Issue #2: clean up axes handling, guess a better default axis

nd2reader/exceptions.py

@@ -15,3 +15,10 @@ class NoImageError(Exception):
 
     """
     pass
+
+
+class EmptyFileError(Exception):
+    """This .nd2 file seems to be empty.
+
+    Raised if no axes are found in the file.
+    """

nd2reader/raw_metadata.py

@@ -39,13 +39,15 @@ class RawMetadata(object):
             "width": self._parse_if_not_none(self.image_attributes, self._parse_width),
             "date": self._parse_if_not_none(self.image_text_info, self._parse_date),
             "fields_of_view": self._parse_fields_of_view(),
-            "frames": np.arange(0, frames_per_channel, 1),
+            "frames": self._parse_frames(),
             "z_levels": self._parse_z_levels(),
             "total_images_per_channel": frames_per_channel,
             "channels": self._parse_channels(),
             "pixel_microns": self._parse_if_not_none(self.image_calibration, self._parse_calibration),
         }
 
+        self._set_default_if_not_empty('fields_of_view')
+        self._set_default_if_not_empty('frames')
         self._metadata_parsed['num_frames'] = len(self._metadata_parsed['frames'])
 
         self._parse_roi_metadata()
@@ -53,6 +55,11 @@ class RawMetadata(object):
 
         return self._metadata_parsed
 
+    def _set_default_if_not_empty(self, entry):
+        if len(self._metadata_parsed[entry]) == 0 and self._metadata_parsed['total_images_per_channel'] > 0:
+            # if the file is not empty, we always have one of this entry
+            self._metadata_parsed[entry] = [0]
+
     @staticmethod
     def _parse_if_not_none(to_check, callback):
         if to_check is not None:
@@ -74,6 +81,14 @@ class RawMetadata(object):
     def _parse_calibration(self):
         return self.image_calibration.get(six.b('SLxCalibration'), {}).get(six.b('dCalibration'))
 
+    def _parse_frames(self):
+        """The number of cycles.
+
+        Returns:
+            list: list of all the frame numbers
+        """
+        return self._parse_dimension(r""".*?T'?\((\d+)\).*?""")
+
     def _parse_channels(self):
         """These are labels created by the NIS Elements user. Typically they may a short description of the filter cube
         used (e.g. 'bright field', 'GFP', etc.)
@@ -154,12 +169,12 @@ class RawMetadata(object):
     def _parse_dimension(self, pattern):
         dimension_text = self._parse_dimension_text()
         if dimension_text is None:
-            return [0]
+            return []
         if six.PY3:
             dimension_text = dimension_text.decode("utf8")
         match = re.match(pattern, dimension_text)
         if not match:
-            return [0]
+            return []
         count = int(match.group(1))
         return list(range(count))
 
@@ -170,7 +185,7 @@ class RawMetadata(object):
 
         """
         if self.image_attributes is None:
-            return None
+            return 0
         return self.image_attributes[six.b('SLxImageAttributes')][six.b('uiSequenceCount')]
 
     def _parse_roi_metadata(self):

nd2reader/reader.py

@@ -1,4 +1,6 @@
 from pims import FramesSequenceND, Frame
+
+from nd2reader.exceptions import EmptyFileError
 from nd2reader.parser import Parser
 import numpy as np
 
@@ -99,17 +101,42 @@ class ND2Reader(FramesSequenceND):
         """Setup the xyctz axes, iterate over t axis by default
 
         """
-        self._init_axis('x', self._get_metadata_property("width", default=0))
-        self._init_axis('y', self._get_metadata_property("height", default=0))
-        self._init_axis('c', len(self._get_metadata_property("channels", default=[])))
-        self._init_axis('t', len(self._get_metadata_property("frames", default=[])))
+        self._init_axis_if_exists('x', self._get_metadata_property("width", default=0))
+        self._init_axis_if_exists('y', self._get_metadata_property("height", default=0))
+        self._init_axis_if_exists('c', len(self._get_metadata_property("channels", default=[])))
+        self._init_axis_if_exists('t', len(self._get_metadata_property("frames", default=[])))
+        self._init_axis_if_exists('z', len(self._get_metadata_property("z_levels", default=[])))
 
-        z_levels = len(self._get_metadata_property("z_levels", default=[]))
-        if z_levels > 1:
-            self._init_axis('z', z_levels)
+        if len(self.sizes) == 0:
+            raise EmptyFileError("No axes were found for this .nd2 file.")
 
         # provide the default
-        self.iter_axes = 't'
+        self.iter_axes = self._guess_default_iter_axis()
+
+    def _init_axis_if_exists(self, axis, size):
+        if size > 0:
+            self._init_axis(axis, size)
+
+    def _guess_default_iter_axis(self):
+        """
+        Guesses the default axis to iterate over based on axis sizes.
+        Returns:
+            the axis to iterate over
+        """
+        priority = ['t', 'z', 'c']
+        found_axes = []
+        for axis in priority:
+            try:
+                current_size = self.sizes[axis]
+            except KeyError:
+                continue
+
+            if current_size > 1:
+                return axis
+
+            found_axes.append(axis)
+
+        return found_axes[0]
 
     def get_timesteps(self):
         """Get the timesteps of the experiment

tests/test_legacy.py

@@ -1,27 +0,0 @@
-import unittest
-from os import path
-
-from nd2reader.artificial import ArtificialND2
-from nd2reader.common import check_or_make_dir
-from nd2reader.legacy import Nd2
-
-
-class TestLegacy(unittest.TestCase):
-    def create_test_nd2(self):
-        with ArtificialND2(self.test_file) as artificial:
-            artificial.close()
-
-    def setUp(self):
-        dir_path = path.dirname(path.realpath(__file__))
-        check_or_make_dir(path.join(dir_path, 'test_data/'))
-        self.test_file = path.join(dir_path, 'test_data/test.nd2')
-
-    def test_can_open_test_file(self):
-        self.create_test_nd2()
-        with Nd2(self.test_file) as reader:
-            self.assertEqual(reader.width, 0)
-            self.assertEqual(reader.height, 0)
-            self.assertEqual(len(reader.z_levels), 1)
-            self.assertEqual(len(reader.channels), 0)
-            self.assertEqual(len(reader.frames), 0)
-

tests/test_reader.py

@@ -4,42 +4,11 @@ import numpy as np
 
 from nd2reader.artificial import ArtificialND2
 from nd2reader.common import check_or_make_dir
+from nd2reader.exceptions import EmptyFileError
 from nd2reader.parser import Parser
 from nd2reader.reader import ND2Reader
 
 
 class TestReader(unittest.TestCase):
-    def create_test_nd2(self):
-        with ArtificialND2(self.test_file) as artificial:
-            artificial.close()
-
-    def setUp(self):
-        dir_path = path.dirname(path.realpath(__file__))
-        check_or_make_dir(path.join(dir_path, 'test_data/'))
-        self.test_file = path.join(dir_path, 'test_data/test.nd2')
-
-    def test_can_open_test_file(self):
-        self.create_test_nd2()
-        with ND2Reader(self.test_file) as reader:
-            self.assertEqual(reader.filename, self.test_file)
-            self.assertEqual(reader.pixel_type, np.float64)
-            self.assertEqual(reader.sizes['x'], 0)
-            self.assertEqual(reader.sizes['y'], 0)
-            self.assertFalse('z' in reader.sizes)
-            self.assertEqual(reader.sizes['c'], 0)
-            self.assertEqual(reader.sizes['t'], 0)
-
     def test_extension(self):
         self.assertTrue('nd2' in ND2Reader.class_exts())
-
-    def test_get_metadata_property(self):
-        self.create_test_nd2()
-        with ND2Reader(self.test_file) as reader:
-            self.assertIsNone(reader._get_metadata_property('kljdf'))
-            self.assertEqual(reader._get_metadata_property('kljdf', 'default'), 'default')
-
-    def test_get_parser(self):
-        self.create_test_nd2()
-        with ND2Reader(self.test_file) as reader:
-            self.assertTrue(type(reader.parser) is Parser)
-