Xmipp

xmipp_transform_range_adjust (v3.0)

Usage

Adjust the grey level value of the pixels to a specified range.

See also
transform_normalize

Parameters

-i, --input <input_file>
Input file: metadata, stack, volume or image.
--mode <mode=overwrite>
Metadata writing mode.
where <mode> can be:
  • overwrite Replace the content of the file with the Metadata
  • append Write the Metadata as a new block, removing the old one
--label <image_label=image>
Label to be used to read/write images.
-o, --output <output_file=>
Output file: metadata, stack, volume or image.
--oroot <root=>
Rootname of output individual images. Output image format can be set adding extension after rootname as ":ext".
--range, -r <min_val> <max_val>
Output minimum and maximum values.
--noise <sigma=0>
Variation of the limit range values.
--mask <mask_type=circular>
Pixels in the mask area are guaranteed to be into the specified range.
where <mask_type> can be:
  • circular <R> circle/sphere mask if R>0 => outside R if R<0 => inside R
  • DWT_circular <R> <smin> <smax> circle/sphere mask smin and smax define the scales to be kept
  • rectangular <Xrect> <Yrect> <Zrect=-1> 2D or 3D rectangle if X,Y,Z > 0 => outside rectangle if X,Y,Z < 0 => inside rectangle
  • crown <R1> <R2> 2D or 3D crown if R1,R2 > 0 => outside crown if R1,R2 < 0 => inside crown
  • cylinder <R> <H> 2D circle or 3D cylinder if R,H > 0 => outside cylinder if R,H < 0 => inside cylinder
  • cone <theta> 3D cone (parallel to Z) if theta > 0 => outside cone if theta < 0 => inside cone
  • wedge <th0> <thF> 3D missing-wedge mask for data collected between tilting angles th0 and thF (around the Y-axis)
  • binary_file <binary_file> Read from file
--center <x0=0> <y0=0> <z0=0>
mask center

Examples and notes

Adjust an image in the range [-1, 1]:
xmipp_transform_range_adjust -i image.xmp -o image_adjust.xmp --range -1 1
Adjust images in a stack applying a circular mask:
xmipp_transform_range_adjust -i images.stk -o image_adjust.stk --range -1 1 --mask circular -32
Adjust a selection file in the range [-100, 100] with sigma noise 10:
xmipp_transform_range_adjust -i selection.sel --oroot images/im_adjust:spi -o selection_adjust.sel --range -100 100 --noise 10

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