RF: Move mmap/keep_file_open parameters to DataobjImage.from_file*

Author: effigies

nibabel/analyze.py

@@ -988,47 +988,6 @@ def from_file_map(klass, file_map, mmap=True, keep_file_open=None):
                            'file_map': copy_file_map(file_map)}
         return img
 
-    @classmethod
-    @kw_only_meth(1)
-    def from_filename(klass, filename, mmap=True, keep_file_open=None):
-        '''Class method to create image from filename `filename`
-
-        .. deprecated:: 2.4.1
-            ``keep_file_open='auto'`` is redundant with `False` and has
-            been deprecated. It will raise an error in nibabel 3.0.
-
-        Parameters
-        ----------
-        filename : str
-            Filename of image to load
-        mmap : {True, False, 'c', 'r'}, optional, keyword only
-            `mmap` controls the use of numpy memory mapping for reading image
-            array data.  If False, do not try numpy ``memmap`` for data array.
-            If one of {'c', 'r'}, try numpy memmap with ``mode=mmap``.  A
-            `mmap` value of True gives the same behavior as ``mmap='c'``.  If
-            image data file cannot be memory-mapped, ignore `mmap` value and
-            read array from file.
-        keep_file_open : { None, True, False }, optional, keyword only
-            `keep_file_open` controls whether a new file handle is created
-            every time the image is accessed, or a single file handle is
-            created and used for the lifetime of this ``ArrayProxy``. If
-            ``True``, a single file handle is created and used. If ``False``,
-            a new file handle is created every time the image is accessed.
-            The default value (``None``) will result in the value of
-            ``nibabel.arrayproxy.KEEP_FILE_OPEN_DEFAULT`` being used.
-
-        Returns
-        -------
-        img : Analyze Image instance
-        '''
-        if mmap not in (True, False, 'c', 'r'):
-            raise ValueError("mmap should be one of {True, False, 'c', 'r'}")
-        file_map = klass.filespec_to_file_map(filename)
-        return klass.from_file_map(file_map, mmap=mmap,
-                                   keep_file_open=keep_file_open)
-
-    load = from_filename
-
     @staticmethod
     def _get_fileholders(file_map):
         """ Return fileholder for header and image

nibabel/brikhead.py

@@ -541,40 +541,6 @@ def from_file_map(klass, file_map, mmap=True, keep_file_open=None):
         return klass(data, hdr.get_affine(), header=hdr, extra=None,
                      file_map=file_map)
 
-    @classmethod
-    @kw_only_meth(1)
-    def from_filename(klass, filename, mmap=True, keep_file_open=None):
-        """
-        Creates an AFNIImage instance from `filename`
-
-        .. deprecated:: 2.4.1
-            ``keep_file_open='auto'`` is redundant with `False` and has
-            been deprecated. It will raise an error in nibabel 3.0.
-
-        Parameters
-        ----------
-        filename : str
-            Path to BRIK or HEAD file to be loaded
-        mmap : {True, False, 'c', 'r'}, optional, keyword only
-            `mmap` controls the use of numpy memory mapping for reading image
-            array data.  If False, do not try numpy ``memmap`` for data array.
-            If one of {'c', 'r'}, try numpy memmap with ``mode=mmap``.  A
-            `mmap` value of True gives the same behavior as ``mmap='c'``.  If
-            image data file cannot be memory-mapped, ignore `mmap` value and
-            read array from file.
-        keep_file_open : {None, True, False}, optional, keyword only
-            `keep_file_open` controls whether a new file handle is created
-            every time the image is accessed, or a single file handle is
-            created and used for the lifetime of this ``ArrayProxy``. If
-            ``True``, a single file handle is created and used. If ``False``,
-            a new file handle is created every time the image is accessed.
-            The default value (``None``) will result in the value of
-            ``nibabel.arrayproxy.KEEP_FILE_OPEN_DEFAULT` being used.
-        """
-        file_map = klass.filespec_to_file_map(filename)
-        return klass.from_file_map(file_map, mmap=mmap,
-                                   keep_file_open=keep_file_open)
-
     @classmethod
     def filespec_to_file_map(klass, filespec):
         """
@@ -620,7 +586,5 @@ def filespec_to_file_map(klass, filespec):
             file_map[key].filename = fname
         return file_map
 
-    load = from_filename
-
 
 load = AFNIImage.load

nibabel/dataobj_images.py

@@ -11,6 +11,7 @@
 import numpy as np
 
 from .filebasedimages import FileBasedImage
+from .keywordonly import kw_only_meth
 from .deprecated import deprecate_with_version
 
 
@@ -404,3 +405,82 @@ def get_shape(self):
         """ Return shape for image
         """
         return self.shape
+
+    @classmethod
+    @kw_only_meth(1)
+    def from_file_map(klass, file_map, mmap=True, keep_file_open=None):
+        ''' Class method to create image from mapping in ``file_map``
+
+        .. deprecated:: 2.4.1
+            ``keep_file_open='auto'`` is redundant with `False` and has
+            been deprecated. It will raise an error in nibabel 3.0.
+
+        Parameters
+        ----------
+        file_map : dict
+            Mapping with (kay, value) pairs of (``file_type``, FileHolder
+            instance giving file-likes for each file needed for this image
+            type.
+        mmap : {True, False, 'c', 'r'}, optional, keyword only
+            `mmap` controls the use of numpy memory mapping for reading image
+            array data.  If False, do not try numpy ``memmap`` for data array.
+            If one of {'c', 'r'}, try numpy memmap with ``mode=mmap``.  A
+            `mmap` value of True gives the same behavior as ``mmap='c'``.  If
+            image data file cannot be memory-mapped, ignore `mmap` value and
+            read array from file.
+        keep_file_open : { None, True, False }, optional, keyword only
+            `keep_file_open` controls whether a new file handle is created
+            every time the image is accessed, or a single file handle is
+            created and used for the lifetime of this ``ArrayProxy``. If
+            ``True``, a single file handle is created and used. If ``False``,
+            a new file handle is created every time the image is accessed.
+            If ``file_map`` refers to an open file handle, this setting has no
+            effect. The default value (``None``) will result in the value of
+            ``nibabel.arrayproxy.KEEP_FILE_OPEN_DEFAULT`` being used.
+
+        Returns
+        -------
+        img : DataobjImage instance
+        '''
+        raise NotImplementedError
+
+    @classmethod
+    @kw_only_meth(1)
+    def from_filename(klass, filename, mmap=True, keep_file_open=None):
+        '''Class method to create image from filename `filename`
+
+        .. deprecated:: 2.4.1
+            ``keep_file_open='auto'`` is redundant with `False` and has
+            been deprecated. It will raise an error in nibabel 3.0.
+
+        Parameters
+        ----------
+        filename : str
+            Filename of image to load
+        mmap : {True, False, 'c', 'r'}, optional, keyword only
+            `mmap` controls the use of numpy memory mapping for reading image
+            array data.  If False, do not try numpy ``memmap`` for data array.
+            If one of {'c', 'r'}, try numpy memmap with ``mode=mmap``.  A
+            `mmap` value of True gives the same behavior as ``mmap='c'``.  If
+            image data file cannot be memory-mapped, ignore `mmap` value and
+            read array from file.
+        keep_file_open : { None, True, False }, optional, keyword only
+            `keep_file_open` controls whether a new file handle is created
+            every time the image is accessed, or a single file handle is
+            created and used for the lifetime of this ``ArrayProxy``. If
+            ``True``, a single file handle is created and used. If ``False``,
+            a new file handle is created every time the image is accessed.
+            The default value (``None``) will result in the value of
+            ``nibabel.arrayproxy.KEEP_FILE_OPEN_DEFAULT`` being used.
+
+        Returns
+        -------
+        img : DataobjImage instance
+        '''
+        if mmap not in (True, False, 'c', 'r'):
+            raise ValueError("mmap should be one of {True, False, 'c', 'r'}")
+        file_map = klass.filespec_to_file_map(filename)
+        return klass.from_file_map(file_map, mmap=mmap,
+                                   keep_file_open=keep_file_open)
+
+    load = from_filename

nibabel/freesurfer/mghformat.py

@@ -536,17 +536,18 @@ def filespec_to_file_map(klass, filespec):
     @classmethod
     @kw_only_meth(1)
     def from_file_map(klass, file_map, mmap=True, keep_file_open=None):
-        '''Load image from ``file_map``
+        ''' Class method to create image from mapping in ``file_map``
 
         .. deprecated:: 2.4.1
             ``keep_file_open='auto'`` is redundant with `False` and has
             been deprecated. It will raise an error in nibabel 3.0.
 
         Parameters
         ----------
-        file_map : None or mapping, optional
-           files mapping.  If None (default) use object's ``file_map``
-           attribute instead
+        file_map : dict
+            Mapping with (kay, value) pairs of (``file_type``, FileHolder
+            instance giving file-likes for each file needed for this image
+            type.
         mmap : {True, False, 'c', 'r'}, optional, keyword only
             `mmap` controls the use of numpy memory mapping for reading image
             array data.  If False, do not try numpy ``memmap`` for data array.
@@ -563,6 +564,10 @@ def from_file_map(klass, file_map, mmap=True, keep_file_open=None):
             If ``file_map`` refers to an open file handle, this setting has no
             effect. The default value (``None``) will result in the value of
             ``nibabel.arrayproxy.KEEP_FILE_OPEN_DEFAULT`` being used.
+
+        Returns
+        -------
+        img : MGHImage instance
         '''
         if mmap not in (True, False, 'c', 'r'):
             raise ValueError("mmap should be one of {True, False, 'c', 'r'}")
@@ -577,47 +582,6 @@ def from_file_map(klass, file_map, mmap=True, keep_file_open=None):
         img = klass(data, affine, header, file_map=file_map)
         return img
 
-    @classmethod
-    @kw_only_meth(1)
-    def from_filename(klass, filename, mmap=True, keep_file_open=None):
-        ''' Class method to create image from filename ``filename``
-
-        .. deprecated:: 2.4.1
-            ``keep_file_open='auto'`` is redundant with `False` and has
-            been deprecated. It will raise an error in nibabel 3.0.
-
-        Parameters
-        ----------
-        filename : str
-            Filename of image to load
-        mmap : {True, False, 'c', 'r'}, optional, keyword only
-            `mmap` controls the use of numpy memory mapping for reading image
-            array data.  If False, do not try numpy ``memmap`` for data array.
-            If one of {'c', 'r'}, try numpy memmap with ``mode=mmap``.  A
-            `mmap` value of True gives the same behavior as ``mmap='c'``.  If
-            image data file cannot be memory-mapped, ignore `mmap` value and
-            read array from file.
-        keep_file_open : { None, True, False }, optional, keyword only
-            `keep_file_open` controls whether a new file handle is created
-            every time the image is accessed, or a single file handle is
-            created and used for the lifetime of this ``ArrayProxy``. If
-            ``True``, a single file handle is created and used. If ``False``,
-            a new file handle is created every time the image is accessed.
-            The default value (``None``) will result in the value of
-            ``nibabel.arrayproxy.KEEP_FILE_OPEN_DEFAULT`` being used.
-
-        Returns
-        -------
-        img : MGHImage instance
-        '''
-        if mmap not in (True, False, 'c', 'r'):
-            raise ValueError("mmap should be one of {True, False, 'c', 'r'}")
-        file_map = klass.filespec_to_file_map(filename)
-        return klass.from_file_map(file_map, mmap=mmap,
-                                   keep_file_open=keep_file_open)
-
-    load = from_filename
-
     def to_file_map(self, file_map=None):
         ''' Write image to `file_map` or contained ``self.file_map``
 

nibabel/tests/test_dataobj_images.py

@@ -16,9 +16,18 @@ class DoNumpyImage(DataobjImage):
     files_types = (('image', '.npy'),)
 
     @classmethod
-    def from_file_map(klass, file_map):
+    def from_file_map(klass, file_map, mmap=True, keep_file_open=None):
+        if mmap not in (True, False, 'c', 'r'):
+            raise ValueError("mmap should be one of {True, False, 'c', 'r'}")
+        if mmap is True:
+            mmap = 'c'
+        elif mmap is False:
+            mmap = None
         with file_map['image'].get_prepare_fileobj('rb') as fobj:
-            arr = np.load(fobj)
+            try:
+                arr = np.load(fobj, mmap=mmap)
+            except:
+                arr = np.load(fobj)
         return klass(arr)
 
     def to_file_map(self, file_map=None):