Skip to content

Commit f9296ff

Browse files
nghia-vonghia-vo
committed
Update
1 parent e2b9114 commit f9296ff

File tree

102 files changed

+11190
-15458
lines changed

Some content is hidden

Large Commits have some content hidden by default. Use the searchbox below for content that may be hidden.

102 files changed

+11190
-15458
lines changed

Diff for: ‎.buildinfo

+1-1
Original file line numberDiff line numberDiff line change
@@ -1,4 +1,4 @@
11
# Sphinx build info version 1
22
# This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
3-
config: fd308dd782c938dd3a3400d245875155
3+
config: 00c2ed1ba70e002916820dacb589eaeb
44
tags: 645f666f9bcd5a90fca523b33c5a78b7

Diff for: ‎.doctrees/environment.pickle

13.1 KB
Binary file not shown.

Diff for: ‎.doctrees/toc/api/algotom.io.loadersaver.doctree

1.62 KB
Binary file not shown.

Diff for: ‎.doctrees/toc/api/algotom.post.postprocessing.doctree

17.7 KB
Binary file not shown.

Diff for: ‎.doctrees/toc/api/algotom.prep.phase.doctree

0 Bytes
Binary file not shown.

Diff for: ‎.doctrees/toc/api/algotom.prep.removal.doctree

1.04 KB
Binary file not shown.

Diff for: ‎.doctrees/toc/api/algotom.rec.reconstruction.doctree

0 Bytes
Binary file not shown.

Diff for: ‎.doctrees/toc/api/algotom.util.simulation.doctree

0 Bytes
Binary file not shown.

Diff for: ‎.doctrees/toc/api/algotom.util.utility.doctree

2.58 KB
Binary file not shown.

Diff for: ‎.doctrees/toc/section2.doctree

228 Bytes
Binary file not shown.

Diff for: ‎.doctrees/toc/section3.doctree

-78 Bytes
Binary file not shown.

Diff for: ‎.doctrees/toc/section5/section5_1.doctree

1.69 KB
Binary file not shown.

Diff for: ‎.doctrees/toc/section6.doctree

653 Bytes
Binary file not shown.

Diff for: ‎.idea/workspace.xml

+102-1
Some generated files are not rendered by default. Learn more about customizing how changed files appear on GitHub.

Diff for: ‎_modules/algotom/io/converter.html

+8-5
Original file line numberDiff line numberDiff line change
@@ -225,8 +225,6 @@ <h1>Source code for algotom.io.converter</h1><div class="highlight"><pre>
225225
<span class="k">else</span><span class="p">:</span>
226226
<span class="n">list_file</span> <span class="o">=</span> <span class="n">losa</span><span class="o">.</span><span class="n">find_file</span><span class="p">(</span><span class="n">input_path</span> <span class="o">+</span> <span class="s2">&quot;/*&quot;</span> <span class="o">+</span> <span class="n">pattern</span> <span class="o">+</span> <span class="s2">&quot;*.tif*&quot;</span><span class="p">)</span>
227227
<span class="n">depth</span> <span class="o">=</span> <span class="nb">len</span><span class="p">(</span><span class="n">list_file</span><span class="p">)</span>
228-
<span class="k">if</span> <span class="n">depth</span> <span class="o">==</span> <span class="mi">0</span><span class="p">:</span>
229-
<span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="s2">&quot;No tif files in the folder: </span><span class="si">{}</span><span class="s2">&quot;</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="n">input_path</span><span class="p">))</span>
230228
<span class="p">(</span><span class="n">height</span><span class="p">,</span> <span class="n">width</span><span class="p">)</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">shape</span><span class="p">(</span><span class="n">losa</span><span class="o">.</span><span class="n">load_image</span><span class="p">(</span><span class="n">list_file</span><span class="p">[</span><span class="mi">0</span><span class="p">]))</span>
231229
<span class="n">file_base</span><span class="p">,</span> <span class="n">file_ext</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">splitext</span><span class="p">(</span><span class="n">output_path</span><span class="p">)</span>
232230
<span class="k">if</span> <span class="ow">not</span> <span class="p">(</span><span class="n">file_ext</span> <span class="o">==</span> <span class="s1">&#39;.hdf&#39;</span> <span class="ow">or</span> <span class="n">file_ext</span> <span class="o">==</span> <span class="s1">&#39;.h5&#39;</span> <span class="ow">or</span> <span class="n">file_ext</span> <span class="o">==</span> <span class="s2">&quot;.nxs&quot;</span><span class="p">):</span>
@@ -235,6 +233,8 @@ <h1>Source code for algotom.io.converter</h1><div class="highlight"><pre>
235233
<span class="n">cr_top</span><span class="p">,</span> <span class="n">cr_bottom</span><span class="p">,</span> <span class="n">cr_left</span><span class="p">,</span> <span class="n">cr_right</span> <span class="o">=</span> <span class="n">crop</span>
236234
<span class="n">cr_height</span> <span class="o">=</span> <span class="n">height</span> <span class="o">-</span> <span class="n">cr_top</span> <span class="o">-</span> <span class="n">cr_bottom</span>
237235
<span class="n">cr_width</span> <span class="o">=</span> <span class="n">width</span> <span class="o">-</span> <span class="n">cr_left</span> <span class="o">-</span> <span class="n">cr_right</span>
236+
<span class="k">if</span> <span class="n">cr_height</span> <span class="o">&lt;</span> <span class="mi">1</span> <span class="ow">or</span> <span class="n">cr_width</span> <span class="o">&lt;</span> <span class="mi">1</span><span class="p">:</span>
237+
<span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="s2">&quot;Can&#39;t crop images with the given parameters !!!&quot;</span><span class="p">)</span>
238238
<span class="n">data_out</span> <span class="o">=</span> <span class="n">losa</span><span class="o">.</span><span class="n">open_hdf_stream</span><span class="p">(</span><span class="n">output_path</span><span class="p">,</span> <span class="p">(</span><span class="n">depth</span><span class="p">,</span> <span class="n">cr_height</span><span class="p">,</span> <span class="n">cr_width</span><span class="p">),</span>
239239
<span class="n">key_path</span><span class="o">=</span><span class="n">key_path</span><span class="p">,</span> <span class="n">overwrite</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span>
240240
<span class="o">**</span><span class="n">options</span><span class="p">)</span>
@@ -280,24 +280,27 @@ <h1>Source code for algotom.io.converter</h1><div class="highlight"><pre>
280280
<span class="n">start</span><span class="p">,</span> <span class="n">stop</span><span class="p">,</span> <span class="n">step</span> <span class="o">=</span> <span class="n">index</span><span class="p">,</span> <span class="n">index</span> <span class="o">+</span> <span class="mi">1</span><span class="p">,</span> <span class="mi">1</span>
281281
<span class="n">cr_top</span><span class="p">,</span> <span class="n">cr_bottom</span><span class="p">,</span> <span class="n">cr_left</span><span class="p">,</span> <span class="n">cr_right</span> <span class="o">=</span> <span class="n">crop</span>
282282
<span class="k">if</span> <span class="n">axis</span> <span class="o">==</span> <span class="mi">1</span><span class="p">:</span>
283-
<span class="k">if</span> <span class="p">(</span><span class="n">stop</span> <span class="o">==</span> <span class="o">-</span><span class="mi">1</span><span class="p">)</span> <span class="ow">or</span> <span class="p">(</span><span class="n">stop</span> <span class="o">&gt;</span> <span class="n">height</span><span class="p">):</span>
283+
<span class="k">if</span> <span class="n">stop</span> <span class="o">&lt;</span> <span class="mi">1</span> <span class="ow">or</span> <span class="n">stop</span> <span class="o">&gt;</span> <span class="n">height</span><span class="p">:</span>
284284
<span class="n">stop</span> <span class="o">=</span> <span class="n">height</span>
285+
<span class="n">start</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">clip</span><span class="p">(</span><span class="n">start</span><span class="p">,</span> <span class="mi">0</span><span class="p">,</span> <span class="n">stop</span> <span class="o">-</span> <span class="mi">1</span><span class="p">)</span>
285286
<span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="n">start</span><span class="p">,</span> <span class="n">stop</span><span class="p">,</span> <span class="n">step</span><span class="p">):</span>
286287
<span class="n">mat</span> <span class="o">=</span> <span class="n">data</span><span class="p">[</span><span class="n">cr_top</span><span class="p">:</span><span class="n">depth</span> <span class="o">-</span> <span class="n">cr_bottom</span><span class="p">,</span> <span class="n">i</span><span class="p">,</span> <span class="n">cr_left</span><span class="p">:</span><span class="n">width</span> <span class="o">-</span> <span class="n">cr_right</span><span class="p">]</span>
287288
<span class="n">out_name</span> <span class="o">=</span> <span class="s2">&quot;0000&quot;</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">i</span><span class="p">)</span>
288289
<span class="n">losa</span><span class="o">.</span><span class="n">save_image</span><span class="p">(</span>
289290
<span class="n">output_path</span> <span class="o">+</span> <span class="s2">&quot;/&quot;</span> <span class="o">+</span> <span class="n">prefix</span> <span class="o">+</span> <span class="s2">&quot;_&quot;</span> <span class="o">+</span> <span class="n">out_name</span><span class="p">[</span><span class="o">-</span><span class="mi">5</span><span class="p">:]</span> <span class="o">+</span> <span class="s2">&quot;.tif&quot;</span><span class="p">,</span> <span class="n">mat</span><span class="p">)</span>
290291
<span class="k">elif</span> <span class="n">axis</span> <span class="o">==</span> <span class="mi">2</span><span class="p">:</span>
291-
<span class="k">if</span> <span class="p">(</span><span class="n">stop</span> <span class="o">==</span> <span class="o">-</span><span class="mi">1</span><span class="p">)</span> <span class="ow">or</span> <span class="p">(</span><span class="n">stop</span> <span class="o">&gt;</span> <span class="n">width</span><span class="p">):</span>
292+
<span class="k">if</span> <span class="n">stop</span> <span class="o">&lt;</span> <span class="mi">1</span> <span class="ow">or</span> <span class="n">stop</span> <span class="o">&gt;</span> <span class="n">width</span><span class="p">:</span>
292293
<span class="n">stop</span> <span class="o">=</span> <span class="n">width</span>
294+
<span class="n">start</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">clip</span><span class="p">(</span><span class="n">start</span><span class="p">,</span> <span class="mi">0</span><span class="p">,</span> <span class="n">stop</span> <span class="o">-</span> <span class="mi">1</span><span class="p">)</span>
293295
<span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="n">start</span><span class="p">,</span> <span class="n">stop</span><span class="p">,</span> <span class="n">step</span><span class="p">):</span>
294296
<span class="n">mat</span> <span class="o">=</span> <span class="n">data</span><span class="p">[</span><span class="n">cr_top</span><span class="p">:</span><span class="n">depth</span> <span class="o">-</span> <span class="n">cr_bottom</span><span class="p">,</span> <span class="n">cr_left</span><span class="p">:</span><span class="n">height</span> <span class="o">-</span> <span class="n">cr_right</span><span class="p">,</span> <span class="n">i</span><span class="p">]</span>
295297
<span class="n">out_name</span> <span class="o">=</span> <span class="s2">&quot;0000&quot;</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">i</span><span class="p">)</span>
296298
<span class="n">losa</span><span class="o">.</span><span class="n">save_image</span><span class="p">(</span>
297299
<span class="n">output_path</span> <span class="o">+</span> <span class="s2">&quot;/&quot;</span> <span class="o">+</span> <span class="n">prefix</span> <span class="o">+</span> <span class="s2">&quot;_&quot;</span> <span class="o">+</span> <span class="n">out_name</span><span class="p">[</span><span class="o">-</span><span class="mi">5</span><span class="p">:]</span> <span class="o">+</span> <span class="s2">&quot;.tif&quot;</span><span class="p">,</span> <span class="n">mat</span><span class="p">)</span>
298300
<span class="k">else</span><span class="p">:</span>
299-
<span class="k">if</span> <span class="p">(</span><span class="n">stop</span> <span class="o">==</span> <span class="o">-</span><span class="mi">1</span><span class="p">)</span> <span class="ow">or</span> <span class="p">(</span><span class="n">stop</span> <span class="o">&gt;</span> <span class="n">depth</span><span class="p">):</span>
301+
<span class="k">if</span> <span class="n">stop</span> <span class="o">&lt;</span> <span class="mi">1</span> <span class="ow">or</span> <span class="n">stop</span> <span class="o">&gt;</span> <span class="n">depth</span><span class="p">:</span>
300302
<span class="n">stop</span> <span class="o">=</span> <span class="n">depth</span>
303+
<span class="n">start</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">clip</span><span class="p">(</span><span class="n">start</span><span class="p">,</span> <span class="mi">0</span><span class="p">,</span> <span class="n">stop</span> <span class="o">-</span> <span class="mi">1</span><span class="p">)</span>
301304
<span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="n">start</span><span class="p">,</span> <span class="n">stop</span><span class="p">,</span> <span class="n">step</span><span class="p">):</span>
302305
<span class="n">mat</span> <span class="o">=</span> <span class="n">data</span><span class="p">[</span><span class="n">i</span><span class="p">,</span> <span class="n">cr_top</span><span class="p">:</span><span class="n">height</span> <span class="o">-</span> <span class="n">cr_bottom</span><span class="p">,</span> <span class="n">cr_left</span><span class="p">:</span><span class="n">width</span> <span class="o">-</span> <span class="n">cr_right</span><span class="p">]</span>
303306
<span class="n">out_name</span> <span class="o">=</span> <span class="s2">&quot;0000&quot;</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">i</span><span class="p">)</span>

0 commit comments

Comments
 (0)