Mkdocs update (#56)

* created pages for all functions and changed site structure.
Updated cone page.
Rest yet to be updated.

* Updated remaining pages. Still require checking and a basic description of the each function needs to be added.

* small change to cone doc

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).                                                                                                                                    
+
+              
+
+
+
+
+

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).                                                                                                                                  
+
+
+
+
+

docs/examples/cuboid.md → 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).                                                                                                                                    
 
 
 

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.                                                                    
+
+
+
+
+

docs/examples/cylinder.md → 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).