266 lines
12 KiB
Diff
266 lines
12 KiB
Diff
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From 07c01ce360fd3bad884f2a3c03c5f33c0f8348cf Mon Sep 17 00:00:00 2001
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From: Eric Prestat <eric.prestat@gmail.com>
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Date: Sat, 22 Jun 2024 20:05:46 +0100
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Subject: [PATCH 2/5] Replace `==/!=` with `is`/`is not` when comparing to
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`None`
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---
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mrcz/ReliablePy.py | 8 ++++----
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mrcz/ioMRC.py | 20 ++++++++++----------
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mrcz/test_mrcz.py | 2 +-
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3 files changed, 15 insertions(+), 15 deletions(-)
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diff --git a/mrcz/ReliablePy.py b/mrcz/ReliablePy.py
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index 64e3274..db0dc6e 100644
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--- a/mrcz/ReliablePy.py
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+++ b/mrcz/ReliablePy.py
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@@ -398,7 +398,7 @@ def pruneParticlesNearImageEdge( self, box = None, shapeImage = [3838,3710] ):
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Image size is not stored anywhere obvious in Relion, so it must be passed in in terms of
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it's shape in [y,x]
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"""
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- if box == None:
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+ if box is None:
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try:
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box = self.star[b'data_model_general'][b'OriginalImageSize']
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except:
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@@ -570,7 +570,7 @@ def saveDataStar( self, outputName, particleKey = b"data_" ):
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Outputs a relion ..._data.star file that has been pruned, regrouped, etc. to outputName
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"""
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- if outputName == None:
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+ if outputName is None:
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# Need to store input star names, and figure out which was the last loaded particles.star file.
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# [outFront, outExt] = os.path.splitext()
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raise IOError( "Default filenames for saveDataStar not implemented yet" )
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@@ -652,11 +652,11 @@ def saveDataAsPar( self, outputPrefix, N_classes = 1, mag = None, pixelsize=None
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# kept track of in Relion with Magnification and DetectorPixelSize (which
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# defaults to 14.0)
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- if pixelsize == None:
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+ if pixelsize is None:
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# Detector pixel size in um, we need pixelsize in Angstrom
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pixelsize = self.star[b'data_'][b'DetectorPixelSize'][0]*1E4 / self.star[b'data_'][b'Magnification'][0]
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print( "Found pixelsize of %0.f" % pixelsize )
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- if mag == None:
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+ if mag is None:
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print( "Using Relion magnification of %.f and DSTEP=%.1f" % ( self.star[b'data_'][b'Magnification'][0], self.star[b'data_'][b'DetectorPixelSize'][0]) )
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print( "For a K2 (DSTEP=5.0) the appropriate magnification would be %0.f" % 50000/pixelsize )
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else:
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diff --git a/mrcz/ioMRC.py b/mrcz/ioMRC.py
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index 998de75..c5b234b 100644
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--- a/mrcz/ioMRC.py
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+++ b/mrcz/ioMRC.py
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@@ -282,16 +282,16 @@ def readMRC(MRCfilename, idx=None, endian='le',
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if ( (header['compressor'] in REVERSE_COMPRESSOR_ENUM)
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and (REVERSE_COMPRESSOR_ENUM[header['compressor']] > 0)
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- and idx == None ):
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+ and idx is None ):
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return __MRCZImport(f, header, slices, endian=endian, fileConvention=fileConvention,
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n_threads=n_threads)
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# Else load as uncompressed MRC file
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- if idx != None:
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+ if idx is not None:
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# If specific images were requested:
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# TO DO: add support to read all images within a range at once
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- if header['compressor'] != None:
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+ if header['compressor'] is not None:
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raise RuntimeError('Reading from arbitrary positions not supported for compressed files. Compressor = %s'%header['compressor'])
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if np.isscalar( idx ):
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indices = np.array([idx, idx], dtype='int')
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@@ -370,7 +370,7 @@ def __MRCZImport(f, header, slices, endian='le', fileConvention='ccpem',
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if not BLOSC_PRESENT:
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raise ImportError( '`blosc` is not installed, cannot decompress file.' )
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- if n_threads == None:
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+ if n_threads is None:
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blosc.nthreads = DEFAULT_N_THREADS
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else:
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blosc.nthreads = n_threads
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@@ -751,7 +751,7 @@ def writeMRC(input_image, MRCfilename, meta=None, endian='le', dtype=None,
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# the file exists, but idx is 'None', it will be replaced by a new file
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# with new header anyway:
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if os.path.isfile(MRCfilename):
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- if idx == None:
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+ if idx is None:
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idxnewfile = True
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else:
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idxnewfile = False
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@@ -760,11 +760,11 @@ def writeMRC(input_image, MRCfilename, meta=None, endian='le', dtype=None,
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if idxnewfile:
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- if dtype == 'uint4' and compressor != None:
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+ if dtype == 'uint4' and compressor is not None:
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raise TypeError('uint4 packing is not compatible with compression, use int8 datatype.')
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header = {'meta': meta}
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- if dtype == None:
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+ if dtype is None:
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if slices > 0:
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header['dtype'] = endchar + input_image[0].dtype.descr[0][1].strip('<>|')
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else:
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@@ -816,7 +816,7 @@ def writeMRC(input_image, MRCfilename, meta=None, endian='le', dtype=None,
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header['compressor'] = compressor
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header['clevel'] = clevel
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- if n_threads == None and BLOSC_PRESENT:
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+ if n_threads is None and BLOSC_PRESENT:
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n_threads = DEFAULT_N_THREADS
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header['n_threads'] = n_threads
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@@ -848,8 +848,8 @@ def writeMRC(input_image, MRCfilename, meta=None, endian='le', dtype=None,
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header['meta'] = meta
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# Now that we have a proper header, we go into the details of writing to a specific position:
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- if idx != None:
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- if header['compressor'] != None:
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+ if idx is not None:
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+ if header['compressor'] is not None:
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raise RuntimeError('Writing at arbitrary positions not supported for compressed files. Compressor = %s' % header['compressor'])
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idx = int(idx)
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diff --git a/mrcz/test_mrcz.py b/mrcz/test_mrcz.py
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index d76f5fa..9701cdc 100644
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--- a/mrcz/test_mrcz.py
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+++ b/mrcz/test_mrcz.py
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@@ -23,7 +23,7 @@ def which(program):
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program_ext = os.path.splitext(program)[1]
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if program_ext == '':
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prog_exe = which(program + '.exe')
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- if prog_exe != None:
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+ if prog_exe is not None:
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return prog_exe
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return which(program + '.com')
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From 92e1b2397e2024c25b61d9eef1ed700c5bc00a4e Mon Sep 17 00:00:00 2001
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From: Eric Prestat <eric.prestat@gmail.com>
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Date: Sat, 22 Jun 2024 20:18:25 +0100
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Subject: [PATCH 3/5] Replace deprecated `disutils.version.StrictVersion` with
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`packaging.version.Version`
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---
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mrcz/ioMRC.py | 8 ++++----
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1 file changed, 4 insertions(+), 4 deletions(-)
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diff --git a/mrcz/ioMRC.py b/mrcz/ioMRC.py
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index c5b234b..115044e 100644
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--- a/mrcz/ioMRC.py
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+++ b/mrcz/ioMRC.py
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@@ -27,7 +27,7 @@
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raise ImportError('Get the backport for `concurrent.futures` for Py2.7 as `pip install futures`')
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raise e
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from mrcz.__version__ import __version__
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-from distutils.version import StrictVersion
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+from packaging.version import Version
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import logging
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logger = logging.getLogger('MRCZ')
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@@ -195,7 +195,7 @@ def _getMRCZVersion(label):
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Returns
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-------
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- version: Optional[distutils.version.StrictVersion]
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+ version: Optional[packaging.version.Version]
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areturns ``None`` if `label` cannot be parsed.
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"""
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if isinstance(label, bytes):
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@@ -207,7 +207,7 @@ def _getMRCZVersion(label):
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label = label[4:]
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try:
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- version = StrictVersion(label)
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+ version = Version(label)
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return version
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except ValueError:
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return None
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@@ -537,7 +537,7 @@ def readMRCHeader(MRCfilename, slices=None, endian='le', fileConvention = 'ccpem
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# is essentially unknown (and wrong). So we have this version
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# check where we force slices to be 1 (i.e. we assume it is a
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# stack of 2D images).
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- if mrcz_version is not None and mrcz_version < StrictVersion('0.5.0'):
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+ if mrcz_version is not None and mrcz_version < Version('0.5.0'):
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logger.warning('MRCZ version < 0.5.0 for file {}, assuming slices == 1.'.format(MRCfilename))
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slices = 1
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else:
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From 1c367b3c3a5bfbffbebf36e2bf6a1eab9a668252 Mon Sep 17 00:00:00 2001
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From: Eric Prestat <eric.prestat@gmail.com>
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Date: Sat, 22 Jun 2024 20:20:13 +0100
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Subject: [PATCH 4/5] Replace deprecated `warn` method with `warning`
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---
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mrcz/ioMRC.py | 8 ++++----
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1 file changed, 4 insertions(+), 4 deletions(-)
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diff --git a/mrcz/ioMRC.py b/mrcz/ioMRC.py
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index 115044e..872ee2e 100644
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--- a/mrcz/ioMRC.py
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+++ b/mrcz/ioMRC.py
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@@ -711,12 +711,12 @@ def writeMRC(input_image, MRCfilename, meta=None, endian='le', dtype=None,
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if z_slice.dtype == np.float64 or z_slice.dtype == float:
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if not WARNED_ABOUT_CASTING_F64:
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- logger.warn('Casting {} to `numpy.float32`, further warnings will be suppressed.'.format(MRCfilename))
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+ logger.warning('Casting {} to `numpy.float32`, further warnings will be suppressed.'.format(MRCfilename))
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WARNED_ABOUT_CASTING_F64 = True
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input_image[J] = z_slice.astype(np.float32)
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elif z_slice.dtype == np.complex128:
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if not WARNED_ABOUT_CASTING_C128:
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- logger.warn('Casting {} to `numpy.complex64`, further warnings will be suppressed.'.format(MRCfilename))
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+ logger.warning('Casting {} to `numpy.complex64`, further warnings will be suppressed.'.format(MRCfilename))
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WARNED_ABOUT_CASTING_C128 = True
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input_image[J] = z_slice.astype(np.complex64)
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else:
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@@ -732,12 +732,12 @@ def writeMRC(input_image, MRCfilename, meta=None, endian='le', dtype=None,
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# Cast float64 -> float32, and complex128 -> complex64
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if input_image.dtype == np.float64 or input_image.dtype == float:
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if not WARNED_ABOUT_CASTING_F64:
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- logger.warn('Casting {} to `numpy.float64`'.format(MRCfilename))
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+ logger.warning('Casting {} to `numpy.float64`'.format(MRCfilename))
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WARNED_ABOUT_CASTING_F64 = True
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input_image = input_image.astype(np.float32)
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elif input_image.dtype == np.complex128:
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if not WARNED_ABOUT_CASTING_C128:
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- logger.warn('Casting {} to `numpy.complex64`'.format(MRCfilename))
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+ logger.warning('Casting {} to `numpy.complex64`'.format(MRCfilename))
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WARNED_ABOUT_CASTING_C128 = True
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input_image = input_image.astype(np.complex64)
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From 97644c4a957946deb1c510d83dba3d3e2fa155ba Mon Sep 17 00:00:00 2001
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From: Eric Prestat <eric.prestat@gmail.com>
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Date: Sat, 22 Jun 2024 20:23:15 +0100
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Subject: [PATCH 5/5] Fix numpy deprecation warning on conversion of an array
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with ndim > 0 to a scalar
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---
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mrcz/ioMRC.py | 4 ++--
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1 file changed, 2 insertions(+), 2 deletions(-)
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diff --git a/mrcz/ioMRC.py b/mrcz/ioMRC.py
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index 872ee2e..7a61b16 100644
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--- a/mrcz/ioMRC.py
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+++ b/mrcz/ioMRC.py
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@@ -542,7 +542,7 @@ def readMRCHeader(MRCfilename, slices=None, endian='le', fileConvention = 'ccpem
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slices = 1
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else:
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f.seek(36)
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- slices = int(np.fromfile(f, dtype=dtype_i4, count=1))
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+ slices = int(np.fromfile(f, dtype=dtype_i4, count=1)[0])
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# Read in pixelsize
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f.seek(40)
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@@ -572,7 +572,7 @@ def readMRCHeader(MRCfilename, slices=None, endian='le', fileConvention = 'ccpem
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# Size of meta-data
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f.seek(92)
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- header['extendedBytes'] = int(np.fromfile(f, dtype=dtype_i4, count=1))
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+ header['extendedBytes'] = int(np.fromfile(f, dtype=dtype_i4, count=1)[0])
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if header['extendedBytes'] > 0:
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f.seek(104)
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header['metaId'] = f.read(4)
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