Add docs for vertical slice reconstruction

algotom · May 7, 2024 · f314099 · f314099
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diff --git a/.doctrees/environment.pickle b/.doctrees/environment.pickle
diff --git a/.doctrees/toc/api.doctree b/.doctrees/toc/api.doctree
diff --git a/.doctrees/toc/api/algotom.io.converter.doctree b/.doctrees/toc/api/algotom.io.converter.doctree
diff --git a/.doctrees/toc/api/algotom.io.loadersaver.doctree b/.doctrees/toc/api/algotom.io.loadersaver.doctree
diff --git a/.doctrees/toc/api/algotom.prep.calculation.doctree b/.doctrees/toc/api/algotom.prep.calculation.doctree
diff --git a/.doctrees/toc/api/algotom.rec.reconstruction.doctree b/.doctrees/toc/api/algotom.rec.reconstruction.doctree
diff --git a/.doctrees/toc/api/algotom.rec.vertrec.doctree b/.doctrees/toc/api/algotom.rec.vertrec.doctree
diff --git a/.doctrees/toc/section2.doctree b/.doctrees/toc/section2.doctree
diff --git a/.doctrees/toc/section3.doctree b/.doctrees/toc/section3.doctree
diff --git a/.doctrees/toc/section4/section4_5.doctree b/.doctrees/toc/section4/section4_5.doctree
diff --git a/.doctrees/toc/section5.doctree b/.doctrees/toc/section5.doctree
diff --git a/.doctrees/toc/section5/section5_2.doctree b/.doctrees/toc/section5/section5_2.doctree
diff --git a/.doctrees/toc/section6.doctree b/.doctrees/toc/section6.doctree
diff --git a/.idea/workspace.xml b/.idea/workspace.xml
diff --git a/_images/fig_2_8.png b/_images/fig_2_8.png
diff --git a/_images/fig_2_9.png b/_images/fig_2_9.png
diff --git a/_images/fig_5_2_1.png b/_images/fig_5_2_1.png
diff --git a/_images/fig_5_2_10.png b/_images/fig_5_2_10.png
diff --git a/_images/fig_5_2_11.png b/_images/fig_5_2_11.png
diff --git a/_images/fig_5_2_12.png b/_images/fig_5_2_12.png
diff --git a/_images/fig_5_2_2.png b/_images/fig_5_2_2.png
diff --git a/_images/fig_5_2_3.png b/_images/fig_5_2_3.png
diff --git a/_images/fig_5_2_4.png b/_images/fig_5_2_4.png
diff --git a/_images/fig_5_2_5.png b/_images/fig_5_2_5.png
diff --git a/_images/fig_5_2_6.png b/_images/fig_5_2_6.png
diff --git a/_images/fig_5_2_7.png b/_images/fig_5_2_7.png
diff --git a/_images/fig_5_2_8.png b/_images/fig_5_2_8.png
diff --git a/_images/fig_5_2_9.png b/_images/fig_5_2_9.png
diff --git a/_modules/algotom/io/converter.html b/_modules/algotom/io/converter.html
diff --git a/_modules/algotom/io/loadersaver.html b/_modules/algotom/io/loadersaver.html
@@ -183,7 +183,7 @@ <h1>Source code for algotom.io.loadersaver</h1><div class="highlight"><pre>
 <span class="kn">import</span> <span class="nn">glob</span>
 <span class="kn">import</span> <span class="nn">warnings</span>
 <span class="kn">import</span> <span class="nn">multiprocessing</span> <span class="k">as</span> <span class="nn">mp</span>
-<span class="kn">from</span> <span class="nn">joblib</span> <span class="kn">import</span> <span class="n">Parallel</span><span class="p">,</span> <span class="n">delayed</span><span class="p">,</span> <span class="n">parallel_backend</span>
+<span class="kn">from</span> <span class="nn">joblib</span> <span class="kn">import</span> <span class="n">Parallel</span><span class="p">,</span> <span class="n">delayed</span>
 <span class="kn">from</span> <span class="nn">collections</span> <span class="kn">import</span> <span class="n">OrderedDict</span><span class="p">,</span> <span class="n">deque</span>
 <span class="kn">import</span> <span class="nn">h5py</span>
 <span class="kn">import</span> <span class="nn">numpy</span> <span class="k">as</span> <span class="nn">np</span>
@@ -1358,6 +1358,8 @@ <h1>Source code for algotom.io.loadersaver</h1><div class="highlight"><pre>
 <span class="sd">        List of output paths or a folder path</span>
 <span class="sd">    image_stack : array_like</span>
 <span class="sd">        3D array.</span>
+<span class="sd">    axis : int</span>
+<span class="sd">        Axis to slice data.</span>
 <span class="sd">    overwrite : bool</span>
 <span class="sd">        Overwrite an existing file if True.</span>
 <span class="sd">    ncore : int or None</span>

diff --git a/_modules/algotom/post/postprocessing.html b/_modules/algotom/post/postprocessing.html
@@ -805,7 +805,7 @@ <h1>Source code for algotom.post.postprocessing</h1><div class="highlight"><pre>
                 <span class="n">data_tmp</span> <span class="o">=</span> <span class="n">ofile</span><span class="o">.</span><span class="n">create_dataset</span><span class="p">(</span><span class="n">out_key</span><span class="p">,</span>
                                                 <span class="p">(</span><span class="n">depth1</span><span class="p">,</span> <span class="n">height1</span><span class="p">,</span> <span class="n">width1</span><span class="p">),</span>
                                                 <span class="n">dtype</span><span class="o">=</span><span class="n">data_type</span><span class="p">,</span>
-                                                <span class="n">chunks</span> <span class="o">=</span> <span class="n">hdf_chunk</span><span class="p">)</span>
+                                                <span class="n">chunks</span><span class="o">=</span><span class="n">hdf_chunk</span><span class="p">)</span>
                 <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="n">np</span><span class="o">.</span><span class="n">arange</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span> <span class="n">depth1</span> <span class="o">-</span> <span class="n">last_chunk</span><span class="p">,</span> <span class="n">chunk</span><span class="p">):</span>
                     <span class="k">if</span> <span class="n">show_progress</span><span class="p">:</span>
                         <span class="n">t1</span> <span class="o">=</span> <span class="n">timeit</span><span class="o">.</span><span class="n">default_timer</span><span class="p">()</span>

diff --git a/_modules/algotom/prep/calculation.html b/_modules/algotom/prep/calculation.html
diff --git a/_modules/algotom/rec/reconstruction.html b/_modules/algotom/rec/reconstruction.html
diff --git a/_modules/algotom/rec/vertrec.html b/_modules/algotom/rec/vertrec.html
diff --git a/_modules/index.html b/_modules/index.html
@@ -153,6 +153,7 @@ <h1>All modules for which code is available</h1>
 <li><a href="algotom/prep/phase.html">algotom.prep.phase</a></li>
 <li><a href="algotom/prep/removal.html">algotom.prep.removal</a></li>
 <li><a href="algotom/rec/reconstruction.html">algotom.rec.reconstruction</a></li>
+<li><a href="algotom/rec/vertrec.html">algotom.rec.vertrec</a></li>
 <li><a href="algotom/util/calibration.html">algotom.util.calibration</a></li>
 <li><a href="algotom/util/correlation.html">algotom.util.correlation</a></li>
 <li><a href="algotom/util/simulation.html">algotom.util.simulation</a></li>

diff --git a/_sources/toc/api.rst.txt b/_sources/toc/api.rst.txt
@@ -32,6 +32,7 @@ Reconstruction
     :maxdepth: 1
 
     api/algotom.rec.reconstruction
+    api/algotom.rec.vertrec
 
 Post-processing
 ---------------

diff --git a/_sources/toc/api/algotom.rec.vertrec.rst.txt b/_sources/toc/api/algotom.rec.vertrec.rst.txt
@@ -0,0 +1,24 @@
+:mod:`algotom.rec.vertrec`
+=================================
+
+.. _vertrec_module:
+
+.. automodule:: algotom.rec.vertrec
+    :members:
+    :show-inheritance:
+    :undoc-members:
+
+    .. rubric:: **Functions:**
+
+    .. autosummary::
+
+        vertical_back_projection_cpu
+        vertical_back_projection_cpu_chunk
+        vertical_back_projection_gpu
+        vertical_back_projection_gpu_chunk
+        vertical_reconstruction
+        vertical_reconstruction_multiple
+        vertical_reconstruction_different_angles
+        find_center_vertical_slice
+        find_center_visual_vertical_slices
+
diff --git a/_sources/toc/section2.rst.txt b/_sources/toc/section2.rst.txt
@@ -78,13 +78,28 @@ Some featuring methods in Algotom are as follows:
        :name: fig_2_7
        :align: center
 
+-   Direct vertical reconstruction for single slice, multiple slices, and multiple slices at
+    different orientations.
+
+    .. image:: section2/figs/fig_2_8.png
+       :width: 100%
+       :name: fig_2_8
+       :align: center
+
+    |
+
+    .. image:: section2/figs/fig_2_9.png
+       :width: 100%
+       :name: fig_2_9
+       :align: center
+
 Development principles
 ----------------------
 
--   While Algotom offers a comprehensive range of tools for tomographic data processing
-    covering raw-data reading, pre-processing, reconstruction, post-processing, and data
-    saving; its development primarily focuses on pre-processing techniques. This distinction
-    makes it a prominent feature among other tomographic software.
+-   While Algotom offers a complete set of tools for tomographic data processing covering
+    pre-processing, reconstruction, post-processing, data simulation, and calibration techniques;
+    its development strongly focuses on pre-processing techniques. This distinction makes it a
+    prominent feature among other tomographic software.
 
 -   To ensure that the software can work across platforms and is easy-to-install; dependencies
     are minimized, and only well-maintained `Python libraries <https://github.com/algotom/algotom/blob/master/requirements.txt>`__

diff --git a/_sources/toc/section3.rst.txt b/_sources/toc/section3.rst.txt
@@ -2,7 +2,7 @@ Installation
 ============
 
 Algotom is installable across operating systems (Windows, Linux, Mac) and
-works with Python >=3.7. It is a Python library not an app. Users have to
+works with Python >=3.8. It is a Python library not an app. Users have to
 write Python codes to process their data. For beginners, a quick way to get started with Python
 programming is to install `Anaconda <https://www.anaconda.com/products/individual>`__,
 then follow instructions `here <https://docs.anaconda.com/anaconda/user-guide/getting-started/>`__.
@@ -45,13 +45,13 @@ If install to an existing environment::
 
     conda install -c conda-forge algotom
 
-or::
+or:
 
 	conda install -c algotom algotom
 
 If install to a new environment::
 
-    conda create -n algotom python>=3.7
+    conda create -n algotom python=3.10
     conda activate algotom
     conda install -c conda-forge algotom
 
@@ -68,7 +68,7 @@ If install to an existing environment::
 
 If install to a new environment::
 
-    conda create -n algotom python>=3.7
+    conda create -n algotom python=3.10
     conda activate algotom
     pip install algotom
 
@@ -83,7 +83,7 @@ Download and install `Miniconda  <https://docs.conda.io/en/latest/miniconda.html
 
 Open Linux terminal or Miniconda/Anaconda Powershell prompt and run the following commands::
 
-    conda create -n algotom python>=3.7
+    conda create -n algotom python=3.10
     conda activate algotom
     cd algotom
     python setup.py install

diff --git a/_sources/toc/section4/section4_5.rst.txt b/_sources/toc/section4/section4_5.rst.txt
@@ -273,6 +273,8 @@ higher resolution scans. This can be achieved by following these steps:
                 out_file = output_base + "/rec_" + ("00000" + str(idx))[-5:] + ".tif"
                 losa.save_image(out_file, rec_img)
 
+.. _find_center:
+
 Finding the center of rotation
 ------------------------------
 

diff --git a/_sources/toc/section5.rst.txt b/_sources/toc/section5.rst.txt
@@ -4,3 +4,4 @@ Technical notes
 .. toctree::
 
     section5/section5_1
+    section5/section5_2