Merge branch 'develop' into 'master'

Add tool scripts

See merge request Florent/idefix!1

.gitignore

@@ -3,3 +3,4 @@ doc/_build
 doc/source
 __pycache__
 log/
+.coverage

idefix/io.py

@@ -64,6 +64,14 @@ def load_las(fname):
             feature_data.append(att)
             feature_dtype.append((spec.name, att.dtype))
 
+    # XXX: Workaround missing num_returns in header
+    try:
+        att = infile.num_returns
+        feature_data.append(att)
+        feature_dtype.append(('num_returns', att.dtype))
+    except Exception:
+        pass
+
     log.debug('Create feature recarray')
     feature = np.core.records.fromarrays(feature_data, dtype=feature_dtype)
     del feature_data, feature_dtype

idefix/tools/txt_to_npz.py

@@ -0,0 +1,48 @@
+#!/usr/bin/env python
+# file txt_to_npz.py
+# author Florent Guiotte <florent.guiotte@uhb.fr>
+# version 0.0
+# date 24 mai 2019
+"""Convert point clouds from text files to Idefix file format.
+
+doc.
+"""
+
+import numpy as np
+import idefix.io as io
+from pathlib import Path
+import argparse
+from tqdm import tqdm
+
+def txt_to_npy(fname, header, delimiter=None, dtype=None, compression=False):
+    oname = fname.stem + '.npz'
+    pc = io.load_txt(fname, header, delimiter, dtype)
+    io.dump_pc(oname, pc, compression)
+
+def main():
+    parser = argparse.ArgumentParser(description='Convert point clouds from text files to Idefix file format.')
+    parser.add_argument('file', type=str, help='file or dir to convert')
+    parser.add_argument('header', type=str, help='field names of the data')
+    parser.add_argument('--dtype', '-t', type=str, help='field data types')
+    parser.add_argument('--delimiter', '-d', type=str, default=',', help='field data delimiter')
+    parser.add_argument('--compress', '-c', action='store_true', default=False, help='enable data compression')
+
+    args = parser.parse_args()
+    header = args.header.split()
+    dtype = [np.dtype(x) for x in args.dtype.split()] if args.dtype else None
+    delimiter = args.delimiter
+    compress = args.compress
+    wd = Path(args.file)
+
+    if wd.is_dir():
+        files = wd.glob('*.txt')
+    else:
+        files = (wd,)
+
+    pbar = tqdm(list(files))
+    for f in pbar:
+        pbar.write('Processing {}...'.format(f))
+        txt_to_npy(f, header, delimiter, dtype, compress)
+
+if __name__ == '__main__':
+    main()

idefix/vxl.py

@@ -131,7 +131,8 @@ def _bin_mean(grid, spatial, feature):
     density, edge = np.histogramdd(spatial, grid)
     weightd, edge = np.histogramdd(spatial, grid, weights=feature)
     mask = density == 0
-    return np.ma.masked_array(np.divide(weightd, density, where=~mask), mask)
+    return np.ma.masked_array(np.divide(weightd, density, where=~mask),
+                              mask, dtype=feature.dtype)
 
 def _bin_mode(grid, spatial, feature):
     '''Bin spatial in a grid, mode method.
@@ -289,7 +290,7 @@ def _squash_position(voxel_grid, method, axis):
     voxel_grid_where = list(xy_where)
     voxel_grid_where.insert(axis%(len(voxel_grid_where)+1), squash_id.compressed())
 
-    raster = np.zeros_like(squash_id)
+    raster = np.zeros_like(squash_id, dtype=voxel_grid.dtype)
     raster[xy_where] = voxel_grid[tuple(voxel_grid_where)]
 
     return raster

setup.py

@@ -11,10 +11,11 @@
 from distutils.core import setup
 
 setup(name='idefix',
-      version='0.0',
+      version='1.4',
       description='Utils and processing pipelines for LiDAR point clouds',
       author='Florent Guiotte',
       author_email='florent.guiotte@uhb.fr',
       url='https://git.guiotte.fr/Florent/Idefix',
-      packages=['idefix'],
+      packages=['idefix', 'idefix.tools'],
+      entry_points = {'console_scripts':['txt2npz = idefix.tools.txt_to_npz:main',]},
       )

test/test_io.py

@@ -15,8 +15,8 @@ from idefix import io
 @pytest.mark.parametrize('fname, exp_point_count, exp_field_count', [
     # TODO: test different LAS version
     # TODO: test LAS without field
-    ('test.las', 58629, 3, ),
-    #('test.laz', 58629, 3, ),
+    ('test.las', 58629, 4, ),
+    ('test.laz', 58629, 4, ),
 ])
 def test_load_las(datadir, fname, exp_point_count, exp_field_count):
     fname = datadir.join(fname)