cars 1.0.0rc2__cp312-cp312-win_amd64.whl

cars/applications/resampling/resampling_algo.py

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+#!/usr/bin/env python
+# coding: utf8
+#
+# Copyright (c) 2020 Centre National d'Etudes Spatiales (CNES).
+#
+# This file is part of CARS
+# (see https://github.com/CNES/cars).
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+#
+"""
+Resampling module:
+contains functions used for epipolar resampling
+"""
+
+# Standard imports
+import math
+
+# Third party imports
+import numpy as np
+import rasterio as rio
+import resample as cresample
+from rasterio.windows import Window, bounds
+
+from cars.conf import mask_cst as msk_cst
+
+# CARS imports
+from cars.core import constants as cst
+from cars.core import datasets, inputs, tiling
+from cars.core.geometry import abstract_geometry
+
+
+def epipolar_rectify_images(  # pylint: disable=too-many-positional-arguments
+    left_imgs,
+    right_imgs,
+    grid1,
+    grid2,
+    region,
+    margins,
+    epipolar_size_x,
+    epipolar_size_y,
+    interpolator_image="bicubic",
+    interpolator_classif="nearest",
+    interpolator_mask="nearest",
+    step=None,
+    mask1=None,
+    mask2=None,
+    left_classifs=None,
+    right_classifs=None,
+    nodata1=0,
+    nodata2=0,
+    add_classif=True,
+):
+    """
+    Resample left and right images
+    """
+
+    # Force region to be float
+    region = [int(x) for x in region]
+
+    # Apply margins to left image
+    # TODO: tiled region should be given in parameter
+    # TODO: keep only rectification here (keep functional unitary approach)
+    left_region = region.copy()
+    left_margins = margins["left_margin"].data
+    left_roi = tiling.crop(
+        left_region, [0, 0, epipolar_size_x, epipolar_size_y]
+    )
+    left_region = tiling.crop(
+        tiling.pad(left_region, left_margins),
+        [0, 0, epipolar_size_x, epipolar_size_y],
+    )
+
+    left_margins = margins["left_margin"].data
+    # Get actual margin taking cropping into account
+    left_margins[0] = left_region[0] - left_roi[0]
+    left_margins[1] = left_region[1] - left_roi[1]
+    left_margins[2] = left_region[2] - left_roi[2]
+    left_margins[3] = left_region[3] - left_roi[3]
+
+    # Apply margins to right image
+    right_region = region.copy()
+    right_margins = margins["right_margin"].data
+    right_roi = tiling.crop(
+        right_region, [0, 0, epipolar_size_x, epipolar_size_y]
+    )
+    right_region = tiling.crop(
+        tiling.pad(right_region, right_margins),
+        [0, 0, epipolar_size_x, epipolar_size_y],
+    )
+
+    # Get actual margin taking cropping into account
+    right_margins[0] = right_region[0] - right_roi[0]
+    right_margins[1] = right_region[1] - right_roi[1]
+    right_margins[2] = right_region[2] - right_roi[2]
+    right_margins[3] = right_region[3] - right_roi[3]
+
+    # Resample left images
+    left_img_transform = inputs.rasterio_get_transform(
+        next(iter(left_imgs)), convention="north"
+    )
+
+    left_dataset = resample_image(
+        left_imgs,
+        grid1,
+        [epipolar_size_x, epipolar_size_y],
+        step=step,
+        region=left_region,
+        nodata=nodata1,
+        mask=mask1,
+        band_coords=cst.BAND_IM,
+        interpolator_img=interpolator_image,
+        interpolator_mask=interpolator_mask,
+        img_transform=left_img_transform,
+    )
+
+    # Update attributes
+    left_dataset.attrs[cst.ROI] = np.array(left_roi)
+    left_dataset.attrs[cst.ROI_WITH_MARGINS] = np.array(left_region)
+    # Remove region key as it duplicates roi_with_margins key
+    # left_dataset.attrs.pop("region", None)
+    left_dataset.attrs[cst.EPI_MARGINS] = np.array(left_margins)
+    if "disp_min" in margins.attrs:
+        left_dataset.attrs[cst.EPI_DISP_MIN] = margins.attrs["disp_min"]
+    if "disp_max" in margins.attrs:
+        left_dataset.attrs[cst.EPI_DISP_MAX] = margins.attrs["disp_max"]
+
+    # Resample right image
+    right_img_transform = inputs.rasterio_get_transform(next(iter(right_imgs)))
+    right_dataset = resample_image(
+        right_imgs,
+        grid2,
+        [epipolar_size_x, epipolar_size_y],
+        step=step,
+        region=right_region,
+        nodata=nodata2,
+        mask=mask2,
+        band_coords=cst.BAND_IM,
+        interpolator_img=interpolator_image,
+        interpolator_mask=interpolator_mask,
+        img_transform=right_img_transform,
+    )
+
+    # Update attributes
+    right_dataset.attrs[cst.ROI] = np.array(right_roi)
+    right_dataset.attrs[cst.ROI_WITH_MARGINS] = np.array(right_region)
+    # Remove region key as it duplicates roi_with_margins key
+    # right_dataset.attrs.pop("region", None)
+    right_dataset.attrs[cst.EPI_MARGINS] = np.array(right_margins)
+    if "disp_min" in margins.attrs:
+        right_dataset.attrs[cst.EPI_DISP_MIN] = margins.attrs["disp_min"]
+    if "disp_max" in margins.attrs:
+        right_dataset.attrs[cst.EPI_DISP_MAX] = margins.attrs["disp_max"]
+
+    # Resample classifications
+    left_classif_dataset = None
+    right_classif_dataset = None
+    if add_classif:
+        if left_classifs:
+            left_classif_dataset = resample_image(
+                left_classifs,
+                grid1,
+                [epipolar_size_x, epipolar_size_y],
+                region=left_region,
+                band_coords=cst.BAND_CLASSIF,
+                interpolator_img=interpolator_classif,
+                interpolator_mask=interpolator_mask,
+                img_transform=left_img_transform,
+            )
+        if right_classifs:
+            right_classif_dataset = resample_image(
+                right_classifs,
+                grid2,
+                [epipolar_size_x, epipolar_size_y],
+                region=right_region,
+                band_coords=cst.BAND_CLASSIF,
+                interpolator_img=interpolator_classif,
+                interpolator_mask=interpolator_mask,
+                img_transform=right_img_transform,
+            )
+
+    return (
+        left_dataset,
+        right_dataset,
+        left_classif_dataset,
+        right_classif_dataset,
+    )
+
+
+# pylint: disable=too-many-positional-arguments
+def resample_image(  # noqa: C901
+    imgs,
+    grid,
+    largest_size,
+    step=None,
+    region=None,
+    nodata=None,
+    mask=None,
+    band_coords=False,
+    interpolator_img="bicubic",
+    interpolator_mask="nearest",
+    img_transform=None,
+):
+    """
+    Resample image according to grid and largest size.
+
+    :param img: Path to the image to resample
+    :type img: string
+    :param grid: rectification grid dict
+    :type grid: dict
+    :param largest_size: Size of full output image
+    :type largest_size: list of two int
+    :param step: horizontal step of resampling (useful for strip resampling)
+    :type step: int
+    :param region: A subset of the output image to produce
+    :type region: None (full output is produced) or array of four floats
+                  [xmin,ymin,xmax,ymax]
+    :param nodata: Nodata value to use (both for input and output)
+    :type nodata: None or float
+    :param mask: Mask to resample as well
+    :type mask: None or path to mask image
+    :param band_coords: Force bands coordinate in output dataset
+    :type band_coords: boolean
+    :param interpolator: interpolator type (bicubic (default) or nearest)
+    :type interpolator: str ("nearest" "linear" "bco")
+    :rtype: xarray.Dataset with resampled image and mask
+    """
+    img_sample = next(iter(imgs))
+    # Handle region is None
+    if region is None:
+        region = [0, 0, largest_size[0], largest_size[1]]
+    else:
+        region = [
+            int(math.floor(region[0])),
+            int(math.floor(region[1])),
+            int(math.ceil(region[2])),
+            int(math.ceil(region[3])),
+        ]
+
+    if img_transform is None:
+        img_transform = inputs.rasterio_get_transform(
+            img_sample, convention="north"
+        )
+
+    # Convert largest_size to int if needed
+    largest_size = [int(x) for x in largest_size]
+
+    # Localize blocks of the tile to resample
+    if step is None:
+        step = region[2] - region[0]
+
+    xmin_of_blocks = np.arange(region[0], region[2], step)
+    xmax_of_blocks = np.append(
+        np.arange(region[0] + step, region[2], step), region[2]
+    )
+
+    ymin_of_blocks = np.arange(region[1], region[3], step)
+    ymax_of_blocks = np.append(
+        np.arange(region[1] + step, region[3], step), region[3]
+    )
+
+    resampled_images_list = []
+    resampled_masks_list = []
+    band_names = []
+    data_types = []
+    nodata_msk = msk_cst.NO_DATA_IN_EPIPOLAR_RECTIFICATION
+    for img in imgs:
+        bands = imgs[img]
+        if "band_id" in bands:
+            nb_bands = len(bands["band_id"])
+        elif "values" in bands:
+            nb_bands = len(bands["values"])
+        else:
+            raise ValueError(
+                "File {} not recognised as an image or classif file".format(
+                    bands
+                )
+            )
+        # Initialize outputs of the entire tile
+        resamp = np.empty(
+            (nb_bands, region[3] - region[1], region[2] - region[0]),
+            dtype=np.float32,
+        )
+        msk = np.empty(
+            (nb_bands, region[3] - region[1], region[2] - region[0]),
+            dtype=np.float32,
+        )
+
+        ystart = 0
+        with rio.open(grid["path"]) as grid_reader, rio.open(img) as img_reader:
+            for ymin, ymax in zip(ymin_of_blocks, ymax_of_blocks):  # noqa: B905
+                ysize = ymax - ymin
+                xstart = 0
+                for xmin, xmax in zip(  # noqa: B905
+                    xmin_of_blocks, xmax_of_blocks
+                ):
+                    block_region = [xmin, ymin, xmax, ymax]
+                    xsize = xmax - xmin
+                    resamp, msk = oversampling_func(
+                        grid_reader,
+                        img_reader,
+                        img_transform,
+                        block_region,
+                        interpolator_img,
+                        band_coords,
+                        nb_bands,
+                        bands,
+                        resamp,
+                        nodata,
+                        msk,
+                        mask,
+                        nodata_msk,
+                        interpolator_mask,
+                        ysize,
+                        xsize,
+                        ystart,
+                        xstart,
+                    )
+                    xstart += xsize
+
+                ystart += ysize
+        if "band_id" in bands:
+            band_names += bands["band_name"]
+        elif "values" in bands:
+            band_names += list(map(str, bands["values"]))
+        else:
+            raise ValueError(
+                "File {} not recognised as an image or classif file".format(
+                    bands
+                )
+            )
+        data_types += [inputs.rasterio_get_image_type(img)] * nb_bands
+        resampled_images_list.append(resamp)
+        resampled_masks_list.append(msk)
+
+    resamp_final = np.concatenate(resampled_images_list, axis=0)
+    msk_final = np.concatenate(resampled_masks_list, axis=0)
+    dataset = datasets.create_im_dataset(
+        resamp_final,
+        region,
+        largest_size,
+        img_sample,
+        band_coords,
+        band_names,
+        data_types,
+        msk_final,
+    )
+
+    return dataset
+
+
+def oversampling_func(  # pylint: disable=too-many-positional-arguments
+    grid_reader,
+    img_reader,
+    img_transform,
+    block_region,
+    interpolator_img,
+    band_coords,
+    nb_bands,
+    bands,
+    resamp,
+    nodata,
+    msk,
+    mask,
+    nodata_msk,
+    interpolator_mask,
+    ysize,
+    xsize,
+    ystart,
+    xstart,
+):
+    """
+    Do the resampling calculus
+    """
+
+    xmin = block_region[0]
+    ymin = block_region[1]
+    xmax = block_region[2]
+    ymax = block_region[3]
+
+    # Build rectification pipelines for images
+    res_x, res_y = grid_reader.res
+    assert res_x == res_y
+    oversampling = int(res_x)
+    assert res_x == oversampling
+
+    grid_origin_x = grid_reader.transform[2]
+    grid_origin_y = grid_reader.transform[5]
+    assert grid_origin_x == grid_origin_y
+    grid_margin = int(-grid_origin_x / oversampling - 0.5)
+
+    grid_margin = int(grid_margin)
+
+    # Convert resampled region to grid region with oversampling
+    grid_region = np.array(
+        [
+            math.floor(xmin / oversampling),
+            math.floor(ymin / oversampling),
+            math.ceil(xmax / oversampling),
+            math.ceil(ymax / oversampling),
+        ]
+    )
+
+    # Out region of epipolar image
+    out_region = oversampling * grid_region
+    # Grid region
+    grid_region += grid_margin
+
+    grid_window = Window.from_slices(
+        (grid_region[1], grid_region[3] + 1),
+        (grid_region[0], grid_region[2] + 1),
+    )
+    grid_as_array = grid_reader.read(window=grid_window)
+    grid_as_array = grid_as_array.astype(np.float32)
+    grid_as_array = grid_as_array.astype(np.float64)
+
+    # get needed source bounding box
+    left = math.floor(np.amin(grid_as_array[0, ...]))
+    right = math.ceil(np.amax(grid_as_array[0, ...]))
+    top = math.floor(np.amin(grid_as_array[1, ...]))
+    bottom = math.ceil(np.amax(grid_as_array[1, ...]))
+
+    transform = rio.Affine(*np.abs(img_transform))
+    # transform xmin and xmax positions to index
+    (top, bottom, left, right) = abstract_geometry.min_max_to_index_min_max(
+        left, right, top, bottom, transform
+    )
+
+    # filter margin for bicubic = 2
+    filter_margin = 2
+    top -= filter_margin
+    bottom += filter_margin
+    left -= filter_margin
+    right += filter_margin
+
+    left, right = list(np.clip([left, right], 0, img_reader.shape[0]))
+    top, bottom = list(np.clip([top, bottom], 0, img_reader.shape[1]))
+
+    img_window = Window.from_slices([left, right], [top, bottom])
+
+    in_sensor = True
+    if right - left == 0 or bottom - top == 0:
+        in_sensor = False
+
+    # round window
+    img_window = img_window.round_offsets()
+    img_window = img_window.round_lengths()
+
+    # compute offset
+    res_x = float(abs(transform[0]))
+    res_y = float(abs(transform[4]))
+    tile_bounds = list(bounds(img_window, transform))
+
+    x_offset = min(tile_bounds[0], tile_bounds[2])
+    y_offset = min(tile_bounds[1], tile_bounds[3])
+
+    if in_sensor:
+        # get sensor data
+        if "band_id" in bands:
+            # image
+            img_as_array = img_reader.read(bands["band_id"], window=img_window)
+        elif "values" in bands:
+            # classification
+            img_as_array = img_reader.read([1], window=img_window)
+        else:
+            raise ValueError(
+                "File {} not recognised as an image or classif file".format(
+                    bands
+                )
+            )
+        # get the nodata mask before blurring
+        img_nan_mask = img_as_array == nodata
+
+        # set the nodata values back
+        if nodata is not None:
+            img_as_array[img_nan_mask] = nodata
+
+        # shift grid regarding the img extraction
+        grid_as_array[0, ...] -= x_offset
+        grid_as_array[1, ...] -= y_offset
+
+        # apply input resolution
+        grid_as_array[0, ...] /= res_x
+        grid_as_array[1, ...] /= res_y
+
+        block_resamp = cresample.grid(
+            img_as_array,
+            grid_as_array,
+            oversampling,
+            interpolator=interpolator_img,
+            nodata=0,
+        ).astype(np.float32)
+
+        if interpolator_img == "bicubic" and band_coords == cst.BAND_CLASSIF:
+            block_resamp = np.where(
+                block_resamp >= 0.5,
+                1,
+                np.where(block_resamp < 0.5, 0, block_resamp),
+            ).astype(int)
+
+        # extract exact region
+        ext_region = block_region - out_region
+        block_resamp = block_resamp[
+            ...,
+            ext_region[1] : ext_region[3] - 1,
+            ext_region[0] : ext_region[2] - 1,
+        ]
+
+        if "values" in bands:
+            # Extract binary bands from mono-band classification
+            multiband_block_resamp = np.zeros(
+                (
+                    nb_bands,
+                    block_region[3] - block_region[1],
+                    block_region[2] - block_region[0],
+                )
+            )
+            for band_id, value in enumerate(bands["values"]):
+                multiband_block_resamp[band_id] = block_resamp == value
+            block_resamp = multiband_block_resamp
+
+    else:
+        block_resamp = np.zeros(
+            (
+                nb_bands,
+                block_region[3] - block_region[1],
+                block_region[2] - block_region[0],
+            )
+        )
+
+    resamp[:, ystart : ystart + ysize, xstart : xstart + xsize] = block_resamp
+
+    # create msk
+    if in_sensor:
+        # get mask in source geometry
+        if mask is not None:
+            with rio.open(mask) as msk_reader:
+                msk_as_array = msk_reader.read(1, window=img_window)
+            msk_as_array = np.array([msk_as_array] * img_as_array.shape[0])
+        else:
+            msk_as_array = np.zeros(img_as_array.shape)
+
+        if nodata is not None:
+            nodata_index = img_as_array == nodata
+            msk_as_array[nodata_index] = nodata_msk
+
+        # resample mask
+        block_msk = cresample.grid(
+            msk_as_array,
+            grid_as_array,
+            oversampling,
+            interpolator=interpolator_mask,
+            nodata=nodata_msk,
+        )
+
+        if interpolator_mask == "bicubic":
+            block_msk = np.where(
+                block_msk >= 0.5,
+                1,
+                np.where(block_msk < 0.5, 0, block_msk),
+            ).astype(int)
+
+        block_msk = block_msk[
+            ...,
+            ext_region[1] : ext_region[3] - 1,
+            ext_region[0] : ext_region[2] - 1,
+        ]
+    else:
+        block_msk = np.full(
+            (
+                nb_bands,
+                block_region[3] - block_region[1],
+                block_region[2] - block_region[0],
+            ),
+            fill_value=nodata_msk,
+        )
+
+    msk[:, ystart : ystart + ysize, xstart : xstart + xsize] = block_msk
+
+    return resamp, msk

cars/applications/resampling/resampling_constants.py

@@ -0,0 +1,36 @@
+#!/usr/bin/env python
+# coding: utf8
+#
+# Copyright (c) 2020 Centre National d'Etudes Spatiales (CNES).
+#
+# This file is part of CARS
+# (see https://github.com/CNES/cars).
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+#
+"""
+this module contains the constants of resampling.
+"""
+
+
+# USED VARIABLES
+
+
+RESAMPLING_RUN_TAG = "resampling"
+
+
+# PARAMS
+METHOD = "method"
+EPI_TILE_SIZE = "epi_tile_size"
+
+# INFOS