update docs

ihrke · ihrke · commit 8a90a8a1bf75 · 2020-06-27T12:20:30.000+02:00
diff --git a/docs/doctrees/docs/blinks.doctree b/docs/doctrees/docs/blinks.doctree
diff --git a/docs/doctrees/docs/pipes.doctree b/docs/doctrees/docs/pipes.doctree
diff --git a/docs/doctrees/docs/plotting.doctree b/docs/doctrees/docs/plotting.doctree
diff --git a/docs/doctrees/docs/summary.doctree b/docs/doctrees/docs/summary.doctree
diff --git a/docs/doctrees/environment.pickle b/docs/doctrees/environment.pickle
diff --git a/docs/doctrees/nbsphinx/docs/blinks.ipynb b/docs/doctrees/nbsphinx/docs/blinks.ipynb
@@ -71,7 +71,7 @@
     "- Second, blinks are defined as everything between two crossings of the velocity profile (from negative to positive).\n",
     "- Finally, detected blinks have to be at least `min_duration` duration (in customizable `units`).\n",
     "\n",
-    "As a consequence, there are several parameters that can be adjusted (see the [API-docs](/docs/api.rst) for details).\n",
+    "As a consequence, there are several parameters that can be adjusted (see the [API-docs](api.html) for details).\n",
     "The most important ones are the following:\n",
     "\n",
     "- `min_duration`: minimum duration for a sequence of missing numbers to be treated as blink\n",
@@ -121,7 +121,7 @@
    "source": [
     "We see that a period of seemingly valid pupil-data (around times 4.05 and 4.15 min) was marked as blink because of a sudden downward change in the pupil signal which might resemble the onset of a blink (a likely source of these artifacts are sudden eye-movements but we would need eyetracking-data to corrobate this hypothesis). \n",
     "\n",
-    "his problem can be fixed by setting a stricter value for the velocity-profile based onset detection `vel_onset` or requiring a more prolonged onset-transient by increasing `min_onset_len`:"
+    "This problem can be fixed by setting a stricter value for the velocity-profile based onset detection `vel_onset` or requiring a more prolonged onset-transient by increasing `min_onset_len`:"
    ]
   },
   {
diff --git a/docs/doctrees/nbsphinx/docs/pipes.ipynb b/docs/doctrees/nbsphinx/docs/pipes.ipynb
@@ -94,7 +94,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "We see that sampling rate, number o datapoints and more is automatically printed along with the history of all operations applied to the dataset. This information can also be retrieved separately and in a form useful for further processing the function `summary()` which returns the information in the form of a `dict`:"
+    "We see that sampling rate, number of datapoints and more is automatically printed along with the history of all operations applied to the dataset. This information can also be retrieved separately and in a form useful for further processing the function `summary()` which returns the information in the form of a `dict`:"
    ]
   },
   {
diff --git a/docs/doctrees/nbsphinx/docs/plotting.ipynb b/docs/doctrees/nbsphinx/docs/plotting.ipynb
@@ -6,7 +6,7 @@
    "source": [
     "# Plotting pupillometric data for exploration\n",
     "\n",
-    "It is crucial to validate preprocessing steps by visually inspecting the results using plots. Therefore, `pypillometry` implements several plotting facilities that encourage active exploration of the dataset. Some of the plotting functions require a Jupyter-notebook with enable widgets (see Installation instructions) so that the plots can be changed interactively, others are purely :mod:`matplotlib`-based."
+    "It is crucial to validate preprocessing steps by visually inspecting the results using plots. Therefore, `pypillometry` implements several plotting facilities that encourage active exploration of the dataset. Some of the plotting functions require a Jupyter-notebook with enable widgets (see Installation instructions) so that the plots can be changed interactively, others are purely `matplotlib`-based."
    ]
   },
   {
diff --git a/docs/doctrees/nbsphinx/docs/summary.ipynb b/docs/doctrees/nbsphinx/docs/summary.ipynb
@@ -22,7 +22,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "The `pypillometry` package provides several functions for summarizing datasets. Simply `print()`ing a :class:`PupilData` object gives a readable summary of the main properties of the dataset and also prints the complete history of operations applied to the dataset."
+    "The `pypillometry` package provides several functions for summarizing datasets. Simply `print()`ing a `PupilData` object gives a readable summary of the main properties of the dataset and also prints the complete history of operations applied to the dataset."
    ]
   },
   {
diff --git a/docs/html/_sources/docs/blinks.ipynb.txt b/docs/html/_sources/docs/blinks.ipynb.txt
@@ -71,7 +71,7 @@
     "- Second, blinks are defined as everything between two crossings of the velocity profile (from negative to positive).\n",
     "- Finally, detected blinks have to be at least `min_duration` duration (in customizable `units`).\n",
     "\n",
-    "As a consequence, there are several parameters that can be adjusted (see the [API-docs](/docs/api.rst) for details).\n",
+    "As a consequence, there are several parameters that can be adjusted (see the [API-docs](api.html) for details).\n",
     "The most important ones are the following:\n",
     "\n",
     "- `min_duration`: minimum duration for a sequence of missing numbers to be treated as blink\n",
@@ -121,7 +121,7 @@
    "source": [
     "We see that a period of seemingly valid pupil-data (around times 4.05 and 4.15 min) was marked as blink because of a sudden downward change in the pupil signal which might resemble the onset of a blink (a likely source of these artifacts are sudden eye-movements but we would need eyetracking-data to corrobate this hypothesis). \n",
     "\n",
-    "his problem can be fixed by setting a stricter value for the velocity-profile based onset detection `vel_onset` or requiring a more prolonged onset-transient by increasing `min_onset_len`:"
+    "This problem can be fixed by setting a stricter value for the velocity-profile based onset detection `vel_onset` or requiring a more prolonged onset-transient by increasing `min_onset_len`:"
    ]
   },
   {
diff --git a/docs/html/_sources/docs/pipes.ipynb.txt b/docs/html/_sources/docs/pipes.ipynb.txt
@@ -94,7 +94,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "We see that sampling rate, number o datapoints and more is automatically printed along with the history of all operations applied to the dataset. This information can also be retrieved separately and in a form useful for further processing the function `summary()` which returns the information in the form of a `dict`:"
+    "We see that sampling rate, number of datapoints and more is automatically printed along with the history of all operations applied to the dataset. This information can also be retrieved separately and in a form useful for further processing the function `summary()` which returns the information in the form of a `dict`:"
    ]
   },
   {
diff --git a/docs/html/_sources/docs/plotting.ipynb.txt b/docs/html/_sources/docs/plotting.ipynb.txt
@@ -6,7 +6,7 @@
    "source": [
     "# Plotting pupillometric data for exploration\n",
     "\n",
-    "It is crucial to validate preprocessing steps by visually inspecting the results using plots. Therefore, `pypillometry` implements several plotting facilities that encourage active exploration of the dataset. Some of the plotting functions require a Jupyter-notebook with enable widgets (see Installation instructions) so that the plots can be changed interactively, others are purely :mod:`matplotlib`-based."
+    "It is crucial to validate preprocessing steps by visually inspecting the results using plots. Therefore, `pypillometry` implements several plotting facilities that encourage active exploration of the dataset. Some of the plotting functions require a Jupyter-notebook with enable widgets (see Installation instructions) so that the plots can be changed interactively, others are purely `matplotlib`-based."
    ]
   },
   {
diff --git a/docs/html/_sources/docs/summary.ipynb.txt b/docs/html/_sources/docs/summary.ipynb.txt
@@ -22,7 +22,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "The `pypillometry` package provides several functions for summarizing datasets. Simply `print()`ing a :class:`PupilData` object gives a readable summary of the main properties of the dataset and also prints the complete history of operations applied to the dataset."
+    "The `pypillometry` package provides several functions for summarizing datasets. Simply `print()`ing a `PupilData` object gives a readable summary of the main properties of the dataset and also prints the complete history of operations applied to the dataset."
    ]
   },
   {
diff --git a/docs/html/docs/blinks.html b/docs/html/docs/blinks.html
@@ -328,7 +328,7 @@ <h2>Blink detection<a class="headerlink" href="#Blink-detection" title="Permalin
 <li><p>Second, blinks are defined as everything between two crossings of the velocity profile (from negative to positive).</p></li>
 <li><p>Finally, detected blinks have to be at least <code class="docutils literal notranslate"><span class="pre">min_duration</span></code> duration (in customizable <code class="docutils literal notranslate"><span class="pre">units</span></code>).</p></li>
 </ul>
-<p>As a consequence, there are several parameters that can be adjusted (see the <a class="reference external" href="/docs/api.rst">API-docs</a> for details). The most important ones are the following:</p>
+<p>As a consequence, there are several parameters that can be adjusted (see the <a class="reference external" href="api.html">API-docs</a> for details). The most important ones are the following:</p>
 <ul class="simple">
 <li><p><code class="docutils literal notranslate"><span class="pre">min_duration</span></code>: minimum duration for a sequence of missing numbers to be treated as blink</p></li>
 <li><p><code class="docutils literal notranslate"><span class="pre">vel_onset</span></code>: negative velocity that needs to be crossed; arbitrary units that depend on sampling rate etc</p></li>
@@ -357,7 +357,7 @@ <h2>Blink detection<a class="headerlink" href="#Blink-detection" title="Permalin
 </div>
 </div>
 <p>We see that a period of seemingly valid pupil-data (around times 4.05 and 4.15 min) was marked as blink because of a sudden downward change in the pupil signal which might resemble the onset of a blink (a likely source of these artifacts are sudden eye-movements but we would need eyetracking-data to corrobate this hypothesis).</p>
-<p>his problem can be fixed by setting a stricter value for the velocity-profile based onset detection <code class="docutils literal notranslate"><span class="pre">vel_onset</span></code> or requiring a more prolonged onset-transient by increasing <code class="docutils literal notranslate"><span class="pre">min_onset_len</span></code>:</p>
+<p>This problem can be fixed by setting a stricter value for the velocity-profile based onset detection <code class="docutils literal notranslate"><span class="pre">vel_onset</span></code> or requiring a more prolonged onset-transient by increasing <code class="docutils literal notranslate"><span class="pre">min_onset_len</span></code>:</p>
 <div class="nbinput docutils container">
 <div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[48]:
 </pre></div>
diff --git a/docs/html/docs/blinks.ipynb b/docs/html/docs/blinks.ipynb
@@ -71,7 +71,7 @@
     "- Second, blinks are defined as everything between two crossings of the velocity profile (from negative to positive).\n",
     "- Finally, detected blinks have to be at least `min_duration` duration (in customizable `units`).\n",
     "\n",
-    "As a consequence, there are several parameters that can be adjusted (see the [API-docs](/docs/api.rst) for details).\n",
+    "As a consequence, there are several parameters that can be adjusted (see the [API-docs](api.html) for details).\n",
     "The most important ones are the following:\n",
     "\n",
     "- `min_duration`: minimum duration for a sequence of missing numbers to be treated as blink\n",
@@ -121,7 +121,7 @@
    "source": [
     "We see that a period of seemingly valid pupil-data (around times 4.05 and 4.15 min) was marked as blink because of a sudden downward change in the pupil signal which might resemble the onset of a blink (a likely source of these artifacts are sudden eye-movements but we would need eyetracking-data to corrobate this hypothesis). \n",
     "\n",
-    "his problem can be fixed by setting a stricter value for the velocity-profile based onset detection `vel_onset` or requiring a more prolonged onset-transient by increasing `min_onset_len`:"
+    "This problem can be fixed by setting a stricter value for the velocity-profile based onset detection `vel_onset` or requiring a more prolonged onset-transient by increasing `min_onset_len`:"
    ]
   },
   {
diff --git a/docs/html/docs/pipes.html b/docs/html/docs/pipes.html
@@ -356,7 +356,7 @@ <h1>Pipeline-based processing in pypillometry<a class="headerlink" href="#Pipeli
 
 </pre></div></div>
 </div>
-<p>We see that sampling rate, number o datapoints and more is automatically printed along with the history of all operations applied to the dataset. This information can also be retrieved separately and in a form useful for further processing the function <code class="docutils literal notranslate"><span class="pre">summary()</span></code> which returns the information in the form of a <code class="docutils literal notranslate"><span class="pre">dict</span></code>:</p>
+<p>We see that sampling rate, number of datapoints and more is automatically printed along with the history of all operations applied to the dataset. This information can also be retrieved separately and in a form useful for further processing the function <code class="docutils literal notranslate"><span class="pre">summary()</span></code> which returns the information in the form of a <code class="docutils literal notranslate"><span class="pre">dict</span></code>:</p>
 <div class="nbinput docutils container">
 <div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[4]:
 </pre></div>
diff --git a/docs/html/docs/pipes.ipynb b/docs/html/docs/pipes.ipynb
@@ -94,7 +94,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "We see that sampling rate, number o datapoints and more is automatically printed along with the history of all operations applied to the dataset. This information can also be retrieved separately and in a form useful for further processing the function `summary()` which returns the information in the form of a `dict`:"
+    "We see that sampling rate, number of datapoints and more is automatically printed along with the history of all operations applied to the dataset. This information can also be retrieved separately and in a form useful for further processing the function `summary()` which returns the information in the form of a `dict`:"
    ]
   },
   {
diff --git a/docs/html/docs/plotting.html b/docs/html/docs/plotting.html
@@ -287,7 +287,7 @@ <h3>Navigation</h3>
 <a href="https://mybinder.org/v2/gh/ihrke/pypillometry/master?filepath=docs/plotting.ipynb"><img alt="Binder badge" src="https://mybinder.org/badge_logo.svg" style="vertical-align:text-bottom"></a>
 </div><div class="section" id="Plotting-pupillometric-data-for-exploration">
 <h1>Plotting pupillometric data for exploration<a class="headerlink" href="#Plotting-pupillometric-data-for-exploration" title="Permalink to this headline">¶</a></h1>
-<p>It is crucial to validate preprocessing steps by visually inspecting the results using plots. Therefore, <code class="docutils literal notranslate"><span class="pre">pypillometry</span></code> implements several plotting facilities that encourage active exploration of the dataset. Some of the plotting functions require a Jupyter-notebook with enable widgets (see Installation instructions) so that the plots can be changed interactively, others are purely :mod:<code class="docutils literal notranslate"><span class="pre">matplotlib</span></code>-based.</p>
+<p>It is crucial to validate preprocessing steps by visually inspecting the results using plots. Therefore, <code class="docutils literal notranslate"><span class="pre">pypillometry</span></code> implements several plotting facilities that encourage active exploration of the dataset. Some of the plotting functions require a Jupyter-notebook with enable widgets (see Installation instructions) so that the plots can be changed interactively, others are purely <code class="docutils literal notranslate"><span class="pre">matplotlib</span></code>-based.</p>
 <div class="nbinput nblast docutils container">
 <div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[62]:
 </pre></div>
diff --git a/docs/html/docs/plotting.ipynb b/docs/html/docs/plotting.ipynb
@@ -6,7 +6,7 @@
    "source": [
     "# Plotting pupillometric data for exploration\n",
     "\n",
-    "It is crucial to validate preprocessing steps by visually inspecting the results using plots. Therefore, `pypillometry` implements several plotting facilities that encourage active exploration of the dataset. Some of the plotting functions require a Jupyter-notebook with enable widgets (see Installation instructions) so that the plots can be changed interactively, others are purely :mod:`matplotlib`-based."
+    "It is crucial to validate preprocessing steps by visually inspecting the results using plots. Therefore, `pypillometry` implements several plotting facilities that encourage active exploration of the dataset. Some of the plotting functions require a Jupyter-notebook with enable widgets (see Installation instructions) so that the plots can be changed interactively, others are purely `matplotlib`-based."
    ]
   },
   {
diff --git a/docs/html/docs/summary.html b/docs/html/docs/summary.html
@@ -298,7 +298,7 @@ <h1>Summarizing pupillometric data<a class="headerlink" href="#Summarizing-pupil
 </pre></div>
 </div>
 </div>
-<p>The <code class="docutils literal notranslate"><span class="pre">pypillometry</span></code> package provides several functions for summarizing datasets. Simply <code class="docutils literal notranslate"><span class="pre">print()</span></code>ing a :class:<code class="docutils literal notranslate"><span class="pre">PupilData</span></code> object gives a readable summary of the main properties of the dataset and also prints the complete history of operations applied to the dataset.</p>
+<p>The <code class="docutils literal notranslate"><span class="pre">pypillometry</span></code> package provides several functions for summarizing datasets. Simply <code class="docutils literal notranslate"><span class="pre">print()</span></code>ing a <code class="docutils literal notranslate"><span class="pre">PupilData</span></code> object gives a readable summary of the main properties of the dataset and also prints the complete history of operations applied to the dataset.</p>
 <div class="nbinput docutils container">
 <div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[6]:
 </pre></div>
diff --git a/docs/html/docs/summary.ipynb b/docs/html/docs/summary.ipynb
@@ -22,7 +22,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "The `pypillometry` package provides several functions for summarizing datasets. Simply `print()`ing a :class:`PupilData` object gives a readable summary of the main properties of the dataset and also prints the complete history of operations applied to the dataset."
+    "The `pypillometry` package provides several functions for summarizing datasets. Simply `print()`ing a `PupilData` object gives a readable summary of the main properties of the dataset and also prints the complete history of operations applied to the dataset."
    ]
   },
   {
diff --git a/docs/html/searchindex.js b/docs/html/searchindex.js

Original file line number	Diff line number	Diff line change
`@@ -94,7 +94,7 @@`
`94`	`94`	`"cell_type": "markdown",`
`95`	`95`	`"metadata": {},`
`96`	`96`	`"source": [`
`97`		- "We see that sampling rate, number o datapoints and more is automatically printed along with the history of all operations applied to the dataset. This information can also be retrieved separately and in a form useful for further processing the function `summary()` which returns the information in the form of a `dict`:"
	`97`	+ "We see that sampling rate, number of datapoints and more is automatically printed along with the history of all operations applied to the dataset. This information can also be retrieved separately and in a form useful for further processing the function `summary()` which returns the information in the form of a `dict`:"
`98`	`98`	`]`
`99`	`99`	`},`
`100`	`100`	`{`
Original file line number	Diff line number	Diff line change
`@@ -6,7 +6,7 @@`
`6`	`6`	`"source": [`
`7`	`7`	`"# Plotting pupillometric data for exploration\n",`
`8`	`8`	`"\n",`
`9`		- "It is crucial to validate preprocessing steps by visually inspecting the results using plots. Therefore, `pypillometry` implements several plotting facilities that encourage active exploration of the dataset. Some of the plotting functions require a Jupyter-notebook with enable widgets (see Installation instructions) so that the plots can be changed interactively, others are purely :mod:`matplotlib`-based."
	`9`	+ "It is crucial to validate preprocessing steps by visually inspecting the results using plots. Therefore, `pypillometry` implements several plotting facilities that encourage active exploration of the dataset. Some of the plotting functions require a Jupyter-notebook with enable widgets (see Installation instructions) so that the plots can be changed interactively, others are purely `matplotlib`-based."
`10`	`10`	`]`
`11`	`11`	`},`
`12`	`12`	`{`
Original file line number	Diff line number	Diff line change
`@@ -22,7 +22,7 @@`
`22`	`22`	`"cell_type": "markdown",`
`23`	`23`	`"metadata": {},`
`24`	`24`	`"source": [`
`25`		- "The `pypillometry` package provides several functions for summarizing datasets. Simply `print()`ing a :class:`PupilData` object gives a readable summary of the main properties of the dataset and also prints the complete history of operations applied to the dataset."
	`25`	+ "The `pypillometry` package provides several functions for summarizing datasets. Simply `print()`ing a `PupilData` object gives a readable summary of the main properties of the dataset and also prints the complete history of operations applied to the dataset."
`26`	`26`	`]`
`27`	`27`	`},`
`28`	`28`	`{`