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Updated schema to the latest version from ISMRMRD #67

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Merged
dchansen merged 6 commits into from
May 1, 2023
Merged

Updated schema to the latest version from ISMRMRD #67

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baf08f2
Updated schema
dchansen Mar 23, 2023
8829b40
Updated xsdata requirements
dchansen Mar 27, 2023
fb01240
Updated conda
dchansen Mar 27, 2023
043a890
Update meta.yaml
dchansen Mar 28, 2023
8c99617
Update meta.yaml
dchansen Apr 24, 2023
e51e909
Update build.sh
dchansen Apr 24, 2023
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1 change: 0 additions & 1 deletion conda/build.sh
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Original file line number Diff line number Diff line change
@@ -1,5 +1,4 @@
#!/bin/bash

set -euo pipefail

pip install .
4 changes: 3 additions & 1 deletion conda/meta.yaml
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Expand Up @@ -13,13 +13,15 @@ requirements:
- numpy>=1.22.0
- h5py>=2.3
- nose>=1.0
- docformatter<=1.4
- xsdata>=22.2

run:
- python
- xsdata>=22.2
- numpy>=1.22.0
- h5py>=2.3
- xsdata>=22.2

test:
source_files:
Expand All @@ -35,4 +37,4 @@ about:
Python interface and utilities for the ISMRM Raw Data (ISMRMRD a.k.a. MRD) format.
dev_url: https://github.com/ismrmrd/ismrmrd-python
doc_url: https://github.com/ismrmrd/ismrmrd-python
doc_source_url: https://github.com/ismrmrd/ismrmrd-python/blob/main/README.md
doc_source_url: https://github.com/ismrmrd/ismrmrd-python/blob/main/README.md
82 changes: 58 additions & 24 deletions schema/ismrmrd.xsd
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Expand Up @@ -22,7 +22,7 @@
<xs:all>
<xs:element minOccurs="0" name="patientName" type="xs:string" />
<xs:element minOccurs="0" name="patientWeight_kg" type="xs:float" />
<xs:element minOccurs="0" name="patientHeight_m" type="xs:float"/>
<xs:element minOccurs="0" name="patientHeight_m" type="xs:float" />
<xs:element minOccurs="0" name="patientID" type="xs:string" />
<xs:element minOccurs="0" name="patientBirthdate" type="xs:date" />
<xs:element minOccurs="0" name="patientGender">
Expand Down Expand Up @@ -67,7 +67,7 @@
<xs:element minOccurs="0" name="seriesDate" type="xs:date" />
<xs:element minOccurs="0" name="seriesTime" type="xs:time" />
<xs:element minOccurs="1" name="patientPosition" type="patientPositionType" />
<xs:element minOccurs="0" name="relativeTablePosition" type="threeDimensionalFloatType" />
<xs:element minOccurs="0" name="relativeTablePosition" type="threeDimensionalFloat" />
<xs:element minOccurs="0" name="initialSeriesNumber" type="xs:long" />
<xs:element minOccurs="0" name="protocolName" type="xs:string" />
<xs:element minOccurs="0" name="sequenceName" type="xs:string" />
Expand Down Expand Up @@ -123,7 +123,6 @@
<xs:element maxOccurs="1" minOccurs="0" name="trajectoryDescription" type="trajectoryDescriptionType" />
<xs:element maxOccurs="1" minOccurs="0" name="parallelImaging" type="parallelImagingType" />
<xs:element maxOccurs="1" minOccurs="0" name="echoTrainLength" type="xs:long" />
<xs:element maxOccurs="1" minOccurs="0" name="multiband" type="multibandType"/>
</xs:all>
</xs:complexType>

Expand All @@ -134,13 +133,6 @@
</xs:all>
</xs:complexType>

<xs:complexType name="multibandType">
<xs:sequence>
<xs:element maxOccurs="unbounded" minOccurs="1" name="spacing" type="xs:float"/>
<xs:element name="phaseShift" type="xs:float"/>
</xs:sequence>
</xs:complexType>

<xs:complexType name="matrixSizeType">
<xs:sequence>
<xs:element default="1" maxOccurs="1" minOccurs="1" name="x" type="xs:unsignedShort" />
Expand Down Expand Up @@ -174,14 +166,6 @@
</xs:all>
</xs:complexType>

<xs:complexType name="threeDimensionalFloatType">
<xs:sequence>
<xs:element maxOccurs="1" minOccurs="1" name="x" type="xs:float" />
<xs:element maxOccurs="1" minOccurs="1" name="y" type="xs:float" />
<xs:element maxOccurs="1" minOccurs="1" name="z" type="xs:float" />
</xs:sequence>
</xs:complexType>

<xs:complexType name="encodingLimitsType">
<xs:all>
<xs:element maxOccurs="1" minOccurs="0" name="kspace_encoding_step_0" type="limitType" />
Expand Down Expand Up @@ -221,6 +205,7 @@
<xs:element maxOccurs="1" minOccurs="1" name="identifier" type="xs:string" />
<xs:element maxOccurs="unbounded" minOccurs="0" name="userParameterLong" type="userParameterLongType" />
<xs:element maxOccurs="unbounded" minOccurs="0" name="userParameterDouble" type="userParameterDoubleType" />
<xs:element maxOccurs="unbounded" minOccurs="0" name="userParameterString" type="userParameterStringType" />
<xs:element maxOccurs="1" minOccurs="0" name="comment" type="xs:string" />
</xs:sequence>
</xs:complexType>
Expand All @@ -233,22 +218,44 @@
<xs:element minOccurs="0" maxOccurs="unbounded" type="xs:float" name="flipAngle_deg" />
<xs:element minOccurs="0" maxOccurs="1" type="xs:string" name="sequence_type" />
<xs:element minOccurs="0" maxOccurs="unbounded" type="xs:float" name="echo_spacing" />
<xs:element minOccurs="0" maxOccurs="unbounded" type="diffusionType" name="diffusion"/>
<xs:element minOccurs="0" maxOccurs="1" type="diffusionDimensionType" name="diffusionDimension" />
<xs:element minOccurs="0" maxOccurs="unbounded" type="diffusionType" name="diffusion" />
<xs:element minOccurs="0" maxOccurs="1" type="xs:string" name="diffusionScheme" />
</xs:sequence>
</xs:complexType>

<xs:complexType name="diffusionType">
<xs:sequence>
<xs:element type="gradientDirectionType" name="gradientDirection" />
<xs:element type="xs:float" name="bvalue"/>
<xs:element type="xs:float" name="bvalue" />
</xs:sequence>
</xs:complexType>


<xs:simpleType name="diffusionDimensionType">
<xs:restriction base="xs:string">
<xs:enumeration value="average" />
<xs:enumeration value="contrast" />
<xs:enumeration value="phase" />
<xs:enumeration value="repetition" />
<xs:enumeration value="set" />
<xs:enumeration value="segment" />
<xs:enumeration value="user_0" />
<xs:enumeration value="user_1" />
<xs:enumeration value="user_2" />
<xs:enumeration value="user_3" />
<xs:enumeration value="user_4" />
<xs:enumeration value="user_5" />
<xs:enumeration value="user_6" />
<xs:enumeration value="user_7" />
</xs:restriction>
</xs:simpleType>

<xs:complexType name="gradientDirectionType">
<xs:all>
<xs:element type="xs:float" name="rl"/>
<xs:element type="xs:float" name="ap"/>
<xs:element type="xs:float" name="fh"/>
<xs:element type="xs:float" name="rl" />
<xs:element type="xs:float" name="ap" />
<xs:element type="xs:float" name="fh" />
</xs:all>
</xs:complexType>

Expand Down Expand Up @@ -295,6 +302,32 @@
</xs:sequence>
</xs:complexType>


<xs:complexType name="multibandType">
<xs:sequence>
<xs:element maxOccurs="unbounded" minOccurs="1" name="spacing" type="multibandSpacingType" />
<xs:element name="deltaKz" minOccurs="1" maxOccurs="1" type="xs:float" />
<xs:element name="multiband_factor" minOccurs="1" maxOccurs="1" type="xs:unsignedInt" />
<xs:element name="calibration" minOccurs="1" maxOccurs="1" type="multibandCalibrationType" />
<xs:element name="calibration_encoding" minOccurs="1" maxOccurs="1" type="xs:unsignedLong" />
</xs:sequence>
</xs:complexType>

<xs:complexType name="multibandSpacingType">
<xs:sequence>
<xs:element maxOccurs="unbounded" minOccurs="1" name="dZ" type="xs:float" />
</xs:sequence>
</xs:complexType>

<xs:simpleType name="multibandCalibrationType">
<xs:restriction base="xs:string">
<xs:enumeration value="separable2D" />
<xs:enumeration value="full3D" />
<xs:enumeration value="other" />
</xs:restriction>
</xs:simpleType>


<xs:complexType name="accelerationFactorType">
<xs:all>
<xs:element name="kspace_encoding_step_1" type="xs:unsignedShort" />
Expand Down Expand Up @@ -327,6 +360,7 @@
<xs:element type="accelerationFactorType" name="accelerationFactor" />
<xs:element maxOccurs="1" minOccurs="0" type="calibrationModeType" name="calibrationMode" />
<xs:element maxOccurs="1" minOccurs="0" type="interleavingDimensionType" name="interleavingDimension" />
<xs:element maxOccurs="1" minOccurs="0" type="multibandType" name="multiband" />
</xs:sequence>
</xs:complexType>

Expand All @@ -349,4 +383,4 @@
<xs:element name="userParameters" type="userParametersType" />
</xs:sequence>
</xs:complexType>
</xs:schema>
</xs:schema>
6 changes: 3 additions & 3 deletions setup.py
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Expand Up @@ -58,7 +58,7 @@ def to_uri(filename):

setup(
name='ismrmrd',
version='1.13.1',
version='1.14.0',
author='ISMRMRD Developers',
description='Python implementation of the ISMRMRD',
license='Public Domain',
Expand All @@ -74,8 +74,8 @@ def to_uri(filename):
'Operating System :: OS Independent',
'Topic :: Scientific/Engineering :: Medical Science Apps.'
],
install_requires=['xsdata>=22.2', 'numpy>=1.22.0', 'h5py>=2.3'],
setup_requires=['nose>=1.0', 'xsdata[cli]>=22.2', 'jinja2 >= 2.11'],
install_requires=['xsdata>=22.12', 'numpy>=1.22.0', 'h5py>=2.3'],
setup_requires=['nose>=1.0', 'xsdata[cli]>=22.12', 'jinja2 >= 2.11'],
test_suite='nose.collector',
cmdclass={'build_py':my_build_py}
)