cars 1.0.0rc1__cp312-cp312-manylinux_2_17_i686.manylinux2014_i686.whl

cars/applications/sparse_matching/sift_app.py

@@ -0,0 +1,735 @@
+#!/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 dense_matching application class.
+"""
+
+# pylint: disable= C0302
+
+# Standard imports
+import logging
+import os
+from typing import Dict, Tuple
+
+# Third party imports
+import numpy as np
+import pandas
+import xarray as xr
+from json_checker import And, Checker, Or
+
+import cars.applications.sparse_matching.sparse_matching_constants as sm_cst
+import cars.orchestrator.orchestrator as ocht
+from cars.applications import application_constants
+
+# CARS imports
+from cars.applications.sparse_matching import sparse_matching_algo
+from cars.applications.sparse_matching.abstract_sparse_matching_app import (
+    SparseMatching,
+)
+from cars.core import constants as cst
+from cars.core.utils import safe_makedirs
+from cars.data_structures import cars_dataset
+
+
+class Sift(SparseMatching, short_name=["sift"]):
+    """
+    SparseMatching
+    """
+
+    # pylint: disable=too-many-instance-attributes
+
+    def __init__(self, conf=None):
+        """
+        Init function of SparseMatching
+
+        :param conf: configuration for matching
+        :return: a application_to_use object
+        """
+
+        super().__init__(conf=conf)
+
+        # check conf
+        self.used_method = self.used_config["method"]
+        self.disparity_margin = self.used_config["disparity_margin"]
+        self.elevation_delta_lower_bound = self.used_config[
+            "elevation_delta_lower_bound"
+        ]
+        self.elevation_delta_upper_bound = self.used_config[
+            "elevation_delta_upper_bound"
+        ]
+        self.strip_margin = self.used_config["strip_margin"]
+        self.epipolar_error_upper_bound = self.used_config[
+            "epipolar_error_upper_bound"
+        ]
+        self.epipolar_error_maximum_bias = self.used_config[
+            "epipolar_error_maximum_bias"
+        ]
+
+        # minimum number of matches to continue with
+        self.minimum_nb_matches = self.used_config["minimum_nb_matches"]
+
+        # sifts
+        self.sift_matching_threshold = self.used_config[
+            "sift_matching_threshold"
+        ]
+        self.sift_n_octave = self.used_config["sift_n_octave"]
+        self.sift_n_scale_per_octave = self.used_config[
+            "sift_n_scale_per_octave"
+        ]
+        self.sift_peak_threshold = self.used_config["sift_peak_threshold"]
+        self.sift_edge_threshold = self.used_config["sift_edge_threshold"]
+        self.sift_magnification = self.used_config["sift_magnification"]
+        self.sift_window_size = self.used_config["sift_window_size"]
+        self.sift_back_matching = self.used_config["sift_back_matching"]
+        self.match_filter_knn = self.used_config["match_filter_knn"]
+        self.match_filter_constant = self.used_config["match_filter_constant"]
+        self.match_filter_mean_factor = self.used_config[
+            "match_filter_mean_factor"
+        ]
+        self.match_filter_dev_factor = self.used_config[
+            "match_filter_dev_factor"
+        ]
+        self.decimation_factor = self.used_config["decimation_factor"]
+        self.used_band = self.used_config["used_band"]
+
+        # Saving files
+        self.save_intermediate_data = self.used_config["save_intermediate_data"]
+
+        self.disparity_bounds_estimation = self.used_config[
+            "disparity_bounds_estimation"
+        ]
+
+        # Init orchestrator
+        self.orchestrator = None
+
+    def check_conf(self, conf):
+        """
+        Check configuration
+
+        :param conf: configuration to check
+        :type conf: dict
+
+        :return: overloaded configuration
+        :rtype: dict
+
+        """
+
+        # init conf
+        if conf is not None:
+            overloaded_conf = conf.copy()
+        else:
+            conf = {}
+            overloaded_conf = {}
+
+        # Overload conf
+        overloaded_conf["method"] = conf.get("method", "sift")
+        overloaded_conf["disparity_margin"] = conf.get("disparity_margin", 0.02)
+        overloaded_conf["elevation_delta_lower_bound"] = conf.get(
+            "elevation_delta_lower_bound", None
+        )
+        overloaded_conf["decimation_factor"] = conf.get("decimation_factor", 30)
+        overloaded_conf["elevation_delta_upper_bound"] = conf.get(
+            "elevation_delta_upper_bound", None
+        )
+        overloaded_conf["strip_margin"] = conf.get("strip_margin", 10)
+        overloaded_conf["epipolar_error_upper_bound"] = conf.get(
+            "epipolar_error_upper_bound", 10.0
+        )
+        overloaded_conf["epipolar_error_maximum_bias"] = conf.get(
+            "epipolar_error_maximum_bias", 50.0
+        )
+
+        # minimum number of matches to continue with
+        overloaded_conf["minimum_nb_matches"] = conf.get(
+            "minimum_nb_matches", 90
+        )
+
+        # sifts params
+        overloaded_conf["sift_matching_threshold"] = conf.get(
+            "sift_matching_threshold", 0.7
+        )
+        overloaded_conf["sift_n_octave"] = conf.get("sift_n_octave", 8)
+        overloaded_conf["sift_n_scale_per_octave"] = conf.get(
+            "sift_n_scale_per_octave", 3
+        )
+        overloaded_conf["sift_peak_threshold"] = conf.get(
+            "sift_peak_threshold", 4.0
+        )
+        overloaded_conf["sift_edge_threshold"] = conf.get(
+            "sift_edge_threshold", 10.0
+        )
+
+        overloaded_conf["sift_magnification"] = conf.get(
+            "sift_magnification", 7.0
+        )
+        overloaded_conf["sift_window_size"] = conf.get("sift_window_size", 2)
+        overloaded_conf["sift_back_matching"] = conf.get(
+            "sift_back_matching", True
+        )
+
+        overloaded_conf["match_filter_knn"] = conf.get("match_filter_knn", 25)
+
+        overloaded_conf["match_filter_constant"] = conf.get(
+            "match_filter_constant", 0.0
+        )
+
+        overloaded_conf["match_filter_mean_factor"] = conf.get(
+            "match_filter_mean_factor", 1.3
+        )
+
+        overloaded_conf["match_filter_dev_factor"] = conf.get(
+            "match_filter_dev_factor", 3.0
+        )
+
+        overloaded_conf["used_band"] = conf.get("used_band", "b0")
+
+        # Saving files
+        overloaded_conf["save_intermediate_data"] = conf.get(
+            "save_intermediate_data", False
+        )
+        self.save_intermediate_data = overloaded_conf["save_intermediate_data"]
+
+        # confidence filtering parameters
+        overloaded_conf["disparity_bounds_estimation"] = conf.get(
+            "disparity_bounds_estimation", {}
+        )
+
+        sparse_matching_schema = {
+            "method": str,
+            "disparity_margin": float,
+            "minimum_nb_matches": And(int, lambda x: x > 0),
+            "elevation_delta_lower_bound": Or(int, float, None),
+            "elevation_delta_upper_bound": Or(int, float, None),
+            "strip_margin": And(int, lambda x: x > 0),
+            "epipolar_error_upper_bound": And(float, lambda x: x > 0),
+            "epipolar_error_maximum_bias": And(float, lambda x: x >= 0),
+            "sift_matching_threshold": And(float, lambda x: x > 0),
+            "sift_n_octave": And(int, lambda x: x > 0),
+            "sift_n_scale_per_octave": And(int, lambda x: x > 0),
+            "sift_peak_threshold": Or(float, int),
+            "sift_edge_threshold": float,
+            "sift_magnification": And(float, lambda x: x > 0),
+            "sift_window_size": And(int, lambda x: x > 0),
+            "decimation_factor": And(int, lambda x: x > 0),
+            "sift_back_matching": bool,
+            "match_filter_knn": int,
+            "match_filter_constant": Or(int, float),
+            "match_filter_mean_factor": Or(int, float),
+            "match_filter_dev_factor": Or(int, float),
+            "used_band": str,
+            "save_intermediate_data": bool,
+            "disparity_bounds_estimation": dict,
+        }
+
+        # Check conf
+        checker = Checker(sparse_matching_schema)
+        checker.validate(overloaded_conf)
+
+        self.check_conf_disparity_bounds_estimation(overloaded_conf)
+
+        # Check consistency between bounds for elevation delta
+        elevation_delta_lower_bound = overloaded_conf[
+            "elevation_delta_lower_bound"
+        ]
+        elevation_delta_upper_bound = overloaded_conf[
+            "elevation_delta_upper_bound"
+        ]
+        if None not in (
+            elevation_delta_lower_bound,
+            elevation_delta_upper_bound,
+        ):
+            if elevation_delta_lower_bound > elevation_delta_upper_bound:
+                raise ValueError(
+                    "Upper bound must be bigger than "
+                    "lower bound for expected elevation delta"
+                )
+
+        return overloaded_conf
+
+    def get_required_bands(self):
+        """
+        Get bands required by this application
+
+        :return: required bands for left and right image
+        :rtype: dict
+        """
+        required_bands = {}
+        required_bands["left"] = [self.used_band]
+        required_bands["right"] = [self.used_band]
+        return required_bands
+
+    def check_conf_disparity_bounds_estimation(self, overloaded_conf):
+        """
+        Check the disparity bounds estimation conf
+        """
+        overloaded_conf["disparity_bounds_estimation"]["activated"] = (
+            overloaded_conf["disparity_bounds_estimation"].get(
+                "activated", True
+            )
+        )
+        overloaded_conf["disparity_bounds_estimation"]["percentile"] = (
+            overloaded_conf["disparity_bounds_estimation"].get("percentile", 1)
+        )
+        overloaded_conf["disparity_bounds_estimation"]["lower_margin"] = (
+            overloaded_conf["disparity_bounds_estimation"].get(
+                "lower_margin", 500
+            )
+        )
+        overloaded_conf["disparity_bounds_estimation"]["upper_margin"] = (
+            overloaded_conf["disparity_bounds_estimation"].get(
+                "upper_margin", 1000
+            )
+        )
+
+        disparity_bounds_estimation_schema = {
+            "activated": bool,
+            "percentile": Or(int, float),
+            "upper_margin": int,
+            "lower_margin": int,
+        }
+
+        checker_disparity_bounds_estimation_schema = Checker(
+            disparity_bounds_estimation_schema
+        )
+        checker_disparity_bounds_estimation_schema.validate(
+            overloaded_conf["disparity_bounds_estimation"]
+        )
+
+    def get_save_matches(self):
+        """
+        Get save_matches parameter
+
+        :return: true is save_matches activated
+        :rtype: bool
+        """
+
+        return self.save_intermediate_data
+
+    def get_disparity_margin(self):
+        """
+        Get disparity margin corresponding to sparse matches
+
+        :return: margin in percent
+
+        """
+        return self.disparity_margin
+
+    def get_strip_margin(self):
+        """
+        Get strip margin corresponding to sparse matches
+
+        :return: margin in percent
+
+        """
+        return self.strip_margin
+
+    def get_epipolar_error_upper_bound(self):
+        """
+        Get epipolar error upper bound corresponding to sparse matches
+
+        :return: margin
+
+        """
+
+        return self.epipolar_error_upper_bound
+
+    def get_minimum_nb_matches(self):
+        """
+        Get minimum_nb_matches :
+        get the minimum number of matches
+
+        :return: minimum_nb_matches
+
+        """
+
+        return self.minimum_nb_matches
+
+    def get_epipolar_error_maximum_bias(self):
+        """
+        Get epipolar error maximum bias corresponding to sparse matches
+
+        :return: margin
+
+        """
+
+        return self.epipolar_error_maximum_bias
+
+    def get_match_filter_knn(self):
+        """
+        Get match_filter_knn :
+        number of neighboors used to measure isolation of matches
+
+        :return: match_filter_knn
+
+        """
+        return self.match_filter_knn
+
+    def get_match_filter_constant(self):
+        """
+        Get get_match_filter_constant :
+        constant in the formula to compute threshold of outliers
+
+        :return: match_filter_constant
+
+        """
+        return self.match_filter_constant
+
+    def get_match_filter_mean_factor(self):
+        """
+        Get match_filter_mean_factor :
+        factor of mean in the formula
+        to compute threshold of outliers
+
+        :return: match_filter_mean_factor
+
+        """
+        return self.match_filter_mean_factor
+
+    def get_match_filter_dev_factor(self):
+        """
+        Get match_filter_dev_factor :
+        factor of deviation in the formula
+        to compute threshold of outliers
+
+        :return: match_filter_dev_factor
+
+        """
+        return self.match_filter_dev_factor
+
+    def get_decimation_factor(self):
+        """
+        Get decimation_factor
+
+        :return: decimation_factor
+
+        """
+        return self.decimation_factor
+
+    def set_decimation_factor(self, value):
+        """
+        set decimation_factor
+
+        """
+        self.decimation_factor = value
+
+    def run(  # pylint: disable=too-many-positional-arguments
+        self,
+        epipolar_image_left,
+        epipolar_image_right,
+        disp_to_alt_ratio,
+        orchestrator=None,
+        pair_folder=None,
+        pair_key="PAIR_0",
+        classif_bands_to_mask=None,
+    ):
+        """
+        Run Matching application.
+
+        Create left and right CarsDataset filled with pandas.DataFrame ,
+        corresponding to epipolar 2D disparities, on the same geometry
+        that epipolar_image_left and epipolar_image_right.
+
+        :param epipolar_image_left: tiled left epipolar. CarsDataset contains:
+
+                - N x M Delayed tiles \
+                    Each tile will be a future xarray Dataset containing:
+
+                    - data with keys : "im", "msk", "texture"
+                    - attrs with keys: "margins" with "disp_min" and "disp_max"
+                        "transform", "crs", "valid_pixels", "no_data_mask",
+                        "no_data_img"
+                - attributes containing:
+                    "largest_epipolar_region","opt_epipolar_tile_size"
+        :type epipolar_image_left: CarsDataset
+        :param epipolar_image_right: tiled right epipolar.CarsDataset contains:
+
+                - N x M Delayed tiles \
+                    Each tile will be a future xarray Dataset containing:
+
+                    - data with keys : "im", "msk", "texture"
+                    - attrs with keys: "margins" with "disp_min" and "disp_max"\
+                        "transform", "crs", "valid_pixels", "no_data_mask",\
+                        "no_data_img"
+                - attributes containing:"largest_epipolar_region", \
+                  "opt_epipolar_tile_size"
+        :type epipolar_image_right: CarsDataset
+        :param disp_to_alt_ratio: disp to alti ratio
+        :type disp_to_alt_ratio: float
+        :param orchestrator: orchestrator used
+        :param pair_folder: folder used for current pair
+        :type pair_folder: str
+        :param pair_key: pair key id
+        :type pair_key: str
+        :param classif_bands_to_mask: bands from classif to mask
+        :type classif_bands_to_mask: list of str / int
+
+        :return left matches, right matches. Each CarsDataset contains:
+
+            - N x M Delayed tiles \
+                Each tile will be a future pandas DataFrame containing:
+                - data : (L, 4) shape matches
+            - attributes containing "disp_lower_bound",  "disp_upper_bound",\
+                "elevation_delta_lower_bound","elevation_delta_upper_bound"
+
+        :rtype: Tuple(CarsDataset, CarsDataset)
+        """
+        # Default orchestrator
+        if orchestrator is None:
+            # Create default sequential orchestrator for current application
+            # be awere, no out_json will be shared between orchestrators
+            # No files saved
+            self.orchestrator = ocht.Orchestrator(
+                orchestrator_conf={"mode": "sequential"}
+            )
+        else:
+            self.orchestrator = orchestrator
+
+        if pair_folder is None:
+            pair_folder = os.path.join(self.orchestrator.out_dir, "tmp")
+
+        if epipolar_image_left.dataset_type == "arrays":
+            # Create CarsDataset
+            # Epipolar_disparity
+            epipolar_disparity_map_left = cars_dataset.CarsDataset(
+                "points", name="sparse_matching_" + pair_key
+            )
+            epipolar_disparity_map_left.create_empty_copy(epipolar_image_left)
+
+            # Update attributes to get epipolar info
+            epipolar_disparity_map_left.attributes.update(
+                epipolar_image_left.attributes
+            )
+
+            # Save disparity maps
+            if self.save_intermediate_data:
+                safe_makedirs(pair_folder)
+
+                self.orchestrator.add_to_save_lists(
+                    os.path.join(pair_folder, "epi_matches_left"),
+                    None,
+                    epipolar_disparity_map_left,
+                    cars_ds_name="epi_matches_left",
+                )
+
+            # Compute disparity range
+            if self.elevation_delta_lower_bound is None:
+                disp_upper_bound = np.inf
+            else:
+                disp_upper_bound = (
+                    -self.elevation_delta_lower_bound / disp_to_alt_ratio
+                )
+            if self.elevation_delta_upper_bound is None:
+                disp_lower_bound = -np.inf
+            else:
+                disp_lower_bound = (
+                    -self.elevation_delta_upper_bound / disp_to_alt_ratio
+                )
+
+            attributes = {
+                "disp_lower_bound": disp_lower_bound,
+                "disp_upper_bound": disp_upper_bound,
+                "elevation_delta_lower_bound": self.elevation_delta_lower_bound,
+                "elevation_delta_upper_bound": self.elevation_delta_upper_bound,
+            }
+
+            epipolar_disparity_map_left.attributes.update(attributes)
+
+            # Get saving infos in order to save tiles when they are computed
+            [saving_info_left] = self.orchestrator.get_saving_infos(
+                [epipolar_disparity_map_left]
+            )
+
+            # Update orchestrator out_json
+            updating_infos = {
+                application_constants.APPLICATION_TAG: {
+                    sm_cst.SPARSE_MATCHING_RUN_TAG: {
+                        pair_key: {
+                            sm_cst.DISP_LOWER_BOUND: disp_lower_bound,
+                            sm_cst.DISP_UPPER_BOUND: disp_upper_bound,
+                        },
+                    }
+                }
+            }
+            orchestrator.update_out_info(updating_infos)
+            logging.info(
+                "Generate disparity: Number tiles: {}".format(
+                    epipolar_disparity_map_left.shape[1]
+                    * epipolar_disparity_map_left.shape[0]
+                )
+            )
+
+            # Add to replace list so tiles will be readable at the same time
+            self.orchestrator.add_to_replace_lists(
+                epipolar_disparity_map_left, cars_ds_name="epi_matches_left"
+            )
+            # Generate disparity maps
+            total_nb_band_sift = epipolar_disparity_map_left.shape[0]
+
+            step = int(np.round(100 / self.decimation_factor))
+
+            if total_nb_band_sift in (1, 2):
+                step = 1
+            elif total_nb_band_sift == 3:
+                step = 2
+
+            for row in range(0, total_nb_band_sift, step):
+                # initialize list of matches
+                full_saving_info_left = ocht.update_saving_infos(
+                    saving_info_left, row=row, col=0
+                )
+                # Compute matches
+                if type(None) not in (
+                    type(epipolar_image_left[row, 0]),
+                    type(epipolar_image_right[row, 0]),
+                ):
+                    (
+                        epipolar_disparity_map_left[row, 0]
+                    ) = self.orchestrator.cluster.create_task(
+                        compute_matches_wrapper, nout=1
+                    )(
+                        epipolar_image_left[row, 0],
+                        epipolar_image_right[row, 0],
+                        used_band=self.used_band,
+                        matching_threshold=self.sift_matching_threshold,
+                        n_octave=self.sift_n_octave,
+                        n_scale_per_octave=self.sift_n_scale_per_octave,
+                        peak_threshold=self.sift_peak_threshold,
+                        edge_threshold=self.sift_edge_threshold,
+                        magnification=self.sift_magnification,
+                        window_size=self.sift_window_size,
+                        backmatching=self.sift_back_matching,
+                        disp_lower_bound=disp_lower_bound,
+                        disp_upper_bound=disp_upper_bound,
+                        saving_info_left=full_saving_info_left,
+                        classif_bands_to_mask=classif_bands_to_mask,
+                    )
+
+        else:
+            logging.error(
+                "SparseMatching application doesn't "
+                "support this input data format"
+            )
+
+        return epipolar_disparity_map_left, None
+
+
+def compute_matches_wrapper(  # pylint: disable=too-many-positional-arguments
+    left_image_object: xr.Dataset,
+    right_image_object: xr.Dataset,
+    used_band="b0",
+    matching_threshold=None,
+    n_octave=None,
+    n_scale_per_octave=None,
+    peak_threshold=None,
+    edge_threshold=None,
+    magnification=None,
+    window_size=None,
+    backmatching=None,
+    disp_lower_bound=None,
+    disp_upper_bound=None,
+    saving_info_left=None,
+    classif_bands_to_mask=None,
+) -> Dict[str, Tuple[xr.Dataset, xr.Dataset]]:
+    """
+    Compute matches from image objects.
+    This function will be run as a delayed task.
+
+    User must provide saving infos to save properly created datasets
+
+    :param left_image_object: tiled Left image dataset with :
+
+            - cst.EPI_IMAGE
+            - cst.EPI_MSK (if given)
+            - cst.EPI_TEXTURE (for left, if given)
+    :type left_image_object: xr.Dataset with :
+
+            - cst.EPI_IMAGE
+            - cst.EPI_MSK (if given)
+            - cst.EPI_TEXTURE (for left, if given)
+    :param right_image_object: tiled Right image
+    :type right_image_object: xr.Dataset
+    :param classif_bands_to_mask: bands from classif to mask
+    :type classif_bands_to_mask: list of str / int
+
+
+    :return: Left matches object, Right matches object (if exists)
+
+    Returned objects are composed of :
+
+        - dataframe (None for right object) with :
+            - TODO
+    """
+
+    # Create mask
+    # TODO : remove overwriting of EPI_MSK
+    saved_left_mask = np.copy(left_image_object[cst.EPI_MSK].values)
+    saved_right_mask = np.copy(right_image_object[cst.EPI_MSK].values)
+
+    # Compute matches
+    matches = sparse_matching_algo.dataset_matching(
+        left_image_object,
+        right_image_object,
+        used_band,
+        matching_threshold=matching_threshold,
+        n_octave=n_octave,
+        n_scale_per_octave=n_scale_per_octave,
+        peak_threshold=peak_threshold,
+        edge_threshold=edge_threshold,
+        magnification=magnification,
+        window_size=window_size,
+        backmatching=backmatching,
+        disp_lower_bound=disp_lower_bound,
+        disp_upper_bound=disp_upper_bound,
+        classif_bands_to_mask=classif_bands_to_mask,
+    )
+
+    # Filter matches outside disparity range
+    if disp_lower_bound is not None and disp_upper_bound is not None:
+        filtered_nb_matches = matches.shape[0]
+
+        matches = matches[matches[:, 2] - matches[:, 0] >= disp_lower_bound]
+        matches = matches[matches[:, 2] - matches[:, 0] <= disp_upper_bound]
+
+        logging.debug(
+            "{} matches discarded because they fall outside of disparity range "
+            "defined by --elevation_delta_lower_bound and "
+            "--elevation_delta_upper_bound: [{} pix., {} pix.]".format(
+                filtered_nb_matches - matches.shape[0],
+                disp_lower_bound,
+                disp_upper_bound,
+            )
+        )
+    else:
+        logging.debug("Matches outside disparity range were not filtered")
+
+    # convert to Dataframe
+    left_matches_dataframe = pandas.DataFrame(matches)
+
+    # recover initial mask data in input images
+    # TODO remove with proper dataset creation
+    left_image_object[cst.EPI_MSK].values = saved_left_mask
+    right_image_object[cst.EPI_MSK].values = saved_right_mask
+
+    cars_dataset.fill_dataframe(
+        left_matches_dataframe, saving_info=saving_info_left, attributes=None
+    )
+
+    return left_matches_dataframe