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MIQA Python Client

This simple python library is intended to allow users of a MIQA instance to interact with the MIQA API programmatically and perform tasks they may not be able to accomplish in the web interface.

The structure of classes in this library closely imitates the structure of models in MIQA, so it is recommended that a user understands this structure before proceeding to use the python client. The documentation explaining this structure can be found at https://openimaging.github.io/miqa/projects/.

In summary, Projects are the top-level objects that act as organizational buckets for experiments. Experiments are collections of scans that may be related in some way. Scans are collections of related 3D medical images. Each scan must have at least one image, or Frame, associated with it. A scan may have multiple Frames representing time steps or some other fourth dimension to the images collected. The purpose of MIQA is to annotate the quality of scans that are currently categorized as usable, unusable, or otherwise. Thus, a Scan Decision is an object that stores those determinations. A Scan can have zero or more Scan Decisions.

Usage

Example usages of available functions are shown in example.py. Reading this example is the best way to understand how functions in this client are used. Below are some further explanations of the usages found in the example.

Explanation of classes

In the MIQA python client, the top-level class, MIQA, refers to an instance of MIQA. For a single organization, this is likely the only active instance you will use. This class holds information for connecting to the API.

Each MIQA object will hold a collection of Project objects, which will each hold a collection of Experiment objects, which will each hold a collection of Scan objects, which will each hold collections of both Frame objects and ScanDecision objects.

The following table displays the available attributes and functions on these classes. Attributes are exactly as they are returned by the API.

Class Name Attributes Functions
MIQA url, headers, token, version, projects, artifact_options login, get_config, get_all_objects, get_project_by_id, create_project, print_all_objects
Project id, name, creator, experiments, total_scans, total_complete, MIQA get_experiment_by_id, add_experiment, print_all_objects, delete
Experiment id, name, scans, project, note get_scan_by_id, add_scan, update_note, print_all_objects
Scan id, name, experiment, decisions, frames, scan_type, subject_id, session_id, scan_link add_frames_from_paths, add_decision, print_all_objects
Frame id, frame_number, frame_evaluation, extension, download_url
ScanDecision id, decision, creator, created, note, user_identified_artifacts, location

Explanation of functions

Each level in the object hierarchy can be accessed from the level above it.

  • Projects can be accessed with MIQA.projects, MIQA.get_project_from_id(id), or MIQA.create_project(name).
  • Experiments can be accessed with Project.experiments, Project.get_experiment_by_id(id), or Project.add_experiment(name).
  • Scans can be accessed with Experiment.scans, Experiment.get_scan_by_id(id), or Experiment.add_scan(name, scan_type, [subject_id, session_id, scan_link]).
  • Frames can be accessed with Scan.frames or Scan.add_frames_from_paths(paths).
  • Scan Decisions can be accessed with Scan.decisions or Scan.add_decision(decision, note, [present_artifacts, absent_artifacts])

print_all_objects: Classes which store more objects (i.e. not Frame nor ScanDecision) have a function which recursively prints all objects below the target object. This is for the convenience of the user to see stored objects quickly. For example, calling print_all_objects on a MIQA object will result in something similar to the following printout:

MIQA Instance http://localhost:8000/api/v1
 Project Guys
   Experiment IXI002
     Scan 0828-DTI
     |Decisions:   []
     |Frames:   [Frame 0, Frame 1, Frame 2, Frame 3, Frame 4, Frame 5, Frame 6, Frame 7, Frame 8, Frame 9, Frame 10, Frame 11, Frame 12, Frame 13, Frame 14, Frame 15, Frame 16]
     Scan 0828-MRA
     |Decisions:   []
     |Frames:   [Frame 0]
     Scan 0828-PD
     |Decisions:   []
     |Frames:   [Frame 0]
     Scan 0828-T1
     |Decisions:   []
     |Frames:   [Frame 0]
     Scan 0828-T2
     |Decisions:   []
     |Frames:   [Frame 0]
   Experiment IXI016
     Scan 0697-MRA
     |Decisions:   []
     |Frames:   [Frame 0]
     Scan 0697-PD
     |Decisions:   []
     |Frames:   [Frame 0]
     Scan 0697-T1
     |Decisions:   []
     |Frames:   [Frame 0]
     Scan 0697-T2
     |Decisions:   []
     |Frames:   [Frame 0]

Whereas calling print_all_objects on a Scan object will produce a much shorter printout:

Scan 0697-T2
 |Decisions:   []
 |Frames:   [Frame 0]