From bd10811aee63acf8368945966a1c1b624d41ec3f Mon Sep 17 00:00:00 2001
From: Ruben Verweij <verweij@physics.leidenuniv.nl>
Date: Wed, 1 Mar 2017 14:28:44 +0100
Subject: [PATCH] Add unit tests for opening files and axis sizes

---
 nd2reader/reader.py  |  7 +++----
 tests/test_reader.py | 42 ++++++++++++++++++++++++++++++++++++++++++
 2 files changed, 45 insertions(+), 4 deletions(-)
 create mode 100644 tests/test_reader.py

diff --git a/nd2reader/reader.py b/nd2reader/reader.py
index ba65de4..9386cd0 100644
--- a/nd2reader/reader.py
+++ b/nd2reader/reader.py
@@ -6,7 +6,6 @@ class ND2Reader(FramesSequenceND):
     """
     PIMS wrapper for the ND2 parser
     """
-
     def __init__(self, filename):
         self.filename = filename
 
@@ -45,7 +44,8 @@ class ND2Reader(FramesSequenceND):
         :param i:
         :return:
         """
-        return self._parser.get_image(i)
+        c_name = self.metadata["channels"][0]
+        return self._parser.get_image_by_attributes(i, 0, c_name, 0, self.metadata["height"], self.metadata["width"])
 
     def get_frame_2D(self, c, t, z):
         """
@@ -56,8 +56,7 @@ class ND2Reader(FramesSequenceND):
         :return:
         """
         c_name = self.metadata["channels"][c]
-
-        return self._parser.get_image_by_attributes(t, 0, c_name, z, self.metadata["width"], self.metadata["height"])
+        return self._parser.get_image_by_attributes(t, 0, c_name, z, self.metadata["height"], self.metadata["width"])
 
     @property
     def pixel_type(self):
diff --git a/tests/test_reader.py b/tests/test_reader.py
new file mode 100644
index 0000000..6e08aae
--- /dev/null
+++ b/tests/test_reader.py
@@ -0,0 +1,42 @@
+import unittest
+
+from nd2reader.reader import ND2Reader
+
+
+class TestReader(unittest.TestCase):
+
+    def setUp(self):
+        self.files = [
+            './test_data/data001.nd2',
+            './test_data/data002.nd2'
+        ]
+
+    def test_sizes_data_001(self):
+        with ND2Reader(self.files[0]) as reader:
+            self.assertEqual(reader.sizes['x'], 128)
+            self.assertEqual(reader.sizes['y'], 128)
+            self.assertEqual(reader.sizes['t'], 982)
+            self.assertEqual(reader.sizes['c'], 1)
+            self.assertEqual(reader.sizes['z'], 1)
+
+    def test_frame_size_data_001(self):
+        with ND2Reader(self.files[0]) as reader:
+            frame = reader[13]
+            self.assertEqual(frame.shape[0], 128)
+            self.assertEqual(frame.shape[1], 128)
+
+    def test_sizes_data_002(self):
+        with ND2Reader(self.files[1]) as reader:
+            self.assertEqual(reader.sizes['x'], 512)
+            self.assertEqual(reader.sizes['y'], 256)
+            self.assertEqual(reader.sizes['t'], 78)
+            self.assertEqual(reader.sizes['c'], 1)
+            self.assertEqual(reader.sizes['z'], 1)
+
+    def test_frame_size_data_002(self):
+        with ND2Reader(self.files[1]) as reader:
+            frame = reader[13]
+            self.assertEqual(frame.shape[1], 512)
+            self.assertEqual(frame.shape[0], 256)
+
+