DOC: Dcstrings

pims/api.py

@@ -30,7 +30,9 @@ def raiser(*args, **kwargs):
     return raiser
 
 
-def wrap_fmt(reader, name, description, extensions=None, modes=None):
+def register_fmt(reader, name, description, extensions=None, modes=None):
+    """Registers a Format with the format manager. Returns a reader
+    for backwards compatibility."""
     formats.add_format(reader(name, description, extensions, modes))
     @wraps(reader)
     def wrapper(filename, **kwargs):
@@ -92,11 +94,10 @@ def wrapper(filename, **kwargs):
 if not pims.tiff_stack.tifffile_available():
     TiffStack_tifffile = not_available("tifffile")
 else:
-    TiffStack_tifffile = wrap_fmt(FormatTiffStack_tifffile,
-                                  'TIFF_tifffile',
-                                  'Reads TIFF files through tifffile.py.',
-                                  'tif tiff lsm stk',
-                                  'iIvV')
+    TiffStack_tifffile = register_fmt(FormatTiffStack_tifffile,
+                                      'TIFF_tifffile',
+                                      'Reads TIFF files through tifffile.py.',
+                                      'tif tiff lsm stk', 'iIvV')
 if not pims.tiff_stack.libtiff_available():
     TiffStack_libtiff = not_available("libtiff")
 if not pims.tiff_stack.PIL_available():

pims/base_frames.py

@@ -670,72 +670,63 @@ def default_axes(sizes, mode):
 
 class _PimsFormat(Format):
     def _can_read(self, request):
+        """Determine whether `request.filename` can be read using this
+        Format.Reader, judging from the imageio.core.Request object."""
         if request.mode[1] in (self.modes + '?'):
             if request.filename.lower().endswith(self.extensions):
                 return True
 
     def _can_write(self, request):
+        """Determine whether file type `request.filename` can be written using
+        this Format.Writer, judging from the imageio.core.Request object."""
         return False
 
     @Slicerator.from_class
     class Reader(with_metaclass(ABCMeta, Format.Reader)):
         def __getitem__(self, key):
             return self.get_data(key)
 
-        @abstractmethod
-        def _get_length(self):
-            pass
+        def get_data(self, index, **kwargs):
+            # This function is a copy of the imageio Format.Reader,
+            # replacing the returned Image object with a PIMS Frame.
+            self._checkClosed()
+            self._BaseReaderWriter_last_index = index
+            im, meta = self._get_data(index, **kwargs)
+            return Frame(im, frame_no=index, metadata=meta)
+
+        def iter_data(self):
+            return iter(self[:])
+
+        def get_meta_data(self, i):
+            # can be overwritten by a reader for better performance
+            return self.get_data(i).metadata
+
+        @property
+        def shape(self):
+            return (len(self),) + tuple(self.frame_shape)
 
         @abstractmethod
         def _open(self, **kwargs):
             pass
 
         @abstractmethod
-        def _get_dtype(self):
+        def _get_data(self, i):
             pass
 
-        @property
-        def dtype(self):
-            return self._get_dtype()
-
-        @property
-        def shape(self):
-            return (len(self),) + self.frame_shape
+        @abstractmethod
+        def __len__(self):
+            pass
 
         @abstractproperty
         def frame_shape(self):
             """ Returns the shape of the frame as returned by get_frame. """
             pass
 
-        @property
-        def ndim(self):
-            """ Returns the number of axes. """
-            return len(self.frame_shape) + 1
-
-        def get_data(self, index, **kwargs):
-            """ get_data(index, **kwargs)
-
-            Read image data from the file, using the image index. The
-            returned image has a 'meta' attribute with the meta data.
-
-            Some formats may support additional keyword arguments. These are
-            listed in the documentation of those formats.
-            """
-            self._checkClosed()
-            self._BaseReaderWriter_last_index = index
-            im, meta = self._get_data(index, **kwargs)
-            return Frame(im, frame_no=index, metadata=meta)
-
-        def iter_data(self):
-            return iter(self[:])
-
-        @abstractmethod
-        def _get_data(self, i):
+        @abstractproperty
+        def pixel_type(self):
+            """Returns a numpy.dtype for the data type of the pixel values"""
             pass
 
-        def _get_meta_data(self, i):
-            return self.get_data(i).metadata
-
 
 class PimsFormat(_PimsFormat):
     class Reader(_PimsFormat.Reader):
@@ -775,14 +766,6 @@ def _init_axis(self, name, size, default=0):
             self.default_coords[name] = int(default)
 
         def get_data(self, index, **kwargs):
-            """ get_data(index, **kwargs)
-
-            Read image data from the file, using the image index. The
-            returned image has a 'meta' attribute with the meta data.
-
-            Some formats may support additional keyword arguments. These are
-            listed in the documentation of those formats.
-            """
             self._checkClosed()
             self._BaseReaderWriter_last_index = index
             return self._get_data(index, **kwargs)
@@ -821,7 +804,7 @@ def _get_data(self, i):
                 dict(axes=self.bundle_axes, coords=metadata_coords))
             return Frame(result, frame_no=i, metadata=metadata)
 
-        def _get_length(self):
+        def __len__(self):
             return int(np.prod([self._sizes[d] for d in self._iter_axes]))
 
         @property
@@ -886,7 +869,7 @@ def bundle_axes(self, value):
             # update the get_frame method
             get_frame = _make_get_frame(self._bundle_axes,
                                         self._get_frame_dict,
-                                        self.sizes, self.dtype)
+                                        self.sizes, self.pixel_type)
             self._get_frame_wrapped = get_frame
 
         @property

pims/tiff_stack.py

@@ -118,8 +118,8 @@ def _open(self, **kwargs):
 
             self.bundle_axes, self.iter_axes = default_axes(self.sizes,
                                                             self.request.mode)
-
-        def _get_dtype(self):
+        @property
+        def pixel_type(self):
             return self._dtype
 
         def _get_frame(self, **inds):