Running an Interferometric Analysis

Here is a detailed description on how to execute an Interferometric Analysis with SCT in three ways:

1. From the Command Line Interface (CLI) → user-facing execution
2. From the Python API → programmatic/scripting/orchestration integration
3. From the Testing Interface → automated validation

From CLI

Interferometric analysis can be performed using the following command just specifying the input product and the output directory.

sct [--config <path_to_config>] interferometry -p <product_path> -out <output_dir> [-g]

where -g is used to enable graphs generation (if added to the command). The input product must be an interferogram product or a coherence map product.

If the user wants to compute the coherence map from two co-registered products, the user must use the following command:

sct [--config <path_to_config>] interferometry -p <product_path_1> -pp <product_path_2> -out <output_dir> [-g]

where -p and -pp are the paths to the two co-registered products.

From Python API

This analysis is also available directly from Python without using the CLI, and can be imported in any python script and executed as follows:

from pathlib import Path
from sct.analyses.interferometry.main import full_interferometric_analysis
from sct.analyses.interferometry.config import SCTInterferometricAnalysisConfig

config = SCTInterferometricAnalysisConfig()  # this is the default, but parameters can be set here

output_netcdf_file = full_interferometric_analysis(
    product=Path("path/to/product"),
    product_2=Path("path/to/product_2"),  # optional, can be None
    output_directory=Path("path/to/output_directory"),
    config=config,  # optional, can be None
    graphs=True,  # optional, can be False
)

From Testing Interface

The interferometric analysis implementation also provides a testing interface, which can be used to run the analysis from the SCT Testing Framework. To do so, a registry .json file containing test cases must be created and provided to the testing CLI interface.

{
    "product-format-type": {
        "test-case-1": {
            "analysis": "interferometry",
            "product": [
                "path/to/co-registered-product/1",
                "path/to/co-registered-product/2"
            ],
            "config": "path/to/config/if/needed",
            "reference_output": "path/to/output/reference/results/coherence_histograms.nc"
        },
        "test-case-2": {
            "analysis": "interferometry",
            "product": "path/to/interferogram-product",
            "config": "path/to/config/if/needed",
            "reference_output": "path/to/output/reference/results/coherence_histograms.nc"
        },
    }
}

Then the testing CLI interface can be used as follows:

sct testing test -r <path_to_registry_file> -out <output_dir> [-g]

When a reference_output is provided, the testing CLI interface will compare the results with the reference output and report any discrepancy.