iMars3D
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Contents:
User Guide
Beginners Guide to iMars3D
imars3d
Development Guide
Release notes
iMars3D
Index
Edit on GitHub
Index
A
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B
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C
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D
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E
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F
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G
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I
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J
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K
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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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X
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Y
A
air_pixels (imars3d.ui.widgets.ifc.IntensityFluctuationCorrection attribute)
algorithm (imars3d.ui.stages.reconstruction.Reconstruction attribute)
apply() (imars3d.ui.stages.reconstruction.Reconstruction method)
(imars3d.ui.widgets.denoise.Denoise method)
(imars3d.ui.widgets.gamma_filter.GammaFilter method)
(imars3d.ui.widgets.ifc.IntensityFluctuationCorrection method)
(imars3d.ui.widgets.normalization.Normalization method)
(imars3d.ui.widgets.ring_removal.RemoveRingArtifact method)
(imars3d.ui.widgets.rotation.FindRotationCenter method)
(imars3d.ui.widgets.tilt.TiltCorrection method)
apply_tilt_correction (class in imars3d.backend.diagnostics.tilt)
as_dict() (imars3d.ui.stages.dataloading.DataLoader method)
(imars3d.ui.stages.metadata.MetaData method)
atol (imars3d.ui.widgets.rotation.FindRotationCenter attribute)
auto_atol (imars3d.ui.widgets.rotation.FindRotationCenter attribute)
auto_cutoff (imars3d.ui.widgets.normalization.Normalization attribute)
auto_detect_air (imars3d.ui.widgets.ifc.IntensityFluctuationCorrection attribute)
auto_reduction_ready() (in module imars3d.backend.autoredux)
auto_threshold (imars3d.ui.widgets.gamma_filter.GammaFilter attribute)
auto_tomopy_threshold (imars3d.ui.widgets.gamma_filter.GammaFilter attribute)
axis (imars3d.ui.widgets.gamma_filter.GammaFilter attribute)
B
bm3d_ring_removal (class in imars3d.backend.corrections.ring_removal)
bottom (imars3d.ui.stages.selectroi.SelectROI attribute)
C
calculate_dissimilarity() (in module imars3d.backend.diagnostics.tilt)
calculate_shift() (in module imars3d.backend.diagnostics.tilt)
calculate_tilt() (in module imars3d.backend.diagnostics.tilt)
colormap (imars3d.ui.stages.preprocess.Preprocess attribute)
(imars3d.ui.stages.reconstruction.Reconstruction attribute)
(imars3d.ui.stages.selectroi.SelectROI attribute)
(imars3d.ui.stages.visualization.Visualization attribute)
colormap_scale (imars3d.ui.stages.preprocess.Preprocess attribute)
(imars3d.ui.stages.reconstruction.Reconstruction attribute)
(imars3d.ui.stages.selectroi.SelectROI attribute)
(imars3d.ui.stages.visualization.Visualization attribute)
config_dict (imars3d.ui.stages.dataloading.DataLoader attribute)
(imars3d.ui.stages.metadata.MetaData attribute)
confirm_ROI_action() (imars3d.ui.stages.selectroi.SelectROI method)
correction_range (imars3d.ui.widgets.ring_removal.RemoveRingArtifact attribute)
crop (class in imars3d.backend.morph.crop)
crop2ROI_action() (imars3d.ui.stages.selectroi.SelectROI method)
crop_to_RIO() (imars3d.ui.stages.selectroi.SelectROI method)
cross_hair_view() (imars3d.ui.stages.preprocess.Preprocess method)
(imars3d.ui.stages.reconstruction.Reconstruction method)
(imars3d.ui.stages.selectroi.SelectROI method)
(imars3d.ui.stages.visualization.Visualization method)
ct (imars3d.ui.stages.preprocess.Preprocess attribute)
(imars3d.ui.stages.reconstruction.Reconstruction attribute)
(imars3d.ui.stages.selectroi.SelectROI attribute)
ct_checkpoint_action() (imars3d.ui.stages.preprocess.Preprocess method)
(imars3d.ui.stages.reconstruction.Reconstruction method)
(imars3d.ui.stages.selectroi.SelectROI method)
ct_viewer() (imars3d.ui.stages.preprocess.Preprocess method)
(imars3d.ui.stages.reconstruction.Reconstruction method)
(imars3d.ui.stages.selectroi.SelectROI method)
cut_off_angle_deg (imars3d.ui.widgets.tilt.TiltCorrection attribute)
cutoff (imars3d.ui.widgets.normalization.Normalization attribute)
D
data_root (imars3d.ui.stages.metadata.MetaData attribute)
DataLoader (class in imars3d.ui.stages.dataloading)
dc (imars3d.ui.stages.preprocess.Preprocess attribute)
(imars3d.ui.stages.selectroi.SelectROI attribute)
dc_viewer() (imars3d.ui.stages.preprocess.Preprocess method)
(imars3d.ui.stages.selectroi.SelectROI method)
denoise (class in imars3d.backend.corrections.denoise)
Denoise (class in imars3d.ui.widgets.denoise)
denoise_action() (imars3d.ui.widgets.denoise.Denoise method)
denoise_bilateral_sigma_color (imars3d.ui.widgets.denoise.Denoise attribute)
denoise_bilateral_sigma_spatial (imars3d.ui.widgets.denoise.Denoise attribute)
denoise_by_bilateral() (in module imars3d.backend.corrections.denoise)
denoise_by_bilateral_2d() (in module imars3d.backend.corrections.denoise)
denoise_by_median() (in module imars3d.backend.corrections.denoise)
denoise_complete_status (imars3d.ui.widgets.denoise.Denoise attribute)
denoise_filter (imars3d.ui.stages.preprocess.Preprocess attribute)
denoise_median_kernel (imars3d.ui.widgets.denoise.Denoise attribute)
denoise_method (imars3d.ui.widgets.denoise.Denoise attribute)
detect_bounds() (in module imars3d.backend.morph.crop)
E
ERROR_GENERAL (imars3d.backend.workflow.engine.WorkflowEngineExitCodes attribute)
ERROR_VALIDATION (imars3d.backend.workflow.engine.WorkflowEngineExitCodes attribute)
execute() (imars3d.ui.stages.reconstruction.Reconstruction method)
(imars3d.ui.widgets.gamma_filter.GammaFilter method)
(imars3d.ui.widgets.ifc.IntensityFluctuationCorrection method)
(imars3d.ui.widgets.normalization.Normalization method)
(imars3d.ui.widgets.ring_removal.RemoveRingArtifact method)
(imars3d.ui.widgets.rotation.FindRotationCenter method)
(imars3d.ui.widgets.tilt.TiltCorrection method)
exit_code (imars3d.backend.workflow.engine.WorkflowEngineError attribute)
(imars3d.backend.workflow.engine.WorkflowValidationError attribute)
extract_info_from_path() (in module imars3d.backend.autoredux)
F
facility (imars3d.ui.stages.metadata.MetaData attribute)
file_selector() (imars3d.ui.stages.dataloading.DataLoader method)
find_180_deg_pairs_idx() (in module imars3d.backend.diagnostics.tilt)
find_rotation_center (class in imars3d.backend.diagnostics.rotation)
FindRotationCenter (class in imars3d.ui.widgets.rotation)
Foldernames (class in imars3d.backend.dataio.data)
frame_width (imars3d.ui.stages.preprocess.Preprocess attribute)
(imars3d.ui.stages.reconstruction.Reconstruction attribute)
(imars3d.ui.stages.selectroi.SelectROI attribute)
(imars3d.ui.stages.visualization.Visualization attribute)
G
gamma_filter (class in imars3d.backend.corrections.gamma_filter)
(imars3d.ui.stages.preprocess.Preprocess attribute)
GammaFilter (class in imars3d.ui.widgets.gamma_filter)
I
idx_active_ct (imars3d.ui.stages.preprocess.Preprocess attribute)
(imars3d.ui.stages.reconstruction.Reconstruction attribute)
(imars3d.ui.stages.selectroi.SelectROI attribute)
idx_active_dc (imars3d.ui.stages.preprocess.Preprocess attribute)
(imars3d.ui.stages.selectroi.SelectROI attribute)
idx_active_ob (imars3d.ui.stages.preprocess.Preprocess attribute)
(imars3d.ui.stages.selectroi.SelectROI attribute)
idx_y (imars3d.ui.stages.visualization.Visualization attribute)
ifc_filter (imars3d.ui.stages.preprocess.Preprocess attribute)
imars3d
module
imars3d.backend
module
imars3d.backend.__main__
module
imars3d.backend.autoredux
module
imars3d.backend.corrections
module
imars3d.backend.corrections.denoise
module
imars3d.backend.corrections.gamma_filter
module
imars3d.backend.corrections.intensity_fluctuation_correction
module
imars3d.backend.corrections.ring_removal
module
imars3d.backend.dataio
module
imars3d.backend.dataio.config
module
imars3d.backend.dataio.data
module
imars3d.backend.dataio.phantom
module
imars3d.backend.diagnostics
module
imars3d.backend.diagnostics.rotation
module
imars3d.backend.diagnostics.tilt
module
imars3d.backend.morph
module
imars3d.backend.morph.crop
module
imars3d.backend.preparation
module
imars3d.backend.preparation.normalization
module
imars3d.backend.reconstruction
module
imars3d.backend.workflow
module
imars3d.backend.workflow.engine
module
imars3d.backend.workflow.validate
module
imars3d.ui
module
imars3d.ui.stages
module
imars3d.ui.stages.dataloading
module
imars3d.ui.stages.metadata
module
imars3d.ui.stages.preprocess
module
imars3d.ui.stages.reconstruction
module
imars3d.ui.stages.selectroi
module
imars3d.ui.stages.visualization
module
imars3d.ui.widgets
module
imars3d.ui.widgets.denoise
module
imars3d.ui.widgets.gamma_filter
module
imars3d.ui.widgets.ifc
module
imars3d.ui.widgets.normalization
module
imars3d.ui.widgets.ring_removal
module
imars3d.ui.widgets.rotation
module
imars3d.ui.widgets.tilt
module
instrument (imars3d.ui.stages.metadata.MetaData attribute)
intensity_fluctuation_correction (class in imars3d.backend.corrections.intensity_fluctuation_correction)
intensity_fluctuation_correction_skimage() (in module imars3d.backend.corrections.intensity_fluctuation_correction)
IntensityFluctuationCorrection (class in imars3d.ui.widgets.ifc)
ipts_num (imars3d.ui.stages.metadata.MetaData attribute)
J
json_editor() (imars3d.ui.stages.dataloading.DataLoader method)
(imars3d.ui.stages.metadata.MetaData method)
JSONValid (class in imars3d.backend.workflow.validate)
JSONValidationError
K
kernel_size (imars3d.ui.widgets.ring_removal.RemoveRingArtifact attribute)
L
left (imars3d.ui.stages.selectroi.SelectROI attribute)
load_data (class in imars3d.backend.dataio.data)
load_template_config() (in module imars3d.backend.autoredux)
M
max_workers (imars3d.backend.reconstruction.recon attribute)
measure_noiseness() (in module imars3d.backend.corrections.denoise)
measure_sharpness() (in module imars3d.backend.corrections.denoise)
median_kernel (imars3d.ui.widgets.gamma_filter.GammaFilter attribute)
MetaData (class in imars3d.ui.stages.metadata)
minus_log (class in imars3d.backend.preparation.normalization)
module
imars3d
imars3d.backend
imars3d.backend.__main__
imars3d.backend.autoredux
imars3d.backend.corrections
imars3d.backend.corrections.denoise
imars3d.backend.corrections.gamma_filter
imars3d.backend.corrections.intensity_fluctuation_correction
imars3d.backend.corrections.ring_removal
imars3d.backend.dataio
imars3d.backend.dataio.config
imars3d.backend.dataio.data
imars3d.backend.dataio.phantom
imars3d.backend.diagnostics
imars3d.backend.diagnostics.rotation
imars3d.backend.diagnostics.tilt
imars3d.backend.morph
imars3d.backend.morph.crop
imars3d.backend.preparation
imars3d.backend.preparation.normalization
imars3d.backend.reconstruction
imars3d.backend.workflow
imars3d.backend.workflow.engine
imars3d.backend.workflow.validate
imars3d.ui
imars3d.ui.stages
imars3d.ui.stages.dataloading
imars3d.ui.stages.metadata
imars3d.ui.stages.preprocess
imars3d.ui.stages.reconstruction
imars3d.ui.stages.selectroi
imars3d.ui.stages.visualization
imars3d.ui.widgets
imars3d.ui.widgets.denoise
imars3d.ui.widgets.gamma_filter
imars3d.ui.widgets.ifc
imars3d.ui.widgets.normalization
imars3d.ui.widgets.ring_removal
imars3d.ui.widgets.rotation
imars3d.ui.widgets.tilt
N
name (imars3d.ui.stages.dataloading.DataLoader attribute)
(imars3d.ui.stages.metadata.MetaData attribute)
(imars3d.ui.stages.preprocess.Preprocess attribute)
(imars3d.ui.stages.reconstruction.Reconstruction attribute)
(imars3d.ui.stages.selectroi.SelectROI attribute)
(imars3d.ui.stages.visualization.Visualization attribute)
(imars3d.ui.widgets.denoise.Denoise attribute)
(imars3d.ui.widgets.gamma_filter.GammaFilter attribute)
(imars3d.ui.widgets.ifc.IntensityFluctuationCorrection attribute)
(imars3d.ui.widgets.normalization.Normalization attribute)
(imars3d.ui.widgets.ring_removal.RemoveRingArtifact attribute)
(imars3d.ui.widgets.rotation.FindRotationCenter attribute)
(imars3d.ui.widgets.tilt.TiltCorrection attribute)
norm_filter (imars3d.ui.stages.preprocess.Preprocess attribute)
normalization (class in imars3d.backend.preparation.normalization)
Normalization (class in imars3d.ui.widgets.normalization)
normalize_roi (class in imars3d.backend.corrections.intensity_fluctuation_correction)
num_pairs (imars3d.backend.diagnostics.rotation.find_rotation_center attribute)
O
ob (imars3d.ui.stages.preprocess.Preprocess attribute)
(imars3d.ui.stages.selectroi.SelectROI attribute)
ob_viewer() (imars3d.ui.stages.preprocess.Preprocess method)
(imars3d.ui.stages.selectroi.SelectROI method)
omegas (imars3d.ui.stages.preprocess.Preprocess attribute)
(imars3d.ui.stages.reconstruction.Reconstruction attribute)
(imars3d.ui.stages.selectroi.SelectROI attribute)
output() (imars3d.ui.stages.preprocess.Preprocess method)
(imars3d.ui.stages.reconstruction.Reconstruction method)
(imars3d.ui.stages.selectroi.SelectROI method)
P
panel() (imars3d.ui.stages.dataloading.DataLoader method)
(imars3d.ui.stages.metadata.MetaData method)
(imars3d.ui.stages.preprocess.Preprocess method)
(imars3d.ui.stages.reconstruction.Reconstruction method)
(imars3d.ui.stages.selectroi.SelectROI method)
(imars3d.ui.stages.visualization.Visualization method)
(imars3d.ui.widgets.denoise.Denoise method)
(imars3d.ui.widgets.gamma_filter.GammaFilter method)
(imars3d.ui.widgets.ifc.IntensityFluctuationCorrection method)
(imars3d.ui.widgets.normalization.Normalization method)
(imars3d.ui.widgets.ring_removal.RemoveRingArtifact method)
(imars3d.ui.widgets.rotation.FindRotationCenter method)
(imars3d.ui.widgets.tilt.TiltCorrection method)
parent (imars3d.ui.widgets.denoise.Denoise attribute)
(imars3d.ui.widgets.gamma_filter.GammaFilter attribute)
(imars3d.ui.widgets.ifc.IntensityFluctuationCorrection attribute)
(imars3d.ui.widgets.normalization.Normalization attribute)
(imars3d.ui.widgets.ring_removal.RemoveRingArtifact attribute)
(imars3d.ui.widgets.rotation.FindRotationCenter attribute)
(imars3d.ui.widgets.tilt.TiltCorrection attribute)
plot_control() (imars3d.ui.stages.preprocess.Preprocess method)
(imars3d.ui.stages.reconstruction.Reconstruction method)
(imars3d.ui.stages.selectroi.SelectROI method)
(imars3d.ui.stages.visualization.Visualization method)
post_recon_filter (imars3d.ui.stages.reconstruction.Reconstruction attribute)
Preprocess (class in imars3d.ui.stages.preprocess)
proj_root (imars3d.ui.stages.metadata.MetaData attribute)
R
recn_name (imars3d.ui.stages.metadata.MetaData attribute)
(imars3d.ui.stages.preprocess.Preprocess attribute)
(imars3d.ui.stages.reconstruction.Reconstruction attribute)
(imars3d.ui.stages.selectroi.SelectROI attribute)
recn_root (imars3d.ui.stages.metadata.MetaData attribute)
(imars3d.ui.stages.preprocess.Preprocess attribute)
(imars3d.ui.stages.reconstruction.Reconstruction attribute)
(imars3d.ui.stages.selectroi.SelectROI attribute)
recon (class in imars3d.backend.reconstruction)
(imars3d.ui.stages.reconstruction.Reconstruction attribute)
(imars3d.ui.stages.visualization.Visualization attribute)
recon_orthorgonal_view() (imars3d.ui.stages.visualization.Visualization method)
recon_panel() (imars3d.ui.stages.reconstruction.Reconstruction method)
recon_save() (imars3d.ui.stages.reconstruction.Reconstruction method)
recon_viewer() (imars3d.ui.stages.reconstruction.Reconstruction method)
Reconstruction (class in imars3d.ui.stages.reconstruction)
registry (imars3d.backend.workflow.engine.WorkflowEngine property)
remove_ring_artifact (class in imars3d.backend.corrections.ring_removal)
remove_ring_artifact_Ketcham (class in imars3d.backend.corrections.ring_removal)
remove_ring_filter (imars3d.ui.stages.preprocess.Preprocess attribute)
RemoveRingArtifact (class in imars3d.ui.widgets.ring_removal)
required() (imars3d.backend.workflow.validate.JSONValid method)
right (imars3d.ui.stages.selectroi.SelectROI attribute)
roi_box (imars3d.ui.stages.selectroi.SelectROI attribute)
roi_box_stream (imars3d.ui.stages.selectroi.SelectROI attribute)
roi_control_pn() (imars3d.ui.stages.selectroi.SelectROI method)
rot_angles (imars3d.backend.dataio.data.save_checkpoint attribute)
(imars3d.backend.dataio.data.save_data attribute)
rot_center (imars3d.ui.widgets.rotation.FindRotationCenter attribute)
rotation_center_finder (imars3d.ui.stages.reconstruction.Reconstruction attribute)
run() (imars3d.backend.workflow.engine.WorkflowEngineAuto method)
S
save_checkpoint (class in imars3d.backend.dataio.data)
save_checkpoint() (imars3d.ui.stages.preprocess.Preprocess method)
(imars3d.ui.stages.reconstruction.Reconstruction method)
(imars3d.ui.stages.selectroi.SelectROI method)
save_config() (in module imars3d.backend.dataio.config)
save_config_file() (imars3d.ui.stages.dataloading.DataLoader method)
(imars3d.ui.stages.metadata.MetaData method)
save_config_to_disk() (imars3d.ui.stages.dataloading.DataLoader method)
(imars3d.ui.stages.metadata.MetaData method)
save_data (class in imars3d.backend.dataio.data)
save_reconstruction_results() (imars3d.ui.stages.reconstruction.Reconstruction method)
selective_median_filter (imars3d.ui.widgets.gamma_filter.GammaFilter attribute)
SelectROI (class in imars3d.ui.stages.selectroi)
sigma (imars3d.ui.widgets.ifc.IntensityFluctuationCorrection attribute)
status (imars3d.ui.stages.reconstruction.Reconstruction attribute)
(imars3d.ui.widgets.gamma_filter.GammaFilter attribute)
(imars3d.ui.widgets.ifc.IntensityFluctuationCorrection attribute)
(imars3d.ui.widgets.normalization.Normalization attribute)
(imars3d.ui.widgets.ring_removal.RemoveRingArtifact attribute)
(imars3d.ui.widgets.rotation.FindRotationCenter attribute)
(imars3d.ui.widgets.tilt.TiltCorrection attribute)
sub_division (imars3d.ui.widgets.ring_removal.RemoveRingArtifact attribute)
substitute_template() (in module imars3d.backend.autoredux)
SUCCESS (imars3d.backend.workflow.engine.WorkflowEngineExitCodes attribute)
summary_pane() (imars3d.ui.stages.metadata.MetaData method)
T
temp_root (imars3d.ui.stages.metadata.MetaData attribute)
(imars3d.ui.stages.preprocess.Preprocess attribute)
(imars3d.ui.stages.reconstruction.Reconstruction attribute)
(imars3d.ui.stages.selectroi.SelectROI attribute)
threshold (imars3d.ui.widgets.gamma_filter.GammaFilter attribute)
tilt_correction (class in imars3d.backend.diagnostics.tilt)
tilt_correction_filter (imars3d.ui.stages.preprocess.Preprocess attribute)
tilt_search_bounds (imars3d.ui.widgets.tilt.TiltCorrection attribute)
TiltCorrection (class in imars3d.ui.widgets.tilt)
todict() (in module imars3d.backend.workflow.validate)
tomopy_threshold (imars3d.ui.widgets.gamma_filter.GammaFilter attribute)
top (imars3d.ui.stages.selectroi.SelectROI attribute)
U
update_config() (imars3d.ui.stages.dataloading.DataLoader method)
update_config_action() (imars3d.ui.stages.dataloading.DataLoader method)
update_ROI() (imars3d.ui.stages.selectroi.SelectROI method)
V
Visualization (class in imars3d.ui.stages.visualization)
W
WorkflowEngine (class in imars3d.backend.workflow.engine)
WorkflowEngineAuto (class in imars3d.backend.workflow.engine)
WorkflowEngineError
WorkflowEngineExitCodes (class in imars3d.backend.workflow.engine)
WorkflowValidationError
X
xy_view() (imars3d.ui.stages.visualization.Visualization method)
xz_view() (imars3d.ui.stages.visualization.Visualization method)
Y
yz_view() (imars3d.ui.stages.visualization.Visualization method)
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