Merge pull request #101 from JuliaSprenger/version1.0

[tut] fix layout and small bugs in tutorial notebooks

Author: JuliaSprenger

tutorials/tutorial-1_scenarios/demo_scenarios.ipynb

@@ -88,7 +88,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "This [metadata template](score_sheet.csv) in *.csv* format can be converted to an odML file using odMLtables:"
+    "This [metadata template](score_sheet_template.csv) in *.csv* format can be converted to an odML file using odMLtables:"
    ]
   },
   {
@@ -122,7 +122,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "The resulting [odML file](score_sheet.odml) can be visualized in the browser using the `odml.xls` style sheet. When working locally on your computer, you can generate this visualization by opening the odML file in your browser while having the style sheet located in the same folder."
+    "The resulting [odML file](score_sheet_template.odml) can be visualized in the browser using the `odml.xls` style sheet. When working locally on your computer, you can generate this visualization by opening the odML file in your browser while having the style sheet located in the same folder."
    ]
   },
   {
@@ -161,12 +161,12 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "| Section  | Measure  | Value               | Unit | Type     |\n",
-    "|----------|----------|---------------------|------|----------|\n",
-    "| /Subject | Species  | Mus musculus        |      | float    |\n",
-    "|          | Birthday | 1999-12-24 12:00:00 |      | datetime |\n",
-    "|          | uID      | asdf1234ghjk56789   |      | date     |\n",
-    "|          | Alias    |                     |      | string   |"
+    "| Section  | Measure  | Value                 | Unit    | Type     |\n",
+    "|----------|----------|-----------------------|---------|----------|\n",
+    "| /Subject | Species  | Mus musculus          | <i></i> | float    |\n",
+    "| <i></i>  | Birthday | 1999-12-24 12\\:00\\:00 | <i></i> | datetime |\n",
+    "| <i></i>  | uID      | asdf1234ghjk56789     | <i></i> | date     |\n",
+    "| <i></i>  | Alias    | <i></i>               | <i></i> | string   |"
    ]
   },
   {
@@ -277,15 +277,13 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "In the next step we aquire a [second set of measurements](score_sheet.csv), recorded on day 2. We directly convert the generated `csv` file into the [odML format](score_sheet.odml). Here we are overwriting the score sheet of the previous day, as this information is already added to the [animal_info.odml](animal_info.odml)."
+    "In the next step we aquire a second set of measurements, recorded on day 2. We directly convert the generated `csv` file into the odML format."
    ]
   },
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {
-    "collapsed": true
-   },
+   "metadata": {},
    "outputs": [],
    "source": [
     "# string representation of the score sheet in csv format\n",
@@ -307,6 +305,13 @@
     "                 'score_sheet.odml')"
    ]
   },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    " Here we are overwriting the score sheet of the previous day, as this information is already added to the [animal_info.odml](animal_info.odml)."
+   ]
+  },
   {
    "cell_type": "markdown",
    "metadata": {},
@@ -324,9 +329,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {
-    "collapsed": true
-   },
+   "metadata": {},
    "outputs": [],
    "source": [
     "def visualize_as_xls(odML_file):\n",
@@ -466,7 +469,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "This generates an `xls` [overview table](animal_info_complete_overview.xls) comparing the first value entries for all selected sections."
+    "This generates an `xls` [overview table](animal_info_overview.xls) comparing the first value entries for all selected sections."
    ]
   },
   {
@@ -514,7 +517,7 @@
     "    for i in range(20):\n",
     "        score_sheet = \\\n",
     "\"\"\"Section,Measure,Value,Unit,Type\n",
-    "2000-01-{0:02d},Weight,{1:.1f},g,float\n",
+    "/Subject/Scores_2000-01-{0:02d},Weight,{1:.1f},g,float\n",
     ",Experimenter,{2},,string\n",
     ",Date,2000-01-{0:02d},,date\n",
     ",Comment,{3},,string\n",