Extend unit tests, remove badge

README.md

@@ -5,7 +5,6 @@
 [![Build Status](https://travis-ci.org/rbnvrw/nd2reader.svg?branch=master)](https://travis-ci.org/rbnvrw/nd2reader)
 [![Test Coverage](https://codeclimate.com/github/rbnvrw/nd2reader/badges/coverage.svg)](https://codeclimate.com/github/rbnvrw/nd2reader/coverage)
 [![Code Climate](https://codeclimate.com/github/rbnvrw/nd2reader/badges/gpa.svg)](https://codeclimate.com/github/rbnvrw/nd2reader)
-![(score out of 4.0)](https://cdn.rawgit.com/rbnvrw/nd2reader/6f4536f1/badge.svg)
 
 ### About
 

badge.svg

@@ -1,59 +0,0 @@
-<?xml version="1.0" encoding="UTF-8" standalone="no"?>
-<svg
-   xmlns:dc="http://purl.org/dc/elements/1.1/"
-   xmlns:cc="http://creativecommons.org/ns#"
-   xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
-   xmlns:svg="http://www.w3.org/2000/svg"
-   xmlns="http://www.w3.org/2000/svg"
-   xmlns:sodipodi="http://sodipodi.sourceforge.net/DTD/sodipodi-0.dtd"
-   xmlns:inkscape="http://www.inkscape.org/namespaces/inkscape"
-   version="1.1"
-   width="107"
-   height="16"
-   id="svg2"
-   inkscape:version="0.91 r13725"
-   sodipodi:docname="badge.svg">
-  <metadata
-     id="metadata12">
-    <rdf:RDF>
-      <cc:Work
-         rdf:about="">
-        <dc:format>image/svg+xml</dc:format>
-        <dc:type
-           rdf:resource="http://purl.org/dc/dcmitype/StillImage" />
-      </cc:Work>
-    </rdf:RDF>
-  </metadata>
-  <defs
-     id="defs10" />
-  <sodipodi:namedview
-     pagecolor="#ffffff"
-     bordercolor="#666666"
-     borderopacity="1"
-     objecttolerance="10"
-     gridtolerance="10"
-     guidetolerance="10"
-     inkscape:pageopacity="0"
-     inkscape:pageshadow="2"
-     inkscape:window-width="1920"
-     inkscape:window-height="1018"
-     id="namedview8"
-     showgrid="false"
-     inkscape:zoom="1"
-     inkscape:cx="50"
-     inkscape:cy="25"
-     inkscape:window-x="-8"
-     inkscape:window-y="-8"
-     inkscape:window-maximized="1"
-     inkscape:current-layer="svg2" />
-  <text
-     font-size="12"
-     x="0.34722221"
-     y="11.666667"
-     id="text4"
-     style="font-size:12px">
-    <tspan
-       id="tspan6"
-       style="fill:#a9a9a9">(score out of 4.0)</tspan>
-  </text>
-</svg>

nd2reader/artificial.py

@@ -24,7 +24,7 @@ class ArtificialND2(object):
 
     def __init__(self, file, version=(3, 0)):
         self.version = version
-        self.raw_text, self.locations, self.data = None, None, None
+        self.raw_text, self.locations, self.data = b'', None, None
         check_or_make_dir(path.dirname(file))
         self._fh = open(file, 'w+b', 0)
         self.write_file()
@@ -53,16 +53,17 @@ class ArtificialND2(object):
 
     def write_file(self):
         self.write_version()
-        self.raw_text, self.locations, self.data = self.write_label_map()
+        self.locations, self.data = self.write_label_map()
+        self._fh.write(self.raw_text)
 
     def write_version(self):
         """Write file header
         """
         # write 16 empty bytes
-        self._fh.write(bytearray(16))
+        self.raw_text += bytearray(16)
 
         # write version info
-        self._fh.write(self._get_version_string())
+        self.raw_text += self._get_version_string()
 
     def _get_version_string(self):
         return six.b('ND2 FILE SIGNATURE CHUNK NAME01!Ver%s.%s' % self.version)
@@ -72,9 +73,9 @@ class ArtificialND2(object):
 
     def write_label_map(self):
         raw_text, locations, data = self.create_label_map_bytes()
-        self._fh.write(raw_text)
+        self.raw_text += raw_text
 
-        return raw_text, locations, data
+        return locations, data
 
     def create_label_map_bytes(self):
         """Construct a binary label map

tests/test_common.py

@@ -8,7 +8,7 @@ import struct
 from nd2reader.artificial import ArtificialND2
 from nd2reader.common import get_version, parse_version, parse_date, _add_to_metadata, _parse_unsigned_char, \
     _parse_unsigned_int, _parse_unsigned_long, _parse_double, check_or_make_dir, _parse_string, _parse_char_array, \
-    get_from_dict_if_exists
+    get_from_dict_if_exists, read_chunk
 from nd2reader.exceptions import InvalidVersionError
 
 
@@ -120,3 +120,36 @@ class TestCommon(unittest.TestCase):
         self.assertIsNone(get_from_dict_if_exists('nowhere', test_dict))
         self.assertEqual(get_from_dict_if_exists('existing', test_dict), 'test')
         self.assertEqual(get_from_dict_if_exists('string', test_dict, convert_key_to_binary=False), 'test2')
+
+    def test_read_chunk(self):
+        with ArtificialND2(self.test_file) as artificial:
+            fh = artificial.file_handle
+            chunk_location = artificial.locations['image_attributes'][0]
+
+            chunk_read = read_chunk(fh, chunk_location)
+            real_data = six.BytesIO(artificial.raw_text)
+
+            real_data.seek(chunk_location)
+
+            # The chunk metadata is always 16 bytes long
+            chunk_metadata = real_data.read(16)
+            header, relative_offset, data_length = struct.unpack("IIQ", chunk_metadata)
+            self.assertEquals(header, 0xabeceda)
+
+            # We start at the location of the chunk metadata, skip over the metadata, and then proceed to the
+            # start of the actual data field, which is at some arbitrary place after the metadata.
+            real_data.seek(chunk_location + 16 + relative_offset)
+
+            real_chunk = real_data.read(data_length)
+
+            self.assertEqual(real_chunk, chunk_read)
+
+    def test_read_chunk_fail_bad_header(self):
+        with ArtificialND2(self.test_file) as artificial:
+            fh = artificial.file_handle
+            chunk_location = artificial.locations['image_attributes'][0]
+
+            with self.assertRaises(ValueError) as context:
+                read_chunk(fh, chunk_location + 1)
+
+            self.assertEquals(str(context.exception), "The ND2 file seems to be corrupted.")

tests/test_raw_metadata.py

@@ -35,6 +35,11 @@ class TestRawMetadata(unittest.TestCase):
         for required in required_keys:
             self.assertTrue(required in metadata)
 
+    def test_cached_metadata(self):
+        metadata_one = self.metadata.get_parsed_metadata()
+        metadata_two = self.metadata.get_parsed_metadata()
+        self.assertEqual(metadata_one, metadata_two)
+
     def test_pfs_status(self):
         self.assertEqual(self.file_data['pfs_status'], self.metadata.pfs_status[0])