python-mrcz/numpy2.patch

From 07c01ce360fd3bad884f2a3c03c5f33c0f8348cf Mon Sep 17 00:00:00 2001
From: Eric Prestat <eric.prestat@gmail.com>
Date: Sat, 22 Jun 2024 20:05:46 +0100
Subject: [PATCH 2/5] Replace `==/!=` with `is`/`is not` when comparing to
 `None`

---
 mrcz/ReliablePy.py |  8 ++++----
 mrcz/ioMRC.py      | 20 ++++++++++----------
 mrcz/test_mrcz.py  |  2 +-
 3 files changed, 15 insertions(+), 15 deletions(-)

diff --git a/mrcz/ReliablePy.py b/mrcz/ReliablePy.py
index 64e3274..db0dc6e 100644
--- a/mrcz/ReliablePy.py
+++ b/mrcz/ReliablePy.py
@@ -398,7 +398,7 @@ def pruneParticlesNearImageEdge( self, box = None, shapeImage = [3838,3710] ):
         Image size is not stored anywhere obvious in Relion, so it must be passed in in terms of 
         it's shape in [y,x]
         """
-        if box == None:
+        if box is None:
             try: 
                 box = self.star[b'data_model_general'][b'OriginalImageSize']
             except:
@@ -570,7 +570,7 @@ def saveDataStar( self, outputName, particleKey = b"data_" ):
         Outputs a relion ..._data.star file that has been pruned, regrouped, etc. to outputName
         """
         
-        if outputName == None:
+        if outputName is None:
             # Need to store input star names, and figure out which was the last loaded particles.star file.
             # [outFront, outExt] = os.path.splitext()
             raise IOError( "Default filenames for saveDataStar not implemented yet" )
@@ -652,11 +652,11 @@ def saveDataAsPar( self, outputPrefix, N_classes = 1, mag = None, pixelsize=None
         # kept track of in Relion with Magnification and DetectorPixelSize (which
         # defaults to 14.0)
         
-        if pixelsize == None:
+        if pixelsize is None:
             # Detector pixel size in um, we need pixelsize in Angstrom
             pixelsize = self.star[b'data_'][b'DetectorPixelSize'][0]*1E4 / self.star[b'data_'][b'Magnification'][0]
             print( "Found pixelsize of %0.f" % pixelsize )
-        if mag == None:
+        if mag is None:
             print( "Using Relion magnification of %.f and DSTEP=%.1f" % ( self.star[b'data_'][b'Magnification'][0], self.star[b'data_'][b'DetectorPixelSize'][0]) )
             print( "For a K2 (DSTEP=5.0) the appropriate magnification would be %0.f" % 50000/pixelsize )
         else:
diff --git a/mrcz/ioMRC.py b/mrcz/ioMRC.py
index 998de75..c5b234b 100644
--- a/mrcz/ioMRC.py
+++ b/mrcz/ioMRC.py
@@ -282,16 +282,16 @@ def readMRC(MRCfilename, idx=None, endian='le',
         
         if ( (header['compressor'] in REVERSE_COMPRESSOR_ENUM) 
             and (REVERSE_COMPRESSOR_ENUM[header['compressor']] > 0) 
-            and idx == None ):
+            and idx is None ):
             return __MRCZImport(f, header, slices, endian=endian, fileConvention=fileConvention, 
                                 n_threads=n_threads)
         # Else load as uncompressed MRC file
 
-        if idx != None:
+        if idx is not None:
         # If specific images were requested:
         # TO DO: add support to read all images within a range at once
 
-            if header['compressor'] != None:
+            if header['compressor'] is not None:
                 raise RuntimeError('Reading from arbitrary positions not supported for compressed files. Compressor = %s'%header['compressor'])
             if np.isscalar( idx ):
                 indices = np.array([idx, idx], dtype='int')
@@ -370,7 +370,7 @@ def __MRCZImport(f, header, slices, endian='le', fileConvention='ccpem',
     if not BLOSC_PRESENT:
         raise ImportError( '`blosc` is not installed, cannot decompress file.' )
         
-    if n_threads == None:
+    if n_threads is None:
         blosc.nthreads = DEFAULT_N_THREADS
     else:
         blosc.nthreads = n_threads
@@ -751,7 +751,7 @@ def writeMRC(input_image, MRCfilename, meta=None, endian='le', dtype=None,
     # the file exists, but idx is 'None', it will be replaced by a new file 
     # with new header anyway:
     if os.path.isfile(MRCfilename):
-        if idx == None:
+        if idx is None:
             idxnewfile = True
         else:
             idxnewfile = False
@@ -760,11 +760,11 @@ def writeMRC(input_image, MRCfilename, meta=None, endian='le', dtype=None,
 
     
     if idxnewfile:
-        if dtype == 'uint4' and compressor != None:
+        if dtype == 'uint4' and compressor is not None:
             raise TypeError('uint4 packing is not compatible with compression, use int8 datatype.')
             
         header = {'meta': meta}
-        if dtype == None:
+        if dtype is None:
             if slices > 0:
                 header['dtype'] = endchar + input_image[0].dtype.descr[0][1].strip('<>|')
             else:
@@ -816,7 +816,7 @@ def writeMRC(input_image, MRCfilename, meta=None, endian='le', dtype=None,
         
         header['compressor'] = compressor
         header['clevel'] = clevel
-        if n_threads == None and BLOSC_PRESENT:
+        if n_threads is None and BLOSC_PRESENT:
             n_threads = DEFAULT_N_THREADS
         header['n_threads'] = n_threads
         
@@ -848,8 +848,8 @@ def writeMRC(input_image, MRCfilename, meta=None, endian='le', dtype=None,
             header['meta'] = meta
 
     # Now that we have a proper header, we go into the details of writing to a specific position:
-    if idx != None:
-        if header['compressor'] != None:
+    if idx is not None:
+        if header['compressor'] is not None:
             raise RuntimeError('Writing at arbitrary positions not supported for compressed files. Compressor = %s' % header['compressor'])
 
         idx = int(idx)
diff --git a/mrcz/test_mrcz.py b/mrcz/test_mrcz.py
index d76f5fa..9701cdc 100644
--- a/mrcz/test_mrcz.py
+++ b/mrcz/test_mrcz.py
@@ -23,7 +23,7 @@ def which(program):
         program_ext = os.path.splitext(program)[1]
         if program_ext == '':
             prog_exe = which(program + '.exe')
-            if prog_exe != None:
+            if prog_exe is not None:
                 return prog_exe
             return which(program + '.com')
             

From 92e1b2397e2024c25b61d9eef1ed700c5bc00a4e Mon Sep 17 00:00:00 2001
From: Eric Prestat <eric.prestat@gmail.com>
Date: Sat, 22 Jun 2024 20:18:25 +0100
Subject: [PATCH 3/5] Replace deprecated `disutils.version.StrictVersion` with
 `packaging.version.Version`

---
 mrcz/ioMRC.py | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/mrcz/ioMRC.py b/mrcz/ioMRC.py
index c5b234b..115044e 100644
--- a/mrcz/ioMRC.py
+++ b/mrcz/ioMRC.py
@@ -27,7 +27,7 @@
         raise ImportError('Get the backport for `concurrent.futures` for Py2.7 as `pip install futures`')
     raise e
 from mrcz.__version__ import __version__
-from distutils.version import StrictVersion
+from packaging.version import Version
 
 import logging
 logger = logging.getLogger('MRCZ')
@@ -195,7 +195,7 @@ def _getMRCZVersion(label):
 
     Returns
     -------
-    version: Optional[distutils.version.StrictVersion]
+    version: Optional[packaging.version.Version]
         areturns ``None`` if `label` cannot be parsed.
     """
     if isinstance(label, bytes):
@@ -207,7 +207,7 @@ def _getMRCZVersion(label):
 
     label = label[4:]
     try:
-        version = StrictVersion(label)
+        version = Version(label)
         return version
     except ValueError:
         return None
@@ -537,7 +537,7 @@ def readMRCHeader(MRCfilename, slices=None, endian='le', fileConvention = 'ccpem
             # is essentially unknown (and wrong). So we have this version 
             # check where we force slices to be 1 (i.e. we assume it is a 
             # stack of 2D images).
-            if mrcz_version is not None and mrcz_version < StrictVersion('0.5.0'):
+            if mrcz_version is not None and mrcz_version < Version('0.5.0'):
                 logger.warning('MRCZ version < 0.5.0 for file {}, assuming slices == 1.'.format(MRCfilename))
                 slices = 1
             else:

From 1c367b3c3a5bfbffbebf36e2bf6a1eab9a668252 Mon Sep 17 00:00:00 2001
From: Eric Prestat <eric.prestat@gmail.com>
Date: Sat, 22 Jun 2024 20:20:13 +0100
Subject: [PATCH 4/5] Replace deprecated `warn` method with `warning`

---
 mrcz/ioMRC.py | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/mrcz/ioMRC.py b/mrcz/ioMRC.py
index 115044e..872ee2e 100644
--- a/mrcz/ioMRC.py
+++ b/mrcz/ioMRC.py
@@ -711,12 +711,12 @@ def writeMRC(input_image, MRCfilename, meta=None, endian='le', dtype=None,
 
             if z_slice.dtype == np.float64 or z_slice.dtype == float:
                 if not WARNED_ABOUT_CASTING_F64:
-                    logger.warn('Casting {} to `numpy.float32`, further warnings will be suppressed.'.format(MRCfilename))
+                    logger.warning('Casting {} to `numpy.float32`, further warnings will be suppressed.'.format(MRCfilename))
                     WARNED_ABOUT_CASTING_F64 = True
                 input_image[J] = z_slice.astype(np.float32)
             elif z_slice.dtype == np.complex128:
                 if not WARNED_ABOUT_CASTING_C128:
-                    logger.warn('Casting {} to `numpy.complex64`, further warnings will be suppressed.'.format(MRCfilename))
+                    logger.warning('Casting {} to `numpy.complex64`, further warnings will be suppressed.'.format(MRCfilename))
                     WARNED_ABOUT_CASTING_C128 = True
                 input_image[J] = z_slice.astype(np.complex64)
             else:
@@ -732,12 +732,12 @@ def writeMRC(input_image, MRCfilename, meta=None, endian='le', dtype=None,
         # Cast float64 -> float32, and complex128 -> complex64
         if input_image.dtype == np.float64 or input_image.dtype == float:
             if not WARNED_ABOUT_CASTING_F64:
-                logger.warn('Casting {} to `numpy.float64`'.format(MRCfilename))
+                logger.warning('Casting {} to `numpy.float64`'.format(MRCfilename))
                 WARNED_ABOUT_CASTING_F64 = True
             input_image = input_image.astype(np.float32)
         elif input_image.dtype == np.complex128:
             if not WARNED_ABOUT_CASTING_C128:
-                logger.warn('Casting {} to `numpy.complex64`'.format(MRCfilename))
+                logger.warning('Casting {} to `numpy.complex64`'.format(MRCfilename))
                 WARNED_ABOUT_CASTING_C128 = True
             input_image = input_image.astype(np.complex64)
 

From 97644c4a957946deb1c510d83dba3d3e2fa155ba Mon Sep 17 00:00:00 2001
From: Eric Prestat <eric.prestat@gmail.com>
Date: Sat, 22 Jun 2024 20:23:15 +0100
Subject: [PATCH 5/5] Fix numpy deprecation warning on conversion of an array
 with ndim > 0 to a scalar

---
 mrcz/ioMRC.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/mrcz/ioMRC.py b/mrcz/ioMRC.py
index 872ee2e..7a61b16 100644
--- a/mrcz/ioMRC.py
+++ b/mrcz/ioMRC.py
@@ -542,7 +542,7 @@ def readMRCHeader(MRCfilename, slices=None, endian='le', fileConvention = 'ccpem
                 slices = 1
             else:
                 f.seek(36)
-                slices = int(np.fromfile(f, dtype=dtype_i4, count=1))
+                slices = int(np.fromfile(f, dtype=dtype_i4, count=1)[0])
 
         # Read in pixelsize
         f.seek(40)
@@ -572,7 +572,7 @@ def readMRCHeader(MRCfilename, slices=None, endian='le', fileConvention = 'ccpem
 
         # Size of meta-data
         f.seek(92)
-        header['extendedBytes'] = int(np.fromfile(f, dtype=dtype_i4, count=1))
+        header['extendedBytes'] = int(np.fromfile(f, dtype=dtype_i4, count=1)[0])
         if header['extendedBytes'] > 0:
             f.seek(104)
             header['metaId'] = f.read(4)