Load LAS file into pcloud format

idefix/io.py

@@ -0,0 +1,74 @@
+#!/usr/bin/env python
+# file io.py
+# author Florent Guiotte <florent.guiotte@uhb.fr>
+# version 0.0
+# date 04 mars 2019
+"""Abstract
+
+doc.
+"""
+
+import logging
+from pathlib import Path
+import numpy as np
+from numpy.lib import recfunctions as rfn
+import laspy
+
+log = logging.getLogger(__name__) 
+
+def load_las(fname):
+    '''Load a LAS file into idefix point cloud format.
+
+    Notes
+    -----
+    The empty fields from LAS format will be automatically stripped. The fields
+    typing are automatically determined.
+
+    Parameters
+    ----------
+    fname : string, Path
+        Path to the LAS file to load.
+
+    Returns
+    -------
+    pcloud : recarray
+        Point cloud respecting structure::
+
+        [(spatial), (feature, [f1, f2, ..., fn])]
+    '''
+    fname = Path(fname)
+    if not fname.is_file():
+        msg = 'No such file: \'{}\''.format(fname)
+        log.error(msg)
+        raise IOError(msg)
+
+    log.info('Loading LAS file \'{}\'...'.format(fname))
+    infile = laspy.file.File(fname)
+
+    log.debug('Extract spatial data')
+    spatial = np.core.records.fromarrays([np.array((infile.x, infile.y, infile.z)).T], 
+                                         dtype=[('spatial', np.float, 3)])
+
+    log.debug('Extract feature data')
+    feature_data, feature_dtype = [], []
+    for spec in infile.reader.point_format:
+        if spec.name in 'XYZ':
+            continue
+        att = infile.reader.get_dimension(spec.name)
+        if (att == 0).all():
+            log.info('Drop empty \'{}\' feature'.format(spec.name))
+        else:
+            log.info('Load \'{}\' feature'.format(spec.name))
+            feature_data.append(att)
+            feature_dtype.append((spec.name, att.dtype))
+
+    log.debug('Create feature recarray')
+    feature = np.core.records.fromarrays(feature_data, dtype=feature_dtype)
+    del feature_data, feature_dtype
+
+    log.debug('Concatenate pcloud')
+    pcloud = rfn.append_fields(spatial, 'feature', feature, usemask=False, asrecarray=True)
+
+    return pcloud
+
+

test/conftest.py

@@ -0,0 +1,35 @@
+#!/usr/bin/env python
+# file conftest.py
+# author Florent Guiotte <florent.guiotte@uhb.fr>
+# version 0.0
+# date 04 mars 2019
+"""Configuration script for PyTest.
+
+Define in this script:
+    - Fixtures shared among tests
+    - Helpers functions for tests
+    - External plugins
+    - Hooks
+"""
+
+from distutils import dir_util
+from pytest import fixture
+import os
+
+@fixture
+def datadir(tmpdir, request):
+    '''
+    Fixture responsible for searching a folder with the same name of test
+    module and, if available, moving all contents to a temporary directory so
+    tests can use them freely.
+
+    from: https://stackoverflow.com/a/29631801
+    '''
+    filename = request.module.__file__
+    test_dir, _ = os.path.splitext(filename)
+
+    if os.path.isdir(test_dir):
+        dir_util.copy_tree(test_dir, str(tmpdir))
+
+    return tmpdir
+

test/test_io.py

@@ -0,0 +1,41 @@
+#!/usr/bin/env python
+# file test_io.py
+# author Florent Guiotte <florent.guiotte@uhb.fr>
+# version 0.0
+# date 04 mars 2019
+"""Idefix IO tests set.
+
+doc.
+"""
+
+import pytest
+import numpy as np
+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, ),
+])
+def test_load_las(datadir, fname, exp_point_count, exp_field_count):
+    fname = datadir.join(fname)
+    
+    # Raise "No such file"
+    with pytest.raises(IOError) as e_info:
+        io.load_las('not_as_file.las')
+
+    # Open file without exception
+    try:
+        result = io.load_las(fname)
+    except IOError:
+        pytest.fail('IO error')
+
+    assert result.size == exp_point_count, "Return correct point count"
+
+    assert result['spatial'].shape[-1] == 3, "Return ndarray with spatial field"
+
+    assert (result['spatial'] == result.spatial).all(), "Quick access with records array"
+
+    assert len(result['feature'].dtype) == exp_field_count, "Return ndarray with attribute fields"
+
+    assert result.spatial.dtype == np.float, "Dtype of spatial is np.float"

test/test_utils.py

@@ -11,9 +11,12 @@ import numpy as np
 import pytest
 from idefix import utils
 
-def test_first():
+@pytest.mark.parametrize("first_input,first_expected", [
-    assert utils.first(1) == -1
+    (1, -1),
-    assert utils.first(-4) == 4
+    (-4, 4),
+])
+def test_first(first_input, first_expected):
+    assert utils.first(first_input) == first_expected
 
 @pytest.fixture
 def fix_data():
@@ -23,3 +26,7 @@ def fix_data():
 def test_bbox(fix_data):
     res = np.array([fix_data.min(axis=0), fix_data.max(axis=0)])
     assert (utils.bbox(fix_data) == res).all()
+
+def test_read(datadir):
+    with open(datadir.join('first.txt')) as f:
+        assert f.read() == 'hullo\n'

test/test_utils/first.txt

@@ -0,0 +1 @@
+hullo