lp:ismrmrd

Author: Michael Hansen
Author Date: 2024-02-14 01:06:50 UTC

Fixed some conan issues

Author: gabuzi
Author Date: 2023-11-07 12:17:10 UTC

Fix argument name in matlab AcquisitionHeader.append() (#243)

Appending to an an acquisition header fails in matlab due to
a typo.

Co-authored-by: David Christoffer Hansen <dchansen@users.noreply.github.com>

Author: Michael Hansen
Author Date: 2023-10-30 21:36:48 UTC

PR comments

Author: David Christoffer Hansen
Author Date: 2023-03-03 13:22:17 UTC

Merge master into debian (#233)

* Add fixed PatientID and generated MeasurementID to header information in generate_cartesian_shepp_logan (#211)

* Add PatientID and random MeasurmentID to header

* Whitespace fixes

* Add header template option

* Update generate_cartesian_shepp_logan.cpp

* Reverting to non-template version with fixed PatientID and generated MeasurementID

* Update ismrmrd_windows_build.yml

Added boost-uuid to the windows test.

* Update CMakeLists.txt

Co-authored-by: David Christoffer Hansen <dchansen@users.noreply.github.com>

* Fixed missing flags in Matlab acquisition header (#212)

* Fixed missing flags in Matlab acquisition header

* Update AcquisitionHeader.m

* Update AcquisitionHeader.m

* Added userParameterString to trajectoryParams (#213)

* Fixed missing flags in Matlab acquisition header

* Added userParameterString to trajectoryParams

* Fixed ACQ bug

* Update CMakeLists.txt

* Conda build (#214)

* First working package build

* Added github workflow for conda packages

* Added build environment

* Fixes to pipeline

* Cleaned working directory

* Fixed phantom generator

* Fixed formatting

* Using matrix strategy

* Fixed YAML bug

Co-authored-by: Michael Hansen <mihansen@microsoft>

* Fix pipeline (#215)

Co-authored-by: Michael Hansen <mihansen@microsoft>

* Another pipeline fix (#216)

Co-authored-by: Michael Hansen <mihansen@microsoft>

* Added support for multiband slices. Added tests for the ISMRMRD header (#209)

* Added support for multiband slices. Added tests for the ISMRMRD header

* Added missing files

* Fixed a bug regarding protocolName

* Removed redundant declaration of EncodingLimits equality operator

* Cachced vcpkg deps

* Fixed float conversion

* Added binary cache

* Updated binary cache

* Updated binary cache

* Updated multiband and added xml tests

* Update xml version

* Added missing test dependency

* Updated multiband

* Updated testing

* Updated testing

* Removed unused variables

* Changed names of types to explicitly define precision

* Update CMakeLists.txt

* Changed Multiband to be part of parallelImaging

* Fixed serialization/deserialization bugs

* Added multiband factor

* Updated schema hash

* Updated multiband

* Removed diffusion

* Update CMakeLists.txt

* Fixed a bug where multiband_factor would be read incorrectly (#219)

* Serialization/Deserialization (#221)

* Added devcontainer

* Started work on serialization

* First draft of serialization and stream converters

* Added stream reconstruction example

* Updated environment to include boost

* Added command line arguments to stream tools and support for converting image series to streams

* Added some explanations to the serialization.h file

* Added basic serialization tests

* Adapted to virtualized interface and implemented e2e test

* Small cleanups and comments

* Fixed ignored return values in tests

* Fixing Mac and Windows build errors

* Fixed comment typo

* Fixes for build errors and code review

* Fixed more windows/mac build problems

* Fixed more windows/mac build problems (2)

* Fixed windows build issues

* Rework to fix compiler warnings

* Fixed bug in image deserialization, fixed EXPORT statement for Windows

* Some restructuring

* Removed unused variable

* Fixed exe detection on Windows

* Path separator for e2e tests

* Path changes for windows tests

* Trying a bash shell for Windows tests

* Fixed slashes in pipeline

* Some fixes for Windows tests

* Only disabling test on Windows run

* Running e3e tests on Windows

* Refactoring for file in and output

* stdin support in stream tools

* Added static asserts for ISMRMRD datatypes

* Removed unneeded formatting changes

* Added C++11 checks and some more layout checks

* Added checks for eof and bad on serialize and deserialize

* Rename Stream to StreamView

* Changed message ids to enum

* Added tests that use binary file intermediates for stream based reconstruction

* Checking that input stream is empty

* Better check for EOF

* Simplified interface for iostream wrappers

* Added serialization/deserialization of configfile, configtext, textmessage

* Added cast to avoid Windows build error

* PR feedback

* Added test to make sure we handle strings with null terminator when deserializing.

* Documentation rework (#210)

* Add ImageHeader flag defines for first/last images of each loop counter

* Initial rework of documentation

* Update index.rst

* Improve formatting of tables

* Update table formatting and overview

* Fix broken links and other cleanup

* Re-add building.md and remove duplicate filestorage.md

* Update streaming protocol to remove config echoing and make numbering consistent with diagram

* Remove null terminator from text sent in most MRD serialization

* Add offset values to fixed headers

* Remove duplicate table for WaveformHeader and correct the size

* Grammar fix

Co-authored-by: Michael Hansen <mihansen@microsoft.com>
Co-authored-by: David Christoffer Hansen <dchansen@users.noreply.github.com>

* Buffered reading and writing MRD files, resulting in 6x speedup on read and 4x on write (#223)

* Buffered reading from MRD file, resulting in 6x read speed

* Added check of the vcpkg version

* Converted to global file buffer for datasets. Not threadsafe, but neither is HDF5

* Adds support for diffusion (#220)

* Added diffusionScheme

* Fixed XML and XSD formatting

* Multiple boost versions (#224)

* Remove PugiXML sources from ISMRMRD and configure build to use system library. (#226)

* Add pugixml as a dependency to various environment configurations.

* Adding PugiXML package to CMake and Windows build, and configure build to use system PugiXML.

* Completely remove option to use locally-provided PugiXML, and there was no way to revert to system PugiXML when build RPMs for Fedora. Now - system-provided PugiXML is the only option.

* Increment patch version to note changes.

* Also need to update patch version for vcpkg for Ubuntu conda, CMake, and RPM builds.

* Fixed a bug where the diffusion header was not correctly read (#225)

Co-authored-by: Michael Hansen <mihansen@microsoft.com>

* Fixed an old reference to USE_SYSTEM_PUGIXML. (#228)

* always include stdint.h on Windows Visual Studio

remove obsolete code that tries to guess some typedefs for ints.

Fixes #217

* Fixed an old reference to USE_SYSTEM_PUGIXML. Removed a duplicate reference to multiband in the schema

* Updated version

* Update vcpkg.json

---------

Co-authored-by: Kris Thielemans <KrisThielemans@users.noreply.github.com>
Co-authored-by: Michael Hansen <mihansen@microsoft.com>
Co-authored-by: roopchansinghv <for_usenet@yahoo.com>

* Updating build docs to be consistent with removal of Pugixml sources from ISMRMRD (#229)

* Updating build docs to explicitly state Pugixml must now be installed externally, as ISMRMRD no longer includes a copy within its source code.

* Update dependency installation in documentation to match what's done in automated workflows.

---------

Co-authored-by: Andrew Dupuis <andrewpdupuis@gmail.com>
Co-authored-by: Michael Hansen <mihansen@microsoft.com>
Co-authored-by: Michael Hansen <mihansen@microsoft>
Co-authored-by: Kelvin Chow <kelvin.chow@gmail.com>
Co-authored-by: roopchansinghv <for_usenet@yahoo.com>
Co-authored-by: Kris Thielemans <KrisThielemans@users.noreply.github.com>

Author: Michael Hansen
Author Date: 2022-10-11 01:16:29 UTC

Work on E2E tests

Author: Michael Hansen
Author Date: 2022-10-07 21:26:49 UTC

Added basic serialization tests

Author: Michael Hansen
Author Date: 2022-08-09 16:00:03 UTC

Another fix for conda pipeline

Author: Michael Hansen
Author Date: 2022-08-08 21:29:04 UTC

Fixed YAML bug

Author: Michael Hansen
Author Date: 2022-03-05 00:11:26 UTC

Renamed some files that are in fact not tests

Author: Michael Hansen
Author Date: 2022-03-04 19:32:16 UTC

Reordered documentation TOC

Author: Michael Hansen
Author Date: 2021-02-18 15:05:18 UTC

Added STATUS back on FFTW3 find

Author: Michael Hansen
Author Date: 2021-02-16 21:19:33 UTC

Fixed case for PugiXML_Found

Author: Michael Hansen
Author Date: 2021-02-14 02:48:01 UTC

Added github actions build status

Author: Hui Xue
Author Date: 2019-01-08 15:22:58 UTC

add a member function to return all keys in a meta container

Author: Michael Hansen
Author Date: 2016-08-08 16:56:13 UTC

Merge pull request #69 from vadre/icp2

Icp2

Author: Michael Hansen
Author Date: 2016-08-08 16:56:13 UTC

Merge pull request #69 from vadre/icp2

Icp2

Author: Hui Xue
Author Date: 2016-06-03 21:48:30 UTC

fix a bug in serializing ismrmrd header

Author: Hui Xue
Author Date: 2015-05-09 13:39:51 UTC

update matlab functions

Author: Hui Xue
Author Date: 2015-05-09 13:39:51 UTC

update matlab functions