] = data
put_object_into_queue_and_raise_error_if_eventually_still_empty(
this_data_packet,
board_queues[0][0],
)
invoke_process_run_and_check_errors(file_writer_process)
actual_file = open_the_generic_h5_file(file_dir)
assert str(UTC_FIRST_TISSUE_DATA_POINT_UUID) not in actual_file.attrs
actual_tissue_data = get_tissue_dataset_from_file(actual_file)
assert actual_tissue_data.shape == (0, )
def test_FileWriterProcess__process_next_data_packet__writes_tissue_data_for_two_packets_when_the_timestamp_idx_starts_part_way_through_the_first_packet__and_sets_timestamp_metadata_for_tissue_since_this_is_first_piece_of_data(
four_board_file_writer_process, ):
file_writer_process = four_board_file_writer_process["fw_process"]
board_queues = four_board_file_writer_process["board_queues"]
from_main_queue = four_board_file_writer_process["from_main_queue"]
file_dir = four_board_file_writer_process["file_dir"]
this_command = copy.deepcopy(GENERIC_BETA_1_START_RECORDING_COMMAND)
this_command["active_well_indices"] = [4]
put_object_into_queue_and_raise_error_if_eventually_still_empty(
this_command,
from_main_queue,
)
num_data_points = 75
data = np.zeros((2, num_data_points), dtype=np.int32)
for this_index in range(num_data_points):
data[0, this_index] = (
this_command["timepoint_to_begin_recording_at"] +
(this_index - 30) * CONSTRUCT_SENSOR_SAMPLING_PERIOD +
DATA_FRAME_PERIOD)
data[1, this_index] = this_index * 2
this_data_packet = copy.deepcopy(GENERIC_TISSUE_DATA_PACKET)
this_data_packet["data"] = data
num_data_points = 15
next_data = np.zeros((2, num_data_points), dtype=np.int32)
for this_index in range(num_data_points):
next_data[0, this_index] = data[
0, -1] + (this_index + 1) * CONSTRUCT_SENSOR_SAMPLING_PERIOD
next_data[1, this_index] = this_index * 2 + 1000
next_data_packet = copy.deepcopy(GENERIC_TISSUE_DATA_PACKET)
next_data_packet["data"] = next_data
board_queues[0][0].put_nowait(this_data_packet)
put_object_into_queue_and_raise_error_if_eventually_still_empty(
next_data_packet,
board_queues[0][0],
)
invoke_process_run_and_check_errors(file_writer_process, num_iterations=2)
actual_file = open_the_generic_h5_file(file_dir)
expected_timestamp = this_command[
"metadata_to_copy_onto_main_file_attributes"][
UTC_BEGINNING_DATA_ACQUISTION_UUID] + datetime.timedelta(
seconds=(this_command["timepoint_to_begin_recording_at"] +
DATA_FRAME_PERIOD) / CENTIMILLISECONDS_PER_SECOND)
assert actual_file.attrs[str(
UTC_FIRST_TISSUE_DATA_POINT_UUID)] == expected_timestamp.strftime(
"%Y-%m-%d %H:%M:%S.%f")
actual_tissue_data = get_tissue_dataset_from_file(actual_file)
assert actual_tissue_data.shape == (60, )
assert actual_tissue_data[0] == 60
assert actual_tissue_data[-1] == 1028
def test_FileWriterProcess_process_magnetometer_data_packet__writes_data_if_the_timestamp_idx_starts_part_way_through_the_chunk__and_sets_timestamp_metadata_for_tissue_since_this_is_first_piece_of_data(
four_board_file_writer_process, ):
fw_process = four_board_file_writer_process["fw_process"]
fw_process.set_beta_2_mode()
populate_calibration_folder(fw_process)
board_queues = four_board_file_writer_process["board_queues"]
from_main_queue = four_board_file_writer_process["from_main_queue"]
file_dir = four_board_file_writer_process["file_dir"]
start_recording_command = copy.deepcopy(
GENERIC_BETA_2_START_RECORDING_COMMAND)
start_recording_command["active_well_indices"] = [4]
put_object_into_queue_and_raise_error_if_eventually_still_empty(
start_recording_command, from_main_queue)
total_num_data_points = 75
num_recorded_data_points = 50
time_index_offset = total_num_data_points - num_recorded_data_points
start_timepoint = start_recording_command[
"timepoint_to_begin_recording_at"] - time_index_offset
test_data_packet = create_simple_data_packet(
start_timepoint,
0,
start_recording_command["active_well_indices"],
total_num_data_points,
)
put_object_into_queue_and_raise_error_if_eventually_still_empty(
test_data_packet, board_queues[0][0])
invoke_process_run_and_check_errors(fw_process)
expected_timestamp = start_recording_command[
"metadata_to_copy_onto_main_file_attributes"][
UTC_BEGINNING_DATA_ACQUISTION_UUID] + datetime.timedelta(seconds=(
start_recording_command["timepoint_to_begin_recording_at"]
) / MICRO_TO_BASE_CONVERSION)
this_file = open_the_generic_h5_file(file_dir, beta_version=2)
assert this_file.attrs[str(
UTC_FIRST_TISSUE_DATA_POINT_UUID)] == expected_timestamp.strftime(
"%Y-%m-%d %H:%M:%S.%f")
actual_time_index_data = get_time_index_dataset_from_file(this_file)
assert actual_time_index_data.shape == (num_recorded_data_points, )
assert actual_time_index_data[0] == start_timepoint + time_index_offset
actual_time_offset_data = get_time_offset_dataset_from_file(this_file)
assert actual_time_offset_data.shape == (GENERIC_NUM_SENSORS_ENABLED,
num_recorded_data_points)
assert actual_time_offset_data[0, 9] == (9 + time_index_offset) * 2
assert actual_time_offset_data[1, 6] == (6 + time_index_offset) * 2
actual_tissue_data = get_tissue_dataset_from_file(this_file)
assert actual_tissue_data.shape == (GENERIC_NUM_CHANNELS_ENABLED,
num_recorded_data_points)
assert actual_tissue_data[0, 9] == (9 + time_index_offset) * 3
assert actual_tissue_data[1, 6] == (6 + time_index_offset) * 4
# close file to avoid issues on Windows
this_file.close()
def test_FileWriterProcess__process_next_data_packet__writes_tissue_data_if_the_whole_data_chunk_is_at_the_timestamp_idx__and_sets_timestamp_metadata_for_tissue_since_this_is_first_piece_of_data(
four_board_file_writer_process, ):
file_writer_process = four_board_file_writer_process["fw_process"]
board_queues = four_board_file_writer_process["board_queues"]
from_main_queue = four_board_file_writer_process["from_main_queue"]
file_dir = four_board_file_writer_process["file_dir"]
this_command = copy.deepcopy(GENERIC_BETA_1_START_RECORDING_COMMAND)
this_command["active_well_indices"] = [3]
put_object_into_queue_and_raise_error_if_eventually_still_empty(
this_command,
from_main_queue,
)
num_data_points = 50
data = np.zeros((2, num_data_points), dtype=np.int32)
for this_index in range(num_data_points):
data[0,
this_index] = (this_command["timepoint_to_begin_recording_at"] +
this_index * CONSTRUCT_SENSOR_SAMPLING_PERIOD)
data[1, this_index] = this_index * 2
this_data_packet = copy.deepcopy(GENERIC_TISSUE_DATA_PACKET)
this_data_packet["well_index"] = 3
this_data_packet["data"] = data
put_object_into_queue_and_raise_error_if_eventually_still_empty(
this_data_packet,
board_queues[0][0],
)
invoke_process_run_and_check_errors(file_writer_process)
actual_file = open_the_generic_h5_file(file_dir, well_name="D1")
expected_timestamp = this_command[
"metadata_to_copy_onto_main_file_attributes"][
UTC_BEGINNING_DATA_ACQUISTION_UUID] + datetime.timedelta(
seconds=this_command["timepoint_to_begin_recording_at"] /
CENTIMILLISECONDS_PER_SECOND)
assert actual_file.attrs[str(
UTC_FIRST_TISSUE_DATA_POINT_UUID)] == expected_timestamp.strftime(
"%Y-%m-%d %H:%M:%S.%f")
actual_tissue_data = get_tissue_dataset_from_file(actual_file)
assert actual_tissue_data.shape == (50, )
assert actual_tissue_data[3] == 6
assert actual_tissue_data[9] == 18
def test_FileWriterProcess_process_magnetometer_data_packet__does_not_write_data_if_data_chunk_is_all_before_the_timestamp_idx(
four_board_file_writer_process, ):
fw_process = four_board_file_writer_process["fw_process"]
fw_process.set_beta_2_mode()
populate_calibration_folder(fw_process)
board_queues = four_board_file_writer_process["board_queues"]
from_main_queue = four_board_file_writer_process["from_main_queue"]
file_dir = four_board_file_writer_process["file_dir"]
start_recording_command = copy.deepcopy(
GENERIC_BETA_2_START_RECORDING_COMMAND)
start_recording_command["active_well_indices"] = [4]
put_object_into_queue_and_raise_error_if_eventually_still_empty(
start_recording_command, from_main_queue)
num_data_points = 30
start_timepoint = start_recording_command[
"timepoint_to_begin_recording_at"] - num_data_points
test_data_packet = create_simple_data_packet(
start_timepoint,
0,
start_recording_command["active_well_indices"],
num_data_points,
)
put_object_into_queue_and_raise_error_if_eventually_still_empty(
test_data_packet, board_queues[0][0])
invoke_process_run_and_check_errors(fw_process)
this_file = open_the_generic_h5_file(file_dir, beta_version=2)
assert str(UTC_FIRST_TISSUE_DATA_POINT_UUID) not in this_file.attrs
actual_time_index_data = get_time_index_dataset_from_file(this_file)
assert actual_time_index_data.shape == (0, )
actual_time_offset_data = get_time_offset_dataset_from_file(this_file)
assert actual_time_offset_data.shape == (GENERIC_NUM_SENSORS_ENABLED, 0)
actual_tissue_data = get_tissue_dataset_from_file(this_file)
assert actual_tissue_data.shape == (GENERIC_NUM_CHANNELS_ENABLED, 0)
# close file to avoid issues on Windows
this_file.close()
def test_FileWriterProcess__process_next_data_packet__adds_a_data_packet_before_the_stop_recording_timepoint__and_does_not_set_tissue_finalization_status_to_true__if_data_packet_is_completely_before_timepoint(
four_board_file_writer_process, ):
file_writer_process = four_board_file_writer_process["fw_process"]
board_queues = four_board_file_writer_process["board_queues"]
from_main_queue = four_board_file_writer_process["from_main_queue"]
file_dir = four_board_file_writer_process["file_dir"]
start_command = copy.deepcopy(GENERIC_BETA_1_START_RECORDING_COMMAND)
start_command["active_well_indices"] = [4]
put_object_into_queue_and_raise_error_if_eventually_still_empty(
start_command,
from_main_queue,
)
num_data_points = 10
data = np.zeros((2, num_data_points), dtype=np.int32)
for this_index in range(num_data_points):
data[0,
this_index] = (start_command["timepoint_to_begin_recording_at"] +
this_index * CONSTRUCT_SENSOR_SAMPLING_PERIOD +
DATA_FRAME_PERIOD)
data[1, this_index] = this_index * 2
this_data_packet = copy.deepcopy(GENERIC_TISSUE_DATA_PACKET)
this_data_packet["data"] = data
put_object_into_queue_and_raise_error_if_eventually_still_empty(
this_data_packet,
board_queues[0][0],
)
invoke_process_run_and_check_errors(file_writer_process)
actual_file = open_the_generic_h5_file(file_dir)
# confirm some data already recorded to file
actual_tissue_data = get_tissue_dataset_from_file(actual_file)
assert actual_tissue_data.shape == (10, )
assert actual_tissue_data[9] == 18
assert actual_tissue_data[3] == 6
stop_command = copy.deepcopy(GENERIC_STOP_RECORDING_COMMAND)
put_object_into_queue_and_raise_error_if_eventually_still_empty(
stop_command,
from_main_queue,
)
data_before_stop = np.zeros((2, num_data_points), dtype=np.int32)
for this_index in range(num_data_points):
data_before_stop[0, this_index] = (
stop_command["timepoint_to_stop_recording_at"] +
(this_index - 10) * CONSTRUCT_SENSOR_SAMPLING_PERIOD)
data_before_stop[1, this_index] = this_index * 5
this_data_packet["data"] = data_before_stop
put_object_into_queue_and_raise_error_if_eventually_still_empty(
this_data_packet,
board_queues[0][0],
)
invoke_process_run_and_check_errors(file_writer_process)
# confirm additional data added to file
actual_data = get_tissue_dataset_from_file(actual_file)
assert actual_data.shape == (20, )
assert actual_data[11] == 5
assert actual_data[14] == 20
tissue_status, _ = file_writer_process.get_recording_finalization_statuses(
)
assert tissue_status[0][4] is False
def test_FileWriterProcess_hard_stop__closes_all_beta_2_files_after_stop_recording_before_all_files_are_finalized__and_files_can_be_opened_after_process_stops(
four_board_file_writer_process, mocker
):
expected_timestamp = "2020_02_09_190359"
expected_barcode = GENERIC_BETA_2_START_RECORDING_COMMAND["metadata_to_copy_onto_main_file_attributes"][
PLATE_BARCODE_UUID
]
fw_process = four_board_file_writer_process["fw_process"]
fw_process.set_beta_2_mode()
populate_calibration_folder(fw_process)
board_queues = four_board_file_writer_process["board_queues"]
from_main_queue = four_board_file_writer_process["from_main_queue"]
tmp_dir = four_board_file_writer_process["file_dir"]
spied_close_all_files = mocker.spy(fw_process, "close_all_files")
put_object_into_queue_and_raise_error_if_eventually_still_empty(
copy.deepcopy(GENERIC_BETA_2_START_RECORDING_COMMAND), from_main_queue
)
invoke_process_run_and_check_errors(fw_process)
# fill files with data
test_num_data_points = 50
start_timepoint = GENERIC_BETA_2_START_RECORDING_COMMAND["timepoint_to_begin_recording_at"]
test_data = np.zeros(test_num_data_points, dtype=np.uint16)
data_packet = {
"data_type": "magnetometer",
"time_indices": np.arange(start_timepoint, start_timepoint + test_num_data_points, dtype=np.uint64),
"is_first_packet_of_stream": False,
}
for well_idx in range(24):
channel_dict = {
"time_offsets": np.zeros((GENERIC_NUM_SENSORS_ENABLED, test_num_data_points), dtype=np.uint16),
SERIAL_COMM_SENSOR_AXIS_LOOKUP_TABLE["A"]["X"]: test_data,
SERIAL_COMM_SENSOR_AXIS_LOOKUP_TABLE["C"]["Z"]: test_data,
}
data_packet[well_idx] = channel_dict
board_queues[0][0].put_nowait(data_packet)
confirm_queue_is_eventually_of_size(board_queues[0][0], 1)
invoke_process_run_and_check_errors(fw_process)
confirm_queue_is_eventually_empty(board_queues[0][0])
stop_recording_command = copy.deepcopy(GENERIC_STOP_RECORDING_COMMAND)
put_object_into_queue_and_raise_error_if_eventually_still_empty(stop_recording_command, from_main_queue)
invoke_process_run_and_check_errors(fw_process)
assert spied_close_all_files.call_count == 0 # confirm precondition
fw_process.hard_stop()
spied_close_all_files.assert_called_once()
# confirm files can be opened and files contains at least one piece of metadata and the correct tissue data
for row_idx in range(4):
for col_idx in range(6):
well_name = WELL_DEF_24.get_well_name_from_row_and_column(row_idx, col_idx)
with h5py.File(
os.path.join(
tmp_dir,
f"{expected_barcode}__{expected_timestamp}",
f"{expected_barcode}__{expected_timestamp}__{well_name}.h5",
),
"r",
) as this_file:
assert (
str(START_RECORDING_TIME_INDEX_UUID) in this_file.attrs
), f"START_RECORDING_TIME_INDEX_UUID missing for Well {well_name}"
assert get_time_index_dataset_from_file(this_file).shape == (
test_num_data_points,
), f"Incorrect time index data shape for Well {well_name}"
assert get_time_offset_dataset_from_file(this_file).shape == (
GENERIC_NUM_SENSORS_ENABLED,
test_num_data_points,
), f"Incorrect time offset data shape for Well {well_name}"
assert get_tissue_dataset_from_file(this_file).shape == (
GENERIC_NUM_CHANNELS_ENABLED,
test_num_data_points,
), f"Incorrect tissue data shape for Well {well_name}"
def test_FileWriterProcess_hard_stop__closes_all_beta_1_files_after_stop_recording_before_all_files_are_finalized__and_files_can_be_opened_after_process_stops(
four_board_file_writer_process, mocker
):
expected_timestamp = "2020_02_09_190935"
expected_barcode = GENERIC_BETA_1_START_RECORDING_COMMAND["metadata_to_copy_onto_main_file_attributes"][
PLATE_BARCODE_UUID
]
fw_process = four_board_file_writer_process["fw_process"]
board_queues = four_board_file_writer_process["board_queues"]
from_main_queue = four_board_file_writer_process["from_main_queue"]
tmp_dir = four_board_file_writer_process["file_dir"]
spied_close_all_files = mocker.spy(fw_process, "close_all_files")
put_object_into_queue_and_raise_error_if_eventually_still_empty(
copy.deepcopy(GENERIC_BETA_1_START_RECORDING_COMMAND), from_main_queue
)
invoke_process_run_and_check_errors(fw_process)
# fill files with data
start_timepoint = GENERIC_BETA_1_START_RECORDING_COMMAND["timepoint_to_begin_recording_at"]
test_data = np.array([[start_timepoint], [0]], dtype=np.int32)
for i in range(24):
tissue_data_packet = {
"well_index": i,
"is_reference_sensor": False,
"data": test_data,
}
board_queues[0][0].put_nowait(tissue_data_packet)
for i in range(6):
ref_data_packet = {
"reference_for_wells": REF_INDEX_TO_24_WELL_INDEX[i],
"is_reference_sensor": True,
"data": test_data,
}
board_queues[0][0].put_nowait(ref_data_packet)
confirm_queue_is_eventually_of_size(board_queues[0][0], 30)
# set to 0 to speed up test
fw_process._minimum_iteration_duration_seconds = 0 # pylint: disable=protected-access
invoke_process_run_and_check_errors(fw_process, num_iterations=30)
confirm_queue_is_eventually_empty(board_queues[0][0])
stop_recording_command = copy.deepcopy(GENERIC_STOP_RECORDING_COMMAND)
put_object_into_queue_and_raise_error_if_eventually_still_empty(stop_recording_command, from_main_queue)
invoke_process_run_and_check_errors(fw_process)
assert spied_close_all_files.call_count == 0 # confirm precondition
fw_process.hard_stop()
spied_close_all_files.assert_called_once()
# confirm files can be opened and files contains at least one piece of metadata and the correct tissue data
for row_idx in range(4):
for col_idx in range(6):
well_name = WELL_DEF_24.get_well_name_from_row_and_column(row_idx, col_idx)
with h5py.File(
os.path.join(
tmp_dir,
f"{expected_barcode}__{expected_timestamp}",
f"{expected_barcode}__{expected_timestamp}__{well_name}.h5",
),
"r",
) as this_file:
assert (
str(START_RECORDING_TIME_INDEX_UUID) in this_file.attrs
), f"START_RECORDING_TIME_INDEX_UUID missing for Well {well_name}"
assert get_tissue_dataset_from_file(this_file).shape == (
test_data.shape[1],
), f"Incorrect tissue data shape for Well {well_name}"
def test_FileWriterProcess_process_magnetometer_data_packet__adds_a_data_packet_completely_before_the_stop_recording_timepoint__and_does_not_set_data_finalization_status_to_true(
four_board_file_writer_process, ):
fw_process = four_board_file_writer_process["fw_process"]
fw_process.set_beta_2_mode()
populate_calibration_folder(fw_process)
board_queues = four_board_file_writer_process["board_queues"]
from_main_queue = four_board_file_writer_process["from_main_queue"]
file_dir = four_board_file_writer_process["file_dir"]
start_recording_command = copy.deepcopy(
GENERIC_BETA_2_START_RECORDING_COMMAND)
start_recording_command["active_well_indices"] = [4]
put_object_into_queue_and_raise_error_if_eventually_still_empty(
start_recording_command, from_main_queue)
stop_command = copy.deepcopy(GENERIC_STOP_RECORDING_COMMAND)
num_data_points_1 = 26
start_timepoint_1 = start_recording_command[
"timepoint_to_begin_recording_at"]
test_data_packet_1 = create_simple_data_packet(
start_timepoint_1,
0,
start_recording_command["active_well_indices"],
num_data_points_1,
)
put_object_into_queue_and_raise_error_if_eventually_still_empty(
test_data_packet_1, board_queues[0][0])
invoke_process_run_and_check_errors(fw_process)
this_file = open_the_generic_h5_file(file_dir, beta_version=2)
# confirm some data already recorded to file
actual_time_index_data = get_time_index_dataset_from_file(this_file)
assert actual_time_index_data.shape == (num_data_points_1, )
assert actual_time_index_data[7] == start_timepoint_1 + 7
actual_time_offset_data = get_time_offset_dataset_from_file(this_file)
assert actual_time_offset_data.shape == (GENERIC_NUM_SENSORS_ENABLED,
num_data_points_1)
assert actual_time_offset_data[0, 15] == 15 * 2
assert actual_time_offset_data[1, 5] == 5 * 2
actual_tissue_data = get_tissue_dataset_from_file(this_file)
assert actual_tissue_data.shape == (GENERIC_NUM_CHANNELS_ENABLED,
num_data_points_1)
assert actual_tissue_data[0, 15] == 15 * 3
assert actual_tissue_data[1, 5] == 5 * 4
put_object_into_queue_and_raise_error_if_eventually_still_empty(
stop_command, from_main_queue)
num_data_points_2 = 24
start_timepoint_2 = stop_command[
"timepoint_to_stop_recording_at"] - num_data_points_2
test_data_packet_2 = create_simple_data_packet(
start_timepoint_2,
num_data_points_1,
start_recording_command["active_well_indices"],
num_data_points_2,
)
assert test_data_packet_2["time_indices"][
-1] == stop_command["timepoint_to_stop_recording_at"] - 1
put_object_into_queue_and_raise_error_if_eventually_still_empty(
test_data_packet_2, board_queues[0][0])
invoke_process_run_and_check_errors(fw_process)
total_num_data_points = num_data_points_1 + num_data_points_2
# confirm additional data added to file
actual_time_index_data = get_time_index_dataset_from_file(this_file)
assert actual_time_index_data.shape == (total_num_data_points, )
assert actual_time_index_data[
-1] == stop_command["timepoint_to_stop_recording_at"] - 1
actual_time_offset_data = get_time_offset_dataset_from_file(this_file)
assert actual_time_offset_data.shape == (GENERIC_NUM_SENSORS_ENABLED,
total_num_data_points)
assert actual_time_offset_data[0, 11] == 11 * 2
assert actual_time_offset_data[1, 14] == 14 * 2
actual_tissue_data = get_tissue_dataset_from_file(this_file)
assert actual_tissue_data.shape == (GENERIC_NUM_CHANNELS_ENABLED,
total_num_data_points)
assert actual_tissue_data[0, 11] == 11 * 3
assert actual_tissue_data[1, 14] == 14 * 4
# TODO Tanner (5/19/21): add assertion about reference data once it is added to Beta 2 files
tissue_status, _ = fw_process.get_recording_finalization_statuses()
assert tissue_status[0][4] is False
# close file to avoid issues on Windows
this_file.close()
def test_FileWriterProcess_process_magnetometer_data_packet__does_not_add_a_data_packet_completely_after_the_stop_recording_timepoint__and_sets_data_finalization_status_to_true(
four_board_file_writer_process, ):
fw_process = four_board_file_writer_process["fw_process"]
fw_process.set_beta_2_mode()
populate_calibration_folder(fw_process)
board_queues = four_board_file_writer_process["board_queues"]
from_main_queue = four_board_file_writer_process["from_main_queue"]
file_dir = four_board_file_writer_process["file_dir"]
start_recording_command = copy.deepcopy(
GENERIC_BETA_2_START_RECORDING_COMMAND)
start_recording_command["active_well_indices"] = [4]
put_object_into_queue_and_raise_error_if_eventually_still_empty(
start_recording_command, from_main_queue)
num_recorded_data_points = 10
start_timepoint = start_recording_command[
"timepoint_to_begin_recording_at"]
recorded_data_packet = create_simple_data_packet(
start_timepoint,
0,
start_recording_command["active_well_indices"],
num_recorded_data_points,
)
put_object_into_queue_and_raise_error_if_eventually_still_empty(
recorded_data_packet, board_queues[0][0])
invoke_process_run_and_check_errors(fw_process)
this_file = open_the_generic_h5_file(file_dir, beta_version=2)
# confirm some data already recorded to file
actual_time_index_data = get_time_index_dataset_from_file(this_file)
assert actual_time_index_data.shape == (num_recorded_data_points, )
assert actual_time_index_data[
-1] == start_timepoint + num_recorded_data_points - 1
actual_time_offset_data = get_time_offset_dataset_from_file(this_file)
assert actual_time_offset_data.shape == (GENERIC_NUM_SENSORS_ENABLED,
num_recorded_data_points)
assert actual_time_offset_data[0, 0] == 0
assert actual_time_offset_data[1, -1] == (num_recorded_data_points - 1) * 2
actual_tissue_data = get_tissue_dataset_from_file(this_file)
assert actual_tissue_data.shape == (GENERIC_NUM_CHANNELS_ENABLED,
num_recorded_data_points)
assert actual_tissue_data[0, 0] == 0
assert actual_tissue_data[1, -1] == (num_recorded_data_points - 1) * 4
stop_command = copy.deepcopy(GENERIC_STOP_RECORDING_COMMAND)
put_object_into_queue_and_raise_error_if_eventually_still_empty(
stop_command, from_main_queue)
ignored_data_packet = create_simple_data_packet(
stop_command["timepoint_to_stop_recording_at"],
num_recorded_data_points,
start_recording_command["active_well_indices"],
15,
)
put_object_into_queue_and_raise_error_if_eventually_still_empty(
ignored_data_packet, board_queues[0][0])
invoke_process_run_and_check_errors(fw_process)
# confirm no additional data added to file
actual_time_index_data = get_time_index_dataset_from_file(this_file)
assert actual_time_index_data.shape == (num_recorded_data_points, )
actual_time_offset_data = get_time_offset_dataset_from_file(this_file)
assert actual_time_offset_data.shape == (GENERIC_NUM_SENSORS_ENABLED,
num_recorded_data_points)
actual_tissue_data = get_tissue_dataset_from_file(this_file)
assert actual_tissue_data.shape == (GENERIC_NUM_CHANNELS_ENABLED,
num_recorded_data_points)
# TODO Tanner (5/19/21): add assertion about reference data once it is added to Beta 2 files
tissue_status, _ = fw_process.get_recording_finalization_statuses()
assert tissue_status[0][4] is True
# close file to avoid issues on Windows
this_file.close()
