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diff --git a/python-panimg.spec b/python-panimg.spec new file mode 100644 index 0000000..cf567e4 --- /dev/null +++ b/python-panimg.spec @@ -0,0 +1,465 @@ +%global _empty_manifest_terminate_build 0 +Name: python-panimg +Version: 0.12.0 +Release: 1 +Summary: Conversion of medical images to MHA and TIFF. +License: Apache-2.0 +URL: https://github.com/DIAGNijmegen/rse-panimg +Source0: https://mirrors.aliyun.com/pypi/web/packages/1f/e3/9401ec58f8700a0d9bcbefa9be87ccfe226a6c65390834d7eacb0c1fb7b6/panimg-0.12.0.tar.gz +BuildArch: noarch + +Requires: python3-pydantic +Requires: python3-numpy +Requires: python3-SimpleITK +Requires: python3-pydicom +Requires: python3-Pillow +Requires: python3-openslide-python +Requires: python3-pyvips +Requires: python3-tifffile +Requires: python3-construct +Requires: python3-click +Requires: python3-pylibjpeg +Requires: python3-pylibjpeg-libjpeg +Requires: python3-pylibjpeg-openjpeg +Requires: python3-wsidicom +Requires: python3-imagecodecs + +%description +# panimg + +[](https://github.com/DIAGNijmegen/rse-panimg/actions/workflows/ci.yml?query=branch%3Amain) +[](https://pypi.org/project/panimg/) +[](https://pypi.org/project/panimg/) +[](https://github.com/psf/black) +[](https://zenodo.org/badge/latestdoi/344730308) + +**NOT FOR CLINICAL USE** + +Conversion of medical images to MHA and TIFF. +Requires Python 3.8, 3.9, 3.10 or 3.11. +`libvips-dev` and `libopenslide-dev` must be installed on your system. + +Under the hood we use: + +* `SimpleITK` +* `pydicom` +* `pylibjpeg` +* `Pillow` +* `openslide-python` +* `pyvips` +* `oct-converter` +* `wsidicom` + +## Usage + +`panimg` takes a directory and tries to convert the containing files to MHA or TIFF. +By default, it will try to convert files from subdirectories as well. +To only convert files in the top level directory, set `recurse_subdirectories` to `False`. +It will try several strategies for loading the contained files, and if an image is found it will output it to the output directory. +It will return a structure containing information about what images were produced, what images were used to form the new images, image metadata, and any errors from any of the strategies. + + +**NOTE: Alpha software, do not run this on directories you do not have a backup of.** + +```python +from pathlib import Path +from panimg import convert + +result = convert( + input_directory=Path("/path/to/files/"), + output_directory=Path("/where/files/will/go/"), +) +``` + +### Command Line Interface + +`panimg` is also accessible from the command line. +Install the package from pip as before, then you can use: + +**NOTE: Alpha software, do not run this on directories you do not have a backup of.** + +```shell +panimg convert /path/to/files/ /where/files/will/go/ +``` + +To access the help test you can use `panimg -h`. + +### Supported Formats + +| Input | Output | Strategy | Notes | +|-------------------------------------| --------| ---------- | -------------------------- | +| `.mha` | `.mha` | `metaio` | | +| `.mhd` with `.raw` or `.zraw` | `.mha` | `metaio` | | +| `.dcm` | `.mha` | `dicom` | | +| `.nii` | `.mha` | `nifti` | | +| `.nii.gz` | `.mha` | `nifti` | | +| `.nrrd` | `.mha` | `nrrd` | <sup>[1](#footnote1)</sup> | +| `.e2e` | `.mha` | `oct` | <sup>[2](#footnote2)</sup> | +| `.fds` | `.mha` | `oct` | <sup>[2](#footnote2)</sup> | +| `.fda` | `.mha` | `oct` | <sup>[2](#footnote2)</sup> | +| `.png` | `.mha` | `fallback` | <sup>[3](#footnote3)</sup> | +| `.jpeg` | `.mha` | `fallback` | <sup>[3](#footnote3)</sup> | +| `.tiff` | `.tiff` | `tiff` | | +| `.svs` (Aperio) | `.tiff` | `tiff` | | +| `.vms`, `.vmu`, `.ndpi` (Hamamatsu) | `.tiff` | `tiff` | | +| `.scn` (Leica) | `.tiff` | `tiff` | | +| `.mrxs` (MIRAX) | `.tiff` | `tiff` | | +| `.biff` (Ventana) | `.tiff` | `tiff` | | +| `.dcm` (DICOM-WSI) | `.tiff` | `tiff` | | + +<a name="footnote1">1</a>: Detached headers are not supported. + +<a name="footnote2">2</a>: Only OCT volume(s), no fundus image(s) will be extracted. + +<a name="footnote3">3</a>: 2D only, unitary dimensions + +#### Post Processors + +You can also define a set of post processors that will operate on each output file. +Post processors will not produce any new image entities, but rather add additional representations of an image, such as DZI or thumbnails. +We provide a `dzi_to_tiff` post processor that is enabled by default, which will produce a DZI file if it is able to. +To customise the post processors that run you can do this with + +```python +result = convert(..., post_processors=[...]) +``` + +You are able to run the post processors directly with + +```python +from panimg import post_process +from panimg.models import PanImgFile + +result = post_process(image_files={PanImgFile(...), ...}, post_processors=[...]) +``` + +#### Using Strategies Directly + +If you want to run a particular strategy directly which returns a generator of images for a set of files you can do this with + +```python +files = {f for f in Path("/foo/").glob("*.dcm") if f.is_file()} + +try: + for result in image_builder_dicom(files=files): + sitk_image = result.image + process(sitk_image) # etc. you can also look at result.name for the name of the file, + # and result.consumed_files to see what files were used for this image +except UnconsumedFilesException as e: + # e.errors is keyed with a Path to a file that could not be consumed, + # with a list of all the errors found with loading it, + # the user can then choose what to do with that information + ... +``` + + +%package -n python3-panimg +Summary: Conversion of medical images to MHA and TIFF. +Provides: python-panimg +BuildRequires: python3-devel +BuildRequires: python3-setuptools +BuildRequires: python3-pip +%description -n python3-panimg +# panimg + +[](https://github.com/DIAGNijmegen/rse-panimg/actions/workflows/ci.yml?query=branch%3Amain) +[](https://pypi.org/project/panimg/) +[](https://pypi.org/project/panimg/) +[](https://github.com/psf/black) +[](https://zenodo.org/badge/latestdoi/344730308) + +**NOT FOR CLINICAL USE** + +Conversion of medical images to MHA and TIFF. +Requires Python 3.8, 3.9, 3.10 or 3.11. +`libvips-dev` and `libopenslide-dev` must be installed on your system. + +Under the hood we use: + +* `SimpleITK` +* `pydicom` +* `pylibjpeg` +* `Pillow` +* `openslide-python` +* `pyvips` +* `oct-converter` +* `wsidicom` + +## Usage + +`panimg` takes a directory and tries to convert the containing files to MHA or TIFF. +By default, it will try to convert files from subdirectories as well. +To only convert files in the top level directory, set `recurse_subdirectories` to `False`. +It will try several strategies for loading the contained files, and if an image is found it will output it to the output directory. +It will return a structure containing information about what images were produced, what images were used to form the new images, image metadata, and any errors from any of the strategies. + + +**NOTE: Alpha software, do not run this on directories you do not have a backup of.** + +```python +from pathlib import Path +from panimg import convert + +result = convert( + input_directory=Path("/path/to/files/"), + output_directory=Path("/where/files/will/go/"), +) +``` + +### Command Line Interface + +`panimg` is also accessible from the command line. +Install the package from pip as before, then you can use: + +**NOTE: Alpha software, do not run this on directories you do not have a backup of.** + +```shell +panimg convert /path/to/files/ /where/files/will/go/ +``` + +To access the help test you can use `panimg -h`. + +### Supported Formats + +| Input | Output | Strategy | Notes | +|-------------------------------------| --------| ---------- | -------------------------- | +| `.mha` | `.mha` | `metaio` | | +| `.mhd` with `.raw` or `.zraw` | `.mha` | `metaio` | | +| `.dcm` | `.mha` | `dicom` | | +| `.nii` | `.mha` | `nifti` | | +| `.nii.gz` | `.mha` | `nifti` | | +| `.nrrd` | `.mha` | `nrrd` | <sup>[1](#footnote1)</sup> | +| `.e2e` | `.mha` | `oct` | <sup>[2](#footnote2)</sup> | +| `.fds` | `.mha` | `oct` | <sup>[2](#footnote2)</sup> | +| `.fda` | `.mha` | `oct` | <sup>[2](#footnote2)</sup> | +| `.png` | `.mha` | `fallback` | <sup>[3](#footnote3)</sup> | +| `.jpeg` | `.mha` | `fallback` | <sup>[3](#footnote3)</sup> | +| `.tiff` | `.tiff` | `tiff` | | +| `.svs` (Aperio) | `.tiff` | `tiff` | | +| `.vms`, `.vmu`, `.ndpi` (Hamamatsu) | `.tiff` | `tiff` | | +| `.scn` (Leica) | `.tiff` | `tiff` | | +| `.mrxs` (MIRAX) | `.tiff` | `tiff` | | +| `.biff` (Ventana) | `.tiff` | `tiff` | | +| `.dcm` (DICOM-WSI) | `.tiff` | `tiff` | | + +<a name="footnote1">1</a>: Detached headers are not supported. + +<a name="footnote2">2</a>: Only OCT volume(s), no fundus image(s) will be extracted. + +<a name="footnote3">3</a>: 2D only, unitary dimensions + +#### Post Processors + +You can also define a set of post processors that will operate on each output file. +Post processors will not produce any new image entities, but rather add additional representations of an image, such as DZI or thumbnails. +We provide a `dzi_to_tiff` post processor that is enabled by default, which will produce a DZI file if it is able to. +To customise the post processors that run you can do this with + +```python +result = convert(..., post_processors=[...]) +``` + +You are able to run the post processors directly with + +```python +from panimg import post_process +from panimg.models import PanImgFile + +result = post_process(image_files={PanImgFile(...), ...}, post_processors=[...]) +``` + +#### Using Strategies Directly + +If you want to run a particular strategy directly which returns a generator of images for a set of files you can do this with + +```python +files = {f for f in Path("/foo/").glob("*.dcm") if f.is_file()} + +try: + for result in image_builder_dicom(files=files): + sitk_image = result.image + process(sitk_image) # etc. you can also look at result.name for the name of the file, + # and result.consumed_files to see what files were used for this image +except UnconsumedFilesException as e: + # e.errors is keyed with a Path to a file that could not be consumed, + # with a list of all the errors found with loading it, + # the user can then choose what to do with that information + ... +``` + + +%package help +Summary: Development documents and examples for panimg +Provides: python3-panimg-doc +%description help +# panimg + +[](https://github.com/DIAGNijmegen/rse-panimg/actions/workflows/ci.yml?query=branch%3Amain) +[](https://pypi.org/project/panimg/) +[](https://pypi.org/project/panimg/) +[](https://github.com/psf/black) +[](https://zenodo.org/badge/latestdoi/344730308) + +**NOT FOR CLINICAL USE** + +Conversion of medical images to MHA and TIFF. +Requires Python 3.8, 3.9, 3.10 or 3.11. +`libvips-dev` and `libopenslide-dev` must be installed on your system. + +Under the hood we use: + +* `SimpleITK` +* `pydicom` +* `pylibjpeg` +* `Pillow` +* `openslide-python` +* `pyvips` +* `oct-converter` +* `wsidicom` + +## Usage + +`panimg` takes a directory and tries to convert the containing files to MHA or TIFF. +By default, it will try to convert files from subdirectories as well. +To only convert files in the top level directory, set `recurse_subdirectories` to `False`. +It will try several strategies for loading the contained files, and if an image is found it will output it to the output directory. +It will return a structure containing information about what images were produced, what images were used to form the new images, image metadata, and any errors from any of the strategies. + + +**NOTE: Alpha software, do not run this on directories you do not have a backup of.** + +```python +from pathlib import Path +from panimg import convert + +result = convert( + input_directory=Path("/path/to/files/"), + output_directory=Path("/where/files/will/go/"), +) +``` + +### Command Line Interface + +`panimg` is also accessible from the command line. +Install the package from pip as before, then you can use: + +**NOTE: Alpha software, do not run this on directories you do not have a backup of.** + +```shell +panimg convert /path/to/files/ /where/files/will/go/ +``` + +To access the help test you can use `panimg -h`. + +### Supported Formats + +| Input | Output | Strategy | Notes | +|-------------------------------------| --------| ---------- | -------------------------- | +| `.mha` | `.mha` | `metaio` | | +| `.mhd` with `.raw` or `.zraw` | `.mha` | `metaio` | | +| `.dcm` | `.mha` | `dicom` | | +| `.nii` | `.mha` | `nifti` | | +| `.nii.gz` | `.mha` | `nifti` | | +| `.nrrd` | `.mha` | `nrrd` | <sup>[1](#footnote1)</sup> | +| `.e2e` | `.mha` | `oct` | <sup>[2](#footnote2)</sup> | +| `.fds` | `.mha` | `oct` | <sup>[2](#footnote2)</sup> | +| `.fda` | `.mha` | `oct` | <sup>[2](#footnote2)</sup> | +| `.png` | `.mha` | `fallback` | <sup>[3](#footnote3)</sup> | +| `.jpeg` | `.mha` | `fallback` | <sup>[3](#footnote3)</sup> | +| `.tiff` | `.tiff` | `tiff` | | +| `.svs` (Aperio) | `.tiff` | `tiff` | | +| `.vms`, `.vmu`, `.ndpi` (Hamamatsu) | `.tiff` | `tiff` | | +| `.scn` (Leica) | `.tiff` | `tiff` | | +| `.mrxs` (MIRAX) | `.tiff` | `tiff` | | +| `.biff` (Ventana) | `.tiff` | `tiff` | | +| `.dcm` (DICOM-WSI) | `.tiff` | `tiff` | | + +<a name="footnote1">1</a>: Detached headers are not supported. + +<a name="footnote2">2</a>: Only OCT volume(s), no fundus image(s) will be extracted. + +<a name="footnote3">3</a>: 2D only, unitary dimensions + +#### Post Processors + +You can also define a set of post processors that will operate on each output file. +Post processors will not produce any new image entities, but rather add additional representations of an image, such as DZI or thumbnails. +We provide a `dzi_to_tiff` post processor that is enabled by default, which will produce a DZI file if it is able to. +To customise the post processors that run you can do this with + +```python +result = convert(..., post_processors=[...]) +``` + +You are able to run the post processors directly with + +```python +from panimg import post_process +from panimg.models import PanImgFile + +result = post_process(image_files={PanImgFile(...), ...}, post_processors=[...]) +``` + +#### Using Strategies Directly + +If you want to run a particular strategy directly which returns a generator of images for a set of files you can do this with + +```python +files = {f for f in Path("/foo/").glob("*.dcm") if f.is_file()} + +try: + for result in image_builder_dicom(files=files): + sitk_image = result.image + process(sitk_image) # etc. you can also look at result.name for the name of the file, + # and result.consumed_files to see what files were used for this image +except UnconsumedFilesException as e: + # e.errors is keyed with a Path to a file that could not be consumed, + # with a list of all the errors found with loading it, + # the user can then choose what to do with that information + ... +``` + + +%prep +%autosetup -n panimg-0.12.0 + +%build +%py3_build + +%install +%py3_install +install -d -m755 %{buildroot}/%{_pkgdocdir} +if [ -d doc ]; then cp -arf doc %{buildroot}/%{_pkgdocdir}; fi +if [ -d docs ]; then cp -arf docs %{buildroot}/%{_pkgdocdir}; fi +if [ -d example ]; then cp -arf example %{buildroot}/%{_pkgdocdir}; fi +if [ -d examples ]; then cp -arf examples %{buildroot}/%{_pkgdocdir}; fi +pushd %{buildroot} +if [ -d usr/lib ]; then + find usr/lib -type f -printf "\"/%h/%f\"\n" >> filelist.lst +fi +if [ -d usr/lib64 ]; then + find usr/lib64 -type f -printf "\"/%h/%f\"\n" >> filelist.lst +fi +if [ -d usr/bin ]; then + find usr/bin -type f -printf "\"/%h/%f\"\n" >> filelist.lst +fi +if [ -d usr/sbin ]; then + find usr/sbin -type f -printf "\"/%h/%f\"\n" >> filelist.lst +fi +touch doclist.lst +if [ -d usr/share/man ]; then + find usr/share/man -type f -printf "\"/%h/%f.gz\"\n" >> doclist.lst +fi +popd +mv %{buildroot}/filelist.lst . +mv %{buildroot}/doclist.lst . + +%files -n python3-panimg -f filelist.lst +%dir %{python3_sitelib}/* + +%files help -f doclist.lst +%{_docdir}/* + +%changelog +* Tue Jun 20 2023 Python_Bot <Python_Bot@openeuler.org> - 0.12.0-1 +- Package Spec generated |