Initial progress #6

dzenanz · 2022-08-30T21:22:05Z

No description provided.

The original is: 216_L2-2019_11_08-10_07_07-seq0-cropSmallRF.nrrd which is a cropped version of: M:\SonoVol\3D RF\2019_11_08\216_L2\B-Mode_3D Scan_2019_11_08-10_07_07\UnfusedRF-a0-seq.mha

dzenanz · 2022-08-30T21:23:36Z

TODO: try Unidata/netcdf-c#2492 here.

thewtex

Please get CI passing

thewtex · 2022-09-06T17:59:25Z

CMakeLists.txt

+#   GIT_REPOSITORY https://github.com/nih-at/libzip
+#   GIT_TAG        v1.9.2
+# )
+# FetchContent_MakeAvailable(libzip)


zstd FetchContent configuration is available here:

https://github.com/InsightSoftwareConsortium/itk-wasm/blob/206802d06015f3002fbb015673b693f90389f0c7/src/io/internal/pipelines/common/compress-stringify/BuildZstd.cmake

thewtex · 2022-09-09T16:18:53Z

CMakeLists.txt

+  It needs to be built of out source, and pointed to a certain ITK build.")
+endif()
+
+function(dump_cmake_variables)


remove debug code

thewtex · 2022-09-09T16:22:15Z

include/itkOMEZarrNGFFImageIO.h

+  /** Run-time type information (and related methods). */
+  itkTypeMacro(OMEZarrNGFFImageIO, ImageIOBase);
+
+  static constexpr unsigned MaximumDimension = 5; // OME-NGFF specifies up to 5D data


5 -> 4 ('c' is the channel / component)

thewtex · 2022-09-09T16:31:04Z

src/itkOMEZarrNGFFImageIO.cxx

+  int r;
+  netCDF_call(nc_create(getNCFilename(this->m_FileName), NC_CLOBBER, &m_NCID));
+
+  const std::vector<std::string> dimensionNames = { "c", "i", "j", "k", "t" };


i j k to x y z per OME-Zarr

thewtex · 2022-09-20T18:41:30Z

-- Building Shared Libraries: ON

We should turn off shared libraries if possible.

thewtex · 2022-09-20T18:42:26Z

Linux todo: use ITK's HDF5:

-- Linking against: hdf5_cpp-shared;hdf5-shared;/usr/lib/x86_64-linux-gnu/libm.so;itkzlib;/usr/lib/x86_64-linux-gnu/libzip.so;/usr/lib/x86_64-linux-gnu/libbz2.so;libcurl;/usr/lib/x86_64-linux-gnu/libxml2.so

thewtex · 2022-09-20T18:44:35Z

ZSTD Support: no

-> yes

https://open.cdash.org/build/8154414/configure

thewtex · 2022-09-20T18:46:46Z

CMake Error at CMakeLists.txt:55 (add_library):
add_library cannot create ALIAS target "ZLIB::ZLIB" because target
"itkzlib" is imported but not globally visible.

thewtex · 2022-09-20T18:51:21Z

For OpenSSL errors, try installing OpenSSL beforehand:

https://github.com/dockcross/dockcross/blob/96d87416f639af0204bdd42553e4b99315ca8476/imagefiles/build-and-install-openssl.sh

Maybe curl on Linux:

https://github.com/dockcross/dockcross/blob/96d87416f639af0204bdd42553e4b99315ca8476/imagefiles/build-and-install-curl.sh

CMake Error at CMakeLists.txt:103 (set_target_properties): set_target_properties can not be used on an ALIAS target.

InsightSoftwareConsortium/ITKModuleTemplate@a465e20

thewtex · 2022-10-04T14:24:16Z

CMakeLists.txt

 FetchContent_MakeAvailable(netCDF)
+set(CMAKE_CXX_FLAGS ${saved_CXX})
+set(CMAKE_C_FLAGS ${saved_C})


We can add warning exceptions here:

ITKIOOMEZarrNGFF/.github/workflows/build-test-package.yml

Lines 98 to 102 in 44f22e2

set(CTEST_CUSTOM_WARNING_EXCEPTION

\${CTEST_CUSTOM_WARNING_EXCEPTION}

# macOS Azure VM Warning

"ld: warning: text-based stub file"

)

dzenanz · 2022-12-27T22:44:35Z

Closing this PR, as I just pushed version ab1a5a4 to master which works fairly well.

dzenanz added 9 commits December 14, 2021 14:57

ENH: add xtensor-zarr as dependency

e975e71

ENH: remove auto-generated content placeholders

cfdcbcf

ENH: create small test image

37861d3

The original is: 216_L2-2019_11_08-10_07_07-seq0-cropSmallRF.nrrd which is a cropped version of: M:\SonoVol\3D RF\2019_11_08\216_L2\B-Mode_3D Scan_2019_11_08-10_07_07\UnfusedRF-a0-seq.mha

ENH: add actual ImageIO content based on IOScanco remote module

6c391ce

ENH: adapt everything to zarr except the IO implementation

bfad090

ENH: xtensor-zarr kind of works, but chokes on Zarr v2 inputs

8cd80bd

ENH: Started switching to netCDF's NCZarr

836bc13

ENH: Adding updated style configuration files

cc2955c

ENH: Code changes to switch from xtensor to netCDF

f7d3f56

dzenanz requested a review from thewtex August 30, 2022 21:22

dzenanz force-pushed the augustProgress branch 2 times, most recently from 78b5a26 to 9b49d76 Compare September 8, 2022 15:29

dzenanz added 7 commits September 8, 2022 11:32

ENH: Make the read/write unit test more general

8829f4f

STYLE: Change links from http into https

534ba21

WIP: Working on unit tests

749444f

ENH: specially handle .zip extension

f02f3ab

EHN: Support zarr v2 extension

6128d83

BUG: Post-test comparison was invoking this as a 6D image

623e6fe

ENH: Update tests to avoid currently unsupported zip format

60de2f7

dzenanz force-pushed the augustProgress branch from 9b49d76 to 60de2f7 Compare September 8, 2022 15:32

dzenanz mentioned this pull request Sep 9, 2022

NCZarr does not support reading of many zarr files Unidata/netcdf-c#2474

Open

thewtex requested changes Sep 9, 2022

View reviewed changes

dzenanz added 2 commits September 13, 2022 08:49

COMP: Linux typename compile fixes

38241d1

COMP: Handle older CMake versions gracefully via if(POLICY)

a30ceb0

WIP: debugging CI

1126a7d

dzenanz mentioned this pull request Sep 22, 2022

Fix Python build #7

Closed

dzenanz added 12 commits September 22, 2022 11:08

ENH: Add Python wrapping definition

60b3c85

COMP: Fix CMake error

9cd10ad

CMake Error at CMakeLists.txt:103 (set_target_properties): set_target_properties can not be used on an ALIAS target.

COMP: Explicitly declare dependence on HDF5

09fb2f3

ENH: Update CI to use latest version of ITK

936d6a0

ENH: Update CI in line with latest ITKModuleTemplate

49d9397

InsightSoftwareConsortium/ITKModuleTemplate@a465e20

ENH: Use .post3 Python wheels

035365e

COMP: Set BUILD_SHARED_LIBS just before fetching netCDF

7b3c43c

WIP: Disable Linux CI for testing Win and MacOS

293d6de

WIP: a commit to test the CI

b1eb00a

ENH: Define a CMake variable disabled in netCDF code

4ba0d98

ENH: Add Python tests

c4ed951

COMP: Disable netCDF warnings

5fca29b

thewtex reviewed Oct 4, 2022

View reviewed changes

dzenanz mentioned this pull request Dec 20, 2022

Clarifying questions regarding building xtensor-zarr xtensor-stack/xtensor-zarr#65

Open

dzenanz closed this Dec 27, 2022

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Initial progress #6

Initial progress #6

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dzenanz commented Dec 27, 2022

	set(CTEST_CUSTOM_WARNING_EXCEPTION
	\${CTEST_CUSTOM_WARNING_EXCEPTION}
	# macOS Azure VM Warning
	"ld: warning: text-based stub file"
	)

Initial progress #6

Initial progress #6

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