Merge pull request #20 from kabilar/main

Update readme.  Fix notebooks.

Author: ttngu207

…Getting_started/00-Getting started.ipynb …Getting_Started/00-Getting Started.ipynb00-Getting_started/00-Getting started.ipynb renamed to 00-Getting_Started/00-Getting Started.ipynb 00-Getting_started/00-Getting started.ipynb renamed to 00-Getting_Started/00-Getting Started.ipynb

@@ -76,6 +76,7 @@
    ]
   },
   {
+   "attachments": {},
    "cell_type": "markdown",
    "metadata": {},
    "source": [
@@ -86,7 +87,7 @@
     "> * In a session of electrophysiology\n",
     ">> * you record electrical activity from a single neuron. You use recording equipment that produces separate data files for each neuron you recorded.\n",
     ">> * Neuron's activities are recorded as raw traces. Neuron's spikes needs to be detected for further analysis to be performed.\n",
-    "> * In a sesssion of calcium imaging\n",
+    "> * In a session of calcium imaging\n",
     ">> * you scan a brain region containing a number of neurons. You use recording equipment that produces separate data files for each scan you performed.\n",
     ">> * you would like to segment the frames and get the regions of interest (ROIs), and save a mask for each ROI\n",
     ">> * finally you would like to extract the trace from each segmented ROI"
@@ -107,6 +108,7 @@
    ]
   },
   {
+   "attachments": {},
    "cell_type": "markdown",
    "metadata": {},
    "source": [
@@ -117,7 +119,7 @@
     "> * In a session of electrophysiology\n",
     ">> * you record electrical activity from a **single neuron**. You use recording equipment that produces separate data files for each neuron you recorded.\n",
     ">> * Neuron's activities are recorded as raw traces. **Neuron's spikes** needs to be detected for further analysis to be performed.\n",
-    "> * In a sesssion of calcium imaging\n",
+    "> * In a session of calcium imaging\n",
     ">> * you scan a brain region containing a number of neurons. You use recording equipment that produces separate data files for each **scan** you performed.\n",
     ">> * you would like to segment the frames and get the **regions of interest (ROIs)**, and save a mask for each ROI\n",
     ">> * finally you would like to extract the **trace** from each segmented ROI"
@@ -225,17 +227,11 @@
    ]
   },
   {
+   "attachments": {},
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "We create the schema using `dj.schema()` function, passing in the name of the schema. For this workshop, you are given the database privilege to create any schema **starting with your username followed by a `_` charcter**. So if your username is `john`, you can make any schema starting with `john_`, such as `john_tutorial`."
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": [
-    "Let's create a schema called `pipeline`, prefixed by `username_`."
+    "We create the schema using `dj.schema()` function, passing in the name of the schema. For this workshop, you are given the database privilege to use any schema name.  Let's create a schema called `tutorial`."
    ]
   },
   {
@@ -244,7 +240,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "schema = dj.schema('{YOUR_USERNAME}_tutorial')"
+    "schema = dj.schema('tutorial')"
    ]
   },
   {
@@ -555,7 +551,7 @@
    "source": [
     "Note that, to uniquely identify an experimental session (or simply a **session**), we need to know the mouse that the session was about. In other words, a session cannot existing without a corresponding mouse! \n",
     "\n",
-    "With **mouse** already represented as a table in our pipeline, we say that the session **depends on** the mouse! We could graphically represent this in an **entity relationship diagram (ERD)** by drawing the line between two tables, with the one below (**session**) dependeing on the one above (**mouse**)."
+    "With **mouse** already represented as a table in our pipeline, we say that the session **depends on** the mouse! We could graphically represent this in an **entity relationship diagram (ERD)** by drawing the line between two tables, with the one below (**session**) depending on the one above (**mouse**)."
    ]
   },
   {
@@ -1181,11 +1177,12 @@
    ]
   },
   {
+   "attachments": {},
    "cell_type": "markdown",
    "metadata": {},
    "source": [
     "### Rename attribute with proj()\n",
-    "Say we want to rename the exisiting attribute `dob` of the `Mouse` table to `date_of_birth`, this can be done using `.proj()`"
+    "Say we want to rename the existing attribute `dob` of the `Mouse` table to `date_of_birth`, this can be done using `.proj()`"
    ]
   },
   {
@@ -1215,10 +1212,11 @@
    ]
   },
   {
+   "attachments": {},
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "Note: as you can see, the projection results keep the primary attributes from the `Mouse * Session` joinning operation, while removing all other non-primary attributes. To Keep all other attributes, you can use the `...` syntax"
+    "Note: as you can see, the projection results keep the primary attributes from the `Mouse * Session` joining operation, while removing all other non-primary attributes. To Keep all other attributes, you can use the `...` syntax"
    ]
   },
   {

…/01-DataJoint Basics - Interactive.ipynb …/01-DataJoint Basics - Interactive.ipynb00-Getting_started/01-DataJoint Basics - Interactive.ipynb renamed to 00-Getting_Started/01-DataJoint Basics - Interactive.ipynb 00-Getting_started/01-DataJoint Basics - Interactive.ipynb renamed to 00-Getting_Started/01-DataJoint Basics - Interactive.ipynb

@@ -45,13 +45,14 @@
    ]
   },
   {
+   "attachments": {},
    "cell_type": "markdown",
    "metadata": {},
    "source": [
     "If you visit the [documentation for DataJoint](https://docs.datajoint.io/introduction/Data-pipelines.html), we define a data pipeline as follows:\n",
     "> A data pipeline is a sequence of steps (more generally a directed acyclic graph) with integrated storage at each step. These steps may be thought of as nodes in a graph.\n",
     "\n",
-    "While this is an accurate description, it may not be the most intuitive definition. Put succinctly, a data pipeline is a listing or a \"map\" of various \"things\" that you work with in a project, with line connecting things to each other to indicate their dependecies. The \"things\" in a data pipeline tends to be the *nouns* you find when describing a project. The \"things\" may include anything from mouse, experimenter, equipment, to experiment session, trial, two-photon scans, electric activities, to receptive fields, neuronal spikes, to figures for a publication! A data pipeline gives you a framework to:\n",
+    "While this is an accurate description, it may not be the most intuitive definition. Put succinctly, a data pipeline is a listing or a \"map\" of various \"things\" that you work with in a project, with line connecting things to each other to indicate their dependencies. The \"things\" in a data pipeline tends to be the *nouns* you find when describing a project. The \"things\" may include anything from mouse, experimenter, equipment, to experiment session, trial, two-photon scans, electric activities, to receptive fields, neuronal spikes, to figures for a publication! A data pipeline gives you a framework to:\n",
     "\n",
     "1. define these \"things\" as tables in which you can store the information about them\n",
     "2. define the relationships (in particular the dependencies) between the \"things\"\n",
@@ -76,6 +77,7 @@
    ]
   },
   {
+   "attachments": {},
    "cell_type": "markdown",
    "metadata": {},
    "source": [
@@ -86,7 +88,7 @@
     "> * In a session of electrophysiology\n",
     ">> * you record electrical activity from a single neuron. You use recording equipment that produces separate data files for each neuron you recorded.\n",
     ">> * Neuron's activities are recorded as raw traces. Neuron's spikes needs to be detected for further analysis to be performed.\n",
-    "> * In a sesssion of calcium imaging\n",
+    "> * In a session of calcium imaging\n",
     ">> * you scan a brain region containing a number of neurons. You use recording equipment that produces separate data files for each scan you performed.\n",
     ">> * you would like to segment the frames and get the regions of interest (ROIs), and save a mask for each ROI\n",
     ">> * finally you would like to extract the trace from each segmented ROI"
@@ -107,6 +109,7 @@
    ]
   },
   {
+   "attachments": {},
    "cell_type": "markdown",
    "metadata": {},
    "source": [
@@ -117,7 +120,7 @@
     "> * In a session of electrophysiology\n",
     ">> * you record electrical activity from a **single neuron**. You use recording equipment that produces separate data files for each neuron you recorded.\n",
     ">> * Neuron's activities are recorded as raw traces. **Neuron's spikes** needs to be detected for further analysis to be performed.\n",
-    "> * In a sesssion of calcium imaging\n",
+    "> * In a session of calcium imaging\n",
     ">> * you scan a brain region containing a number of neurons. You use recording equipment that produces separate data files for each **scan** you performed.\n",
     ">> * you would like to segment the frames and get the **regions of interest (ROIs)**, and save a mask for each ROI\n",
     ">> * finally you would like to extract the **trace** from each segmented ROI"
@@ -225,17 +228,11 @@
    ]
   },
   {
+   "attachments": {},
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "We create the schema using `dj.schema()` function, passing in the name of the schema. For this workshop, you are given the database privilege to create any schema **starting with your username followed by a `_` charcter**. So if your username is `john`, you can make any schema starting with `john_`, such as `john_tutorial`."
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": [
-    "Let's create a schema called `pipeline`, prefixed by `username_`."
+    "We create the schema using `dj.schema()` function, passing in the name of the schema. For this workshop, you are given the database privilege to use any schema name.  Let's create a schema called `tutorial`."
    ]
   },
   {
@@ -252,7 +249,7 @@
     }
    ],
    "source": [
-    "schema = dj.schema('{YOUR_USERNAME}_tutorial')"
+    "schema = dj.schema('tutorial')"
    ]
   },
   {
@@ -1059,12 +1056,13 @@
    ]
   },
   {
+   "attachments": {},
    "cell_type": "markdown",
    "metadata": {},
    "source": [
     "Note that, to uniquely identify an experimental session (or simply a **session**), we need to know the mouse that the session was about. In other words, a session cannot existing without a corresponding mouse! \n",
     "\n",
-    "With **mouse** already represented as a table in our pipeline, we say that the session **depends on** the mouse! We could graphically represent this in an **entity relationship diagram (ERD)** by drawing the line between two tables, with the one below (**session**) dependeing on the one above (**mouse**)."
+    "With **mouse** already represented as a table in our pipeline, we say that the session **depends on** the mouse! We could graphically represent this in an **entity relationship diagram (ERD)** by drawing the line between two tables, with the one below (**session**) depending on the one above (**mouse**)."
    ]
   },
   {
@@ -1109,47 +1107,7 @@
    "outputs": [
     {
      "data": {
-      "image/svg+xml": [
-       "<svg height=\"114pt\" viewBox=\"0.00 0.00 66.69 114.00\" width=\"67pt\" xmlns=\"http://www.w3.org/2000/svg\" xmlns:xlink=\"http://www.w3.org/1999/xlink\">\n",
-       "<g class=\"graph\" id=\"graph0\" transform=\"scale(1 1) rotate(0) translate(4 110)\">\n",
-       "<title>%3</title>\n",
-       "<polygon fill=\"#ffffff\" points=\"-4,4 -4,-110 62.6914,-110 62.6914,4 -4,4\" stroke=\"transparent\"/>\n",
-       "<!-- Mouse -->\n",
-       "<g class=\"node\" id=\"node1\">\n",
-       "<title>Mouse</title>\n",
-       "<g id=\"a_node1\"><a xlink:title=\"mouse_id             \r",
-       "------------------------------\r",
-       "dob=null             \r",
-       "sex=&quot;unknown&quot;        \r",
-       "\">\n",
-       "<polygon fill=\"#00ff00\" fill-opacity=\"0.188235\" points=\"55.3633,-106 3.3281,-106 3.3281,-71 55.3633,-71 55.3633,-106\" stroke=\"#00ff00\" stroke-opacity=\"0.188235\"/>\n",
-       "<text fill=\"#006400\" font-family=\"arial\" font-size=\"12.00\" text-anchor=\"start\" text-decoration=\"underline\" x=\"11.3369\" y=\"-86.7994\">Mouse</text>\n",
-       "</a>\n",
-       "</g>\n",
-       "</g>\n",
-       "<!-- Session -->\n",
-       "<g class=\"node\" id=\"node2\">\n",
-       "<title>Session</title>\n",
-       "<g id=\"a_node2\"><a xlink:title=\"→ Mouse\r",
-       "session_date         \r",
-       "------------------------------\r",
-       "experiment_setup     \r",
-       "experimenter         \r",
-       "data_path=&quot;&quot;         \r",
-       "\">\n",
-       "<polygon fill=\"#00ff00\" fill-opacity=\"0.188235\" points=\"58.5379,-35 .1535,-35 .1535,0 58.5379,0 58.5379,-35\" stroke=\"#00ff00\" stroke-opacity=\"0.188235\"/>\n",
-       "<text fill=\"#006400\" font-family=\"arial\" font-size=\"12.00\" text-anchor=\"start\" text-decoration=\"underline\" x=\"8\" y=\"-15.7994\">Session</text>\n",
-       "</a>\n",
-       "</g>\n",
-       "</g>\n",
-       "<!-- Mouse&#45;&gt;Session -->\n",
-       "<g class=\"edge\" id=\"edge1\">\n",
-       "<title>Mouse-&gt;Session</title>\n",
-       "<path d=\"M29.3457,-70.9494C29.3457,-60.1083 29.3457,-46.2366 29.3457,-35.3418\" fill=\"none\" stroke=\"#000000\" stroke-opacity=\"0.250980\" stroke-width=\".75\"/>\n",
-       "</g>\n",
-       "</g>\n",
-       "</svg>"
-      ],
+      "image/svg+xml": "<svg height=\"114pt\" viewBox=\"0.00 0.00 66.69 114.00\" width=\"67pt\" xmlns=\"http://www.w3.org/2000/svg\" xmlns:xlink=\"http://www.w3.org/1999/xlink\">\n<g class=\"graph\" id=\"graph0\" transform=\"scale(1 1) rotate(0) translate(4 110)\">\n<title>%3</title>\n<polygon fill=\"#ffffff\" points=\"-4,4 -4,-110 62.6914,-110 62.6914,4 -4,4\" stroke=\"transparent\"/>\n<!-- Mouse -->\n<g class=\"node\" id=\"node1\">\n<title>Mouse</title>\n<g id=\"a_node1\"><a xlink:title=\"mouse_id             \r\n------------------------------\r\ndob=null             \r\nsex=&quot;unknown&quot;        \r\n\">\n<polygon fill=\"#00ff00\" fill-opacity=\"0.188235\" points=\"55.3633,-106 3.3281,-106 3.3281,-71 55.3633,-71 55.3633,-106\" stroke=\"#00ff00\" stroke-opacity=\"0.188235\"/>\n<text fill=\"#006400\" font-family=\"arial\" font-size=\"12.00\" text-anchor=\"start\" text-decoration=\"underline\" x=\"11.3369\" y=\"-86.7994\">Mouse</text>\n</a>\n</g>\n</g>\n<!-- Session -->\n<g class=\"node\" id=\"node2\">\n<title>Session</title>\n<g id=\"a_node2\"><a xlink:title=\"→ Mouse\r\nsession_date         \r\n------------------------------\r\nexperiment_setup     \r\nexperimenter         \r\ndata_path=&quot;&quot;         \r\n\">\n<polygon fill=\"#00ff00\" fill-opacity=\"0.188235\" points=\"58.5379,-35 .1535,-35 .1535,0 58.5379,0 58.5379,-35\" stroke=\"#00ff00\" stroke-opacity=\"0.188235\"/>\n<text fill=\"#006400\" font-family=\"arial\" font-size=\"12.00\" text-anchor=\"start\" text-decoration=\"underline\" x=\"8\" y=\"-15.7994\">Session</text>\n</a>\n</g>\n</g>\n<!-- Mouse&#45;&gt;Session -->\n<g class=\"edge\" id=\"edge1\">\n<title>Mouse-&gt;Session</title>\n<path d=\"M29.3457,-70.9494C29.3457,-60.1083 29.3457,-46.2366 29.3457,-35.3418\" fill=\"none\" stroke=\"#000000\" stroke-opacity=\"0.250980\" stroke-width=\".75\"/>\n</g>\n</g>\n</svg>",
       "text/plain": [
        "<datajoint.diagram.Diagram at 0xa1d699588>"
       ]
@@ -1160,7 +1118,7 @@
     }
    ],
    "source": [
-    "dj.ERD(schema)"
+    "dj.Diagram(schema)"
    ]
   },
   {
@@ -4052,11 +4010,12 @@
    ]
   },
   {
+   "attachments": {},
    "cell_type": "markdown",
    "metadata": {},
    "source": [
     "### Rename attribute with proj()\n",
-    "Say we want to rename the exisiting attribute `dob` of the `Mouse` table to `date_of_birth`, this can be done using `.proj()`"
+    "Say we want to rename the existing attribute `dob` of the `Mouse` table to `date_of_birth`, this can be done using `.proj()`"
    ]
   },
   {
@@ -4284,10 +4243,11 @@
    ]
   },
   {
+   "attachments": {},
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "Note: as you can see, the projection results keep the primary attributes from the `Mouse * Session` joinning operation, while removing all other non-primary attributes. To Keep all other attributes, you can use the `...` syntax"
+    "Note: as you can see, the projection results keep the primary attributes from the `Mouse * Session` joining operation, while removing all other non-primary attributes. To Keep all other attributes, you can use the `...` syntax"
    ]
   },
   {