LOCI- Crop on import

[Glen MacDonald-2]

Hello,

Using LOCI with 'Crop on Import' does not correctly control the height of the region. All other parameters seem to work whether passed as variables or written into the command.  The 2 lines below have the same behavior - the region opens with either the full original height of the file, or some multiple of the specified height.  

swidth=256;sheight=128;
sx=128;sy=128;
lowwer=1; tilll=99;

run("Bio-Formats Importer", "open=[] autoscale color_mode=Default crop specify_range split_channels view=Hyperstack stack_order=XYCZT z_begin=lowwer z_end=tilll z_step =1 t_begin=lowwer t_end=tilll t_step=1 x_coordinate_1=sx y_coordinate_1=sy width_1=swidth heigth_1=sheight");

               
run("Bio-Formats Importer", "open=[] autoscale color_mode=Default crop specify_range split_channels view=Hyperstack stack_order=XYCZT z_begin=1 z_end=99 z_step =1 t_begin=lowwer t_end=tilll t_step=1 x_coordinate_1=sx y_coordinate_1=sy width_1=256 heigth_1=128");

Am I doing something wrong or is there a bug in the plugin?

Glen MacDonald
Core for Communication Research
Virginia Merrill Bloedel Hearing Research Center
Box 357923
University of Washington
Seattle, WA 98195-7923
[phone]

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[Melissa Linkert-2]

Hi Glen,

> Using LOCI with 'Crop on Import' does not correctly control the height of the region. All other parameters seem to work whether passed as variables or written into the command.  The 2 lines below have the same behavior - the region opens with either the full original height of the file, or some multiple of the specified height.  
>
> swidth=256;sheight=128;
> sx=128;sy=128;
> lowwer=1; tilll=99;
>
> run("Bio-Formats Importer", "open=[] autoscale color_mode=Default crop specify_range split_channels view=Hyperstack stack_order=XYCZT z_begin=lowwer z_end=tilll z_step =1 t_begin=lowwer t_end=tilll t_step=1 x_coordinate_1=sx y_coordinate_1=sy width_1=swidth heigth_1=sheight");
>
>
> run("Bio-Formats Importer", "open=[] autoscale color_mode=Default crop specify_range split_channels view=Hyperstack stack_order=XYCZT z_begin=1 z_end=99 z_step =1 t_begin=lowwer t_end=tilll t_step=1 x_coordinate_1=sx y_coordinate_1=sy width_1=256 heigth_1=128");

It looks like in both cases, you're specifying "heigth_1=128", when it
should be "height_1=128".  Does changing the spelling there solve the
problem?

Regards,
-Melissa

On Fri, Nov 16, 2012 at 01:23:44PM -0800, Glen H MacDonald wrote:

> Hello,
>
> Using LOCI with 'Crop on Import' does not correctly control the height of the region. All other parameters seem to work whether passed as variables or written into the command.  The 2 lines below have the same behavior - the region opens with either the full original height of the file, or some multiple of the specified height.  
>
> swidth=256;sheight=128;
> sx=128;sy=128;
> lowwer=1; tilll=99;
>
> run("Bio-Formats Importer", "open=[] autoscale color_mode=Default crop specify_range split_channels view=Hyperstack stack_order=XYCZT z_begin=lowwer z_end=tilll z_step =1 t_begin=lowwer t_end=tilll t_step=1 x_coordinate_1=sx y_coordinate_1=sy width_1=swidth heigth_1=sheight");
>
>
> run("Bio-Formats Importer", "open=[] autoscale color_mode=Default crop specify_range split_channels view=Hyperstack stack_order=XYCZT z_begin=1 z_end=99 z_step =1 t_begin=lowwer t_end=tilll t_step=1 x_coordinate_1=sx y_coordinate_1=sy width_1=256 heigth_1=128");
>
> Am I doing something wrong or is there a bug in the plugin?
>
> Glen MacDonald
> Core for Communication Research
> Virginia Merrill Bloedel Hearing Research Center
> Box 357923
> University of Washington
> Seattle, WA 98195-7923
> [phone]
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html

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ImageJ mailing list: http://imagej.nih.gov/ij/list.html