Merge branch 'master' into enh-diff-dtype

Author: effigies

.travis.yml

@@ -4,29 +4,31 @@
 # for it to be on multiple physical lines, so long as you remember: - There
 # can't be any leading "-"s - All newlines will be removed, so use ";"s
 
+dist: xenial
+sudo: true
 language: python
 
-# Run jobs on container-based infrastructure, can be overridden per job
-sudo: false
-
 cache:
   directories:
     - $HOME/.cache/pip
 env:
     global:
-        - DEPENDS="six numpy scipy matplotlib h5py pillow pydicom hypothesis"
+        - DEPENDS="six numpy scipy matplotlib h5py pillow pydicom"
         - OPTIONAL_DEPENDS=""
         - INSTALL_TYPE="setup"
         - EXTRA_WHEELS="https://5cf40426d9f06eb7461d-6fe47d9331aba7cd62fc36c7196769e4.ssl.cf2.rackcdn.com"
         - PRE_WHEELS="https://7933911d6844c6c53a7d-47bd50c35cd79bd838daf386af554a83.ssl.cf2.rackcdn.com"
         - EXTRA_PIP_FLAGS="--find-links=$EXTRA_WHEELS"
         - PRE_PIP_FLAGS="--pre $EXTRA_PIP_FLAGS --find-links $PRE_WHEELS"
 python:
-    - 3.4
     - 3.5
     - 3.6
+    - 3.7
 matrix:
   include:
+    - python: 3.4
+      dist: trusty
+      sudo: false
     - python: 2.7
       env:
         - COVERAGE=1
@@ -95,7 +97,7 @@ before_install:
     - source venv/bin/activate
     - python --version # just to check
     - pip install -U pip wheel  # needed at one point
-    - retry pip install nose flake8 mock hypothesis  # always
+    - retry pip install nose flake8 mock  # always
     - pip install $EXTRA_PIP_FLAGS $DEPENDS $OPTIONAL_DEPENDS
     - if [ "${COVERAGE}" == "1" ]; then
       pip install coverage;

appveyor.yml

@@ -12,6 +12,8 @@ environment:
     - PYTHON: C:\Python35-x64
     - PYTHON: C:\Python36
     - PYTHON: C:\Python36-x64
+    - PYTHON: C:\Python37
+    - PYTHON: C:\Python37-x64
 
 install:
   # Prepend newly installed Python to the PATH of this build (this cannot be
@@ -20,7 +22,7 @@ install:
   - SET PATH=%PYTHON%;%PYTHON%\Scripts;%PATH%
 
   # Install the dependencies of the project.
-  - pip install numpy scipy matplotlib nose h5py mock hypothesis pydicom
+  - pip install numpy scipy matplotlib nose h5py mock pydicom
   - pip install .
   - SET NIBABEL_DATA_DIR=%CD%\nibabel-data
 

dev-requirements.txt

@@ -2,4 +2,3 @@
 -r requirements.txt
 nose
 mock
-hypothesis

nibabel/cmdline/diff.py

@@ -67,26 +67,53 @@ def get_opt_parser():
 
 
 def are_values_different(*values):
-    """Generically compares values, returns true if different"""
+    """Generically compare values, return True if different
+
+    Note that comparison is targetting reporting of comparison of the headers
+    so has following specifics:
+    - even a difference in data types is considered a difference, i.e. 1 != 1.0
+    - nans are considered to be the "same", although generally nan != nan
+    """
     value0 = values[0]
-    # to ensure that the first value isn't compared with itself
-    values = values[1:]
-
-    for value in values:
-        try:  # we sometimes don't want NaN values
-            if np.any(np.isnan(value0)) and np.any(np.isnan(value)):  # if they're both NaN
-                break
-            elif np.any(np.isnan(value0)) or np.any(np.isnan(value)):  # if only 1 is NaN
-                return True
 
-        except TypeError:
-            pass
+    # to not recompute over again
+    if isinstance(value0, np.ndarray):
+        try:
+            # np.asarray for elderly numpys, e.g. 1.7.1 where for
+            # degenerate arrays (shape ()) it would return a pure scalar
+            value0_nans = np.asanyarray(np.isnan(value0))
+            value0_nonnans = np.asanyarray(np.logical_not(value0_nans))
+            # if value0_nans.size == 1:
+            #     import pdb; pdb.set_trace()
+            if not np.any(value0_nans):
+                value0_nans = None
+        except TypeError as exc:
+            str_exc = str(exc)
+            # Not implemented in numpy 1.7.1
+            if "not supported" in str_exc or "ot implemented" in str_exc:
+                value0_nans = None
+            else:
+                raise
 
+    for value in values[1:]:
         if type(value0) != type(value):  # if types are different, then we consider them different
             return True
         elif isinstance(value0, np.ndarray):
-            return np.any(value0 != value)
-
+            if value0.dtype != value.dtype or \
+               value0.shape != value.shape:
+                return True
+            # there might be nans and they need special treatment
+            if value0_nans is not None:
+                value_nans = np.isnan(value)
+                if np.any(value0_nans != value_nans):
+                    return True
+                if np.any(value0[value0_nonnans] != value[value0_nonnans]):
+                    return True
+            elif np.any(value0 != value):
+                return True
+        elif value0 is np.nan:
+            if value is not np.nan:
+                return True
         elif value0 != value:
             return True
 

nibabel/deprecated.py

@@ -52,8 +52,8 @@ class FutureWarningMixin(object):
 
     >>> with warnings.catch_warnings(record=True) as warns:
     ...     d = D()
-    ...     warns[0].message
-    FutureWarning("Please, don't use this class",)
+    ...     warns[0].message.args[0]
+    "Please, don't use this class"
     """
     warn_message = 'This class will be removed in future versions'
 

nibabel/freesurfer/io.py

@@ -81,24 +81,24 @@ def _read_volume_info(fobj):
     return volume_info
 
 
-def _pack_rgba(rgba):
-    """Pack an RGBA sequence into a single integer.
+def _pack_rgb(rgb):
+    """Pack an RGB sequence into a single integer.
 
     Used by :func:`read_annot` and :func:`write_annot` to generate
     "annotation values" for a Freesurfer ``.annot`` file.
 
     Parameters
     ----------
-    rgba : ndarray, shape (n, 4)
-        RGBA colors
+    rgb : ndarray, shape (n, 3)
+        RGB colors
 
     Returns
     -------
     out : ndarray, shape (n, 1)
         Annotation values for each color.
     """
-    bitshifts = 2 ** np.array([[0], [8], [16], [24]], dtype=rgba.dtype)
-    return rgba.dot(bitshifts)
+    bitshifts = 2 ** np.array([[0], [8], [16]], dtype=rgb.dtype)
+    return rgb.dot(bitshifts)
 
 
 def read_geometry(filepath, read_metadata=False, read_stamp=False):
@@ -333,9 +333,13 @@ def read_annot(filepath, orig_ids=False):
     Annotation file format versions 1 and 2 are supported, corresponding to
     the "old-style" and "new-style" color table layout.
 
+    Note that the output color table ``ctab`` is in RGBT form, where T
+    (transparency) is 255 - alpha.
+
     See:
      * https://surfer.nmr.mgh.harvard.edu/fswiki/LabelsClutsAnnotationFiles#Annotation
      * https://github.com/freesurfer/freesurfer/blob/dev/matlab/read_annotation.m
+     * https://github.com/freesurfer/freesurfer/blob/8b88b34/utils/colortab.c
 
     Parameters
     ----------
@@ -352,7 +356,7 @@ def read_annot(filepath, orig_ids=False):
         Annotation id at each vertex. If a vertex does not belong
         to any label and orig_ids=False, its id will be set to -1.
     ctab : ndarray, shape (n_labels, 5)
-        RGBA + label id colortable array.
+        RGBT + label id colortable array.
     names : list of str (python 2), list of bytes (python 3)
         The names of the labels. The length of the list is n_labels.
     """
@@ -384,7 +388,7 @@ def read_annot(filepath, orig_ids=False):
             ctab, names = _read_annot_ctab_new_format(fobj, -n_entries)
 
     # generate annotation values for each LUT entry
-    ctab[:, [4]] = _pack_rgba(ctab[:, :4])
+    ctab[:, [4]] = _pack_rgb(ctab[:, :3])
 
     if not orig_ids:
         ord = np.argsort(ctab[:, -1])
@@ -397,6 +401,9 @@ def read_annot(filepath, orig_ids=False):
 def _read_annot_ctab_old_format(fobj, n_entries):
     """Read in an old-style Freesurfer color table from `fobj`.
 
+    Note that the output color table ``ctab`` is in RGBT form, where T
+    (transparency) is 255 - alpha.
+
     This function is used by :func:`read_annot`.
 
     Parameters
@@ -412,7 +419,7 @@ def _read_annot_ctab_old_format(fobj, n_entries):
     -------
 
     ctab : ndarray, shape (n_entries, 5)
-        RGBA colortable array - the last column contains all zeros.
+        RGBT colortable array - the last column contains all zeros.
     names : list of str
         The names of the labels. The length of the list is n_entries.
     """
@@ -430,7 +437,7 @@ def _read_annot_ctab_old_format(fobj, n_entries):
         name_length = np.fromfile(fobj, dt, 1)[0]
         name = np.fromfile(fobj, "|S%d" % name_length, 1)[0]
         names.append(name)
-        # read RGBA for this entry
+        # read RGBT for this entry
         ctab[i, :4] = np.fromfile(fobj, dt, 4)
 
     return ctab, names
@@ -439,6 +446,9 @@ def _read_annot_ctab_old_format(fobj, n_entries):
 def _read_annot_ctab_new_format(fobj, ctab_version):
     """Read in a new-style Freesurfer color table from `fobj`.
 
+    Note that the output color table ``ctab`` is in RGBT form, where T
+    (transparency) is 255 - alpha.
+
     This function is used by :func:`read_annot`.
 
     Parameters
@@ -454,7 +464,7 @@ def _read_annot_ctab_new_format(fobj, ctab_version):
     -------
 
     ctab : ndarray, shape (n_labels, 5)
-        RGBA colortable array - the last column contains all zeros.
+        RGBT colortable array - the last column contains all zeros.
     names : list of str
         The names of the labels. The length of the list is n_labels.
     """
@@ -480,7 +490,7 @@ def _read_annot_ctab_new_format(fobj, ctab_version):
         name_length = np.fromfile(fobj, dt, 1)[0]
         name = np.fromfile(fobj, "|S%d" % name_length, 1)[0]
         names.append(name)
-        # RGBA
+        # RGBT
         ctab[idx, :4] = np.fromfile(fobj, dt, 4)
 
     return ctab, names
@@ -489,9 +499,13 @@ def _read_annot_ctab_new_format(fobj, ctab_version):
 def write_annot(filepath, labels, ctab, names, fill_ctab=True):
     """Write out a "new-style" Freesurfer annotation file.
 
+    Note that the color table ``ctab`` is in RGBT form, where T (transparency)
+    is 255 - alpha.
+
     See:
      * https://surfer.nmr.mgh.harvard.edu/fswiki/LabelsClutsAnnotationFiles#Annotation
      * https://github.com/freesurfer/freesurfer/blob/dev/matlab/write_annotation.m
+     * https://github.com/freesurfer/freesurfer/blob/8b88b34/utils/colortab.c
 
     Parameters
     ----------
@@ -500,7 +514,7 @@ def write_annot(filepath, labels, ctab, names, fill_ctab=True):
     labels : ndarray, shape (n_vertices,)
         Annotation id at each vertex.
     ctab : ndarray, shape (n_labels, 5)
-        RGBA + label id colortable array.
+        RGBT + label id colortable array.
     names : list of str
         The names of the labels. The length of the list is n_labels.
     fill_ctab : {True, False} optional
@@ -523,8 +537,8 @@ def write_string(s):
 
         # Generate annotation values for each ctab entry
         if fill_ctab:
-            ctab = np.hstack((ctab[:, :4], _pack_rgba(ctab[:, :4])))
-        elif not np.array_equal(ctab[:, [4]], _pack_rgba(ctab[:, :4])):
+            ctab = np.hstack((ctab[:, :4], _pack_rgb(ctab[:, :3])))
+        elif not np.array_equal(ctab[:, [4]], _pack_rgb(ctab[:, :3])):
             warnings.warn('Annotation values in {} will be incorrect'.format(
                 filepath))
 

nibabel/freesurfer/tests/test_io.py

@@ -16,7 +16,7 @@
 
 from .. import (read_geometry, read_morph_data, read_annot, read_label,
                 write_geometry, write_morph_data, write_annot)
-from ..io import _pack_rgba
+from ..io import _pack_rgb
 
 from ...tests.nibabel_data import get_nibabel_data, needs_nibabel_data
 from ...fileslice import strided_scalar
@@ -236,8 +236,7 @@ def test_read_write_annot():
     # Generate the annotation values for each LUT entry
     rgbal[:, 4] = (rgbal[:, 0] +
                    rgbal[:, 1] * (2 ** 8) +
-                   rgbal[:, 2] * (2 ** 16) +
-                   rgbal[:, 3] * (2 ** 24))
+                   rgbal[:, 2] * (2 ** 16))
     annot_path = 'c.annot'
     with InTemporaryDirectory():
         write_annot(annot_path, labels, rgbal, names, fill_ctab=False)
@@ -287,8 +286,7 @@ def test_write_annot_fill_ctab():
         rgbal = np.hstack((rgba, np.zeros((nlabels, 1), dtype=np.int32)))
         rgbal[:, 4] = (rgbal[:, 0] +
                        rgbal[:, 1] * (2 ** 8) +
-                       rgbal[:, 2] * (2 ** 16) +
-                       rgbal[:, 3] * (2 ** 24))
+                       rgbal[:, 2] * (2 ** 16))
         with clear_and_catch_warnings() as w:
             write_annot(annot_path, labels, rgbal, names, fill_ctab=False)
         assert_true(
@@ -307,7 +305,7 @@ def gen_old_annot_file(fpath, nverts, labels, rgba, names):
         dt = '>i'
         vdata = np.zeros((nverts, 2), dtype=dt)
         vdata[:, 0] = np.arange(nverts)
-        vdata[:, [1]] = _pack_rgba(rgba[labels, :])
+        vdata[:, [1]] = _pack_rgb(rgba[labels, :3])
         fbytes = b''
         # number of vertices
         fbytes += struct.pack(dt, nverts)