recheck all the paths, fix pathing errors when deployed on codebook

Author: ttngu207

01-Calcium_Imaging/02-Imported Tables - Interactive.ipynb

@@ -50,7 +50,6 @@
    "source": [
     "import numpy as np\n",
     "import matplotlib.pyplot as plt\n",
-    "\n",
     "%matplotlib inline"
    ]
   },
@@ -67,8 +66,6 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "import os\n",
-    "if os.path.basename(os.getcwd())!='notebooks': os.chdir('/home/notebooks')\n",
     "from tutorial_pipeline.mouse_session import schema, Mouse, Session"
    ]
   },
@@ -176,7 +173,18 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "ls data"
+    "from tutorial_pipeline import data_dir\n",
+    "data_dir"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "for f in data_dir.glob('*.tif'):\n",
+    "    print(f)"
    ]
   },
   {
@@ -229,8 +237,9 @@
    "metadata": {},
    "outputs": [],
    "source": [
+    "import os\n",
     "from skimage import io\n",
-    "im = io.imread('data/example_scan_01.tif')\n",
+    "im = io.imread(data_dir / 'example_scan_01.tif')\n",
     "print(im.shape)"
    ]
   },
@@ -705,7 +714,12 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.7.3"
+   "version": "3.7.16"
+  },
+  "vscode": {
+   "interpreter": {
+    "hash": "949777d72b0d2535278d3dc13498b2535136f6dfe0678499012e853ee9abcab1"
+   }
   }
  },
  "nbformat": 4,

01-Calcium_Imaging/03-Computed Table, Lookup Table, and Part Table - Interactive.ipynb

@@ -69,8 +69,6 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "import os\n",
-    "if os.path.basename(os.getcwd())!='notebooks': os.chdir('/home/notebooks')\n",
     "from tutorial_pipeline.imaging import schema, Mouse, Session, Scan, AverageFrame"
    ]
   },
@@ -1033,7 +1031,12 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.7.3"
+   "version": "3.7.16"
+  },
+  "vscode": {
+   "interpreter": {
+    "hash": "949777d72b0d2535278d3dc13498b2535136f6dfe0678499012e853ee9abcab1"
+   }
   }
  },
  "nbformat": 4,

02-Electrophysiology/02-Imported Tables - Interactive.ipynb

@@ -66,8 +66,6 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "import os\n",
-    "if os.path.basename(os.getcwd())!='notebooks': os.chdir('/home/notebooks')\n",
     "from tutorial_pipeline.mouse_session import schema, Mouse, Session"
    ]
   },
@@ -129,6 +127,16 @@
     "So `data_100_2017-05-25.npy` is the data for session identified by `mouse_id = 100` and `session_date = \"2017-05-25\"`."
    ]
   },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "from tutorial_pipeline import data_dir\n",
+    "data_dir"
+   ]
+  },
   {
    "cell_type": "markdown",
    "metadata": {},
@@ -199,7 +207,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "filename = 'data/data_{mouse_id}_{session_date}.npy'.format(**key)\n",
+    "filename = '{data_dir}/data_{mouse_id}_{session_date}.npy'.format(**key, data_dir=data_dir)\n",
     "filename"
    ]
   },
@@ -489,7 +497,7 @@
     "    \"\"\"\n",
     "    def make(self, key):\n",
     "        # use key dictionary to determine the data file path\n",
-    "        data_file = \"data/data_{mouse_id}_{session_date}.npy\".format(**key)\n",
+    "        data_file = '{data_dir}/data_{mouse_id}_{session_date}.npy'.format(**key, data_dir=data_dir)\n",
     "\n",
     "        # load the data\n",
     "        data = np.load(data_file)\n",
@@ -663,7 +671,7 @@
    "formats": "ipynb,py:light"
   },
   "kernelspec": {
-   "display_name": "Python 3 (ipykernel)",
+   "display_name": "Python 3",
    "language": "python",
    "name": "python3"
   },
@@ -677,7 +685,12 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.8.12"
+   "version": "3.7.16"
+  },
+  "vscode": {
+   "interpreter": {
+    "hash": "949777d72b0d2535278d3dc13498b2535136f6dfe0678499012e853ee9abcab1"
+   }
   }
  },
  "nbformat": 4,

02-Electrophysiology/02-Imported Tables - Interactive.py

@@ -34,8 +34,6 @@
 
 # Now we would like to continue working with the tables we defined in the previous notebook. To do so, we would need the classes for each table: `Mouse` and `Session`. We can either redefine it here, but for your convenience, we have included the schema and table class definitions in a package called `tutorial_pipeline.mouse_session`, from which you can import the classes as well as the schema object. We will use the schema object again to define more tables.
 
-import os
-if os.path.basename(os.getcwd())!='notebooks': os.chdir('/home/notebooks')
 from tutorial_pipeline.mouse_session import schema, Mouse, Session
 
 Mouse()
@@ -76,7 +74,7 @@
 key = keys[0]
 key
 
-filename = 'data/data_{mouse_id}_{session_date}.npy'.format(**key)
+filename = '../data/data_{mouse_id}_{session_date}.npy'.format(**key)
 filename
 
 # Here we have made use of Python's dictionary unpacking and `format` method on strings to generate the filename from the `key`.
@@ -184,7 +182,7 @@ class Neuron(dj.Imported):
     """
     def make(self, key):
         # use key dictionary to determine the data file path
-        data_file = "data/data_{mouse_id}_{session_date}.npy".format(**key)
+        data_file = "../data/data_{mouse_id}_{session_date}.npy".format(**key)
 
         # load the data
         data = np.load(data_file)

02-Electrophysiology/03-Computed Table, Lookup Table, and Part Table - Interactive.ipynb

@@ -69,8 +69,6 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "import os\n",
-    "if os.path.basename(os.getcwd())!='notebooks': os.chdir('/home/notebooks')\n",
     "from tutorial_pipeline.ephys_cell_activity import schema, Mouse, Session, Neuron"
    ]
   },
@@ -1098,7 +1096,7 @@
    "formats": "ipynb,py:light"
   },
   "kernelspec": {
-   "display_name": "Python 3 (ipykernel)",
+   "display_name": "Python 3",
    "language": "python",
    "name": "python3"
   },
@@ -1112,7 +1110,12 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.8.12"
+   "version": "3.7.16"
+  },
+  "vscode": {
+   "interpreter": {
+    "hash": "949777d72b0d2535278d3dc13498b2535136f6dfe0678499012e853ee9abcab1"
+   }
   }
  },
  "nbformat": 4,

02-Electrophysiology/03-Computed Table, Lookup Table, and Part Table - Interactive.py

@@ -37,8 +37,6 @@
 
 # Similarly as before, to continue working with the tables we defined in the previous notebook, we can either redefine the classes for each table `Mouse`, `Session`, `Neuron` and populate them. Or, again for your convenience, we can import them from the `tutorial_pipeline.ephys_cell_activity` module.
 
-import os
-if os.path.basename(os.getcwd())!='notebooks': os.chdir('/home/notebooks')
 from tutorial_pipeline.ephys_cell_activity import schema, Mouse, Session, Neuron
 
 Session()