specpipe 0.3.0

A file-based pipeline for efficient batch processing and modeling of hyperspectral images.

SpecPipe

A high-performance, file-based pipeline for batch processing and modeling of hyperspectral images.

SpecPipe streamlines the batch testing and optimization of hyperspectral analysis workflows. It provides a structured framework to apply various image processing techniques (calibration, baseline correction, denoising, feature engineering, etc.) in combination with various machine learning models. The pipeline employs a comprehensive full-factorial design to evaluate all method combinations and generates standard reports on performance metrics, residual analysis, influence anlaysis and visualizations.

Core features:

• Batch processing: Automate numerous data processing and modeling workflows in a single batch operation.
• File-based: A resumable, file-based processing pipeline with full-scale auditability and break tolerance.
• High-performance: Optimized for hyperspectral images with minimal memory consumption and options of GPU acceleration and pipeline-level multiprocessing.
• Simple extensible integration: Intuitive data management and straightforward integration for custom processing functions and Scikit-learn-style models.

Table of Contents

• Installation
• Usage
• Contributing
• License

Installation

Follow these steps to install the project:

1. Prerequisites: Ensure you have Python 3.9 or higher installed.

2. Install from PyPI (Recommended):

   pip install specpipe
   

3. Install from source (for development):

   git clone https://github.com/siwei66/SpecPipe.git
   cd SpecPipe
   pip install -e specpipe
   

Usage

1. Data preparation

• Setup a demo directory in current working directory

  import os
  demo_dir = os.getcwd() + "/SpecPipeDemo/"
  

• Create a data directory and download real-world demo data

  data_dir = demo_dir + "demo_data/"
  os.makedirs(data_dir)
  
  from specpipe import download_demo_data
  download_demo_data(data_dir)
  

• Create a directory for pipeline results

  report_dir = demo_dir + "/demo_results_classification/"
  os.makedirs(report_dir)
  

2. Configure your experiment data

2.1 Create a spectral experiment instance

• Create a SpecExp instance:

  from specpipe import SpecExp
  exp = SpecExp(report_dir)
  

The instance stores and organizes the data loading configurations of an experiment, which faciliates lazy-loading.

• Check report directory:

  exp.report_directory
  

  Output:

  '~/SpecPipeDemo/demo_results_classification/'
  

2.2. Experiment group management

• Add experiment groups:

  exp.add_groups(['group_1', 'group_2', 'group_3'])
  

• Check groups:

  exp.groups
  

  Output:

  ['group_1', 'group_2', 'group_3']
  

• Remove a group:

  exp.rm_group('group_3')
  

  Output:

  Following group is removed:
  group_3
  

2.3. Raster image management

• Add raster images:

  Use parameter name:

  exp.add_images_by_name(image_name="demo.", image_directory=data_dir, group="group_1")
  

  Output:

  Following image items are added:
      Group    Image    Mask
  0   group_1  demo.tiff
  

  Or use parameter position:

  exp.add_images_by_name("demo.", data_dir, "group_2")
  

  Output:

  Following image items are added:
       Group    Image    Mask
  0    group_2  demo.tiff     
  

• Check added images:

  exp.ls_images()
  

  Output:

      Group    Image    Mask
  0   group_1  demo.tiff     
  1   group_2  demo.tiff     
  

2.4. Region of interest (ROI) management

• Load image ROIs using suffix to image names:

  # By parameter name
  exp.add_rois_by_suffix(roi_filename_suffix="_[12].xml", search_directory=data_dir, group="group_1")
  # Or by parameter position
  exp.add_rois_by_suffix("_[345].xml", data_dir, "group_2")
  

  Output:

  Following ROI items loaded:
     Group    Image    ROI_name    ROI_type    ROI_source_file
  0  group_1  demo.tiff      1-1   sample      demo_1.xml
  1  group_1  demo.tiff      1-2   sample      demo_1.xml
  ...
  9  group_1  demo.tiff      2-5   sample      demo_2.xml
  

• Remove ROIs by name:

  exp.rm_rois(roi_name='5-5')
  

• Remove ROIs by source file name:

  exp.rm_rois(roi_source_file_name='demo_5.xml')
  

• Load ROIs to a image using ROI files by paths:

  exp.add_rois_by_file([f"{data_dir}/demo_5.xml"], image_name="example.tif", group="group_2")
  

• Check added ROIs:

  exp.ls_rois()
  

      Group    Image    ROI_name    ROI_type
  0   group_1  demo.tiff      1-1   sample
  1   group_1  demo.tiff      1-2   sample
  ...
  24  group_2  demo.tiff      5-5   sample
  

• Show raster RGB preview with associated ROIs:

  exp.show_image("demo.tiff", "group_1", rgb_band_index=(19, 12, 6), output_path=report_dir + "demo_rast_rgb1.png")
  

  Output:

  

  exp.show_image("demo.tiff", "group_2", rgb_band_index=(19, 12, 6), output_path=report_dir + "demo_rast_rgb2.png")
  

  Output:

  

2.5. Sample labels and target values

2.5.1 Set sample labels

• Get current sample label dataframe:

  labels = exp.ls_labels()
  

• Set new sample labels in the dataframe:

  Here we use sample ROI names as sample labels:

  labels.iloc[:, 1] = exp.ls_rois_sample(return_dataframe=True, print_result=False)["ROI_name"]
  

• Update sample labels:

  exp.sample_labels = labels
  

• Check sample labels:

  exp.ls_labels()["Label"]
  

  Output:

  0     1-1
  1     1-2
  ...
  24    5-5
  

2.5.2 Set target values

• List target value dataframe:

  targets = exp.ls_sample_targets()
  

• Create mock target values for regression and update target dataframe:

  Here we use leaf number:

  targets["Target_value"] = [f"leaf_{labl[0]}" for labl in targets['Label']]
  

• Load target values from updated target dataframe:

  exp.sample_targets_from_df(targets)
  

• Check target values:

  exp.ls_targets()[["Label", "Target_value"]]
  

  Output:

      Label Target_value
  0    1-1       leaf_1
  1    1-2       leaf_1
  ...
  24   5-5       leaf_5
  

3. Design testing pipeline

• SpecPipe follows a structured data processing workflow with these sequential data levels:

  Raster image data -> ROI spectra -> ROI statistics -> Traits to model
  

• The technical data levels in SpecPipe includes:

  Images: 
      0 - "image", input image path and output processed image path.
  
  Image pixel spectra: 
      1 - "pixel_spec", 1D spectrum of image pixel (simple)
  
      2 - "pixel_specs_array", 2D spectra array of image pixels (fast)
  
      3 - "pixel_specs_tensor", 2D spectra tensor of image pixels (fast)
  
      4 - "pixel_hyperspecs_tensor", 2D hyperspectra tensor of image pixels (fastest)
  
      (See "rasterop.pixel_apply" - apply processing functions to spectra of image pixels)
  
  Image ROIs:
      5 - "image_roi", raster with sample ROIs, for spectrum extraction
  
      6 - "roispecs", 2D array of ROI spectra
  
      7 - "spec1d", arbitrary 1D data of samples, e.g. 1D spectra, spectra statistics
  
  Models:
      8 - "model", model evaluation with standard report output as files
  

• The corresponding data processing workflow is:

  Raster image data:    0 ~ 4
      ↓
  Extract ROI spectra:  5 - "image_roi"
      ↓
  ROI spectra:          6 - "roispecs"
      ↓
  ROI statistics:       7 - "spec1d"
      ↓
  Model evaluation:     8 - "model"
  

The processing functions are wrapped in the pipeline according to the specified "data levels". Parallel processes can be added with identical "data level" and "application sequence", and they are arranged using full-factorial approach in the pipeline.

3.1 Create processing pipeline

• Create processing pipeline from SpecExp instance configured above:

  from specpipe import SpecPipe
  pipe = SpecPipe(exp)
  

3.2 Image processing

• Create some image processing functions, such as:

• Standard normal variate:

  def snv(v):
      import numpy as np
      vmean = np.mean(v, axis=1, keepdims=True)
      vstd = np.std(v, axis=1, keepdims=True)
      snv = (v - vmean) / vstd
      return snv
  

  TIP: Import working function dependency inside for multiprocessing.

• Raw data for performance comparison:

  def raw(v):
      return v
  

• Add these processing functions to the pipeline:

  pipe.add_process(
      input_data_level="pixel_specs_array",
      output_data_level="pixel_specs_array",
      application_sequence=0,
      method=snv,
  )
  

• Or we can specify the data level using the corresponding number:

  pipe.add_process(2, 2, 0, raw)
  

3.3 ROI statistics

• Import some ROI spectral statistic metrics:

  from specpipe import roi_mean, roi_median
  

• Add these processes to the pipeline:

  Specify data level using name:

  pipe.add_process(
      input_data_level='image_roi', 
      output_data_level='spec1d', 
      application_sequence=0, 
      method=roi_mean
      )
  

  Or specify data level using number:

  pipe.add_process(5, 7, 0, roi_median)
  

3.4 Sample data wrangling

• Create a function to remove nan and inf values:

  import numpy as np
  def replace_nan(v: np.ndarray, np=np) -> np.ndarray:
      return np.nan_to_num(v, nan=0.0, posinf=0.0, neginf=0.0)
  

  TIP: Instead of import inside, you can also passing working function dependencies as parameters with default values for multiprocessing.

• Add the process to the pipeline:

  pipe.add_process('spec1d', 'spec1d', 0, replace_nan)
  

• Check all added preprocessing processes:

  pipe.ls_process()
  

  Output:

     ID        Process_label       Input_data_level    Output_data_level    Application_sequence    Method
  0  2_0_%#1                       pixel_specs_array  pixel_specs_array     0                       snv
  1  2_0_%#2                       pixel_specs_array  pixel_specs_array     0                       raw
  2  5_0_%#1                       image_roi          spec1d                0                       roi_mean
  3  5_0_%#2                       image_roi          spec1d                0                       roi_median
  4  7_0_%#1                       spec1d             spec1d                0                       replace_nan
  

• To remove added processes from the pipeline:

  pipe.rm_process(method='replace_nan')
  

Processes can be removed by various criteria, the example removes the function 'replace_nan' by its name.

3.5 Add models to the pipeline

• Create some models:

  from sklearn.ensemble import RandomForestClassifier
  from sklearn.neighbors import KNeighborsClassifier
  
  rf_classifier = RandomForestRegressor(n_estimators=10)
  knn_classifier = KNeighborsRegressor(n_neighbors=3)
  

• Add models to the pipeline:

  pipe.add_model(knn_classifier, validation_method="2-fold")
  pipe.add_model(rf_classifier, validation_method="2-fold")
  

• Check added models:

  pipe.ls_model()
  

• Check all processes including models:

  pipe.ls_process()
  

  Output:

     ID Process_label    Input_data_level    Output_data_level    Application_sequence    Method
  0  7_0_%#1             spec1d              model                0                       KNeighborsClassifier
  1  7_0_%#2             spec1d              model                0                       RandomForestClassifier
  

4 Run pipeline

• Check processing chains of the pipeline:

  pipe.ls_chains()
  

  Output:

       Step_0    Step_1         Step_2
  0    snv       roi_mean       KNeighborsClassifier
  1    snv       roi_mean       RandomForestClassifier
  2    snv       roi_median     KNeighborsClassifier
  3    snv       roi_median     RandomForestClassifier
  4    raw       roi_mean       KNeighborsClassifier
  5    raw       roi_mean       RandomForestClassifier
  6    raw       roi_median     KNeighborsClassifier
  7    raw       roi_median     RandomForestClassifier
  

• Run pipeline:

  pipe.run()
  

• Enable resume after interruption:

  pipe.run(resume=True)
  

If the implementation is interrupted or forcibly terminated, running the pipeline again with resume=True to continue from last completed step.

5 Running results

• The pipeline produces following results for every processing chain, including:

  • Final and intermediate processing results
  • Configurations
  • Validation and application models
  • Model evaluation reports
  • Visualization
  

• The resulting file structure is as follows:

• For input data:

  report_directory/
  ├── SpecExp_configuration/
  │    ├── Loading_history/
  │    │   ├── Loaded_images.csv
  │    │   └── Loaded_ROIs.csv
  │    └── SpecExp_data_configuration.dill
  └── SpecPipe_configuration/
       ├── SpecPipe_added_process.csv
       ├── SpecPipe_exec_chains_in_ID.csv
       ├── SpecPipe_exec_chains_in_label.csv
       ├── SpecPipe_full_factorial_chains_in_ID.csv
       ├── SpecPipe_full_factorial_chains_in_label.csv
       └── SpecPipe_pipeline_configuration.dill
  

• For classification tasks, the pipeline generates:

  report_directory/
  ├── Modeling/
  │    └── Model_evaluation_reports/
  │        ├── Data_chain_Preprocessing_#0_Model_(model label 0)/
  │        │   ├── Model_for_application/
  │        │   ├── Model_in_validation/
  │        │   ├── Classification_performance.csv
  │        │   ├── Validation_results.csv
  │        │   ├── Residual_analysis.csv
  │        │   ├── Influence_analysis.csv
  │        │   └── ROC_curve.png
  │        ├── Data_chain_Preprocessing_#0_Model_(model label 1)/
  │        ├── Data_chain_Preprocessing_#1_Model_(model label 0)/
  │        ├── Data_chain_Preprocessing_#1_Model_(model label 1)/
  │        ├── Macro_avg_performance_summary.csv
  │        ├── Micro_avg_performance_summary.csv
  │        ├── Marginal_macro_avg_AUC_stats_(process step).csv
  │        ├── Marginal_micro_avg_AUC_stats_(process step).csv
  │        ├── Preprocessing_#0.txt
  │        └── Preprocessing_#1.txt
  ├── Pre_execution_test_data/
  ├── Preprocessing/
  │    ├── Step_results/
  │    ├── PreprocessingChainResult_chain_0.csv
  │    ├── PreprocessingChainResult_chain_0_X_(stats metrics).csv
  │    └── PreprocessingChainResult_chain_1.csv
  ├── SpecPipe_configuration/
  └── test_run/
  

• Retrieve reports in console

  result_summary = pipe.report_summary()
  chain_results = pipe.report_chains()
  

• Check summary reports The summary reports include:

  result_summary.keys()
  

  Output:

  dict_keys([
      'Macro_avg_performance_summary',
      'Marginal_macro_avg_AUC_stats_step_0',
      'Marginal_macro_avg_AUC_stats_step_1',
      'Marginal_macro_avg_AUC_stats_step_2',
      'Marginal_micro_avg_AUC_stats_step_0',
      'Marginal_micro_avg_AUC_stats_step_1',
      'Marginal_micro_avg_AUC_stats_step_2',
      'Micro_avg_performance_summary',
      'sample_targets_stats'])
  

  Demonstration of macro-average performance metrics of classification:

  result_summary['Macro_avg_performance_summary']
  

  Output:

      Step_0   Step_1   Step_2  Precision  Recall  F1_Score  Accuracy    AUC
  0  2_0_%#1  5_0_%#1  7_0_%#1   0.860000    0.84  0.842828     0.936  0.947
  ...
  7  2_0_%#2  5_0_%#2  7_0_%#2   0.769524    0.72  0.684242     0.888  0.829
  

  Demonstration of marginal macro-average performance metrics of classification:

  result_summary['Marginal_macro_avg_AUC_stats_step_0']
  

  Output:

           Process_ID       All   2_0_%#1   2_0_%#2
  0     Process_label       All       snv       raw
  1         n_records         8         4         4
  2    Mean_AUC_macro   0.85425   0.95275   0.75575
  3     Min_AUC_macro     0.631     0.942     0.631
  4  Median_AUC_macro     0.906    0.9495     0.761
  5     Max_AUC_macro      0.97      0.97      0.87
  6               All       1.0  0.199557  0.199557
  7           2_0_%#1  0.199557       1.0  0.028571
  8           2_0_%#2  0.199557  0.028571       1.0
  

  The processes of the step (here raw image and standard normal variates) are compared using non-parametric Mann-Whitney-U test.

• Check processing chain reports It's reports of every processing chains:

  len(chain_results)
  

  Output:

  8
  

  For each chain, the reports include:

  chain_results[0].keys()
  

  Output:

  dict_keys([
      'Chain_processes',
      'Classification_performance',
      'Influence_analysis',
      'Residual_analysis',
      'ROC_curve',
      'Validation_results'])
  

  Demonstration of Receiver-Operating-Characteristic curve:

  chain_results[0]['ROC_curve']
  

  Output:

  

6 Regression demonstration

6.1 Create a directory for regression results

• Create a directory for regression results

  report_dir_reg = demo_dir + "/demo_results_regression/"
  os.makedirs(report_dir_reg)
  

6.2 Copy and update the pipeline data manager to regression

• Copy and update SpecExp and SpecPipe instances

  import copy
  
  exp_reg = copy.deepcopy(exp)
  pipe_reg = copy.deepcopy(pipe)
  targets_reg = copy.deepcopy(targets)
  

• Update report directory of SpecExp

  exp_reg.report_directory = report_dir_reg
  

• Modify targets to numeric, here the numbers approaximate the age of the leaves

  targets_reg["Target_value"] = [(5 - int(labl[0])) for labl in targets['Label']]
  exp_reg.sample_targets_from_df(targets_reg)
  

• Check target values

  exp_reg.ls_targets()[["Sample_ID", "Target_value"]]
  

6.3 Update the pipeline models to regressors

• Check and remove classification models

  pipe_reg.ls_model()
  pipe_reg.rm_model()
  

• Update the data manager

  pipe_reg.spec_exp = exp_reg
  

• Add regressors to the pipeline Create some regressors:

  from sklearn.ensemble import RandomForestRegressor
  from sklearn.neighbors import KNeighborsRegressor
  
  rf_regressor = RandomForestRegressor(n_estimators=10)
  knn_regressor = KNeighborsRegressor(n_neighbors=3)
  

  The pipeline supports sklearn-style models, wrap into the style for arbitrary models.

  Let's skip the time-consuming influence analysis:

  pipe_reg.add_model(knn_regressor, validation_method="2-fold", influence_analysis_config=None)
  pipe_reg.add_model(rf_regressor, validation_method="2-fold", influence_analysis_config=None)
  

  TIP: Influence analysis adopts leave-one-out approach, which is often the slowest step of model evaluation.

6.4 Check and run new pipeline

• Check processing chains

  pipe_reg.ls_chains()
  

• Run regression pipeline

  pipe_reg.run()
  

6.5 Check results of a regression pipeline

• For regression tasks, the pipeline generates:

  report_directory/
  ├── Modeling/
  │    ├── sample_targets.csv
  │    ├── sample_targets_stats.csv
  │    └── Model_evaluation_reports/
  │        ├── Data_chain_Preprocessing_#0_Model_(model label 0)/
  │        │   ├── Model_for_application/
  │        │   ├── Model_in_validation/
  │        │   ├── Regression_performance.csv
  │        │   ├── Validation_results.csv
  │        │   ├── Residual_analysis.csv
  │        │   ├── Influence_analysis.csv
  │        │   ├── Scatter_plot.png
  │        │   └── Residual_plot.png
  │        ├── Data_chain_Preprocessing_#0_Model_(model label 1)/
  │        ├── Data_chain_Preprocessing_#1_Model_(model label 0)/
  │        ├── Data_chain_Preprocessing_#1_Model_(model label 1)/
  │        ├── Performance_summary.csv
  │        ├── Marginal_R2_stats_(process step).csv
  │        ├── Preprocessing_#0.txt
  │        ├── Preprocessing_#0.txt
  │        └── Preprocessing_#1.txt
  ├── Pre_execution_test_data/
  ├── Preprocessing/
  │    ├── Step_results/
  │    ├── PreprocessingChainResult_chain_0.csv
  │    ├── PreprocessingChainResult_chain_0_X_(stats metrics).csv
  │    └── PreprocessingChainResult_chain_1.csv
  ├── SpecPipe_configuration/
  └── test_run/
  

• Retrieve reports in console

  result_summary_reg = pipe_reg.report_summary()
  chain_results_reg = pipe_reg.report_chains()
  

• Check summary reports The summary reports include:

  result_summary_reg.keys()
  

  Output:

  dict_keys([
      'Marginal_R2_stats_step_0',
      'Marginal_R2_stats_step_1',
      'Marginal_R2_stats_step_2',
      'Performance_summary',
      'sample_targets_stats'])
  

  Demonstration of performance summary content:

  result_summary_reg['Performance_summary'].columns
  

  Output:

  Index([
      'Step_0', 'Step_1', 'Step_2',
      'Mean_Error', 'Standard_Deviation_of_Error', 'Mean_Absolute_Error',
      'Normalized_MAE', 'CV_MAE',
      'Mean_Squared_Error', 'Root_Mean_Squared_Error',
      'Normalized_RMSE', 'CV_RMSE',
      'Residual_Prediction_Deviation', 'R2'
  ], dtype='object')
  

• Check processing chain reports For each chain, the reports include:

  chain_results_reg[0].keys()
  

  Output:

  dict_keys([
      'Chain_processes',
      'Regression_performance',
      'Residual_analysis',
      'Residual_plot',
      'Scatter_plot',
      'Validation_results'])
  

  The influence analysis is absent, because we skip it in model addition.

  Demonstration of the scatter plot of the processing chain:

  chain_results_reg[0]['Scatter_plot']
  

  Output:

  

7 Test feature engineering fittables

Feature engineering fittables (data transformers) are fitted during the model validation process and function as integrated parts of the model. To incorporate these transformers, use the model connector functions 'combine_transformer_classifier' or 'combine_transformer_regressor' (similar to sklearn.pipeline).

The SpecPipe module also includes a composer that generates batchwise combined models using a full factorial design. Each component within these combined models automatically supports all marginal statistics and testing features available in the module.

• For example:

  from sklearn.preprocessing import StandardScaler
  from sklearn.feature_selection import SelectKBest, f_classif
  from specpipe.modelconnector import IdentityTransformer  # Passthrough transformer for comparison
  
  selector1 = SelectKBest(f_classif, k=5)  # Select 5 features
  selector2 = IdentityTransformer()  # For passthrough (no selection)
  
  from specpipe import factorial_transformer_chains
  
  models = factorial_transformer_chains(
      [StandardScaler(), IdentityTransformer()],  # Model step 1: test data scalers
      {'Feat5': selector1, 'FeatAll': selector2},  # Model step 2: test feature selection fittables
      # ...
      estimators={'KNN': knn_classifier, 'RF': rf_classifier},  # Estimators (specify custom labels using dictionary input)
      is_regression=False
  )
  print(models)
  

  Output:

  [TransClassifier_StandardScaler_Feat5_KNN,
   TransClassifier_StandardScaler_Feat5_RF,
   TransClassifier_StandardScaler_FeatAll_KNN,
   TransClassifier_StandardScaler_FeatAll_RF,
   TransClassifier_IdentityTransformer_Feat5_KNN,
   TransClassifier_IdentityTransformer_Feat5_RF,
   TransClassifier_IdentityTransformer_FeatAll_KNN,
   TransClassifier_IdentityTransformer_FeatAll_RF]
  

• Finally, add the generated models to your pipeline:

  for model in models:
      pipe.add_model(model, validation_method="2-fold")
  

Contributing

This is an initial release of SpecPipe. Your experience applying this toolset in your specialized field is extremely valuable. Any feedback and contributions are highly welcomed!

• Report bugs: Found an issue? Please open a GitHub issue with details
• Share your domain expertise: Tell us how SpecPipe works (or doesn't work) in your specific application area in discussions
• Suggest features: Have ideas for improvements? Use the GitHub discussions or issues tab
• Submit pull requests: Feel free to fork and submit PRs for bug fixes or small features
• Test and provide feedback: Try it out and let us know about your experience in discussions

License

This project is licensed under the MIT License - see the LICENSE file for details.