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| {"config":{"lang":["en"],"separator":"[\\s\\-]+","pipeline":["stopWordFilter"]},"docs":[{"location":"","title":"Overview","text":"<p>Read IMOD model files as pandas dataframes in Python.</p>"},{"location":"#usage","title":"Usage","text":"<pre><code>import imodmodel\n\ndf = imodmodel.read('my_model_file.mod')\n</code></pre> <pre><code>In [3]: df.head()\nOut[3]: \n object_id contour_id x y z\n0 0 0 64.333336 64.666664 80.0\n1 0 0 47.000000 77.333336 80.0\n2 0 0 51.333332 45.666668 80.0\n3 0 0 87.333336 49.666668 80.0\n4 0 0 76.000000 82.000000 80.0\n</code></pre> <p>Annotations made in the slicer window are stored in the IMOD binary file with both centerpoints and angles.</p> <p>These annotations can be read in by setting <code>annotation='slan'</code> when calling <code>imodmodel.read()</code></p> <pre><code>import imodmodel\n\ndf = imodmodel.read('file_with_slicer_angles.mod', annotation='slan')\n</code></pre> <pre><code>In [3]: df.head()\nOut[3]:\n object_id slan_id time x_rot y_rot z_rot center_x center_y center_z label\n0 0 0 1 13.100000 0.0 -30.200001 235.519577 682.744141 302.0\n0 0 1 1 -41.400002 0.0 -47.700001 221.942444 661.193237 327.0\n0 0 2 1 -41.400002 0.0 -41.799999 232.790726 671.332031 327.0\n0 0 3 1 -35.500000 0.0 -36.000000 240.129181 679.927795 324.0\n</code></pre> <p>That's it!</p>"},{"location":"#installation","title":"Installation","text":"<p><code>imodmodel</code> can be installed from the Python Package Index (PyPI)</p> <pre><code>pip install imodmodel\n</code></pre> <p>We recommend installing into a clean virtual environment.</p>"}]} | ||
| {"config":{"lang":["en"],"separator":"[\\s\\-]+","pipeline":["stopWordFilter"]},"docs":[{"location":"","title":"Overview","text":"<p>Read IMOD model files as pandas dataframes in Python.</p>"},{"location":"#usage","title":"Usage","text":"<pre><code>import imodmodel\n\ndf = imodmodel.read('my_model_file.mod')\n</code></pre> <pre><code>In [3]: df.head()\nOut[3]: \n object_id contour_id x y z\n0 0 0 64.333336 64.666664 80.0\n1 0 0 47.000000 77.333336 80.0\n2 0 0 51.333332 45.666668 80.0\n3 0 0 87.333336 49.666668 80.0\n4 0 0 76.000000 82.000000 80.0\n</code></pre> <p>Slicer angles saved in the slicer window are stored in the IMOD binary file with both centerpoints and angles.</p> <p>These annotations can be read in by setting <code>annotation='slicer_angle'</code> when calling <code>imodmodel.read()</code></p> <pre><code>import imodmodel\n\ndf = imodmodel.read('file_with_slicer_angles.mod', annotation='slicer_angles')\n</code></pre> <pre><code>In [3]: df.head()\nOut[3]:\n object_id slicer_angle_id time x_rot y_rot z_rot center_x center_y center_z label\n0 0 0 1 13.100000 0.0 -30.200001 235.519577 682.744141 302.0\n0 0 1 1 -41.400002 0.0 -47.700001 221.942444 661.193237 327.0\n0 0 2 1 -41.400002 0.0 -41.799999 232.790726 671.332031 327.0\n0 0 3 1 -35.500000 0.0 -36.000000 240.129181 679.927795 324.0\n</code></pre>"},{"location":"#imodmodel","title":"ImodModel","text":"<p>The resulting dataframe from <code>imodmodel.read()</code> contains only information about the contours or slicer angles. The full set of information from the imod model file can be parsed using <code>ImodModel</code></p> <pre><code>from imodmodel import ImodModel\n\nmy_model = ImodModel.from_file(\"my_model_file.mod\")\n</code></pre> <pre><code>in [3]: my_model.model_field_set\nout[3]: \n{'id', 'extra', 'objects', 'slicer_angles', 'header'}\n</code></pre>"},{"location":"#my_modelid","title":"my_model.id","text":"<p><code>my_model.id</code> contains the IMOD file id and the version id</p> <pre><code>in [4]: my_model.id\nout[4]: \nID(IMOD_file_id='IMOD', version_id='V1.2')\n</code></pre>"},{"location":"#my_modelheader","title":"my_model.header","text":"<p><code>my_model.header</code> is contains the model structure data mainly used by IMOD.</p> <pre><code>in [5]: my_model.header\nout[5]:\nModelHeader(name='IMOD-NewModel', xmax=956, ymax=924, zmax=300, objsize=3, flags=62976, drawmode=1,\nmousemode=1, blacklevel=145, whitelevel=173, xoffset=0.0, yoffset=0.0, zoffset=0.0, xscale=1.0, yscale=10,\nzscale=1.0, object=2, contour=-1, point=-1, res=3, thresh=128, pixelsize=1.9733333587646484, units=-9,\ncsum=704518946, alpha=0.0, beta=0.0, gamma=0.0)\n</code></pre>"},{"location":"#my_modelobjects","title":"my_model.objects","text":"<p><code>my_model.objects</code> is a <code>list</code> IMOD objects.</p> <pre><code>in [6]: my_model.objects[0].header\nout[6]: \nObjectHeader(name='', extra_data=[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], contsize=0,\nflags=402653184, axis=0, drawmode=1, red=0.0, green=1.0, blue=0.0, pdrawsize=0, symbol=1, symsize=3,\nlinewidth2=1, linewidth=1, linesty=0, symflags=0, sympad=0, trans=0, meshsize=0, surfsize=0)\n</code></pre> <p>This is where object values like contours, meshes, and IMAT information are located.</p> <pre><code>in [7]: my_model.objects[1].meshes[0].indices\nout[7]: \narray([[38, 40, 52],\n [38, 52, 50],\n [50, 52, 64],\n [50, 64, 60],\n ...,\n [ 4, 10, 26],\n [ 4, 26, 20],\n [20, 26, 38],\n [20, 38, 32]])\n</code></pre> <pre><code>in [8]: my_model.objects[1].imat\nout[8]: \nIMAT(ambient=102, diffuse=255, specular=127, shininess=4, fillred=0, fillgreen=0, fillblue=0,\nquality=0, mat2=0, valblack=0, valwhite=255, matflags2=0, mat3b3=0)\n</code></pre> <pre><code>in [9]: my_model.objects[1].contours[0].points\nout[9]:\narray([[367.00006104, 661.83343506, 134. ],\n [415.66674805, 667.83343506, 134. ],\n [474.33340454, 662.50012207, 134. ]])\n</code></pre>"},{"location":"#my_modelslicer_angles","title":"my_model.slicer_angles","text":"<p><code>my_model.slicer_angles</code> is a <code>list</code> of slicer angles.</p> <pre><code>in [10]: my_model.slicer_angles[0]\nout[10]:\nSLAN(time=1, angles=(0.0, 0.0, 0.0), center=(533.5, 717.0, 126.0), label='\\x00')\n</code></pre> <p>That's it!</p>"},{"location":"#installation","title":"Installation","text":"<p><code>imodmodel</code> can be installed from the Python Package Index (PyPI)</p> <pre><code>pip install imodmodel\n</code></pre> <p>We recommend installing into a clean virtual environment.</p>"}]} |
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