sfftk
stable
EMDB-SFF Toolkit (
sfftk
)
Converting Files To EMDB-SFF
Annotating EMDB-SFF Segmentations
Miscellaneous Operations Using sfftk
Developing with
sfftk
Extending sfftk
sfftk
packages
sfftk
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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H
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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
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Z
A
AbstractGlobalNote (class in sfftk.notes.modify)
AbstractNote (class in sfftk.notes.modify)
add_cont() (sfftk.readers.modreader.OBJT method)
add_mesh() (sfftk.readers.modreader.OBJT method)
add_note() (in module sfftk.notes.modify)
add_objt() (sfftk.readers.modreader.IMOD method)
add_size() (sfftk.readers.modreader.CONT method)
add_to_segment() (sfftk.notes.modify.AbstractNote method)
add_to_segmentation() (sfftk.notes.modify.AbstractGlobalNote method)
add_view() (sfftk.readers.modreader.IMOD method)
AmiraHyperSurfaceAnnotation (class in sfftk.formats.surf)
AmiraHyperSurfaceHeader (class in sfftk.formats.surf)
AmiraHyperSurfaceMesh (class in sfftk.formats.surf)
AmiraHyperSurfaceSegment (class in sfftk.formats.surf)
AmiraHyperSurfaceSegmentation (class in sfftk.formats.surf)
AmiraMeshAnnotation (class in sfftk.formats.am)
AmiraMeshHeader (class in sfftk.formats.am)
AmiraMeshMesh (class in sfftk.formats.am)
AmiraMeshSegment (class in sfftk.formats.am)
AmiraMeshSegmentation (class in sfftk.formats.am)
AmiraMeshVolume (class in sfftk.formats.am)
angstrom_multiplier() (in module sfftk.readers.modreader)
annotation (sfftk.formats.am.AmiraMeshSegment property)
(sfftk.formats.map.BinaryMaskSegment property)
(sfftk.formats.map.MapSegment property)
(sfftk.formats.map.MergedMaskSegment property)
(sfftk.formats.mod.IMODSegment property)
(sfftk.formats.stl.STLSegment property)
(sfftk.formats.surf.AmiraHyperSurfaceSegment property)
ArgsNote (class in sfftk.notes.modify)
B
BaseNote (class in sfftk.notes.modify)
bin_map() (in module sfftk.core.prep)
BinaryMaskSegment (class in sfftk.formats.map)
BinaryMaskSegmentation (class in sfftk.formats.map)
C
check_mask_is_binary() (in module sfftk.core.prep)
check_multi_file_formats() (in module sfftk.core.parser)
clear() (sfftk.core.configs.Configs method)
clear_notes() (in module sfftk.notes.modify)
cli() (in module sfftk.core.parser)
CLIP (class in sfftk.readers.modreader)
CLIP_FLAGS (class in sfftk.readers.modreader)
colour (sfftk.formats.am.AmiraMeshAnnotation property)
(sfftk.formats.map.MapAnnotation property)
(sfftk.formats.map.MaskAnnotation property)
(sfftk.formats.mod.IMODAnnotation property)
(sfftk.formats.surf.AmiraHyperSurfaceAnnotation property)
(sfftk.readers.surfreader.HxSurfSegment property)
colours (sfftk.readers.survosreader.SuRVoSSegmentation property)
columns (sfftk.readers.starreader.StarTable property)
compute_bounding_box() (in module sfftk.readers.stlreader)
compute_transform() (in module sfftk.readers.mapreader)
Configs (class in sfftk.core.configs)
construct_transformation_matrix() (in module sfftk.core.prep)
CONT (class in sfftk.readers.modreader)
CONTOUR_FLAGS (class in sfftk.readers.modreader)
convert() (sfftk.formats.am.AmiraMeshAnnotation method)
(sfftk.formats.am.AmiraMeshHeader method)
(sfftk.formats.am.AmiraMeshMesh method)
(sfftk.formats.am.AmiraMeshSegment method)
(sfftk.formats.am.AmiraMeshSegmentation method)
(sfftk.formats.am.AmiraMeshVolume method)
(sfftk.formats.map.BinaryMaskSegment method)
(sfftk.formats.map.BinaryMaskSegmentation method)
(sfftk.formats.map.MapAnnotation method)
(sfftk.formats.map.MapSegment method)
(sfftk.formats.map.MapSegmentation method)
(sfftk.formats.map.MaskAnnotation method)
(sfftk.formats.map.MergedMaskSegment method)
(sfftk.formats.map.MergedMaskSegmentation method)
(sfftk.formats.mod.IMODAnnotation method)
(sfftk.formats.mod.IMODEllipsoid method)
(sfftk.formats.mod.IMODHeader method)
(sfftk.formats.mod.IMODMesh method)
(sfftk.formats.mod.IMODMeshes method)
(sfftk.formats.mod.IMODSegment method)
(sfftk.formats.mod.IMODSegmentation method)
(sfftk.formats.mod.IMODShapes method)
(sfftk.formats.seg.SeggerAnnotation method)
(sfftk.formats.seg.SeggerSegment method)
(sfftk.formats.seg.SeggerSegmentation method)
(sfftk.formats.seg.SeggerVolume method)
(sfftk.formats.star.RelionMultiStarSegmentation method)
(sfftk.formats.star.RelionStarSegment method)
(sfftk.formats.star.RelionStarSegmentation method)
(sfftk.formats.stl.STLAnnotation method)
(sfftk.formats.stl.STLHeader method)
(sfftk.formats.stl.STLMesh method)
(sfftk.formats.stl.STLSegment method)
(sfftk.formats.stl.STLSegmentation method)
(sfftk.formats.surf.AmiraHyperSurfaceAnnotation method)
(sfftk.formats.surf.AmiraHyperSurfaceHeader method)
(sfftk.formats.surf.AmiraHyperSurfaceMesh method)
(sfftk.formats.surf.AmiraHyperSurfaceSegment method)
(sfftk.formats.surf.AmiraHyperSurfaceSegmentation method)
(sfftk.formats.survos.SuRVoSSegment method)
(sfftk.formats.survos.SuRVoSSegmentation method)
copy_notes() (in module sfftk.notes.modify)
COST (class in sfftk.readers.modreader)
COST_FLAGS (class in sfftk.readers.modreader)
CSVRow (class in sfftk.notes.find)
CSVTable (class in sfftk.notes.find)
D
data (sfftk.readers.survosreader.SuRVoSSegmentation property)
del_configs() (in module sfftk.core.configs)
del_from_segment() (sfftk.notes.modify.AbstractNote method)
del_from_segmentation() (sfftk.notes.modify.AbstractGlobalNote method)
del_note() (in module sfftk.notes.modify)
description (sfftk.formats.am.AmiraMeshAnnotation property)
(sfftk.formats.map.MapAnnotation property)
(sfftk.formats.map.MaskAnnotation property)
(sfftk.formats.mod.IMODAnnotation property)
descriptions (sfftk.readers.segreader.SeggerSegmentation property)
E
edit_in_segment() (sfftk.notes.modify.AbstractNote method)
edit_in_segmentation() (sfftk.notes.modify.AbstractGlobalNote method)
edit_note() (in module sfftk.notes.modify)
ExternalReference (class in sfftk.notes.modify)
extract_segments() (in module sfftk.readers.surfreader)
F
file_name (sfftk.readers.segreader.SeggerSegmentation property)
file_path (sfftk.formats.seg.SeggerHeader property)
(sfftk.readers.segreader.SeggerSegmentation property)
find_chunk_length() (in module sfftk.readers.modreader)
fix_mask() (sfftk.readers.mapreader.Map method)
FLAGS (class in sfftk.readers.modreader)
format (sfftk.readers.segreader.SeggerSegmentation property)
format_version (sfftk.readers.segreader.SeggerSegmentation property)
G
get_config_file_path() (in module sfftk.core.configs)
get_configs() (in module sfftk.core.configs)
get_data() (in module sfftk.readers.amreader)
(in module sfftk.readers.mapreader)
(in module sfftk.readers.modreader)
(in module sfftk.readers.segreader)
(in module sfftk.readers.stlreader)
(in module sfftk.readers.surfreader)
(in module sfftk.readers.survosreader)
get_parent_id() (sfftk.readers.segreader.SeggerSegmentation method)
get_region_ids() (sfftk.readers.segreader.SeggerSegmentation method)
get_root() (in module sfftk.readers.segreader)
get_url() (sfftk.notes.find.SearchResource method)
GlobalArgsNote (class in sfftk.notes.modify)
GlobalSimpleNote (class in sfftk.notes.modify)
H
handle_config() (in module sfftk.sff)
handle_convert() (in module sfftk.sff)
handle_notes() (in module sfftk.sff)
handle_notes_add() (in module sfftk.sff)
handle_notes_clear() (in module sfftk.sff)
handle_notes_copy() (in module sfftk.sff)
handle_notes_del() (in module sfftk.sff)
handle_notes_edit() (in module sfftk.sff)
handle_notes_list() (in module sfftk.sff)
handle_notes_merge() (in module sfftk.sff)
handle_notes_save() (in module sfftk.sff)
handle_notes_search() (in module sfftk.sff)
handle_notes_show() (in module sfftk.sff)
handle_notes_trash() (in module sfftk.sff)
handle_prep() (in module sfftk.sff)
handle_prep_mergemask() (in module sfftk.sff)
handle_prep_starcrop() (in module sfftk.sff)
handle_prep_starsplit() (in module sfftk.sff)
handle_tests() (in module sfftk.sff)
handle_view() (in module sfftk.sff)
has_mesh_or_shapes (sfftk.formats.mod.IMODSegmentation property)
header (sfftk.formats.am.AmiraMeshSegmentation property)
(sfftk.formats.map.BinaryMaskSegmentation property)
(sfftk.formats.map.MapSegmentation property)
(sfftk.formats.map.MergedMaskSegmentation property)
(sfftk.formats.mod.IMODSegmentation property)
(sfftk.formats.seg.SeggerSegmentation property)
(sfftk.formats.star.RelionMultiStarSegmentation property)
(sfftk.formats.star.RelionStarSegmentation property)
(sfftk.formats.stl.STLSegmentation property)
(sfftk.formats.surf.AmiraHyperSurfaceSegmentation property)
(sfftk.readers.segreader.SeggerSegmentation property)
(sfftk.readers.starreader.StarTable property)
HeaderView (class in sfftk.notes.view)
HxSurfSegment (class in sfftk.readers.surfreader)
I
id (sfftk.formats.surf.AmiraHyperSurfaceSegment property)
(sfftk.readers.surfreader.HxSurfSegment property)
ijk_to_xyz_transform (sfftk.formats.seg.SeggerHeader property)
(sfftk.readers.segreader.SeggerSegmentation property)
IMAT (class in sfftk.readers.modreader)
IMAT_FLAGS (class in sfftk.readers.modreader)
IMOD (class in sfftk.readers.modreader)
IMODAnnotation (class in sfftk.formats.mod)
IMODEllipsoid (class in sfftk.formats.mod)
IMODHeader (class in sfftk.formats.mod)
IMODMesh (class in sfftk.formats.mod)
IMODMeshes (class in sfftk.formats.mod)
IMODSegment (class in sfftk.formats.mod)
IMODSegmentation (class in sfftk.formats.mod)
IMODShapes (class in sfftk.formats.mod)
invert() (sfftk.readers.mapreader.Map method)
iri (sfftk.notes.modify.ExternalReference property)
is_index (sfftk.notes.find.TableField property)
is_mask (sfftk.readers.mapreader.Map property)
J
justify() (sfftk.notes.find.TableField method)
K
keys() (sfftk.readers.starreader.StarReader method)
L
labels (sfftk.readers.mapreader.Map property)
(sfftk.readers.survosreader.SuRVoSSegmentation property)
list_notes() (in module sfftk.notes.view)
load_configs() (in module sfftk.core.configs)
M
Map (class in sfftk.readers.mapreader)
map_level (sfftk.readers.segreader.SeggerSegmentation property)
map_path (sfftk.formats.seg.SeggerHeader property)
(sfftk.readers.segreader.SeggerSegmentation property)
map_size (sfftk.formats.seg.SeggerHeader property)
(sfftk.readers.segreader.SeggerSegmentation property)
MapAnnotation (class in sfftk.formats.map)
MapHeader (class in sfftk.formats.map)
MapSegment (class in sfftk.formats.map)
MapSegmentation (class in sfftk.formats.map)
mask (sfftk.readers.segreader.SeggerSegmentation property)
MaskAnnotation (class in sfftk.formats.map)
MaskHeader (class in sfftk.formats.map)
material (sfftk.formats.am.AmiraMeshSegment property)
maximum_tomograms (sfftk.core.prep.RelionCompositeStarReader attribute)
MCLP (class in sfftk.readers.modreader)
MCLP_FLAGS (class in sfftk.readers.modreader)
MEPA (class in sfftk.readers.modreader)
MEPA_FLAGS (class in sfftk.readers.modreader)
merge() (in module sfftk.notes.modify)
(sfftk.core.prep.MergedMask method)
MergedMask (class in sfftk.core.prep)
MergedMaskSegment (class in sfftk.formats.map)
MergedMaskSegmentation (class in sfftk.formats.map)
mergemask() (in module sfftk.core.prep)
MESH (class in sfftk.readers.modreader)
MESH_FLAGS (class in sfftk.readers.modreader)
meshes (sfftk.formats.mod.IMODSegment property)
(sfftk.formats.stl.STLSegment property)
(sfftk.formats.surf.AmiraHyperSurfaceSegment property)
MEST (class in sfftk.readers.modreader)
MINX (class in sfftk.readers.modreader)
MODEL_FLAGS (class in sfftk.readers.modreader)
module
sfftk.__init__
sfftk.core.configs
sfftk.core.parser
sfftk.core.prep
sfftk.formats.am
sfftk.formats.map
sfftk.formats.mod
sfftk.formats.seg
sfftk.formats.star
sfftk.formats.stl
sfftk.formats.surf
sfftk.formats.survos
sfftk.notes.find
sfftk.notes.modify
sfftk.notes.view
sfftk.readers.amreader
sfftk.readers.mapreader
sfftk.readers.modreader
sfftk.readers.segreader
sfftk.readers.starreader
sfftk.readers.stlreader
sfftk.readers.surfreader
sfftk.readers.survosreader
sfftk.sff
MOST (class in sfftk.readers.modreader)
N
name (sfftk.formats.am.AmiraMeshAnnotation property)
(sfftk.formats.map.MapAnnotation property)
(sfftk.formats.map.MaskAnnotation property)
(sfftk.formats.seg.SeggerHeader property)
(sfftk.formats.stl.STLSegment property)
(sfftk.formats.surf.AmiraHyperSurfaceAnnotation property)
(sfftk.readers.segreader.SeggerSegmentation property)
(sfftk.readers.surfreader.HxSurfSegment property)
names (sfftk.readers.survosreader.SuRVoSSegmentation property)
normals (sfftk.formats.mod.IMODMesh property)
NoteAttr (class in sfftk.notes.modify)
NoteView (class in sfftk.notes.view)
O
OBJECT_FLAGS (class in sfftk.readers.modreader)
OBJECT_SYM_FLAGS (class in sfftk.readers.modreader)
OBJT (class in sfftk.readers.modreader)
OBST (class in sfftk.readers.modreader)
P
parent_ids (sfftk.formats.seg.SeggerHeader property)
(sfftk.readers.segreader.SeggerSegmentation property)
parse() (sfftk.readers.starreader.StarReader method)
parse_args() (in module sfftk.core.parser)
pc (sfftk.notes.find.TableField property)
polygons (sfftk.formats.mod.IMODMesh property)
(sfftk.formats.stl.STLMesh property)
(sfftk.formats.surf.AmiraHyperSurfaceMesh property)
print_model() (in module sfftk.readers.modreader)
print_progress() (in module sfftk.readers.starreader)
R
radius (sfftk.formats.mod.IMODEllipsoid property)
raw_data() (sfftk.readers.starreader.StarTableRow method)
read() (sfftk.core.configs.Configs method)
(sfftk.readers.mapreader.Map method)
(sfftk.readers.modreader.CLIP method)
(sfftk.readers.modreader.CONT method)
(sfftk.readers.modreader.COST method)
(sfftk.readers.modreader.IMAT method)
(sfftk.readers.modreader.IMOD method)
(sfftk.readers.modreader.MCLP method)
(sfftk.readers.modreader.MEPA method)
(sfftk.readers.modreader.MESH method)
(sfftk.readers.modreader.MEST method)
(sfftk.readers.modreader.MINX method)
(sfftk.readers.modreader.MOST method)
(sfftk.readers.modreader.OBJT method)
(sfftk.readers.modreader.OBST method)
(sfftk.readers.modreader.SLAN method)
(sfftk.readers.modreader.STORE method)
(sfftk.readers.modreader.VIEW method)
ref_points (sfftk.readers.segreader.SeggerSegmentation property)
region_colours (sfftk.readers.segreader.SeggerSegmentation property)
region_ids (sfftk.formats.seg.SeggerHeader property)
(sfftk.readers.segreader.SeggerSegmentation property)
RelionCompositeStarReader (class in sfftk.core.prep)
RelionMultiStarSegmentation (class in sfftk.formats.star)
RelionStarHeader (class in sfftk.formats.star)
RelionStarReader (class in sfftk.readers.starreader)
RelionStarSegment (class in sfftk.formats.star)
RelionStarSegmentation (class in sfftk.formats.star)
render() (sfftk.notes.find.TableField method)
ResultsTable (class in sfftk.notes.find)
root_parent_ids (sfftk.formats.seg.SeggerHeader property)
(sfftk.readers.segreader.SeggerSegmentation property)
S
save() (in module sfftk.notes.modify)
search() (sfftk.notes.find.SearchResource method)
SearchResource (class in sfftk.notes.find)
SearchResults (class in sfftk.notes.find)
SeggerAnnotation (class in sfftk.formats.seg)
SeggerHeader (class in sfftk.formats.seg)
SeggerSegment (class in sfftk.formats.seg)
SeggerSegmentation (class in sfftk.formats.seg)
(class in sfftk.readers.segreader)
SeggerVolume (class in sfftk.formats.seg)
segment_id (sfftk.formats.survos.SuRVoSSegment property)
segment_ids() (sfftk.readers.survosreader.SuRVoSSegmentation method)
segments (sfftk.formats.am.AmiraMeshSegmentation property)
(sfftk.formats.map.BinaryMaskSegmentation property)
(sfftk.formats.map.MapSegmentation property)
(sfftk.formats.map.MergedMaskSegmentation property)
(sfftk.formats.mod.IMODSegmentation property)
(sfftk.formats.seg.SeggerSegmentation property)
(sfftk.formats.star.RelionMultiStarSegmentation property)
(sfftk.formats.star.RelionStarSegmentation property)
(sfftk.formats.stl.STLSegmentation property)
(sfftk.formats.surf.AmiraHyperSurfaceSegmentation property)
(sfftk.formats.survos.SuRVoSSegmentation property)
set_configs() (in module sfftk.core.configs)
setattr() (sfftk.readers.starreader.StarTableRow method)
sfftk.__init__
module
sfftk.core.configs
module
sfftk.core.parser
module
sfftk.core.prep
module
sfftk.formats.am
module
sfftk.formats.map
module
sfftk.formats.mod
module
sfftk.formats.seg
module
sfftk.formats.star
module
sfftk.formats.stl
module
sfftk.formats.surf
module
sfftk.formats.survos
module
sfftk.notes.find
module
sfftk.notes.modify
module
sfftk.notes.view
module
sfftk.readers.amreader
module
sfftk.readers.mapreader
module
sfftk.readers.modreader
module
sfftk.readers.segreader
module
sfftk.readers.starreader
module
sfftk.readers.stlreader
module
sfftk.readers.surfreader
module
sfftk.readers.survosreader
module
sfftk.sff
module
shape (sfftk.readers.survosreader.SuRVoSSegmentation property)
shapes (sfftk.formats.mod.IMODSegment property)
show_chunks() (in module sfftk.readers.modreader)
show_notes() (in module sfftk.notes.view)
SimpleNote (class in sfftk.notes.modify)
simplify_mask() (sfftk.readers.segreader.SeggerSegmentation method)
skew_matrix (sfftk.readers.mapreader.Map property)
skew_matrix_data (sfftk.readers.mapreader.Map property)
skew_translation (sfftk.readers.mapreader.Map property)
skew_translation_data (sfftk.readers.mapreader.Map property)
SLAN (class in sfftk.readers.modreader)
smoothing_levels (sfftk.readers.segreader.SeggerSegmentation property)
starcrop() (in module sfftk.core.prep)
StarReader (class in sfftk.readers.starreader)
starsplit() (in module sfftk.core.prep)
StarTable (class in sfftk.readers.starreader)
StarTableRow (class in sfftk.readers.starreader)
STLAnnotation (class in sfftk.formats.stl)
STLHeader (class in sfftk.formats.stl)
STLMesh (class in sfftk.formats.stl)
STLSegment (class in sfftk.formats.stl)
STLSegmentation (class in sfftk.formats.stl)
STORE (class in sfftk.readers.modreader)
SuRVoSSegment (class in sfftk.formats.survos)
SuRVoSSegmentation (class in sfftk.formats.survos)
(class in sfftk.readers.survosreader)
T
Table (class in sfftk.notes.find)
TableField (class in sfftk.notes.find)
TableHeaderView (class in sfftk.notes.view)
TableRow (class in sfftk.notes.find)
tables (sfftk.readers.starreader.StarReader property)
tabulate() (sfftk.notes.find.SearchResults method)
to_affine_transform() (sfftk.readers.starreader.StarTableRow method)
transform (sfftk.formats.mod.IMODEllipsoid property)
transform() (in module sfftk.core.prep)
transform_stl_mesh() (in module sfftk.core.prep)
translate_indexes() (sfftk.formats.surf.AmiraHyperSurfaceMesh static method)
trash() (in module sfftk.notes.modify)
triangles (sfftk.formats.am.AmiraMeshMesh property)
(sfftk.formats.mod.IMODMesh property)
(sfftk.readers.surfreader.HxSurfSegment property)
U
UpperAction (class in sfftk.core.parser)
V
version (sfftk.formats.seg.SeggerHeader property)
vertices (sfftk.formats.am.AmiraMeshMesh property)
(sfftk.formats.mod.IMODMesh property)
(sfftk.formats.stl.STLMesh property)
(sfftk.formats.surf.AmiraHyperSurfaceMesh property)
(sfftk.readers.surfreader.HxSurfSegment property)
View (class in sfftk.notes.view)
VIEW (class in sfftk.readers.modreader)
VIEW_FLAGS (class in sfftk.readers.modreader)
volume (sfftk.formats.am.AmiraMeshSegment property)
voxels (sfftk.readers.mapreader.Map property)
W
width (sfftk.notes.find.TableField property)
write() (sfftk.core.configs.Configs method)
(sfftk.readers.mapreader.Map method)
X
x_length (sfftk.readers.modreader.IMOD property)
Y
y_length (sfftk.readers.modreader.IMOD property)
Z
z_length (sfftk.readers.modreader.IMOD property)
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