automatic import of python-zmesh

3 files changed, 386 insertions, 0 deletions

diff --git a/.gitignore b/.gitignore
index e69de29..97ddd2d 100644
--- a/.gitignore
+++ b/.gitignore
@@ -0,0 +1 @@
+/zmesh-1.6.2.tar.gz
diff --git a/python-zmesh.spec b/python-zmesh.spec
new file mode 100644
index 0000000..e4399c5
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+%global _empty_manifest_terminate_build 0
+Name:		python-zmesh
+Version:	1.6.2
+Release:	1
+Summary:	Multilabel marching cubes and simplification of volumetric data.
+License:	GPLv3+
+URL:		https://github.com/seung-lab/zmesh/
+Source0:	https://mirrors.nju.edu.cn/pypi/web/packages/f8/4d/3be291deda3cadf04fc346b52cc1ff12e7f5b8d1d9716ffbb0edf91a4ced/zmesh-1.6.2.tar.gz
+
+Requires:	python3-numpy
+
+%description
+## zmesh: Multi-Label Marching Cubes & Mesh Simplification
+[![Tests](https://github.com/seung-lab/zmesh/actions/workflows/test.yml/badge.svg?branch=master)](https://github.com/seung-lab/zmesh/actions/workflows/test.yml) [![PyPI version](https://badge.fury.io/py/zmesh.svg)](https://badge.fury.io/py/zmesh)  
+
+```python
+from zmesh import Mesher
+
+labels = ... # some dense volumetric labeled image
+mesher = Mesher( (4,4,40) ) # anisotropy of image
+
+# initial marching cubes pass
+# close controls whether meshes touching
+# the image boundary are left open or closed
+mesher.mesh(labels, close=False) 
+
+meshes = []
+for obj_id in mesher.ids():
+  meshes.append(
+    mesher.get_mesh(
+      obj_id, 
+      normals=False, # whether to calculate normals or not
+
+      # tries to reduce triangles by this factor
+      # 0 disables simplification
+      simplification_factor=100, 
+
+      # Max tolerable error in physical distance
+      max_simplification_error=8,
+      # whether meshes should be centered in the voxel
+      # on (0,0,0) [False] or (0.5,0.5,0.5) [True]
+      voxel_centered=False, 
+    )
+  )
+  mesher.erase(obj_id) # delete high res mesh
+
+mesher.clear() # clear memory retained by mesher
+
+mesh = meshes[0]
+mesh = mesher.simplify(
+  mesh, 
+  # same as simplification_factor in get_mesh
+  reduction_factor=100, 
+  # same as max_simplification_error in get_mesh
+  max_error=40, 
+  compute_normals=False, # whether to also compute face normals
+) # apply simplifier to a pre-existing mesh
+
+# compute normals without simplifying
+mesh = mesher.compute_normals(mesh) 
+
+mesh.vertices
+mesh.faces 
+mesh.normals
+mesh.triangles() # compute triangles from vertices and faces
+
+# Extremely common obj format
+with open('iconic_doge.obj', 'wb') as f:
+  f.write(mesh.to_obj())
+
+# Common binary format
+with open('iconic_doge.ply', 'wb') as f:
+  f.write(mesh.to_ply())
+
+# Neuroglancer Precomputed format
+with open('10001001:0', 'wb') as f:
+  f.write(mesh.to_precomputed())
+```
+
+## Installation 
+
+If binaries are not available for your system, ensure you have a C++ compiler installed.
+
+```bash
+pip install zmesh
+```
+
+## Performance Tuning & Notes
+
+- The mesher will consume about double memory in 64 bit mode if the size of the 
+object exceeds <1023, 1023, 511> on the x, y, or z axes. This is due to a limitation 
+of the 32-bit format. 
+- The mesher is ambidextrous, it can handle C or Fortran order arrays.
+- The maximum vertex range supported `.simplify` after converting to voxel space is 2<sup>20</sup> (appx. 1M) due to the packed 64-bit vertex format.
+- There is a longstanding design flaw in `cMesher.hpp` that transposes the returned mesh and resolution. We're working on a backwards compatible solution. That's why you need to do `mesher.mesh(data.T)`.
+
+## Related Projects 
+
+- [zi_lib](https://github.com/zlateski/zi_lib) - zmesh makes heavy use of Aleks' C++ library.
+- [Igneous](https://github.com/seung-lab/igneous) - Visualization of connectomics data using cloud computing.
+
+## Credits
+
+Thanks to Aleks Zlateski for creating and sharing this beautiful mesher.  
+
+Later changes by Will Silversmith, Nico Kemnitz, and Jingpeng Wu. 
+
+## References  
+
+1. W. Lorensen and H. Cline. "Marching Cubes: A High Resolution 3D Surface Construction Algorithm". pp 163-169. Computer Graphics, Volume 21, Number 4, July 1987. ([link](https://people.eecs.berkeley.edu/~jrs/meshpapers/LorensenCline.pdf))  
+2. M. Garland and P. Heckbert. "Surface simplification using quadric error metrics". SIGGRAPH '97: Proceedings of the 24th annual conference on Computer graphics and interactive techniques. Pages 209–216. August 1997. doi: 10.1145/258734.258849 ([link](https://mgarland.org/files/papers/quadrics.pdf))  
+3. H. Hoppe. "New Quadric Metric for Simplifying Meshes with Appearance Attributes". IEEE Visualization 1999 Conference. pp. 59-66. doi: 10.1109/VISUAL.1999.809869 ([link](http://hhoppe.com/newqem.pdf))
+
+
+
+
+
+%package -n python3-zmesh
+Summary:	Multilabel marching cubes and simplification of volumetric data.
+Provides:	python-zmesh
+BuildRequires:	python3-devel
+BuildRequires:	python3-setuptools
+BuildRequires:	python3-pip
+BuildRequires:	python3-cffi
+BuildRequires:	gcc
+BuildRequires:	gdb
+%description -n python3-zmesh
+## zmesh: Multi-Label Marching Cubes &amp; Mesh Simplification
+[![Tests](https://github.com/seung-lab/zmesh/actions/workflows/test.yml/badge.svg?branch=master)](https://github.com/seung-lab/zmesh/actions/workflows/test.yml) [![PyPI version](https://badge.fury.io/py/zmesh.svg)](https://badge.fury.io/py/zmesh)  
+
+```python
+from zmesh import Mesher
+
+labels = ... # some dense volumetric labeled image
+mesher = Mesher( (4,4,40) ) # anisotropy of image
+
+# initial marching cubes pass
+# close controls whether meshes touching
+# the image boundary are left open or closed
+mesher.mesh(labels, close=False) 
+
+meshes = []
+for obj_id in mesher.ids():
+  meshes.append(
+    mesher.get_mesh(
+      obj_id, 
+      normals=False, # whether to calculate normals or not
+
+      # tries to reduce triangles by this factor
+      # 0 disables simplification
+      simplification_factor=100, 
+
+      # Max tolerable error in physical distance
+      max_simplification_error=8,
+      # whether meshes should be centered in the voxel
+      # on (0,0,0) [False] or (0.5,0.5,0.5) [True]
+      voxel_centered=False, 
+    )
+  )
+  mesher.erase(obj_id) # delete high res mesh
+
+mesher.clear() # clear memory retained by mesher
+
+mesh = meshes[0]
+mesh = mesher.simplify(
+  mesh, 
+  # same as simplification_factor in get_mesh
+  reduction_factor=100, 
+  # same as max_simplification_error in get_mesh
+  max_error=40, 
+  compute_normals=False, # whether to also compute face normals
+) # apply simplifier to a pre-existing mesh
+
+# compute normals without simplifying
+mesh = mesher.compute_normals(mesh) 
+
+mesh.vertices
+mesh.faces 
+mesh.normals
+mesh.triangles() # compute triangles from vertices and faces
+
+# Extremely common obj format
+with open('iconic_doge.obj', 'wb') as f:
+  f.write(mesh.to_obj())
+
+# Common binary format
+with open('iconic_doge.ply', 'wb') as f:
+  f.write(mesh.to_ply())
+
+# Neuroglancer Precomputed format
+with open('10001001:0', 'wb') as f:
+  f.write(mesh.to_precomputed())
+```
+
+## Installation 
+
+If binaries are not available for your system, ensure you have a C++ compiler installed.
+
+```bash
+pip install zmesh
+```
+
+## Performance Tuning & Notes
+
+- The mesher will consume about double memory in 64 bit mode if the size of the 
+object exceeds <1023, 1023, 511> on the x, y, or z axes. This is due to a limitation 
+of the 32-bit format. 
+- The mesher is ambidextrous, it can handle C or Fortran order arrays.
+- The maximum vertex range supported `.simplify` after converting to voxel space is 2<sup>20</sup> (appx. 1M) due to the packed 64-bit vertex format.
+- There is a longstanding design flaw in `cMesher.hpp` that transposes the returned mesh and resolution. We're working on a backwards compatible solution. That's why you need to do `mesher.mesh(data.T)`.
+
+## Related Projects 
+
+- [zi_lib](https://github.com/zlateski/zi_lib) - zmesh makes heavy use of Aleks' C++ library.
+- [Igneous](https://github.com/seung-lab/igneous) - Visualization of connectomics data using cloud computing.
+
+## Credits
+
+Thanks to Aleks Zlateski for creating and sharing this beautiful mesher.  
+
+Later changes by Will Silversmith, Nico Kemnitz, and Jingpeng Wu. 
+
+## References  
+
+1. W. Lorensen and H. Cline. "Marching Cubes: A High Resolution 3D Surface Construction Algorithm". pp 163-169. Computer Graphics, Volume 21, Number 4, July 1987. ([link](https://people.eecs.berkeley.edu/~jrs/meshpapers/LorensenCline.pdf))  
+2. M. Garland and P. Heckbert. "Surface simplification using quadric error metrics". SIGGRAPH '97: Proceedings of the 24th annual conference on Computer graphics and interactive techniques. Pages 209–216. August 1997. doi: 10.1145/258734.258849 ([link](https://mgarland.org/files/papers/quadrics.pdf))  
+3. H. Hoppe. "New Quadric Metric for Simplifying Meshes with Appearance Attributes". IEEE Visualization 1999 Conference. pp. 59-66. doi: 10.1109/VISUAL.1999.809869 ([link](http://hhoppe.com/newqem.pdf))
+
+
+
+
+
+%package help
+Summary:	Development documents and examples for zmesh
+Provides:	python3-zmesh-doc
+%description help
+## zmesh: Multi-Label Marching Cubes &amp; Mesh Simplification
+[![Tests](https://github.com/seung-lab/zmesh/actions/workflows/test.yml/badge.svg?branch=master)](https://github.com/seung-lab/zmesh/actions/workflows/test.yml) [![PyPI version](https://badge.fury.io/py/zmesh.svg)](https://badge.fury.io/py/zmesh)  
+
+```python
+from zmesh import Mesher
+
+labels = ... # some dense volumetric labeled image
+mesher = Mesher( (4,4,40) ) # anisotropy of image
+
+# initial marching cubes pass
+# close controls whether meshes touching
+# the image boundary are left open or closed
+mesher.mesh(labels, close=False) 
+
+meshes = []
+for obj_id in mesher.ids():
+  meshes.append(
+    mesher.get_mesh(
+      obj_id, 
+      normals=False, # whether to calculate normals or not
+
+      # tries to reduce triangles by this factor
+      # 0 disables simplification
+      simplification_factor=100, 
+
+      # Max tolerable error in physical distance
+      max_simplification_error=8,
+      # whether meshes should be centered in the voxel
+      # on (0,0,0) [False] or (0.5,0.5,0.5) [True]
+      voxel_centered=False, 
+    )
+  )
+  mesher.erase(obj_id) # delete high res mesh
+
+mesher.clear() # clear memory retained by mesher
+
+mesh = meshes[0]
+mesh = mesher.simplify(
+  mesh, 
+  # same as simplification_factor in get_mesh
+  reduction_factor=100, 
+  # same as max_simplification_error in get_mesh
+  max_error=40, 
+  compute_normals=False, # whether to also compute face normals
+) # apply simplifier to a pre-existing mesh
+
+# compute normals without simplifying
+mesh = mesher.compute_normals(mesh) 
+
+mesh.vertices
+mesh.faces 
+mesh.normals
+mesh.triangles() # compute triangles from vertices and faces
+
+# Extremely common obj format
+with open('iconic_doge.obj', 'wb') as f:
+  f.write(mesh.to_obj())
+
+# Common binary format
+with open('iconic_doge.ply', 'wb') as f:
+  f.write(mesh.to_ply())
+
+# Neuroglancer Precomputed format
+with open('10001001:0', 'wb') as f:
+  f.write(mesh.to_precomputed())
+```
+
+## Installation 
+
+If binaries are not available for your system, ensure you have a C++ compiler installed.
+
+```bash
+pip install zmesh
+```
+
+## Performance Tuning & Notes
+
+- The mesher will consume about double memory in 64 bit mode if the size of the 
+object exceeds <1023, 1023, 511> on the x, y, or z axes. This is due to a limitation 
+of the 32-bit format. 
+- The mesher is ambidextrous, it can handle C or Fortran order arrays.
+- The maximum vertex range supported `.simplify` after converting to voxel space is 2<sup>20</sup> (appx. 1M) due to the packed 64-bit vertex format.
+- There is a longstanding design flaw in `cMesher.hpp` that transposes the returned mesh and resolution. We're working on a backwards compatible solution. That's why you need to do `mesher.mesh(data.T)`.
+
+## Related Projects 
+
+- [zi_lib](https://github.com/zlateski/zi_lib) - zmesh makes heavy use of Aleks' C++ library.
+- [Igneous](https://github.com/seung-lab/igneous) - Visualization of connectomics data using cloud computing.
+
+## Credits
+
+Thanks to Aleks Zlateski for creating and sharing this beautiful mesher.  
+
+Later changes by Will Silversmith, Nico Kemnitz, and Jingpeng Wu. 
+
+## References  
+
+1. W. Lorensen and H. Cline. "Marching Cubes: A High Resolution 3D Surface Construction Algorithm". pp 163-169. Computer Graphics, Volume 21, Number 4, July 1987. ([link](https://people.eecs.berkeley.edu/~jrs/meshpapers/LorensenCline.pdf))  
+2. M. Garland and P. Heckbert. "Surface simplification using quadric error metrics". SIGGRAPH '97: Proceedings of the 24th annual conference on Computer graphics and interactive techniques. Pages 209–216. August 1997. doi: 10.1145/258734.258849 ([link](https://mgarland.org/files/papers/quadrics.pdf))  
+3. H. Hoppe. "New Quadric Metric for Simplifying Meshes with Appearance Attributes". IEEE Visualization 1999 Conference. pp. 59-66. doi: 10.1109/VISUAL.1999.809869 ([link](http://hhoppe.com/newqem.pdf))
+
+
+
+
+
+%prep
+%autosetup -n zmesh-1.6.2
+
+%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-zmesh -f filelist.lst
+%dir %{python3_sitearch}/*
+
+%files help -f doclist.lst
+%{_docdir}/*
+
+%changelog
+* Wed May 31 2023 Python_Bot <Python_Bot@openeuler.org> - 1.6.2-1
+- Package Spec generated
diff --git a/sources b/sources
new file mode 100644
index 0000000..cbd8d44
--- /dev/null
+++ b/sources
@@ -0,0 +1 @@
+0c55a7acebe55b062364bf5ab41eeafb  zmesh-1.6.2.tar.gz