Mercurial > repos > iuc > imagej2_make_binary

annotate imagej2_make_binary.xml @ 0:66d9e595dff2 draft

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author iuc
date Tue, 04 Aug 2015 13:20:29 -0400
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1 <?xml version='1.0' encoding='UTF-8'?>
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2 <tool id="imagej2_make_binary" name="Convert to binary" version="1.0.0">
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3 <description>(black and white) with ImageJ2</description>
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4 <macros>
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5 <import>imagej2_macros.xml</import>
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6 </macros>
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7 <expand macro="fiji_20141125_requirements" />
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8 <command>
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9 <![CDATA[
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10 python $__tool_directory__/imagej2_make_binary.py
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11 --input "$input"
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12 --input_datatype $input.ext
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13 @make_binary_args@
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14 @max_heap_size_args@
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15 --jython_script $__tool_directory__/jython_script.py
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16 --output_datatype $output_datatype
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17 --output "$output"
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18 ]]>
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19 </command>
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20 <inputs>
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21 <param format="bmp,eps,gif,jpg,pcx,pgm,png,psd,tiff" name="input" type="data" label="Select image"/>
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22 <expand macro="make_binary_params" />
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23 <param name="output_datatype" type="select" label="Save as format">
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24 <expand macro="image_datatypes" />
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25 </param>
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26 <expand macro="max_heap_size_type_conditional" />
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27 </inputs>
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28 <outputs>
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29 <data name="output" format_source="input" label="${tool.name} on ${on_string}">
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30 <actions>
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31 <action type="format">
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32 <option type="from_param" name="output_datatype" />
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33 </action>
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34 </actions>
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35 </data>
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36 </outputs>
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37 <tests>
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38 <test>
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39 <param name="input" value="clown.jpg" />
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40 <param name="input_datatype" value="jpg" />
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41 <param name="iterations" value="1" />
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42 <param name="count" value="1" />
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43 <param name="black_background" value="no" />
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44 <param name="pad_edges_when_eroding" value="no" />
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45 <param name="output_datatype" value="jpg" />
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46 <output name="output" file="clown_binary.jpg" compare="sim_size" />
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47 </test>
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48 </tests>
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49 <help>
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50 **What it does**
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51
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52 <![CDATA[
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53 Converts an image into a binary (black and white) image by analyzing the histogram of
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54 the entire image and setting an automatic threshold level to create the binary image.
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55
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56 - **Iterations** - Specifies the number of times erosion, dilation, opening, and closing are performed.
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57 - **Count** - Specifies the number of adjacent background pixels necessary before a pixel is removed from the edge of an object during erosion and the number of adjacent foreground pixels necessary before a pixel is added to the edge of an object during dilation.
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58 - **Black background** - If **Yes**, binary images will be created without using an inverted LUT and an assumption that the input image contains white objects on a black background will be made.
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59 - **Pad edges when eroding** - If **Yes**, eroding does not erode from the edges of the image.
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60
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61 ]]>
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62
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63 </help>
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64 <expand macro="fiji_headless_citations" />
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65 </tool>