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# -*- coding: utf-8 -*-
"""
Image preprocessing functions.
This module consolidates preprocessing functions that were previously scattered
across different modules (exposure, geometry, fourier). All functions in this
module operate on high-level ImageObj objects and use parameter classes from
the sigima.proc framework.
"""
from __future__ import annotations
import guidata.dataset as gds
import numpy as np
import sigima.enums
import sigima.tools.image
from sigima.config import _
from sigima.enums import PadLocation2D
from sigima.objects.image import ImageObj
from sigima.proc.decorator import computation_function
from sigima.proc.image.base import dst_1_to_1
__all__ = [
"BinningParam",
"ZeroPadding2DParam",
"binning",
"zero_padding",
]
class BinningParam(gds.DataSet):
"""Binning parameters."""
sx = gds.IntItem(
_("Cluster size (X)"),
default=2,
min=2,
help=_("Number of adjacent pixels to be combined together along X-axis."),
)
sy = gds.IntItem(
_("Cluster size (Y)"),
default=2,
min=2,
help=_("Number of adjacent pixels to be combined together along Y-axis."),
)
operation = gds.ChoiceItem(
_("Operation"),
sigima.enums.BinningOperation,
default=sigima.enums.BinningOperation.SUM,
)
dtypes = ["dtype"] + ImageObj.get_valid_dtypenames()
dtype_str = gds.ChoiceItem(
_("Data type"),
list(zip(dtypes, dtypes)),
help=_("Output image data type."),
)
change_pixel_size = gds.BoolItem(
_("Change pixel size"),
default=True,
help=_(
"If checked, pixel size is updated according to binning factors. "
"Users who prefer to work with pixel coordinates may want to uncheck this."
),
)
@computation_function()
def binning(src: ImageObj, p: BinningParam) -> ImageObj:
"""Binning: image pixel binning (or aggregation).
Depending on the algorithm, the input image may be cropped to fit an integer
number of blocks.
Args:
src: source image
p: parameters
Returns:
Output image
Raises:
ValueError: if source image has non-uniform coordinates
"""
if not src.is_uniform_coords:
raise ValueError("Binning only works with images having uniform coordinates")
# Create destination image
dst = dst_1_to_1(
src,
"binning",
f"{p.sx}x{p.sy},{p.operation},change_pixel_size={p.change_pixel_size}",
)
dst.data = sigima.tools.image.binning(
src.data,
sx=p.sx,
sy=p.sy,
operation=p.operation,
dtype=None if p.dtype_str == "dtype" else p.dtype_str,
)
if p.change_pixel_size:
if not np.isnan(src.dx) and not np.isnan(src.dy):
# Update coordinates with new pixel spacing
new_dx = src.dx * p.sx
new_dy = src.dy * p.sy
dst.set_uniform_coords(new_dx, new_dy, src.x0, src.y0)
return dst
class ZeroPadding2DParam(gds.DataSet):
"""Zero padding parameters for 2D images"""
def __init__(self, *args, **kwargs) -> None:
super().__init__(*args, **kwargs)
self.__obj: ImageObj | None = None
def update_from_obj(self, obj: ImageObj) -> None:
"""Update parameters from image"""
self.__obj = obj
self.choice_callback(None, self.strategy)
def choice_callback(self, item, value): # pylint: disable=unused-argument
"""Callback to update padding values"""
if self.__obj is None:
return
rows, cols = self.__obj.data.shape
if value == "next_pow2":
self.rows = 2 ** int(np.ceil(np.log2(rows))) - rows
self.cols = 2 ** int(np.ceil(np.log2(cols))) - cols
elif value == "multiple_of_64":
self.rows = (64 - rows % 64) if rows % 64 != 0 else 0
self.cols = (64 - cols % 64) if cols % 64 != 0 else 0
strategies = ("next_pow2", "multiple_of_64", "custom")
_prop = gds.GetAttrProp("strategy")
strategy = gds.ChoiceItem(
_("Padding strategy"), zip(strategies, strategies), default=strategies[-1]
).set_prop("display", store=_prop, callback=choice_callback)
_func_prop = gds.FuncProp(_prop, lambda x: x == "custom")
rows = gds.IntItem(_("Rows to add"), min=0, default=0).set_prop(
"display", active=_func_prop
)
cols = gds.IntItem(_("Columns to add"), min=0, default=0).set_prop(
"display", active=_func_prop
)
position = gds.ChoiceItem(
_("Padding position"), PadLocation2D, default=PadLocation2D.BOTTOM_RIGHT
)
@computation_function()
def zero_padding(
src: ImageObj,
p: ZeroPadding2DParam | None = None,
) -> ImageObj:
"""Zero-padding: add zeros to image borders.
Args:
src: input image object
p: parameters
Returns:
Output image object
"""
if p is None:
p = ZeroPadding2DParam.create()
if p.strategy == "custom":
suffix = f"rows={p.rows}, cols={p.cols}"
else:
suffix = f"strategy={p.strategy}"
suffix += f", position={p.position}"
dst = dst_1_to_1(src, "zero_padding", suffix)
result = sigima.tools.image.zero_padding(
src.data,
rows=p.rows,
cols=p.cols,
position=p.position,
)
dst.data = result
return dst
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