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C
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D
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E
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G
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H
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I
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L
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M
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N
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O
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P
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R
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S
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T
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U
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V
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W
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Z
_
_emi (ncempy.io.ser.fileSER attribute)
_file_hdl (ncempy.io.emdVelox.fileEMDVelox attribute)
(ncempy.io.ser.fileSER attribute)
A
allTags (ncempy.io.dm.fileDM attribute)
appendData() (in module ncempy.io.mrc)
applyLatticeLimit() (in module ncempy.algo.peak_find)
axisOrientations (ncempy.io.mrc.fileMRC attribute)
B
bandpass_filter() (in module ncempy.algo.fourier_operations)
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)
cellAngles (ncempy.io.mrc.fileMRC attribute)
comments (ncempy.io.emd.fileEMD attribute)
const() (in module ncempy.algo.math)
correct_distortion() (in module ncempy.algo.radial_profile)
cur_eva_vers (in module ncempy.eval.ring_diff)
cur_set_vers (in module ncempy.eval.ring_diff)
D
data (ncempy.io.emd.fileEMD attribute)
dataOffset (ncempy.io.dm.fileDM attribute)
(ncempy.io.mrc.fileMRC attribute)
dataOut (ncempy.io.mrc.fileMRC attribute)
dataShape (ncempy.io.dm.fileDM attribute)
dataSize (ncempy.io.dm.fileDM attribute)
(ncempy.io.mrc.fileMRC attribute)
dataType (ncempy.io.mrc.fileMRC attribute)
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)
extra (ncempy.io.mrc.fileMRC attribute)
extract_dimension() (in module ncempy.command_line.ncem2png)
ExtractRawSignalsFromBrukerSequence() (in module ncempy.edstomo.bruker)
F
FEIinfo (ncempy.io.mrc.fileMRC attribute)
fid (ncempy.io.dm.fileDM attribute)
(ncempy.io.mrc.fileMRC attribute)
file_hdl (ncempy.io.emd.fileEMD attribute)
file_name (ncempy.io.dm.fileDM attribute)
(ncempy.io.emd.fileEMD attribute)
(ncempy.io.emdVelox.fileEMDVelox attribute)
(ncempy.io.mrc.fileMRC attribute)
(ncempy.io.ser.fileSER attribute)
file_path (ncempy.io.dm.fileDM attribute)
(ncempy.io.emd.fileEMD attribute)
(ncempy.io.emdVelox.fileEMDVelox attribute)
(ncempy.io.mrc.fileMRC attribute)
(ncempy.io.ser.fileSER attribute)
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)
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)
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)
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.dm.fileDM method)
(ncempy.io.mrc.fileMRC method)
(ncempy.io.ser.fileSER method)
GetElamFluorescenceLines() (in module ncempy.edstomo.CharacteristicEmission)
GetEnergyDimension() (in module ncempy.edstomo.bruker)
GetFluorescenceLineEnergy() (in module ncempy.edstomo.CharacteristicEmission)
getMemmap() (ncempy.io.dm.fileDM method)
(ncempy.io.mrc.fileMRC method)
getMetadata() (ncempy.io.dm.fileDM method)
getSlice() (ncempy.io.dm.fileDM method)
(ncempy.io.mrc.fileMRC method)
GetSpatialDimension() (in module ncempy.edstomo.bruker)
getThumbnail() (ncempy.io.dm.fileDM method)
GetTiltsFromBrukerSequence() (in module ncempy.edstomo.bruker)
GetWeightedSum() (in module ncempy.edstomo.CharacteristicEmission)
gridSize (ncempy.io.mrc.fileMRC attribute)
H
head (ncempy.io.ser.fileSER attribute)
I
im_and_fft() (in module ncempy.viz)
im_calibrated() (in module ncempy.viz)
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)
list_data (ncempy.io.emdVelox.fileEMDVelox attribute)
list_emds (ncempy.io.emd.fileEMD attribute)
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)
match_lattice_peaks() (in module ncempy.algo.peak_find)
MatrixQuaternionRot() (in module ncempy.algo.gaussND)
metaDataJSON (ncempy.io.emdVelox.fileEMDVelox attribute)
microscope (ncempy.io.emd.fileEMD attribute)
min_dummy_settings (in module ncempy.eval.ring_diff)
minMaxMean (ncempy.io.mrc.fileMRC attribute)
mrc2emd() (in module ncempy.io.mrc)
mrc2raw() (in module ncempy.io.mrc)
mrcReader() (in module ncempy.io.mrc)
mrcType (ncempy.io.mrc.fileMRC attribute)
mrcWriter() (in module ncempy.io.mrc)
N
ncempy.algo.distortion (module)
ncempy.algo.fourier_operations (module)
ncempy.algo.gaussND (module)
ncempy.algo.local_max (module)
ncempy.algo.math (module)
ncempy.algo.moments (module)
ncempy.algo.multicorr_funcs (module)
ncempy.algo.peak_find (module)
ncempy.algo.radial_profile (module)
ncempy.algo.rebin (module)
ncempy.command_line (module)
ncempy.command_line.ncem2png (module)
ncempy.edstomo (module)
ncempy.edstomo.bruker (module)
ncempy.edstomo.CharacteristicEmission (module)
ncempy.eval.line_profile (module)
ncempy.eval.ring_diff (module)
ncempy.eval.stack_align (module)
ncempy.io.dm (module)
ncempy.io.emd (module)
ncempy.io.emdVelox (module)
ncempy.io.mrc (module)
ncempy.io.read (module)
ncempy.io.ser (module)
ncempy.viz (module)
NotSERError
numObjects (ncempy.io.dm.fileDM attribute)
O
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)
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_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)
powlaw() (in module ncempy.algo.math)
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_emi() (in module ncempy.io.ser)
readHeader() (ncempy.io.ser.fileSER method)
refineLattice2D() (in module ncempy.algo.peak_find)
refineLattice3D() (in module ncempy.algo.peak_find)
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.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
sample (ncempy.io.emd.fileEMD attribute)
scale (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.fourier_operations)
shiftImage() (in module ncempy.algo.fourier_operations)
stack_align() (in module ncempy.eval.stack_align)
stack_view (class in ncempy.viz)
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
upsampled_correlation() (in module ncempy.algo.multicorr_funcs)
upsampleFFT() (in module ncempy.algo.multicorr_funcs)
user (ncempy.io.emd.fileEMD attribute)
V
v (ncempy.io.mrc.fileMRC attribute)
version (ncempy.io.emd.fileEMD attribute)
voigt() (in module ncempy.algo.math)
volumeSize (ncempy.io.mrc.fileMRC attribute)
voxelSize (ncempy.io.mrc.fileMRC attribute)
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)
Z
zSize2 (ncempy.io.dm.fileDM attribute)
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