Command-line interface¶
check¶
Implementation of CLI check command.
-
treem.commands.check.
check
(args)[source]¶ Checks morphology reconstruction for structural consistency.
usage: swc check [-h] [-q] [-o <str>] file
positional arguments:
file input morphology file (swc)
optional arguments:
-h, --help show this help message and exit
-q disable output
-o <str> save output to file (json)
prints out error codes and IDs of error nodes; returns the number of errors
convert¶
Implementation of CLI convert command.
usage: swc convert [-h] [-p <int> [<int> ...]] [-o <str>] [-q] file
positional arguments:
file input morphology file (swc)
optional arguments:
-h, --help show this help message and exit
-p <int> [<int> ...] point type {1,2,3,4} [all]
-o <str> converted morphology file (swc) [inp.swc]
-q disable output
find¶
Implementation of CLI find command.
usage: swc find [-h] [-p <int> [<int> ...]] [-e <int> [<int> ...]]
[-b <int> [<int> ...]] [-g <int> [<int> ...]] [-s]
[-d <float>] [-l <float>] [-z <float>] [--comp <str>]
[-c <float>] [--bottom-up] [--sec]
file
positional arguments:
file input morphology file (swc)
optional arguments:
-h, --help show this help message and exit
-p <int> [<int> ...] point type {1,2,3,4} [any]
-e <int> [<int> ...] branch order
-b <int> [<int> ...] branch breadth
-g <int> [<int> ...] node degree
-s stem branches (same as: -e 1 --sec -p 2 3 4)
-d <float> diameter threshold, um
-l <float> segment length threshold, um
-z <float> z-jump threshold, um
--comp <str> comparison condition for threshold {lt,eq,gt} [gt]
-c <float> cut plane thickness, um (z axis)
--bottom-up slice surface down (z axis)
--sec section start ids only
prints out point ids
measure¶
Implementation of CLI measure command.
-
treem.commands.measure.
get_morphometry
(reconstruction, args)[source]¶ Computes morphometric features of a reconstruction.
-
treem.commands.measure.
measure
(args)[source]¶ Computes morphometric features of multiple reconstructions.
usage: swc measure [-h] [-p <int> [<int> ...]] [-o <str>] file [file ...]
positional arguments:
file input morphology file (swc)
optional arguments:
-h, --help show this help message and exit
-p <int> [<int> ...] point type {1,2,3,4} [all]
-o <str> output morphometric file (json)
modify¶
Implementation of CLI modify command.
usage: swc modify [-h] [-p <int> [<int> ...]] [-e <int> [<int> ...]]
[-b <int> [<int> ...]] [-i <int> [<int> ...]]
[-s <float> <float> <float>] [-r <float>] [-t <float>]
[-m <int>] [-j <float>] [--sec] [-w <float>] [-u] [-a]
[--seed <int>] [-o <str>]
file
positional arguments:
file input morphology file (swc)
optional arguments:
-h, --help show this help message and exit
-p <int> [<int> ...] point type {2,3,4} [all]
-e <int> [<int> ...] branch order
-b <int> [<int> ...] branch breadth
-i <int> [<int> ...] input ids
-s <float> <float> <float>
scaling factors (x,y,z axes)
-r <float> radius scaling factor
-t <float> stretching strength, rel.
-m <int> smoothing strength, iter.
-j <float> random coordinate jitter, um (max)
--sec apply jitter per section
-w <float> random branch twisting, deg. (max)
-u prune branches
-a swap branches
--seed <int> random seed
-o <str> output morphology file (swc) [mod.swc]
render¶
usage: swc [-h] {check,view,find,modify,repair,measure,convert} ...
swc: error: invalid choice: 'render' (choose from 'check', 'view', 'find', 'modify', 'repair', 'measure', 'convert')
repair¶
Implementation of CLI repair command.
usage: swc repair [-h] [-n] [-t <float> <float> <float>]
[-a <float> <float> <float>] [-k <float>] [-kxy <float>]
[--bottom-up] [--seed <int>] [-c <int> [<int> ...]]
[--force-repair] [-d <int> [<int> ...]] [--diam <str>]
[--pool <str> [<str> ...]] [-l <int> [<int> ...]]
[-z <int> [<int> ...]] [--zjump <str>] [-r <float>]
[-o <str>] [-v]
file
positional arguments:
file input morphology file (swc)
optional arguments:
-h, --help show this help message and exit
-n center root
-t <float> <float> <float>
translate morphology, um (x,y,z)
-a <float> <float> <float>
rotate morphology, deg. (x,y,z axes)
-k <float> shrinkage correction factor (z axis)
-kxy <float> shrinkage correction factor (x,y plane)
--bottom-up slice surface down (z axis)
--seed <int> random seed
-c <int> [<int> ...] cut points ids
--force-repair repair cuts using branches of any order
-d <int> [<int> ...] set diameter in points ids
--diam <str> correction mode {joint,sec,order,breadth} [joint]
--pool <str> [<str> ...]
reference reconstructions for repair
-l <int> [<int> ...] delete nodes in points ids
-z <int> [<int> ...] z-jump points ids
--zjump <str> correction mode {align,split,tilt,join} [align]
-r <float> sampling resolution, um
-o <str> output morphology file (swc) [rep.swc]
-v verbose output
view¶
Implementation of CLI view command.
usage: swc view [-h] [-p <int> [<int> ...]] [-b <int> [<int> ...]]
[-s <int> [<int> ...]] [-m <int> [<int> ...]] [--show-id]
[-t <str>] [--no-axes] [--scale <float>] [-c <str>]
[--shadow-color <str>] [--shadow-width <float>]
[-a <float> <float>] [-d <float>] [-j <str>] [-o <str>]
file [file ...]
positional arguments:
file input morphology file (swc)
optional arguments:
-h, --help show this help message and exit
-p <int> [<int> ...] point type {1,2,3,4} [all]
-b <int> [<int> ...] branch start id
-s <int> [<int> ...] section start id
-m <int> [<int> ...] marker point id
--show-id show id labels
-t <str> set figure title
--no-axes disable axes
--scale <float> show scale bars, um
-c <str> color mode {neurites,cells,shadow} [neurites]
--shadow-color <str> shadow color [lightgray]
--shadow-width <float>
shadow width [3.0]
-a <float> <float> initial rotation angles, deg. (elevation, azimuth)
-d <float> initial distance to object, rel. [10.0]
-j <str> projection {xy,xz,yz}
-o <str> save image to file