Update links for new folder structure

Author: CBroz1

00-Getting_started/00-Getting started.ipynb

@@ -316,18 +316,18 @@
     "The next step in the tutorial is to:\n",
     "1. learn the basic of the DataJoint framework with [01-DataJoint Basics](./01-DataJoint%20Basics%20-%20Interactive.ipynb)\n",
     "2. data ingestion in a pipeline, with practical examples in 2 domains:\n",
-    "    + [02-electrophysiology](./electrophysiology/02-Imported%20Tables%20-%20Interactive.ipynb)\n",
-    "    + [02-calcium imaging](./calcium_imaging/02-Imported%20Tables%20-%20Interactive.ipynb)\n",
+    "    + [02-electrophysiology](/02-Electrophysiology/02-Imported%20Tables%20-%20Interactive.ipynb)\n",
+    "    + [02-calcium imaging](./01-Calcium_Imaging/02-Imported%20Tables%20-%20Interactive.ipynb)\n",
     "3. more advanced topics on built-in automatic computation of the pipeline with DataJoint, also with practical examples from:\n",
-    "    + [03-electrophysiology](./electrophysiology/03-Computed%20Table%2C%20Lookup%20Table%2C%20and%20Part%20Table%20-%20Completed.ipynb)\n",
-    "    + [03-calcium imaging](./calcium_imaging/03-Computed%20Table%2C%20Lookup%20Table%2C%20and%20Part%20Table%20-%20Completed.ipynb)"
+    "    + [03-electrophysiology](/02-Electrophysiology/03-Computed%20Table%2C%20Lookup%20Table%2C%20and%20Part%20Table%20-%20Completed.ipynb)\n",
+    "    + [03-calcium imaging](./01-Calcium_Imaging/03-Computed%20Table%2C%20Lookup%20Table%2C%20and%20Part%20Table%20-%20Completed.ipynb)"
    ]
   },
   {
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "As you will find out that these tutorial notebooks are meant to be interactive. There will be empty cells meant for you to write the code yourself, as mini exercises. To access the notebooks with complete solutions, visit this [folder](./completed)."
+    "As you will find out that these tutorial notebooks are meant to be interactive. There will be empty cells meant for you to write the code yourself, as mini exercises. To access the notebooks with complete solutions, visit this [folder](../03-Completed_Exercises)."
    ]
   }
  ],

00-Getting_started/01-DataJoint Basics - Interactive.ipynb

@@ -1535,8 +1535,8 @@
     "In the next session, we are going to extend our data pipeline with tables to represent **imported data** and define new tables to **compute and hold analysis results**.\n",
     "\n",
     "We will use both ephys and calcium imaging as example pipelines:\n",
-    "+ [02-electrophysiology](./electrophysiology/02-Imported%20Tables%20-%20Interactive.ipynb)\n",
-    "+ [02-calcium imaging](./calcium_imaging/02-Imported%20Tables%20-%20Interactive.ipynb)"
+    "+ [02-electrophysiology](../02-Electrophysiology/02-Imported%20Tables%20-%20Interactive.ipynb)\n",
+    "+ [02-calcium imaging](../01-Calcium_Imaging/02-Imported%20Tables%20-%20Interactive.ipynb)"
    ]
   },
   {

00-Getting_started/01-DataJoint Basics - Interactive.py

@@ -556,7 +556,7 @@ class Session(dj.Manual):
 # In the next session, we are going to extend our data pipeline with tables to represent **imported data** and define new tables to **compute and hold analysis results**.
 #
 # We will use both ephys and calcium imaging as example pipelines:
-# + [02-electrophysiology](./electrophysiology/02-Imported%20Tables%20-%20Interactive.ipynb)
-# + [02-calcium imaging](./calcium_imaging/02-Imported%20Tables%20-%20Interactive.ipynb)
+# + [02-calcium imaging](.../01-Calcium_Imaging/02-Imported%20Tables%20-%20Interactive.ipynb)
+# + [02-electrophysiology](../02-Electrophysiology/02-Imported%20Tables%20-%20Interactive.ipynb)
 
 

…a/02-Imported Tables - Interactive.ipynb …g/02-Imported Tables - Interactive.ipynb01-Calcium_Imaging_Data/02-Imported Tables - Interactive.ipynb renamed to 01-Calcium_Imaging/02-Imported Tables - Interactive.ipynb 01-Calcium_Imaging_Data/02-Imported Tables - Interactive.ipynb renamed to 01-Calcium_Imaging/02-Imported Tables - Interactive.ipynb

@@ -11,7 +11,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "Welcome back! In this session, we are going to continue working with the pipeline for the mouse electrophysiology example. \n",
+    "Welcome back! In this session, we are going to continue working with the pipeline for the mouse calcium imaging example. \n",
     "\n",
     "In this session, we will learn to:\n",
     "\n",
@@ -1013,7 +1013,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "We have covered most of the building elements of data pipeline design. Using these elements, we could design more sophiscated pipelines that facillitates your experimental recordings and data analyses."
+    "We have covered most of the building elements of data pipeline design. Using these elements, we could design more sophiscated pipelines that facillitates your experimental recordings and data analyses. To see these concepts in the context of another methodology, see the next folder on [Electrophysiology](../02-Electrophysiology)"
    ]
   }
  ],

…able, and Part Table - Interactive.ipynb …able, and Part Table - Interactive.ipynb01-Calcium_Imaging_Data/03-Computed Table, Lookup Table, and Part Table - Interactive.ipynb renamed to 01-Calcium_Imaging/03-Computed Table, Lookup Table, and Part Table - Interactive.ipynb 01-Calcium_Imaging_Data/03-Computed Table, Lookup Table, and Part Table - Interactive.ipynb renamed to 01-Calcium_Imaging/03-Computed Table, Lookup Table, and Part Table - Interactive.ipynb

@@ -464,7 +464,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "Here we have prepared two tif files of scanning in the [data](../data/calcium_imaging) folder `example_scan_01.tif` and `example_scan_02.tif` "
+    "Here we have prepared two tif files of scanning in the [data](../data/01-Calcium_Imaging) folder `example_scan_01.tif` and `example_scan_02.tif` "
    ]
   },
   {
@@ -481,7 +481,7 @@
     }
    ],
    "source": [
-    "ls ../calcium_imaging/data"
+    "ls ../01-Calcium_Imaging/data"
    ]
   },
   {
@@ -658,7 +658,7 @@
    ],
    "source": [
     "from skimage import io\n",
-    "im = io.imread('../calcium_imaging/data/example_scan_01.tif')\n",
+    "im = io.imread('../01-Calcium_Imaging/data/example_scan_01.tif')\n",
     "print(im.shape)"
    ]
   },
@@ -1261,7 +1261,7 @@
     "    \"\"\"\n",
     "    def make(self, key):  # key is the primary key of one of the entries in the table `Scan`\n",
     "        # fetch data directory from table Session\n",
-    "        data_path = '../calcium_imaging/' + (Session & key).fetch1('data_path')\n",
+    "        data_path = '../01-Calcium_Imaging/' + (Session & key).fetch1('data_path')\n",
     "        \n",
     "        # fetch data file name from table Scan\n",
     "        file_name = (Scan & key).fetch1('file_name')\n",

…um_Imaging_Data/data/example_scan_01.tif …Calcium_Imaging/data/example_scan_01.tif01-Calcium_Imaging_Data/data/example_scan_01.tif renamed to 01-Calcium_Imaging/data/example_scan_01.tif 01-Calcium_Imaging_Data/data/example_scan_01.tif renamed to 01-Calcium_Imaging/data/example_scan_01.tif

@@ -556,7 +556,7 @@
     }
    ],
    "source": [
-    "filename = '../electrophysiology/data/data_{mouse_id}_{session_date}.npy'.format(**key)\n",
+    "filename = '../02-Electrophysiology/data/data_{mouse_id}_{session_date}.npy'.format(**key)\n",
     "filename"
    ]
   },
@@ -1469,7 +1469,7 @@
     "    \"\"\"\n",
     "    def make(self, key):\n",
     "        # use key dictionary to determine the data file path\n",
-    "        data_file = \"../electrophysiology/data/data_{mouse_id}_{session_date}.npy\".format(**key)\n",
+    "        data_file = \"../02-Electrophysiology/data/data_{mouse_id}_{session_date}.npy\".format(**key)\n",
     "\n",
     "        # load the data\n",
     "        data = np.load(data_file)\n",