Merge branch 'develop'

gazelib/__init__.py

@@ -3,3 +3,9 @@
 Gazelib, a toolkit for gaze analysis.
 '''
 from gazelib.package import version as __version__  # noqa
+import gazelib.containers  # noqa
+import gazelib.io  # noqa
+import gazelib.legacy  # noqa
+import gazelib.settings  # noqa
+import gazelib.statistics  # noqa
+import gazelib.validation  # noqa

gazelib/containers.py

@@ -2,10 +2,11 @@
 '''
 Classes that store the gaze data and can be fed to analysis functions.
 '''
-from .validation import is_list_of_strings, is_real
-from .settings import min_event_slice_overlap_seconds as min_overlap
-from .statistics.utils import arithmetic_mean, deltas
-from .io import load_json, write_json, write_fancy_json, write_dictlist_as_csv
+from gazelib.validation import is_list_of_strings, is_real
+from gazelib.settings import min_event_slice_overlap_seconds as min_overlap
+from gazelib.statistics import arithmetic_mean, deltas
+from gazelib.io import (load_json, write_json, write_fancy_json,
+                        write_dictlist_as_csv)
 from time import time as get_current_posix_time
 from deepdiff import DeepDiff
 from bisect import bisect_left  # binary tree search tool
@@ -303,6 +304,13 @@ def get_relative_end_time(self):
 
         return max(tl_max, ev_max)
 
+    def get_relative_time_by_index(self, timeline_name, index):
+        '''
+        Return relative time on the timeline at index.
+        '''
+        tl = self.get_timeline(timeline_name)
+        return tl[index]
+
     def get_duration(self):
         '''
         Difference in seconds between the smallest and largest time point.
@@ -522,6 +530,10 @@ def slice_by_tag(self, tag, index=0):
         return self.slice_by_relative_time(range_start, range_end)
 
     def iter_slices_by_tag(self, tag, limit_to=None):
+        '''DEPRECATED. Use iter_by_tag instead.'''
+        return self.iter_by_tag(tag, limit_to)
+
+    def iter_by_tag(self, tag, limit_to=None):
         '''
         Slice to multiple portions. E.g. if there is ten events with "trial"
         tag, returns iterable over ten slices, one for each tag.

gazelib/legacy/__init__.py

@@ -0,0 +1,4 @@
+'''
+Tools from the previous igazelib project
+'''
+import gazelib.legacy.igazelib  # noqa

gazelib/package.py

@@ -1,7 +1,7 @@
 # -*- coding: utf-8 -*-
 
 name = 'gazelib'
-version = '1.2.0'
+version = '1.2.1'
 description = 'Software tools to manage and analyze data from eye-trackers'
 url = 'https://github.com/infant-cognition-tampere/gazelib'
 author = 'Akseli Palen'

gazelib/statistics/__init__.py

@@ -1,3 +1,4 @@
 '''
 Statistical tools and methods.
 '''
+from .utils import arithmetic_mean, weighted_arithmetic_mean, deltas  # noqa

tests/test_containers.py

@@ -12,27 +12,11 @@
 import gazelib
 from gazelib.containers import CommonV1
 
-from .utils import get_temp_filepath, remove_temp_file, frange
-import jsonschema
-import difflib
+from .utils import (get_temp_filepath, remove_temp_file, frange,
+    get_fixture_filepath, load_sample, assert_files_equal)
+import jsonschema  # import ValidationError
 import os
 
-def get_fixture_filepath(sample_name):
-    '''
-    Create absolute filepath from sample filename.
-    '''
-    this_dir = os.path.dirname(os.path.realpath(__file__))
-    full_path = os.path.join(this_dir, 'fixtures', sample_name)
-    return full_path
-
-def load_sample(sample_name):
-    '''
-    Reads from fixtures/ directory
-    Access e.g. by: load_sample('sample.common.json')
-    '''
-    full_path = get_fixture_filepath(sample_name)
-    return gazelib.io.load_json(full_path)
-
 
 def assert_valid(self, common_raw, msg='Invalid CommonV1 structure'):
     '''
@@ -44,32 +28,6 @@ def assert_valid(self, common_raw, msg='Invalid CommonV1 structure'):
         self.fail(msg)
 
 
-def assert_files_equal(self, filepath1, filepath2,
-                       msg='Files should be equal but are not'):
-    '''
-    Assert the content of two files are equal. Do not care about empty spaces
-    at the end of the files.
-    '''
-    with open(filepath1, 'r') as f1, open(filepath2, 'r') as f2:
-        # Two lists of lines. Each element is a string that ends with '\n'
-        s1 = list(f1.readlines())
-        s2 = list(f2.readlines())
-    # Trim new lines because it causes problems because
-    # hand-written JSON includes trailing empty line where
-    # the generated JSON does not.
-    s1 = list(map(lambda l: l.rstrip('\n'), s1))
-    s2 = list(map(lambda l: l.rstrip('\n'), s2))
-    # File names for nice message.
-    b1 = filepath1
-    b2 = filepath2
-    diffs = list(difflib.unified_diff(s1, s2, b1, b2, lineterm='', n=0))
-    if len(diffs) != 0:
-        # Files not equal
-        diffmsg = '\n'.join(diffs)
-        msg = msg + ':\n' + diffmsg
-        self.fail(msg)
-
-
 class TestCommonV1(unittest.TestCase):
 
     def test_empty_init(self):
@@ -123,6 +81,15 @@ def test_get_start_end_time(self):
         self.assertEqual(t1, 0.5)
         self.assertEqual(dur, 1.0)
 
+    def test_get_relative_time_by_index(self):
+        c = CommonV1(get_fixture_filepath('sample.common.json'))
+
+        t = c.get_relative_time_by_index('ecg', 3)
+        self.assertEqual(t, 0.03)
+
+        f = lambda: c.get_relative_time_by_index('ecg', 100)
+        self.assertRaises(IndexError, f)
+
     def test_slice_by_relative_time(self):
 
         raw = load_sample('sample.common.json')
@@ -186,12 +153,12 @@ def test_slice_by_tag(self):
         slicec = g.slice_by_tag('test/center', index=1)
         self.assertEqual(len(slicec.get_timeline('eyetracker')), 1)
 
-    def test_iter_slices_by_tag(self):
+    def test_iter_by_tag(self):
 
         raw = load_sample('sample.common.json')
         g = gazelib.containers.CommonV1(raw)
 
-        slices = list(g.iter_slices_by_tag('test/center'))
+        slices = list(g.iter_by_tag('test/center'))
 
         self.assertEqual(len(slices), 2)
         self.assertEqual(len(slices[0].raw['events']), 5)

tests/test_statistics.py

@@ -5,34 +5,34 @@
 
 from gazelib import statistics as unit
 
-class TestUtils(unittest.TestCase):
+class TestStatistics(unittest.TestCase):
 
     def test_deltas(self):
 
         l = [1, 2, 3, 4, 5]
-        self.assertListEqual(unit.utils.deltas(l), [1, 1, 1, 1])
+        self.assertListEqual(unit.deltas(l), [1, 1, 1, 1])
         l = [-1, 0, 1, 2]
-        self.assertListEqual(unit.utils.deltas(l), [1, 1, 1])
+        self.assertListEqual(unit.deltas(l), [1, 1, 1])
         l = [1, 0, 1, 0, -1]
-        self.assertListEqual(unit.utils.deltas(l), [-1, 1, -1, -1])
+        self.assertListEqual(unit.deltas(l), [-1, 1, -1, -1])
 
     def test_arithmetic_mean(self):
 
         l = [1, 2, 3]
-        self.assertEqual(unit.utils.arithmetic_mean(l), 2.0)
+        self.assertEqual(unit.arithmetic_mean(l), 2.0)
         l = []
-        self.assertEqual(unit.utils.arithmetic_mean(l), None)
+        self.assertEqual(unit.arithmetic_mean(l), None)
         l = [None, 1]
-        self.assertEqual(unit.utils.arithmetic_mean(l), 1.0)
+        self.assertEqual(unit.arithmetic_mean(l), 1.0)
 
     def test_weighted_arithmetic_mean(self):
 
         l = [1, 5, 1]
         w = [1, 0, 1]
-        self.assertEqual(unit.utils.weighted_arithmetic_mean(l, w), 1.0)
+        self.assertEqual(unit.weighted_arithmetic_mean(l, w), 1.0)
         l = [2, 5, 0]
         w = [1, None, 1]
-        self.assertEqual(unit.utils.weighted_arithmetic_mean(l, w), 1.0)
+        self.assertEqual(unit.weighted_arithmetic_mean(l, w), 1.0)
 
 if __name__ == '__main__':
     unittest.main()

tests/utils/__init__.py

@@ -1,6 +1,9 @@
 import os
 import tempfile
+import gazelib
 from sys import float_info
+import difflib
+
 
 def get_temp_filepath(file_name):
     '''
@@ -10,6 +13,7 @@ def get_temp_filepath(file_name):
     p = tempfile.mkdtemp()
     return os.path.join(p, file_name)
 
+
 def remove_temp_file(abs_filepath):
     '''
     Remove file created by the tempfile.mkdtemp
@@ -19,6 +23,7 @@ def remove_temp_file(abs_filepath):
     os.remove(abs_filepath)
     os.rmdir(d)
 
+
 def frange(x, y, jump=1.0):
     '''
     Range for floats.
@@ -30,3 +35,47 @@ def frange(x, y, jump=1.0):
         yield x
         i += 1
         x = x0 + i * jump
+
+
+def get_fixture_filepath(sample_name):
+    '''
+    Create absolute filepath from sample filename.
+    '''
+    this_dir = os.path.dirname(os.path.dirname(os.path.realpath(__file__)))
+    full_path = os.path.join(this_dir, 'fixtures', sample_name)
+    return full_path
+
+
+def load_sample(sample_name):
+    '''
+    Reads from fixtures/ directory
+    Access e.g. by: load_sample('sample.common.json')
+    '''
+    full_path = get_fixture_filepath(sample_name)
+    return gazelib.io.load_json(full_path)
+
+
+def assert_files_equal(self, filepath1, filepath2,
+                       msg='Files should be equal but are not'):
+    '''
+    Assert the content of two files are equal. Do not care about empty spaces
+    at the end of the files.
+    '''
+    with open(filepath1, 'r') as f1, open(filepath2, 'r') as f2:
+        # Two lists of lines. Each element is a string that ends with '\n'
+        s1 = list(f1.readlines())
+        s2 = list(f2.readlines())
+    # Trim new lines because it causes problems because
+    # hand-written JSON includes trailing empty line where
+    # the generated JSON does not.
+    s1 = list(map(lambda l: l.rstrip('\n'), s1))
+    s2 = list(map(lambda l: l.rstrip('\n'), s2))
+    # File names for nice message.
+    b1 = filepath1
+    b2 = filepath2
+    diffs = list(difflib.unified_diff(s1, s2, b1, b2, lineterm='', n=0))
+    if len(diffs) != 0:
+        # Files not equal
+        diffmsg = '\n'.join(diffs)
+        msg = msg + ':\n' + diffmsg
+        self.fail(msg)