From: Roland Mas 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)