PyPI - pyimgal - Versions diffs - 0.1.0__tar.gz - Mend

pyimgal 0.1.0__tar.gz

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.

Files changed (77) hide show

pyimgal-0.1.0/Cargo.lock +488 -0
pyimgal-0.1.0/Cargo.toml +16 -0
pyimgal-0.1.0/PKG-INFO +82 -0
pyimgal-0.1.0/README.md +54 -0
pyimgal-0.1.0/imgal/Cargo.toml +22 -0
pyimgal-0.1.0/imgal/README.md +97 -0
pyimgal-0.1.0/imgal/src/colocalization/mod.rs +3 -0
pyimgal-0.1.0/imgal/src/colocalization/saca.rs +591 -0
pyimgal-0.1.0/imgal/src/distribution/gaussian.rs +55 -0
pyimgal-0.1.0/imgal/src/distribution/mod.rs +2 -0
pyimgal-0.1.0/imgal/src/error/array.rs +98 -0
pyimgal-0.1.0/imgal/src/error/mod.rs +2 -0
pyimgal-0.1.0/imgal/src/filter/convolve.rs +142 -0
pyimgal-0.1.0/imgal/src/filter/mod.rs +2 -0
pyimgal-0.1.0/imgal/src/integration/mod.rs +6 -0
pyimgal-0.1.0/imgal/src/integration/rectangle.rs +28 -0
pyimgal-0.1.0/imgal/src/integration/simpson.rs +97 -0
pyimgal-0.1.0/imgal/src/kernel/mod.rs +1 -0
pyimgal-0.1.0/imgal/src/kernel/neighborhood.rs +233 -0
pyimgal-0.1.0/imgal/src/lib.rs +12 -0
pyimgal-0.1.0/imgal/src/parameter/diffraction.rs +29 -0
pyimgal-0.1.0/imgal/src/parameter/mod.rs +5 -0
pyimgal-0.1.0/imgal/src/parameter/omega.rs +29 -0
pyimgal-0.1.0/imgal/src/phasor/calibration.rs +183 -0
pyimgal-0.1.0/imgal/src/phasor/mod.rs +3 -0
pyimgal-0.1.0/imgal/src/phasor/plot.rs +165 -0
pyimgal-0.1.0/imgal/src/phasor/time_domain.rs +231 -0
pyimgal-0.1.0/imgal/src/simulation/decay.rs +377 -0
pyimgal-0.1.0/imgal/src/simulation/instrument.rs +31 -0
pyimgal-0.1.0/imgal/src/simulation/mod.rs +3 -0
pyimgal-0.1.0/imgal/src/simulation/noise.rs +232 -0
pyimgal-0.1.0/imgal/src/statistics/kendall_tau.rs +163 -0
pyimgal-0.1.0/imgal/src/statistics/mod.rs +8 -0
pyimgal-0.1.0/imgal/src/statistics/sample.rs +35 -0
pyimgal-0.1.0/imgal/src/statistics/sort.rs +145 -0
pyimgal-0.1.0/imgal/src/statistics/sum.rs +37 -0
pyimgal-0.1.0/imgal/src/threshold/manual.rs +33 -0
pyimgal-0.1.0/imgal/src/threshold/mod.rs +2 -0
pyimgal-0.1.0/imgal/src/traits/mod.rs +1 -0
pyimgal-0.1.0/imgal/src/traits/numeric.rs +40 -0
pyimgal-0.1.0/imgal/tests/test_distribution.rs +12 -0
pyimgal-0.1.0/imgal/tests/test_filter.rs +68 -0
pyimgal-0.1.0/imgal/tests/test_integration.rs +34 -0
pyimgal-0.1.0/imgal/tests/test_kernel.rs +49 -0
pyimgal-0.1.0/imgal/tests/test_parameter.rs +14 -0
pyimgal-0.1.0/imgal/tests/test_phasor.rs +264 -0
pyimgal-0.1.0/imgal/tests/test_simulation.rs +261 -0
pyimgal-0.1.0/imgal/tests/test_statistics.rs +27 -0
pyimgal-0.1.0/imgal_python/Cargo.toml +18 -0
pyimgal-0.1.0/imgal_python/README.md +54 -0
pyimgal-0.1.0/imgal_python/src/child_modules/colocalization_module.rs +25 -0
pyimgal-0.1.0/imgal_python/src/child_modules/distribution_module.rs +21 -0
pyimgal-0.1.0/imgal_python/src/child_modules/filter_module.rs +25 -0
pyimgal-0.1.0/imgal_python/src/child_modules/integration_module.rs +29 -0
pyimgal-0.1.0/imgal_python/src/child_modules/kernel_module.rs +36 -0
pyimgal-0.1.0/imgal_python/src/child_modules/mod.rs +10 -0
pyimgal-0.1.0/imgal_python/src/child_modules/parameter_module.rs +25 -0
pyimgal-0.1.0/imgal_python/src/child_modules/phasor_module.rs +74 -0
pyimgal-0.1.0/imgal_python/src/child_modules/simulation_module.rs +78 -0
pyimgal-0.1.0/imgal_python/src/child_modules/statistics_module.rs +33 -0
pyimgal-0.1.0/imgal_python/src/child_modules/threshold_module.rs +21 -0
pyimgal-0.1.0/imgal_python/src/error.rs +48 -0
pyimgal-0.1.0/imgal_python/src/functions/colocalization_functions.rs +162 -0
pyimgal-0.1.0/imgal_python/src/functions/distribution_functions.rs +37 -0
pyimgal-0.1.0/imgal_python/src/functions/filter_functions.rs +54 -0
pyimgal-0.1.0/imgal_python/src/functions/integration_functions.rs +64 -0
pyimgal-0.1.0/imgal_python/src/functions/kernel_functions.rs +113 -0
pyimgal-0.1.0/imgal_python/src/functions/mod.rs +10 -0
pyimgal-0.1.0/imgal_python/src/functions/parameter_functions.rs +37 -0
pyimgal-0.1.0/imgal_python/src/functions/phasor_functions.rs +334 -0
pyimgal-0.1.0/imgal_python/src/functions/simulation_functions.rs +462 -0
pyimgal-0.1.0/imgal_python/src/functions/statistics_functions.rs +133 -0
pyimgal-0.1.0/imgal_python/src/functions/threshold_functions.rs +41 -0
pyimgal-0.1.0/imgal_python/src/lib.rs +5 -0
pyimgal-0.1.0/imgal_python/src/parent_module.rs +23 -0
pyimgal-0.1.0/imgal_python/src/utils.rs +25 -0
pyimgal-0.1.0/pyproject.toml +39 -0

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+dependencies = [
+ "wit-bindgen-rt",
+]
+[[package]]
+name = "wit-bindgen-rt"
+version = "0.39.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "6f42320e61fe2cfd34354ecb597f86f413484a798ba44a8ca1165c58d42da6c1"
+dependencies = [
+ "bitflags",
+]
+[[package]]
+name = "zerocopy"
+version = "0.8.26"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "1039dd0d3c310cf05de012d8a39ff557cb0d23087fd44cad61df08fc31907a2f"
+dependencies = [
+ "zerocopy-derive",
+]
+[[package]]
+name = "zerocopy-derive"
+version = "0.8.26"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "9ecf5b4cc5364572d7f4c329661bcc82724222973f2cab6f050a4e5c22f75181"
+dependencies = [
+ "proc-macro2",
+ "quote",
+ "syn",
+]

pyimgal-0.1.0/Cargo.toml ADDED Viewed

@@ -0,0 +1,16 @@
+[workspace]
+members = ["imgal", "imgal_python"]
+resolver = "3"
+[profile.dev]
+debug = true
+lto = "off"
+opt-level = 0
+panic = "unwind"
+[profile.release]
+codegen-units = 1
+debug = false
+lto = "thin"
+opt-level = 3
+panic = "unwind"

pyimgal-0.1.0/PKG-INFO ADDED Viewed

@@ -0,0 +1,82 @@
+Metadata-Version: 2.4
+Name: pyimgal
+Version: 0.1.0
+Classifier: Development Status :: 3 - Alpha
+Classifier: Intended Audience :: Developers
+Classifier: Intended Audience :: Education
+Classifier: Intended Audience :: Science/Research
+Classifier: Operating System :: Microsoft :: Windows
+Classifier: Operating System :: Unix
+Classifier: Operating System :: MacOS
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.9
+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: Programming Language :: Rust
+Classifier: Topic :: Scientific/Engineering
+Classifier: Topic :: Scientific/Engineering :: Image Processing
+Requires-Dist: maturin>=1.8.3
+Summary: Python wrapper and bindings for imgal.
+Keywords: image-processing,algorithm,rust
+Author-email: Edward Evans <elevans2@wisc.edu>
+License-Expression: Unlicense
+Requires-Python: >=3.9
+Description-Content-Type: text/markdown; charset=UTF-8; variant=GFM
+# pyimgal
+The `pyimgal` package serves as the Python bindings wrapper for [imgal](https://github.com/imgal-sc/imgal).
+## Installation
+### `pyimgal` from PyPI
+You can install `pyimgal` from PyPI with:
+```bash
+pip install pyimgal
+```
+### `imgal_python` from source
+To build the `pyimgal` Python bindings from source, use the `maturin` build tool. If you're using `uv` you can do the following in the `imgal_python` crate directory to build the Python bindings:
+```bash
+$ cd imgal_python
+$ uv run maturin develop --release
+```
+This will create a `.venv` in the local directory, compile the `imgal` Rust library and the `imgal_python` PyO3 bindings and install the bindings in the venv as `pyimgal`.
+Alternatively if you're using `conda` or `mamba` you can do the following:
+```bash
+$ cd imgal_python
+$ mamba activate myenv
+(myenv) $ mamba install maturin
+...
+(myenv) $ maturin develop --release
+```
+### Using `imgal` with Python
+Once `pyimgal` has been installed in a compatiable Python environment, `imgal` will be available to import. The example below demonstrates how to obtain a colocalization z-score (_i.e._ colocalization and
+anti-colocalization strength) using the [Spatially Adaptive Colocalization Analysis (SACA)](https://doi.org/10.1109/TIP.2019.2909194) framework. The two number values after the channels are threshold values for channels `a` and `b` respectively.
+```python
+import imgal.colocalization as coloc
+from tifffile import imread
+# load some data
+image = imread("path/to/data.tif")
+# slice channels to perform colocalization analysis
+ch_a = image[:, :, 0]
+ch_b = image[:, :, 1]
+# perform SACA 2D
+coloc_zscore = coloc.saca_2d(ch_a, ch_b, 500.0, 500.0)
+```

pyimgal-0.1.0/README.md ADDED Viewed

@@ -0,0 +1,54 @@
+# pyimgal
+The `pyimgal` package serves as the Python bindings wrapper for [imgal](https://github.com/imgal-sc/imgal).
+## Installation
+### `pyimgal` from PyPI
+You can install `pyimgal` from PyPI with:
+```bash
+pip install pyimgal
+```
+### `imgal_python` from source
+To build the `pyimgal` Python bindings from source, use the `maturin` build tool. If you're using `uv` you can do the following in the `imgal_python` crate directory to build the Python bindings:
+```bash
+$ cd imgal_python
+$ uv run maturin develop --release
+```
+This will create a `.venv` in the local directory, compile the `imgal` Rust library and the `imgal_python` PyO3 bindings and install the bindings in the venv as `pyimgal`.
+Alternatively if you're using `conda` or `mamba` you can do the following:
+```bash
+$ cd imgal_python
+$ mamba activate myenv
+(myenv) $ mamba install maturin
+...
+(myenv) $ maturin develop --release
+```
+### Using `imgal` with Python
+Once `pyimgal` has been installed in a compatiable Python environment, `imgal` will be available to import. The example below demonstrates how to obtain a colocalization z-score (_i.e._ colocalization and
+anti-colocalization strength) using the [Spatially Adaptive Colocalization Analysis (SACA)](https://doi.org/10.1109/TIP.2019.2909194) framework. The two number values after the channels are threshold values for channels `a` and `b` respectively.
+```python
+import imgal.colocalization as coloc
+from tifffile import imread
+# load some data
+image = imread("path/to/data.tif")
+# slice channels to perform colocalization analysis
+ch_a = image[:, :, 0]
+ch_b = image[:, :, 1]
+# perform SACA 2D
+coloc_zscore = coloc.saca_2d(ch_a, ch_b, 500.0, 500.0)
+```

pyimgal-0.1.0/imgal/Cargo.toml ADDED Viewed

@@ -0,0 +1,22 @@
+[package]
+name = "imgal"
+description = "A fast and open-source scientific image processing and algorithm library."
+version = "0.1.0"
+authors = ["Edward Evans"]
+edition = "2024"
+license = "Unlicense"
+homepage = "https://docs.rs/imgal"
+repository = "https://github.com/imgal-sc/imgal"
+readme = "README.md"
+categories = ["algorithms", "mathematics", "science"]
+[lib]
+name = "imgal"
+crate-type = ["rlib"]
+[dependencies]
+ndarray = { version = "0.16.1", features = ["rayon"] }
+rand = "0.9.1"
+rand_distr = "0.5.1"
+rayon = "1.10.0"
+rustfft = "6.3"