Merge pull request #48 from AlonDaks/master

Fixed scene_slicer tests to be in passing shape

.travis.yml

@@ -17,7 +17,6 @@ install:
   - python --version # just to check
   - retry pip install nose # always
   - sudo apt-get update
-  - sudo apt-get upgrade
   - sudo apt-get install libblas-dev liblapack-dev libatlas3gf-base
   - wheelhouse_pip_install ${DEPENDS} --trusted-host travis-wheels.scikit-image.org
   - if [ "${COVERAGE}" == "1" ]; then

code/utils/linear_modeling.py

@@ -5,7 +5,7 @@
 import numpy.linalg as npl
 from scipy.stats import t as t_dist
 from scipy.ndimage import gaussian_filter
-import scene_slicer as ssm
+from . import scene_slicer as ssm
 import nibabel as nib
 
 

code/utils/scene_slicer.py

@@ -11,15 +11,8 @@
                   'int-ext': {'INT': 0,
                               'EXT': 1}}
 
-DAY_NIGHT_IND = 0
-INT_EXT_IND = 1
-
 TUNING_SECONDS_OFFSET = 17
 
-# with open('../../data/data_path.json', 'r') as fh:
-#     data_paths = json.load(fh)
-# path_to_subject_image = "../../" + data_paths['bold_dico_7Tad2grpbold7Tad']['sub1']['runs'][0]['path']
-
 
 class SceneSlicer:
     def __init__(self, path_to_subject_image, path_to_scene_csv):
@@ -40,15 +33,15 @@ def generate_scene_desc_dict_(self):
                     INTEGER_LABELS['int-ext'][row['int-ext']])
 
     def generate_scene_slices_(self):
-        num_offset_slices = int(math.floor(TUNING_SECONDS_OFFSET / 2))
+        num_offset_slices = int(math.ceil(TUNING_SECONDS_OFFSET / 2))
         day_night = num_offset_slices * [None]
         int_ext = num_offset_slices * [None]
         current_scene_start_time = TUNING_SECONDS_OFFSET
         for i in range(num_offset_slices, self.image.shape[-1]):
-            if i * 2 + 1 in self.scene_desc:
-                current_scene_start_time = i * 2 + 1
-            elif i * 2 + 2 in self.scene_desc:
-                current_scene_start_time = i * 2 + 2
+            if i * 2 in self.scene_desc:
+                current_scene_start_time = i * 2
+            elif i * 2 - 1 in self.scene_desc:
+                current_scene_start_time = i * 2 - 1
             day_night.append(self.scene_desc[current_scene_start_time][0])
             int_ext.append(self.scene_desc[current_scene_start_time][1])
         self.scene_slices = (day_night, int_ext)
@@ -60,10 +53,9 @@ def get_scene_slices(self):
             self.generate_scene_slices_()
         return self.scene_slices
 
-    def get_day_night(self, slice):
+    def get_labels_by_slice(self, slice):
         if not self.scene_slices:
             self.get_scene_slices()
-        day_label = self.scene_slices[DAY_NIGHT_IND][slice]
-        int_label = self.scene_slices[INT_EXT_IND][slice]
-        return (day_label, int_label)
-
+        day_label = self.scene_slices[0][slice]
+        int_label = self.scene_slices[1][slice]
+        return (day_label, int_label)

code/utils/tests/test_linear_modeling.py

@@ -68,7 +68,7 @@ def test_get_top_32():
 
 def test_get_index_4d():
     actual = linear_modeling.get_index_4d([0, 2], data)
-    assert_equal(actual, [(0, 0), (0, 2)])
+    assert_equal(list(actual), [(0, 0), (0, 2)])
 
     # def test_plot_single_voxel():
     # 	not sure how to test plots

code/utils/tests/test_scene_slicer.py

@@ -1,60 +1,63 @@
-# Python 3 compatibility
 from __future__ import absolute_import, division, print_function
-
 from .. import scene_slicer
 import os
 import nibabel as nib
 import csv
 import numpy as np
 
-IS_DAY = 0
-IS_INT = 1
-
 
-def test_prepare():
-    data = np.array([[[[7, 9], [7, 8]], [[1, 2], [1, 8]]], [[[2, 3], [2, 1]],
-                                                            [[5, 4], [4, 3]]]])
+def setup_test():
+    data = np.zeros((2, 2, 2, 50))
     img = nib.Nifti1Image(data, affine=np.diag([1, 1, 1, 1]))
     nib.save(img, 'test_data.nii')
-    with open('scene.csv', 'w') as csvfile:
+    with open('test_scenes.csv', 'w') as csvfile:
         scenewriter = csv.writer(csvfile, delimiter=',', quotechar='"')
-        scenewriter.writerow([17.0, "SAVANNAH", "DAY", "EXT"])
-        scenewriter.writerow([272.0, "DOCTORS OFFICE", "DAY", "INT"])
-    ss = scene_slicer.SceneSlicer('test_data.nii', 'scene.csv')
-    return ss
+        scenewriter.writerow([17.0, 'SAVANNAH', 'DAY', 'EXT'])
+        scenewriter.writerow([40.0, 'DOCTORS OFFICE', 'NIGHT', 'INT'])
+        scenewriter.writerow([61.0, 'GUMP', 'DAY', 'EXT'])
+        scenewriter.writerow([82.0, 'GUMP', 'DAY', 'EXT'])
+        scenewriter.writerow([91.0, 'GUMP', 'NIGHT', 'INT'])
+    return scene_slicer.SceneSlicer('test_data.nii', 'test_scenes.csv')
 
 
-def delete_files():
+def teardown_test():
     os.remove('test_data.nii')
-    os.remove('scene.csv')
+    os.remove('test_scenes.csv')
+
+
+def test_constants():
+    assert scene_slicer.INTEGER_LABELS == {'day-night': {'DAY': 0,
+                                                         'NIGHT': 1,
+                                                         'DAWN': 2},
+                                           'int-ext': {'INT': 0,
+                                                       'EXT': 1}}
+    assert scene_slicer.TUNING_SECONDS_OFFSET == 17
 
 
 def test_scene_slicer_init():
-    ss = test_prepare()
-    assert ss.scene_desc is not None
-    assert ss.scene_keys is not None
-    delete_files()
-
-
-def test_scene_slicer_dict():
-    ss = test_prepare()
-    ss.generate_scene_desc_dict()
-    for i in ss.scene_desc:
-        assert len(ss.scene_desc[i]) == 2
-        assert ss.scene_desc[i][IS_DAY] == 0 or ss.scene_desc[i][IS_DAY] == 1
-        assert ss.scene_desc[i][IS_INT] == 0 or ss.scene_desc[i][IS_INT] == 1
-    delete_files()
-
-
-def test_scene_slicer_slices():
-    ss = test_prepare()
-    ss.get_scene_slices()
-    assert len(ss.scene_slices) != 0
-    delete_files()
-
-
-def test_scene_slicer_day_night():
-    ss = test_prepare()
-    scene_tup = ss.get_day_night(0)
-    assert scene_tup == (True, False)
-    delete_files()
+    ss = setup_test()
+    assert ss.path_to_scene_csv == 'test_scenes.csv'
+    np.testing.assert_array_equal(ss.image.get_data(), np.zeros((2, 2, 2, 50)))
+    assert ss.scene_slices == []
+    assert ss.scene_desc == {}
+    teardown_test()
+
+
+def test_get_scene_slices():
+    ss = setup_test()
+    scene_slices = ss.get_scene_slices()
+    day_night_labels = 9*[None] + 11*[0] + 11*[1] + 15*[0] + 4*[1] 
+    int_ext_labels = 9*[None] + 11*[1] + 11*[0] + 15*[1] + 4*[0] 
+    assert scene_slices[0] == day_night_labels
+    assert scene_slices[1] == int_ext_labels
+    teardown_test()
+
+def test_get_labels_by_slice():
+    ss = setup_test()
+    assert (None, None) == ss.get_labels_by_slice(0)
+    assert (None, None) == ss.get_labels_by_slice(8)
+    assert (0, 1) == ss.get_labels_by_slice(10)
+    assert (1, 0) == ss.get_labels_by_slice(48)
+    teardown_test()
+
+