sem2surface 0.2.0__tar.gz

sem2surface-0.2.0/LICENSE

@@ -0,0 +1,30 @@
+BSD 3-Clause License
+
+Copyright (c) 2023-2026, Vladislav A. Yastrebov
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+1. Redistributions of source code must retain the above copyright notice,
+   this list of conditions and the following disclaimer.
+
+2. Redistributions in binary form must reproduce the above copyright notice,
+   this list of conditions and the following disclaimer in the documentation
+   and/or other materials provided with the distribution.
+
+3. Neither the name of the copyright holder nor the names of its
+   contributors may be used to endorse or promote products derived from
+   this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE
+LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
+SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
+INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
+CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
+POSSIBILITY OF SUCH DAMAGE.

sem2surface-0.2.0/PKG-INFO

@@ -0,0 +1,306 @@
+Metadata-Version: 2.4
+Name: sem2surface
+Version: 0.2.0
+Summary: 3D surface reconstruction from multi-detector SEM/BSE images
+Author: Vladislav A. Yastrebov
+License-Expression: BSD-3-Clause
+Project-URL: Homepage, https://github.com/vyastreb/sem2surface
+Project-URL: Repository, https://github.com/vyastreb/sem2surface
+Project-URL: Issues, https://github.com/vyastreb/sem2surface/issues
+Keywords: SEM,BSE,surface reconstruction,metrology,microscopy
+Classifier: Development Status :: 4 - Beta
+Classifier: Environment :: Console
+Classifier: Environment :: X11 Applications
+Classifier: Intended Audience :: Science/Research
+Classifier: Operating System :: MacOS
+Classifier: Operating System :: Microsoft :: Windows
+Classifier: Operating System :: POSIX :: Linux
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Topic :: Scientific/Engineering :: Image Processing
+Requires-Python: >=3.10
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: numpy>=1.23
+Requires-Dist: matplotlib>=3.7
+Requires-Dist: scipy>=1.10
+Requires-Dist: scikit-image>=0.21
+Requires-Dist: pillow>=9.0
+Provides-Extra: vtk
+Requires-Dist: vtk>=9.2; extra == "vtk"
+Provides-Extra: test
+Requires-Dist: build>=1.2; extra == "test"
+Requires-Dist: pytest>=8; extra == "test"
+Requires-Dist: twine>=5; extra == "test"
+Dynamic: license-file
+
+# sem2surface
+
+`sem2surface` reconstructs a three-dimensional surface from three to five
+multi-detector SEM/BSE images. It extracts two normalized principal images,
+identifies their orientation with a Radon transform, and integrates the resulting
+gradients using the Frankot-Chellappa FFT method.
+
+<!-- PyPI cannot resolve repository-relative images. Keep this absolute URL. -->
+![3D surface reconstruction from multi-detector SEM images](https://raw.githubusercontent.com/vyastreb/sem2surface/master/img/explication.jpg)
+
+The reconstruction can be used qualitatively with an arbitrary vertical scale.
+Quantitative measurements require a calibrated Z scaling factor for the imaging
+configuration. The included Vickers-indentation example demonstrates that
+calibration procedure.
+
+## Installation
+
+Python 3.10 or newer is required. An isolated virtual environment is strongly
+recommended so the application does not conflict with system Python packages.
+
+### Linux and macOS
+
+Create an environment and install a released version:
+
+```bash
+python3 -m venv .venv
+source .venv/bin/activate
+python -m pip install --upgrade pip
+python -m pip install sem2surface
+sem2surface-gui
+```
+
+Until a release is uploaded to PyPI, run the final installation command from
+this source checkout instead:
+
+```bash
+python -m pip install .
+```
+
+On Linux, Tkinter may be packaged separately. For example, Ubuntu and Debian
+users can install it with their system package manager as `python3-tk` before
+creating the environment.
+
+### Windows
+
+Install Python 3.10 or newer from
+[python.org](https://www.python.org/downloads/windows/). Keep the standard
+`pip`, Tcl/Tk, and Python Launcher components enabled. Then open PowerShell in
+the folder where you want the environment and run:
+
+```powershell
+py -3 -m venv .venv
+.\.venv\Scripts\Activate.ps1
+python -m pip install --upgrade pip
+python -m pip install sem2surface
+sem2surface-gui
+```
+
+If PowerShell blocks the activation script, allow it only for the current
+PowerShell process and retry activation:
+
+```powershell
+Set-ExecutionPolicy -Scope Process -ExecutionPolicy Bypass
+.\.venv\Scripts\Activate.ps1
+```
+
+In Command Prompt, activate the same environment with:
+
+```bat
+.venv\Scripts\activate.bat
+```
+
+Activation is optional. The GUI can always be launched directly:
+
+```powershell
+.\.venv\Scripts\sem2surface-gui.exe
+```
+
+Before the PyPI release, install either from a source checkout with
+`python -m pip install .` or from the provided wheel:
+
+```powershell
+python -m pip install "C:\path\to\sem2surface-0.2.0-py3-none-any.whl"
+```
+
+Use `deactivate` to leave the environment on any platform. Do not copy a
+virtual environment between computers or move it after creation; create a new
+one and reinstall the package instead.
+
+VTK export is optional because VTK is a large dependency:
+
+```bash
+python -m pip install "sem2surface[vtk]"
+# From this source checkout instead: python -m pip install ".[vtk]"
+```
+
+The application does not require ImageMagick or a LaTeX installation. Tkinter is
+included with the standard Python installers on Windows and macOS.
+
+## Desktop application
+
+After installation, launch the graphical interface from a terminal:
+
+```bash
+sem2surface-gui
+```
+
+Select three to five detector images, confirm the pixel size and scaling factor,
+choose an output directory, and start the reconstruction. TIFF, PNG, JPEG, and
+BMP images are supported. The work runs in the background so the window remains
+responsive.
+
+The GUI intentionally provides only the FFT reconstruction. Atomic-number
+correction and direct profile integration have been removed.
+
+## Command line
+
+Installation also provides a `sem2surface` executable:
+
+```bash
+sem2surface detector_A.tif detector_B.tif detector_C.tif \
+  --z-scale 217.27243 \
+  --save npz \
+  --output-dir results
+```
+
+Pixel size is read from the first TIFF by default. For images without compatible
+SEM metadata, provide it in micrometres:
+
+```bash
+sem2surface detector_A.png detector_B.png detector_C.png \
+  --pixel-size-um 0.325521 \
+  --curvature none
+```
+
+Run `sem2surface --help` for the complete list of options. VTK output requires
+the optional `vtk` installation described above.
+
+## Python API
+
+```python
+from pathlib import Path
+
+from sem2surface import construct_surface
+
+images = [Path("detector_A.tif"), Path("detector_B.tif"), Path("detector_C.tif")]
+preview, X, Y, Z, warning = construct_surface(
+    images,
+    z_scaling_factor_per_pixel=217.27243,
+    remove_curvature=True,
+    save_file_type="NPZ",
+    output_dir="results",
+)
+```
+
+Pixel size and manual curvature radii use metres in the Python API. Returned
+coordinate and height arrays use micrometres. The old `constructSurface`
+function remains as a compatibility wrapper for version 0.1 scripts, but only
+FFT reconstruction is accepted and the old atomic-number arguments are ignored.
+
+## Outputs
+
+Every reconstruction creates:
+
+- a colour PNG of the reconstructed surface;
+- a grayscale PNG suitable for further image analysis;
+- a UTF-8 log containing parameters, input names, angles, and surface RMS.
+
+Surface arrays can additionally be saved as CSV, compressed NumPy NPZ, or VTK
+structured-grid data. Optional diagnostic output includes the detector/PCA
+decomposition, Radon search, and oriented gradients.
+
+When timestamps are disabled, an existing output with the same name is replaced.
+Choose a dedicated output folder or enable timestamps when results must be kept.
+
+## Reference examples and scaling
+
+The [examples directory](https://github.com/vyastreb/sem2surface/tree/master/examples)
+contains the reference analyses:
+
+- `Surface_1` and `Surface_2`: representative reconstructed surfaces;
+- `Vickers_imprint`: reconstruction of a Vickers indentation;
+- `Vickers_imprint_scaling`: identification of the Z scaling factor from the
+  known Vickers geometry.
+
+After installing the package with the VTK extra, an example can be run from any
+working directory:
+
+```bash
+python examples/Surface_1/test_without_gui.py
+```
+
+<!-- PyPI cannot resolve repository-relative images. Keep this absolute URL. -->
+![Reconstruction of the indented surface](https://raw.githubusercontent.com/vyastreb/sem2surface/master/img/indent_superposition.jpg)
+
+## Development
+
+Create an isolated environment and install the editable project with its test
+tools:
+
+```bash
+python -m venv .venv
+source .venv/bin/activate
+python -m pip install -e ".[test]"
+python -m pytest
+python -m build
+python -m twine check dist/*
+```
+
+Continuous integration tests Python 3.10 and 3.13 on Linux, Windows, and macOS,
+and verifies both the source distribution and universal wheel.
+
+### Maintainer release checklist
+
+Use a clean virtual environment and update the version in both
+`pyproject.toml` and `src/sem2surface.py`. PyPI does not allow an uploaded file
+or release version to be replaced.
+
+```bash
+python -m pytest -q
+python -m build
+python -m twine check dist/*
+```
+
+For a first trial, create a separate account and API token on
+[TestPyPI](https://test.pypi.org/), then upload only the files for the new
+version:
+
+```bash
+python -m twine upload --repository testpypi dist/sem2surface-0.2.0*
+```
+
+When prompted, use `__token__` as the username and the complete TestPyPI token,
+including its `pypi-` prefix, as the password. Test the uploaded wheel in a new
+environment without resolving dependencies from TestPyPI:
+
+```bash
+python -m pip install --index-url https://test.pypi.org/simple/ --no-deps sem2surface==0.2.0
+sem2surface --version
+```
+
+For the real release, create a PyPI account and API token at
+[pypi.org](https://pypi.org/), then run:
+
+```bash
+python -m twine upload dist/sem2surface-0.2.0*
+```
+
+PyPI and TestPyPI use separate accounts and tokens. Never commit a token or put
+one directly in a command. For later automated releases, prefer
+[PyPI Trusted Publishing](https://docs.pypi.org/trusted-publishers/).
+
+## Method references
+
+1. Neggers, J. et al. (2021). Principal image decomposition for multi-detector
+   backscatter electron topography reconstruction. *Ultramicroscopy*, 227,
+   113200. [DOI](https://doi.org/10.1016/j.ultramic.2020.113200)
+2. Frankot, R. T. and Chellappa, R. (1988). A method for enforcing integrability
+   in shape from shading algorithms. *IEEE Transactions on Pattern Analysis and
+   Machine Intelligence*, 10(4), 439-451.
+   [DOI](https://doi.org/10.1109/34.3909)
+
+## Author and license
+
+Developed by Vladislav A. Yastrebov, CNRS, Mines Paris – PSL, Centre des
+matériaux. Distributed under the
+[BSD 3-Clause License](https://github.com/vyastreb/sem2surface/blob/master/LICENSE).

sem2surface-0.2.0/README.md

@@ -0,0 +1,267 @@
+# sem2surface
+
+`sem2surface` reconstructs a three-dimensional surface from three to five
+multi-detector SEM/BSE images. It extracts two normalized principal images,
+identifies their orientation with a Radon transform, and integrates the resulting
+gradients using the Frankot-Chellappa FFT method.
+
+<!-- PyPI cannot resolve repository-relative images. Keep this absolute URL. -->
+![3D surface reconstruction from multi-detector SEM images](https://raw.githubusercontent.com/vyastreb/sem2surface/master/img/explication.jpg)
+
+The reconstruction can be used qualitatively with an arbitrary vertical scale.
+Quantitative measurements require a calibrated Z scaling factor for the imaging
+configuration. The included Vickers-indentation example demonstrates that
+calibration procedure.
+
+## Installation
+
+Python 3.10 or newer is required. An isolated virtual environment is strongly
+recommended so the application does not conflict with system Python packages.
+
+### Linux and macOS
+
+Create an environment and install a released version:
+
+```bash
+python3 -m venv .venv
+source .venv/bin/activate
+python -m pip install --upgrade pip
+python -m pip install sem2surface
+sem2surface-gui
+```
+
+Until a release is uploaded to PyPI, run the final installation command from
+this source checkout instead:
+
+```bash
+python -m pip install .
+```
+
+On Linux, Tkinter may be packaged separately. For example, Ubuntu and Debian
+users can install it with their system package manager as `python3-tk` before
+creating the environment.
+
+### Windows
+
+Install Python 3.10 or newer from
+[python.org](https://www.python.org/downloads/windows/). Keep the standard
+`pip`, Tcl/Tk, and Python Launcher components enabled. Then open PowerShell in
+the folder where you want the environment and run:
+
+```powershell
+py -3 -m venv .venv
+.\.venv\Scripts\Activate.ps1
+python -m pip install --upgrade pip
+python -m pip install sem2surface
+sem2surface-gui
+```
+
+If PowerShell blocks the activation script, allow it only for the current
+PowerShell process and retry activation:
+
+```powershell
+Set-ExecutionPolicy -Scope Process -ExecutionPolicy Bypass
+.\.venv\Scripts\Activate.ps1
+```
+
+In Command Prompt, activate the same environment with:
+
+```bat
+.venv\Scripts\activate.bat
+```
+
+Activation is optional. The GUI can always be launched directly:
+
+```powershell
+.\.venv\Scripts\sem2surface-gui.exe
+```
+
+Before the PyPI release, install either from a source checkout with
+`python -m pip install .` or from the provided wheel:
+
+```powershell
+python -m pip install "C:\path\to\sem2surface-0.2.0-py3-none-any.whl"
+```
+
+Use `deactivate` to leave the environment on any platform. Do not copy a
+virtual environment between computers or move it after creation; create a new
+one and reinstall the package instead.
+
+VTK export is optional because VTK is a large dependency:
+
+```bash
+python -m pip install "sem2surface[vtk]"
+# From this source checkout instead: python -m pip install ".[vtk]"
+```
+
+The application does not require ImageMagick or a LaTeX installation. Tkinter is
+included with the standard Python installers on Windows and macOS.
+
+## Desktop application
+
+After installation, launch the graphical interface from a terminal:
+
+```bash
+sem2surface-gui
+```
+
+Select three to five detector images, confirm the pixel size and scaling factor,
+choose an output directory, and start the reconstruction. TIFF, PNG, JPEG, and
+BMP images are supported. The work runs in the background so the window remains
+responsive.
+
+The GUI intentionally provides only the FFT reconstruction. Atomic-number
+correction and direct profile integration have been removed.
+
+## Command line
+
+Installation also provides a `sem2surface` executable:
+
+```bash
+sem2surface detector_A.tif detector_B.tif detector_C.tif \
+  --z-scale 217.27243 \
+  --save npz \
+  --output-dir results
+```
+
+Pixel size is read from the first TIFF by default. For images without compatible
+SEM metadata, provide it in micrometres:
+
+```bash
+sem2surface detector_A.png detector_B.png detector_C.png \
+  --pixel-size-um 0.325521 \
+  --curvature none
+```
+
+Run `sem2surface --help` for the complete list of options. VTK output requires
+the optional `vtk` installation described above.
+
+## Python API
+
+```python
+from pathlib import Path
+
+from sem2surface import construct_surface
+
+images = [Path("detector_A.tif"), Path("detector_B.tif"), Path("detector_C.tif")]
+preview, X, Y, Z, warning = construct_surface(
+    images,
+    z_scaling_factor_per_pixel=217.27243,
+    remove_curvature=True,
+    save_file_type="NPZ",
+    output_dir="results",
+)
+```
+
+Pixel size and manual curvature radii use metres in the Python API. Returned
+coordinate and height arrays use micrometres. The old `constructSurface`
+function remains as a compatibility wrapper for version 0.1 scripts, but only
+FFT reconstruction is accepted and the old atomic-number arguments are ignored.
+
+## Outputs
+
+Every reconstruction creates:
+
+- a colour PNG of the reconstructed surface;
+- a grayscale PNG suitable for further image analysis;
+- a UTF-8 log containing parameters, input names, angles, and surface RMS.
+
+Surface arrays can additionally be saved as CSV, compressed NumPy NPZ, or VTK
+structured-grid data. Optional diagnostic output includes the detector/PCA
+decomposition, Radon search, and oriented gradients.
+
+When timestamps are disabled, an existing output with the same name is replaced.
+Choose a dedicated output folder or enable timestamps when results must be kept.
+
+## Reference examples and scaling
+
+The [examples directory](https://github.com/vyastreb/sem2surface/tree/master/examples)
+contains the reference analyses:
+
+- `Surface_1` and `Surface_2`: representative reconstructed surfaces;
+- `Vickers_imprint`: reconstruction of a Vickers indentation;
+- `Vickers_imprint_scaling`: identification of the Z scaling factor from the
+  known Vickers geometry.
+
+After installing the package with the VTK extra, an example can be run from any
+working directory:
+
+```bash
+python examples/Surface_1/test_without_gui.py
+```
+
+<!-- PyPI cannot resolve repository-relative images. Keep this absolute URL. -->
+![Reconstruction of the indented surface](https://raw.githubusercontent.com/vyastreb/sem2surface/master/img/indent_superposition.jpg)
+
+## Development
+
+Create an isolated environment and install the editable project with its test
+tools:
+
+```bash
+python -m venv .venv
+source .venv/bin/activate
+python -m pip install -e ".[test]"
+python -m pytest
+python -m build
+python -m twine check dist/*
+```
+
+Continuous integration tests Python 3.10 and 3.13 on Linux, Windows, and macOS,
+and verifies both the source distribution and universal wheel.
+
+### Maintainer release checklist
+
+Use a clean virtual environment and update the version in both
+`pyproject.toml` and `src/sem2surface.py`. PyPI does not allow an uploaded file
+or release version to be replaced.
+
+```bash
+python -m pytest -q
+python -m build
+python -m twine check dist/*
+```
+
+For a first trial, create a separate account and API token on
+[TestPyPI](https://test.pypi.org/), then upload only the files for the new
+version:
+
+```bash
+python -m twine upload --repository testpypi dist/sem2surface-0.2.0*
+```
+
+When prompted, use `__token__` as the username and the complete TestPyPI token,
+including its `pypi-` prefix, as the password. Test the uploaded wheel in a new
+environment without resolving dependencies from TestPyPI:
+
+```bash
+python -m pip install --index-url https://test.pypi.org/simple/ --no-deps sem2surface==0.2.0
+sem2surface --version
+```
+
+For the real release, create a PyPI account and API token at
+[pypi.org](https://pypi.org/), then run:
+
+```bash
+python -m twine upload dist/sem2surface-0.2.0*
+```
+
+PyPI and TestPyPI use separate accounts and tokens. Never commit a token or put
+one directly in a command. For later automated releases, prefer
+[PyPI Trusted Publishing](https://docs.pypi.org/trusted-publishers/).
+
+## Method references
+
+1. Neggers, J. et al. (2021). Principal image decomposition for multi-detector
+   backscatter electron topography reconstruction. *Ultramicroscopy*, 227,
+   113200. [DOI](https://doi.org/10.1016/j.ultramic.2020.113200)
+2. Frankot, R. T. and Chellappa, R. (1988). A method for enforcing integrability
+   in shape from shading algorithms. *IEEE Transactions on Pattern Analysis and
+   Machine Intelligence*, 10(4), 439-451.
+   [DOI](https://doi.org/10.1109/34.3909)
+
+## Author and license
+
+Developed by Vladislav A. Yastrebov, CNRS, Mines Paris – PSL, Centre des
+matériaux. Distributed under the
+[BSD 3-Clause License](https://github.com/vyastreb/sem2surface/blob/master/LICENSE).

sem2surface-0.2.0/pyproject.toml

@@ -0,0 +1,60 @@
+[build-system]
+requires = ["setuptools>=77", "wheel"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "sem2surface"
+version = "0.2.0"
+description = "3D surface reconstruction from multi-detector SEM/BSE images"
+readme = "README.md"
+requires-python = ">=3.10"
+license = "BSD-3-Clause"
+authors = [
+  { name = "Vladislav A. Yastrebov" },
+]
+keywords = ["SEM", "BSE", "surface reconstruction", "metrology", "microscopy"]
+classifiers = [
+  "Development Status :: 4 - Beta",
+  "Environment :: Console",
+  "Environment :: X11 Applications",
+  "Intended Audience :: Science/Research",
+  "Operating System :: MacOS",
+  "Operating System :: Microsoft :: Windows",
+  "Operating System :: POSIX :: Linux",
+  "Programming Language :: Python :: 3",
+  "Programming Language :: Python :: 3.10",
+  "Programming Language :: Python :: 3.11",
+  "Programming Language :: Python :: 3.12",
+  "Programming Language :: Python :: 3.13",
+  "Topic :: Scientific/Engineering :: Image Processing",
+]
+dependencies = [
+  "numpy>=1.23",
+  "matplotlib>=3.7",
+  "scipy>=1.10",
+  "scikit-image>=0.21",
+  "pillow>=9.0",
+]
+
+[project.optional-dependencies]
+vtk = ["vtk>=9.2"]
+test = ["build>=1.2", "pytest>=8", "twine>=5"]
+
+[project.urls]
+Homepage = "https://github.com/vyastreb/sem2surface"
+Repository = "https://github.com/vyastreb/sem2surface"
+Issues = "https://github.com/vyastreb/sem2surface/issues"
+
+[project.scripts]
+sem2surface = "sem2surface_cli:main"
+
+[project.gui-scripts]
+sem2surface-gui = "sem2surface_gui:main"
+
+[tool.setuptools]
+package-dir = { "" = "src" }
+py-modules = ["sem2surface", "sem2surface_cli", "sem2surface_gui"]
+
+[tool.pytest.ini_options]
+addopts = "-ra"
+testpaths = ["tests"]

sem2surface-0.2.0/setup.cfg

@@ -0,0 +1,4 @@
+[egg_info]
+tag_build = 
+tag_date = 0
+