diff --git a/docs/examples/cone.md b/docs/examples/cone.md deleted file mode 100644 index fd62175..0000000 --- a/docs/examples/cone.md +++ /dev/null @@ -1,27 +0,0 @@ -# Cone - -To view the available options for the cone command, make use of the '--help' provision. - -```shell - -ttmask cone --help - -``` - -## Commands and Options - -Option | Usage | ------------- |-----------------------------------------------------------------------------------| ---sidelength | This specifies the your box size. e.g. a 100 x 100 x 100 pixel array. | ---cone-height | The height of your cone in angstrom. | ---cone-base-diameter | The diameter of the base (i.e. widest diameter) of the cone. ---soft-edge-width | The number of pixels over which a soft edge will be added. | ---pixel-size | The desired pixel size of your output. If left blank, 1 will be taken as default. | ---output | Name of your output file, e.g. cone1.mrc | - -Note : Currently hollow cones are not available due to some quirks as to how this needs to be specified. - - - - - \ No newline at end of file diff --git a/docs/examples/cube.md b/docs/examples/cube.md deleted file mode 100644 index fa07586..0000000 --- a/docs/examples/cube.md +++ /dev/null @@ -1,25 +0,0 @@ -# Cube - -To view the available options for the cube command, make use of the '--help' provision. - -```shell - -ttmask cube --help - -``` - -## Commands and Options - -Option | Usage | ------------- |------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------| ---sidelength | This specifies the your box size. e.g. a 100 x 100 x 100 pixel array. | ---cube-sidelength | The edge length of your cube in angstrom. | ---soft-edge-width | The number of pixels over which a soft edge will be added. | ---pixel-size | The desired pixel size of your output. If left blank, 1 will be taken as default. | ---output | Name of your output file, e.g. cube5.mrc | ---wall-thickness | If specified (in angstrom), the cube will be hollow. The walls of the cube will be given this thickness, but will be added inwards of the boundary, such that cube-sidelength dimensions are not exceeded. | - - - - - \ No newline at end of file diff --git a/docs/functions/cone.md b/docs/functions/cone.md new file mode 100644 index 0000000..f1eea15 --- /dev/null +++ b/docs/functions/cone.md @@ -0,0 +1,29 @@ +# Cone + +To view the available options for the cone command, make use of the '--help' provision. Note : Hollow cones are not supported currently due to artefacts at the tip of the cone. + +```shell + +ttmask cone --help + +``` + +## Commands and Options + +Option | Usage | +------------ |------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------| +--sidelength | This specifies the box size. e.g. "--sidelength 100" for a 100 x 100 x 100 pixel array. | +--cone-height | The height of your cone in angstroms. | +--cone-base-diameter | The diameter of the base (i.e. widest diameter) of the cone. +--soft-edge-width | The number of pixels over which a soft edge will be added. | +--pixel-size | The desired pixel size of your output in angstroms. | +--output | Name of your output file | +--centering | The default is "--centering standard", in which the shape is placed at the center of the box (i.e. [sidelength/2, sidelength/2, sidelength/2]). However, if you would like the shape to 'appear' centered within an even box size then use "--centering visual", which shifts the center half a pixel. Alternatively, one may use "--centering custom" together with the "--center" flag (see next table entry). +--center | If using "--centering custom" then specify the custom center here. E.g. for a box size of 100, if you want to shift the mask 10 pixels in Z, then specify the new center using "--center 40 50 50". The convention here is "--center z y x" (depth, height, width). + + + + + + + \ No newline at end of file diff --git a/docs/functions/cube.md b/docs/functions/cube.md new file mode 100644 index 0000000..ead8561 --- /dev/null +++ b/docs/functions/cube.md @@ -0,0 +1,27 @@ +# Cube + +To view the available options for the cube command, make use of the '--help' provision. + +```shell + +ttmask cube --help + +``` + +## Commands and Options + +Option | Usage | +------------ |------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------| +--sidelength | This specifies the box size. e.g. "--sidelength 100" for a 100 x 100 x 100 pixel array. | +--cube-sidelength | The edge length of your cube in angstrom. | +--soft-edge-width | The number of pixels over which a soft edge will be added. | +--pixel-size | The desired pixel size of your output in angstroms. | +--output | Name of your output file | +--wall-thickness | If specified (in angstrom), the cube will be hollow. The walls of the cube will be given this thickness, but will be added inwards of the boundary, such that cube-sidelength dimensions are not exceeded. | +--centering | The default is "--centering standard", in which the shape is placed at the center of the box (i.e. [sidelength/2, sidelength/2, sidelength/2]). However, if you would like the shape to 'appear' centered within an even box size then use "--centering visual", which shifts the center half a pixel. Alternatively, one may use "--centering custom" together with the "--center" flag (see next table entry). +--center | If using "--centering custom" then specify the custom center here. E.g. for a box size of 100, if you want to shift the mask 10 pixels in Z, then specify the new center using "--center 40 50 50". The convention here is "--center z y x" (depth, height, width). + + + + + \ No newline at end of file diff --git a/docs/examples/cuboid.md b/docs/functions/cuboid.md similarity index 56% rename from docs/examples/cuboid.md rename to docs/functions/cuboid.md index 17811d0..c1faee9 100644 --- a/docs/examples/cuboid.md +++ b/docs/functions/cuboid.md @@ -12,12 +12,14 @@ ttmask cuboid --help Option | Usage | ------------ |-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------| ---sidelength | This specifies the your box size. e.g. a 100 x 100 x 100 pixel array. | +--sidelength | This specifies the box size. e.g. "--sidelength 100" for a 100 x 100 x 100 pixel array. | --cuboid-sidelengths | The edge lengths of your cuboid in angstrom, specied as three space seperated floats e.g. 50 50 50. These correspond to the depth, height and width of your cuboid respectively (i.e. zyx) | --soft-edge-width | The number of pixels over which a soft edge will be added. | ---pixel-size | The desired pixel size of your output. If left blank, 1 will be taken as default. | ---output | Name of your output file, e.g. cuboid5.mrc | +--pixel-size | The desired pixel size of your output in angstroms. | +--output | Name of your output file | --wall-thickness | If specified (in angstrom), the cuboid will be hollow. The walls of the cube will be given this thickness, but will be added inwards of the boundary, such that cuboid-sidelengths dimensions are not exceeded. | +--centering | The default is "--centering standard", in which the shape is placed at the center of the box (i.e. [sidelength/2, sidelength/2, sidelength/2]). However, if you would like the shape to 'appear' centered within an even box size then use "--centering visual", which shifts the center half a pixel. Alternatively, one may use "--centering custom" together with the "--center" flag (see next table entry). +--center | If using "--centering custom" then specify the custom center here. E.g. for a box size of 100, if you want to shift the mask 10 pixels in Z, then specify the new center using "--center 40 50 50". The convention here is "--center z y x" (depth, height, width). diff --git a/docs/functions/curved_surface.md b/docs/functions/curved_surface.md new file mode 100644 index 0000000..4e35092 --- /dev/null +++ b/docs/functions/curved_surface.md @@ -0,0 +1,29 @@ +# Curved Surface + +To view the available options for the curved_surface command, make use of the '--help' provision. + +```shell + +ttmask curved_surface --help + +``` + +## Commands and Options + +Option | Usage | +------------ |-----------------------------------------------------------------------------------| +--sidelength | This specifies the box size. e.g. "--sidelength 100" for a 100 x 100 x 100 pixel array. | +--fit-sphere-diameter | This is the diameter of the sphere that would fit the curvature of the desired membrane surface. i.e. a larger value results in reduced curvature of the surface, with a lower value increasing surface curvature. +--surface-thickness | The thickness of the curved surface in angstrom. +--soft-edge-width | The number of pixels over which a soft edge will be added. | +--pixel-size | The desired pixel size of your output in angstroms. | +--output | Name of your output file | +--centering | The default is "--centering standard", in which the shape is placed at the center of the box (i.e. [sidelength/2, sidelength/2, sidelength/2]). However, if you would like the shape to 'appear' centered within an even box size then use "--centering visual", which shifts the center half a pixel. Alternatively, one may use "--centering custom" together with the "--center" flag (see next table entry). +--center | If using "--centering custom" then specify the custom center here. E.g. for a box size of 100, if you want to shift the mask 10 pixels in Z, then specify the new center using "--center 40 50 50". The convention here is "--center z y x" (depth, height, width). + +Note : Currently hollow cones are not available due to some quirks as to how this needs to be specified. + + + + + \ No newline at end of file diff --git a/docs/examples/cylinder.md b/docs/functions/cylinder.md similarity index 56% rename from docs/examples/cylinder.md rename to docs/functions/cylinder.md index 4f18d4a..b3f4bfd 100644 --- a/docs/examples/cylinder.md +++ b/docs/functions/cylinder.md @@ -12,12 +12,15 @@ ttmask cylinder --help Option | Usage | ------------ |------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------| ---sidelength | This specifies the your box size. e.g. a 100 x 100 x 100 pixel array. | +--sidelength | This specifies the box size. e.g. "--sidelength 100" for a 100 x 100 x 100 pixel array. | +--cylinder-height | The height of your cylinder in angstrom. --cylinder-diameter | The diameter of your cylinder in angstrom, measured from outermost edge to edge. | --soft-edge-width | The number of pixels over which a soft edge will be added. | ---pixel-size | The desired pixel size of your output. If left blank, 1 will be taken as default. | ---output | Name of your output file, e.g. cyl1.mrc | +--pixel-size | The desired pixel size of your output in angstroms. | +--output | Name of your output file | --wall-thickness | If specified (in angstrom), the cylinder will be hollow, with this thickness wall. The thickness is not added to the cylinder-diameter, but instead is added inward of that boundary such that your specified diameter still remains accurate. | +--centering | The default is "--centering standard", in which the shape is placed at the center of the box (i.e. [sidelength/2, sidelength/2, sidelength/2]). However, if you would like the shape to 'appear' centered within an even box size then use "--centering visual", which shifts the center half a pixel. Alternatively, one may use "--centering custom" together with the "--center" flag (see next table entry). +--center | If using "--centering custom" then specify the custom center here. E.g. for a box size of 100, if you want to shift the mask 10 pixels in Z, then specify the new center using "--center 40 50 50". The convention here is "--center z y x" (depth, height, width). diff --git a/docs/examples/ellipsoid.md b/docs/functions/ellipsoid.md similarity index 61% rename from docs/examples/ellipsoid.md rename to docs/functions/ellipsoid.md index 3759829..ee22c8d 100644 --- a/docs/examples/ellipsoid.md +++ b/docs/functions/ellipsoid.md @@ -12,12 +12,14 @@ ttmask ellipsoid --help Option | Usage | ------------ |-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------| ---sidelength | This specifies the your box size. e.g. a 100 x 100 x 100 pixel array. | +--sidelength | This specifies the box size. e.g. "--sidelength 100" for a 100 x 100 x 100 pixel array. | --ellipsoid-dimensions | The lengths of your ellipsoid in angstrom, specied as three space seperated floats e.g. 50 30 30. These correspond to the depth, height and width of your ellipsoid respectively (i.e. zyx) | --soft-edge-width | The number of pixels over which a soft edge will be added. | ---pixel-size | The desired pixel size of your output. If left blank, 1 will be taken as default. | ---output | Name of your output file, e.g. ellipsoid1.mrc | +--pixel-size | The desired pixel size of your output in angstroms. | +--output | Name of your output file | --wall-thickness | If specified (in angstrom), the ellipsoid will be hollow, with this thickness wall. The thickness is not added to the ellipsoid-dimensions, but instead is added inward of that boundary such that your specified dimensions still remain accurate. | +--centering | The default is "--centering standard", in which the shape is placed at the center of the box (i.e. [sidelength/2, sidelength/2, sidelength/2]). However, if you would like the shape to 'appear' centered within an even box size then use "--centering visual", which shifts the center half a pixel. Alternatively, one may use "--centering custom" together with the "--center" flag (see next table entry). +--center | If using "--centering custom" then specify the custom center here. E.g. for a box size of 100, if you want to shift the mask 10 pixels in Z, then specify the new center using "--center 40 50 50". The convention here is "--center z y x" (depth, height, width). diff --git a/docs/functions/map2mask.md b/docs/functions/map2mask.md new file mode 100644 index 0000000..7d26a71 --- /dev/null +++ b/docs/functions/map2mask.md @@ -0,0 +1,26 @@ +# Map to Mask + +To view the available options for the map2mask command, make use of the '--help' provision. + +```shell + +ttmask map2mask --help + +``` + +## Commands and Options + +Option | Usage | +---------------------------|------------------------------------------------------------------------------------------------------| +--input-map | The input map to be binarized (mrc file format). | +--binarization-threshold | All values greater than this threshold are set to 1 and all values below this threshold are set to 0 | +--padding-width | The number of pixels by which to extend the mask, adding a given number of 1s. | +--soft-edge-width | The number of pixels over which a soft edge will be added. | +--pixel-size | The desired pixel size of your output. If left blank, 1 will be taken as default. | +--output-mask | Name of your output file | + + + + + + \ No newline at end of file diff --git a/docs/examples/sphere.md b/docs/functions/sphere.md similarity index 56% rename from docs/examples/sphere.md rename to docs/functions/sphere.md index 919f25a..e2ed67b 100644 --- a/docs/examples/sphere.md +++ b/docs/functions/sphere.md @@ -12,12 +12,14 @@ ttmask sphere --help Option | Usage | ------------ |--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------| ---sidelength | This specifies the your box size. e.g. a 100 x 100 x 100 pixel array. | +--sidelength | This specifies the box size. e.g. "--sidelength 100" for a 100 x 100 x 100 pixel array. | --sphere-diameter | The diameter of your sphere in angstrom, measured from outermost edge to edge. | --soft-edge-width | The number of pixels over which a soft edge will be added. | ---pixel-size | The desired pixel size of your output. If left blank, 1 will be taken as default. | ---output | Name of your output file, e.g. sphere5.mrc | +--pixel-size | The desired pixel size of your output in angstroms. | +--output | Name of your output file | --wall-thickness | If specified (in angstrom), the sphere will be hollow, with this thickness wall. The thickness is not added to the sphere-diameter, but instead is added inward of that boundary such that your specified diameter still remains accurate. | +--centering | The default is "--centering standard", in which the shape is placed at the center of the box (i.e. [sidelength/2, sidelength/2, sidelength/2]). However, if you would like the shape to 'appear' centered within an even box size then use "--centering visual", which shifts the center half a pixel. Alternatively, one may use "--centering custom" together with the "--center" flag (see next table entry). +--center | If using "--centering custom" then specify the custom center here. E.g. for a box size of 100, if you want to shift the mask 10 pixels in Z, then specify the new center using "--center 40 50 50". The convention here is "--center z y x" (depth, height, width). diff --git a/docs/functions/tube.md b/docs/functions/tube.md new file mode 100644 index 0000000..212a7a6 --- /dev/null +++ b/docs/functions/tube.md @@ -0,0 +1,29 @@ +# Tube + +To view the available options for the tube command, make use of the '--help' provision. + +```shell + +ttmask tube --help + +``` + +## Commands and Options + +Option | Usage | +------------ |------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------| +--sidelength | This specifies the box size. e.g. "--sidelength 100" for a 100 x 100 x 100 pixel array. | +--tube-height | The height of your tube in angstrom. +--tube-diameter | The diameter of your tube in angstrom, measured from outermost edge to edge. | +--soft-edge-width | The number of pixels over which a soft edge will be added. | +--pixel-size | The desired pixel size of your output in angstroms. | +--output | Name of your output file | +--wall-thickness | If specified (in angstrom), the tube will be hollow, with this thickness wall. The thickness is not added to the tube-diameter, but instead is added inward of that boundary such that your specified diameter still remains accurate. | +--centering | The default is "--centering standard", in which the shape is placed at the center of the box (i.e. [sidelength/2, sidelength/2, sidelength/2]). However, if you would like the shape to 'appear' centered within an even box size then use "--centering visual", which shifts the center half a pixel. Alternatively, one may use "--centering custom" together with the "--center" flag (see next table entry). +--center | If using "--centering custom" then specify the custom center here. E.g. for a box size of 100, if you want to shift the mask 10 pixels in Z, then specify the new center using "--center 40 50 50". The convention here is "--center z y x" (depth, height, width). + + + + + + \ No newline at end of file diff --git a/mkdocs.yml b/mkdocs.yml index 62a8844..c6643b7 100644 --- a/mkdocs.yml +++ b/mkdocs.yml @@ -12,14 +12,17 @@ copyright: Copyright © 2022 - 2022 teamtomo # Custom navigation can be specified nav: - Overview: overview.md - - Examples: + - Functions: - - Cone: examples/cone.md - - Cube: examples/cube.md - - Cuboid: examples/cuboid.md - - Cylinder: examples/cylinder.md - - Ellipsoid: examples/ellipsoid.md - - Sphere: examples/sphere.md + - Cone: functions/cone.md + - Cube: functions/cube.md + - Cuboid: functions/cuboid.md + - Curved Surface: functions/curved_surface.md + - Cylinder: functions/cylinder.md + - Ellipsoid: functions/ellipsoid.md + - Map to Mask: functions/map2mask.md + - Sphere: functions/sphere.md + - Tube: functions/tube.md theme: icon: logo: material/cube-outline