Run, report, and translate with pc_align for multi-processed altimetry

asp_plot/alignment.py

@@ -0,0 +1,224 @@
+import logging
+import os
+
+import numpy as np
+from osgeo import gdal, osr
+
+from asp_plot.utils import Raster, glob_file, run_subprocess_command
+
+logging.basicConfig(level=logging.WARNING)
+logger = logging.getLogger(__name__)
+
+
+class Alignment:
+    def __init__(
+        self,
+        directory,
+        dem_fn,
+        # aligned_dem_fn=None,
+        **kwargs,
+    ):
+        self.directory = directory
+
+        if not os.path.exists(dem_fn):
+            raise ValueError(f"DEM file not found: {dem_fn}")
+        self.dem_fn = dem_fn
+
+        # if aligned_dem_fn is not None and not os.path.exists(aligned_dem_fn):
+        #     raise ValueError(f"Aligned DEM file not found: {aligned_dem_fn}")
+        # self.aligned_dem_fn = aligned_dem_fn
+
+    # TODO: move all pc_align steps and dem translations to separate class
+    # call this alignment for different processing levels, with some minimum number
+    # of required points (a ~500 point parameter).
+    # Report all translation results to user via a dictionary and printing.
+    # If translation agrees within some tolerance (a 5% or 10% parameter) in XYZ components,
+    # apply the translation of the points found closest in time to the DEM.
+    def pc_align_dem_to_atl06sr(
+        self,
+        max_displacement=20,
+        max_source_points=10000000,
+        alignment_method="point-to-point",
+        atl06sr_csv=None,
+        output_prefix="pc_align/pc_align",
+    ):
+        if atl06sr_csv is None or not os.path.exists(atl06sr_csv):
+            raise ValueError(
+                f"\nATL06 filtered CSV file not found: {atl06sr_csv}\nWe need this to run pc_align. It can be created with the to_csv_for_pc_align() function in the Altimetry module.\n"
+            )
+
+        pc_align_folder = os.path.join(self.directory, output_prefix)
+
+        print(
+            f"Running pc_align on {self.dem_fn} and {atl06sr_csv}\nWriting to {pc_align_folder}*"
+        )
+
+        command = [
+            "pc_align",
+            "--max-displacement",
+            str(max_displacement),
+            "--max-num-source-points",
+            str(max_source_points),
+            "--alignment-method",
+            alignment_method,
+            "--csv-format",
+            "1:lon 2:lat 3:height_above_datum",
+            "--compute-translation-only",
+            "--output-prefix",
+            pc_align_folder,
+            self.dem_fn,
+            atl06sr_csv,
+        ]
+
+        run_subprocess_command(command)
+
+    def pc_align_report(self, output_prefix="pc_align/pc_align"):
+        pc_align_log = glob_file(self.directory, f"{output_prefix}-log-pc_align*.txt")
+
+        with open(pc_align_log, "r") as file:
+            content = file.readlines()
+
+        report = ""
+        for line in content:
+            if "Input: error percentile of smallest errors (meters):" in line:
+                report_line = line.split("[ console ] : ")[1]
+                report += report_line
+            if "Input: mean of smallest errors (meters):" in line:
+                report_line = line.split("[ console ] : ")[1]
+                report += report_line
+            if "Output: error percentile of smallest errors (meters):" in line:
+                report_line = line.split("[ console ] : ")[1]
+                report += report_line
+            if "Output: mean of smallest errors (meters):" in line:
+                report_line = line.split("[ console ] : ")[1]
+                report += report_line
+            if "Translation vector (Cartesian, meters):" in line:
+                report_line = line.split("[ console ] : ")[1]
+                report += report_line
+                ecef_shift = np.genfromtxt(
+                    [line.split("Vector3")[1][1:-2]], delimiter=","
+                )
+                report += f"\nECEF shift: {ecef_shift}\n"
+            if "Translation vector magnitude (meters):" in line:
+                report_line = line.split("[ console ] : ")[1]
+                report += report_line
+
+        return report
+
+    def apply_dem_translation(self, output_prefix="pc_align/pc_align", inv_trans=True):
+        def get_proj_shift(src_c, src_shift, s_srs, t_srs, inv_trans=True):
+            if s_srs.IsSame(t_srs):
+                proj_shift = src_shift
+            else:
+                src_c_shift = src_c + src_shift
+                src2proj = osr.CoordinateTransformation(s_srs, t_srs)
+                proj_c = np.array(src2proj.TransformPoint(*src_c))
+                proj_c_shift = np.array(src2proj.TransformPoint(*src_c_shift))
+                if inv_trans:
+                    proj_shift = proj_c - proj_c_shift
+                else:
+                    proj_shift = proj_c_shift - proj_c
+            # Reduce unnecessary precision
+            proj_shift = np.around(proj_shift, 3)
+            return proj_shift
+
+        pc_align_log = glob_file(self.directory, f"{output_prefix}-log-pc_align*.txt")
+
+        src = Raster(self.dem_fn)
+        src_a = src.read_array()
+        src_ndv = src.get_ndv()
+
+        # Need to extract from log to know how to compute translation
+        # if ref is csv and src is dem, want to transform source_center + shift
+        # if ref is dem and src is csv, want to inverse transform ref by shift applied at (source_center - shift)
+
+        llz_c = None
+        with open(pc_align_log, "r") as file:
+            content = file.readlines()
+
+        for line in content:
+            if "Centroid of source points (Cartesian, meters):" in line:
+                ecef_c = np.genfromtxt([line.split("Vector3")[1][1:-2]], delimiter=",")
+            if "Centroid of source points (lat,lon,z):" in line:
+                llz_c = np.genfromtxt([line.split("Vector3")[1][1:-2]], delimiter=",")
+            if "Translation vector (Cartesian, meters):" in line:
+                ecef_shift = np.genfromtxt(
+                    [line.split("Vector3")[1][1:-2]], delimiter=","
+                )
+            if "Translation vector (lat,lon,z):" in line:
+                llz_shift = np.genfromtxt(
+                    [line.split("Vector3")[1][1:-2]], delimiter=","
+                )
+                break
+
+        if llz_c is None:
+            raise ValueError(
+                f"\nLog file does not contain necessary translation information: {pc_align_log}\n"
+            )
+
+        # Reorder lat,lon,z to lon,lat,z (x,y,z)
+        i = [1, 0, 2]
+        llz_c = llz_c[i]
+        llz_shift = llz_shift[i]
+
+        ecef_srs = osr.SpatialReference()
+        ecef_srs.ImportFromEPSG(4978)
+
+        s_srs = ecef_srs
+        src_c = ecef_c
+        src_shift = ecef_shift
+
+        # Determine shift in original dataset coords
+        t_srs = osr.SpatialReference()
+        t_srs.ImportFromWkt(src.ds.crs.to_wkt())
+        proj_shift = get_proj_shift(src_c, src_shift, s_srs, t_srs, inv_trans)
+
+        aligned_dem_fn = self.dem_fn.replace(".tif", "_pc_align_translated.tif")
+        print(f"\nWriting out: {aligned_dem_fn}\n")
+
+        gdal_opt = ["COMPRESS=LZW", "TILED=YES", "PREDICTOR=3", "BIGTIFF=IF_SAFER"]
+        dst_ds = gdal.GetDriverByName("GTiff").CreateCopy(
+            aligned_dem_fn, gdal.Open(self.dem_fn), strict=0, options=gdal_opt
+        )
+        # Apply vertical shift
+        dst_b = dst_ds.GetRasterBand(1)
+        dst_b.SetNoDataValue(float(src_ndv))
+        dst_b.WriteArray(np.around((src_a + proj_shift[2]).filled(src_ndv), decimals=3))
+
+        dst_gt = list(dst_ds.GetGeoTransform())
+        # Apply horizontal shift directly to geotransform
+        dst_gt[0] += proj_shift[0]
+        dst_gt[3] += proj_shift[1]
+        dst_ds.SetGeoTransform(dst_gt)
+        dst_ds = None
+
+        return aligned_dem_fn
+
+    # DEPRECATED: Very slow, better to use apply_dem_translation().
+    # def generate_translated_dem(self, pc_align_output, dem_out_fn):
+    #     """
+    #     Very slow, better to use apply_dem_translation().
+    #     """
+    #     if not os.path.exists(pc_align_output):
+    #         raise ValueError(
+    #             f"\npc_align output not found: {pc_align_output}\n\nWe need this to generate the translated DEM.\n"
+    #         )
+
+    #     rast = Raster(self.dem_fn)
+    #     gsd = rast.get_gsd()
+    #     epsg = rast.get_epsg_code()
+
+    #     command = [
+    #         "point2dem",
+    #         "--tr",
+    #         str(gsd),
+    #         "--t_srs",
+    #         f"EPSG:{epsg}",
+    #         "--nodata-value",
+    #         str(-9999),
+    #         "-o",
+    #         dem_out_fn,
+    #         pc_align_output,
+    #     ]
+
+    #     run_subprocess_command(command)