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RELEASE_NOTES.md

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0.2.3

  • Fixed error in CTF formula of CTF() of focustools/util.py - thanks to Harshit Gupta for spotting it

0.2.2

  • Fixed bug in focus.postprocess (reading masks)

0.2.1

  • Fixed bug in focus.postprocess (reading half-maps)

0.2.0

  • Renamed bin/focus.ctfapply to bin/focus.ctf
  • Added option --randomize_beyond to focus.postprocess
  • Added options --transparent and --svg to focus.ctf
  • Included bin/focus.resample
  • Included bin/focus.project

0.1.4

Fixed default argument bugs in AutoMask() of focustools/util.py

0.1.3

Fixed x-label in CTF plots of bin/focus.ctfapply

0.1.2

Another bugfix in focustools/util.py

0.1.1

Bug fixes in:

  • bin/focus.ctfapply
  • bin/focus.mrcz
  • focustools/util.py
  • RELEASE_NOTES.md

0.1.0

Initial release containing:

  • bin/

    • focus.ctfapply
    • focus.mrcz
    • focus.postprocess

  • focustools/utils.py

    • AdhocSSNR(imsize=[100, 100], apix=1.0, DF=1000.0, WGH=0.1, Cs=2.7, kV=300.0, S=1.0, F=1.0, hp_frac=0.01, lp=True)
    • AutoMask(img, apix=1.0, lp=-1, gaussian=False, cosine=True, cosine_edge_width=3.0, absolute_threshold=None, fraction_threshold=None, sigma_threshold=1.0, expand_width=3.0, expand_soft_width=3.0, floodfill_rad=-1, floodfill_xyz=[0, 0, 0], floodfill_fraction=-1, verbose=False)
    • BackProject(img, pose=[0, 0, 0, 0, 0], interpolation='trilinear', pad=2, do_sinc=True, res_max=-1, apix=-1, return_weights=True, is_fft=False, DF1=1000.0, DF2=None, AST=0.0, WGH=0.10, invert_contrast=False, Cs=2.7, kV=300.0, phase_flip=False, ctf_multiply=False, wiener_filter=False, C=1.0)
    • BandPassCrossCorrelation(img1, img2, apix=1.0, lp=-1, hp=-1, weights=None, rounding=True, eps=1e-8)
    • CistemAutoMask(img, apix=1.0)
    • CorrectCTF(img, DF1=1000.0, DF2=None, AST=0.0, WGH=0.10, invert_contrast=False, Cs=2.7, kV=300.0, apix=1.0, phase_flip=False, ctf_multiply=False, wiener_filter=False, C=1.0, return_ctf=False)
    • CrossCorrelation(img1, img2)
    • CTF(imsize=[100, 100], DF1=1000.0, DF2=None, AST=0.0, WGH=0.10, Cs=2.7, kV=300.0, apix=1.0, B=0.0, rfft=True)
    • ElectronWavelength(kV=300.0)
    • FCC(volume1, volume2, phiArray=[0.0], invertCone=False)
    • FilterBfactor(img, apix=1.0, B=0.0, return_filter=False)
    • FilterCosine(img, apix=1.0, lp=-1, hp=-1, width=6.0, return_filter=False)
    • FilterDoseWeight(stack, apix=1.0, frame_dose=1.0, pre_dose=0.0, total_dose=-1, kv=300.0)
    • FilterGauss(img, apix=1.0, lp=-1, hp=-1, return_filter=False)
    • FilterTophat(img, apix=1.0, lp=-1, hp=-1, return_filter=False)
    • FilterWhiten(img, return_filter=False, ps=False)
    • FirstZeroCTF(DF=1000.0, WGH=0.10, Cs=2.7, kV=300.0)
    • FloodFilling(img, inimask, thr=0.0)
    • FRC(image1, image2, phiArray=[0.0])
    • FSC(volume1, volume2, phiArray=[0.0])
    • Fsc2Xml(filename, x, y)
    • GetFreqArray(NSAM=256, apix=1.0)
    • GetNumberOfFourierSamples(imsize)
    • HalfBitCurve(imsize=[100, 100], nsym=1, D=2.0, L=3.0, count=False)
    • HighResolutionNoiseSubstitution(img, apix=1.0, lp=-1, random_seed=123456789, parallel=False)
    • MaskAutoExpand(map1, map2, apix=1.0, init_lp=15, fraction_threshold=0.01, init_hard_edge=0, init_soft_edge=3, randomize_below_fsc=0.8, fsc_thr=0.143, random_seed=123456789, interp=False, verbose=False)
    • MatchAmplitudes(img1, img2)
    • MatchPowerSpectra(img1, img2)
    • NormalizeImg(img, mean=0.0, std=1.0, radius=-1)
    • Project(img, pose=[0, 0, 0, 0, 0], interpolation='trilinear', pad=2, do_sinc=True, res_max=-1, apix=-1, is_fft=False, DF1=1000.0, DF2=None, AST=0.0, WGH=0.10, invert_contrast=False, Cs=2.7, kV=300.0, phase_flip=False, ctf_multiply=False)
    • RadialFilter(img, filt, return_filter=False)
    • RadialIndices(imsize=[100, 100], rounding=True, normalize=False, rfft=False, xyz=[0, 0, 0], nozero=True)
    • RadialProfile(img, amps=False)
    • Resample(img, newsize=None, apix=1.0, newapix=None)
    • Resize(img, newsize=None, padval=None, xyz=[0, 0, 0])
    • ResolutionAtThreshold(freq, fsc, thr, interp=True, nyquist_is_fine=False, )
    • Rotate(img, rot=[0, 0, 0], interpolation='trilinear', pad=1)
    • RotateFFT(img, rot=[0, 0, 0], interpolation='trilinear', pad=1)
    • RotationalAverage(img, nomean=False)
    • Shift(img, shift=[0, 0, 0])
    • SigmaCurve(imsize=[100, 100], sigma=3.0, nsym=1, D=2.0, L=3.0, count=False)
    • SoftMask(imsize=[100, 100], radius=0.5, width=6.0, rounding=False, xyz=[0, 0, 0], rfft=False)
    • VoxelsPerShell(imsize=[100, 100], count=False)