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|
From: Roland Mas <roland.mas@entierement.net>
Date: Sat, 14 Mar 2026 12:09:10 +0100
Subject: Fix SyntaxWarnings
---
mrcz/ReliablePy.py | 12 ++++++------
mrcz/ioMRC.py | 14 +++++++-------
mrcz/test_mrcz.py | 38 +++++++++++++++++++-------------------
3 files changed, 32 insertions(+), 32 deletions(-)
diff --git a/mrcz/ReliablePy.py b/mrcz/ReliablePy.py
index 78f067a..5658f54 100644
--- a/mrcz/ReliablePy.py
+++ b/mrcz/ReliablePy.py
@@ -359,7 +359,7 @@ class ReliablePy(object):
plt.plot( self.star['data_fsc']['Resolution'], self.star['data_fsc']['CorrectedFourierShellCorrelationPhaseRandomizedMaskedMaps'],
'.-', color='goldenrod', label="Random-phase corrected FSC" )
except: pass
- plt.xlabel( "Resolution ($\AA^{-1}$)" )
+ plt.xlabel( r"Resolution ($\AA^{-1}$)" )
plt.ylabel( "Fourier Shell Correlation" )
plt.legend( loc='upper right', fontsize=16 )
plt.xlim( np.min(self.star['data_fsc']['Resolution']), np.max(self.star['data_fsc']['Resolution']) )
@@ -382,7 +382,7 @@ class ReliablePy(object):
plt.semilogy( Resolution, SSNR+1.0,
label="Class %d: %d" %(K+1,N_particles*self.star[b'data_model_classes'][b'ClassDistribution'][K]) )
plt.legend( loc = 'best' )
- plt.xlabel( "Resolution ($\AA^{-1}$)" )
+ plt.xlabel( r"Resolution ($\AA^{-1}$)" )
plt.ylabel( "Spectral Signal-to-Noise Ratio" )
# Let's also display the class distributions in the legend
@@ -534,7 +534,7 @@ class ReliablePy(object):
if self.verbose >= 2:
plt.figure()
plt.scatter( DefocusMean, part_GroupScaleCorrection, c=k_predict)
- plt.xlabel( "Defocus ($\AA$)" )
+ plt.xlabel( r"Defocus ($\AA$)" )
plt.ylabel( "Group scale correction (a.u.)" )
plt.title("K-means on Defocus")
@@ -827,13 +827,13 @@ class ReliablePy(object):
plt.figure()
plt.fill_between( cDefocus, hDefocus, np.zeros(len(hDefocus)), facecolor='steelblue', alpha=0.5 )
plt.plot( [defocusThreshold, defocusThreshold], [0, np.max(hDefocus)], "--", color='firebrick' )
- plt.xlabel( "Defocus, $C_1 (\AA)$" )
+ plt.xlabel( r"Defocus, $C_1 (\AA)$" )
plt.ylabel( "Histogram counts" )
plt.figure()
plt.fill_between( cAstig, hAstig, np.zeros(len(hAstig)), facecolor='forestgreen', alpha=0.5 )
plt.plot( [astigThreshold, astigThreshold], [0, np.max(hAstig)], "--", color='firebrick' )
- plt.xlabel( "Astigmatism, $A_1 (\AA)$" )
+ plt.xlabel( r"Astigmatism, $A_1 (\AA)$" )
plt.ylabel( "Histogram counts" )
plt.figure()
@@ -845,7 +845,7 @@ class ReliablePy(object):
plt.figure()
plt.fill_between( cRes, hRes, np.zeros(len(hRes)), facecolor='purple', alpha=0.5 )
plt.plot( [resThreshold, resThreshold], [0, np.max(hRes)], "--", color='firebrick' )
- plt.xlabel( "Fitted Resolution, $r (\AA)$" )
+ plt.xlabel( r"Fitted Resolution, $r (\AA)$" )
plt.ylabel( "Histogram counts" )
diff --git a/mrcz/ioMRC.py b/mrcz/ioMRC.py
index 998de75..05d7376 100644
--- a/mrcz/ioMRC.py
+++ b/mrcz/ioMRC.py
@@ -216,7 +216,7 @@ def _getMRCZVersion(label):
def readMRC(MRCfilename, idx=None, endian='le',
pixelunits=u'\\AA', fileConvention='ccpem',
useMemmap=False, n_threads=None, slices=None):
- '''
+ r'''
Imports an MRC/Z file as a NumPy array and a meta-data dict.
Parameters
@@ -552,9 +552,9 @@ def readMRCHeader(MRCfilename, slices=None, endian='le', fileConvention = 'ccpem
header['pixelunits'] = pixelunits
# '\AA' will eventually be deprecated, please cease using it.
- if header['pixelunits'] == u'\\AA' or header['pixelunits'] == u'\AA':
+ if header['pixelunits'] == r'\\AA' or header['pixelunits'] == r'\AA':
pass
- elif header['pixelunits'] == u'\mum':
+ elif header['pixelunits'] == r'\mum':
header['pixelsize'] *= 1E-5
elif header['pixelunits'] == u'pm':
header['pixelsize'] *= 100.0
@@ -602,7 +602,7 @@ def writeMRC(input_image, MRCfilename, meta=None, endian='le', dtype=None,
pixelsize=[0.1,0.1,0.1], pixelunits=u'\\AA', shape=None,
voltage=0.0, C3=0.0, gain=1.0, compressor=None, clevel=1,
n_threads=None, quickStats=True, idx=None):
- '''
+ r'''
Write a conventional MRC file, or a compressed MRCZ file to disk. If
compressor is ``None``, then backwards compatibility with other MRC libraries
should be preserved. Other libraries will not, however, recognize
@@ -1047,9 +1047,9 @@ def writeMRCHeader(f, header, slices, endchar='<'):
# Print cellsize = pixelsize * dimensions
# '\AA' will eventually be deprecated (probably in Python 3.7/8), please cease using it.
- if header['pixelunits'] == '\\AA' or header['pixelunits'] == '\AA':
+ if header['pixelunits'] == r'\\AA' or header['pixelunits'] == r'\AA':
AApixelsize = np.array(header['pixelsize'])
- elif header['pixelunits'] == '\mum':
+ elif header['pixelunits'] == r'\mum':
AApixelsize = np.array(header['pixelsize'])*10000.0
elif header['pixelunits'] == 'pm':
AApixelsize = np.array(header['pixelsize'])/100.0
@@ -1190,4 +1190,4 @@ def asyncWriteMRC(*args, **kwargs):
time.sleep(0.001)
# File is written to disk
'''
- return _asyncExecutor.submit(writeMRC, *args, **kwargs)
\ No newline at end of file
+ return _asyncExecutor.submit(writeMRC, *args, **kwargs)
diff --git a/mrcz/test_mrcz.py b/mrcz/test_mrcz.py
index 30165fd..f2f0070 100644
--- a/mrcz/test_mrcz.py
+++ b/mrcz/test_mrcz.py
@@ -63,18 +63,18 @@ class PythonMrczTests(unittest.TestCase):
pixelsize = np.array([1.2, 2.6, 3.4])
mrcz.writeMRC(testMage, mrcName, dtype=casttype,
- pixelsize=pixelsize, pixelunits=u'\AA',
+ pixelsize=pixelsize, pixelunits=r'\AA',
voltage=300.0, C3=2.7, gain=1.05,
compressor=compressor, clevel=clevel)
- rereadMage, rereadHeader = mrcz.readMRC(mrcName, pixelunits=u'\AA')
+ rereadMage, rereadHeader = mrcz.readMRC(mrcName, pixelunits=r'\AA')
# `tempfile.TemporaryDirectory` would be better but Python 2.7 doesn't support it
try: os.remove(mrcName)
except IOError: log.info('Warning: file {} left on disk'.format(mrcName))
npt.assert_array_almost_equal(testMage, rereadMage)
npt.assert_array_almost_equal(rereadHeader['pixelsize'], pixelsize)
- assert(rereadHeader['pixelunits'] == u'\AA')
+ assert(rereadHeader['pixelunits'] == r'\AA')
npt.assert_almost_equal(rereadHeader['voltage'], 300.0)
npt.assert_almost_equal(rereadHeader['C3'], 2.7)
npt.assert_almost_equal(rereadHeader['gain'], 1.05)
@@ -146,11 +146,11 @@ class PythonMrczTests(unittest.TestCase):
pixelsize = [1.2, 5.6, 3.4]
mrcz.writeMRC(testMage, mrcName, meta=meta,
- pixelsize=pixelsize, pixelunits=u'\AA',
+ pixelsize=pixelsize, pixelunits=r'\AA',
voltage=300.0, C3=2.7, gain=1.05,
compressor='zstd', clevel=1, n_threads=1)
- rereadMage, rereadHeader = mrcz.readMRC(mrcName, pixelunits=u'\AA')
+ rereadMage, rereadHeader = mrcz.readMRC(mrcName, pixelunits=r'\AA')
try: os.remove(mrcName)
except IOError: log.info('Warning: file {} left on disk'.format(mrcName))
@@ -163,7 +163,7 @@ class PythonMrczTests(unittest.TestCase):
npt.assert_array_almost_equal(testMage, rereadMage)
npt.assert_almost_equal(rereadHeader['voltage'], 300.0)
npt.assert_array_almost_equal(rereadHeader['pixelsize'], pixelsize)
- assert(rereadHeader['pixelunits'] == u'\AA')
+ assert(rereadHeader['pixelunits'] == r'\AA')
npt.assert_almost_equal(rereadHeader['C3'], 2.7)
npt.assert_almost_equal(rereadHeader['gain'], 1.05)
@@ -175,13 +175,13 @@ class PythonMrczTests(unittest.TestCase):
pixelsize = [1.2, 5.6, 3.4]
worker = mrcz.asyncWriteMRC(testMage, mrcName, meta=meta,
- pixelsize=pixelsize, pixelunits=u'\AA',
+ pixelsize=pixelsize, pixelunits=r'\AA',
voltage=300.0, C3=2.7, gain=1.05,
compressor='zstd', clevel=1, n_threads=1)
worker.result() # Wait for write to finish
- worker = mrcz.asyncReadMRC(mrcName, pixelunits=u'\AA')
+ worker = mrcz.asyncReadMRC(mrcName, pixelunits=r'\AA')
rereadMage, rereadHeader = worker.result()
try: os.remove(mrcName)
@@ -195,7 +195,7 @@ class PythonMrczTests(unittest.TestCase):
npt.assert_array_almost_equal(testMage, rereadMage)
npt.assert_almost_equal(rereadHeader['voltage'], 300.0)
npt.assert_array_almost_equal(rereadHeader['pixelsize'], pixelsize)
- assert(rereadHeader['pixelunits'] == u'\AA')
+ assert(rereadHeader['pixelunits'] == r'\AA')
npt.assert_almost_equal(rereadHeader['C3'], 2.7)
npt.assert_almost_equal(rereadHeader['gain'], 1.05)
@@ -208,7 +208,7 @@ class PythonMrczTests(unittest.TestCase):
pixelsize = [5.6, 3.4]
mrcz.writeMRC(testMage, mrcName, pixelsize=pixelsize, compressor=None)
- rereadMage, _ = mrcz.readMRC(mrcName, pixelunits=u'\AA')
+ rereadMage, _ = mrcz.readMRC(mrcName, pixelunits=r'\AA')
try: os.remove(mrcName)
except IOError: log.info('Warning: file {} left on disk'.format(mrcName))
@@ -229,7 +229,7 @@ class PythonMrczTests(unittest.TestCase):
mrcz.writeMRC(testMage, mrcName, pixelsize=pixelsize,
compressor='zstd', clevel=1, n_threads=1)
- rereadMage, _ = mrcz.readMRC(mrcName, pixelunits=u'\AA')
+ rereadMage, _ = mrcz.readMRC(mrcName, pixelunits=r'\AA')
try: os.remove(mrcName)
except IOError: log.info('Warning: file {} left on disk'.format(mrcName))
@@ -248,7 +248,7 @@ class PythonMrczTests(unittest.TestCase):
mrcz.writeMRC(testMage, mrcName, pixelsize=pixelsize, compressor=None)
- rereadMage, _ = mrcz.readMRC(mrcName, pixelunits=u'\AA')
+ rereadMage, _ = mrcz.readMRC(mrcName, pixelunits=r'\AA')
try: os.remove(mrcName)
except IOError: log.info('Warning: file {} left on disk'.format(mrcName))
@@ -268,7 +268,7 @@ class PythonMrczTests(unittest.TestCase):
mrcz.writeMRC(testMage, mrcName, pixelsize=pixelsize,
compressor='zstd', clevel=1, n_threads=1)
- rereadMage, _ = mrcz.readMRC(mrcName, pixelunits=u'\AA')
+ rereadMage, _ = mrcz.readMRC(mrcName, pixelunits=r'\AA')
try: os.remove(mrcName)
except IOError: log.info('Warning: file {} left on disk'.format(mrcName))
@@ -290,7 +290,7 @@ class PythonMrczTests(unittest.TestCase):
mrcz.writeMRC(testMage, mrcName, pixelsize=pixelsize,
compressor=None)
- rereadMage, _ = mrcz.readMRC(mrcName, pixelunits=u'\AA', slices=slices)
+ rereadMage, _ = mrcz.readMRC(mrcName, pixelunits=r'\AA', slices=slices)
try: os.remove(mrcName)
except IOError: log.info('Warning: file {} left on disk'.format(mrcName))
@@ -308,7 +308,7 @@ class PythonMrczTests(unittest.TestCase):
mrcz.writeMRC(testMage, mrcName, pixelsize=pixelsize,
compressor='zstd', clevel=1, n_threads=1)
- rereadMage, _ = mrcz.readMRC(mrcName, pixelunits=u'\AA', slices=slices)
+ rereadMage, _ = mrcz.readMRC(mrcName, pixelunits=r'\AA', slices=slices)
try: os.remove(mrcName)
except IOError: log.info('Warning: file {} left on disk'.format(mrcName))
@@ -444,7 +444,7 @@ class PythonMrczTests(unittest.TestCase):
for j,I in enumerate(f32_stack):
mrcz.writeMRC(I, mrcName, pixelsize=pixelsize, compressor=None, idx = j)
- rereadMage, _ = mrcz.readMRC(mrcName, pixelunits=u'\AA')
+ rereadMage, _ = mrcz.readMRC(mrcName, pixelunits=r'\AA')
try: os.remove(mrcName)
except IOError: log.info('Warning: file {} left on disk'.format(mrcName))
@@ -484,14 +484,14 @@ else:
pixelsize = [1.2, 2.6, 3.4]
mrcz.writeMRC(testMage, mrcInput,
- pixelsize=pixelsize, pixelunits=u'\AA',
+ pixelsize=pixelsize, pixelunits=r'\AA',
voltage=300.0, C3=2.7, gain=1.05,
compressor=compressor)
sub.call(cmrczProg + ' -i %s -o %s -c %s -B %d -l %d'
%(mrcInput, mrcOutput, compressor, blocksize, clevel), shell=True)
- rereadMage, rereadHeader = mrcz.readMRC(mrcOutput, pixelunits=u'\AA')
+ rereadMage, rereadHeader = mrcz.readMRC(mrcOutput, pixelunits=r'\AA')
os.remove(mrcOutput)
os.remove(mrcInput)
@@ -502,7 +502,7 @@ else:
npt.assert_array_almost_equal(testMage, rereadMage)
npt.assert_array_equal(rereadHeader['voltage'], 300.0)
npt.assert_array_almost_equal(rereadHeader['pixelsize'], pixelsize)
- npt.assert_array_equal(rereadHeader['pixelunits'], u'\AA')
+ npt.assert_array_equal(rereadHeader['pixelunits'], r'\AA')
npt.assert_array_equal(rereadHeader['C3'], 2.7)
npt.assert_array_equal(rereadHeader['gain'], 1.05)
|
