Add zstd support to Analyze format images.

- Add zstandard compression for analyze format images via pyzstd.
- Add zstd option under setup.cfg options.extra_requires.

Author: vanandrew

nibabel/analyze.py

@@ -907,6 +907,11 @@ class AnalyzeImage(SpatialImage):
     files_types = (('image', '.img'), ('header', '.hdr'))
     valid_exts = ('.img', '.hdr')
     _compressed_suffixes = ('.gz', '.bz2')
+    try: # If pyzstd installed., add .zst suffix
+        import pyzstd
+        _compressed_suffixes = (*_compressed_suffixes, '.zst')
+    except ImportError:
+        pass
 
     makeable = True
     rw = True

nibabel/openers.py

@@ -39,6 +39,11 @@
     IndexedGzipFile = gzip.GzipFile
     HAVE_INDEXED_GZIP = False
 
+# Enable .zst support if pyzstd installed.
+try:
+    from pyzstd import ZstdFile
+except ImportError:
+    pass
 
 def _gzip_open(filename, mode='rb', compresslevel=9, keep_open=False):
 
@@ -77,13 +82,19 @@ class Opener(object):
     """
     gz_def = (_gzip_open, ('mode', 'compresslevel', 'keep_open'))
     bz2_def = (BZ2File, ('mode', 'buffering', 'compresslevel'))
+    zstd_def = (ZstdFile, ('mode', 'level_or_option'))
     compress_ext_map = {
         '.gz': gz_def,
         '.bz2': bz2_def,
+        '.zst': zstd_def,
         None: (open, ('mode', 'buffering'))  # default
     }
     #: default compression level when writing gz and bz2 files
     default_compresslevel = 1
+    #: default option for zst files
+    default_zst_compresslevel = 3
+    default_level_or_option = {"rb": None, "r": None,
+        "wb": default_zst_compresslevel, "w": default_zst_compresslevel}
     #: whether to ignore case looking for compression extensions
     compress_ext_icase = True
 
@@ -100,10 +111,15 @@ def __init__(self, fileish, *args, **kwargs):
         full_kwargs.update(dict(zip(arg_names[:n_args], args)))
         # Set default mode
         if 'mode' not in full_kwargs:
-            kwargs['mode'] = 'rb'
+            mode = 'rb'
+            kwargs['mode'] = mode
+        else:
+            mode = full_kwargs['mode']
         # Default compression level
         if 'compresslevel' in arg_names and 'compresslevel' not in kwargs:
             kwargs['compresslevel'] = self.default_compresslevel
+        if 'level_or_option' in arg_names and 'level_or_option' not in kwargs:
+            kwargs['level_or_option'] = self.default_level_or_option[mode]
         # Default keep_open hint
         if 'keep_open' in arg_names:
             kwargs.setdefault('keep_open', False)

nibabel/volumeutils.py

@@ -40,6 +40,12 @@
 #: file-like classes known to hold compressed data
 COMPRESSED_FILE_LIKES = (gzip.GzipFile, BZ2File, IndexedGzipFile)
 
+# Enable .zst support if pyzstd installed.
+try:
+    from pyzstd import ZstdFile
+    COMPRESSED_FILE_LIKES = (*COMPRESSED_FILE_LIKES, ZstdFile)
+except ImportError:
+    pass
 
 class Recoder(object):
     """ class to return canonical code(s) from code or aliases

setup.cfg

@@ -60,6 +60,8 @@ test =
     pytest !=5.3.4
     pytest-cov
     pytest-doctestplus
+zstd =
+    pyzstd >= 0.14.3
 all =
     %(dicomfs)s
     %(dev)s