stouputils 1.14.0__py3-none-any.whl
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.
- stouputils/__init__.py +40 -0
- stouputils/__main__.py +86 -0
- stouputils/_deprecated.py +37 -0
- stouputils/all_doctests.py +160 -0
- stouputils/applications/__init__.py +22 -0
- stouputils/applications/automatic_docs.py +634 -0
- stouputils/applications/upscaler/__init__.py +39 -0
- stouputils/applications/upscaler/config.py +128 -0
- stouputils/applications/upscaler/image.py +247 -0
- stouputils/applications/upscaler/video.py +287 -0
- stouputils/archive.py +344 -0
- stouputils/backup.py +488 -0
- stouputils/collections.py +244 -0
- stouputils/continuous_delivery/__init__.py +27 -0
- stouputils/continuous_delivery/cd_utils.py +243 -0
- stouputils/continuous_delivery/github.py +522 -0
- stouputils/continuous_delivery/pypi.py +130 -0
- stouputils/continuous_delivery/pyproject.py +147 -0
- stouputils/continuous_delivery/stubs.py +86 -0
- stouputils/ctx.py +408 -0
- stouputils/data_science/config/get.py +51 -0
- stouputils/data_science/config/set.py +125 -0
- stouputils/data_science/data_processing/image/__init__.py +66 -0
- stouputils/data_science/data_processing/image/auto_contrast.py +79 -0
- stouputils/data_science/data_processing/image/axis_flip.py +58 -0
- stouputils/data_science/data_processing/image/bias_field_correction.py +74 -0
- stouputils/data_science/data_processing/image/binary_threshold.py +73 -0
- stouputils/data_science/data_processing/image/blur.py +59 -0
- stouputils/data_science/data_processing/image/brightness.py +54 -0
- stouputils/data_science/data_processing/image/canny.py +110 -0
- stouputils/data_science/data_processing/image/clahe.py +92 -0
- stouputils/data_science/data_processing/image/common.py +30 -0
- stouputils/data_science/data_processing/image/contrast.py +53 -0
- stouputils/data_science/data_processing/image/curvature_flow_filter.py +74 -0
- stouputils/data_science/data_processing/image/denoise.py +378 -0
- stouputils/data_science/data_processing/image/histogram_equalization.py +123 -0
- stouputils/data_science/data_processing/image/invert.py +64 -0
- stouputils/data_science/data_processing/image/laplacian.py +60 -0
- stouputils/data_science/data_processing/image/median_blur.py +52 -0
- stouputils/data_science/data_processing/image/noise.py +59 -0
- stouputils/data_science/data_processing/image/normalize.py +65 -0
- stouputils/data_science/data_processing/image/random_erase.py +66 -0
- stouputils/data_science/data_processing/image/resize.py +69 -0
- stouputils/data_science/data_processing/image/rotation.py +80 -0
- stouputils/data_science/data_processing/image/salt_pepper.py +68 -0
- stouputils/data_science/data_processing/image/sharpening.py +55 -0
- stouputils/data_science/data_processing/image/shearing.py +64 -0
- stouputils/data_science/data_processing/image/threshold.py +64 -0
- stouputils/data_science/data_processing/image/translation.py +71 -0
- stouputils/data_science/data_processing/image/zoom.py +83 -0
- stouputils/data_science/data_processing/image_augmentation.py +118 -0
- stouputils/data_science/data_processing/image_preprocess.py +183 -0
- stouputils/data_science/data_processing/prosthesis_detection.py +359 -0
- stouputils/data_science/data_processing/technique.py +481 -0
- stouputils/data_science/dataset/__init__.py +45 -0
- stouputils/data_science/dataset/dataset.py +292 -0
- stouputils/data_science/dataset/dataset_loader.py +135 -0
- stouputils/data_science/dataset/grouping_strategy.py +296 -0
- stouputils/data_science/dataset/image_loader.py +100 -0
- stouputils/data_science/dataset/xy_tuple.py +696 -0
- stouputils/data_science/metric_dictionnary.py +106 -0
- stouputils/data_science/metric_utils.py +847 -0
- stouputils/data_science/mlflow_utils.py +206 -0
- stouputils/data_science/models/abstract_model.py +149 -0
- stouputils/data_science/models/all.py +85 -0
- stouputils/data_science/models/base_keras.py +765 -0
- stouputils/data_science/models/keras/all.py +38 -0
- stouputils/data_science/models/keras/convnext.py +62 -0
- stouputils/data_science/models/keras/densenet.py +50 -0
- stouputils/data_science/models/keras/efficientnet.py +60 -0
- stouputils/data_science/models/keras/mobilenet.py +56 -0
- stouputils/data_science/models/keras/resnet.py +52 -0
- stouputils/data_science/models/keras/squeezenet.py +233 -0
- stouputils/data_science/models/keras/vgg.py +42 -0
- stouputils/data_science/models/keras/xception.py +38 -0
- stouputils/data_science/models/keras_utils/callbacks/__init__.py +20 -0
- stouputils/data_science/models/keras_utils/callbacks/colored_progress_bar.py +219 -0
- stouputils/data_science/models/keras_utils/callbacks/learning_rate_finder.py +148 -0
- stouputils/data_science/models/keras_utils/callbacks/model_checkpoint_v2.py +31 -0
- stouputils/data_science/models/keras_utils/callbacks/progressive_unfreezing.py +249 -0
- stouputils/data_science/models/keras_utils/callbacks/warmup_scheduler.py +66 -0
- stouputils/data_science/models/keras_utils/losses/__init__.py +12 -0
- stouputils/data_science/models/keras_utils/losses/next_generation_loss.py +56 -0
- stouputils/data_science/models/keras_utils/visualizations.py +416 -0
- stouputils/data_science/models/model_interface.py +939 -0
- stouputils/data_science/models/sandbox.py +116 -0
- stouputils/data_science/range_tuple.py +234 -0
- stouputils/data_science/scripts/augment_dataset.py +77 -0
- stouputils/data_science/scripts/exhaustive_process.py +133 -0
- stouputils/data_science/scripts/preprocess_dataset.py +70 -0
- stouputils/data_science/scripts/routine.py +168 -0
- stouputils/data_science/utils.py +285 -0
- stouputils/decorators.py +605 -0
- stouputils/image.py +441 -0
- stouputils/installer/__init__.py +18 -0
- stouputils/installer/common.py +67 -0
- stouputils/installer/downloader.py +101 -0
- stouputils/installer/linux.py +144 -0
- stouputils/installer/main.py +223 -0
- stouputils/installer/windows.py +136 -0
- stouputils/io.py +486 -0
- stouputils/parallel.py +483 -0
- stouputils/print.py +482 -0
- stouputils/py.typed +1 -0
- stouputils/stouputils/__init__.pyi +15 -0
- stouputils/stouputils/_deprecated.pyi +12 -0
- stouputils/stouputils/all_doctests.pyi +46 -0
- stouputils/stouputils/applications/__init__.pyi +2 -0
- stouputils/stouputils/applications/automatic_docs.pyi +106 -0
- stouputils/stouputils/applications/upscaler/__init__.pyi +3 -0
- stouputils/stouputils/applications/upscaler/config.pyi +18 -0
- stouputils/stouputils/applications/upscaler/image.pyi +109 -0
- stouputils/stouputils/applications/upscaler/video.pyi +60 -0
- stouputils/stouputils/archive.pyi +67 -0
- stouputils/stouputils/backup.pyi +109 -0
- stouputils/stouputils/collections.pyi +86 -0
- stouputils/stouputils/continuous_delivery/__init__.pyi +5 -0
- stouputils/stouputils/continuous_delivery/cd_utils.pyi +129 -0
- stouputils/stouputils/continuous_delivery/github.pyi +162 -0
- stouputils/stouputils/continuous_delivery/pypi.pyi +53 -0
- stouputils/stouputils/continuous_delivery/pyproject.pyi +67 -0
- stouputils/stouputils/continuous_delivery/stubs.pyi +39 -0
- stouputils/stouputils/ctx.pyi +211 -0
- stouputils/stouputils/decorators.pyi +252 -0
- stouputils/stouputils/image.pyi +172 -0
- stouputils/stouputils/installer/__init__.pyi +5 -0
- stouputils/stouputils/installer/common.pyi +39 -0
- stouputils/stouputils/installer/downloader.pyi +24 -0
- stouputils/stouputils/installer/linux.pyi +39 -0
- stouputils/stouputils/installer/main.pyi +57 -0
- stouputils/stouputils/installer/windows.pyi +31 -0
- stouputils/stouputils/io.pyi +213 -0
- stouputils/stouputils/parallel.pyi +216 -0
- stouputils/stouputils/print.pyi +136 -0
- stouputils/stouputils/version_pkg.pyi +15 -0
- stouputils/version_pkg.py +189 -0
- stouputils-1.14.0.dist-info/METADATA +178 -0
- stouputils-1.14.0.dist-info/RECORD +140 -0
- stouputils-1.14.0.dist-info/WHEEL +4 -0
- stouputils-1.14.0.dist-info/entry_points.txt +3 -0
stouputils/image.py
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"""
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This module provides little utilities for image processing.
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- image_resize: Resize an image while preserving its aspect ratio by default.
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- auto_crop: Automatically crop an image to remove zero/uniform regions.
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- numpy_to_gif: Generate a '.gif' file from a 3D numpy array for visualization.
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- numpy_to_obj: Generate a '.obj' file from a 3D numpy array using marching cubes.
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See stouputils.data_science.data_processing for lots more image processing utilities.
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"""
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# Imports
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import os
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from collections.abc import Callable
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from typing import TYPE_CHECKING, Any, TypeVar, cast
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from .io import super_open
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from .print import debug, info
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if TYPE_CHECKING:
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import numpy as np
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from numpy.typing import NDArray
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from PIL import Image
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PIL_Image_or_NDArray = TypeVar("PIL_Image_or_NDArray", bound="Image.Image | NDArray[np.number]")
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# Functions
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def image_resize[PIL_Image_or_NDArray](
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image: PIL_Image_or_NDArray,
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max_result_size: int,
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resampling: "Image.Resampling | None" = None,
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min_or_max: Callable[[int, int], int] = max,
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return_type: type[PIL_Image_or_NDArray] | str = "same",
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keep_aspect_ratio: bool = True,
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) -> Any:
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""" Resize an image while preserving its aspect ratio by default.
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Scales the image so that its largest dimension equals max_result_size.
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Args:
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image (Image.Image | np.ndarray): The image to resize.
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max_result_size (int): Maximum size for the largest dimension.
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resampling (Image.Resampling | None): PIL resampling filter to use (default: Image.Resampling.LANCZOS).
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min_or_max (Callable): Function to use to get the minimum or maximum of the two ratios.
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return_type (type | str): Type of the return value (Image.Image, np.ndarray, or "same" to match input type).
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keep_aspect_ratio (bool): Whether to keep the aspect ratio.
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Returns:
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Image.Image | NDArray[np.number]: The resized image with preserved aspect ratio.
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Examples:
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>>> # Test with (height x width x channels) numpy array
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>>> import numpy as np
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>>> array = np.random.randint(0, 255, (100, 50, 3), dtype=np.uint8)
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>>> image_resize(array, 100).shape
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(100, 50, 3)
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>>> image_resize(array, 100, min_or_max=max).shape
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(100, 50, 3)
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>>> image_resize(array, 100, min_or_max=min).shape
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(200, 100, 3)
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>>> # Test with PIL Image
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>>> from PIL import Image
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>>> pil_image: Image.Image = Image.new('RGB', (200, 100))
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>>> image_resize(pil_image, 50).size
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(50, 25)
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>>> # Test with different return types
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>>> resized_array = image_resize(array, 50, return_type=np.ndarray)
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>>> isinstance(resized_array, np.ndarray)
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True
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>>> resized_array.shape
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(50, 25, 3)
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>>> # Test with different resampling methods
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>>> image_resize(pil_image, 50, resampling=Image.Resampling.NEAREST).size
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(50, 25)
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"""
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# Imports
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import numpy as np
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from PIL import Image
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# Set default resampling method if not provided
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if resampling is None:
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resampling = Image.Resampling.LANCZOS
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# Store original type for later conversion
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original_was_pil: bool = isinstance(image, Image.Image)
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# Convert numpy array to PIL Image if needed
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if not original_was_pil:
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image = Image.fromarray(image)
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if keep_aspect_ratio:
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# Get original image dimensions
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width: int = image.size[0]
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height: int = image.size[1]
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# Determine which dimension to use for scaling based on min_or_max function
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max_dimension: int = min_or_max(width, height)
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# Calculate scaling factor
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scale: float = max_result_size / max_dimension
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# Calculate new dimensions while preserving aspect ratio
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new_width: int = int(width * scale)
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new_height: int = int(height * scale)
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# Resize the image with the calculated dimensions
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new_image: Image.Image = image.resize((new_width, new_height), resampling)
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else:
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# If not keeping aspect ratio, resize to square with max_result_size
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new_image: Image.Image = image.resize((max_result_size, max_result_size), resampling)
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# Return the image in the requested format
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if return_type == "same":
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# Return same type as input
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if original_was_pil:
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return new_image
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else:
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return np.array(new_image)
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elif return_type != Image.Image:
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return np.array(new_image)
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else:
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return new_image
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def auto_crop[PIL_Image_or_NDArray](
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image: PIL_Image_or_NDArray,
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mask: "NDArray[np.bool_] | None" = None,
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threshold: int | float | Callable[["NDArray[np.number]"], int | float] | None = None,
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return_type: type[PIL_Image_or_NDArray] | str = "same",
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contiguous: bool = True,
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) -> Any:
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""" Automatically crop an image to remove zero or uniform regions.
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This function crops the image to keep only the region where pixels are non-zero
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(or above a threshold). It can work with a mask or directly analyze the image.
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Args:
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image (Image.Image | NDArray): The image to crop.
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mask (NDArray[bool] | None): Optional binary mask indicating regions to keep.
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threshold (int | float | Callable): Threshold value or function (default: np.min).
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return_type (type | str): Type of the return value (Image.Image, NDArray[np.number], or "same" to match input type).
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contiguous (bool): If True (default), crop to bounding box. If False, remove entire rows/columns with no content.
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Returns:
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Image.Image | NDArray[np.number]: The cropped image.
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Examples:
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>>> # Test with numpy array with zeros on edges
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>>> import numpy as np
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>>> array = np.zeros((100, 100, 3), dtype=np.uint8)
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>>> array[20:80, 30:70] = 255 # White rectangle in center
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>>> cropped = auto_crop(array, return_type=np.ndarray)
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>>> cropped.shape
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(60, 40, 3)
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>>> # Test with custom mask
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>>> mask = np.zeros((100, 100), dtype=bool)
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>>> mask[10:90, 10:90] = True
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>>> cropped_with_mask = auto_crop(array, mask=mask, return_type=np.ndarray)
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>>> cropped_with_mask.shape
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(80, 80, 3)
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>>> # Test with PIL Image
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>>> from PIL import Image
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>>> pil_image = Image.new('RGB', (100, 100), (0, 0, 0))
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>>> from PIL import ImageDraw
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>>> draw = ImageDraw.Draw(pil_image)
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>>> draw.rectangle([25, 25, 75, 75], fill=(255, 255, 255))
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>>> cropped_pil = auto_crop(pil_image)
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>>> cropped_pil.size
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(51, 51)
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>>> # Test with threshold
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>>> array_gray = np.ones((100, 100), dtype=np.uint8) * 10
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>>> array_gray[20:80, 30:70] = 255
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>>> cropped_threshold = auto_crop(array_gray, threshold=50, return_type=np.ndarray)
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>>> cropped_threshold.shape
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(60, 40)
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>>> # Test with callable threshold (using lambda to avoid min value)
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>>> array_gray2 = np.ones((100, 100), dtype=np.uint8) * 10
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>>> array_gray2[20:80, 30:70] = 255
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>>> cropped_max = auto_crop(array_gray2, threshold=lambda x: 50, return_type=np.ndarray)
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>>> cropped_max.shape
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(60, 40)
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>>> # Test with non-contiguous crop
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>>> array_sparse = np.zeros((100, 100, 3), dtype=np.uint8)
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|
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>>> array_sparse[10, 10] = 255
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>>> array_sparse[50, 50] = 255
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>>> array_sparse[90, 90] = 255
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|
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>>> cropped_contiguous = auto_crop(array_sparse, contiguous=True, return_type=np.ndarray)
|
|
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|
+
>>> cropped_contiguous.shape # Bounding box from (10,10) to (90,90)
|
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|
+
(81, 81, 3)
|
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|
+
>>> cropped_non_contiguous = auto_crop(array_sparse, contiguous=False, return_type=np.ndarray)
|
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+
>>> cropped_non_contiguous.shape # Only rows/cols 10, 50, 90
|
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|
+
(3, 3, 3)
|
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+
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+
>>> # Test with 3D crop on depth dimension
|
|
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|
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>>> array_3d = np.zeros((50, 50, 10), dtype=np.uint8)
|
|
199
|
+
>>> array_3d[10:40, 10:40, 2:8] = 255 # Content only in depth slices 2-7
|
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|
+
>>> cropped_3d = auto_crop(array_3d, contiguous=True, return_type=np.ndarray)
|
|
201
|
+
>>> cropped_3d.shape # Should crop all 3 dimensions
|
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(30, 30, 6)
|
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"""
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|
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# Imports
|
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import numpy as np
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from PIL import Image
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# Convert to numpy array and store original type
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+
original_was_pil: bool = isinstance(image, Image.Image)
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|
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image_array: NDArray[np.number] = np.array(image) if original_was_pil else image
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+
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# Create mask if not provided
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if mask is None:
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if threshold is None:
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threshold = cast(Callable[["NDArray[np.number]"], int | float], np.min)
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threshold_value: int | float = threshold(image_array) if callable(threshold) else threshold
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# Create a 2D mask for both 2D and 3D arrays
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|
+
if image_array.ndim == 2:
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mask = image_array > threshold_value
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else: # 3D array
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mask = np.any(image_array > threshold_value, axis=2)
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+
|
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# Find rows, columns, and depth with content
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rows_with_content: NDArray[np.bool_] = np.any(mask, axis=1)
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|
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cols_with_content: NDArray[np.bool_] = np.any(mask, axis=0)
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+
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# For 3D arrays, also find which depth slices have content
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|
+
depth_with_content: NDArray[np.bool_] | None = None
|
|
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|
+
if image_array.ndim == 3:
|
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# Create a 1D mask for depth dimension
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depth_with_content = np.any(image_array > (threshold(image_array) if callable(threshold) else threshold if threshold is not None else np.min(image_array)), axis=(0, 1))
|
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+
|
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|
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# Return original if no content found
|
|
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|
+
if not (np.any(rows_with_content) and np.any(cols_with_content)):
|
|
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|
+
return image_array if return_type != Image.Image else (image if original_was_pil else Image.fromarray(image_array))
|
|
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|
+
|
|
237
|
+
# Crop based on contiguous parameter
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|
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|
+
if contiguous:
|
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239
|
+
row_idx, col_idx = np.where(rows_with_content)[0], np.where(cols_with_content)[0]
|
|
240
|
+
if image_array.ndim == 3 and depth_with_content is not None and np.any(depth_with_content):
|
|
241
|
+
depth_idx = np.where(depth_with_content)[0]
|
|
242
|
+
cropped_array: NDArray[np.number] = image_array[row_idx[0]:row_idx[-1]+1, col_idx[0]:col_idx[-1]+1, depth_idx[0]:depth_idx[-1]+1]
|
|
243
|
+
else:
|
|
244
|
+
cropped_array: NDArray[np.number] = image_array[row_idx[0]:row_idx[-1]+1, col_idx[0]:col_idx[-1]+1]
|
|
245
|
+
else:
|
|
246
|
+
if image_array.ndim == 3 and depth_with_content is not None:
|
|
247
|
+
# np.ix_ needs index arrays, not boolean arrays
|
|
248
|
+
row_indices = np.where(rows_with_content)[0]
|
|
249
|
+
col_indices = np.where(cols_with_content)[0]
|
|
250
|
+
depth_indices = np.where(depth_with_content)[0]
|
|
251
|
+
ix = np.ix_(row_indices, col_indices, depth_indices)
|
|
252
|
+
else:
|
|
253
|
+
row_indices = np.where(rows_with_content)[0]
|
|
254
|
+
col_indices = np.where(cols_with_content)[0]
|
|
255
|
+
ix = np.ix_(row_indices, col_indices)
|
|
256
|
+
cropped_array = image_array[ix]
|
|
257
|
+
|
|
258
|
+
# Return in requested format
|
|
259
|
+
if return_type == "same":
|
|
260
|
+
return Image.fromarray(cropped_array) if original_was_pil else cropped_array
|
|
261
|
+
return cropped_array if return_type != Image.Image else Image.fromarray(cropped_array)
|
|
262
|
+
|
|
263
|
+
|
|
264
|
+
def numpy_to_gif(
|
|
265
|
+
path: str,
|
|
266
|
+
array: "NDArray[np.integer | np.floating | np.bool_]",
|
|
267
|
+
duration: int = 100,
|
|
268
|
+
loop: int = 0,
|
|
269
|
+
mkdir: bool = True,
|
|
270
|
+
**kwargs: Any
|
|
271
|
+
) -> None:
|
|
272
|
+
""" Generate a '.gif' file from a numpy array for 3D/4D visualization.
|
|
273
|
+
|
|
274
|
+
Args:
|
|
275
|
+
path (str): Path to the output .gif file.
|
|
276
|
+
array (NDArray): Numpy array to be dumped (must be 3D or 4D).
|
|
277
|
+
3D: (depth, height, width) - e.g. (64, 1024, 1024)
|
|
278
|
+
4D: (depth, height, width, channels) - e.g. (50, 64, 1024, 3)
|
|
279
|
+
duration (int): Duration between frames in milliseconds.
|
|
280
|
+
loop (int): Number of loops (0 = infinite).
|
|
281
|
+
mkdir (bool): Create the directory if it does not exist.
|
|
282
|
+
**kwargs (Any): Additional keyword arguments for PIL.Image.save().
|
|
283
|
+
|
|
284
|
+
Examples:
|
|
285
|
+
|
|
286
|
+
.. code-block:: python
|
|
287
|
+
|
|
288
|
+
> # 3D array example
|
|
289
|
+
> array = np.random.randint(0, 256, (10, 100, 100), dtype=np.uint8)
|
|
290
|
+
> numpy_to_gif("output_10_frames_100x100.gif", array, duration=200, loop=0)
|
|
291
|
+
|
|
292
|
+
> # 4D array example (batch of 3D images)
|
|
293
|
+
> array_4d = np.random.randint(0, 256, (5, 10, 100, 3), dtype=np.uint8)
|
|
294
|
+
> numpy_to_gif("output_50_frames_100x100.gif", array_4d, duration=200)
|
|
295
|
+
|
|
296
|
+
> total_duration = 1000 # 1 second
|
|
297
|
+
> numpy_to_gif("output_1s.gif", array, duration=total_duration // len(array))
|
|
298
|
+
"""
|
|
299
|
+
# Imports
|
|
300
|
+
import numpy as np
|
|
301
|
+
from PIL import Image
|
|
302
|
+
|
|
303
|
+
# Assertions
|
|
304
|
+
assert array.ndim in (3, 4), f"The input array must be 3D or 4D, got shape {array.shape} instead."
|
|
305
|
+
if array.ndim == 4:
|
|
306
|
+
assert array.shape[-1] in (1, 3), f"For 4D arrays, the last dimension must be 1 or 3 (channels), got shape {array.shape} instead."
|
|
307
|
+
|
|
308
|
+
# Create directory if needed
|
|
309
|
+
if mkdir:
|
|
310
|
+
dirname: str = os.path.dirname(path)
|
|
311
|
+
if dirname != "":
|
|
312
|
+
os.makedirs(dirname, exist_ok=True)
|
|
313
|
+
|
|
314
|
+
# Normalize array if outside [0-255] range to [0-1]
|
|
315
|
+
array = array.astype(np.float32)
|
|
316
|
+
mini, maxi = np.min(array), np.max(array)
|
|
317
|
+
if mini < 0 or maxi > 255:
|
|
318
|
+
array = ((array - mini) / (maxi - mini + 1e-8))
|
|
319
|
+
|
|
320
|
+
# Scale to [0-255] if in [0-1] range
|
|
321
|
+
mini, maxi = np.min(array), np.max(array)
|
|
322
|
+
if mini >= 0.0 and maxi <= 1.0:
|
|
323
|
+
array = (array * 255)
|
|
324
|
+
|
|
325
|
+
# Ensure array is uint8 for PIL compatibility
|
|
326
|
+
array = array.astype(np.uint8)
|
|
327
|
+
|
|
328
|
+
# Convert each slice to PIL Image
|
|
329
|
+
pil_images: list[Image.Image] = [
|
|
330
|
+
Image.fromarray(z_slice)
|
|
331
|
+
for z_slice in array
|
|
332
|
+
]
|
|
333
|
+
|
|
334
|
+
# Save as GIF
|
|
335
|
+
pil_images[0].save(
|
|
336
|
+
path,
|
|
337
|
+
save_all=True,
|
|
338
|
+
append_images=pil_images[1:],
|
|
339
|
+
duration=duration,
|
|
340
|
+
loop=loop,
|
|
341
|
+
**kwargs
|
|
342
|
+
)
|
|
343
|
+
|
|
344
|
+
|
|
345
|
+
def numpy_to_obj(
|
|
346
|
+
path: str,
|
|
347
|
+
array: "NDArray[np.integer | np.floating | np.bool_]",
|
|
348
|
+
threshold: float = 0.5,
|
|
349
|
+
step_size: int = 1,
|
|
350
|
+
pad_array: bool = True,
|
|
351
|
+
verbose: int = 0
|
|
352
|
+
) -> None:
|
|
353
|
+
""" Generate a '.obj' file from a numpy array for 3D visualization using marching cubes.
|
|
354
|
+
|
|
355
|
+
Args:
|
|
356
|
+
path (str): Path to the output .obj file.
|
|
357
|
+
array (NDArray): Numpy array to be dumped (must be 3D).
|
|
358
|
+
threshold (float): Threshold level for marching cubes (0.5 for binary data).
|
|
359
|
+
step_size (int): Step size for marching cubes (higher = simpler mesh, faster generation).
|
|
360
|
+
pad_array (bool): If True, pad array with zeros to ensure closed volumes for border cells.
|
|
361
|
+
verbose (int): Verbosity level (0 = no output, 1 = some output, 2 = full output).
|
|
362
|
+
|
|
363
|
+
Examples:
|
|
364
|
+
|
|
365
|
+
.. code-block:: python
|
|
366
|
+
|
|
367
|
+
> array = np.random.rand(64, 64, 64) > 0.5 # Binary volume
|
|
368
|
+
> numpy_to_obj("output_mesh.obj", array, threshold=0.5, step_size=2, pad_array=True, verbose=1)
|
|
369
|
+
|
|
370
|
+
> array = my_3d_data # Some 3D numpy array (e.g. human lung scan)
|
|
371
|
+
> numpy_to_obj("output_mesh.obj", array, threshold=0.3)
|
|
372
|
+
"""
|
|
373
|
+
# Imports
|
|
374
|
+
import numpy as np
|
|
375
|
+
from numpy.typing import NDArray
|
|
376
|
+
from skimage import measure
|
|
377
|
+
|
|
378
|
+
# Assertions
|
|
379
|
+
assert array.ndim == 3, f"The input array must be 3D, got shape {array.shape} instead."
|
|
380
|
+
assert step_size > 0, f"Step size must be positive, got {step_size}."
|
|
381
|
+
if verbose > 1:
|
|
382
|
+
debug(
|
|
383
|
+
f"Generating 3D mesh from array of shape {array.shape}, "
|
|
384
|
+
f"threshold={threshold}, step_size={step_size}, pad_array={pad_array}, "
|
|
385
|
+
f"non-zero voxels={np.count_nonzero(array):,}"
|
|
386
|
+
)
|
|
387
|
+
|
|
388
|
+
# Convert to float for marching cubes, if needed
|
|
389
|
+
volume: NDArray[np.floating] = array.astype(np.float32)
|
|
390
|
+
if np.issubdtype(array.dtype, np.bool_):
|
|
391
|
+
threshold = 0.5
|
|
392
|
+
elif np.issubdtype(array.dtype, np.integer):
|
|
393
|
+
# For integer arrays, normalize to 0-1 range
|
|
394
|
+
array = array.astype(np.float32)
|
|
395
|
+
min_val, max_val = np.min(array), np.max(array)
|
|
396
|
+
if min_val != max_val:
|
|
397
|
+
volume = (array - min_val) / (max_val - min_val)
|
|
398
|
+
|
|
399
|
+
# Pad array with zeros to ensure closed volumes for border cells
|
|
400
|
+
if pad_array:
|
|
401
|
+
volume = np.pad(volume, pad_width=step_size, mode='constant', constant_values=0.0)
|
|
402
|
+
|
|
403
|
+
# Apply marching cubes algorithm to extract mesh
|
|
404
|
+
verts, faces, _, _ = cast(
|
|
405
|
+
tuple[NDArray[np.floating], NDArray[np.integer], NDArray[np.floating], NDArray[np.floating]],
|
|
406
|
+
measure.marching_cubes(volume, level=threshold, step_size=step_size, allow_degenerate=False) # type: ignore
|
|
407
|
+
)
|
|
408
|
+
|
|
409
|
+
# Shift vertices back by step_size to account for padding
|
|
410
|
+
if pad_array:
|
|
411
|
+
verts = verts - step_size
|
|
412
|
+
|
|
413
|
+
if verbose > 1:
|
|
414
|
+
debug(f"Generated mesh with {len(verts):,} vertices and {len(faces):,} faces")
|
|
415
|
+
if step_size > 1:
|
|
416
|
+
debug(f"Mesh complexity reduced by ~{step_size ** 3}x compared to step_size=1")
|
|
417
|
+
|
|
418
|
+
# Build content using list for better performance
|
|
419
|
+
content_lines: list[str] = [
|
|
420
|
+
"# OBJ file generated from 3D numpy array",
|
|
421
|
+
f"# Array shape: {array.shape}",
|
|
422
|
+
f"# Threshold: {threshold}",
|
|
423
|
+
f"# Step size: {step_size}",
|
|
424
|
+
f"# Vertices: {len(verts)}",
|
|
425
|
+
f"# Faces: {len(faces)}",
|
|
426
|
+
""
|
|
427
|
+
]
|
|
428
|
+
|
|
429
|
+
# Add vertices
|
|
430
|
+
content_lines.extend(f"v {a:.6f} {b:.6f} {c:.6f}" for a, b, c in verts)
|
|
431
|
+
|
|
432
|
+
# Add faces (OBJ format is 1-indexed, simple format without normals)
|
|
433
|
+
content_lines.extend(f"f {a+1} {b+1} {c+1}" for a, b, c in faces)
|
|
434
|
+
|
|
435
|
+
# Write to .obj file
|
|
436
|
+
with super_open(path, "w") as f:
|
|
437
|
+
f.write("\n".join(content_lines) + "\n")
|
|
438
|
+
|
|
439
|
+
if verbose > 0:
|
|
440
|
+
info(f"Successfully exported 3D mesh to: '{path}'")
|
|
441
|
+
|
|
@@ -0,0 +1,18 @@
|
|
|
1
|
+
""" Installer module for stouputils.
|
|
2
|
+
|
|
3
|
+
Provides functions for platform-agnostic installation tasks by dispatching
|
|
4
|
+
to platform-specific implementations (Windows, Linux/macOS).
|
|
5
|
+
|
|
6
|
+
It handles getting installation paths, adding programs to the PATH environment variable,
|
|
7
|
+
and installing programs from local zip files or URLs.
|
|
8
|
+
"""
|
|
9
|
+
# ruff: noqa: F403
|
|
10
|
+
# ruff: noqa: F405
|
|
11
|
+
|
|
12
|
+
# Imports
|
|
13
|
+
from .common import *
|
|
14
|
+
from .downloader import *
|
|
15
|
+
from .linux import *
|
|
16
|
+
from .main import *
|
|
17
|
+
from .windows import *
|
|
18
|
+
|
|
@@ -0,0 +1,67 @@
|
|
|
1
|
+
""" Common functions used by the Linux and Windows installers modules. """
|
|
2
|
+
# Imports
|
|
3
|
+
from typing import Literal
|
|
4
|
+
|
|
5
|
+
from ..print import warning
|
|
6
|
+
|
|
7
|
+
|
|
8
|
+
# Functions
|
|
9
|
+
def prompt_for_path(prompt_message: str, default_path: str) -> str:
|
|
10
|
+
""" Prompt the user to override a default path.
|
|
11
|
+
|
|
12
|
+
Args:
|
|
13
|
+
prompt_message (str): The message to display to the user.
|
|
14
|
+
default_path (str): The default path to suggest.
|
|
15
|
+
|
|
16
|
+
Returns:
|
|
17
|
+
str: The path entered by the user, or the default path if they pressed Enter.
|
|
18
|
+
"""
|
|
19
|
+
warning(f"{prompt_message}\nPress Enter to use this path, or type a new path to override it: ")
|
|
20
|
+
return input() or default_path
|
|
21
|
+
|
|
22
|
+
|
|
23
|
+
def ask_install_type(ask_global: int, default_local_path: str, default_global_path: str | None) -> Literal["g", "l"]:
|
|
24
|
+
""" Determine the installation type (global 'g' or local 'l') based on user input.
|
|
25
|
+
|
|
26
|
+
Args:
|
|
27
|
+
ask_global (int): 0 = ask, 1 = force global, 2 = force local.
|
|
28
|
+
default_local_path (str): The default local path.
|
|
29
|
+
default_global_path (str | None): The default global path (if applicable).
|
|
30
|
+
|
|
31
|
+
Returns:
|
|
32
|
+
Literal["g", "l"]: 'g' for global install, 'l' for local install.
|
|
33
|
+
|
|
34
|
+
Examples:
|
|
35
|
+
.. code-block:: python
|
|
36
|
+
|
|
37
|
+
> # Ask the user while providing default paths
|
|
38
|
+
> install_choice: str = ask_install_type(0, f"{os.getcwd()}/MyProgram", "C:\\Program Files\\MyProgram")
|
|
39
|
+
g
|
|
40
|
+
|
|
41
|
+
> # Don't ask, force global
|
|
42
|
+
> install_choice: str = ask_install_type(1, ...)
|
|
43
|
+
g
|
|
44
|
+
|
|
45
|
+
> # Don't ask, force local
|
|
46
|
+
> install_choice: str = ask_install_type(2, ...)
|
|
47
|
+
l
|
|
48
|
+
"""
|
|
49
|
+
install_choice: str = ""
|
|
50
|
+
if ask_global == 0:
|
|
51
|
+
if default_global_path:
|
|
52
|
+
global_prompt: str = f"(Globally would target '{default_global_path}')"
|
|
53
|
+
else:
|
|
54
|
+
global_prompt: str = "(Global install not well-defined)"
|
|
55
|
+
warning(
|
|
56
|
+
f"Install globally (requires admin/sudo, suggests adding to PATH) or locally? (G/l):\n"
|
|
57
|
+
f"{global_prompt}, locally would be '{default_local_path}')"
|
|
58
|
+
)
|
|
59
|
+
install_choice = input().lower()
|
|
60
|
+
elif ask_global == 1:
|
|
61
|
+
install_choice = "g"
|
|
62
|
+
elif ask_global == 2:
|
|
63
|
+
install_choice = "l"
|
|
64
|
+
|
|
65
|
+
# Default to global unless user explicitly chooses local ('l')
|
|
66
|
+
return 'l' if install_choice == 'l' else 'g'
|
|
67
|
+
|
|
@@ -0,0 +1,101 @@
|
|
|
1
|
+
""" Downloader module for the installer subpackage.
|
|
2
|
+
|
|
3
|
+
Provides functions for downloading and installing programs from URLs.
|
|
4
|
+
It handles platform-specific downloads, checking if programs are already installed,
|
|
5
|
+
and setting up the downloaded programs for use.
|
|
6
|
+
|
|
7
|
+
This module works with the main installer module to provide a complete installation
|
|
8
|
+
solution for programs that need to be downloaded from the internet.
|
|
9
|
+
"""
|
|
10
|
+
# Imports
|
|
11
|
+
import os
|
|
12
|
+
import platform
|
|
13
|
+
import subprocess
|
|
14
|
+
import sys
|
|
15
|
+
|
|
16
|
+
from ..print import info, warning
|
|
17
|
+
from .main import install_program
|
|
18
|
+
|
|
19
|
+
|
|
20
|
+
# Functions
|
|
21
|
+
def download_executable(download_urls: dict[str, str], program_name: str, append_to_path: str = "") -> bool:
|
|
22
|
+
""" Ask the user if they want to download the program (ex: waifu2x-ncnn-vulkan).
|
|
23
|
+
If yes, try to download the program from the GitHub releases page.
|
|
24
|
+
|
|
25
|
+
Args:
|
|
26
|
+
download_urls (dict[str, str]): The URLs to download the program from.
|
|
27
|
+
program_name (str): The name of the program to download.
|
|
28
|
+
|
|
29
|
+
Returns:
|
|
30
|
+
bool: True if the program is now ready to use, False otherwise.
|
|
31
|
+
"""
|
|
32
|
+
# Ask the user if they want to download the upscaler
|
|
33
|
+
program_url: str = next(iter(download_urls.values())).split("/download/")[0]
|
|
34
|
+
warning(
|
|
35
|
+
f"Program executable not found, would you like to download it automatically from GitHub? (Y/n) :\n"
|
|
36
|
+
f"({program_url})"
|
|
37
|
+
)
|
|
38
|
+
|
|
39
|
+
# Handle the user's response
|
|
40
|
+
if input().lower() == "n":
|
|
41
|
+
info("User declined to download the upscaler.")
|
|
42
|
+
return False
|
|
43
|
+
|
|
44
|
+
# Get the platform
|
|
45
|
+
system: str = platform.system()
|
|
46
|
+
download_url: str = download_urls.get(system, "")
|
|
47
|
+
if not download_url:
|
|
48
|
+
warning(
|
|
49
|
+
f"Unsupported platform: {system}, please download the program manually from the following URL:\n"
|
|
50
|
+
f" {program_url}"
|
|
51
|
+
)
|
|
52
|
+
return False
|
|
53
|
+
|
|
54
|
+
# Download the upscaler
|
|
55
|
+
if not install_program(download_url, program_name=program_name, append_to_path=append_to_path):
|
|
56
|
+
warning("Failed to download the upscaler, please download it manually from the following URL:")
|
|
57
|
+
print(f" {download_url}")
|
|
58
|
+
return False
|
|
59
|
+
|
|
60
|
+
return True
|
|
61
|
+
|
|
62
|
+
def check_executable(
|
|
63
|
+
executable: str,
|
|
64
|
+
executable_help_text: str,
|
|
65
|
+
download_urls: dict[str, str],
|
|
66
|
+
append_to_path: str = ""
|
|
67
|
+
) -> None:
|
|
68
|
+
""" Check if the executable exists, optionally download it if it doesn't.
|
|
69
|
+
|
|
70
|
+
Args:
|
|
71
|
+
executable (str): The path to the executable.
|
|
72
|
+
executable_help_text (str): The help text to check for in the executable's output.
|
|
73
|
+
download_urls (dict[str, str]): The URLs to download the executable from.
|
|
74
|
+
append_to_path (str): The path to append to the executable's path.
|
|
75
|
+
(ex: "bin" if executables are in the bin folder)
|
|
76
|
+
"""
|
|
77
|
+
program_name: str = os.path.basename(executable)
|
|
78
|
+
try_download: bool = True
|
|
79
|
+
|
|
80
|
+
# Run the command, capture output, don't check exit code immediately
|
|
81
|
+
try:
|
|
82
|
+
result: subprocess.CompletedProcess[str] = subprocess.run(
|
|
83
|
+
[executable, "-h"],
|
|
84
|
+
capture_output=True,
|
|
85
|
+
text=True, # Decode stdout/stderr as text
|
|
86
|
+
check=False # Don't raise exception on non-zero exit code
|
|
87
|
+
)
|
|
88
|
+
|
|
89
|
+
# If the command failed (no help text matching), try to download the upscaler
|
|
90
|
+
try_download: bool = executable_help_text.lower() not in result.stdout.lower()
|
|
91
|
+
except FileNotFoundError:
|
|
92
|
+
try_download: bool = True
|
|
93
|
+
|
|
94
|
+
# If the command failed, try to download the upscaler
|
|
95
|
+
if try_download:
|
|
96
|
+
if not download_executable(download_urls, program_name, append_to_path=append_to_path):
|
|
97
|
+
warning(f"'{program_name}' is required but not available. Exiting.")
|
|
98
|
+
else:
|
|
99
|
+
info(f"'{program_name}' downloaded successfully, please restart the script.")
|
|
100
|
+
sys.exit(1)
|
|
101
|
+
|