SMQTK v0.10.0 Release Notes

This minor release represents the merger of public release request 88ABW-2018-3703. This large updated adds a number of functionality improvements and API changes, docker image improvements and expansions (see the new classifier service), FAISS algorithm wrapper improvements, NearestNeighborIndex update and removal support, a switch to py.test testing framework, generalized classification probability adjustment function, code clean-up, bug fixes and more.

Updates / New Features since v0.9.0


  • Classifier
    • Added ClassifierCollection support class. This assists with aggregating multiple SMQTK classifier implementations and applying one or more of those classifiers to input descriptors.
    • Split contents of the file into multiple component files. This file was growing too large with the multiple abstract classes and a new utility class.
    • Changed classify abstract method to raise a ValueError instead of a RuntimeError upon being given an empty DescriptorElement.
    • Updated SupervisedClassifier abstract interface to use the template pattern with the train method. Now, implementing classes need to define _train. The train method is not abstract anymore and calls the _train method after the input data consolidation.
    • Update API of classifier to support use of generic extra training parameters.
    • Updated libSVM classifier algorithm to weight classes based on the geometric mean of class counts divided by specific class count to more properly handle weighting even if there is class imbalance.
  • Hash Index
    • Made to be its own interface descending from SmqtkAlgorithm instead of NearestNeighborsIndex. While the functionality of a NN-Index and a HashIndex are very similar, all method interfaces are different in terms of the types they accept and return and the HashIndex implementation redefined and documented them to the point where there was no shared functionality.
    • Switched to using the template method for abstract methods.
    • Add update and remove methods to abstract interface. Implemented new interface methods in all subclasses.
    • Added model concurrency protection to implementations.
  • Nearest-Neighbors
    • Switched to using the template method for abstract methods.
    • Add update and remove methods to abstract interface. Implemented new interface methods in all subclasses.
    • Fix imports in FAISS wrapper module.
    • Added model concurrency protection to implementations.
    • FAISS
      • Add model persistence via optionally provided DataElement.
      • Fixed use of strings for python 2/3 compatibility.
      • Changed default factory string to “IVF1,Flat”.
      • Added initial GPU support to wrapper. Currently only supports one GPU with explicit GPU ID specification.


  • Descriptor Index
    • Added __contains__ method to abstract class to call the has method. This should usually be more efficient than scanning the iteration of the index which is what was happening before. For some implementations, at worst, the runtime for checking for inclusion will be the same (some implementations may have to iterate).
  • Descriptor Element
    • Interface
      • Hash value for an element is now only composed of UID value. This is an initial step in deprecating the use of the type-string property on descriptor elements.
      • Equality check between elements now just vector equality.
      • Added base implementation of __getstate__ and __setstate__. Updated implementations to handle this as well as be backward compatible with their previous serialization formats.
      • Added a return of self to vector setting method for easier in-line setting after construction.
    • PostgreSQL
      • Updated to use PsqlConnectionHelper class.
  • KeyValueStore
    • Added remove and remove_many abstract methods to the interface. Added implementations to current subclasses.
    • Added __getitem__ implementation.


  • Caffe
    • Updated docker images for CPU or GPU execution.
    • Updated Caffe version built to 1.0.0.
  • Added Classifier service docker images for CPU or GPU execution.
    • Inherits from the Caffe docker images.
    • Uses MSRA’s ResNet-50 deep learning models.
  • IQR Playground
    • Updated configuration files.
    • Now only runs IQR RESTful service and IQR GUI web app (removed nearest- neighbors service).
    • Simplified source image mount point to /images.
    • Updated run_container.*.sh helper scripts.
    • Change deep-learning model used from AlexNet to MSRA’s RestNet-50 model.
  • Versioning changes to, by default, encode date built instead of arbitrary separate versioning compared to SMQTK’s versioning.
  • Classifier and IQR docker images now use the local SMQTK checkout on the host system instead of cloning from the internet.

IQR module

  • Added serialization load/save methods to the IqrSession class.


  • generate_image_transform
    • Added stride parameter to image tile cropping feature to allow for more than just discrete, abutting tile cropping.
  • runApplication
    • Add ability to get more than individual app description from providing the -l option. Now includes the title portion of each web app’s doc-string.
  • Added smqtk-make-train-test-sets
    • Create train/test splits from the output of the compute_many_descriptors tool, usually for training and testing a classifier.


  • Remove use of nose-exclude since there are now actual tests in the web sub-module.
  • Switch to using pytest as the test running instead of nose. Nose is now in “maintenance mode” and recommends a move to a different testing framework. Pytest is a popular a new powerful testing framework alternative with a healthy ecosystem of extensions.
  • Travis CI
    • Removed use of Miniconda installation since it wasn’t being utilized in special way.
  • Added more tests for Flask-based web services.

Utilities module

  • Added mimetype utilities sub-module.
  • Added a web utilities module.
    • Added common function for making response Flask JSON instances.
  • Added an iter_validation utility submodule.
  • Plugin utilities
    • Updated plugin discovery function to be more descriptive as to why a module or class was ignored. This helps debugging and understanding why an implementation for an interface is not available at runtime.
  • PostgreSQL
    • Added locking to table creation upsert call.
  • Added probability utils submodule and initial probability adjustment function.


  • Added new classifier service for managing multiple SMQTK classifier instances via a RESTful interface as well as describe arbitrary new data with the stored classifiers. This service also has the ability to take in saved IQR session states and train a new binary classifier from it.
    • Able to query the service with arbitrary data to be described and classified by one or more managed classifiers.
    • Able to get and set serializations of classifier models for archival.
    • Added example directory of show how to run and to interact with the classifier service via curl.
    • Optionally take a new parameter on the classify endpoint to adjust the precision/recall balance of results.
  • IQR Search Dispatcher (GUI web app)
    • Refactored to use RESTful IQR service.
    • Added GUI and JS to load an IQR state from file.
    • Update sample JSON configuration file at python/smqtk/web/search_app/sample_configs/config.IqrSearchApp.json.
    • Added /is_ready endpoint for determining that the service is alive.
  • IQR service
    • Added ability to an IQR state serialization into a session.
    • Added sample JSON configuration file to python/smqtk/web/search_app/sample_configs/config.IqrRestService.json.
    • Added /is_ready endpoint for determining that the service is alive.
    • Move class out of the file and into its own dedicated file.
    • Make IQR state getter endpoint return a JSON containing the base64 of the state instead of directly returning the serialization bytes.
    • Added endpoints to update, remove from and query against the global nearest-neighbors index.

Fixes since v0.9.0


  • Nearest-Neighbor Index
    • LSH
      • Fix bug where it was reporting the size of the nested descriptor index as the size of the neighbor index when the actual index state is defined by the hash-to-uids key-value mapping.


  • DataElement
    • Fixed bug where write_temp() would fail if the content_type() was unknown (i.e. when it returned None).
  • Descriptor Index
    • PostgreSQL
      • Fix bug where an instance would create a table even though the create_table parameter was set to false.
  • Descriptor Elements
    • PostgreSQL implementation
      • Fix set_vector method to be able to take in sequences that are not explicitly numpy arrays.
  • KeyValue
    • PostgreSQL
      • Fix bug where an instance would create a table even though the create_table parameter was set to false.


  • classifier_model_validation
    • Fixed confidence interval plotting.
    • Fixed confusion matrix plot value range to the [0,1] range which causes the matrix colors to have meaning across plots.

  • Add smqtk- to some scripts with camel-case names in order to cause them to be successfully removed upon uninstallation of the SMQTK package.


  • Fixed ambiguous ordering check in libsvm-hik implementation of RelevancyIndex algorithm.


  • IQR Search Dispatcher (GUI web app)
    • Fix use of StringIO to using BytesIO.
    • Protect against potential deadlock issues by wrapping intermediate code with try/finally clauses.
    • Fixed off-by-one bug in javascript DataView construction.
  • IQR Service
    • Gracefully handle no-positive-descriptors error on working index initialization.
    • Fix use of StringIO to using BytesIO.