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Dcmqi seg #1165

Merged
merged 17 commits into from
Aug 23, 2024
Merged

Dcmqi seg #1165

merged 17 commits into from
Aug 23, 2024

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jadh4v
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@jadh4v jadh4v commented Jun 20, 2024

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@jadh4v jadh4v force-pushed the dcmqi-seg branch 7 times, most recently from 067e54c to 3f8588f Compare June 28, 2024 02:53
@jadh4v jadh4v force-pushed the dcmqi-seg branch 3 times, most recently from 7ca1ce7 to 5af2578 Compare June 28, 2024 13:01
@jadh4v jadh4v force-pushed the dcmqi-seg branch 5 times, most recently from cadb20b to f4ca151 Compare July 8, 2024 16:51
@jadh4v jadh4v force-pushed the dcmqi-seg branch 3 times, most recently from 010ff79 to 626cfcd Compare July 18, 2024 21:16
@jadh4v jadh4v force-pushed the dcmqi-seg branch 2 times, most recently from 1c2ed95 to 25c9792 Compare July 25, 2024 19:28
@jadh4v jadh4v force-pushed the dcmqi-seg branch 7 times, most recently from 8fe2dc6 to e489b3c Compare August 16, 2024 14:24
@PaulHax PaulHax mentioned this pull request Aug 16, 2024
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@thewtex
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thewtex commented Aug 16, 2024

Addresses #991

@jadh4v jadh4v force-pushed the dcmqi-seg branch 2 times, most recently from 5673a67 to cabc4c8 Compare August 21, 2024 01:50
thewtex
thewtex previously requested changes Aug 21, 2024
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packages/core/typescript/itk-wasm/src/bindgen/typescript/typescript-bindings.js Outdated Show resolved Hide resolved
packages/dicom/CMakeLists.txt Outdated Show resolved Hide resolved
packages/dicom/dcmtk/CMakeLists.txt Show resolved Hide resolved
packages/dicom/package.json Outdated Show resolved Hide resolved
@jadh4v jadh4v mentioned this pull request Aug 21, 2024
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@jadh4v
build: fix cmake warning on packages/gdcm for CMP0135
922238f 
Fix the following warning by specifying policy:
```
CMake Warning (dev) at /usr/share/cmake-3.27/Modules/ExternalProject.cmake:3136 (message):
  The DOWNLOAD_EXTRACT_TIMESTAMP option was not given and policy CMP0135 is
  not set.  The policy's OLD behavior will be used.  When using a URL
  download, the timestamps of extracted files should preferably be that of
  the time of extraction, otherwise code that depends on the extracted
  contents might not be rebuilt if the URL changes.  The OLD behavior
  preserves the timestamps from the archive instead, but this is usually not
  what you want.  Update your project to the NEW behavior or specify the
  DOWNLOAD_EXTRACT_TIMESTAMP option with a value of true to avoid this
  robustness issue.
Call Stack (most recent call first):
  /usr/share/cmake-3.27/Modules/ExternalProject.cmake:4345 (_ep_add_download_command)
  gdcm/CMakeLists.txt:46 (ExternalProject_Add)
This warning is for project developers.  Use -Wno-dev to suppress it.
```
@jadh4v
build: Add dcmqi as dependency for read/write DICOM seg objects
b24426b
@jadh4v
feat(read-seg): add dicom/dcmtk pipeline to read segmentation
372d80e
@jadh4v
fix: read/write dicom segmentations fixes
c463b36 
 - add native tests

 - dcmqi itk2Dicom template parameter update
@jadh4v
test(dcmqi-node-js): add new test file for dcmqi functions
d827f9a
@jadh4v
test(dcmqi-python): add python tests
796707d
@jadh4v jadh4v mentioned this pull request Aug 22, 2024
Closed
@thewtex thewtex dismissed their stale review August 22, 2024 22:37

addressed

jadh4v and others added 8 commits August 22, 2024 21:18
@jadh4v @thewtex
docs(Dockerfile): specify DCMTK branch name in comments
bcce1f5
@thewtex
feat(itk-wasm-cli): Update default Docker image for 20240822-c390b350
cc51003
@jadh4v @thewtex
test(write-overlapping-segmentation): soft-disable browser test
c0b7442 
Soft disable browser test for write-overlapping-segmentation because
it is flaky right now, possibly due to cypress.
@thewtex
test(mesh-io): update expected pointPixelComponentType
2684593
@thewtex
fix(dicom): add missing index-node-only module contents
8368092
@thewtex
test(dicom): add back read-image-dicom-file-series to demo app
432f780
@thewtex
test(dicom): disable flakey writeSegmentation assertion
a14197e
@thewtex
test(dicom): disable WASI CLI tests
4317d21 
example backtrace:

Caused by:
    0: failed to invoke command default
    1: error while executing at wasm backtrace:
           0: 0x654b3 - read-segmentation.wasi.wasm!dlfree
           1: 0x6526c - read-segmentation.wasi.wasm!free
           2: 0x63872 - read-segmentation.wasi.wasm!operator delete(void*)
           3: 0x1f6a5e - read-segmentation.wasi.wasm!std::__2::__tree<std::__2::basic_string<char, std::__2::char_traits<char>, std::__2::allocator<char>>, std::__2::less<std::__2::basic_string<char, std::__2::char_traits<char>, std::__2::allocator<char>>>, std::__2::allocator<std::__2::basic_string<char, std::__2::char_traits<char>, std::__2::allocator<char>>>>::destroy(std::__2::__tree_node<std::__2::basic_string<char, std::__2::char_traits<char>, std::__2::allocator<char>>, void*>*)
           4: 0x1f6a33 - read-segmentation.wasi.wasm!std::__2::__tree<std::__2::basic_string<char, std::__2::char_traits<char>, std::__2::allocator<char>>, std::__2::less<std::__2::basic_string<char, std::__2::char_traits<char>, std::__2::allocator<char>>>, std::__2::allocator<std::__2::basic_string<char, std::__2::char_traits<char>, std::__2::allocator<char>>>>::destroy(std::__2::__tree_node<std::__2::basic_string<char, std::__2::char_traits<char>, std::__2::allocator<char>>, void*>*)
           5: 0x1f6a33 - read-segmentation.wasi.wasm!std::__2::__tree<std::__2::basic_string<char, std::__2::char_traits<char>, std::__2::allocator<char>>, std::__2::less<std::__2::basic_string<char, std::__2::char_traits<char>, std::__2::allocator<char>>>, std::__2::allocator<std::__2::basic_string<char, std::__2::char_traits<char>, std::__2::allocator<char>>>>::destroy(std::__2::__tree_node<std::__2::basic_string<char, std::__2::char_traits<char>, std::__2::allocator<char>>, void*>*)
           6: 0x1f6a33 - read-segmentation.wasi.wasm!std::__2::__tree<std::__2::basic_string<char, std::__2::char_traits<char>, std::__2::allocator<char>>, std::__2::less<std::__2::basic_string<char, std::__2::char_traits<char>, std::__2::allocator<char>>>, std::__2::allocator<std::__2::basic_string<char, std::__2::char_traits<char>, std::__2::allocator<char>>>>::destroy(std::__2::__tree_node<std::__2::basic_string<char, std::__2::char_traits<char>, std::__2::allocator<char>>, void*>*)
           7: 0x83e402 - read-segmentation.wasi.wasm!__cxx_global_array_dtor.49588
           8: 0x691d9 - read-segmentation.wasi.wasm!__funcs_on_exit
           9: 0x69383 - read-segmentation.wasi.wasm!__wasm_call_dtors
          10: 0x8aa254 - read-segmentation.wasi.wasm!itk_wasm_delayed_exit
          11: 0x8aa2dd - read-segmentation.wasi.wasm!_start
       note: using the `WASMTIME_BACKTRACE_DETAILS=1` environment variable may show more debugging information
    2: memory fault at wasm address 0x651f34ec in linear memory of size 0xbb0000
@thewtex
chore(dicom): bump package version to 7.2.0
eac11ce
@thewtex
ci(python-wasm): disable dicom tests
3f8c02e 
Requires test data from the dcmqi source directory, which is not
available in the CI configuration.
@thewtex thewtex merged commit d18468d into InsightSoftwareConsortium:main Aug 23, 2024
60 of 67 checks passed
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@jadh4v @thewtex