Masking : Mask creation tool for 2D or 3D masks.

Usage in command line

sp_mask.py  input_volume  output_directory  --prefix=PREFIX  --overwrite  --low_pass_filter_resolution=LOW_PASS_FILTER_RESOLUTION  --low_pass_filter_falloff=LOW_PASS_FILTER_FALLOFF  --pixel_size=PIXEL_SIZE  --threshold=THRESHOLD --nsigma=NSIGMA  --mol_mass=MOL_MASS  --ndilation=NDILATION  --nerosion=NEROSION  --edge_width=EDGE_WIDTH  --edge_type=EDGE_TYPE  --do_old --allow_disconnected  --fill_mask --second_mask=SECOND_MASK  --second_mask_shape=SECOND_MASK_SHAPE  --s_radius=S_RADIUS  --s_nx=S_NX  --s_ny=S_NY  --s_nz=S_NZ  --s_threshold=THRESHOLD --s_nsigma=NSIGMA  --s_mol_mass=MOL_MASS  --s_ndilation=NDILATION  --s_nerosion=NEROSION  --s_edge_width=EDGE_WIDTH  --s_edge_type=EDGE_TYPE  --s_do_old  --s_allow_disconnected  --s_invert=S_INVERT --s_fill_mask

sp_mask.py exists only in non-MPI version.

Create a binary mask dilated by 2 pixel using the binary threshold from chimera

sp_mask.py input_volume output_directory --threshold=0.3 --edge_width=0 --ndilation=1

Create an adapted mask dilated by 2 pixel and a soft edge of 5 pixel using the binary threshold from chimera

sp_mask.py input_volume output_directory --threshold=0.3 --edge_width=5 --ndilation=1

Create an adapted mask dilated by 2 pixel and a soft edge of 5 pixel using the binary threshold from chimera and masked by a soft edged cylinder to 80% (e.g. for helical reconstruction with a box size of 300)

sp_mask.py input_volume output_directory --threshold=0.3 --edge_width=5 --ndilation=1 --second_mask_shape=cylinder --s_radius=40 --s_nx=240 --s_ny=240 --s_nz=240 --s_ndilation=1 --s_edge_width=5

input_volume

Input image

Path to the 2D image or 3D Volume (default required string)

output_directory

Output directory

Output directory path (default required string)

--prefix

Output prefix

Prefix of the produced files (default sp_mask)

--overwrite

Overwrite outputs

Overwrite the output mask in case it exists already. (default False)

--use_mol_mass

Use molecular mass

GUI OPTION ONLY - Define if one want to use the molecular mass option as a masking threshold. (default False)

--threshold==none --nsigma==none

--mol_mass

Molecular mass [kDa]: The estimated molecular mass of the target particle in kilodalton. This is used to calculate the binarization threshold automatically. (default none)

--use_mol_mass==True

--threshold

Binarization threshold: Defines the threshold used in the first step of the processing to generate a binary version of the input structure. If the value is lower-equal than the default, the option will be ignored and the threshold will be set according to nsigma method above. (default none)

--nsigma==none --use_mol_mass==False

--nsigma

Density standard deviation threshold: Defines the threshold used in the first step of the processing to generate a binary version of the structure. The threshold is set to ⇐ mean + (nsigma x standard deviations). This option will not be used if the option threshold is none. (default none)

--threshold==none --use_mol_mass==False

--ndilation

Number of dilations

The pixel width to dilate the 3D binary volume corresponding to the specified molecular mass or density threshold prior to softening the edge. One circle of dilation will add about 2 pixels to the mask. (default 3)

--nerosion

Number of erosions

Number of times to erode binarized volume. One circle of erosion will remove about 2 pixels from the mask. (default 0)

--edge_width

Soft-edge width [Pixels]: The pixel width of transition area for soft-edged masking. If the width is 0, a binary mask is returned. (default 5)

--edge_type

Soft-edge type: The type of soft-edge. Available methods are (1) \'cosine\' for cosine soft-edged (used in PostRefiner) and (2) \'gaussian\' for gaussian soft-edge. (default cosine)

--edge_width!=0

--allow_disconnected

Allow disconnected regions

Allow disconnected region in the mask. (default False)

--fill_mask

Fill mask

Fills empty spaces inside a map. (default True question reversed in GUI)

--do_old

Old behaviour

Restore the old masking behaviour, which is a bit less smooth. (default False)

--edge_width!=0

--low_pass_filter_resolution

Low pass filter resolution [A]

Low pass filter resolution in angstrom. If set, the volume will be filtered prior to create a mask. (default none)

--low_pass_filter_falloff

Low pass filter falloff [1/Pixel]

Low pass filter falloff in absolute frequencies. If set, the volume will be filtered prior to create a mask. (default 0.01)

--low_pass_filter_resolution!=none

--pixel_size

Pixel size [A/px]

Pixel size of the volume. Used for filtering. (default 1.0)

--low_pass_filter_resolution!=none

--use_second_mask

Use a second mask

ONLY A GUI OPTION. The second mask can be used to mask the first one after creation. This is useful to create soft edged regions of the mask. (default False)

--second_mask

Second mask path

Path to the second mask used for masking the mask. (default none)

--use_second_mask==True --second_mask_shape==none

--second_mask_shape

Second mask shape

Shape of the second mask. Possible values: sphere, cylinder, cube. (default none)

--use_second_mask==True --second_mask==none

--s_radius

Second - Radius of the mask

The estimated molecular mass of the target particle in kilodalton. This is used to calculate the binarization threshold automatically. (default none)

--second_mask_shape!=none --second_mask_shape!=cube --use_second_mask==True

--s_nx

Second - X dimension of the mask

The estimated molecular mass of the target particle in kilodalton. This is used to calculate the binarization threshold automatically. (default none)

--second_mask_shape!=none --use_second_mask==True

--s_ny

Second - Y dimension of the mask

The estimated molecular mass of the target particle in kilodalton. This is used to calculate the binarization threshold automatically. (default none)

--second_mask_shape!=none --use_second_mask==True

--s_nz

Second - Z dimension of the mask

The estimated molecular mass of the target particle in kilodalton. This is used to calculate the binarization threshold automatically. (default none)

--second_mask_shape!=none --use_second_mask==True

--s_use_mol_mass

Second - Use molecular mass

GUI OPTION ONLY - Define if one want to use the molecular mass option as a masking threshold. (default False)

--s_threshold==none --s_nsigma==none --use_second_mask==True --second_mask!=none ; –s_mol_mass : Second - Molecular mass [kDa] : The estimated molecular mass of the target particle in kilodalton. This is used to calculate the binarization threshold automatically. (default none) : –s_use_mol_mass==True –use_second_mask==True –second_mask!=none

--s_threshold

Second - Binarization threshold: Defines the threshold used in the first step of the processing to generate a binary version of the input structure. If the value is lower-equal than the default, the option will be ignored and the threshold will be set according to nsigma method above. (default none)

--s_nsigma==none --s_use_mol_mass==False --use_second_mask==True --second_mask!=none ; –s_nsigma : Second - Density standard deviation threshold: Defines the threshold used in the first step of the processing to generate a binary version of the structure. The threshold is set to <= mean + (nsigma x standard deviations). This option will not be used if the option threshold is none. (default none) : –s_threshold==none –s_use_mol_mass==False –use_second_mask==True –second_mask!=none

--s_ndilation

Second - Number of dilations

The pixel width to dilate the 3D binary volume corresponding to the specified molecular mass or density threshold prior to softening the edge. One round of erosion will add about 2 pixels to the mask (default 3)

--use_second_mask==True

--s_nerosion

Second - Number of erosions

Number of times to erode binarized volume. One round of erosion will remove about 2 pixels from the mask (default 0)

--use_second_mask==True

--s_edge_width

Second - Soft-edge width [Pixels]: The pixel width of transition area for soft-edged masking.(default 5)

--use_second_mask==True

--s_edge_type

Second - Soft-edge type: The type of soft-edge for the 3D mask. Available methods are (1) \'cosine\' for cosine soft-edged (used in PostRefiner) and (2) \'gaussian\' for gaussian soft-edge. (default cosine)

--use_second_mask==True --s_edge_width!=0

--s_do_old

Second - Old behaviour

Restore the old masking behaviour, which is a bit less smooth. (default False)

--use_second_mask==True --s_edge_width!=0

--s_allow_disconnected

Second - Allow disconnected regions

Allow disconnected region in the mask. (default False)

--use_second_mask==True

--s_fill_mask

Second - Fill mask

Fills empty spaces inside a map. (default True question reversed in GUI)

--s_invert

Second - Invert masking

If True, the mask will remove everything that is inside instead of leaving it. (default False)

--use_second_mask==True

Markus Stabrin

Category 1:: APPLICATIONS

sparx/bin/sp_mask.py

Beta:: Under evaluation and testing. Please let us know if there are any bugs.

There are no known bugs so far.