refactoring for file names, adjusting tests appropriately

code/utils/scene_slicer.py

@@ -9,21 +9,24 @@
 INT_IND = 2
 EXT_IND = 3
 
+# with open('../../data/data_path.json', 'r') as fh:
+#     data_paths = json.load(fh)
+# path_to_images = []
+# for i in range(8):
+#     path_to_images.append("../../" + data_paths['bold_dico_7Tad2grpbold7Tad']['sub1']['runs'][0]['path'])
 
 class SceneSlicer:
-    def __init__(self, sub_num, path_to_root):
-        self.path_to_root = path_to_root
-        with open(self.path_to_root + 'data/data_path.json', 'r') as fh:
-            self.data_paths = json.load(fh)
-        self.images = [0] * 8
-        self.scene_slices = [0] * 8
-        self.sub_num = sub_num
+    def __init__(self, path_to_images, path_to_scene_csv="../../ds113_study_description/stimulus/task001/annotations/scenes.csv"):
+        self.path_to_images = path_to_images
+        self.path_to_scene_csv = path_to_scene_csv
+        self.images = [0] * len(path_to_images)
+        self.scene_slices = [0] * len(path_to_images)
         self.segment_duration = [902, 882, 876, 976, 924, 878, 1086, 673.4]
         self.scene_desc = {}
         self.scene_keys = []
 
     def generate_scene_desc_dict(self):
-        with open(self.path_to_root + 'ds113_study_description/stimulus/task001/annotations/scenes.csv', 'rb') as csvfile:
+        with open(self.path_to_scene_csv, 'rb') as csvfile:
             reader = csv.DictReader(csvfile, fieldnames=['seconds', 'scene', 'day-night', 'int-ext'])
             for row in reader:
                 scene_time = int(float(row['seconds']))
@@ -33,9 +36,7 @@ def generate_scene_desc_dict(self):
 
     def get_image(self, run_num):
         if self.images[run_num] == 0:
-            sub_str = 'sub' + str(self.sub_num)
-            img_path = self.path_to_root + self.data_paths['bold_dico_7Tad2grpbold7Tad'][sub_str]['runs'][run_num]["path"]
-            img = nib.load(img_path)
+            img = nib.load(self.path_to_images[run_num])
             self.images[run_num] = img
         return self.images[run_num]
 
@@ -76,3 +77,4 @@ def get_day_night(self, run_num, slice):
         is_day_slice = slice in scene_slices[DAY_IND]
         is_int_slice = slice in scene_slices[INT_IND]
         return (is_day_slice, is_int_slice)
+

code/utils/tests/test_scene_slicer.py

@@ -2,43 +2,64 @@
 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]]]])
+    img = nib.Nifti1Image(data, affine=np.diag([1, 1, 1, 1]))
+    nib.save(img, 'test_data.nii')
+    with open('scene.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
+
+
+def delete_files():
+    os.remove('test_data.nii')
+    os.remove('scene.csv')
+
+
 def test_scene_slicer_init():
-    ss = scene_slicer.SceneSlicer(1, "")
-    assert ss.sub_num == 1
-    assert len(ss.images) == 8
-    assert len(ss.scene_slices) == 8
+    ss = test_prepare()
     assert ss.scene_desc is not None
     assert ss.scene_keys is not None
     assert ss.segment_duration == [902, 882, 876, 976, 924, 878, 1086, 673.4]
-
+    delete_files()
 
 def test_scene_slicer_dict():
-    ss = scene_slicer.SceneSlicer(1, "")
+    ss = test_prepare()
     ss.generate_scene_desc_dict()
     for i in ss.scene_desc:
-        len(ss.scene_desc[i]) == 2
+        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_image():
-    ss = scene_slicer.SceneSlicer(1, "")
-    ss.get_image(2)
-    assert ss.images[2] != 0
-
+    ss = test_prepare()
+    ss.get_image(0)
+    assert ss.images[0] != 0
+    delete_files()
 
 def test_scene_slicer_slices():
-    ss = scene_slicer.SceneSlicer(1, "")
-    ss.get_scene_slices(4)
-    assert ss.scene_slices[4] != 0
-
+    ss = test_prepare()
+    ss.get_scene_slices(0)
+    assert ss.scene_slices[0] != 0
+    delete_files()
 
 def test_scene_slicer_day_night():
-    ss = scene_slicer.SceneSlicer(1, "")
-    scene_tup = ss.get_day_night(1, 0)
+    ss = test_prepare()
+    scene_tup = ss.get_day_night(0, 0)
     assert scene_tup == (True, False)
+    delete_files()
+