mrd-python 2.0.0rc1__py3-none-any.whl

mrd/protocols.py

@@ -0,0 +1,180 @@
+# This file was generated by the "yardl" tool. DO NOT EDIT.
+
+# pyright: reportUnusedImport=false
+
+import abc
+import collections.abc
+import datetime
+import typing
+
+import numpy as np
+import numpy.typing as npt
+
+from .types import *
+from .yardl_types import ProtocolError
+from . import yardl_types as yardl
+
+class MrdWriterBase(abc.ABC):
+    """Abstract writer for the Mrd protocol."""
+
+
+    def __init__(self) -> None:
+        self._state = 0
+
+    schema = r"""{"protocol":{"name":"Mrd","sequence":[{"name":"header","type":[null,"Mrd.Header"]},{"name":"data","type":{"stream":{"items":"Mrd.StreamItem"}}}]},"types":[{"name":"AccelerationFactorType","fields":[{"name":"kspaceEncodingStep1","type":"uint32"},{"name":"kspaceEncodingStep2","type":"uint32"}]},{"name":"Acquisition","fields":[{"name":"flags","type":"Mrd.AcquisitionFlags"},{"name":"idx","type":"Mrd.EncodingCounters"},{"name":"measurementUid","type":"uint32"},{"name":"scanCounter","type":[null,"uint32"]},{"name":"acquisitionTimeStamp","type":[null,"uint32"]},{"name":"physiologyTimeStamp","type":{"vector":{"items":"uint32"}}},{"name":"channelOrder","type":{"vector":{"items":"uint32"}}},{"name":"discardPre","type":[null,"uint32"]},{"name":"discardPost","type":[null,"uint32"]},{"name":"centerSample","type":[null,"uint32"]},{"name":"encodingSpaceRef","type":[null,"uint32"]},{"name":"sampleTimeUs","type":[null,"float32"]},{"name":"position","type":{"array":{"items":"float32","dimensions":[{"length":3}]}}},{"name":"readDir","type":{"array":{"items":"float32","dimensions":[{"length":3}]}}},{"name":"phaseDir","type":{"array":{"items":"float32","dimensions":[{"length":3}]}}},{"name":"sliceDir","type":{"array":{"items":"float32","dimensions":[{"length":3}]}}},{"name":"patientTablePosition","type":{"array":{"items":"float32","dimensions":[{"length":3}]}}},{"name":"userInt","type":{"vector":{"items":"int32"}}},{"name":"userFloat","type":{"vector":{"items":"float32"}}},{"name":"data","type":"Mrd.AcquisitionData"},{"name":"trajectory","type":"Mrd.TrajectoryData"}]},{"name":"AcquisitionData","type":{"array":{"items":"complexfloat32","dimensions":[{"name":"coils"},{"name":"samples"}]}}},{"name":"AcquisitionFlags","base":"uint64","values":[{"symbol":"firstInEncodeStep1","value":1},{"symbol":"lastInEncodeStep1","value":2},{"symbol":"firstInEncodeStep2","value":4},{"symbol":"lastInEncodeStep2","value":8},{"symbol":"firstInAverage","value":16},{"symbol":"lastInAverage","value":32},{"symbol":"firstInSlice","value":64},{"symbol":"lastInSlice","value":128},{"symbol":"firstInContrast","value":256},{"symbol":"lastInContrast","value":512},{"symbol":"firstInPhase","value":1024},{"symbol":"lastInPhase","value":2048},{"symbol":"firstInRepetition","value":4096},{"symbol":"lastInRepetition","value":8192},{"symbol":"firstInSet","value":16384},{"symbol":"lastInSet","value":32768},{"symbol":"firstInSegment","value":65536},{"symbol":"lastInSegment","value":131072},{"symbol":"isNoiseMeasurement","value":262144},{"symbol":"isParallelCalibration","value":524288},{"symbol":"isParallelCalibrationAndImaging","value":1048576},{"symbol":"isReverse","value":2097152},{"symbol":"isNavigationData","value":4194304},{"symbol":"isPhasecorrData","value":8388608},{"symbol":"lastInMeasurement","value":16777216},{"symbol":"isHpfeedbackData","value":33554432},{"symbol":"isDummyscanData","value":67108864},{"symbol":"isRtfeedbackData","value":134217728},{"symbol":"isSurfacecoilcorrectionscanData","value":268435456},{"symbol":"isPhaseStabilizationReference","value":536870912},{"symbol":"isPhaseStabilization","value":1073741824}]},{"name":"AcquisitionSystemInformationType","fields":[{"name":"systemVendor","type":[null,"string"]},{"name":"systemModel","type":[null,"string"]},{"name":"systemFieldStrengthT","type":[null,"float32"]},{"name":"relativeReceiverNoiseBandwidth","type":[null,"float32"]},{"name":"receiverChannels","type":[null,"uint32"]},{"name":"coilLabel","type":{"vector":{"items":"Mrd.CoilLabelType"}}},{"name":"institutionName","type":[null,"string"]},{"name":"stationName","type":[null,"string"]},{"name":"deviceID","type":[null,"string"]},{"name":"deviceSerialNumber","type":[null,"string"]}]},{"name":"Calibration","values":[{"symbol":"separable2D","value":0},{"symbol":"full3D","value":1},{"symbol":"other","value":2}]},{"name":"CalibrationMode","values":[{"symbol":"embedded","value":0},{"symbol":"interleaved","value":1},{"symbol":"separate","value":2},{"symbol":"external","value":3},{"symbol":"other","value":4}]},{"name":"CoilLabelType","fields":[{"name":"coilNumber","type":"uint32"},{"name":"coilName","type":"string"}]},{"name":"DiffusionDimension","values":[{"symbol":"average","value":0},{"symbol":"contrast","value":1},{"symbol":"phase","value":2},{"symbol":"repetition","value":3},{"symbol":"set","value":4},{"symbol":"segment","value":5},{"symbol":"user0","value":6},{"symbol":"user1","value":7},{"symbol":"user2","value":8},{"symbol":"user3","value":9},{"symbol":"user4","value":10},{"symbol":"user5","value":11},{"symbol":"user6","value":12},{"symbol":"user7","value":13}]},{"name":"DiffusionType","fields":[{"name":"gradientDirection","type":"Mrd.GradientDirectionType"},{"name":"bvalue","type":"float32"}]},{"name":"EncodingCounters","fields":[{"name":"kspaceEncodeStep1","type":[null,"uint32"]},{"name":"kspaceEncodeStep2","type":[null,"uint32"]},{"name":"average","type":[null,"uint32"]},{"name":"slice","type":[null,"uint32"]},{"name":"contrast","type":[null,"uint32"]},{"name":"phase","type":[null,"uint32"]},{"name":"repetition","type":[null,"uint32"]},{"name":"set","type":[null,"uint32"]},{"name":"segment","type":[null,"uint32"]},{"name":"user","type":{"vector":{"items":"uint32"}}}]},{"name":"EncodingLimitsType","fields":[{"name":"kspaceEncodingStep0","type":[null,"Mrd.LimitType"]},{"name":"kspaceEncodingStep1","type":[null,"Mrd.LimitType"]},{"name":"kspaceEncodingStep2","type":[null,"Mrd.LimitType"]},{"name":"average","type":[null,"Mrd.LimitType"]},{"name":"slice","type":[null,"Mrd.LimitType"]},{"name":"contrast","type":[null,"Mrd.LimitType"]},{"name":"phase","type":[null,"Mrd.LimitType"]},{"name":"repetition","type":[null,"Mrd.LimitType"]},{"name":"set","type":[null,"Mrd.LimitType"]},{"name":"segment","type":[null,"Mrd.LimitType"]},{"name":"user0","type":[null,"Mrd.LimitType"]},{"name":"user1","type":[null,"Mrd.LimitType"]},{"name":"user2","type":[null,"Mrd.LimitType"]},{"name":"user3","type":[null,"Mrd.LimitType"]},{"name":"user4","type":[null,"Mrd.LimitType"]},{"name":"user5","type":[null,"Mrd.LimitType"]},{"name":"user6","type":[null,"Mrd.LimitType"]},{"name":"user7","type":[null,"Mrd.LimitType"]}]},{"name":"EncodingSpaceType","fields":[{"name":"matrixSize","type":"Mrd.MatrixSizeType"},{"name":"fieldOfViewMm","type":"Mrd.FieldOfViewMm"}]},{"name":"EncodingType","fields":[{"name":"encodedSpace","type":"Mrd.EncodingSpaceType"},{"name":"reconSpace","type":"Mrd.EncodingSpaceType"},{"name":"encodingLimits","type":"Mrd.EncodingLimitsType"},{"name":"trajectory","type":"Mrd.Trajectory"},{"name":"trajectoryDescription","type":[null,"Mrd.TrajectoryDescriptionType"]},{"name":"parallelImaging","type":[null,"Mrd.ParallelImagingType"]},{"name":"echoTrainLength","type":[null,"int64"]}]},{"name":"ExperimentalConditionsType","fields":[{"name":"h1resonanceFrequencyHz","type":"int64"}]},{"name":"FieldOfViewMm","fields":[{"name":"x","type":"float32"},{"name":"y","type":"float32"},{"name":"z","type":"float32"}]},{"name":"GradientDirectionType","fields":[{"name":"rl","type":"float32"},{"name":"ap","type":"float32"},{"name":"fh","type":"float32"}]},{"name":"Header","fields":[{"name":"version","type":[null,"int64"]},{"name":"subjectInformation","type":[null,"Mrd.SubjectInformationType"]},{"name":"studyInformation","type":[null,"Mrd.StudyInformationType"]},{"name":"measurementInformation","type":[null,"Mrd.MeasurementInformationType"]},{"name":"acquisitionSystemInformation","type":[null,"Mrd.AcquisitionSystemInformationType"]},{"name":"experimentalConditions","type":"Mrd.ExperimentalConditionsType"},{"name":"encoding","type":{"vector":{"items":"Mrd.EncodingType"}}},{"name":"sequenceParameters","type":[null,"Mrd.SequenceParametersType"]},{"name":"userParameters","type":[null,"Mrd.UserParametersType"]},{"name":"waveformInformation","type":{"vector":{"items":"Mrd.WaveformInformationType"}}}]},{"name":"Image","typeParameters":["T"],"fields":[{"name":"flags","type":"Mrd.ImageFlags"},{"name":"measurementUid","type":"uint32"},{"name":"fieldOfView","type":{"array":{"items":"float32","dimensions":[{"length":3}]}}},{"name":"position","type":{"array":{"items":"float32","dimensions":[{"length":3}]}}},{"name":"colDir","type":{"array":{"items":"float32","dimensions":[{"length":3}]}}},{"name":"lineDir","type":{"array":{"items":"float32","dimensions":[{"length":3}]}}},{"name":"sliceDir","type":{"array":{"items":"float32","dimensions":[{"length":3}]}}},{"name":"patientTablePosition","type":{"array":{"items":"float32","dimensions":[{"length":3}]}}},{"name":"average","type":[null,"uint32"]},{"name":"slice","type":[null,"uint32"]},{"name":"contrast","type":[null,"uint32"]},{"name":"phase","type":[null,"uint32"]},{"name":"repetition","type":[null,"uint32"]},{"name":"set","type":[null,"uint32"]},{"name":"acquisitionTimeStamp","type":[null,"uint32"]},{"name":"physiologyTimeStamp","type":{"vector":{"items":"uint32"}}},{"name":"imageType","type":"Mrd.ImageType"},{"name":"imageIndex","type":[null,"uint32"]},{"name":"imageSeriesIndex","type":[null,"uint32"]},{"name":"userInt","type":{"vector":{"items":"int32"}}},{"name":"userFloat","type":{"vector":{"items":"float32"}}},{"name":"data","type":{"name":"Mrd.ImageData","typeArguments":["T"]}},{"name":"meta","type":{"map":{"keys":"string","values":{"vector":{"items":"string"}}}}}]},{"name":"ImageComplexDouble","type":{"name":"Mrd.Image","typeArguments":["complexfloat64"]}},{"name":"ImageComplexFloat","type":{"name":"Mrd.Image","typeArguments":["complexfloat32"]}},{"name":"ImageData","typeParameters":["Y"],"type":{"array":{"items":"Y","dimensions":[{"name":"channel"},{"name":"z"},{"name":"y"},{"name":"x"}]}}},{"name":"ImageDouble","type":{"name":"Mrd.Image","typeArguments":["float64"]}},{"name":"ImageFlags","base":"uint64","values":[{"symbol":"isNavigationData","value":1},{"symbol":"firstInAverage","value":16},{"symbol":"lastInAverage","value":32},{"symbol":"firstInSlice","value":64},{"symbol":"lastInSlice","value":128},{"symbol":"firstInContrast","value":256},{"symbol":"lastInContrast","value":512},{"symbol":"firstInPhase","value":1024},{"symbol":"lastInPhase","value":2048},{"symbol":"firstInRepetition","value":4096},{"symbol":"lastInRepetition","value":8192},{"symbol":"firstInSet","value":16384},{"symbol":"lastInSet","value":32768}]},{"name":"ImageFloat","type":{"name":"Mrd.Image","typeArguments":["float32"]}},{"name":"ImageInt","type":{"name":"Mrd.Image","typeArguments":["int32"]}},{"name":"ImageInt16","type":{"name":"Mrd.Image","typeArguments":["int16"]}},{"name":"ImageType","values":[{"symbol":"magnitude","value":1},{"symbol":"phase","value":2},{"symbol":"real","value":3},{"symbol":"imag","value":4},{"symbol":"complex","value":5}]},{"name":"ImageUint","type":{"name":"Mrd.Image","typeArguments":["uint32"]}},{"name":"ImageUint16","type":{"name":"Mrd.Image","typeArguments":["uint16"]}},{"name":"InterleavingDimension","values":[{"symbol":"phase","value":0},{"symbol":"repetition","value":1},{"symbol":"contrast","value":2},{"symbol":"average","value":3},{"symbol":"other","value":4}]},{"name":"LimitType","fields":[{"name":"minimum","type":"uint32"},{"name":"maximum","type":"uint32"},{"name":"center","type":"uint32"}]},{"name":"MatrixSizeType","fields":[{"name":"x","type":"uint32"},{"name":"y","type":"uint32"},{"name":"z","type":"uint32"}]},{"name":"MeasurementDependencyType","fields":[{"name":"dependencyType","type":"string"},{"name":"measurementID","type":"string"}]},{"name":"MeasurementInformationType","fields":[{"name":"measurementID","type":[null,"string"]},{"name":"seriesDate","type":[null,"date"]},{"name":"seriesTime","type":[null,"time"]},{"name":"patientPosition","type":"Mrd.PatientPosition"},{"name":"relativeTablePosition","type":[null,"Mrd.ThreeDimensionalFloat"]},{"name":"initialSeriesNumber","type":[null,"int64"]},{"name":"protocolName","type":[null,"string"]},{"name":"sequenceName","type":[null,"string"]},{"name":"seriesDescription","type":[null,"string"]},{"name":"measurementDependency","type":{"vector":{"items":"Mrd.MeasurementDependencyType"}}},{"name":"seriesInstanceUIDRoot","type":[null,"string"]},{"name":"frameOfReferenceUID","type":[null,"string"]},{"name":"referencedImageSequence","type":[null,"Mrd.ReferencedImageSequenceType"]}]},{"name":"MultibandSpacingType","fields":[{"name":"dZ","type":{"vector":{"items":"float32"}}}]},{"name":"MultibandType","fields":[{"name":"spacing","type":{"vector":{"items":"Mrd.MultibandSpacingType"}}},{"name":"deltaKz","type":"float32"},{"name":"multibandFactor","type":"uint32"},{"name":"calibration","type":"Mrd.Calibration"},{"name":"calibrationEncoding","type":"uint64"}]},{"name":"ParallelImagingType","fields":[{"name":"accelerationFactor","type":"Mrd.AccelerationFactorType"},{"name":"calibrationMode","type":[null,"Mrd.CalibrationMode"]},{"name":"interleavingDimension","type":[null,"Mrd.InterleavingDimension"]},{"name":"multiband","type":[null,"Mrd.MultibandType"]}]},{"name":"PatientGender","values":[{"symbol":"m","value":0},{"symbol":"f","value":1},{"symbol":"o","value":2}]},{"name":"PatientPosition","values":[{"symbol":"hFP","value":0},{"symbol":"hFS","value":1},{"symbol":"hFDR","value":2},{"symbol":"hFDL","value":3},{"symbol":"fFP","value":4},{"symbol":"fFS","value":5},{"symbol":"fFDR","value":6},{"symbol":"fFDL","value":7}]},{"name":"ReferencedImageSequenceType","fields":[{"name":"referencedSOPInstanceUID","type":{"vector":{"items":"string"}}}]},{"name":"SequenceParametersType","fields":[{"name":"tR","type":{"vector":{"items":"float32"}}},{"name":"tE","type":{"vector":{"items":"float32"}}},{"name":"tI","type":{"vector":{"items":"float32"}}},{"name":"flipAngleDeg","type":{"vector":{"items":"float32"}}},{"name":"sequenceType","type":[null,"string"]},{"name":"echoSpacing","type":{"vector":{"items":"float32"}}},{"name":"diffusionDimension","type":[null,"Mrd.DiffusionDimension"]},{"name":"diffusion","type":{"vector":{"items":"Mrd.DiffusionType"}}},{"name":"diffusionScheme","type":[null,"string"]}]},{"name":"StreamItem","type":[{"tag":"Acquisition","type":"Mrd.Acquisition"},{"tag":"WaveformUint32","type":"Mrd.WaveformUint32"},{"tag":"ImageUint16","type":"Mrd.ImageUint16"},{"tag":"ImageInt16","type":"Mrd.ImageInt16"},{"tag":"ImageUint","type":"Mrd.ImageUint"},{"tag":"ImageInt","type":"Mrd.ImageInt"},{"tag":"ImageFloat","type":"Mrd.ImageFloat"},{"tag":"ImageDouble","type":"Mrd.ImageDouble"},{"tag":"ImageComplexFloat","type":"Mrd.ImageComplexFloat"},{"tag":"ImageComplexDouble","type":"Mrd.ImageComplexDouble"}]},{"name":"StudyInformationType","fields":[{"name":"studyDate","type":[null,"date"]},{"name":"studyTime","type":[null,"time"]},{"name":"studyID","type":[null,"string"]},{"name":"accessionNumber","type":[null,"int64"]},{"name":"referringPhysicianName","type":[null,"string"]},{"name":"studyDescription","type":[null,"string"]},{"name":"studyInstanceUID","type":[null,"string"]},{"name":"bodyPartExamined","type":[null,"string"]}]},{"name":"SubjectInformationType","fields":[{"name":"patientName","type":[null,"string"]},{"name":"patientWeightKg","type":[null,"float32"]},{"name":"patientHeightM","type":[null,"float32"]},{"name":"patientID","type":[null,"string"]},{"name":"patientBirthdate","type":[null,"date"]},{"name":"patientGender","type":[null,"Mrd.PatientGender"]}]},{"name":"ThreeDimensionalFloat","fields":[{"name":"x","type":"float32"},{"name":"y","type":"float32"},{"name":"z","type":"float32"}]},{"name":"Trajectory","values":[{"symbol":"cartesian","value":0},{"symbol":"epi","value":1},{"symbol":"radial","value":2},{"symbol":"goldenangle","value":3},{"symbol":"spiral","value":4},{"symbol":"other","value":5}]},{"name":"TrajectoryData","type":{"array":{"items":"float32","dimensions":[{"name":"basis"},{"name":"samples"}]}}},{"name":"TrajectoryDescriptionType","fields":[{"name":"identifier","type":"string"},{"name":"userParameterLong","type":{"vector":{"items":"Mrd.UserParameterLongType"}}},{"name":"userParameterDouble","type":{"vector":{"items":"Mrd.UserParameterDoubleType"}}},{"name":"userParameterString","type":{"vector":{"items":"Mrd.UserParameterStringType"}}},{"name":"comment","type":[null,"string"]}]},{"name":"UserParameterBase64Type","fields":[{"name":"name","type":"string"},{"name":"value","type":"string"}]},{"name":"UserParameterDoubleType","fields":[{"name":"name","type":"string"},{"name":"value","type":"float64"}]},{"name":"UserParameterLongType","fields":[{"name":"name","type":"string"},{"name":"value","type":"int64"}]},{"name":"UserParameterStringType","fields":[{"name":"name","type":"string"},{"name":"value","type":"string"}]},{"name":"UserParametersType","fields":[{"name":"userParameterLong","type":{"vector":{"items":"Mrd.UserParameterLongType"}}},{"name":"userParameterDouble","type":{"vector":{"items":"Mrd.UserParameterDoubleType"}}},{"name":"userParameterString","type":{"vector":{"items":"Mrd.UserParameterStringType"}}},{"name":"userParameterBase64","type":{"vector":{"items":"Mrd.UserParameterBase64Type"}}}]},{"name":"Waveform","typeParameters":["T"],"fields":[{"name":"flags","type":"uint64"},{"name":"measurementUid","type":"uint32"},{"name":"scanCounter","type":"uint32"},{"name":"timeStamp","type":"uint32"},{"name":"sampleTimeUs","type":"float32"},{"name":"waveformId","type":"uint32"},{"name":"data","type":{"name":"Mrd.WaveformSamples","typeArguments":["T"]}}]},{"name":"WaveformInformationType","fields":[{"name":"waveformName","type":"string"},{"name":"waveformType","type":"Mrd.WaveformType"},{"name":"userParameters","type":"Mrd.UserParametersType"}]},{"name":"WaveformSamples","typeParameters":["T"],"type":{"array":{"items":"T","dimensions":[{"name":"channels"},{"name":"samples"}]}}},{"name":"WaveformType","values":[{"symbol":"ecg","value":0},{"symbol":"pulse","value":1},{"symbol":"respiratory","value":2},{"symbol":"trigger","value":3},{"symbol":"gradientwaveform","value":4},{"symbol":"other","value":5}]},{"name":"WaveformUint32","type":{"name":"Mrd.Waveform","typeArguments":["uint32"]}}]}"""
+
+    def close(self) -> None:
+        if self._state == 3:
+            try:
+                self._end_stream()
+                return
+            finally:
+                self._close()
+        self._close()
+        if self._state != 4:
+            expected_method = self._state_to_method_name((self._state + 1) & ~1)
+            raise ProtocolError(f"Protocol writer closed before all steps were called. Expected to call to '{expected_method}'.")
+
+    def __enter__(self):
+        return self
+
+    def __exit__(self, exc_type: typing.Optional[type[BaseException]], exc: typing.Optional[BaseException], traceback: object) -> None:
+        try:
+            self.close()
+        except Exception as e:
+            if exc is None:
+                raise e
+
+    def write_header(self, value: typing.Optional[Header]) -> None:
+        """Ordinal 0"""
+
+        if self._state != 0:
+            self._raise_unexpected_state(0)
+
+        self._write_header(value)
+        self._state = 2
+
+    def write_data(self, value: collections.abc.Iterable[StreamItem]) -> None:
+        """Ordinal 1"""
+
+        if self._state & ~1 != 2:
+            self._raise_unexpected_state(2)
+
+        self._write_data(value)
+        self._state = 3
+
+    @abc.abstractmethod
+    def _write_header(self, value: typing.Optional[Header]) -> None:
+        raise NotImplementedError()
+
+    @abc.abstractmethod
+    def _write_data(self, value: collections.abc.Iterable[StreamItem]) -> None:
+        raise NotImplementedError()
+
+    @abc.abstractmethod
+    def _close(self) -> None:
+        pass
+
+    @abc.abstractmethod
+    def _end_stream(self) -> None:
+        pass
+
+    def _raise_unexpected_state(self, actual: int) -> None:
+        expected_method = self._state_to_method_name(self._state)
+        actual_method = self._state_to_method_name(actual)
+        raise ProtocolError(f"Expected to call to '{expected_method}' but received call to '{actual_method}'.")
+
+    def _state_to_method_name(self, state: int) -> str:
+        if state == 0:
+            return 'write_header'
+        if state == 2:
+            return 'write_data'
+        return "<unknown>"
+
+class MrdReaderBase(abc.ABC):
+    """Abstract reader for the Mrd protocol."""
+
+
+    def __init__(self) -> None:
+        self._state = 0
+
+    def close(self) -> None:
+        self._close()
+        if self._state != 4:
+            if self._state % 2 == 1:
+                previous_method = self._state_to_method_name(self._state - 1)
+                raise ProtocolError(f"Protocol reader closed before all data was consumed. The iterable returned by '{previous_method}' was not fully consumed.")
+            else:
+                expected_method = self._state_to_method_name(self._state)
+                raise ProtocolError(f"Protocol reader closed before all data was consumed. Expected call to '{expected_method}'.")
+            	
+
+    schema = MrdWriterBase.schema
+
+    def __enter__(self):
+        return self
+
+    def __exit__(self, exc_type: typing.Optional[type[BaseException]], exc: typing.Optional[BaseException], traceback: object) -> None:
+        try:
+            self.close()
+        except Exception as e:
+            if exc is None:
+                raise e
+
+    @abc.abstractmethod
+    def _close(self) -> None:
+        raise NotImplementedError()
+
+    def read_header(self) -> typing.Optional[Header]:
+        """Ordinal 0"""
+
+        if self._state != 0:
+            self._raise_unexpected_state(0)
+
+        value = self._read_header()
+        self._state = 2
+        return value
+
+    def read_data(self) -> collections.abc.Iterable[StreamItem]:
+        """Ordinal 1"""
+
+        if self._state != 2:
+            self._raise_unexpected_state(2)
+
+        value = self._read_data()
+        self._state = 3
+        return self._wrap_iterable(value, 4)
+
+    def copy_to(self, writer: MrdWriterBase) -> None:
+        writer.write_header(self.read_header())
+        writer.write_data(self.read_data())
+
+    @abc.abstractmethod
+    def _read_header(self) -> typing.Optional[Header]:
+        raise NotImplementedError()
+
+    @abc.abstractmethod
+    def _read_data(self) -> collections.abc.Iterable[StreamItem]:
+        raise NotImplementedError()
+
+    T = typing.TypeVar('T')
+    def _wrap_iterable(self, iterable: collections.abc.Iterable[T], final_state: int) -> collections.abc.Iterable[T]:
+        yield from iterable
+        self._state = final_state
+
+    def _raise_unexpected_state(self, actual: int) -> None:
+        actual_method = self._state_to_method_name(actual)
+        if self._state % 2 == 1:
+            previous_method = self._state_to_method_name(self._state - 1)
+            raise ProtocolError(f"Received call to '{actual_method}' but the iterable returned by '{previous_method}' was not fully consumed.")
+        else:
+            expected_method = self._state_to_method_name(self._state)
+            raise ProtocolError(f"Expected to call to '{expected_method}' but received call to '{actual_method}'.")
+        	
+    def _state_to_method_name(self, state: int) -> str:
+        if state == 0:
+            return 'read_header'
+        if state == 2:
+            return 'read_data'
+        return "<unknown>"
+

mrd/tools/export_png_images.py

@@ -0,0 +1,39 @@
+import sys
+import argparse
+import numpy as np
+from PIL import Image
+
+import mrd
+
+
+def export(input, output):
+    with mrd.BinaryMrdReader(input) as r:
+        header = r.read_header()
+        image_count = 0
+        for item in r.read_data():
+            if not isinstance(item, mrd.StreamItem.ImageFloat):
+                raise RuntimeError("Stream must contain only floating point images")
+
+            image = item.value
+            image.data *= 255 / image.data.max()
+            pixels = image.data.astype(np.uint8)
+
+            for c in range(image.channels()):
+                for s in range(image.slices()):
+                    im = Image.fromarray(pixels[c, s, :, :], 'L')
+                    filename = f"{output}{image_count:04d}.png"
+                    im.save(filename, format='PNG')
+                    image_count += 1
+
+
+if __name__ == "__main__":
+    parser = argparse.ArgumentParser(description="Reconstructs an MRD stream")
+    parser.add_argument('-i', '--input', type=str, required=False,
+                        help="Input file (default stdin)")
+    parser.add_argument('-o', '--output-prefix', type=str, required=False,
+                        help="Output filename prefix", default="image_")
+    args = parser.parse_args()
+
+    input = open(args.input, "rb") if args.input is not None else sys.stdin.buffer
+
+    export(input, args.output_prefix)

mrd/tools/phantom.py

@@ -0,0 +1,161 @@
+import sys
+import argparse
+import numpy as np
+
+from typing import Generator
+
+import mrd
+from mrd.tools import simulation
+from mrd.tools.transform import image_to_kspace
+
+
+def generate(output_file, matrix, coils, oversampling, repetitions, noise_level):
+    output = sys.stdout.buffer
+    if output_file is not None:
+        output = output_file
+
+    nx = matrix
+    ny = matrix
+    nkx = oversampling * nx
+    nky = ny
+    fov = 300
+    slice_thickness = 5
+
+    h = mrd.Header()
+
+    s = mrd.SubjectInformationType()
+    s.patient_id = "1234BGVF"
+    s.patient_name = "John Doe"
+    h.subject_information = s
+
+    exp = mrd.ExperimentalConditionsType()
+    exp.h1resonance_frequency_hz = 128000000
+    h.experimental_conditions = exp
+
+    sys_info = mrd.AcquisitionSystemInformationType()
+    sys_info.receiver_channels = coils
+    h.acquisition_system_information = sys_info
+
+    e = mrd.EncodingSpaceType()
+    e.matrix_size = mrd.MatrixSizeType(x=nkx, y=nky, z=1)
+    e.field_of_view_mm = mrd.FieldOfViewMm(x=oversampling*fov, y=fov, z=slice_thickness)
+
+    r = mrd.EncodingSpaceType()
+    r.matrix_size = mrd.MatrixSizeType(x=nx, y=ny, z=1)
+    r.field_of_view_mm = mrd.FieldOfViewMm(x=fov, y=fov, z=slice_thickness)
+
+    limits1 = mrd.LimitType()
+    limits1.minimum = 0
+    limits1.center = round(ny / 2)
+    limits1.maximum = ny - 1
+
+    limits_rep = mrd.LimitType()
+    limits_rep.minimum = 0
+    limits_rep.center = round(repetitions / 2)
+    limits_rep.maximum = repetitions - 1
+
+    limits = mrd.EncodingLimitsType()
+    limits.kspace_encoding_step_1 = limits1
+    limits.repetition = limits_rep
+
+    enc = mrd.EncodingType()
+    enc.trajectory = mrd.Trajectory.CARTESIAN
+    enc.encoded_space = e
+    enc.recon_space = r
+    enc.encoding_limits = limits
+    h.encoding.append(enc)
+
+    phantom = generate_coil_kspace(matrix, coils, oversampling)
+
+    def generate_data() -> Generator[mrd.StreamItem, None, None]:
+        # We'll reuse this Acquisition object
+        acq = mrd.Acquisition()
+
+        acq.data.resize((coils, nkx))
+        acq.channel_order = list(range(coils))
+        acq.center_sample = round(nkx / 2)
+        acq.read_dir[0] = 1.0
+        acq.phase_dir[1] = 1.0
+        acq.slice_dir[2] = 1.0
+
+        scan_counter = 0
+
+        # Write out a few noise scans
+        for n in range(32):
+            noise = generate_noise((coils, nkx), noise_level)
+            # Here's where we would make the noise correlated
+            acq.scan_counter = scan_counter
+            scan_counter += 1
+            acq.flags = mrd.AcquisitionFlags.IS_NOISE_MEASUREMENT
+            acq.data[:] = noise
+            yield mrd.StreamItem.Acquisition(acq)
+
+        # Loop over the repetitions, add noise and serialize
+        # Simulating a T-SENSE type scan
+        for r in range(repetitions):
+            noise = generate_noise(phantom.shape, noise_level)
+            # Here's where we would make the noise correlated
+            kspace = phantom + noise
+
+            for line in range(nky):
+                acq.scan_counter = scan_counter
+                scan_counter += 1
+
+                acq.flags = mrd.AcquisitionFlags(0)
+                if line == 0:
+                    acq.flags |= mrd.AcquisitionFlags.FIRST_IN_ENCODE_STEP_1
+                    acq.flags |= mrd.AcquisitionFlags.FIRST_IN_SLICE
+                    acq.flags |= mrd.AcquisitionFlags.FIRST_IN_REPETITION
+                if line == nky - 1:
+                    acq.flags |= mrd.AcquisitionFlags.LAST_IN_ENCODE_STEP_1
+                    acq.flags |= mrd.AcquisitionFlags.LAST_IN_SLICE
+                    acq.flags |= mrd.AcquisitionFlags.LAST_IN_REPETITION
+
+                acq.idx.kspace_encode_step_1 = line
+                acq.idx.kspace_encode_step_2 = 0
+                acq.idx.slice = 0
+                acq.idx.repetition = r
+                acq.data[:] = kspace[:, 0, line, :]
+                yield mrd.StreamItem.Acquisition(acq)
+
+    with mrd.BinaryMrdWriter(output) as w:
+        w.write_header(h)
+        w.write_data(generate_data())
+
+
+def generate_noise(shape, noise_sigma, mean=0.0):
+    rng = np.random.default_rng()
+    noise = rng.normal(mean, noise_sigma, shape) + 1j * rng.normal(mean, noise_sigma, shape)
+    return noise.astype(np.complex64)
+
+def generate_coil_kspace(matrix_size, ncoils, oversampling):
+    phan = simulation.generate_shepp_logan_phantom(matrix_size)
+    coils = simulation.generate_birdcage_sensitivities(matrix_size, ncoils, 1.5)
+    coils = phan * coils
+    if oversampling > 1:
+        c = (0,0)
+        padding = round((oversampling * matrix_size - matrix_size) / 2)
+        coils = np.pad(coils, (c, c, c, (padding,padding)), mode='constant')
+    coils = image_to_kspace(coils, dim=(-1, -2)).astype(np.complex64)
+    return coils
+
+
+if __name__ == "__main__":
+    parser = argparse.ArgumentParser(description="Generates a phantom dataset in MRD format")
+    parser.add_argument('-o', '--output', type=str, required=False, help="Output file, defaults to stdout")
+    parser.add_argument('-m', '--matrix', type=int, required=False, help="Matrix size")
+    parser.add_argument('-c', '--coils', type=int, required=False, help="Number of coils")
+    parser.add_argument('-s', '--oversampling', type=int, required=False, help="Oversampling")
+    parser.add_argument('-r', '--repetitions', type=int, required=False, help="Number of repetitions")
+    # parser.add_argument('-a', '--acceleration', type=int, required=False, help="Acceleration", default=1)
+    parser.add_argument('-n', '--noise-level', type=float, required=False, help="Noise level")
+    parser.set_defaults(
+        output=None,
+        coils=8,
+        matrix=256,
+        oversampling=2,
+        repetitions=1,
+        noise_level=0.05
+    )
+    args = parser.parse_args()
+    generate(args.output, args.matrix, args.coils, args.oversampling, args.repetitions, args.noise_level)

mrd/tools/simulation.py

@@ -0,0 +1,173 @@
+"""
+Tools for generating coil sensitivities and phantoms
+"""
+import numpy as np
+from mrd.tools.transform import kspace_to_image, image_to_kspace
+
+
+def generate_shepp_logan_phantom(matrix_size) -> np.ndarray:
+    """Generates a modified Shepp Logan phantom with improved contrast"""
+    return generate_phantom(matrix_size, modified_shepp_logan_ellipses())
+
+
+def generate_phantom(matrix_size, ellipses):
+    """
+    Create a Shepp-Logan or modified Shepp-Logan phantom::
+
+        phantom (n = 256, phantom_type = 'Modified Shepp-Logan', ellipses = None)
+
+    Parameters
+    ----------
+    matrix_size: int
+        Size of imaging matrix in pixels
+
+    ellipses: list of PhantomEllipse
+        Custom set of ellipses to use.
+
+    Returns
+    -------
+    np.ndarray
+        Phantom image with shape (1, 1, matrix_size, matrix_size)
+
+    Notes
+    -----
+    The image bounding box in the algorithm is ``[-1, -1], [1, 1]``,
+    so the values of ``a``, ``b``, ``x0``, ``y0`` should all be specified with
+    respect to this box.
+
+    References:
+
+    Shepp, L. A.; Logan, B. F.; Reconstructing Interior Head Tissue
+    from X-Ray Transmissions, IEEE Transactions on Nuclear Science,
+    Feb. 1974, p. 232.
+
+    Toft, P.; "The Radon Transform - Theory and Implementation",
+    Ph.D. thesis, Department of Mathematical Modelling, Technical
+    University of Denmark, June 1996.
+    """
+    shape = (1, 1, matrix_size, matrix_size)
+    out = np.zeros(shape, dtype=np.complex64)
+    for e in ellipses:
+        for y in range(matrix_size):
+            y_co = (float(y) - (matrix_size >> 1))  / (matrix_size >> 1)
+            for x in range(matrix_size):
+                x_co = (float(x) - (matrix_size >> 1))  / (matrix_size >> 1)
+                if e.is_inside(x_co, y_co):
+                    out[0, 0, y, x] += e.get_amplitude() + 0.j
+    return out
+
+def generate_birdcage_sensitivities(matrix_size, ncoils, relative_radius=1.5) -> np.ndarray:
+    """Generates birdcage coil sensitivities.
+
+    This function is heavily inspired by the mri_birdcage.m Matlab script in
+    Jeff Fessler's IRT package: http://web.eecs.umich.edu/~fessler/code/
+
+    Parameters
+    ----------
+    matrix_size: int
+        Size of imaging matrix in pixels
+    ncoils: int
+        Number of simulated coils
+    relative_radius: float, optional
+        Relative radius of birdcage (default 1.5)
+
+    Returns
+    -------
+    np.ndarray
+        Birdcage coil sensitivities with shape (ncoils, 1, matrix_size, matrix_size)
+    """
+    shape = (ncoils, 1, matrix_size, matrix_size)
+    out = np.zeros(shape, dtype=np.complex64)
+    for c in range(ncoils):
+        coilx = relative_radius * np.cos(c * (2 * np.pi / ncoils))
+        coily = relative_radius * np.sin(c * (2 * np.pi / ncoils))
+        coil_phase = -1.0 * c * (2 * np.pi / ncoils)
+        for y in range(matrix_size):
+            y_co = (float(y) - (matrix_size >> 1)) / (matrix_size >> 1) - coily
+            for x in range(matrix_size):
+                x_co = (float(x) - (matrix_size >> 1)) / (matrix_size >> 1) - coilx
+                rr = np.sqrt(x_co * x_co + y_co * y_co)
+                phi = np.arctan2(x_co, -y_co) + coil_phase
+                out[c, 0, y, x] = complex(1 / rr * np.cos(phi), 1 / rr * np.sin(phi))
+    return out
+
+
+class PhantomEllipse:
+    """Ellipse object for phantom generation"""
+
+    def __init__(self, A, a, b, x0, y0, phi):
+        """Construct a PhantomEllipse
+
+        Parameters
+        ----------
+        A: float
+            Additive intensity of the ellipse.
+        a: float
+            Length of the major axis.
+        b: float
+            Length of the minor axis.
+        x0: float
+            Horizontal offset of the centre of the ellipse.
+        y0: float
+            Vertical offset of the centre of the ellipse.
+        phi: float
+            Counterclockwise rotation of the ellipse in degrees,
+            measured as the angle between the horizontal axis and
+            the ellipse major axis.
+        """
+        self.A = A
+        self.a = a
+        self.b = b
+        self.x0 = x0
+        self.y0 = y0
+        self.phi = phi
+
+    def is_inside(self, x, y):
+        """Determine whether an (x,y) coordinate is inside the ellipse"""
+        asq = self.a * self.a
+        bsq = self.b * self.b
+        phi = self.phi * np.pi / 180
+        x0 = x - self.x0
+        y0 = y - self.y0
+        cosp = np.cos(phi)
+        sinp = np.sin(phi)
+        return (
+            ((x0 * cosp + y0 * sinp) * (x0 * cosp + y0 * sinp)) / asq +
+            ((y0 * cosp - x0 * sinp) * (y0 * cosp - x0 * sinp)) / bsq
+            <= 1)
+
+    def get_amplitude(self):
+        return self.A
+
+
+def shepp_logan_ellipses():
+    """Standard head phantom, taken from Shepp & Logan"""
+    return [
+        PhantomEllipse(1.0, 0.6900, 0.9200, 0.00, 0.0000, 0.0),
+        PhantomEllipse(-0.98, 0.6624, 0.8740, 0.00, -0.0184, 0.0),
+        PhantomEllipse(-0.02, 0.1100, 0.3100, 0.22, 0.0000, -18.0),
+        PhantomEllipse(-0.02, 0.1600, 0.4100, -0.22, 0.0000, 18.0),
+        PhantomEllipse(0.01, 0.2100, 0.2500, 0.00, 0.3500, 0.0),
+        PhantomEllipse(0.01, 0.0460, 0.0460, 0.00, 0.1000, 0.0),
+        PhantomEllipse(0.01, 0.0460, 0.0460, 0.00, -0.1000, 0.0),
+        PhantomEllipse(0.01, 0.0460, 0.0230, -0.08, -0.6050, 0.0),
+        PhantomEllipse(0.01, 0.0230, 0.0230, 0.00, -0.6060, 0.0),
+        PhantomEllipse(0.01, 0.0230, 0.0460, 0.06, -0.6050, 0.0),
+    ]
+
+def modified_shepp_logan_ellipses():
+    """Modified version of Shepp & Logan's head phantom, adjusted to
+    improve contrast. Taken from Toft.
+    """
+    return [
+        PhantomEllipse(1.0, .6900, .9200, 0.00, 0.0000, 0.0),
+        PhantomEllipse(-0.8, .6624, .8740, 0.00, -0.0184, 0.0),
+        PhantomEllipse(-0.2, .1100, .3100, 0.22, 0.0000, -18.0),
+        PhantomEllipse(-0.2, .1600, .4100, -0.22, 0.0000, 18.0),
+        PhantomEllipse(0.1, .2100, .2500, 0.00, 0.3500, 0.0),
+        PhantomEllipse(0.1, .0460, .0460, 0.00, 0.1000, 0.0),
+        PhantomEllipse(0.1, .0460, .0460, 0.00, -0.1000, 0.0),
+        PhantomEllipse(0.1, .0460, .0230, -0.08, -0.6050, 0.0),
+        PhantomEllipse(0.1, .0230, .0230, 0.00, -0.6060, 0.0),
+        PhantomEllipse(0.1, .0230, .0460, 0.06, -0.6050, 0.0),
+    ]