add fix geotransform function from old preprocessor and adapt it for jp2 driver open & close

core/registrar/source.py

@@ -67,7 +67,7 @@ class SwiftSource(Source):
 
     def get_container_and_path(self, path: str):
         container = self.container
-        if container is None:
+        if container is None or container == '':
             parts = (path[1:] if path.startswith('/') else path).split('/')
             container, path = parts[0], '/'.join(parts[1:])
 

preprocessor/preprocessor/config-schema.yaml

@@ -125,7 +125,7 @@ definitions:
               type:
                 description: The type of georeferencing to apply.
                 type: string
-                enum: [gcp, rpc, corner, world, no_op] # TODO: more
+                enum: [gcp, rpc, corner, world, no_op, fix_geotrans] # TODO: more
               options:
                 description: Additional options for the georeferencing. Depends on the type of georeferencing.
                 type: object

preprocessor/preprocessor/steps/georeference.py

@@ -26,6 +26,8 @@ def georeference_step(source_dir: os.PathLike, target_dir: os.PathLike, preproce
             georef_func = corner_georef
         elif type_name == 'no_op':
             georef_func = no_op
+        elif type_name == 'fix_geotrans':
+            georef_func = fix_geotrans
         else:
             raise Exception('Invalid georeference type %s' % type_name)
         try:
@@ -166,6 +168,57 @@ def no_op(input_filename: os.PathLike, target_filename: os.PathLike):
     shutil.move(input_filename, target_filename)
 
 
+def fix_geotrans(input_filename: os.PathLike, target_filename: os.PathLike, warp_options: dict=None):
+    # assumes already existing geotransform and if xres=0,yres=0, fixes it
+    try:
+        ds = gdal.Open(input_filename, gdal.GA_Update)
+    except RuntimeError:
+        logger.warn('Can not open file by GDAL %s' % (input_filename))
+        return
+    ds = correct_geo_transform(ds)
+    if ds.GetDriver().ShortName == 'JP2OpenJPEG':
+        # workaround for rewriting jp2 files and exception thrown by "USE_SRC_CODESTREAM=YES specified, but no codestream found"
+        # then needs .vrt configured in data_file_globs too
+        target_filename = replace_ext(target_filename, '.vrt'),
+    gdal.Warp(
+        target_filename,
+        ds,
+        **(warp_options or {}),
+    )
+
+
+def correct_geo_transform(src_ds):
+    # input - gdal dataset
+    # sets new geotransform if necessary by creating control points of a raster with switched height and width
+    # returns - gdal dataset
+    ulx, xres, xskew, uly, yskew, yres = src_ds.GetGeoTransform()
+    logger.debug("Testing for malformed geotransform")
+    # test geotransform if necessary to shift
+    if xres == 0.0 and yres == 0.0:
+        logger.info("Malformed geotransform xres,yres=0 detected, correcting.")
+        # malformed image, compute xres and yres switched in geotransform
+        lrx = ulx + (src_ds.RasterXSize * xskew)
+        lry = uly + (src_ds.RasterYSize * yskew)
+        # [ulx, lrx, lry, uly] - bounds = lon_min, lon_max, lat_min, lat_max
+        fp = [[0, src_ds.RasterXSize, src_ds.RasterXSize, 0], [0, 0, src_ds.RasterYSize, src_ds.RasterYSize]]
+        tp = [[ulx, lrx, lrx, ulx], [lry, lry, uly, uly]]
+        pix = list(zip(fp[0], fp[1]))
+        coor = list(zip(tp[0], tp[1]))
+        # compute the gdal.GCP parameters
+        gcps = []
+        for index, txt in enumerate(pix):
+            gcps.append(gdal.GCP())
+            gcps[index].GCPPixel = pix[index][0]
+            gcps[index].GCPLine = src_ds.RasterYSize - int(pix[index][1])
+            gcps[index].GCPX = coor[index][0]
+            gcps[index].GCPY = coor[index][1]
+        # get correct geotransform from gcps
+        geotransform_new = gdal.GCPsToGeoTransform(gcps)
+        # overwrite geotransform with new
+        src_ds.SetGeoTransform(geotransform_new)
+    return src_ds
+
+
 def gcps_from_borders(size: Tuple[float, float], coords: List[Tuple[float, float]], orbit_direction: str, force_north_up: bool=False):
     x_size, y_size = size
     # expects coordinates in dict(.*border_left.*:[lat,lon],...)