stop using functions and data dirs

BMClab · Oct 23, 2023 · 0855f09 · 0855f09
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diff --git a/notebooks/DataFiltering.ipynb b/notebooks/DataFiltering.ipynb
diff --git a/notebooks/ResidualAnalysis.ipynb b/notebooks/ResidualAnalysis.ipynb
@@ -17,7 +17,7 @@
    "source": [
     "A common problem in signal processing is to automatically determine the optimal cutoff frequency that should be employed in a low-pass filter to attenuate as much as possible the noise without compromising the signal content of the data.   \n",
     "\n",
-    "Before we continue, see [this Jupyter notebook](http://nbviewer.ipython.org/github/demotu/BMC/blob/master/notebooks/DataFiltering.ipynb) for an overview about data filtering if needed.\n",
+    "Before we continue, see [this Jupyter notebook](https://nbviewer.org/github/BMClab/BMC/blob/master/notebooks/DataFiltering.ipynb) for an overview about data filtering if needed.\n",
     "\n",
     "Unfortunately, there is no definite solution for this problem, but there are some techniques, with different degrees of success, to try to determine the optimal cutoff frequency.  \n",
     "\n",
@@ -31,8 +31,14 @@
     "\n",
     "Let's test this function with benchmark data.   \n",
     "\n",
-    "In 1977, Pezzack, Norman and Winter published a paper where they investigated the effects of differentiation and filtering processes on experimental data (the angle of a bar manipulated in space). Since then, these data have became a benchmark to test new algorithms. Let's work with these data (available at [http://isbweb.org/data/pezzack/index.html](http://isbweb.org/data/pezzack/index.html)). The data have the angular displacement measured by video and the angular acceleration  directly measured by an accelerometer, which we will consider as the true acceleration.   \n",
-    "Part of these data are showing next:"
+    "In 1977, Pezzack, Norman and Winter published a paper where they investigated the effects of differentiation and filtering processes on experimental data (the angle of a bar manipulated in space). Since then, these data have became a benchmark to test new algorithms. Let's work with these data (available at [https://isbweb.org/data/pezzack/index.html](http://isbweb.org/data/pezzack/index.html)). The data have the angular displacement measured by video and the angular acceleration  directly measured by an accelerometer, which we will consider as the true acceleration."
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## Setup"
    ]
   },
   {
@@ -284,7 +290,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 4,
+   "execution_count": 3,
    "metadata": {
     "ExecuteTime": {
      "end_time": "2017-12-29T19:22:48.275312Z",
@@ -329,7 +335,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 5,
+   "execution_count": 4,
    "metadata": {
     "ExecuteTime": {
      "end_time": "2017-12-29T19:22:53.522401Z",
@@ -363,7 +369,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 6,
+   "execution_count": 5,
    "metadata": {
     "ExecuteTime": {
      "end_time": "2017-12-29T19:23:32.085684Z",
@@ -407,7 +413,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "The performance seems satisfactory (see [this Jupyter notebook](http://nbviewer.ipython.org/github/demotu/BMC/blob/master/notebooks/DataFiltering.ipynb) for a comparison using other filters), but it is known that this residual analysis algorithm results in oversmoothing the kinematic data (see  [http://www.clinicalgaitanalysis.com/faq/cutoff.html](http://www.clinicalgaitanalysis.com/faq/cutoff.html))."
+    "The performance seems satisfactory (see [this Jupyter notebook](https://nbviewer.org/github/BMClab/BMC/blob/master/notebooks/DataFiltering.ipynb) for a comparison using other filters), but it is known that this residual analysis algorithm results in oversmoothing the kinematic data (see  [https://www.clinicalgaitanalysis.com/faq/cutoff.html](http://www.clinicalgaitanalysis.com/faq/cutoff.html))."
    ]
   },
   {
@@ -416,10 +422,10 @@
    "source": [
     "To read more about the determination of the optimal cutoff frequency, see the following papers:  \n",
     "\n",
-    "- Pezzack, Norman, & Winter (1977). [An assessment of derivative determining techniques used for motion analysis](http://www.health.uottawa.ca/biomech/courses/apa7305/JB-Pezzack-Norman-Winter-1977.pdf). Journal of Biomechanics, 10, 377-382.\n",
-    "- Giakas & Baltizopoulos (1997) [A comparison of automatic filtering techniques applied to biomechanical walking data](http://www.pe.uth.gr/sk_cms/scriptlib/getblob.php?redir=../sk_cms/images/notfound.htm&table=pepublications&field=doc&id=30). J. Biomech. 30, 847-850.\n",
-    "- Alonso, Salgado, Cuadrado & Pintado (2009) [Automatic smoothing of raw kinematic signals using SSA and cluster analysis](http://lim.ii.udc.es/docs/proceedings/2009_09_EUROMECH_Automatic.pdf). 7th EUROMECH Solid Mechanics Conference.\n",
-    "- Kristianslund, Krosshaug & Bogert (2012) [Effect of low pass filtering on joint moments from inverse dynamics: Implications for injury prevention](http://www.klokavskade.no/upload/Publication/Kristianslund_2012_J%20Biomechan_Effect%20of%20low-pass%20filtering%20on%20joint%20moments%20from%20inverse%20dynamics.pdf). J. Biomech. 45, 666-671."
+    "- Pezzack, Norman, & Winter (1977). An assessment of derivative determining techniques used for motion analysis. Journal of Biomechanics, 10, 377-382.\n",
+    "- Giakas & Baltizopoulos (1997) A comparison of automatic filtering techniques applied to biomechanical walking data. J. Biomech. 30, 847-850.\n",
+    "- Alonso, Salgado, Cuadrado & Pintado (2009) [Automatic smoothing of raw kinematic signals using SSA and cluster analysis](https://lim.ii.udc.es/docs/proceedings/2009_09_EUROMECH_Automatic.pdf). 7th EUROMECH Solid Mechanics Conference.\n",
+    "- Kristianslund, Krosshaug & Bogert (2012) Effect of low pass filtering on joint moments from inverse dynamics: Implications for injury prevention. J. Biomech. 45, 666-671."
    ]
   },
   {
@@ -428,8 +434,8 @@
    "source": [
     "## References\n",
     "\n",
-    "- Pezzack JC, Norman RW, & Winter DA (1977). [An assessment of derivative determining techniques used for motion analysis](http://www.health.uottawa.ca/biomech/courses/apa7305/JB-Pezzack-Norman-Winter-1977.pdf). Journal of Biomechanics, 10, 377-382. [PubMed](http://www.ncbi.nlm.nih.gov/pubmed/893476).\n",
-    "- Winter DA (2009) [Biomechanics and motor control of human movement](http://books.google.com.br/books?id=_bFHL08IWfwC&printsec=frontcover&source=gbs_ge_summary_r&cad=0#v=onepage&q&f=false). 4 ed. Hoboken, EUA: Wiley."
+    "- Pezzack JC, Norman RW, & Winter DA (1977). An assessment of derivative determining techniques used for motion analysis. Journal of Biomechanics, 10, 377-382. [PubMed](https://www.ncbi.nlm.nih.gov/pubmed/893476).\n",
+    "- Winter DA (2009) [Biomechanics and motor control of human movement](https://books.google.com.br/books?id=_bFHL08IWfwC&printsec=frontcover&source=gbs_ge_summary_r&cad=0#v=onepage&q&f=false). 4 ed. Hoboken, EUA: Wiley."
    ]
   }
  ],