Applications

ImageMath

Regression-based unmixing (synthMix)

You can find the Regression-based unmixing in the menu bar Applications ‣ Regression-based unmixing (synthMix)

See also

Have a look at the Urban Unmixing Tutorial for a use case example of the Regression-based unmixing Application.

Input Parameters:

  • Inputs
    • Endmember Library: Select spectral library
    • Class Attribute: Specify the attribute which contains class/material information.
    • Spectral Image: Specify spectral image on which unmixing should be applied.
  • Class Selection
    • Target Classes combo: Specify the desired target classes (which are derived from the Class Attribute field specified above). Can be used to select only a subset of target classes from a spectral library.
  • Mixing Parameters
    • Number of Synthetic Mixtures per Class: Amount of mixtures to be generated per class.
    • Include Original Library Endmembers cb0: Whether to include the original spectra in the training library.
    • Mixing Complexity Likelihoods: Defines the likelihood of creating a binary, ternary or fourfold mixture. For example, by specifing the likelihoods as 0.5, 0.5, 0, it is equally likely that binary and ternary mixtures are created, whereas no fourfold mixtures will be generated. Enter decimals between 0.0-1.0 (all three likelihoods need to sum up to 1).
      • 2EM: Likelihood of creating a binary mixture (2 endmembers)
      • 3EM: Likelihood of creating a ternary mixture (3 endmembers)
      • 4EM: Likelihood of creating a fourfold mixture (4 endmembers)
    • Allow Within-Class Mixtures cb0: Whether to allow mixtures between signatures of the same endmember.
    • Class Likelihoods combo (Proportional | Equalized): In case of proportional class likelihoods the number of mixtures of a class in the output library will be proportional to the number of spectra in the input library of that class. In case of equalized, all classes will be represented equally.
  • Regression Algorithm
  • In the Regressor combo dropdown menu you can choose different regressors (e.g. Random Forest, Support Vector Regression, Kernel Ridge Regression)
  • mIconCollapse Model parameters: Specify the parameters of the selected regressor.

    Hint

    Scikit-learn python syntax is used here, which means you can specify model parameters accordingly. Have a look at the scikit-learn documentation on the individual parameters, e.g. for the RandomForestRegressor

  • Use Ensemble cb0: If enabled, more than one iteration of mixing, training and prediction will be performed. The results of each iteration will be combined into a final ensemble result (see Decision Fusion (Ensemble) on how results should be combined).

  • Ensemble Size: Specify the size of the ensemble (number of iterations).

  • Outputs
  • Folder: Specify an output folder where results will be written to.
  • Name: Basename of the output files
  • mIconCollapse Advanced
    • Decision Fusion (Ensemble) combo (median | mean | iqr | std): Select one or multiple options of the kind of decision fusion (how individal predictions of the ensemble will be combined)
    • Save Check the following to save additional outputs …
      • Training Samples cb0: Save the training samples
      • Predictions cb0: Save the individual predictions of the ensemble
      • Models cb0: Save the model files
    • Create Class Fraction RGB cb0: Generates a RGB visualisation based on the weighted sum of class colors and corresponding fractions
    • Derive Classification from Fraction Map cb0: Save classification from fraction map (class with the highest fraction will be assigned)

Run the regression-based unmixing

Once all parameters are entered, press the action button to start the regression-based unmixing.




Classification Workflow

You can find this application in the menu bar Applications ‣ Classification Workflow

The Classification Workflow application let’s you easily perform classification analysis and mapping tasks using remote sensing data.

Quick Mapping

In the Quick Mapping section you can very easily define your training dataset, fit a classifier and predict a classification layer, with only a few clicks.

E.g. use EnMAP-Box testdata together with a Random Forest classifier:

../../_images/categorized_vector_layer_21.png ../../_images/raster_layer1.png ../../_images/categorized_raster_layer1.png

For a more elaborated analysis see the Detailed Analysis section.

Detailed Analysis

In the Detailed Analysis section you have more control over individual analysis steps. When performing a detailed analysis, you can basically go through every subsection from left to right. But, depending on the usecase, it is also possible to skip individual steps you’re not interested in.

Dataset

You have various options to create a dataset for subsequent analysis: select a Source option and click create dataset to create a new dataset`.

In the Editor, category colors and names, and feature names can be changed and saved.

By using the various controls in the Draw samples section, you can easily define a training-test-split setup. The number of training and test samples to be drawn for each category are listed, and also editable, inside the Editor.

Click split dataset to perform the split, resulting in a training and a test dataset, that can be used in subsequent analysis.

Classifier

In the Classifier section you can either select a Predifined classifier or provide a user-defined Python Code snipped. See the https://scikit-learn.org/ documentation for a complete overview.

Click create classifier to create an (unfitted) classifier, that can be used in subsequent analysis.

Feature Clustering

In the Feature Clustering section you can perform an unsupervised Feature redundancy analysis, that clusters similar features together: select a Dataset, an Algorithm and click cluster features to create and an Output report.

After inspecting the report you can perform a Feature subset selection: select a suitable Number of features and click select features to create a training and a test dataset with fewer features, that are less correlated and can be used in subsequent analysis.

Feature Ranking

In the Feature Ranking section you can perform a supervised Feature importance analysis, that ranks features in terms of their importance for the classification task at hand: select a Dataset, an Algorithm and click :guilabel:`rank features to create and an Output report.

After inspecting the report you can perform a Feature subset selection: select a suitable Number of features and click select features to create a training and a test dataset with fewer features, that are most important and can be used in subsequent analysis.

Model

In the Model section you can perform Model fitting: select a Dataset and click fit classifier to create a fitted Output classifier, that is used in subsequent analysis.

For Model performance analysis select an Algorithm and click assess performance to create an Output report.

Classification

In the Classification section you can perform Map prediction: select a Raster layer with features that matches the features used in Model fitting. Click predict output products to create an Output classification layer and/or an Output class probability layer. Note that outputs are opened inside the EnMAP-Box Data Sources panel.

For Map accuracy and area estimation select a Ground truth categorized layer and click assess performance to create an Output report.

Settings

In the Settings section you can specify the Output directory (e.g. C:/Users/USERNAME/AppData/Local/Temp/EnMAPBox/ClassificationWorkflow), that is used as the default file destination path, when creating file outputs. Note that each output file wigdet (e.g. Output dataset) has a default basename (e.g. dataset.pkl), that is used to create a default file destination (e.g. C:/Users/USERNAME/AppData/Local/Temp/EnMAPBox/ClassificationWorkflow/dataset.pkl). If the default file destination already exists, the basename is enumerated (e.g. .dataset_2.pkl) to avoid overwriting existing outputs.

Log


Classification Workflow Classic

You can find this application in the menu bar Applications ‣ Classification Workflow Classic

../../_images/classification_workflow.png

Classification Workflow Application

See also

Have a look at the Getting Started for a use case example of the Classification Workflow Application.

Input Parameters:

  • Training Inputs

    • Type combo

      Three different types of input data sources are supported and have to be specified beforehand in the dropdown menu. Depending on the selected input type the user interface shows different options.

      • Raster / Classification:
        • Raster: Specify input raster based on which samples will be drawn for training a classifier.
        • Classification: Specify input raster which holds class information.
      • Raster / Vector Classification:
        • Raster: Specify input raster based on which samples will be drawn for training a classifier.
        • Reference: Specify vector dataset with reference information. Has to have a column in the attribute table with a unique class identifier (numeric). The class colors and labels are derived from the current Symbology. To set or change those settings, click the rendererCategorizedSymbol button or go to the Layer Properties (Layer properties ‣ Symbology). The vector dataset is rasterized/burned on-the-fly onto the grid of the input raster in order to extract the sample. If the vector source is a polygon dataset, only polygons which cover more than 75% of a pixel in the target grid are rasterized.
      • labelled Library:
        • Library: Specify input spectral library.
  • Sampling

    Once you specified all inputs in the Training inputs section, you can edit the class colors, names and class sample sizes in the Sampling submenu.

    Note

    If set, the class labels and color information is automatically retrieved from the layers current renderer settings (Layer properties ‣ Symbology).

    • Sample size combo spin Specify the sample size per class, either relative in percent or in absolute pixel counts.
    • The total sample size is shown below
    • cb0 Save sample: Activate this option and specify an output path to save the sample as a raster.
  • Training

    • In the Classifier combo dropdown menu you can choose different classifiers (e.g. Random Forest, Support Vector Machine)

    • mIconCollapse Model parameters: Specify the parameters of the selected classifier.

      Hint

      Scikit-learn python syntax is used here, which means you can specify model parameters accordingly. Have a look at the scikit-learn documentation on the individual parameters, e.g. for the RandomForestClassifier

    • cb0 Save model: Activate this option to save the model file (.pkl) to disk.

  • Mapping

    • Raster: Specify the raster you would like to apply the trained classifier to (usually -but not necessarily- this is the same as used for training)

    • Mask: Specify a mask layer if you want to exclude certain areas from the prediction.

      • Outputs:

        • Classification: Output path where to write the classification image to.

        • Probability: Output path of the class probability image.

          Hint

          This outputs the result of a classifiers predict_proba method. Note that depending on the classifier this option might not be available or has to be activated in the model parameters (e.g. for the Support Vector Machine, the line svc = SVC(probability=False) has to be altered to svc = SVC(probability=True)

        • RGB: Generates a RGB visualisation based on the weighted sum of class colors and class probabilities.

  • Cross-validation Accuracy Assessment

    • cb0 Cross-validation with n-folds spin: Activate this setting to assess the accuracy of the classification by performing cross validation. Specify the desired number of folds (default: 3). HTML report will be generated at the specified output path.

Run the classification workflow

Once all parameters are entered, press the action button to start the classification workflow.




Regression Workflow

You can find the Regression Workflow in the menu bar Applications ‣ Classification Workflow

See also

Have a look at the Biomass Mapping Tutorial for a use case example of the Regression Workflow Application.

Input Parameters:

  • Training Inputs

    • Raster: Specify input raster based on which samples will be drawn for training a regressor.
    • Reference: Specify vector or raster dataset with reference information (regression target). In case of vector input, dataset has to have a numeric column in the attribute table with a target variable of interest. This vector dataset is rasterized/burned on-the-fly onto the grid of the input raster in order to extract the sample. If the vector source is a polygon dataset, all pixels will be drawn which intersect the polygon.
    • Attribute: Attribute field in the reference vector layer which contains the regression target variable.
  • Sampling

    • Number of Strata spin: Specify the desired number of strata sampling. If you don’t want to use stratified sampling, just enter 1.

    • Min & Max: Defines the value range in which samples should be drawn.

    • Sample size combo spin: Specify the sample size per stratum, either relative in percent or in absolute pixel counts.

      Every stratum is listed below with the value range that is covered by this stratum depicted in square brackets (e.g., Stratum 1: [1.0, 4.33]). Furthermore, you can see and alter the number of pixels/samples for each stratum using the spin spinboxes.

    • cb0 Save sample: Activate this option and specify an output path to save the sample as a raster.

  • Training

    • In the Regressor combo dropdown menu you can choose different regressors (e.g. Random Forest, Support Vector Regression, Kernel Ridge Regression)

    • mIconCollapse Model parameters: Specify the parameters of the selected regressor.

      Hint

      Scikit-learn python syntax is used here, which means you can specify model parameters accordingly. Have a look at the scikit-learn documentation on the individual parameters, e.g. for the RandomForestRegressor

    • cb0 Save model: Activate this option to save the model file (.pkl) to disk.

  • Mapping

    • Input Raster: Specify the raster you would like to apply the trained regressor to (usually -but not necessarily- this is the same as used for training)
  • Cross-validation Accuracy Assessment

    • cb0 Cross-validation with n-folds spin: Activate this setting to assess the accuracy of the regression by performing cross validation. Specify the desired number of folds (default: 3). HTML report will be generated at the specified output path.

Run the regression workflow

Once all parameters are entered, press the action button to start the regression workflow.

EO Time Series Viewer

Please visit EO Time Series Viewer Documentation for more information.

Agricultural Applications

Please visit LMU Vegetation Apps Documentation for more information.