From 1c1b7fa57ab0c377e0ca6e4b398696d80669095f Mon Sep 17 00:00:00 2001
From: Scott Lowe <scott.code.lowe@gmail.com>
Date: Tue, 15 Jun 2021 09:30:43 +0100
Subject: [PATCH] JNB: Change to using datetime for the output directory

---
 examples/Basic usage - Functional.ipynb | 29 +++++++++++++++++++++----
 examples/Basic usage.ipynb              | 29 ++++++++++++++++++++++++-
 2 files changed, 53 insertions(+), 5 deletions(-)

diff --git a/examples/Basic usage - Functional.ipynb b/examples/Basic usage - Functional.ipynb
index 43fad97c..25075caf 100644
--- a/examples/Basic usage - Functional.ipynb	
+++ b/examples/Basic usage - Functional.ipynb	
@@ -252,12 +252,33 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "# Define the folder where FISSA's outputs will be cached.\n",
+    "# Define the folder where FISSA's outputs will be cached, so they can be\n",
+    "# quickly reloaded in the future without having to recompute them.\n",
+    "#\n",
+    "# This argument is optional; if it is not provided, FISSA will not save its\n",
+    "# results for later use.\n",
     "#\n",
     "# Note: you *must* use a different folder for each experiment.\n",
+    "#\n",
+    "# In this example, we will use the current datetime as the\n",
+    "# name of the experiment, but you can name your experiments\n",
+    "# however you want to.\n",
+    "\n",
+    "import datetime\n",
     "\n",
-    "output_folder = \"fissa_example\"\n",
+    "output_folder = \"fissa-example_{}\".format(\n",
+    "    datetime.datetime.now().strftime(\"%Y-%m-%d_%H-%M-%S\")\n",
+    ")\n",
     "\n",
+    "print(output_folder)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
     "# Run FISSA, saving to the output directory\n",
     "result = fissa.run_fissa(images_location, rois_location, output_folder)"
    ]
@@ -313,7 +334,7 @@
     "These interface similarly as `experiment.ROIs`, `experiment.raw`, and `experiment.result` described above. However, Matlab counts from 1 (as opposed to Python counting from 0), such that the ROI, raw trace, and decontaminated trace are all found for cell 0 trial 0 as:\n",
     "\n",
     "```octave\n",
-    "data = load(\"fissa_example/matlab.mat\")\n",
+    "data = load(\"experiment_results.mat\")\n",
     "data.ROIs.cell0.trial0{1}  % polygon for the ROI\n",
     "data.ROIs.cell0.trial0{2}  % polygon for first neuropil subregion\n",
     "data.result.cell0.trial0(1, :)  % final extracted cell signal\n",
@@ -363,7 +384,7 @@
     "alpha = 0.1\n",
     "\n",
     "# If you change the experiment parameters, you need to change the cache directory too\n",
-    "output_folder2 = \"fissa_example2\"\n",
+    "output_folder2 = \"fissa-example-alt\"\n",
     "\n",
     "# Run FISSA with these parameters\n",
     "result = fissa.run_fissa(\n",
diff --git a/examples/Basic usage.ipynb b/examples/Basic usage.ipynb
index f5bb8585..093e79d8 100755
--- a/examples/Basic usage.ipynb	
+++ b/examples/Basic usage.ipynb	
@@ -82,7 +82,34 @@
     "```\n",
     "Defining a different roiset per image can be useful if you need to adjust for motion drift for example.\n",
     "\n",
-    "Then, we can define out experiment:"
+    "Then, we can define our experiment:"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# Define the folder where FISSA's outputs will be cached, so they can be\n",
+    "# quickly reloaded in the future without having to recompute them.\n",
+    "#\n",
+    "# This argument is optional; if it is not provided, FISSA will not save its\n",
+    "# results for later use.\n",
+    "#\n",
+    "# Note: you *must* use a different folder for each experiment.\n",
+    "#\n",
+    "# In this example, we will use the current datetime as the\n",
+    "# name of the experiment, but you can name your experiments\n",
+    "# however you want to.\n",
+    "\n",
+    "import datetime\n",
+    "\n",
+    "output_folder = \"fissa-example_{}\".format(\n",
+    "    datetime.datetime.now().strftime(\"%Y-%m-%d_%H-%M-%S\")\n",
+    ")\n",
+    "\n",
+    "print(output_folder)"
    ]
   },
   {