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General Information

  • PACFISH
    • Software Architecture
  • Examples and use cases
    • Use case: using the tool to read and write HDF5 files
    • Use case: Implement a conversion adapter
  • List of contributors
  • How to contribute
    • License
    • Copyright
    • Developer’s Certificate of Origin
    • Coding conventions
    • Practical Workflow

API reference

  • pacfish
    • api
      • adapters
        • NrrdFileConverter
      • BaseAdapter
        • BaseAdapter.add_custom_meta_datum_field()
        • BaseAdapter.generate_acquisition_meta_data()
        • BaseAdapter.generate_binary_data()
        • BaseAdapter.generate_device_meta_data()
        • BaseAdapter.generate_pa_data()
        • BaseAdapter.set_metadata_value()
    • core
      • DetectionElementCreator
        • DetectionElementCreator.get_dictionary()
        • DetectionElementCreator.set_angular_response()
        • DetectionElementCreator.set_detector_geometry()
        • DetectionElementCreator.set_detector_geometry_type()
        • DetectionElementCreator.set_detector_orientation()
        • DetectionElementCreator.set_detector_position()
        • DetectionElementCreator.set_frequency_response()
      • DeviceMetaDataCreator
        • DeviceMetaDataCreator.add_detection_element()
        • DeviceMetaDataCreator.add_illumination_element()
        • DeviceMetaDataCreator.finalize_device_meta_data()
        • DeviceMetaDataCreator.set_general_information()
      • IlluminationElementCreator
        • IlluminationElementCreator.get_dictionary()
        • IlluminationElementCreator.set_beam_divergence_angles()
        • IlluminationElementCreator.set_beam_energy_profile()
        • IlluminationElementCreator.set_beam_intensity_profile()
        • IlluminationElementCreator.set_beam_stability_profile()
        • IlluminationElementCreator.set_illuminator_geometry()
        • IlluminationElementCreator.set_illuminator_geometry_type()
        • IlluminationElementCreator.set_illuminator_orientation()
        • IlluminationElementCreator.set_illuminator_position()
        • IlluminationElementCreator.set_pulse_width()
        • IlluminationElementCreator.set_wavelength_range()
      • DIMENSIONALITY_STRINGS
      • EnumeratedString
        • EnumeratedString.evaluate_value_range()
      • MetaDatum
        • MetaDatum.evaluate_value_range()
      • MetadataAcquisitionTags
        • MetadataAcquisitionTags.ACOUSTIC_COUPLING_AGENT
        • MetadataAcquisitionTags.ACQUISITION_WAVELENGTHS
        • MetadataAcquisitionTags.AD_SAMPLING_RATE
        • MetadataAcquisitionTags.COMPRESSION
        • MetadataAcquisitionTags.DATA_TYPE
        • MetadataAcquisitionTags.DIMENSIONALITY
        • MetadataAcquisitionTags.ELEMENT_DEPENDENT_GAIN
        • MetadataAcquisitionTags.ENCODING
        • MetadataAcquisitionTags.FREQUENCY_DOMAIN_FILTER
        • MetadataAcquisitionTags.MEASUREMENTS_PER_IMAGE
        • MetadataAcquisitionTags.MEASUREMENT_SPATIAL_POSES
        • MetadataAcquisitionTags.MEASUREMENT_TIMESTAMPS
        • MetadataAcquisitionTags.OVERALL_GAIN
        • MetadataAcquisitionTags.PHOTOACOUSTIC_IMAGING_DEVICE_REFERENCE
        • MetadataAcquisitionTags.PULSE_ENERGY
        • MetadataAcquisitionTags.REGIONS_OF_INTEREST
        • MetadataAcquisitionTags.SCANNING_METHOD
        • MetadataAcquisitionTags.SIZES
        • MetadataAcquisitionTags.SPEED_OF_SOUND
        • MetadataAcquisitionTags.TAGS
        • MetadataAcquisitionTags.TAGS_ACQUISITION
        • MetadataAcquisitionTags.TAGS_BINARY
        • MetadataAcquisitionTags.TAGS_CONTAINER
        • MetadataAcquisitionTags.TEMPERATURE_CONTROL
        • MetadataAcquisitionTags.TIME_GAIN_COMPENSATION
        • MetadataAcquisitionTags.UUID
      • MetadataDeviceTags
        • MetadataDeviceTags.ANGULAR_RESPONSE
        • MetadataDeviceTags.BEAM_DIVERGENCE_ANGLES
        • MetadataDeviceTags.BEAM_ENERGY_PROFILE
        • MetadataDeviceTags.BEAM_INTENSITY_PROFILE
        • MetadataDeviceTags.BEAM_STABILITY_PROFILE
        • MetadataDeviceTags.DETECTION_ELEMENT
        • MetadataDeviceTags.DETECTORS
        • MetadataDeviceTags.DETECTOR_GEOMETRY
        • MetadataDeviceTags.DETECTOR_GEOMETRY_TYPE
        • MetadataDeviceTags.DETECTOR_ORIENTATION
        • MetadataDeviceTags.DETECTOR_POSITION
        • MetadataDeviceTags.FIELD_OF_VIEW
        • MetadataDeviceTags.FREQUENCY_RESPONSE
        • MetadataDeviceTags.GENERAL
        • MetadataDeviceTags.ILLUMINATION_ELEMENT
        • MetadataDeviceTags.ILLUMINATORS
        • MetadataDeviceTags.ILLUMINATOR_GEOMETRY
        • MetadataDeviceTags.ILLUMINATOR_GEOMETRY_TYPE
        • MetadataDeviceTags.ILLUMINATOR_ORIENTATION
        • MetadataDeviceTags.ILLUMINATOR_POSITION
        • MetadataDeviceTags.INTENSITY_PROFILE_DISTANCE
        • MetadataDeviceTags.NUMBER_OF_DETECTION_ELEMENTS
        • MetadataDeviceTags.NUMBER_OF_ILLUMINATION_ELEMENTS
        • MetadataDeviceTags.PULSE_WIDTH
        • MetadataDeviceTags.TAGS
        • MetadataDeviceTags.TAGS_DETECTORS
        • MetadataDeviceTags.TAGS_GENERAL
        • MetadataDeviceTags.TAGS_ILLUMINATORS
        • MetadataDeviceTags.UNIQUE_IDENTIFIER
        • MetadataDeviceTags.WAVELENGTH_RANGE
      • NDimensionalNumpyArray
        • NDimensionalNumpyArray.evaluate_value_range()
      • NDimensionalNumpyArrayWithMElements
        • NDimensionalNumpyArrayWithMElements.evaluate_value_range()
      • NonNegativeNumber
        • NonNegativeNumber.evaluate_value_range()
      • NonNegativeNumbersInArray
        • NonNegativeNumbersInArray.evaluate_value_range()
      • NonNegativeWholeNumber
        • NonNegativeWholeNumber.evaluate_value_range()
      • NumberWithUpperAndLowerLimit
        • NumberWithUpperAndLowerLimit.evaluate_value_range()
      • UnconstrainedMetaDatum
        • UnconstrainedMetaDatum.evaluate_value_range()
      • Units
        • Units.DIMENSIONLESS_UNIT
        • Units.HERTZ
        • Units.JOULES
        • Units.KELVIN
        • Units.METERS
        • Units.METERS_PER_SECOND
        • Units.NO_UNIT
        • Units.RADIANS
        • Units.SECONDS
      • PAData
        • PAData.get_acoustic_coupling_agent()
        • PAData.get_acquisition_meta_datum()
        • PAData.get_acquisition_wavelengths()
        • PAData.get_angular_response()
        • PAData.get_beam_divergence()
        • PAData.get_beam_energy_profile()
        • PAData.get_beam_profile()
        • PAData.get_beam_profile_distance()
        • PAData.get_beam_stability_profile()
        • PAData.get_compression()
        • PAData.get_custom_meta_datum()
        • PAData.get_data_UUID()
        • PAData.get_data_type()
        • PAData.get_detector_attribute_for_tag()
        • PAData.get_detector_geometry()
        • PAData.get_detector_geometry_type()
        • PAData.get_detector_ids()
        • PAData.get_detector_orientation()
        • PAData.get_detector_position()
        • PAData.get_device_uuid()
        • PAData.get_dimensionality()
        • PAData.get_element_dependent_gain()
        • PAData.get_encoding()
        • PAData.get_field_of_view()
        • PAData.get_frequency_domain_filter()
        • PAData.get_frequency_response()
        • PAData.get_illuminator_attribute_for_tag()
        • PAData.get_illuminator_geometry()
        • PAData.get_illuminator_geometry_type()
        • PAData.get_illuminator_ids()
        • PAData.get_illuminator_orientation()
        • PAData.get_illuminator_position()
        • PAData.get_measurement_spatial_poses()
        • PAData.get_measurement_time_stamps()
        • PAData.get_measurements_per_image()
        • PAData.get_number_of_detectors()
        • PAData.get_number_of_illuminators()
        • PAData.get_overall_gain()
        • PAData.get_photoacoustic_imaging_device_reference()
        • PAData.get_pulse_energy()
        • PAData.get_pulse_width()
        • PAData.get_regions_of_interest()
        • PAData.get_sampling_rate()
        • PAData.get_scanning_method()
        • PAData.get_sizes()
        • PAData.get_speed_of_sound()
        • PAData.get_temperature()
        • PAData.get_time_gain_compensation()
        • PAData.get_wavelength_range()
    • iohandler
      • load_data()
      • write_data()
    • qualitycontrol
      • CompletenessChecker
        • CompletenessChecker.check_acquisition_meta_data()
        • CompletenessChecker.check_device_meta_data()
        • CompletenessChecker.check_metadatum_from_dict()
      • ConsistencyChecker
        • ConsistencyChecker.check_acquisition_meta_data()
        • ConsistencyChecker.check_binary_data()
        • ConsistencyChecker.check_device_meta_data()
      • quality_check_pa_data()
    • visualize_device()

Glossary

  • Possible Metadata Attributes
    • Condition
    • Description
    • dtype
    • Measurement Device Attribute
      • Calibration Date
      • Measurement Device Manufacturer
      • Measurement Device Serial Number
      • Measurement Device Type
    • Method Name
    • Necessity
    • Nested Attribute
    • Units
  • Binary Data Metadata
    • Data Type
    • Dimensionality
    • Sizes
  • File Container Format
    • Encoding
    • Compression
    • Universally Unique Identifier
  • Acquisition Metadata
    • A/D (Analog/Digital) Sampling Rate
    • Acoustic Coupling Agent
    • Acquisition Optical Wavelengths
    • Element-dependent Gain
    • Frequency Domain Filter
    • Measurements Per Image
    • Measurement Spatial Pose
    • Measurement Timestamps
    • Overall Gain
    • Photoacoustic Imaging Device Reference
    • Pulse Laser Energy
    • Regions of Interest
    • Scanning Method
    • Speed of Sound
    • Temperature Control
    • Time Gain Compensation
  • Device Metadata
    • General Parameters
      • Field of View
      • Number of Detection Elements
      • Number of Illumination Elements
      • Universally Unique Identifier
    • Detection Element
      • Detector Geometry
      • Detector Geometry Type
      • Detector Orientation
      • Detector Position
      • Detection Element Properties
        • Angular Response
        • Frequency Response
    • Illumination Element
      • Illuminator Geometry
      • Illuminator Geometry Type
      • Illuminator Orientation
      • Illuminator Position
      • Illuminator Properties
        • Beam Divergence Angles
        • Beam Intensity Profile
        • Intensity Profile Distance
        • Laser Energy Profile
        • Laser Stability Profile
        • Pulse Duration / Width
        • Wavelength Range
PACFISH
  • Overview: module code

All modules for which code is available

  • pacfish.api.BaseAdapter
  • pacfish.api.adapters.Nrrd_File_Converter
  • pacfish.core.DeviceMetaDataCreator
  • pacfish.core.Metadata
  • pacfish.core.PAData
  • pacfish.iohandler.file_reader
  • pacfish.iohandler.file_writer
  • pacfish.qualitycontrol.CompletenessChecker
  • pacfish.qualitycontrol.ConsistencyChecker
  • pacfish.qualitycontrol.PADataIntegrityCheck
  • pacfish.visualize_device

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