Window_micrograph

micrograph_window

Purpose

This utility windows a micrograph, in the sense of cutting it to a smaller size. This is used for marking particles in a downsampled micrograph and cutting them from the original micrograph. If the original micrograph is not of a dimension which is multiple of the downsampling factor (Xstep and Ystep in Downsample) then the coordinate conversion will not be well done and particles will be biased. For instance, assume we have a micrograph of 3002x3001 pixels, downsample it by 3 to 1000x1000. Then the particles cut from the original micrograph will be shifted towards the top left corner by (32,31) pixels. This is avoided if the original micrograph has a size multiple of (Xstep,Ystep).

Usage

micrograph_window -i [micrograph_in] -o [micrograph_out] -size [new X dimension] [new Y dimension] ...

Parameters

• `` Micrograph to window
• `` Output micrograph, it will be rewritten and have the same bits/pixel as the input one
• `` Output dimension. The image is windowed (cut) starting from the left corner of the input image, ie, the right columns and the bottom rows are lost. The output dimensions cannot be bigger than the input ones
• -top_left_corner [X0] [Y=0] = Starting corner for the window. The top left corner of the image is (0,0). X is the horizontal direction and Y the vertical one

Notes and examples

Window a micrograph of 3002x3001 to 3000x3000

$ micrograph_window -i micrograph.raw -o micrograph_w.raw -size 3000 3000

window between 2 points in 3D (physical coordinates)

xmipp_window  -i rec_fourier.vol  -o kk.vol -r0  10 10 10  -rF  40 40 40  -physical 

window between 2 points in 3D (logical coordinates)

xmipp_window  -i rec_fourier.vol  -o kk2.vol -r0  -20 -20 -20  -rF  10 10 10 

USER's COMMENTS

--Main.AlfredoSolano - 16 Jan 2007