RF: remove EcatMlist class, write mlist as int32

Remove EcatMlist class for simplicity, replace with functions on mlist
array.

The CTI code has the mlist as an int32 array, use int32s throughout, and
hope.

Author: matthew-brett

nibabel/ecat.py

@@ -405,7 +405,7 @@ def get_frame_order(mlist):
     >>> ecat_file = os.path.join(nibabel_dir,'tests','data','tinypet.v')
     >>> img = ecat.load(ecat_file)
     >>> mlist = img.get_mlist()
-    >>> mlist.get_frame_order()
+    >>> get_frame_order(mlist)
     {0: [0, 16842758]}
     """
     ids = mlist[:, 0].copy()
@@ -449,7 +449,7 @@ def get_series_framenumbers(mlist):
     >>> ecat_file = os.path.join(nibabel_dir,'tests','data','tinypet.v')
     >>> img = ecat.load(ecat_file)
     >>> mlist = img.get_mlist()
-    >>> mlist.get_series_framenumbers()
+    >>> get_series_framenumbers(mlist)
     {0: 1}
     """
     nframes = len(mlist)
@@ -502,46 +502,6 @@ def read_subheaders(fileobj, mlist, endianness):
     return subheaders
 
 
-class EcatMlist(object):
-    # Can we do without this object, just using the functions?
-
-    def __init__(self,fileobj, hdr):
-        """ gets list of frames and subheaders in pet file
-
-        Container for Ecat mlist
-
-        Data for mlist is numpy array shape (frames, 4)
-
-        Columns are:
-
-        * 0 - Matrix identifier.
-        * 1 - subheader block number
-        * 2 - Last block number of matrix data block.
-        * 3 - Matrix status:
-          * 1 - exists - rw
-          * 2 - exists - ro
-          * 3 - matrix deleted
-
-        A block above is 512 bytes in the image data file
-
-        Parameters
-        -----------
-        fileobj : file-like
-            ECAT file <filename>.v  fileholder or file object with read, seek
-            methods
-        """
-        self.hdr = hdr
-        self._mlist = np.zeros((hdr['num_frames'], 4), dtype='uint32')
-        mlist_data = read_mlist(fileobj, hdr.endianness)
-        self._mlist[:len(mlist_data)] = mlist_data
-
-    def get_frame_order(self):
-        return get_frame_order(self._mlist)
-
-    def get_series_framenumbers(self):
-        return get_series_framenumbers(self._mlist)
-
-
 class EcatSubHeader(object):
 
     _subhdrdtype = subhdr_dtype
@@ -554,17 +514,17 @@ def __init__(self, hdr, mlist, fileobj):
         Parameters
         -----------
         hdr : EcatHeader
-
-        mlist : EcatMlist
-
+            ECAT main header
+        mlist : array shape (N, 4)
+            Matrix list
         fileobj : ECAT file <filename>.v  fileholder or file object
                   with read, seek methods
         """
         self._header = hdr
         self.endianness = hdr.endianness
         self._mlist = mlist
         self.fileobj = fileobj
-        self.subheaders = read_subheaders(fileobj, mlist._mlist, hdr.endianness)
+        self.subheaders = read_subheaders(fileobj, mlist, hdr.endianness)
 
     def get_shape(self, frame=0):
         """ returns shape of given frame"""
@@ -576,11 +536,9 @@ def get_shape(self, frame=0):
 
     def get_nframes(self):
         """returns number of frames"""
-        mlist = self._mlist
-        framed = mlist.get_frame_order()
+        framed = get_frame_order(self._mlist)
         return len(framed)
 
-
     def _check_affines(self):
         """checks if all affines are equal across frames"""
         nframes = self.get_nframes()
@@ -625,9 +583,7 @@ def _get_data_dtype(self, frame):
         return self._data_type_codes.dtype[dtcode]
 
     def _get_frame_offset(self, frame=0):
-        mlist = self._mlist._mlist
-        offset = (mlist[frame][1]) * BLOCK_SIZE
-        return int(offset)
+        return int(self._mlist[frame][1] * BLOCK_SIZE)
 
     def _get_oriented_data(self, raw_data, orientation=None):
         '''
@@ -725,7 +681,7 @@ def __array__(self):
         (``__getitem__``) below, or ``subheader.data_from_fileobj(frame)``
         '''
         data = np.empty(self.shape)
-        frame_mapping = self._subheader._mlist.get_frame_order()
+        frame_mapping = get_frame_order(self._subheader._mlist)
         for i in sorted(frame_mapping):
             data[:,:,:,i] = self._subheader.data_from_fileobj(frame_mapping[i][0])
         return data
@@ -737,7 +693,7 @@ def __getitem__(self, sliceobj):
         # Indices into sliceobj referring to image axes
         ax_inds = [i for i, obj in enumerate(sliceobj) if not obj is None]
         assert len(ax_inds) == len(self.shape)
-        frame_mapping = self._subheader._mlist.get_frame_order()
+        frame_mapping = get_frame_order(self._subheader._mlist)
         # Analyze index for 4th axis
         slice3 = sliceobj[ax_inds[3]]
         # We will load volume by volume.  Make slicer into volume by dropping
@@ -769,7 +725,6 @@ class EcatImage(SpatialImage):
     _header = EcatHeader
     header_class = _header
     _subheader = EcatSubHeader
-    _mlist = EcatMlist
     files_types = (('image', '.v'), ('header', '.v'))
 
     ImageArrayProxy = EcatImageArrayProxy
@@ -795,8 +750,8 @@ def __init__(self, dataobj, affine, header,
             meta data for this image format
         subheader : None or subheader instance
             meta data for each sub-image for frame in the image
-        mlist : None or mlist instance
-            meta data with array giving offset and order of data in file
+        mlist : None or array
+            Matrix list array giving offset and order of data in file
         extra : None or mapping, optional
             metadata associated with this image that cannot be
             stored in header or subheader
@@ -871,7 +826,8 @@ def shape(self):
         return(x, y, z, nframes)
 
     def get_mlist(self):
-        """ get access to the mlist """
+        """ get access to the mlist
+        """
         return self._mlist
 
     def get_subheaders(self):
@@ -904,29 +860,29 @@ def from_file_map(klass, file_map):
         header = klass._header.from_fileobj(hdr_fid)
         hdr_copy = header.copy()
         ### LOAD MLIST
-        mlist = klass._mlist(hdr_fid, hdr_copy)
+        mlist = np.zeros((header['num_frames'], 4), dtype=np.int32)
+        mlist_data = read_mlist(hdr_fid, hdr_copy.endianness)
+        mlist[:len(mlist_data)] = mlist_data
         ### LOAD SUBHEADERS
-        subheaders = klass._subheader(hdr_copy,
-                                      mlist,
-                                      hdr_fid)
+        subheaders = klass._subheader(hdr_copy, mlist, hdr_fid)
         ### LOAD DATA
         ##  Class level ImageArrayProxy
         data = klass.ImageArrayProxy(subheaders)
-
         ## Get affine
         if not subheaders._check_affines():
-            warnings.warn('Affines different across frames, loading affine from FIRST frame',
-                          UserWarning )
+            warnings.warn('Affines different across frames, loading affine '
+                          'from FIRST frame', UserWarning )
         aff = subheaders.get_frame_affine()
-        img = klass(data, aff, header, subheaders, mlist, extra=None, file_map = file_map)
+        img = klass(data, aff, header, subheaders, mlist,
+                    extra=None, file_map=file_map)
         return img
 
     def _get_empty_dir(self):
         '''
         Get empty directory entry of the form
         [numAvail, nextDir, previousDir, numUsed]
         '''
-        return np.array([31, 2, 0, 0], dtype=np.uint32)
+        return np.array([31, 2, 0, 0], dtype=np.int32)
 
     def _write_data(self, data, stream, pos, dtype=None, endianness=None):
         '''
@@ -962,9 +918,11 @@ def to_file_map(self, file_map=None):
         if file_map is None:
             file_map = self.file_map
 
+        # It appears to be necessary to load the data before saving even if the
+        # data itself is not used.
         data = self.get_data()
         hdr = self.get_header()
-        mlist = self.get_mlist()._mlist
+        mlist = self._mlist
         subheaders = self.get_subheaders()
         dir_pos = 512
         entry_pos = dir_pos + 16 #528
@@ -999,8 +957,7 @@ def to_file_map(self, file_map=None):
             self._write_data(image, imgf, pos+2, endianness='>')
 
             #Move to dictionnary offset and write dictionnary entry
-            self._write_data(mlist[index], imgf, entry_pos,
-                np.uint32, endianness='>')
+            self._write_data(mlist[index], imgf, entry_pos, endianness='>')
 
             entry_pos = entry_pos + 16
 
@@ -1022,7 +979,7 @@ def to_file_map(self, file_map=None):
         #Fill directory with empty data until directory is full
         while current_dir[0] > 0:
             entry_pos = dir_pos + 16 + (16 * current_dir[3])
-            self._write_data(np.array([0,0,0,0]), imgf, entry_pos, np.uint32)
+            self._write_data(np.zeros(4, dtype=np.int32), imgf, entry_pos)
             current_dir[0] = current_dir[0] - 1
             current_dir[3] = current_dir[3] + 1
 

nibabel/tests/test_ecat.py

@@ -13,11 +13,11 @@
 import numpy as np
 
 from ..openers import Opener
-from ..ecat import EcatHeader, EcatMlist, EcatSubHeader, EcatImage
+from ..ecat import (EcatHeader, EcatSubHeader, EcatImage, read_mlist,
+                    get_frame_order, get_series_framenumbers)
 
 from unittest import TestCase
-from nose.tools import (assert_true, assert_false, assert_equal,
-                        assert_not_equal, assert_raises)
+from nose.tools import (assert_true, assert_false, assert_equal, assert_raises)
 
 from numpy.testing import assert_array_equal, assert_array_almost_equal
 
@@ -79,13 +79,12 @@ def test_from_eg_file(self):
 
 class TestEcatMlist(TestCase):
     header_class = EcatHeader
-    mlist_class = EcatMlist
     example_file = ecat_file
 
     def test_mlist(self):
         fid = open(self.example_file, 'rb')
         hdr = self.header_class.from_fileobj(fid)
-        mlist =  self.mlist_class(fid, hdr)
+        mlist = read_mlist(fid, hdr.endianness)
         fid.seek(0)
         fid.seek(512)
         dat=fid.read(128*32)
@@ -95,68 +94,64 @@ def test_mlist(self):
         fid.close()
         #tests
         assert_true(mats['matlist'][0,0] +  mats['matlist'][0,3] == 31)
-        assert_true(mlist.get_frame_order()[0][0] == 0)
-        assert_true(mlist.get_frame_order()[0][1] == 16842758.0)
+        assert_true(get_frame_order(mlist)[0][0] == 0)
+        assert_true(get_frame_order(mlist)[0][1] == 16842758.0)
         # test badly ordered mlist
-        badordermlist = mlist
-        badordermlist._mlist = np.array([[  1.68427540e+07,   3.00000000e+00,
-                                            1.20350000e+04,   1.00000000e+00],
-                                         [  1.68427530e+07,   1.20360000e+04,
-                                            2.40680000e+04,   1.00000000e+00],
-                                         [  1.68427550e+07,   2.40690000e+04,
-                                            3.61010000e+04,   1.00000000e+00],
-                                         [  1.68427560e+07,   3.61020000e+04,
-                                            4.81340000e+04,   1.00000000e+00],
-                                         [  1.68427570e+07,   4.81350000e+04,
-                                            6.01670000e+04,   1.00000000e+00],
-                                         [  1.68427580e+07,   6.01680000e+04,
-                                            7.22000000e+04,   1.00000000e+00]])
+        badordermlist = np.array([[1.68427540e+07,   3.00000000e+00,
+                                   1.20350000e+04,   1.00000000e+00],
+                                  [1.68427530e+07,   1.20360000e+04,
+                                   2.40680000e+04,   1.00000000e+00],
+                                  [1.68427550e+07,   2.40690000e+04,
+                                   3.61010000e+04,   1.00000000e+00],
+                                  [1.68427560e+07,   3.61020000e+04,
+                                   4.81340000e+04,   1.00000000e+00],
+                                  [1.68427570e+07,   4.81350000e+04,
+                                   6.01670000e+04,   1.00000000e+00],
+                                  [1.68427580e+07,   6.01680000e+04,
+                                   7.22000000e+04,   1.00000000e+00]])
         with suppress_warnings():  # STORED order
-            assert_true(badordermlist.get_frame_order()[0][0] == 1)
+            assert_true(get_frame_order(badordermlist)[0][0] == 1)
 
     def test_mlist_errors(self):
         fid = open(self.example_file, 'rb')
         hdr = self.header_class.from_fileobj(fid)
         hdr['num_frames'] = 6
-        mlist =  self.mlist_class(fid, hdr)    
-        mlist._mlist = np.array([[  1.68427540e+07,   3.00000000e+00,
-                                    1.20350000e+04,   1.00000000e+00],
-                                 [  1.68427530e+07,   1.20360000e+04,
-                                    2.40680000e+04,   1.00000000e+00],
-                                 [  1.68427550e+07,   2.40690000e+04,
-                                    3.61010000e+04,   1.00000000e+00],
-                                 [  1.68427560e+07,   3.61020000e+04,
-                                    4.81340000e+04,   1.00000000e+00],
-                                 [  1.68427570e+07,   4.81350000e+04,
-                                    6.01670000e+04,   1.00000000e+00],
-                                 [  1.68427580e+07,   6.01680000e+04,
-                                    7.22000000e+04,   1.00000000e+00]])        
+        mlist = read_mlist(fid, hdr.endianness)
+        mlist = np.array([[1.68427540e+07,   3.00000000e+00,
+                           1.20350000e+04,   1.00000000e+00],
+                          [1.68427530e+07,   1.20360000e+04,
+                           2.40680000e+04,   1.00000000e+00],
+                          [1.68427550e+07,   2.40690000e+04,
+                           3.61010000e+04,   1.00000000e+00],
+                          [1.68427560e+07,   3.61020000e+04,
+                           4.81340000e+04,   1.00000000e+00],
+                          [1.68427570e+07,   4.81350000e+04,
+                           6.01670000e+04,   1.00000000e+00],
+                          [1.68427580e+07,   6.01680000e+04,
+                           7.22000000e+04,   1.00000000e+00]])
         with suppress_warnings():  # STORED order
-            series_framenumbers = mlist.get_series_framenumbers()
+            series_framenumbers = get_series_framenumbers(mlist)
         # first frame stored was actually 2nd frame acquired
         assert_true(series_framenumbers[0] == 2)
         order = [series_framenumbers[x] for x in sorted(series_framenumbers)]
         # true series order is [2,1,3,4,5,6], note counting starts at 1
         assert_true(order == [2, 1, 3, 4, 5, 6])
-        mlist._mlist[0,0] = 0
+        mlist[0,0] = 0
         with suppress_warnings():
-            frames_order = mlist.get_frame_order()
+            frames_order = get_frame_order(mlist)
         neworder =[frames_order[x][0] for x in sorted(frames_order)] 
         assert_true(neworder == [1, 2, 3, 4, 5])
         with suppress_warnings():
-            assert_raises(IOError,
-                          mlist.get_series_framenumbers)
-        
-        
+            assert_raises(IOError, get_series_framenumbers, mlist)
+
 
 class TestEcatSubHeader(TestCase):
     header_class = EcatHeader
-    mlist_class = EcatMlist
     subhdr_class = EcatSubHeader
     example_file = ecat_file
     fid = open(example_file, 'rb')
     hdr = header_class.from_fileobj(fid)
-    mlist =  mlist_class(fid, hdr)
+    mlist = read_mlist(fid, hdr.endianness)
     subhdr = subhdr_class(hdr, mlist, fid)
 
     def test_subheader_size(self):
@@ -269,5 +264,5 @@ def test_data_regression(self):
 
     def test_mlist_regreesion(self):
         # Test mlist is as same as for nibabel 1.3.0
-        assert_array_equal(self.img.get_mlist()._mlist,
+        assert_array_equal(self.img.get_mlist(),
                            [[16842758, 3, 3011, 1]])