Remove osgeo.utils dependency, smoke test pass

opendm/dem/commands.py

@@ -12,7 +12,7 @@ from opendm import system
 from opendm.concurrency import get_max_memory, parallel_map
 from scipy import ndimage
 from datetime import datetime
-from osgeo.utils.gdal_fillnodata import main as gdal_fillnodata
+from opendm.vendor.gdal_fillnodata import main as gdal_fillnodata
 from opendm import log
 try:
     import Queue as queue

opendm/vendor/gdal_fillnodata.py

@@ -0,0 +1,216 @@
+#!/usr/bin/env python3
+# ******************************************************************************
+#  $Id: gdal_fillnodata.py 124baa7f71f15396a661014a81b6c5b0c82c8004 2020-10-14 17:29:39 +0300 Idan Miara $
+#
+#  Project:  GDAL Python Interface
+#  Purpose:  Application for filling nodata areas in a raster by interpolation
+#  Author:   Frank Warmerdam, warmerdam@pobox.com
+#
+# ******************************************************************************
+#  Copyright (c) 2008, Frank Warmerdam
+#  Copyright (c) 2009-2011, Even Rouault <even dot rouault at spatialys.com>
+#
+#  Permission is hereby granted, free of charge, to any person obtaining a
+#  copy of this software and associated documentation files (the "Software"),
+#  to deal in the Software without restriction, including without limitation
+#  the rights to use, copy, modify, merge, publish, distribute, sublicense,
+#  and/or sell copies of the Software, and to permit persons to whom the
+#  Software is furnished to do so, subject to the following conditions:
+#
+#  The above copyright notice and this permission notice shall be included
+#  in all copies or substantial portions of the Software.
+#
+#  THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS
+#  OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+#  FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
+#  THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+#  LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+#  FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+#  DEALINGS IN THE SOFTWARE.
+# ******************************************************************************
+
+import sys
+
+from osgeo import gdal
+
+
+def CopyBand(srcband, dstband):
+    for line in range(srcband.YSize):
+        line_data = srcband.ReadRaster(0, line, srcband.XSize, 1)
+        dstband.WriteRaster(0, line, srcband.XSize, 1, line_data,
+                            buf_type=srcband.DataType)
+
+
+def Usage():
+    print("""
+gdal_fillnodata [-q] [-md max_distance] [-si smooth_iterations]
+                [-o name=value] [-b band]
+                srcfile [-nomask] [-mask filename] [-of format] [-co name=value]* [dstfile]
+""")
+    sys.exit(1)
+
+
+def main(argv):
+    max_distance = 100
+    smoothing_iterations = 0
+    options = []
+    quiet_flag = 0
+    src_filename = None
+    src_band = 1
+
+    dst_filename = None
+    frmt = 'GTiff'
+    creation_options = []
+
+    mask = 'default'
+
+    gdal.AllRegister()
+    argv = gdal.GeneralCmdLineProcessor(argv)
+    if argv is None:
+        sys.exit(0)
+
+    # Parse command line arguments.
+    i = 1
+    while i < len(argv):
+        arg = argv[i]
+
+        if arg == '-of' or arg == '-f':
+            i = i + 1
+            frmt = argv[i]
+
+        elif arg == '-co':
+            i = i + 1
+            creation_options.append(argv[i])
+
+        elif arg == '-q' or arg == '-quiet':
+            quiet_flag = 1
+
+        elif arg == '-si':
+            i = i + 1
+            smoothing_iterations = int(argv[i])
+
+        elif arg == '-b':
+            i = i + 1
+            src_band = int(argv[i])
+
+        elif arg == '-md':
+            i = i + 1
+            max_distance = float(argv[i])
+
+        elif arg == '-nomask':
+            mask = 'none'
+
+        elif arg == '-mask':
+            i = i + 1
+            mask = argv[i]
+
+        elif arg == '-mask':
+            i = i + 1
+            mask = argv[i]
+
+        elif arg[:2] == '-h':
+            Usage()
+
+        elif src_filename is None:
+            src_filename = argv[i]
+
+        elif dst_filename is None:
+            dst_filename = argv[i]
+
+        else:
+            Usage()
+
+        i = i + 1
+
+    if src_filename is None:
+        Usage()
+
+    # =============================================================================
+    # 	Verify we have next gen bindings with the sievefilter method.
+    # =============================================================================
+    try:
+        gdal.FillNodata
+    except AttributeError:
+        print('')
+        print('gdal.FillNodata() not available.  You are likely using "old gen"')
+        print('bindings or an older version of the next gen bindings.')
+        print('')
+        sys.exit(1)
+
+    # =============================================================================
+    # Open source file
+    # =============================================================================
+
+    if dst_filename is None:
+        src_ds = gdal.Open(src_filename, gdal.GA_Update)
+    else:
+        src_ds = gdal.Open(src_filename, gdal.GA_ReadOnly)
+
+    if src_ds is None:
+        print('Unable to open %s' % src_filename)
+        sys.exit(1)
+
+    srcband = src_ds.GetRasterBand(src_band)
+
+    if mask == 'default':
+        maskband = srcband.GetMaskBand()
+    elif mask == 'none':
+        maskband = None
+    else:
+        mask_ds = gdal.Open(mask)
+        maskband = mask_ds.GetRasterBand(1)
+
+    # =============================================================================
+    #       Create output file if one is specified.
+    # =============================================================================
+
+    if dst_filename is not None:
+
+        drv = gdal.GetDriverByName(frmt)
+        dst_ds = drv.Create(dst_filename, src_ds.RasterXSize, src_ds.RasterYSize, 1,
+                            srcband.DataType, creation_options)
+        wkt = src_ds.GetProjection()
+        if wkt != '':
+            dst_ds.SetProjection(wkt)
+        gt = src_ds.GetGeoTransform(can_return_null=True)
+        if gt:
+            dst_ds.SetGeoTransform(gt)
+
+        dstband = dst_ds.GetRasterBand(1)
+        CopyBand(srcband, dstband)
+        ndv = srcband.GetNoDataValue()
+        if ndv is not None:
+            dstband.SetNoDataValue(ndv)
+
+        color_interp = srcband.GetColorInterpretation()
+        dstband.SetColorInterpretation(color_interp)
+        if color_interp == gdal.GCI_PaletteIndex:
+            color_table = srcband.GetColorTable()
+            dstband.SetColorTable(color_table)
+
+    else:
+        dstband = srcband
+
+    # =============================================================================
+    # Invoke algorithm.
+    # =============================================================================
+
+    if quiet_flag:
+        prog_func = None
+    else:
+        prog_func = gdal.TermProgress_nocb
+
+    result = gdal.FillNodata(dstband, maskband,
+                             max_distance, smoothing_iterations, options,
+                             callback=prog_func)
+
+
+    src_ds = None
+    dst_ds = None
+    mask_ds = None
+
+    return result
+
+
+if __name__ == '__main__':
+    sys.exit(main(sys.argv))

requirements.txt

@@ -11,7 +11,7 @@ laspy==1.7.0
 lxml==4.6.1
 matplotlib==3.3.3
 networkx==2.5
-numpy==1.19.4
+numpy==1.21.1
 Pillow==8.0.1
 vmem==1.0.1
 pyodm==1.5.6

run.py

@@ -6,6 +6,13 @@ if sys.version_info.major < 3:
     print("Ups! ODM needs to run with Python 3. It seems you launched it with Python 2. Try using: python3 run.py ... ")
     sys.exit(1)
 
+# Set PROJ_LIB explicitly unless already set to fix Fiona imports
+# when multiple versions of the proj database are installed
+import os
+import pyproj
+if os.environ.get('PROJ_LIB') is None:
+    os.environ['PROJ_LIB'] = pyproj.datadir.get_data_dir()
+
 from opendm import log
 from opendm import config
 from opendm import system
@@ -14,8 +21,6 @@ from opendm.progress import progressbc
 from opendm.utils import double_quote, get_processing_results_paths
 from opendm.loghelpers import args_to_dict
 
-import os
-
 from stages.odm_app import ODMApp
 
 if __name__ == '__main__':