Added pre- and post-sampling dependent on ADC dead time #149

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schote wants to merge 12 commits into main from adc-presampling

src/console/interfaces/rx_data.py

            
                      Original file line number
                      Diff line number
                      Diff line change
                  
    @@ -18,6 +18,7 @@ class RxData:
  
        # Data characteristics, defined by the ADC event in sequence definition

        num_samples: int

        num_samples_raw: int

        num_samples_discard: int    # Number of samples to be discarded before and after ADC, defined by dead time

        dwell_time: float

        dwell_time_raw: float

    @@ -137,10 +138,10 @@ def process_data(self, store_unprocessed: bool = True) -> None:
  
            # Creating the processed data output array first and copying the values of the output of the decimation

            # avoids an apparent memory leak when using the scipy.decimate with the 'iir' ftype

            output_shape = list(np.shape(demod_data))

            output_shape[-1] = self.num_samples

            # Note that the processed data may contain samples from pre and post sampling

            output_shape = (*np.shape(demod_data)[:-1], self.num_samples + int(2*self.num_samples_discard))

            self.processed_data = np.zeros(output_shape, dtype=complex)

            self.processed_data[:] = self.decimate_data(demod_data)[:]

            self.processed_data[:] = self.decimate_data(demod_data)

            if not store_unprocessed:

                self.raw_data = None

src/console/pulseq_interpreter/sequence_provider.py

            
                      Original file line number
                      Diff line number
                      Diff line change
                  
    @@ -2,6 +2,8 @@
  
    import logging

    import operator

    from collections.abc import Callable

    from dataclasses import dataclass

    from math import floor

    from types import SimpleNamespace

    from typing import Any

    @@ -34,6 +36,13 @@ def profile(func: Callable[..., Any]) -> Callable[..., Any]:
  
    default_fov_offset: Dimensions = Dimensions(0, 0, 0)

    default_orientation: Dimensions = Dimensions(1, 2, 3)

    @dataclass

    class ADCGate:

        """Define precalculated attributes of an ADC gate."""

        start: int

        num_samples_discard: int

        num_samples_raw: int

    class SequenceProvider(Sequence):

        """Sequence provider class.

    @@ -189,7 +198,7 @@ def dict(self) -> dict:
  
                "output_limits": self.output_limits,

            }

        def get_adc_events(self) -> list:

        def get_adc_events(self) -> list[ADCGate]:

            """Extract ADC 'waveforms' from the sequence.

            TODO: Add error checks

    @@ -199,18 +208,30 @@ def get_adc_events(self) -> list:
  
                list: List of with waveform ID, gate signal and reference signal for each unique ADC event.

            """

            adc_waveforms = self.adc_library

            adc_list = []

            for adc_waveform in adc_waveforms.data.items():

                num_samples = adc_waveform[1][0]

                dwell_time = adc_waveform[1][1]

                delay = adc_waveform[1][2]

                delay_samples = round(delay * self.spcm_freq)

                gate_duration = num_samples * dwell_time

                gate_samples = round(gate_duration * self.spcm_freq)

                waveform = np.zeros(delay_samples + gate_samples, dtype=np.uint16)

                waveform[delay_samples:] = 2**15

                adc_list.append((adc_waveform[0], waveform, gate_samples))

            for adc_props in self.adc_library.data.values():

                # Implementation compatible to version 1.4.X and 1.5.X -> dead time is always appended

                num_samples, adc_dwell_time, delay = adc_props[:3]

                dead_time = adc_props[-1]

                # Calculate the number of samples to be discarded from the decimated signal

                num_samples_discard = floor(dead_time / adc_dwell_time)

                # Calculate the total gate duration, given by number of samples

                # and two times the number of discarded samples for symmetric adc dead time

                # Note that the total gate duration is only increased if the dead time is a multiple of the adc dwell time

                total_gate_duration = (num_samples + 2*num_samples_discard) * adc_dwell_time

                num_raw_samples = round(total_gate_duration * self.spcm_freq)

                # Remaining delay = dead_time minus pre- and post-sampling fractions

                remaining_delay = delay - num_samples_discard * adc_dwell_time

                num_delay_samples = round(remaining_delay * self.spcm_freq)

                adc_list.append(ADCGate(

                    start=num_delay_samples,

                    num_samples_raw=num_raw_samples,

                    num_samples_discard=num_samples_discard,

                ))

            return adc_list

        def get_rf_events(self) -> list:

    @@ -281,7 +302,7 @@ def unroll_sequence(self, parameter: AcquisitionParameter) -> UnrolledSequence:
  
            # Get list of all events and list of unique RF and ADC events, since they are frequently reused

            events_list = self.block_events

            adc_events = self.get_adc_events()

            adc_events: list[ADCGate] = self.get_adc_events()

            rf_events = self.get_rf_events()

            # Calculate rf pulse and unblanking waveforms from RF event

    @@ -410,22 +431,22 @@ def unroll_sequence(self, parameter: AcquisitionParameter) -> UnrolledSequence:
  
                        labels[label.label] = label.value

                if block.adc is not None:  # ADC event

                    # Grab the ADC event from the pre-calculated list

                    # Grab the ADC gate from the pre-calculated list

                    # Pulseq is 1 indexed, shift idx by -1 for correct event

                    adc_event = adc_events[event[5] - 1]

                    adc_waveform = adc_event[1]

                    adc_gate: ADCGate = adc_events[event[5] - 1]

                    # Calculate ADC start and end positions according to block position

                    adc_start = block_pos[event_idx] * 4

                    adc_end = (block_pos[event_idx] + np.size(adc_waveform)) * 4

                    adc_start = (block_pos[event_idx] + adc_gate.start) * 4

                    adc_end = (block_pos[event_idx] + adc_gate.start + adc_gate.num_samples_raw) * 4

                    # Add ADC gate to X gradient

                    _seq[adc_start + 1:adc_end + 1:4] = _seq[adc_start + 1:adc_end + 1:4] | adc_waveform

                    _seq[adc_start + 1:adc_end + 1:4] = _seq[adc_start + 1:adc_end + 1:4] | np.uint16(2**15)

                    _rx_data.append(RxData(

                        index=adc_count,

                        num_samples=block.adc.num_samples,

                        num_samples_raw=adc_event[2],

                        num_samples_raw=adc_gate.num_samples_raw,

                        num_samples_discard=adc_gate.num_samples_discard,

                        dwell_time=block.adc.dwell,

                        dwell_time_raw=self.spcm_dwell_time,

                        phase_offset=block.adc.phase_offset,

src/console/utilities/data/write_acquisition_to_mrd.py

-Original file line number
+Diff line change
@@ Expand Up / @@ -56,6 +56,11 @@ def write_acquisition_to_mrd( @@
                 acq.center_sample = rx_data.num_samples // 2
                 # Readout bandwidth, as time between samples in microseconds
                 acq.sample_time_us = rx_data.dwell_time * 1e6
+                # Number of samples to be discarded, defined by adc_dead_time
+                # Since adc_dead_time is arrange symmetrically around ADC, the
+                # number of discarded pre and post sample is identical
+                acq.discard_pre = rx_data.num_samples_discard
+                acq.discard_post = rx_data.num_samples_discard
                 # Timestamp of readout
                 if rx_data.time_stamp is not None:
                     acq.acquisition_time_stamp = int(rx_data.time_stamp * 1e6)  # timestamp in us
@@ Expand Down @@

tests/conftest.py

-Original file line number
+Diff line change
@@ Expand Up @@
                             average_index=k_average,
                             num_samples=num_samples,
                             num_samples_raw=num_raw_samples,
+                            num_samples_discard=0,
                             dwell_time=1 / 20e3,
                             dwell_time_raw=1 / 20e6,
                             phase_offset=0,
@@ Expand Down @@

tests/sequence_tests/test_sequence_provider.py

-Original file line number
+Diff line change
@@ Expand Up / @@ -6,6 +6,7 @@ @@
     import pypulseq as pp
     import pytest
+    from console.interfaces.acquisition_parameter import AcquisitionParameter
     from console.interfaces.rx_data import RxData
     from console.interfaces.unrolled_sequence import UnrolledSequence
     from console.pulseq_interpreter.sequence_provider import SequenceProvider
@@ Expand Down Expand Up / @@ -260,7 +261,7 @@ def test_get_rf_events(seq_provider, test_sequence): @@
         assert rf_block.type == "rf"
-    def test_sequence_rx_data(seq_provider: SequenceProvider, acquisition_parameter):
+    def test_sequence_rx_data(seq_provider: SequenceProvider, acquisition_parameter: AcquisitionParameter):
         """Labels in blocks must be propagated into RxData.labels for each ADC event."""
         n_samples = 1000
         bw = 20e3
@@ Expand All @@
         assert rx0.num_samples == n_samples
         assert rx0.num_samples_raw == n_samples / (bw*seq_provider.spcm_dwell_time)
         assert rx0.dwell_time == 1/bw
+    @pytest.mark.parametrize("dead_time", [0., 10e-3])
+    def test_adc_presampling(seq_provider: SequenceProvider, acquisition_parameter: AcquisitionParameter, dead_time: float):
+        """Verify that dead_time is used for pre and post samples which are to be discarded after decimation."""
+        adc_bw = 20e3
+        adc_dwell = 1/adc_bw
+        num_samples_discard = round(dead_time/adc_dwell)
+        num_samples = 100
+        # Define adc event
+        adc = pp.make_adc(
+            delay=dead_time,
+            num_samples=num_samples,
+            dwell=adc_dwell,
+            system=pp.Opts(adc_dead_time=dead_time),
+        )
+        # Unroll sequence
+        seq_provider.add_block(adc)
+        seq_unrolled = seq_provider.unroll_sequence(acquisition_parameter)
+        rx_data = seq_unrolled.rx_data[0]
+        assert rx_data.num_samples == num_samples
+        assert rx_data.num_samples_discard == num_samples_discard

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