Merge pull request #3 from vferat/dev

spi rework

Author: vferat

.gitignore

@@ -58,3 +58,6 @@ docs/_build/
 
 # PyBuilder
 target/
+test.sef
+pycartool/tests/data/sample_test_write_spi.spi
+pycartool/tests/data/sample_test_write_ris.ris

pycartool/io/roi.py

@@ -18,6 +18,12 @@ def read_roi(filename):
     rois : list, shape(n_roi, 2)
         A list of ROIs which each element is a list [roi name, elements]
 
+    Warning
+    -------
+    Indexes start from 1, not 0 as Cartools does. When using
+    with combination of source space, you way need to tranform
+    to 0 base indices.
+
     """
     with open(filename) as f:
         Roi_type = f.readline().strip()

pycartool/io/source_space.py

@@ -29,4 +29,28 @@ def read_spi(filename):
         coord = [elem[:-1] for elem in d]
         coord = np.array(coord)
         coord = coord.astype(np.float)
-    return(coord, names)
+        solution_points = {'names': names,
+                           'coordinates': coord}
+    return(solution_points)
+
+
+def write_spi(filename, solution_points):
+    """Write Cartool spi file.
+
+    Parameters
+    ----------
+    filename : str
+        The spi file to write.
+    solution_points : dict of str
+        The solution points info. Keys are:
+            names : list of str
+                the solutions point names.
+            coordinates : np.array, shape (n_solutions_points, 3)
+                the x,y,z coordinates of each solution point.
+    """
+    names = solution_points['names']
+    x, y, z = solution_points['coordinates'].T
+    with open(filename, 'w', newline='') as f:
+        writer = csv.writer(f, delimiter='\t')
+        for s in enumerate(zip(x, y, z, names)):
+            writer.writerow(s[1])

pycartool/tests/test_spi.py

@@ -4,16 +4,33 @@
 # License: BSD (3-clause)
 
 import os
-from ..io.source_space import read_spi
+import numpy as np
+from ..io.source_space import read_spi, write_spi
 
 dir_path = os.path.dirname(os.path.realpath(__file__))
-data_path = os.path.join(dir_path, "data")
+data_path = os.path.join(dir_path, 'data')
 
 
 def test_read_spi():
-    file_path = os.path.join(data_path, "sample_test_spi.spi")
-    spi = read_spi(file_path)
-    if not (len(spi[0]) == 5006):
+    """Test read_spi"""
+    file_path = os.path.join(data_path, 'sample_test_spi.spi')
+    solution_points = read_spi(file_path)
+    if not len(solution_points['names']) == 5006:
         raise AssertionError()
-    if not (len(spi[1]) == 5006):
+    if not solution_points['coordinates'].shape[0] == 5006:
         raise AssertionError()
+
+
+def test_write_spi():
+    """Test write_spi"""
+    filename = os.path.join(data_path, 'sample_test_write_spi.spi')
+    coordinates = np.random.rand(5000, 3)
+    names = [('S' + str(i)) for i in range(0, 5000)]
+    write_solution_points = {'names': names,
+                             'coordinates': coordinates}
+    write_spi(filename, write_solution_points)
+    read_solution_points = read_spi(filename)
+    if names != read_solution_points['names']:
+        raise AssertionError
+    if (coordinates != read_solution_points['coordinates']).any():
+        raise AssertionError