Hyperspectral Landcover Classification

A Computer Vision Model For Classifying Terrain
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Table of Contents

1. About The Project
2. Contributors
3. Detailed Analysis and Results
4. Web Based App

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About The Project

A Larger Initiative: BioSCape

This project is part of the larger BioSCape initiative, a collaboration aimed at understanding biodiversity in the Greater Cape Floristic Region of South Africa. It utilizes hyperspectral images captured by the NASA‐SANSA AVIRIS-NG remote sensor to classify land cover types across diverse ecological categories.

Learn more about BioSCape.

• Biodiversity Survey of the Cape: A NASA-SANSA research project focusing on hyperspectral data of the Greater Cape Floristic Region.
• Sensor: AVIRIS-NG capturing 432 frequency bands per pixel, enabling detailed classification (Should be noted only 373 bands using a range of 4-7m resolution).

Land Cover Classification Categories

1. Annual Crops
2. Built-up (urban/man-made structures)
3. Consolidated Barren (rocks, salt pans, etc.)
4. Natural Grassland
5. Natural Wooded Land
6. Permanent Crops (vineyards, orchards)
7. Planted Forest
8. Shrubs
9. Unconsolidated Barren (loose soil, beaches)
10. Waterbodies
11. Wetlands

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Contributors

• Ben Harris - LinkedIn
• Sam Hobbs - LinkedIn
• Blake Marshall - LinkedIn
• Jacob Sellers - LinkedIn
• Sean Farmer - LinkedIn
• Ian Swallow - LinkedIn
• Collins Senaya - LinkedIn
• Isauro Ramos - LinkedIn

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Docs

This section provides an in-depth overview of how hyperspectral data were handled, the outlier detection process, the CNN implementation, and key results and metrics. It concludes with a discussion of performance, challenges, and future directions.

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1. Dataset & Distribution

We gathered image‐level samples from google earth images in the Greater Cape Floristic Region, labeling each image according to its terrain class. Below is a snapshot of the overall distribution (count of samples/scenes) across our classes:

Initial Label Counts (image-Level)

• Shrubs: 670
• Annual Crops: 298
• Waterbodies: 239
• Natural Wooded Land: 192
• Planted Forest: 171
• Permanent Crops: 153
• Natural Grassland: 123
• Built-up: 125
• Wetlands: 112
• Consolidated Barren: 105
• Unconsolidated Barren: 89
• Mixed or Not Classified: 145

For training–testing splits, ensured stratification at the sample (image) level:

• Training split (80% of image samples):
• Testing split (20% of image samples):

Data Imbalance: Some classes (e.g., Shrubs ) have substantially more samples than others (e.g., Unconsolidated Barren). This imbalance impacted model training, especially for lower‐frequency classes such as Wetlands or Consolidated Barren.

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2. Preprocessing & Outlier Removal

Our preprocessing pipeline focused on data cleaning and outlier detection to remove “noisy” or invalid pixels before model training.

2.1 Data Cleaning

1. Remove “Mixed or Not Classified” Labels
   Rows with ambiguous or unreliable class designations were discarded.

2. Handle Missing Frequency Data

   • Any pixel with missing reflectance values in the 373 hyperspectral bands was removed.

3. One-Hot / Encoded Labels

   • Class names were stored as integer encodings for downstream processing and model training/testing.

2.2 PCA‐Based Outlier Detection

Employed a PCA + Mahalanobis distance approach per image sample:

1. Scaling via a RobustScaler (reduces sensitivity to outliers).
2. Principal Component Analysis retaining 95% of variance to compress high-dimensional reflectance data.
3. Mahalanobis Distance in PCA space to flag points exceeding a chi-square threshold (e.g., (\alpha=0.05)).
4. Pixels classified as outliers were removed from the dataset.

Below are visual examples showing removed outlier pixels in black:

Figure: Shown in order from left to right, Example outlier removal for three different samples.

• Sample 7981: Before=308 pixels, After=283, Removed=21
• Sample 5722: Before=128 pixels, After=108, Removed=16
• Sample 30: Before=110 pixels, After=92, Removed=18

This process helped reduce noisy signals and improved overall classification consistency.

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2. Morphological Post-Processing

Although the 1D CNN provides detailed per-pixel classifications, small patches of noise or isolated mislabeled pixels can appear. To mitigate this, dilation‐based morphological filter only to the majority class in each image is applied. This helps smooth out noise while minimally affecting overall image predictions.

1. Majority-Class Detection
   Each image is analyzed to find the most frequent label.

2. Targeted Dilation
   We dilate only the majority-class regions using a small (3 \times 3) structuring element. Surrounding pixels become assigned to that majority class if they fall within the dilated mask.

3. Per-Pixel vs. Per-Image Effect

   • Per-Pixel: Accuracy can improve due to the removal of spurious outliers which are absorbed by the dominant class.
   • Per-Image: Because majority voting already often selects the dominant label, the final image-level classification is not significantly impacted.

Example Outputs

Below are three examples illustrating the original CNN predictions (left) vs. post‐morphology (right). Note how small, disjoint misclassifications within large homogeneous regions are eliminated:

Figure: Post-processing visually “cleans” each labeled map by expanding the majority class (green in these examples), removing small scattered patches of confusion.

In practice, morphological post-processing is optional and can be tuned via alternative structuring elements (e.g., disk, diamond), operation types (e.g., opening/closing), or window sizes. For our dataset, we found minimal changes in image-level metrics, but reduced noise at the per-pixel scale.

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3. 1D CNN Implementation

Built a 1D Convolutional Neural Network to leverage the spectral dimension (373 channels) for classification:

Figure: 1D CNN Architecture

Key Model Details

• Input Shape: ((\text{# of frequency bands}, 1))
• Layers:
  • 4 × Conv1D layers (512 → 256 → 256 → 128 filters), with ReLU activation
  • MaxPooling1D layers after each convolution for dimension reduction
  • Batch Normalization to stabilize and speed up training
  • Several Dense layers (128 → 64 → 32) with Dropout to mitigate overfitting
  • Output: Dense layer with softmax for multi-class classification
• Optimizer: Adam (init. learning rate = .0001)
• Loss Function: Categorical Crossentropy
• Callbacks: EarlyStopping, ReduceLROnPlateau, ModelCheckpoint

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4. Results & Discussion

We evaluated performance at the image level, i.e., each test image’s class assigned via majority voting on pixel predictions.

4.1 Retaining “Shrubs” and “Natural Grassland” as Separate Classes

When Shrubs and Natural Grassland remain distinct:

Figure: Image-Level Confusion Matrix (Counts) — Shrubs and Natural Grassland kept separate

Classification Report (Dropdown)

Class	Precision	Recall	F1-Score
Annual Crops	0.78	0.92	0.84
Built-up	0.86	1.00	0.93
Consolidated Barren	0.68	0.55	0.61
Natural Grassland	0.75	0.21	0.32
Natural Wooded Land	0.61	0.69	0.65
Permanent Crops	0.86	0.58	0.70
Planted Forest	0.77	0.65	0.70
Shrubs	0.65	0.81	0.72
Unconsolidated Barren	0.80	0.70	0.74
Waterbodies	0.94	1.00	0.97
Wetlands	0.75	0.35	0.48

Overall Image‐Level Accuracy: 78%

• Classes like Built‐up and Waterbodies achieve near‐perfect recall.
• Shrubs and Natural Grassland see significant confusion, hurting recall for Grassland.
• Wetlands and Consolidated Barren also struggle.

4.2 Merging “Shrubs” and “Natural Grassland” into a Single Class

To reduce confusion between these visually/spectrally similar categories, we merged them into one label: “Shrubs and Natural Grassland.”

Figure: Image-Level Confusion Matrix (Counts) — Shrubs & Natural Grassland merged

Classification Report (Dropdown)

Class	Precision	Recall	F1-Score
Annual Crops	0.86	0.90	0.88
Built-up	0.90	1.00	0.95
Consolidated Barren	0.75	0.50	0.60
Natural Wooded Land	0.70	0.83	0.76
Permanent Crops	0.86	0.68	0.76
Planted Forest	0.81	0.59	0.68
Shrubs and Natural Grassland	0.79	0.89	0.83
Unconsolidated Barren	0.80	0.67	0.73
Waterbodies	0.93	0.96	0.95
Wetlands	0.75	0.35	0.48

Overall Image‐Level Accuracy: 82%

• Merging significantly boosted accuracy and F1 for that combined class.
• Built‐up and Waterbodies remain strong, with near‐perfect scores.
• Challenges persist for Wetlands and Consolidated Barren.

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5. Key Takeaways & Limitations

1. Outlier Removal Helps
   • PCA+Mahalanobis filtering prunes noisy spectral pixels, improving class separation.
2. Merging Similar Classes
   • Combining Shrubs and Natural Grassland alleviated confusion, yielding an 82% image‐level accuracy.
3. Data Imbalance Issues
   • Classes like Wetlands, Unconsolidated Barren, etc., remain underrepresented, hurting recall and F1. Techniques like oversampling or advanced class weighting could further help.
4. Spectral Complexity
   • Hyperspectral data benefits from 1D CNN approaches but visually similar or spectrally close classes remain difficult to discriminate.

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Hyperspectral Land Cover Classification Visualization App

Geospatial Visualization with Google Maps

The platform uses the Google Maps API for an intuitive spatial interface:

• Marker-based Visualization:
  Classified sample points are displayed as markers on a satellite basemap. Green markers indicate correctly predicted labels (based on ground truth), while red markers indicate discrepancies.

  Example (Marker Map with Predictions):

  

• Category-Based Filtering:
  A sidebar allows users to filter land cover samples by category. Choosing a category (e.g., "Shrubs and Natural Grassland") highlights only those samples, making pattern recognition straightforward.

• Interactive Info Windows:
  Clicking a marker displays detailed metadata: sample number, ground truth label, predicted label, and options to add the sample to further analytical plots (e.g., scatter or bar plots).

  

Hexagon Layer Visualization

Beyond simple markers, the tool can display aggregated frequency data using a hexagonal binning layer powered by deck.gl:

• Pre-Aggregated Frequency Sums:
  Frequency values from hyperspectral samples are aggregated and stored in a MongoDB backend, enabling quick retrieval of summarized data. This reduces memory load and improves performance.

• 3D Hexagon Layer:
  A HexagonLayer renders vertical columns at sample locations, with height and color encoding frequency sums. This provides an immediate sense of spatial distribution and intensity patterns across the landscape.

  

• Adjustable Parameters:
  A control panel allows real-time adjustments of coverage, radius, and upper percentile parameters, enabling dynamic exploration of spatial frequency distributions.

Bar and Scatter Plots for Detailed Analysis

For deeper dives into spectral distributions:

• Bar Plot:
  Users can select individual samples and generate histograms (bar plots) of frequency distributions.

  

  This allows closer inspection of the underlying spectral frequency ranges for a chosen sample, revealing how spectral values cluster within intervals.

  

• Scatter Plot (for Frequencies):
  Users can also view scatter plots for selected frequency bands or combinations thereof, helping them identify relationships or anomalies in spectral signatures.

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