Base ImageIOReader on FramesSequenceND

.gitignore

@@ -7,6 +7,7 @@
 build/*
 dist/*
 pims.egg-info/*
+PIMS.egg-info/*
 pims/version.py
 pims/loci_tools.jar
 examples/.ipynb_checkpoints

pims/base_frames.py

@@ -606,3 +606,28 @@ def __repr__(self):
             s += "Axis '{0}' size: {1}\n".format(dim, self._sizes[dim])
         s += """Pixel Datatype: {dtype}""".format(dtype=self.pixel_type)
         return s
+
+    def _init_axis_if_exists(self, axis, size, min_size=1):
+        if size >= min_size:
+            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', 'v']
+        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]

pims/imageio_reader.py

@@ -3,7 +3,7 @@
 
 import six
 
-from pims.base_frames import FramesSequence
+from pims.base_frames import FramesSequenceND
 from pims.frame import Frame
 
 try:
@@ -16,8 +16,12 @@ def available():
     return imageio is not None
 
 
-class ImageIOReader(FramesSequence):
+class ImageIOReader(FramesSequenceND):
     class_priority = 6
+
+    propagate_attrs = ['frame_shape', 'pixel_type', 'metadata',
+                       'get_metadata_raw', 'reader_class_name']
+
     @classmethod
     def class_exts(cls):
         return {'tiff', 'bmp', 'cut', 'dds', 'exr', 'g3', 'hdr', 'iff', 'j2k',
@@ -31,6 +35,9 @@ def class_exts(cls):
     def __init__(self, filename, **kwargs):
         if imageio is None:
             raise ImportError('The ImageIOReader requires imageio to work.')
+
+        super(self.__class__, self).__init__()
+
         self.reader = imageio.get_reader(filename, **kwargs)
         self.filename = filename
         self._len = self.reader.get_length()
@@ -39,6 +46,23 @@ def __init__(self, filename, **kwargs):
         self._shape = first_frame.shape
         self._dtype = first_frame.dtype
 
+        self._setup_axes()
+        self._register_get_frame(self.get_frame, 'tyx')
+
+    def _setup_axes(self):
+        """Setup the xyctz axes, iterate over t axis by default
+
+        """
+        self._init_axis_if_exists('x', self._shape[1])
+        self._init_axis_if_exists('y', self._shape[0])
+        self._init_axis_if_exists('t', self._len)
+
+        if len(self.sizes) == 0:
+            raise EmptyFileError("No axes were found for this file.")
+
+        # provide the default
+        self.iter_axes = self._guess_default_iter_axis()
+
     def get_frame(self, i):
         frame = self.reader.get_data(i)
         return Frame(frame, frame_no=i, metadata=frame.meta)