update docs

docs/build/doctest/output.txt

@@ -1,12 +1,12 @@
-Results of doctest builder run on 2020-05-04 18:23:07
+Results of doctest builder run on 2020-05-04 19:15:02
 =====================================================
 
-Document: generated/seg1d.optimized_funcs.vcor
-----------------------------------------------
+Document: generated/seg1d.Segmenter.clear_reference
+---------------------------------------------------
 1 items passed all tests:
-   5 tests in default
-5 tests in 1 items.
-5 passed and 0 failed.
+   7 tests in default
+7 tests in 1 items.
+7 passed and 0 failed.
 Test passed.
 
 Document: generated/seg1d.optimized_funcs.rcor
@@ -17,36 +17,20 @@ Document: generated/seg1d.optimized_funcs.rcor
 5 passed and 0 failed.
 Test passed.
 
-Document: api_ecg
------------------
-1 items passed all tests:
-  25 tests in default
-25 tests in 1 items.
-25 passed and 0 failed.
-Test passed.
-
-Document: generated/seg1d.Segmenter
------------------------------------
-1 items passed all tests:
-   6 tests in default
-6 tests in 1 items.
-6 passed and 0 failed.
-Test passed.
-
-Document: generated/seg1d.algorithm.uniques
--------------------------------------------
+Document: generated/seg1d.optimized_funcs.vcor
+----------------------------------------------
 1 items passed all tests:
    5 tests in default
 5 tests in 1 items.
 5 passed and 0 failed.
 Test passed.
 
-Document: generated/seg1d.algorithm.combine_corr
-------------------------------------------------
+Document: generated/seg1d.Segmenter.add_reference
+-------------------------------------------------
 1 items passed all tests:
-  11 tests in default
-11 tests in 1 items.
-11 passed and 0 failed.
+  10 tests in default
+10 tests in 1 items.
+10 passed and 0 failed.
 Test passed.
 
 Document: generated/seg1d.Segmenter.t_segments
@@ -57,16 +41,8 @@ Document: generated/seg1d.Segmenter.t_segments
 11 passed and 0 failed.
 Test passed.
 
-Document: generated/seg1d.Segmenter.add_reference
--------------------------------------------------
-1 items passed all tests:
-  10 tests in default
-10 tests in 1 items.
-10 passed and 0 failed.
-Test passed.
-
-Document: generated/seg1d.algorithm.get_peaks
----------------------------------------------
+Document: generated/seg1d.algorithm.resample
+--------------------------------------------
 1 items passed all tests:
    6 tests in default
 6 tests in 1 items.
@@ -81,32 +57,16 @@ Document: api_basic
 13 passed and 0 failed.
 Test passed.
 
-Document: generated/seg1d.algorithm.rolling_corr
-------------------------------------------------
-1 items passed all tests:
-   6 tests in default
-6 tests in 1 items.
-6 passed and 0 failed.
-Test passed.
-
-Document: api_tune
-------------------
-1 items passed all tests:
-  27 tests in default
-27 tests in 1 items.
-27 passed and 0 failed.
-Test passed.
-
-Document: code_simple
----------------------
+Document: api_ecg
+-----------------
 1 items passed all tests:
-   6 tests in default
-6 tests in 1 items.
-6 passed and 0 failed.
+  25 tests in default
+25 tests in 1 items.
+25 passed and 0 failed.
 Test passed.
 
-Document: generated/seg1d.algorithm.resample
---------------------------------------------
+Document: generated/seg1d.Segmenter
+-----------------------------------
 1 items passed all tests:
    6 tests in default
 6 tests in 1 items.
@@ -121,20 +81,28 @@ Document: generated/seg1d.algorithm.cluster
 8 passed and 0 failed.
 Test passed.
 
-Document: generated/seg1d.Segmenter.segment
+Document: api_feat
+------------------
+1 items passed all tests:
+  17 tests in default
+17 tests in 1 items.
+17 passed and 0 failed.
+Test passed.
+
+Document: generated/seg1d.algorithm.uniques
 -------------------------------------------
 1 items passed all tests:
    5 tests in default
 5 tests in 1 items.
 5 passed and 0 failed.
 Test passed.
 
-Document: generated/seg1d.Segmenter.set_target
-----------------------------------------------
+Document: api_tune
+------------------
 1 items passed all tests:
-  10 tests in default
-10 tests in 1 items.
-10 passed and 0 failed.
+  29 tests in default
+29 tests in 1 items.
+29 passed and 0 failed.
 Test passed.
 
 Document: start
@@ -170,25 +138,57 @@ Got:
 37 passed and 1 failed.
 ***Test Failed*** 1 failures.
 
-Document: api_feat
-------------------
+Document: generated/seg1d.algorithm.rolling_corr
+------------------------------------------------
 1 items passed all tests:
-  17 tests in default
-17 tests in 1 items.
-17 passed and 0 failed.
+   6 tests in default
+6 tests in 1 items.
+6 passed and 0 failed.
 Test passed.
 
-Document: generated/seg1d.Segmenter.clear_reference
----------------------------------------------------
+Document: code_simple
+---------------------
 1 items passed all tests:
-   7 tests in default
-7 tests in 1 items.
-7 passed and 0 failed.
+   6 tests in default
+6 tests in 1 items.
+6 passed and 0 failed.
+Test passed.
+
+Document: generated/seg1d.Segmenter.set_target
+----------------------------------------------
+1 items passed all tests:
+  10 tests in default
+10 tests in 1 items.
+10 passed and 0 failed.
+Test passed.
+
+Document: generated/seg1d.Segmenter.segment
+-------------------------------------------
+1 items passed all tests:
+   5 tests in default
+5 tests in 1 items.
+5 passed and 0 failed.
+Test passed.
+
+Document: generated/seg1d.algorithm.combine_corr
+------------------------------------------------
+1 items passed all tests:
+  11 tests in default
+11 tests in 1 items.
+11 passed and 0 failed.
+Test passed.
+
+Document: generated/seg1d.algorithm.get_peaks
+---------------------------------------------
+1 items passed all tests:
+   6 tests in default
+6 tests in 1 items.
+6 passed and 0 failed.
 Test passed.
 
 Doctest summary
 ===============
-  227 tests
+  229 tests
     1 failure in tests
     0 failures in setup code
     0 failures in cleanup code

docs/build/html/api_basic-1.py

@@ -5,7 +5,7 @@
 # Then we generate some data
 
 x = np.linspace(-np.pi*2, np.pi*2, 2000) #create an array of data
-targ = np.sin(x)  # target data from a sin function
+targ = np.sin(x)  # target data from a sin function 
 t_s,t_e = 200,400 # define a sub-series
 
 # To assign the data to the Segmenter, first we create an instance of it and then

docs/build/html/api_basic.html

@@ -93,7 +93,7 @@
 </div>
 <p>Then we generate some data</p>
 <div class="doctest highlight-default notranslate"><div class="highlight"><pre><span></span><span class="gp">&gt;&gt;&gt; </span><span class="n">x</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">linspace</span><span class="p">(</span><span class="o">-</span><span class="n">np</span><span class="o">.</span><span class="n">pi</span><span class="o">*</span><span class="mi">2</span><span class="p">,</span> <span class="n">np</span><span class="o">.</span><span class="n">pi</span><span class="o">*</span><span class="mi">2</span><span class="p">,</span> <span class="mi">2000</span><span class="p">)</span> <span class="c1">#create an array of data</span>
-<span class="gp">&gt;&gt;&gt; </span><span class="n">targ</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">sin</span><span class="p">(</span><span class="n">x</span><span class="p">)</span>  <span class="c1"># target data from a sin function</span>
+<span class="gp">&gt;&gt;&gt; </span><span class="n">targ</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">sin</span><span class="p">(</span><span class="n">x</span><span class="p">)</span>  <span class="c1"># target data from a sin function </span>
 <span class="gp">&gt;&gt;&gt; </span><span class="n">t_s</span><span class="p">,</span><span class="n">t_e</span> <span class="o">=</span> <span class="mi">200</span><span class="p">,</span><span class="mi">400</span> <span class="c1"># define a sub-series</span>
 </pre></div>
 </div>

docs/build/html/api_ecg-1.py

@@ -42,4 +42,7 @@
 
 plt.figure(figsize=(5,3))  # doctest: +SKIP
 plt.plot(refs.T)  # doctest: +SKIP
+plt.xlabel("time in s")  # doctest: +SKIP
+plt.ylabel("ECG in mV")  # doctest: +SKIP
+plt.tight_layout()  # doctest: +SKIP
 plt.show()  # doctest: +SKIP

docs/build/html/api_ecg-2.py

@@ -4,4 +4,7 @@
 
 plt.figure(figsize=(15,3))  # doctest: +SKIP
 plt.plot(s.t_masked.T)  # doctest: +SKIP
+plt.xlabel("time in s")  # doctest: +SKIP
+plt.ylabel("ECG in mV")  # doctest: +SKIP
+plt.tight_layout()  # doctest: +SKIP
 plt.show()  # doctest: +SKIP

docs/build/html/api_ecg-3.py

@@ -7,4 +7,7 @@
 
 plt.figure(figsize=(5,3))  # doctest: +SKIP
 plt.plot(refs.T)  # doctest: +SKIP
+plt.xlabel("time in s")  # doctest: +SKIP
+plt.ylabel("ECG in mV")  # doctest: +SKIP
+plt.tight_layout()  # doctest: +SKIP
 plt.show()  # doctest: +SKIP

docs/build/html/api_ecg-4.py

@@ -21,4 +21,7 @@
 
 plt.figure(figsize=(15,3))  # doctest: +SKIP
 plt.plot(res.T)  # doctest: +SKIP
-plt.show() # doctest: +SKIP
+plt.xlabel("time in s")  # doctest: +SKIP
+plt.ylabel("ECG in mV")  # doctest: +SKIP
+plt.tight_layout()  # doctest: +SKIP
+plt.show()  # doctest: +SKIP

docs/build/html/api_ecg.html

@@ -137,6 +137,9 @@
 </div>
 <div class="doctest highlight-default notranslate"><div class="highlight"><pre><span></span><span class="gp">&gt;&gt;&gt; </span><span class="n">plt</span><span class="o">.</span><span class="n">figure</span><span class="p">(</span><span class="n">figsize</span><span class="o">=</span><span class="p">(</span><span class="mi">5</span><span class="p">,</span><span class="mi">3</span><span class="p">))</span>  
 <span class="gp">&gt;&gt;&gt; </span><span class="n">plt</span><span class="o">.</span><span class="n">plot</span><span class="p">(</span><span class="n">refs</span><span class="o">.</span><span class="n">T</span><span class="p">)</span>  
+<span class="gp">&gt;&gt;&gt; </span><span class="n">plt</span><span class="o">.</span><span class="n">xlabel</span><span class="p">(</span><span class="s2">&quot;time in s&quot;</span><span class="p">)</span>  
+<span class="gp">&gt;&gt;&gt; </span><span class="n">plt</span><span class="o">.</span><span class="n">ylabel</span><span class="p">(</span><span class="s2">&quot;ECG in mV&quot;</span><span class="p">)</span>  
+<span class="gp">&gt;&gt;&gt; </span><span class="n">plt</span><span class="o">.</span><span class="n">tight_layout</span><span class="p">()</span>  
 <span class="gp">&gt;&gt;&gt; </span><span class="n">plt</span><span class="o">.</span><span class="n">show</span><span class="p">()</span>  
 </pre></div>
 </div>
@@ -148,6 +151,9 @@
 target data as an ndarray with NaN values for areas not found to be segments.</p>
 <div class="doctest highlight-default notranslate"><div class="highlight"><pre><span></span><span class="gp">&gt;&gt;&gt; </span><span class="n">plt</span><span class="o">.</span><span class="n">figure</span><span class="p">(</span><span class="n">figsize</span><span class="o">=</span><span class="p">(</span><span class="mi">15</span><span class="p">,</span><span class="mi">3</span><span class="p">))</span>  
 <span class="gp">&gt;&gt;&gt; </span><span class="n">plt</span><span class="o">.</span><span class="n">plot</span><span class="p">(</span><span class="n">s</span><span class="o">.</span><span class="n">t_masked</span><span class="o">.</span><span class="n">T</span><span class="p">)</span>  
+<span class="gp">&gt;&gt;&gt; </span><span class="n">plt</span><span class="o">.</span><span class="n">xlabel</span><span class="p">(</span><span class="s2">&quot;time in s&quot;</span><span class="p">)</span>  
+<span class="gp">&gt;&gt;&gt; </span><span class="n">plt</span><span class="o">.</span><span class="n">ylabel</span><span class="p">(</span><span class="s2">&quot;ECG in mV&quot;</span><span class="p">)</span>  
+<span class="gp">&gt;&gt;&gt; </span><span class="n">plt</span><span class="o">.</span><span class="n">tight_layout</span><span class="p">()</span>  
 <span class="gp">&gt;&gt;&gt; </span><span class="n">plt</span><span class="o">.</span><span class="n">show</span><span class="p">()</span>  
 </pre></div>
 </div>
@@ -166,6 +172,9 @@
 </div>
 <div class="doctest highlight-default notranslate"><div class="highlight"><pre><span></span><span class="gp">&gt;&gt;&gt; </span><span class="n">plt</span><span class="o">.</span><span class="n">figure</span><span class="p">(</span><span class="n">figsize</span><span class="o">=</span><span class="p">(</span><span class="mi">5</span><span class="p">,</span><span class="mi">3</span><span class="p">))</span>  
 <span class="gp">&gt;&gt;&gt; </span><span class="n">plt</span><span class="o">.</span><span class="n">plot</span><span class="p">(</span><span class="n">refs</span><span class="o">.</span><span class="n">T</span><span class="p">)</span>  
+<span class="gp">&gt;&gt;&gt; </span><span class="n">plt</span><span class="o">.</span><span class="n">xlabel</span><span class="p">(</span><span class="s2">&quot;time in s&quot;</span><span class="p">)</span>  
+<span class="gp">&gt;&gt;&gt; </span><span class="n">plt</span><span class="o">.</span><span class="n">ylabel</span><span class="p">(</span><span class="s2">&quot;ECG in mV&quot;</span><span class="p">)</span>  
+<span class="gp">&gt;&gt;&gt; </span><span class="n">plt</span><span class="o">.</span><span class="n">tight_layout</span><span class="p">()</span>  
 <span class="gp">&gt;&gt;&gt; </span><span class="n">plt</span><span class="o">.</span><span class="n">show</span><span class="p">()</span>  
 </pre></div>
 </div>
@@ -200,7 +209,10 @@
 </div>
 <div class="doctest highlight-default notranslate"><div class="highlight"><pre><span></span><span class="gp">&gt;&gt;&gt; </span><span class="n">plt</span><span class="o">.</span><span class="n">figure</span><span class="p">(</span><span class="n">figsize</span><span class="o">=</span><span class="p">(</span><span class="mi">15</span><span class="p">,</span><span class="mi">3</span><span class="p">))</span>  
 <span class="gp">&gt;&gt;&gt; </span><span class="n">plt</span><span class="o">.</span><span class="n">plot</span><span class="p">(</span><span class="n">res</span><span class="o">.</span><span class="n">T</span><span class="p">)</span>  
-<span class="gp">&gt;&gt;&gt; </span><span class="n">plt</span><span class="o">.</span><span class="n">show</span><span class="p">()</span> 
+<span class="gp">&gt;&gt;&gt; </span><span class="n">plt</span><span class="o">.</span><span class="n">xlabel</span><span class="p">(</span><span class="s2">&quot;time in s&quot;</span><span class="p">)</span>  
+<span class="gp">&gt;&gt;&gt; </span><span class="n">plt</span><span class="o">.</span><span class="n">ylabel</span><span class="p">(</span><span class="s2">&quot;ECG in mV&quot;</span><span class="p">)</span>  
+<span class="gp">&gt;&gt;&gt; </span><span class="n">plt</span><span class="o">.</span><span class="n">tight_layout</span><span class="p">()</span>  
+<span class="gp">&gt;&gt;&gt; </span><span class="n">plt</span><span class="o">.</span><span class="n">show</span><span class="p">()</span>  
 </pre></div>
 </div>
 <p>(<a class="reference external" href=".//api_ecg-4.py">Source code</a>)</p>

docs/build/html/api_tune-1.py

@@ -22,5 +22,8 @@
 # Plot the target
 plt.figure(figsize=(10,3)) #doctest: +SKIP
 plt.plot(x, targ,linewidth=4,alpha=0.5,label='Target')#doctest: +SKIP
+plt.xlabel('Angle [rad]')#doctest: +SKIP
+plt.ylabel('sin(x)')#doctest: +SKIP
 plt.legend()#doctest: +SKIP
+plt.tight_layout()#doctest: +SKIP
 plt.show()#doctest: +SKIP

docs/build/html/api_tune-2.py

@@ -13,5 +13,8 @@
 plt.figure(figsize=(3,3)) #doctest: +SKIP
 # Plot the reference
 plt.plot(x[t_s:t_e], refData,linewidth=4,alpha=0.5,label='Reference')#doctest: +SKIP
+plt.xlabel('Angle [rad]')#doctest: +SKIP
+plt.ylabel('sin(x)')#doctest: +SKIP
 plt.legend()#doctest: +SKIP
+plt.tight_layout()#doctest: +SKIP
 plt.show()#doctest: +SKIP

docs/build/html/api_tune-3.py

@@ -27,9 +27,15 @@
 # NOTE this is just the location, the actual reference data is shown above
 plt.plot(x[t_s:t_e], targ[t_s:t_e],linewidth=6,alpha=0.7,label='Reference')#doctest: +SKIP
 #plot all segments found
+seg_num = 1
 for seg in segments:
     st = seg[0]
     e = seg[1]
-    plt.plot(x[st:e], targ[st:e],dashes=[1,1],linewidth=2,alpha=0.8,label='Segment')#doctest: +SKIP
+    plt.plot(x[st:e], targ[st:e],dashes=[1,1],linewidth=2,alpha=0.8, #doctest: +SKIP
+             label='Segment {}'.format(seg_num)) #doctest: +SKIP
+    seg_num += 1
+plt.xlabel('Angle [rad]')#doctest: +SKIP
+plt.ylabel('sin(x)')#doctest: +SKIP
 plt.legend()#doctest: +SKIP
+plt.tight_layout()#doctest: +SKIP
 plt.show()#doctest: +SKIP

docs/build/html/api_tune-4.py

@@ -61,9 +61,15 @@
 #plot the original reference segment
 plt.plot(x[t_s:t_e], targ[t_s:t_e],linewidth=6,alpha=0.7,label='Reference')#doctest: +SKIP
 #plot all segments found
+seg_num = 1
 for seg in segments:
-    s = seg[0]
+    st = seg[0]
     e = seg[1]
-    plt.plot(x[s:e], targ[s:e],dashes=[1,1],linewidth=2,alpha=0.8,label='Segment')#doctest: +SKIP
+    plt.plot(x[st:e], targ[st:e],dashes=[1,1],linewidth=2,alpha=0.8, #doctest: +SKIP
+             label='Segment {}'.format(seg_num)) #doctest: +SKIP
+    seg_num += 1
+plt.xlabel('Angle [rad]')#doctest: +SKIP
+plt.ylabel('sin(x)')#doctest: +SKIP
 plt.legend()#doctest: +SKIP
+plt.tight_layout()#doctest: +SKIP
 plt.show()#doctest: +SKIP