Mercurial > repos > gregor.m > spyboat

annotate SpyBOAT.xml @ 3:4d7f30a7e2f6 draft

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"planemo upload commit d070f1ba04a5141a65487f45b29c22767639e44b"
author gregor.m
date Tue, 24 Nov 2020 13:06:26 +0000
parents c59d1373230e
children a4c6fcf2c456
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1 <tool id="SpyBOAT" name="SpyBOAT" version="0.1.0">
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2 <requirements>
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3 <requirement type="package" version="0.1.0">spyboat</requirement>
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4 </requirements>
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5 <version_command>python $__tool_directory__/spyboat_cli.py --version</version_command>
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6 <command detect_errors="exit_code"><![CDATA[
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7 python $__tool_directory__/spyboat_cli.py
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8 --input_path '$movie'
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9 #if $gauss_sigma:
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10 --gauss_sigma $gauss_sigma
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11 #end if
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12 #if $rescale_factor:
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13 --rescale $rescale_factor
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14 #end if
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15
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16 #if $masking.selection_mode == "create_static_mask":
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17 --masking static
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18 --mask_frame $masking.mask_frame
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19 --mask_thresh $masking.mask_thresh
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20 #else if $masking.selection_mode == "create_dynamic_mask":
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21 --masking dynamic
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22 --mask_thresh $masking.mask_thresh
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23 #end if
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24
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25 --dt $dt
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26 --Tmin $tmin
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27 --Tmax $tmax
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28 --nT $nt
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29 #if $tcutoff
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30 --Tcutoff $tcutoff
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31 #end if
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32 #if $win_size:
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33 --win_size $win_size
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34 #end if
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35
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36 --phase_out $phase_out
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37 --period_out $period_out
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38 --power_out $power_out
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39 --amplitude_out $amplitude_out
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40 #if $preprocessed_out:
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41 --preprocessed_out $preprocessed_out
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42 #end if
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43
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44 --html_fname $html_out
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45 --report_img_path '$html_out.extra_files_path'
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46
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47 --ncpu "\${GALAXY_SLOTS:-8}"
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48 > $log
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49
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50 ]]></command>
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51 <inputs>
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52 <param name="movie" type="data" format="tiff" label="Movie to process"
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53 help="Select a movie to Wavelet process"/>
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54
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55 <!--
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56 The following Wavelet parameters must have the same numerical type as defined in the
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57 argparse parser in spyboat_cli.py
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58 -->
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59
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60 <param name="gauss_sigma" type="float" label="Sigma"
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61 help="Width of the Gaussian smoothing kernel, leave blank if no pre-smoothing desired." optional="true">
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62 <validator type="in_range" min="0" max="9999999"/>
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63 </param>
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64
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65 <param name="rescale_factor" type="integer" value="" label="Rescale factor"
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66 help="Downsamples the input movie by this factor given in %, leave blank to disable downsampling"
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67 optional="true">
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68 <validator type="in_range" min="0" max="99"/>
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69 </param>
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70
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71 <conditional name="masking">
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72 <param label="Masking the output" name="selection_mode" type="select" help="Create a mask from the (blurred/rescaled) input to mask out regions without oscillations/signal in the output">
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73 <option selected="true" value="no_masking">No masking</option>
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74 <option value="create_static_mask">Create a static mask</option>
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75 <option value="create_dynamic_mask">Create a dynamic mask</option>
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76 </param>
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77 <when value="create_static_mask">
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78 <param name="mask_frame" type="integer" value="1" label="Create mask from frame"
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79 help="Creates a static mask from the chosen frame of the input movie.">
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80 <validator type="in_range" min="1" max="99999"/>
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81 </param>
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82 <param name="mask_thresh" type="float" value="0" label="Threshold"
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83 help="All pixels below this threshold will be masked in the output.">
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84 <validator type="in_range" min="0" max="999999"/>
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85 </param>
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86 </when>
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87 <when value="create_dynamic_mask">
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88 <param name="mask_thresh" type="float" value="0" label="Threshold"
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89 help="For each frame of the input, all pixels below this threshold will be masked in the output.">
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90 <validator type="in_range" min="0" max="999999"/>
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91 </param>
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92 </when>
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93 </conditional>
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94
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95 <param name="dt" type="float" value="1" label="Sampling interval" help="Time span between two frames">
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96 <validator type="in_range" min="0" max="9999999"/>
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97 </param>
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98 <param name="tmin" type="float" value="2" label="Smallest period" help="Minimal period to scan for">
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99 <validator type="in_range" min="0" max="9999999"/>
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100 </param>
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101
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102 <param name="tmax" type="float" value="30" label="Largest period"
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103 help="Maximal period to scan for">
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104 <validator type="in_range" min="0" max="9999999"/>
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105 </param>
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106
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107 <param name="nt" type="integer" value="150" label="Number of periods to scan for"
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108 help="Determines period resolution of the Wavelet power spectra">
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109 <validator type="in_range" min="0" max="9999999"/>
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110 </param>
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111
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112 <param name="tcutoff" type="float" value="40" label="Tcutoff"
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113 help="Cut-off-period for sinc filter detrending, a blank field disables detrending" optional="true">
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114 <validator type="in_range" min="0" max="9999999"/>
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115 </param>
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116
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117 <param name="win_size" type="float" value="" label="Sliding window size"
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118 help="Window size for amplitude envelope estimation, leave blank to disable normalization "
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119 optional="true">
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120 <validator type="in_range" min="0" max="9999999"/>
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121 </param>
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122
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123 <conditional name="save_preprocessed">
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124 <param label="Save preprocessed input" name="selection" type="select" help="Save the blurred/rescaled input to history? ">
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125 <option selected="true" value="No">No</option>
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126 <option value="Yes">Yes</option>
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127 </param>
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128 </conditional>
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129 </inputs>
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130
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131 <outputs>
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132 <data name="phase_out" format="tiff" label="phase_${movie.name}"/>
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133 <data name="period_out" format="tiff" label="period_${movie.name}"/>
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134 <data name="power_out" format="tiff" label="power_${movie.name}"/>
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135 <data name="amplitude_out" format="tiff" label="amplitude_${movie.name}"/>
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136 <data name="preprocessed_out" format="tiff" label="preproc_${movie.name}">
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137 <filter>save_preprocessed['selection'] == 'Yes'</filter>
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138 </data>
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139
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140 <data name="log" format="txt" label="log_${movie.name}.txt"/>
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141 <data format="html" name="html_out" label="Report_${movie.name}"/>
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142
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143 </outputs>
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144
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145 <tests>
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146 <test>
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147 <param name="movie" value="test_movie.tif" ftype="tiff"/>
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148 <output name="phase_out" file="phase_out.tif" ftype="tiff" compare="sim_size"/>
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149 <output name="period_out" file="period_out.tif" ftype="tiff" compare="sim_size"/>
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150 <output name="power_out" file="power_out.tif" ftype="tiff" compare="sim_size"/>
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151 <output name="amplitude_out" file="amplitude_out.tif" ftype="tiff" compare="sim_size"/>
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152 </test>
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153 </tests>
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154 <help><![CDATA[
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155 **What it does**
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156
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157 Wavelet transforms a 3d-image stack (time,Y,X) pixel by pixel along the time axis and extracts/evaluates the wavelet ridge. Removal of low-frequency trends is provided via sinc filtering.
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158 There are four output movies generated (phase, period, amplitude and power). They have exactly the same dimensions (time,Y,X) as the (rescaled) input.
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159
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160 Pre-smoothing of the data with Gaussian kernels is supported and often recommendable.
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161
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162 To limit the number of Wavelet transformations (computing time), downscaling of the input movie resolution is recommended.
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163 Trimming away parts of the movie with no relevant data (e.g. outer dark edges) also speeds up the processing.
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164
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165 If multiple channels are present in your data, extract the channel of interest beforehand (e.g. with Fiji).
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166
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167 **Author**: Gregor Mönke (gregor.moenke@embl.de).
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168
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169 **Wrapper by**: Jelle Scholtalbers (jelle.scholtalbers@embl.de).
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170
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171 **Know what you are doing**
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172
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173 .. class:: warningmark
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174
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175 You will want to have understood the basics of time-frequency analysis with Wavelets, find more information about the analysis strategy employed at https://github.com/tensionhead/pyBOAT
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176
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177 **Parameter List**
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178
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179 - Sigma:
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180
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181 The Kernel bandwidth (in pixels) for the Gaussian kernels to use for pre-smoothing the input data. The default value of zero means that no pre-smoothing is done. Set this number to a desired kernel width to turn on pre-smoothing.
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182
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183 - Rescale factor:
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184
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185 Given in %, downsamples the spatial resolution of the input movie. This speeds
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186 up the whole analysis by a lot.
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187
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188 - Masking:
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189 SpyBOAT offers 'static' and 'dynamic' masking. 'static' means that a single mask is created by thresholding from a user selected frame. 'dynamic' creates a mask for each frame by thresholding, works better for moving/expanding/shrinking oscillatory fields.
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190 - Sampling interval:
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191
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192 Time passed between consecutive measurements, e.g 'an image every 10 minutes'.
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193
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194 - Smallest Period:
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195
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196 The minimal period to scan for, this is the higher (in frequency) end of the spectrum. A warning will be given during processing if the chosen value deceeds the Nyquist limit (2 times the sampling interval).
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197
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198 - Largest period:
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199
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200 The maximal period to scan for, this is the lower (in frequency) end of the spectrum. The inbuild Sinc filter will remove any periods larger than this form the data. Due to the 'roll off' of the filter, this value should be chosen generously. A warning will be given during processing if the chosen value exceeds the length of the time series.
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201
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202 - Number of periods to scan for:
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203
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204 This is the the number of convolutions computed per pixel.
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205
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206 Spectral resolution = ( biggest period - smallest period ) / number of periods
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207
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208 - Tcutoff:
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209
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210 The cut-off period for the sinc filter, periods larger than this one will
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211 be removed from the signal before the transform. If no value is given,
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212 no detrending is performed. At least a gracious cut-off of around ~3 times
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213 the largest period to be expected is recommended.
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214
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215 - Sliding window size
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216
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217 Length (in time units, e.g. hours) of the sliding window to estimate
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218 an amplitude envelope. The signal then gets normalized by this envelope,
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219 meaning that all amplitudes will be around ~1 after the transform. The
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220 advantage is that signal with strong amplitude trends will have more
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221 meaningful Wavelet powers after normalization.
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222
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223 ]]></help>
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224 </tool>