Merge pull request #125 from sustrev/main

More DICOM conversion
- for  e2e, img,boct, poct

examples/demo_boct_extraction.py

@@ -1,3 +1,4 @@
+from oct_converter.dicom import create_dicom_from_oct
 from oct_converter.readers import BOCT
 
 filepath = "../sample_files/sample.OCT"
@@ -11,3 +12,13 @@
     oct.save(
         "boct_testing.png"
     )  # save volume as a set of sequential images, fds_testing_[1...N].png
+
+# create DICOM from .OCT
+dcm = create_dicom_from_oct(filepath)
+# Output dir can be specified, otherwise will
+# default to current working directory.
+# If multiple volumes are identified within the file,
+# multiple DICOMs will be outputted.
+# Additionally, diskbuffered can be specified to store
+# volume on disk using HDF5 to reduce memory usage
+dcm = create_dicom_from_oct(filepath, diskbuffered=True)

examples/demo_e2e_extraction.py

@@ -1,5 +1,6 @@
 import json
 
+from oct_converter.dicom import create_dicom_from_oct
 from oct_converter.readers import E2E
 
 filepath = "../sample_files/sample.E2E"
@@ -21,3 +22,10 @@
 metadata = file.read_all_metadata()
 with open("metadata.json", "w") as outfile:
     outfile.write(json.dumps(metadata, indent=4))
+
+# create a DICOM from E2E
+dcm = create_dicom_from_oct(filepath)
+# Output dir can be specified, otherwise will
+# default to current working directory.
+# If multiple volumes are present in the E2E file,
+# multiple files will be created.

examples/demo_fda_extraction.py

@@ -38,5 +38,3 @@
 dcm = create_dicom_from_oct(filepath)
 # Output dir can be specified, otherwise will
 # default to current working directory.
-# Output filename can be specified, otherwise
-# will default to the input filename.

examples/demo_fds_extraction.py

@@ -32,5 +32,3 @@
 dcm = create_dicom_from_oct(filepath)
 # Output dir can be specified, otherwise will
 # default to current working directory.
-# Output filename can be specified, otherwise
-# will default to the input filename.

examples/demo_img_extraction.py

@@ -1,3 +1,4 @@
+from oct_converter.dicom import create_dicom_from_oct
 from oct_converter.readers import IMG
 
 filepath = "../sample_files/file.img"
@@ -7,3 +8,11 @@
 )  # returns an OCT volume with additional metadata if available
 oct_volume.peek()  # plots a montage of the volume
 oct_volume.save("img_testing.avi")  # save volume
+
+# create a DICOM from .img
+dcm = create_dicom_from_oct(filepath)
+# Output dir can be specified, otherwise will
+# default to current working directory.
+# Additionally, rows, columns, and interlaced can
+# be specified to more accurately create an image.
+dcm = create_dicom_from_oct(filepath, interlaced=True)

examples/demo_optovue_extraction.py

@@ -1,3 +1,4 @@
+from oct_converter.dicom import create_dicom_from_oct
 from oct_converter.readers import POCT
 
 filepath = "../sample_files/sample.OCT"
@@ -7,3 +8,10 @@
 for volume in oct_volumes:
     volume.peek()  # plots a montage of the volume
 print("debug")
+
+# create DICOM from .OCT
+dcm = create_dicom_from_oct(filepath)
+# Output dir can be specified, otherwise will
+# default to current working directory.
+# If multiple volumes are identified within the file,
+# multiple DICOMs will be outputted.

oct_converter/dicom/boct_meta.py

@@ -0,0 +1,108 @@
+from oct_converter.dicom.metadata import (
+    DicomMetadata,
+    ImageGeometry,
+    ManufacturerMeta,
+    OCTDetectorType,
+    OCTImageParams,
+    OPTAcquisitionDevice,
+    OPTAnatomyStructure,
+    PatientMeta,
+    SeriesMeta,
+)
+from oct_converter.image_types import OCTVolumeWithMetaData
+
+
+def boct_series_meta(boct: OCTVolumeWithMetaData) -> SeriesMeta:
+    """Creates SeriesMeta from Bioptigen OCT metadata
+
+    Args:
+        boct: OCTVolumeWithMetaData with laterality and acquisition_date attributes
+    Returns:
+        SeriesMeta: Series metadata populated with laterality and acquisition_date
+    """
+    series = SeriesMeta()
+
+    series.study_id = ""
+    series.series_id = 0
+    series.laterality = boct.laterality
+    series.acquisition_date = boct.acquisition_date
+    series.opt_anatomy = OPTAnatomyStructure.Retina
+
+    return series
+
+
+def boct_manu_meta() -> ManufacturerMeta:
+    """Creates base ManufacturerMeta for Bioptigen
+
+    Args:
+        None
+    Returns:
+        ManufacturerMeta: base Bioptigen manufacture metadata
+    """
+
+    manufacture = ManufacturerMeta()
+
+    manufacture.manufacturer = "Bioptigen"
+    manufacture.manufacturer_model = ""
+    manufacture.device_serial = ""
+    manufacture.software_version = ""
+
+    return manufacture
+
+
+def boct_image_geom() -> ImageGeometry:
+    """Creates ImageGeometry from Bioptigen OCT metadata
+
+    Args:
+        pixel_spacing: Pixel spacing calculated in the boct reader
+    Returns:
+        ImageGeometry: Geometry data populated by pixel_spacing
+    """
+    image_geom = ImageGeometry()
+    image_geom.pixel_spacing = [0.02, 0.02]  # Placeholder value
+    image_geom.slice_thickness = 0.2  # Placeholder value
+    image_geom.image_orientation = [1, 0, 0, 0, 1, 0]
+
+    return image_geom
+
+
+def boct_image_params() -> OCTImageParams:
+    """Creates OCTImageParams specific to Bioptigen
+
+    Args:
+        None
+    Returns:
+        OCTImageParams: Image params populated with Bioptigen defaults
+    """
+    image_params = OCTImageParams()
+    image_params.opt_acquisition_device = OPTAcquisitionDevice.OCTScanner
+    image_params.DetectorType = OCTDetectorType.CCD
+    image_params.IlluminationWaveLength = 880
+    image_params.IlluminationPower = 1200
+    image_params.IlluminationBandwidth = 50
+    image_params.DepthSpatialResolution = 7
+    image_params.MaximumDepthDistortion = 0.5
+    image_params.AlongscanSpatialResolution = []
+    image_params.MaximumAlongscanDistortion = []
+    image_params.AcrossscanSpatialResolution = []
+    image_params.MaximumAcrossscanDistortion = []
+
+    return image_params
+
+
+def boct_dicom_metadata(boct: OCTVolumeWithMetaData) -> DicomMetadata:
+    """Creates DicomMetadata and populates each module
+
+    Args:
+        oct: OCTVolumeWithMetaData created by the boct reader
+    Returns:
+        DicomMetadata: Populated DicomMetadata created with OCT metadata
+    """
+    meta = DicomMetadata
+    meta.patient_info = PatientMeta()
+    meta.series_info = boct_series_meta(boct)
+    meta.manufacturer_info = boct_manu_meta()
+    meta.image_geometry = boct_image_geom()
+    meta.oct_image_params = boct_image_params()
+
+    return meta