Adding Youtube video, and some PEP8 changes

nasa-nccs-hpda · Oct 6, 2023 · 3e11390 · 3e11390
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diff --git a/README.rst b/README.rst
@@ -202,11 +202,10 @@ Teams' Validation Example on the Science Managed Cloud Environment
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
 The following is an example workflow using the Science Managed Cloud Environment. Depending on your environment,
-you will need to modify some of these steps.
+you will need to modify some of these steps. If you have been notified that a tutorial environment is already 
+generated for you, feel free to skip to step 3.
 
-If you have been notified that a tutorial environment is already generated for you, feel free to skip to step 3.
-
-#. Setup the working environment - Only done by the Team Administrator
+**1. Setup the working environment - Only done by the Team Administrator**
 
 For this first step we will setup the working directories for your team. In this case we need 3 main directories.
 When using the Daskhub system, we have a directory called /home/jovyan, which is your personal home directory. Then
@@ -219,27 +218,26 @@ setup your Daskhub working environment.
 
   wget https://raw.githubusercontent.com/nasa-nccs-hpda/eo-validation/main/notebooks/ValidationEnvironmentSetup.ipynb
 
-Then, we will setup our data, labels, and original points directories:
-
-.. code:: bash
 
-  mkdir -p /efs/projects/<project_name>/data /efs/projects/<project_name>/labels /efs/projects/<project_name>/validation/original_points
-
-#. Upload the data to your system of choice - Only done by the Team Administrator
+**2. Upload the data to your system of choice - Only done by the Team Administrator**
 
 In this step you will need to upload the data you will be using in the validation exercise. In general this will require
 you to upload a pair of data (GeoTIFF satellite imagery) and labels (GeoTIFF single band label), and locate them in a 
 general location. To upload the data to SMCE, you can use scp from a terminal within Daskhub, or manually uploading the
 imagery using Drag and Drop options.
 
-#. Start working on your environment
+**3. Start working on your environment**
 
 In this step users can start working on their personal notebooks. These notebooks can be accessed by opening the 
 ValidationDashboard.ipynb file from your working directory. For example, if you are part of Dr. Peng group, you can
 access your personal tutorial notebook under /efs/Bin_UIUC/<your_username>/ValidationDashboard.ipynb.
 
 If you need additional help walking through the notebook, here is a short video on how to get started `YouTube <https://youtu.be/3tG7bQ-10ac>`__.
 
+.. image:: https://img.youtube.com/vi/3tG7bQ-10ac/maxresdefault.jpg
+    :alt: eo-validation demo
+    :target: https://www.youtube.com/watch?v=3tG7bQ-10ac
+
 Overall Validation Workflow
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 

diff --git a/docs/conf.py b/docs/conf.py
@@ -1,27 +1,14 @@
-# Configuration file for the Sphinx documentation builder.
-#
-# For the full list of built-in configuration values, see the documentation:
-# https://www.sphinx-doc.org/en/master/usage/configuration.html
 import os
 import sys
 
 sys.path.insert(0, os.path.abspath('..'))
 
 import eo_validation
 
-# package_path = os.path.abspath('..')
-# os.environ['PYTHONPATH'] = ':'.join((package_path, os.environ.get('PYTHONPATH', '')))
-
-# -- Project information -----------------------------------------------------
-# https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information
-
 project = 'eo-validation'
 copyright = '2023, Jordan A. Caraballo-Vega'
 author = 'Jordan A. Caraballo-Vega'
 
-# -- General configuration ---------------------------------------------------
-# https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration
-
 extensions = [
     'sphinx.ext.autodoc',
     'sphinx_autodoc_typehints',
@@ -46,23 +33,10 @@
 templates_path = ['_templates']
 exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store']
 
-# -- Options for HTML output -------------------------------------------------
-# https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output
-
-#source_suffix ={
-#    '.rst': 'restructuredtext',
-#    '.txt': 'markdown',
-#    '.md': 'markdown',
-#    '.ipynb': 'myst-nb'
-#}
 master_doc = "index"
-
 version = release = eo_validation.__version__
-
 pygments_style = "sphinx"
-
 todo_include_todos = False
-
 html_theme = 'sphinx_rtd_theme'
 
 # html_static_path = ['_static/']
@@ -74,4 +48,4 @@
     "dollarmath",
     "html_image",
 ]
-myst_url_schemes = ("http", "https", "mailto")
+myst_url_schemes = ("http", "https", "mailto")
diff --git a/eo_validation/__init__.py b/eo_validation/__init__.py
@@ -1,3 +1,3 @@
 __author__ = """Jordan A. Caraballo-Vega"""
 __email__ = "jordan.a.caraballo-vega@nasa.gov"
-__version__ = "0.0.1"
+__version__ = "0.1.1"
diff --git a/eo_validation/validation_dashboard.py b/eo_validation/validation_dashboard.py
@@ -300,7 +300,8 @@ def generate_points(
             # Make sure expected accuracies match size of classes found
             if len(self.expected_accuracies) != raster_prediction['predicted'].max() + 1:
                 self.expected_accuracies = \
-                    [self.expected_accuracies[0]] * (raster_prediction['predicted'].max() + 1)
+                    [self.expected_accuracies[0]] * \
+                        (raster_prediction['predicted'].max() + 1)
 
             print("self.expected_accuracies", self.expected_accuracies)
             print("unique_counts", unique_counts)
@@ -336,8 +337,9 @@ def generate_points(
             if unique_counts['n_point'].sum() < val_total_points:
                 unique_counts.at[0, 'n_point'] += \
                     val_total_points - unique_counts['n_point'].sum()
-            elif unique_counts['n_point'].sum() > val_total_points:                
-                unique_counts.at[unique_counts['n_point'].idxmax(), 'n_point'] -= \
+            elif unique_counts['n_point'].sum() > val_total_points:               
+                unique_counts.at[
+                    unique_counts['n_point'].idxmax(), 'n_point'] -= \
                     unique_counts['n_point'].sum() - val_total_points
 
             for class_id, row in unique_counts.iterrows():
@@ -362,8 +364,10 @@ def generate_points(
             # Convert to dataframe and filter no-data
             raster_prediction = \
                 raster_prediction.squeeze().to_dataframe().reset_index()
+
+            # drop some unecessary columns
             raster_prediction = raster_prediction.drop(
-                ['band', 'spatial_ref'], axis=1)  # drop some unecessary columns
+                ['band', 'spatial_ref'], axis=1)
 
             # Only select appropiate values, remove no-data
             raster_prediction = raster_prediction[
@@ -373,7 +377,7 @@ def generate_points(
             raster_prediction = raster_prediction.astype({'predicted': 'int'})
 
             # Generate random points (drop randomly from the dataset
-            raster_prediction = raster_prediction.sample(n = n_points)
+            raster_prediction = raster_prediction.sample(n=n_points)
 
         # Generate geometry dataframe
         geometry = gpd.points_from_xy(raster_prediction.x, raster_prediction.y)
@@ -400,15 +404,15 @@ def add_markers(
             mask_filename = mask_filename[0]
         else:
             mask_filename = None
-        
+
         original_points_filename = os.path.join(
             self.points_dir, f'{Path(in_raster).stem}.gpkg')
-        
+
         # Extract output filename if None available and doing offline points
         if self.output_filename is None or offline:
             self.output_filename = os.path.join(
                 self.output_dir, f"{Path(in_raster).stem}.gpkg")
-            
+
         # Case #1: student is already working on the points
         if not gen_points or os.path.isfile(self.output_filename):
             validation_points = self.load_gpkg(self.output_filename)
@@ -515,7 +519,8 @@ def add_markers(
                 cell = ipysheet.cell(index, 3, point['burnt'])
                 widgets.jslink((cell, 'value'), (radio_burn_widget, 'value'))
                 cell = ipysheet.cell(index, 4, point['confidence'])
-                widgets.jslink((cell, 'value'), (radio_confidence_widget, 'value'))
+                widgets.jslink(
+                    (cell, 'value'), (radio_confidence_widget, 'value'))
                 cell = ipysheet.cell(index, 5, verified_option)
                 widgets.jslink((cell, 'value'), (checked_widget, 'value'))