sigima 0.0.1.dev0__py3-none-any.whl → 1.0.0__py3-none-any.whl

sigima/proc/image/__init__.py

@@ -0,0 +1,513 @@
+# Copyright (c) DataLab Platform Developers, BSD 3-Clause license, see LICENSE file.
+
+"""
+Basic image processing
+~~~~~~~~~~~~~~~~~~~~~~
+
+.. automodule:: sigima.proc.image.base
+    :members:
+    :no-index:
+
+Arithmetic
+~~~~~~~~~~
+
+.. automodule:: sigima.proc.image.arithmetic
+    :members:
+    :no-index:
+
+Mathematical Operations
+~~~~~~~~~~~~~~~~~~~~~~~
+
+.. automodule:: sigima.proc.image.mathops
+    :members:
+    :no-index:
+
+Measurements
+~~~~~~~~~~~~
+
+.. automodule:: sigima.proc.image.measurement
+    :members:
+    :no-index:
+
+Extraction
+~~~~~~~~~~
+
+.. automodule:: sigima.proc.image.extraction
+    :members:
+    :no-index:
+
+Filtering
+~~~~~~~~~
+
+.. automodule:: sigima.proc.image.filtering
+    :members:
+    :no-index:
+
+Fourier
+~~~~~~~
+
+.. automodule:: sigima.proc.image.fourier
+    :members:
+    :no-index:
+
+Thresholding
+~~~~~~~~~~~~
+
+.. automodule:: sigima.proc.image.threshold
+    :members:
+    :no-index:
+
+Exposure correction
+~~~~~~~~~~~~~~~~~~~
+
+.. automodule:: sigima.proc.image.exposure
+    :members:
+    :no-index:
+
+Preprocessing
+~~~~~~~~~~~~~
+
+.. automodule:: sigima.proc.image.preprocessing
+    :members:
+    :no-index:
+
+Restoration
+~~~~~~~~~~~
+
+.. automodule:: sigima.proc.image.restoration
+    :members:
+    :no-index:
+
+Noise
+~~~~~
+
+.. automodule:: sigima.proc.image.noise
+    :members:
+    :no-index:
+
+Morphology
+~~~~~~~~~~
+
+.. automodule:: sigima.proc.image.morphology
+    :members:
+    :no-index:
+
+Edge detection
+~~~~~~~~~~~~~~
+
+.. automodule:: sigima.proc.image.edges
+    :members:
+    :no-index:
+
+Detection
+~~~~~~~~~
+
+.. automodule:: sigima.proc.image.detection
+    :members:
+    :no-index:
+
+Geometry
+~~~~~~~~
+
+.. automodule:: sigima.proc.image.geometry
+    :members:
+    :no-index:
+
+Transformation features
+^^^^^^^^^^^^^^^^^^^^^^^
+
+.. automodule:: sigima.proc.image.transformations
+    :members:
+    :no-index:
+"""
+
+# pylint: disable=invalid-name  # Allows short reference names like x, y, ...
+
+# MARK: Important notes
+# ---------------------
+# - All `guidata.dataset.DataSet` classes must also be imported
+#   in the `sigima.params` module.
+# - All functions decorated by `computation_function` defined in the other modules
+#   of this package must be imported right here.
+
+from __future__ import annotations
+
+import guidata.dataset as gds
+
+from sigima.config import _
+from sigima.enums import PadLocation2D
+from sigima.proc.image.arithmetic import (
+    addition,
+    addition_constant,
+    arithmetic,
+    average,
+    difference,
+    difference_constant,
+    division,
+    division_constant,
+    product,
+    product_constant,
+    quadratic_difference,
+    standard_deviation,
+)
+from sigima.proc.image.base import (
+    Wrap1to1Func,
+    compute_geometry_from_obj,
+    dst_1_to_1_signal,
+    restore_data_outside_roi,
+)
+from sigima.proc.image.detection import (
+    BlobDOGParam,
+    BlobDOHParam,
+    BlobLOGParam,
+    BlobOpenCVParam,
+    ContourShapeParam,
+    HoughCircleParam,
+    Peak2DDetectionParam,
+    blob_dog,
+    blob_doh,
+    blob_log,
+    blob_opencv,
+    contour_shape,
+    hough_circle_peaks,
+    peak_detection,
+)
+from sigima.proc.image.edges import (
+    CannyParam,
+    canny,
+    farid,
+    farid_h,
+    farid_v,
+    laplace,
+    prewitt,
+    prewitt_h,
+    prewitt_v,
+    roberts,
+    scharr,
+    scharr_h,
+    scharr_v,
+    sobel,
+    sobel_h,
+    sobel_v,
+)
+from sigima.proc.image.exposure import (
+    AdjustGammaParam,
+    AdjustLogParam,
+    AdjustSigmoidParam,
+    EqualizeAdaptHistParam,
+    EqualizeHistParam,
+    FlatFieldParam,
+    NormalizeParam,
+    RescaleIntensityParam,
+    adjust_gamma,
+    adjust_log,
+    adjust_sigmoid,
+    clip,
+    equalize_adapthist,
+    equalize_hist,
+    flatfield,
+    histogram,
+    normalize,
+    offset_correction,
+    rescale_intensity,
+)
+from sigima.proc.image.extraction import (
+    AverageProfileParam,
+    Direction,
+    LineProfileParam,
+    RadialProfileParam,
+    ROIGridParam,
+    SegmentProfileParam,
+    average_profile,
+    extract_roi,
+    extract_rois,
+    generate_image_grid_roi,
+    line_profile,
+    radial_profile,
+    segment_profile,
+)
+from sigima.proc.image.filtering import (
+    ButterworthParam,
+    GaussianFreqFilterParam,
+    butterworth,
+    gaussian_filter,
+    gaussian_freq_filter,
+    moving_average,
+    moving_median,
+    wiener,
+)
+from sigima.proc.image.fourier import (
+    fft,
+    ifft,
+    magnitude_spectrum,
+    phase_spectrum,
+    psd,
+)
+from sigima.proc.image.geometry import (
+    Resampling2DParam,
+    ResizeParam,
+    RotateParam,
+    TranslateParam,
+    UniformCoordsParam,
+    XYZCalibrateParam,
+    calibration,
+    fliph,
+    flipv,
+    resampling,
+    resize,
+    rotate,
+    rotate90,
+    rotate270,
+    set_uniform_coords,
+    translate,
+    transpose,
+)
+from sigima.proc.image.mathops import (
+    DataTypeIParam,
+    Log10ZPlusNParam,
+    absolute,
+    astype,
+    complex_from_magnitude_phase,
+    complex_from_real_imag,
+    convolution,
+    deconvolution,
+    exp,
+    imag,
+    inverse,
+    log10,
+    log10_z_plus_n,
+    phase,
+    real,
+)
+from sigima.proc.image.measurement import (
+    centroid,
+    enclosing_circle,
+    horizontal_projection,
+    stats,
+    vertical_projection,
+)
+from sigima.proc.image.morphology import (
+    MorphologyParam,
+    black_tophat,
+    closing,
+    dilation,
+    erosion,
+    opening,
+    white_tophat,
+)
+from sigima.proc.image.noise import (
+    add_gaussian_noise,
+    add_poisson_noise,
+    add_uniform_noise,
+)
+from sigima.proc.image.preprocessing import (
+    BinningParam,
+    ZeroPadding2DParam,
+    binning,
+    zero_padding,
+)
+from sigima.proc.image.restoration import (
+    DenoiseBilateralParam,
+    DenoiseTVParam,
+    DenoiseWaveletParam,
+    denoise_bilateral,
+    denoise_tophat,
+    denoise_tv,
+    denoise_wavelet,
+    erase,
+)
+from sigima.proc.image.threshold import (
+    ThresholdParam,
+    threshold,
+    threshold_isodata,
+    threshold_li,
+    threshold_mean,
+    threshold_minimum,
+    threshold_otsu,
+    threshold_triangle,
+    threshold_yen,
+)
+from sigima.proc.image.transformations import transformer
+
+__all__ = [
+    "AdjustGammaParam",
+    "AdjustLogParam",
+    "AdjustSigmoidParam",
+    "AverageProfileParam",
+    "BinningParam",
+    "BlobDOGParam",
+    "BlobDOHParam",
+    "BlobLOGParam",
+    "BlobOpenCVParam",
+    "ButterworthParam",
+    "CannyParam",
+    "ContourShapeParam",
+    "DataTypeIParam",
+    "DenoiseBilateralParam",
+    "DenoiseTVParam",
+    "DenoiseWaveletParam",
+    "Direction",
+    "EqualizeAdaptHistParam",
+    "EqualizeHistParam",
+    "FlatFieldParam",
+    "GaussianFreqFilterParam",
+    "GridParam",
+    "HoughCircleParam",
+    "LineProfileParam",
+    "Log10ZPlusNParam",
+    "MorphologyParam",
+    "NormalizeParam",
+    "PadLocation2D",
+    "Peak2DDetectionParam",
+    "ROIGridParam",
+    "RadialProfileParam",
+    "Resampling2DParam",
+    "RescaleIntensityParam",
+    "ResizeParam",
+    "RotateParam",
+    "SegmentProfileParam",
+    "ThresholdParam",
+    "TranslateParam",
+    "UniformCoordsParam",
+    "Wrap1to1Func",
+    "XYZCalibrateParam",
+    "ZeroPadding2DParam",
+    "absolute",
+    "add_gaussian_noise",
+    "add_poisson_noise",
+    "add_uniform_noise",
+    "addition",
+    "addition_constant",
+    "adjust_gamma",
+    "adjust_log",
+    "adjust_sigmoid",
+    "arithmetic",
+    "astype",
+    "average",
+    "average_profile",
+    "binning",
+    "black_tophat",
+    "blob_dog",
+    "blob_doh",
+    "blob_log",
+    "blob_opencv",
+    "butterworth",
+    "calibration",
+    "canny",
+    "centroid",
+    "clip",
+    "closing",
+    "complex_from_magnitude_phase",
+    "complex_from_real_imag",
+    "compute_geometry_from_obj",
+    "contour_shape",
+    "convolution",
+    "deconvolution",
+    "denoise_bilateral",
+    "denoise_tophat",
+    "denoise_tv",
+    "denoise_wavelet",
+    "difference",
+    "difference_constant",
+    "dilation",
+    "division",
+    "division_constant",
+    "dst_1_to_1_signal",
+    "enclosing_circle",
+    "equalize_adapthist",
+    "equalize_hist",
+    "erase",
+    "erosion",
+    "exp",
+    "extract_roi",
+    "extract_rois",
+    "farid",
+    "farid_h",
+    "farid_v",
+    "fft",
+    "flatfield",
+    "fliph",
+    "flipv",
+    "gaussian_filter",
+    "gaussian_freq_filter",
+    "generate_image_grid_roi",
+    "histogram",
+    "horizontal_projection",
+    "hough_circle_peaks",
+    "ifft",
+    "imag",
+    "inverse",
+    "laplace",
+    "line_profile",
+    "log10",
+    "log10_z_plus_n",
+    "magnitude_spectrum",
+    "moving_average",
+    "moving_median",
+    "normalize",
+    "offset_correction",
+    "opening",
+    "peak_detection",
+    "phase",
+    "phase_spectrum",
+    "prewitt",
+    "prewitt_h",
+    "prewitt_v",
+    "product",
+    "product_constant",
+    "psd",
+    "quadratic_difference",
+    "radial_profile",
+    "real",
+    "resampling",
+    "rescale_intensity",
+    "resize",
+    "restore_data_outside_roi",
+    "roberts",
+    "rotate",
+    "rotate90",
+    "rotate270",
+    "scharr",
+    "scharr_h",
+    "scharr_v",
+    "segment_profile",
+    "set_uniform_coords",
+    "sobel",
+    "sobel_h",
+    "sobel_v",
+    "standard_deviation",
+    "stats",
+    "threshold",
+    "threshold_isodata",
+    "threshold_li",
+    "threshold_mean",
+    "threshold_minimum",
+    "threshold_otsu",
+    "threshold_triangle",
+    "threshold_yen",
+    "transformer",
+    "translate",
+    "transpose",
+    "vertical_projection",
+    "white_tophat",
+    "wiener",
+    "zero_padding",
+]
+
+
+class GridParam(gds.DataSet):
+    """Grid parameters"""
+
+    _prop = gds.GetAttrProp("direction")
+    _directions = (("col", _("columns")), ("row", _("rows")))
+    direction = gds.ChoiceItem(_("Distribute over"), _directions, radio=True).set_prop(
+        "display", store=_prop
+    )
+    cols = gds.IntItem(_("Columns"), default=1, nonzero=True).set_prop(
+        "display", active=gds.FuncProp(_prop, lambda x: x == "col")
+    )
+    rows = gds.IntItem(_("Rows"), default=1, nonzero=True).set_prop(
+        "display", active=gds.FuncProp(_prop, lambda x: x == "row")
+    )
+    colspac = gds.FloatItem(_("Column spacing"), default=0.0, min=0.0)
+    rowspac = gds.FloatItem(_("Row spacing"), default=0.0, min=0.0)