imars3d.ui.stages package

Reconstruction stages’ UIs.

Submodules

imars3d.ui.stages.dataloading module

Data loading stage for iMars3D.

class imars3d.ui.stages.dataloading.DataLoader(**params)[source]

Bases: Parameterized

Data loading stage for iMars3D.

as_dict()[source]: Return as dict.

config_dict = {'facility': 'TBD', 'instrument': 'TBD', 'ipts': 0, 'name': 'TBD', 'outputdir': 'TBD', 'projectdir': 'TBD', 'tasks': [], 'workingdir': 'TBD'}

file_selector()[source]: File selector.

json_editor()[source]: JSON editor app for viewing config.

name = 'DataLoader'

panel()[source]: App panel view.

save_config_file()[source]: Save config file to disk.

save_config_to_disk()

update_config()[source]: Update config dict.

update_config_action()

imars3d.ui.stages.metadata module

First stage to generate interactive reconstruction.

class imars3d.ui.stages.metadata.MetaData(**params)[source]

Bases: Parameterized

Collect metadata from users.

as_dict()[source]: Return config dict.

config_dict = {'facility': 'TBD', 'instrument': 'TBD', 'ipts': 0, 'name': 'TBD', 'outputdir': 'TBD', 'projectdir': 'TBD', 'tasks': [], 'workingdir': 'TBD'}

data_root = '/home/docs'

facility = 'HFIR'

instrument = 'CG1D'

ipts_num = 0

json_editor()[source]: Return a json editor pane.

name = 'MetaData'

panel(width=250)[source]: App panel view.

proj_root = '/home/docs'

recn_name = 'myrecon'

recn_root = '/home/docs'

save_config_file()[source]: Save config file to disk.

save_config_to_disk()

summary_pane()[source]: Return a summary pane.

temp_root: intermediate results save location

imars3d.ui.stages.preprocess module

Preprocessing stage for iMars3D.

class imars3d.ui.stages.preprocess.Preprocess(**params)[source]

Bases: Parameterized

Preprocessing stage for iMars3D.

colormap = 'gray'

colormap_scale = 'linear'

cross_hair_view(x, y)[source]: Cross hair view.

ct = None

ct_checkpoint_action()

ct_viewer()[source]: Radiograph (CT) viewer.

dc = None

dc_viewer()[source]: Dark current viewer.

denoise_filter = Denoise(denoise_action=<function Denoise.<lambda>>, denoise_bilateral_sigma_color=0.02, denoise_bilateral_sigma_spatial=5, denoise_complete_status=False, denoise_median_kernel=3, denoise_method='bilateral', name='Denoise00205', parent=None)

frame_width = 500

gamma_filter = GammaFilter(auto_threshold=True, auto_tomopy_threshold=True, axis=0, execute=<function GammaFilter.<lambda>>, median_kernel=5, name='GammaFilter00203', parent=None, selective_median_filter=True, status=False, threshold=65530, tomopy_threshold=13107)

idx_active_ct = 0

idx_active_dc = 0

idx_active_ob = 0

ifc_filter = IntensityFluctuationCorrection(air_pixels=5, auto_detect_air=False, execute=<function IntensityFluctuationCorrection.<lambda>>, name='IntensityFluctuationCorrection00206', parent=None, sigma=3, status=False)

name = 'Preprocess'

norm_filter = Normalization(auto_cutoff=True, cutoff=1.0, execute=<function Normalization.<lambda>>, name='Normalization00204', parent=None, status=False)

ob = None

ob_viewer()[source]: Open beam viewer.

omegas = None

output()[source]: Output data for next step.

panel()[source]: Panel view.

plot_control(width=80)[source]: Plot control panel.

recn_name = 'myrecon'

recn_root = '/home/docs'

remove_ring_filter = RemoveRingArtifact(correction_range=(0.9, 1.1), execute=<function RemoveRingArtifact.<lambda>>, kernel_size=5, name='RemoveRingArtifact00208', parent=None, status=False, sub_division=10)

save_checkpoint()[source]: Save current state to checkpoint.

temp_root: intermedia results save location

tilt_correction_filter = TiltCorrection(cut_off_angle_deg=0.001, execute=<function TiltCorrection.<lambda>>, name='TiltCorrection00207', parent=None, status=False, tilt_search_bounds=(-5.0, 5.0))

imars3d.ui.stages.reconstruction module

Reconstruction stage for iMars3D.

class imars3d.ui.stages.reconstruction.Reconstruction(**params)[source]

Bases: Parameterized

Panel for conduction guided reconstruction with iMars3D.

algorithm = 'gridrec'

apply()[source]: Run reconstruction.

colormap = 'gray'

colormap_scale = 'linear'

cross_hair_view(x, y)[source]: Return cross hair view of the image.

ct = None

ct_checkpoint_action()

ct_viewer()[source]: Radiograph viewer.

execute()

frame_width = 500

idx_active_ct = 0

name = 'Reconstruction'

omegas = None

output()[source]: Return reconstruction results to next step.

panel()[source]: App panel view.

plot_control(width=80)[source]: Plot control panel.

post_recon_filter = 'hann'

recn_name = 'myrecon'

recn_root = '/home/docs'

recon = None

recon_panel(width=200)[source]: Reconstruction panel.

recon_save()

recon_viewer()[source]: Reconstruction viewer.

rotation_center_finder = FindRotationCenter(atol=0.2, auto_atol=True, execute=<function FindRotationCenter.<lambda>>, name='FindRotationCenter00209', parent=None, rot_center=0.0, status=False)

save_checkpoint()[source]: Save current ct to checkpoint.

save_reconstruction_results()[source]: Save reconstruction results to disk.

status = False

temp_root: intermedia results save location

imars3d.ui.stages.selectroi module

Select region of interest stage for iMars3D.

class imars3d.ui.stages.selectroi.SelectROI(**params)[source]

Bases: Parameterized

Stage for selecting region of interest.

bottom = 0

colormap = 'gray'

colormap_scale = 'linear'

confirm_ROI_action()

crop2ROI_action()

crop_to_RIO()[source]: Crop to ROI.

cross_hair_view(x, y)[source]: Return cross hair view.

ct = None

ct_checkpoint_action()

ct_viewer()[source]: Radiograph viewer.

dc = None

dc_viewer()[source]: Dark current viewer.

frame_width = 500

idx_active_ct = 0

idx_active_dc = 0

idx_active_ob = 0

left = 0

name = 'SelectROI'

ob = None

ob_viewer()[source]: Open beam viewer.

omegas = None

output()[source]: Return output data for next step.

panel()[source]: App panel view.

plot_control(width=80)[source]: Plot control panel.

recn_name = 'myrecon'

recn_root = '/home/docs'

right = 0

roi_box = :Polygons [x,y]

roi_box_stream = BoxEdit(data=None)

roi_control_pn(width=80)[source]: Return panel for ROI control.

save_checkpoint()[source]: Save current ct, ob, dc, omegas.

temp_root: intermedia results save location

top = 0

update_ROI()[source]: Update ROI box.

imars3d.ui.stages.visualization module

Visualization stage for iMars3D.

class imars3d.ui.stages.visualization.Visualization(**params)[source]

Bases: Parameterized

Visualization stage for iMars3D.

colormap = 'gray'

colormap_scale = 'linear'

cross_hair_view(x, y)[source]: Cross hair view.

frame_width = 500

idx_y = 0

name = 'Visualization'

panel()[source]: App panel view.

plot_control(width=80)[source]: Plot control.

recon = None

recon_orthorgonal_view()[source]: Orthogonal view of the reconstruction.

xy_view(x, y)[source]: XY view.

xz_view()[source]: XZ view.

yz_view(x, y)[source]: YZ view.