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51  <h1>Source code for sas.dataloader.readers.tiff_reader</h1><div class="highlight"><pre>
52<span class="c">#####################################################################</span>
53<span class="c">#This software was developed by the University of Tennessee as part of the</span>
54<span class="c">#Distributed Data Analysis of Neutron Scattering Experiments (DANSE)</span>
55<span class="c">#project funded by the US National Science Foundation. </span>
56<span class="c">#See the license text in license.txt</span>
57<span class="c">#copyright 2008, University of Tennessee</span>
58<span class="c">######################################################################</span>
59<span class="sd">&quot;&quot;&quot;</span>
60<span class="sd">    Image reader. Untested.</span>
61<span class="sd">&quot;&quot;&quot;</span>
62<span class="c">#TODO: load and check data and orientation of the image (needs rendering)</span>
63<span class="kn">import</span> <span class="nn">math</span>
64<span class="kn">import</span> <span class="nn">logging</span>
65<span class="kn">import</span> <span class="nn">os</span>
66<span class="kn">import</span> <span class="nn">numpy</span>
67<span class="kn">from</span> <span class="nn">sas.dataloader.data_info</span> <span class="kn">import</span> <span class="n">Data2D</span>
68<span class="kn">from</span> <span class="nn">sas.dataloader.manipulations</span> <span class="kn">import</span> <span class="n">reader2D_converter</span>
69   
70<div class="viewcode-block" id="Reader"><a class="viewcode-back" href="../../../../dev/api/sas.dataloader.readers.html#sas.dataloader.readers.tiff_reader.Reader">[docs]</a><span class="k">class</span> <span class="nc">Reader</span><span class="p">:</span>
71    <span class="sd">&quot;&quot;&quot;</span>
72<span class="sd">    Example data manipulation</span>
73<span class="sd">    &quot;&quot;&quot;</span>
74    <span class="c">## File type</span>
75    <span class="n">type_name</span> <span class="o">=</span> <span class="s">&quot;TIF&quot;</span>
76    <span class="c">## Wildcards</span>
77    <span class="nb">type</span> <span class="o">=</span> <span class="p">[</span><span class="s">&quot;TIF files (*.tif)|*.tif&quot;</span><span class="p">,</span>
78            <span class="s">&quot;TIFF files (*.tiff)|*.tiff&quot;</span><span class="p">,</span>
79            <span class="p">]</span>
80    <span class="c">## Extension</span>
81    <span class="n">ext</span> <span class="o">=</span> <span class="p">[</span><span class="s">&#39;.tif&#39;</span><span class="p">,</span> <span class="s">&#39;.tiff&#39;</span><span class="p">]</span>
82       
83<div class="viewcode-block" id="Reader.read"><a class="viewcode-back" href="../../../../dev/api/sas.dataloader.readers.html#sas.dataloader.readers.tiff_reader.Reader.read">[docs]</a>    <span class="k">def</span> <span class="nf">read</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">filename</span><span class="o">=</span><span class="bp">None</span><span class="p">):</span>
84        <span class="sd">&quot;&quot;&quot;</span>
85<span class="sd">        Open and read the data in a file</span>
86<span class="sd">        </span>
87<span class="sd">        :param file: path of the file</span>
88<span class="sd">        &quot;&quot;&quot;</span>
89        <span class="k">try</span><span class="p">:</span>
90            <span class="kn">import</span> <span class="nn">Image</span>
91            <span class="kn">import</span> <span class="nn">TiffImagePlugin</span>
92            <span class="n">Image</span><span class="o">.</span><span class="n">_initialized</span><span class="o">=</span><span class="mi">2</span>
93        <span class="k">except</span><span class="p">:</span>
94            <span class="n">msg</span> <span class="o">=</span> <span class="s">&quot;tiff_reader: could not load file. Missing Image module.&quot;</span>
95            <span class="k">raise</span> <span class="ne">RuntimeError</span><span class="p">,</span> <span class="n">msg</span>
96       
97        <span class="c"># Instantiate data object</span>
98        <span class="n">output</span> <span class="o">=</span> <span class="n">Data2D</span><span class="p">()</span>
99        <span class="n">output</span><span class="o">.</span><span class="n">filename</span> <span class="o">=</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">basename</span><span class="p">(</span><span class="n">filename</span><span class="p">)</span>
100           
101        <span class="c"># Read in the image</span>
102        <span class="k">try</span><span class="p">:</span>
103            <span class="n">im</span> <span class="o">=</span> <span class="n">Image</span><span class="o">.</span><span class="n">open</span><span class="p">(</span><span class="n">filename</span><span class="p">)</span>
104        <span class="k">except</span><span class="p">:</span>
105            <span class="k">raise</span>  <span class="ne">RuntimeError</span><span class="p">,</span> <span class="s">&quot;cannot open </span><span class="si">%s</span><span class="s">&quot;</span><span class="o">%</span><span class="p">(</span><span class="n">filename</span><span class="p">)</span>
106        <span class="n">data</span> <span class="o">=</span> <span class="n">im</span><span class="o">.</span><span class="n">getdata</span><span class="p">()</span>
107
108        <span class="c"># Initiazed the output data object</span>
109        <span class="n">output</span><span class="o">.</span><span class="n">data</span> <span class="o">=</span> <span class="n">numpy</span><span class="o">.</span><span class="n">zeros</span><span class="p">([</span><span class="n">im</span><span class="o">.</span><span class="n">size</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="n">im</span><span class="o">.</span><span class="n">size</span><span class="p">[</span><span class="mi">1</span><span class="p">]])</span>
110        <span class="n">output</span><span class="o">.</span><span class="n">err_data</span> <span class="o">=</span> <span class="n">numpy</span><span class="o">.</span><span class="n">zeros</span><span class="p">([</span><span class="n">im</span><span class="o">.</span><span class="n">size</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="n">im</span><span class="o">.</span><span class="n">size</span><span class="p">[</span><span class="mi">1</span><span class="p">]])</span>
111        <span class="n">output</span><span class="o">.</span><span class="n">mask</span> <span class="o">=</span> <span class="n">numpy</span><span class="o">.</span><span class="n">ones</span><span class="p">([</span><span class="n">im</span><span class="o">.</span><span class="n">size</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="n">im</span><span class="o">.</span><span class="n">size</span><span class="p">[</span><span class="mi">1</span><span class="p">]],</span> <span class="n">dtype</span><span class="o">=</span><span class="nb">bool</span><span class="p">)</span>
112       
113        <span class="c"># Initialize</span>
114        <span class="n">x_vals</span> <span class="o">=</span> <span class="p">[]</span>
115        <span class="n">y_vals</span> <span class="o">=</span> <span class="p">[]</span>
116
117        <span class="c"># x and y vectors</span>
118        <span class="k">for</span> <span class="n">i_x</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="n">im</span><span class="o">.</span><span class="n">size</span><span class="p">[</span><span class="mi">0</span><span class="p">]):</span>
119            <span class="n">x_vals</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">i_x</span><span class="p">)</span>
120           
121        <span class="n">itot</span> <span class="o">=</span> <span class="mi">0</span>
122        <span class="k">for</span> <span class="n">i_y</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="n">im</span><span class="o">.</span><span class="n">size</span><span class="p">[</span><span class="mi">1</span><span class="p">]):</span>
123            <span class="n">y_vals</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">i_y</span><span class="p">)</span>
124
125        <span class="k">for</span> <span class="n">val</span> <span class="ow">in</span> <span class="n">data</span><span class="p">:</span>
126            <span class="k">try</span><span class="p">:</span>
127                <span class="n">value</span> <span class="o">=</span> <span class="nb">float</span><span class="p">(</span><span class="n">val</span><span class="p">)</span>
128            <span class="k">except</span><span class="p">:</span>
129                <span class="n">logging</span><span class="o">.</span><span class="n">error</span><span class="p">(</span><span class="s">&quot;tiff_reader: had to skip a non-float point&quot;</span><span class="p">)</span>
130                <span class="k">continue</span>
131           
132            <span class="c"># Get bin number</span>
133            <span class="k">if</span> <span class="n">math</span><span class="o">.</span><span class="n">fmod</span><span class="p">(</span><span class="n">itot</span><span class="p">,</span> <span class="n">im</span><span class="o">.</span><span class="n">size</span><span class="p">[</span><span class="mi">0</span><span class="p">])</span> <span class="o">==</span> <span class="mi">0</span><span class="p">:</span>
134                <span class="n">i_x</span> <span class="o">=</span> <span class="mi">0</span>
135                <span class="n">i_y</span> <span class="o">+=</span> <span class="mi">1</span>
136            <span class="k">else</span><span class="p">:</span>
137                <span class="n">i_x</span> <span class="o">+=</span> <span class="mi">1</span>
138               
139            <span class="n">output</span><span class="o">.</span><span class="n">data</span><span class="p">[</span><span class="n">im</span><span class="o">.</span><span class="n">size</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="o">-</span> <span class="mi">1</span> <span class="o">-</span> <span class="n">i_y</span><span class="p">][</span><span class="n">i_x</span><span class="p">]</span> <span class="o">=</span> <span class="n">value</span>
140           
141            <span class="n">itot</span> <span class="o">+=</span> <span class="mi">1</span>
142               
143        <span class="n">output</span><span class="o">.</span><span class="n">xbins</span> <span class="o">=</span> <span class="n">im</span><span class="o">.</span><span class="n">size</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span>
144        <span class="n">output</span><span class="o">.</span><span class="n">ybins</span> <span class="o">=</span> <span class="n">im</span><span class="o">.</span><span class="n">size</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span>
145        <span class="n">output</span><span class="o">.</span><span class="n">x_bins</span> <span class="o">=</span> <span class="n">x_vals</span>
146        <span class="n">output</span><span class="o">.</span><span class="n">y_bins</span> <span class="o">=</span> <span class="n">y_vals</span>
147        <span class="n">output</span><span class="o">.</span><span class="n">qx_data</span> <span class="o">=</span> <span class="n">numpy</span><span class="o">.</span><span class="n">array</span><span class="p">(</span><span class="n">x_vals</span><span class="p">)</span>
148        <span class="n">output</span><span class="o">.</span><span class="n">qy_data</span> <span class="o">=</span> <span class="n">numpy</span><span class="o">.</span><span class="n">array</span><span class="p">(</span><span class="n">y_vals</span><span class="p">)</span>
149        <span class="n">output</span><span class="o">.</span><span class="n">xmin</span> <span class="o">=</span> <span class="mi">0</span>
150        <span class="n">output</span><span class="o">.</span><span class="n">xmax</span> <span class="o">=</span> <span class="n">im</span><span class="o">.</span><span class="n">size</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="o">-</span> <span class="mi">1</span>
151        <span class="n">output</span><span class="o">.</span><span class="n">ymin</span> <span class="o">=</span> <span class="mi">0</span>
152        <span class="n">output</span><span class="o">.</span><span class="n">ymax</span> <span class="o">=</span> <span class="n">im</span><span class="o">.</span><span class="n">size</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="o">-</span> <span class="mi">1</span>
153       
154        <span class="c"># Store loading process information</span>
155        <span class="n">output</span><span class="o">.</span><span class="n">meta_data</span><span class="p">[</span><span class="s">&#39;loader&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">type_name</span>
156        <span class="n">output</span> <span class="o">=</span> <span class="n">reader2D_converter</span><span class="p">(</span><span class="n">output</span><span class="p">)</span>
157        <span class="k">return</span> <span class="n">output</span></div></div>
158</pre></div>
159
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