Index

A

adaptive_background() (in module ncempy.algo.eels) allTags (ncempy.io.dm.fileDM attribute)

appendData() (in module ncempy.io.mrc) applyLatticeLimit() (in module ncempy.algo.peak_find)

B

bandpass_filter() (in module ncempy.algo.fourier_operations)

bandpass_interactive() (in module ncempy.viz.widgets)

C

calc_polarcoords() (in module ncempy.algo.radial_profile) calc_radialprofile() (in module ncempy.algo.radial_profile) calculate_unit_cell() (in module ncempy.algo.peak_find) centroid() (in module ncempy.algo)

const() (in module ncempy.algo.math) correct_distortion() (in module ncempy.algo.radial_profile) create_rgb() (in module ncempy.algo.eels) cur_eva_vers (in module ncempy.eval.ring_diff) cur_set_vers (in module ncempy.eval.ring_diff)

D

dataOffset (ncempy.io.dm.fileDM attribute) dataShape (ncempy.io.dm.fileDM attribute) dataSize (ncempy.io.dm.fileDM attribute) dataType (ncempy.io.dm.fileDM attribute) dectrisReader() (in module ncempy.io.dectris)

defaultDims() (in module ncempy.io.emd) dftUpsample() (in module ncempy.algo.multicorr_funcs) dm_to_png() (in module ncempy.command_line.ncem2png) dmReader() (in module ncempy.io.dm) doubleRoll() (in module ncempy.algo.peak_find) dummy_settings (in module ncempy.eval.ring_diff)

E

ElamPrint() (in module ncempy.edstomo.CharacteristicEmission) emd2mrc() (in module ncempy.io.mrc) emdReader() (in module ncempy.io.emd)

emdVeloxReader() (in module ncempy.io.emdVelox) emdWriter() (in module ncempy.io.emd) enforceMinDist() (in module ncempy.algo.peak_find) extract_dimension() (in module ncempy.command_line.ncem2png)

F

fid (ncempy.io.dm.fileDM attribute) file_name (ncempy.io.dm.fileDM attribute) file_path (ncempy.io.dm.fileDM attribute) fileDECTRIS (class in ncempy.io.dectris) fileDM (class in ncempy.io.dm) fileEMD (class in ncempy.io.emd) fileEMDVelox (class in ncempy.io.emdVelox) fileMRC (class in ncempy.io.mrc) fileSER (class in ncempy.io.ser)

fileSize (ncempy.io.dm.fileDM attribute) fileSMV (class in ncempy.io.smv) filter_ring() (in module ncempy.algo.distortion) find_emdgroups() (ncempy.io.emd.fileEMD method) fit_peaks_gauss2d() (in module ncempy.algo.peak_find) fit_peaks_gauss3d() (in module ncempy.algo.peak_find) fit_radialprofile() (in module ncempy.algo.radial_profile) fourDstem_interactive() (in module ncempy.viz.widgets) fromfile() (ncempy.io.dm.fileDM method)

G

gauss1D() (in module ncempy.algo.gaussND) gauss2D() (in module ncempy.algo.gaussND) gauss2D_FIT() (in module ncempy.algo.gaussND) gauss2D_poly_FIT() (in module ncempy.algo.gaussND) gauss2D_theta() (in module ncempy.algo.gaussND) gauss2D_theta_FIT() (in module ncempy.algo.gaussND) gauss3D() (in module ncempy.algo.gaussND) gauss3D_FIT() (in module ncempy.algo.gaussND) gauss3D_poly() (in module ncempy.algo.gaussND) gauss3D_poly_FIT() (in module ncempy.algo.gaussND) gauss3DGEN_FIT() (in module ncempy.algo.gaussND) gaussian_lorentz() (in module ncempy.algo.eels) gaussLorentz1D() (in module ncempy.algo.gaussND) generateLatticeFromRefinement() (in module ncempy.algo.peak_find) get_dataset() (ncempy.io.emdVelox.fileEMDVelox method) get_emddims() (ncempy.io.emd.fileEMD method) get_emdgroup() (ncempy.io.emd.fileEMD method) get_memmap() (ncempy.io.emd.fileEMD method) get_settings() (in module ncempy.eval.ring_diff) getDataset() (ncempy.io.dectris.fileDECTRIS method) (ncempy.io.dm.fileDM method) (ncempy.io.emdVelox.fileEMDVelox method) (ncempy.io.mrc.fileMRC method) (ncempy.io.ser.fileSER method) (ncempy.io.smv.fileSMV method)

GetElamFluorescenceLines() (in module ncempy.edstomo.CharacteristicEmission) GetFluorescenceLineEnergy() (in module ncempy.edstomo.CharacteristicEmission) getMemmap() (ncempy.io.dm.fileDM method) (ncempy.io.mrc.fileMRC method) getMetadata() (ncempy.io.dectris.fileDECTRIS method) (ncempy.io.dm.fileDM method) (ncempy.io.emd.fileEMD method) (ncempy.io.emdVelox.fileEMDVelox method) (ncempy.io.mrc.fileMRC method) (ncempy.io.ser.fileSER method) (ncempy.io.smv.fileSMV method) getSlice() (ncempy.io.dm.fileDM method) (ncempy.io.mrc.fileMRC method) getThumbnail() (ncempy.io.dm.fileDM method) GetWeightedSum() (in module ncempy.edstomo.CharacteristicEmission)

I

im_and_fft() (in module ncempy.viz) im_calibrated() (in module ncempy.viz) image_and_plot() (in module ncempy.viz.widgets) image_correlate() (in module ncempy.algo) image_cross_corr() (in module ncempy.algo)

image_phase_correlate() (in module ncempy.algo) imageShifter() (in module ncempy.algo.multicorr_funcs) imfft() (in module ncempy.viz) imrfft() (in module ncempy.viz) imsd() (in module ncempy.viz) initial_correlation_image() (in module ncempy.algo.multicorr_funcs)

L

lattice2D() (in module ncempy.algo.peak_find) lattice2D_2() (in module ncempy.algo.peak_find) lattice2D_norm() (in module ncempy.algo.peak_find) lattice3D() (in module ncempy.algo.peak_find) lattice3D_2() (in module ncempy.algo.peak_find)

latticeDisplacements() (in module ncempy.algo.peak_find) line_profile() (in module ncempy.eval.line_profile) linear() (in module ncempy.algo.math) lkp_funcs (in module ncempy.algo.math) local_max() (in module ncempy.algo.local_max) lorentz1D() (in module ncempy.algo.gaussND)

M

main() (in module ncempy.command_line.ncem2png) map_background() (in module ncempy.algo.eels) map_sum() (in module ncempy.algo.eels) match_lattice_peaks() (in module ncempy.algo.peak_find) MatrixQuaternionRot() (in module ncempy.algo.gaussND) metadata (ncempy.io.dm.fileDM attribute) min_dummy_settings (in module ncempy.eval.ring_diff) module ncempy ncempy.algo ncempy.algo.distortion ncempy.algo.eels ncempy.algo.fourier_operations ncempy.algo.gaussND ncempy.algo.local_max ncempy.algo.math ncempy.algo.multicorr_funcs ncempy.algo.peak_find ncempy.algo.radial_profile ncempy.command_line ncempy.command_line.ncem2png ncempy.edstomo ncempy.edstomo.CharacteristicEmission ncempy.eval ncempy.eval.line_profile ncempy.eval.multicorr ncempy.eval.ring_diff ncempy.eval.stack_align ncempy.io ncempy.io.dectris ncempy.io.dm ncempy.io.emd ncempy.io.emdVelox ncempy.io.mrc ncempy.io.ser ncempy.io.smv ncempy.viz ncempy.viz.widgets

moment_angle() (in module ncempy.algo) moments() (in module ncempy.algo) moments_central() (in module ncempy.algo) mrc2emd() (in module ncempy.io.mrc) mrc2raw() (in module ncempy.io.mrc) mrcReader() (in module ncempy.io.mrc) mrcWriter() (in module ncempy.io.mrc) multicorr() (in module ncempy.eval.multicorr)

N

ncempy module ncempy.algo module ncempy.algo.distortion module ncempy.algo.eels module ncempy.algo.fourier_operations module ncempy.algo.gaussND module ncempy.algo.local_max module ncempy.algo.math module ncempy.algo.multicorr_funcs module ncempy.algo.peak_find module ncempy.algo.radial_profile module ncempy.command_line module ncempy.command_line.ncem2png module ncempy.edstomo module ncempy.edstomo.CharacteristicEmission module ncempy.eval module

ncempy.eval.line_profile module ncempy.eval.multicorr module ncempy.eval.ring_diff module ncempy.eval.stack_align module ncempy.io module ncempy.io.dectris module ncempy.io.dm module ncempy.io.emd module ncempy.io.emdVelox module ncempy.io.mrc module ncempy.io.ser module ncempy.io.smv module ncempy.viz module ncempy.viz.widgets module NoEmdDataSets NotSERError numObjects (ncempy.io.dm.fileDM attribute)

O

on_memory (ncempy.io.dm.fileDM attribute) optimize_center() (in module ncempy.algo.distortion)

optimize_distortion() (in module ncempy.algo.distortion) origin (ncempy.io.dm.fileDM attribute)

P

parseHeader() (ncempy.io.dm.fileDM method) (ncempy.io.mrc.fileMRC method) (ncempy.io.smv.fileSMV method) parseMetaData() (ncempy.io.emdVelox.fileEMDVelox method) peak3View() (in module ncempy.algo.peak_find) peakFind2D() (in module ncempy.algo.peak_find) peakFind3D() (in module ncempy.algo.peak_find) peakPlot3D() (in module ncempy.algo.peak_find) peaksToImage() (in module ncempy.algo.peak_find) peaksToVolume() (in module ncempy.algo.peak_find) plot() (in module ncempy.viz) plot_distpolar() (in module ncempy.viz)

plot_fit() (in module ncempy.viz) plot_points() (in module ncempy.viz) plot_radialprofile() (in module ncempy.viz) plot_ringpolar() (in module ncempy.viz) points_todim() (in module ncempy.algo.local_max) points_topolar() (in module ncempy.algo.distortion) powerFit() (in module ncempy.algo.eels) powlaw() (in module ncempy.algo.math) pre_post_fit() (in module ncempy.algo.eels) put_comment() (ncempy.io.emd.fileEMD method) put_emdgroup() (ncempy.io.emd.fileEMD method) put_settings() (in module ncempy.eval.ring_diff) put_sglgroup() (in module ncempy.eval.ring_diff)

R

rad_dis() (in module ncempy.algo.distortion) read() (in module ncempy.io) read_emi() (in module ncempy.io.ser) readHeader() (ncempy.io.ser.fileSER method) (ncempy.io.smv.fileSMV method) rebin() (in module ncempy.algo) refineLattice2D() (in module ncempy.algo.peak_find) refineLattice3D() (in module ncempy.algo.peak_find) remove_bad_pixels() (ncempy.io.dectris.fileDECTRIS method)

remove_xrays() (in module ncempy.algo.peak_find) residuals_center() (in module ncempy.algo.distortion) residuals_dis() (in module ncempy.algo.distortion) residuals_fit() (in module ncempy.algo.radial_profile) rotateImage() (in module ncempy.algo) (in module ncempy.algo.fourier_operations) run_all() (in module ncempy.eval.ring_diff) run_sglgroup() (in module ncempy.eval.ring_diff) run_singleImage() (in module ncempy.algo.radial_profile)

S

scale (ncempy.io.dm.fileDM attribute) scaleOrigin (ncempy.io.dm.fileDM attribute) scaleUnit (ncempy.io.dm.fileDM attribute) seek() (ncempy.io.dm.fileDM method) ser_to_png() (in module ncempy.command_line.ncem2png) serReader() (in module ncempy.io.ser) shearImage() (in module ncempy.algo) (in module ncempy.algo.fourier_operations) shiftImage() (in module ncempy.algo) (in module ncempy.algo.fourier_operations)

SI_interactive() (in module ncempy.viz.widgets) smvReader() (in module ncempy.io.smv) smvWriter() (in module ncempy.io.smv) stack_align() (in module ncempy.algo) (in module ncempy.eval.stack_align) stack_browse() (in module ncempy.viz.widgets) stack_view (class in ncempy.viz) stemtomo_browse() (in module ncempy.viz.widgets) sum_functions() (in module ncempy.algo.math)

T

tell() (ncempy.io.dm.fileDM method)

thumbnail (ncempy.io.dm.fileDM attribute) tripleRoll() (in module ncempy.algo.peak_find)

U

UnsupportedEmdVersion

upsampled_correlation() (in module ncempy.algo.multicorr_funcs) upsampleFFT() (in module ncempy.algo.multicorr_funcs)

V

verbose (ncempy.io.dm.fileDM attribute)

voigt() (in module ncempy.algo.math) volume_slicer() (in module ncempy.viz.widgets)

W

write_dim() (ncempy.io.emd.fileEMD method) writeEMD() (ncempy.io.ser.fileSER method)

writeHeader() (in module ncempy.io.mrc) writeTags() (ncempy.io.dm.fileDM method) writeXYZ() (in module ncempy.algo.peak_find)

X

xSize (ncempy.io.dm.fileDM attribute)

Y

ySize (ncempy.io.dm.fileDM attribute)

Z

zSize (ncempy.io.dm.fileDM attribute)

zSize2 (ncempy.io.dm.fileDM attribute)