Metadata support#

[1]:

import os
import numpy as np
import cupy as cp
from matplotlib import pyplot as plt

Setting resource folder

[2]:

resources_dir = os.getenv("PYNVIMGCODEC_EXAMPLES_RESOURCES_DIR", "../assets/images/")

Import nvImageCodec module and create Decoder

[3]:

#os.environ['PYNVIMGCODEC_VERBOSITY'] = '5' uncomment for verbose log output

[4]:

from nvidia import nvimgcodec
decoder = nvimgcodec.Decoder()

Geo#

[11]:

img_full_path = os.path.abspath(os.path.join(resources_dir, "Alex_2016-01-14_1300Z_(Geotiff).tif"))
cs = nvimgcodec.CodeStream(img_full_path)
print("Number of images:", cs.num_images)
print("img.width", cs.width)
print("img.height", cs.height)

for code_stream_idx in range(0, cs.num_images):
    scs = cs.getSubCodeStream(code_stream_idx)
    metadata = decoder.getMetadata(scs)
    for m in metadata:
        print(m)
        print(" "*5, m.buffer)

Number of images: 1
img.width 5000
img.height 6400
Metadata(kind=GEO format=JSON buffer_size=276)
      b'{"MODEL_PIXEL_SCALE":[0.00259611,0.0022483,0],"MODEL_TIEPOINT":[0,0,0,-35.489,39.1935,0],"GT_MODEL_TYPE":2,"GT_RASTER_TYPE":1,"GEODETIC_CRS":4326,"GEODETIC_CITATION":"WGS 84","GEOG_ANGULAR_UNITS":9102,"ELLIPSOID_SEMI_MAJOR_AXIS":6.37814e+06,"ELLIPSOID_INV_FLATTENING":298.257}'

Decode image

[6]:

img = decoder.decode(cs)
print(img.__cuda_array_interface__)
plt.figure()
plt.imshow(img.cpu())

{'shape': (6400, 5000, 3), 'strides': None, 'typestr': '|u1', 'data': (64424509440, False), 'version': 3, 'stream': 1}

[6]:

<matplotlib.image.AxesImage at 0x7f35f0723bf0>

Aperio#

Aorta tissue, brightfield, JPEG 2000, YCbCr

[7]:

img_full_path = os.path.abspath(os.path.join(resources_dir, "JP2K-33003-1.svs"))
cs = nvimgcodec.CodeStream(img_full_path)
print("Number of images:", cs.num_images)
print("img.width", cs.width)
print("img.height", cs.height)

for code_stream_idx in range(0, cs.num_images):
    scs = cs.getSubCodeStream(code_stream_idx)
    metadata = decoder.getMetadata(scs)
    for m in metadata:
        print(m)
        print(" "*5, m.buffer.decode('utf-8'))

Number of images: 6
img.width 15374
img.height 17497
Metadata(kind=MED_APERIO format=RAW buffer_size=530)
      Aperio Image Library v10.0.50
16000x17597 [0,100 15374x17497] (256x256) J2K/YUV16 Q=70|AppMag = 40|StripeWidth = 1000|ScanScope ID = SS1283|Filename = 6797|Title = univ missouri 07.15.09|Date = 07/16/09|Time = 18:15:06|User = 93d70f65-3b32-4072-ba6a-bd6785a781be|MPP = 0.2498|Left = 39.010742|Top = 14.299895|LineCameraSkew = -0.003035|LineAreaXOffset = 0.000000|LineAreaYOffset = 0.000000|Focus Offset = -0.001000|DSR ID = homer|ImageID = 6797|OriginalWidth = 16000|Originalheight = 17597|Filtered = 3|ICC Profile = ScanScope v1
Metadata(kind=MED_APERIO format=RAW buffer_size=498)
      Aperio Image Library v10.0.50
15374x17497 -> 674x768 - |AppMag = 40|StripeWidth = 1000|ScanScope ID = SS1283|Filename = 6797|Title = univ missouri 07.15.09|Date = 07/16/09|Time = 18:15:06|User = 93d70f65-3b32-4072-ba6a-bd6785a781be|MPP = 0.2498|Left = 39.010742|Top = 14.299895|LineCameraSkew = -0.003035|LineAreaXOffset = 0.000000|LineAreaYOffset = 0.000000|Focus Offset = -0.001000|DSR ID = homer|ImageID = 6797|OriginalWidth = 16000|Originalheight = 17597|Filtered = 3|ICC Profile = ScanScope v1
Metadata(kind=MED_APERIO format=RAW buffer_size=100)
      Aperio Image Library v10.0.50
16000x17597 [0,100 15374x17497] (256x256) -> 3843x4374 J2K/YUV16 Q=70
Metadata(kind=MED_APERIO format=RAW buffer_size=100)
      Aperio Image Library v10.0.50
16000x17597 [0,100 15374x17497] (256x256) -> 1921x2187 J2K/YUV16 Q=70
Metadata(kind=MED_APERIO format=RAW buffer_size=43)
      Aperio Image Library v10.0.50
label 415x422
Metadata(kind=MED_APERIO format=RAW buffer_size=44)
      Aperio Image Library v10.0.50
macro 1280x421

Decode all subimages

[8]:

for code_stream_idx in range(0, cs.num_images):
    scs = cs.getSubCodeStream(code_stream_idx)
    img = decoder.decode(scs)
    plt.figure()
    plt.imshow(img.cpu())

Philips#

Lymph node section, H&E stain, brightfield, BigTIFF, barcode attribute, from CAMELYON16 data set

[9]:

img_full_path = os.path.abspath(os.path.join(resources_dir, "Philips-1.tiff"))
cs = nvimgcodec.CodeStream(img_full_path)
print("Number of images:", cs.num_images)
print("img.width", cs.width)
print("img.height", cs.height)
for code_stream_idx in range(0, cs.num_images):
    scs = cs.getSubCodeStream(code_stream_idx)
    metadata = decoder.getMetadata(scs)
    for m in metadata:
        print(m)
        print(" "*5, m.buffer.decode('utf-8'))

Number of images: 8
img.width 45056
img.height 35840
Metadata(kind=MED_PHILIPS format=XML buffer_size=9335)
      <?xml version="1.0" encoding="UTF-8" ?>
<DataObject ObjectType="DPUfsImport">
        <Attribute Name="DICOM_MANUFACTURER" Group="0x0008" Element="0x0070" PMSVR="IString">Hamamatsu</Attribute>
        <Attribute Name="PIM_DP_SCANNED_IMAGES" Group="0x301D" Element="0x1003" PMSVR="IDataObjectArray">
                <Array>
                        <DataObject ObjectType="DPScannedImage">
                                <Attribute Name="PIM_DP_IMAGE_TYPE" Group="0x301D" Element="0x1004" PMSVR="IString">WSI</Attribute>
                                <Attribute Name="UFS_IMAGE_PIXEL_TRANSFORMATION_METHOD" Group="0x301D" Element="0x2013" PMSVR="IString">0</Attribute>
                                <Attribute Name="DICOM_BITS_ALLOCATED" Group="0x0028" Element="0x0100" PMSVR="IUInt16">8</Attribute>
                                <Attribute Name="DICOM_BITS_STORED" Group="0x0028" Element="0x0101" PMSVR="IUInt16">8</Attribute>
                                <Attribute Name="DICOM_DERIVATION_DESCRIPTION" Group="0x0008" Element="0x2111" PMSVR="IString">tiff-useBigTIFF=1-useRgb=0-levels=10003,10002,10000,10001-processing=0-q80-sourceFilename=&quot;T14-03469_3311940 - 2015-12-09 17.29.29.ndpi&quot;</Attribute>
                                <Attribute Name="DICOM_HIGH_BIT" Group="0x0028" Element="0x0102" PMSVR="IUInt16">7</Attribute>
                                <Attribute Name="DICOM_LOSSY_IMAGE_COMPRESSION" Group="0x0028" Element="0x2110" PMSVR="IString">01</Attribute>
                                <Attribute Name="DICOM_LOSSY_IMAGE_COMPRESSION_METHOD" Group="0x0028" Element="0x2114" PMSVR="IStringArray">&quot;PHILIPS_TIFF_1_0&quot;</Attribute>
                                <Attribute Name="DICOM_LOSSY_IMAGE_COMPRESSION_RATIO" Group="0x0028" Element="0x2112" PMSVR="IDoubleArray">&quot;3&quot;</Attribute>
                                <Attribute Name="DICOM_PHOTOMETRIC_INTERPRETATION" Group="0x0028" Element="0x0004" PMSVR="IString">RGB</Attribute>
                                <Attribute Name="DICOM_PIXEL_REPRESENTATION" Group="0x0028" Element="0x0103" PMSVR="IUInt16">0</Attribute>
                                <Attribute Name="DICOM_PIXEL_SPACING" Group="0x0028" Element="0x0030" PMSVR="IDoubleArray">&quot;0.000226891&quot; &quot;0.000226907&quot;</Attribute>
                                <Attribute Name="DICOM_PLANAR_CONFIGURATION" Group="0x0028" Element="0x0006" PMSVR="IUInt16">0</Attribute>
                                <Attribute Name="DICOM_SAMPLES_PER_PIXEL" Group="0x0028" Element="0x0002" PMSVR="IUInt16">3</Attribute>
                                <Attribute Name="PIIM_PIXEL_DATA_REPRESENTATION_SEQUENCE" Group="0x1001" Element="0x8B01" PMSVR="IDataObjectArray">
                                        <Array>
                                                <DataObject ObjectType="PixelDataRepresentation">
                                                        <Attribute Name="DICOM_PIXEL_SPACING" Group="0x0028" Element="0x0030" PMSVR="IDoubleArray">&quot;0.000227273&quot; &quot;0.000227273&quot;</Attribute>
                                                        <Attribute Name="PIIM_DP_PIXEL_DATA_REPRESENTATION_POSITION" Group="0x101D" Element="0x100B" PMSVR="IDoubleArray">&quot;0&quot; &quot;0&quot; &quot;0&quot;</Attribute>
                                                        <Attribute Name="PIIM_PIXEL_DATA_REPRESENTATION_COLUMNS" Group="0x2001" Element="0x115E" PMSVR="IUInt32">45056</Attribute>
                                                        <Attribute Name="PIIM_PIXEL_DATA_REPRESENTATION_NUMBER" Group="0x1001" Element="0x8B02" PMSVR="IUInt16">0</Attribute>
                                                        <Attribute Name="PIIM_PIXEL_DATA_REPRESENTATION_ROWS" Group="0x2001" Element="0x115D" PMSVR="IUInt32">35840</Attribute>
                                                </DataObject>
                                                <DataObject ObjectType="PixelDataRepresentation">
                                                        <Attribute Name="DICOM_PIXEL_SPACING" Group="0x0028" Element="0x0030" PMSVR="IDoubleArray">&quot;0.000454545&quot; &quot;0.000454545&quot;</Attribute>
                                                        <Attribute Name="PIIM_DP_PIXEL_DATA_REPRESENTATION_POSITION" Group="0x101D" Element="0x100B" PMSVR="IDoubleArray">&quot;0&quot; &quot;0&quot; &quot;0&quot;</Attribute>
                                                        <Attribute Name="PIIM_PIXEL_DATA_REPRESENTATION_COLUMNS" Group="0x2001" Element="0x115E" PMSVR="IUInt32">22528</Attribute>
                                                        <Attribute Name="PIIM_PIXEL_DATA_REPRESENTATION_NUMBER" Group="0x1001" Element="0x8B02" PMSVR="IUInt16">1</Attribute>
                                                        <Attribute Name="PIIM_PIXEL_DATA_REPRESENTATION_ROWS" Group="0x2001" Element="0x115D" PMSVR="IUInt32">17920</Attribute>
                                                </DataObject>
                                                <DataObject ObjectType="PixelDataRepresentation">
                                                        <Attribute Name="DICOM_PIXEL_SPACING" Group="0x0028" Element="0x0030" PMSVR="IDoubleArray">&quot;0.000909091&quot; &quot;0.000909091&quot;</Attribute>
                                                        <Attribute Name="PIIM_DP_PIXEL_DATA_REPRESENTATION_POSITION" Group="0x101D" Element="0x100B" PMSVR="IDoubleArray">&quot;0&quot; &quot;0&quot; &quot;0&quot;</Attribute>
                                                        <Attribute Name="PIIM_PIXEL_DATA_REPRESENTATION_COLUMNS" Group="0x2001" Element="0x115E" PMSVR="IUInt32">11264</Attribute>
                                                        <Attribute Name="PIIM_PIXEL_DATA_REPRESENTATION_NUMBER" Group="0x1001" Element="0x8B02" PMSVR="IUInt16">2</Attribute>
                                                        <Attribute Name="PIIM_PIXEL_DATA_REPRESENTATION_ROWS" Group="0x2001" Element="0x115D" PMSVR="IUInt32">9216</Attribute>
                                                </DataObject>
                                                <DataObject ObjectType="PixelDataRepresentation">
                                                        <Attribute Name="DICOM_PIXEL_SPACING" Group="0x0028" Element="0x0030" PMSVR="IDoubleArray">&quot;0.00181818&quot; &quot;0.00181818&quot;</Attribute>
                                                        <Attribute Name="PIIM_DP_PIXEL_DATA_REPRESENTATION_POSITION" Group="0x101D" Element="0x100B" PMSVR="IDoubleArray">&quot;0&quot; &quot;0&quot; &quot;0&quot;</Attribute>
                                                        <Attribute Name="PIIM_PIXEL_DATA_REPRESENTATION_COLUMNS" Group="0x2001" Element="0x115E" PMSVR="IUInt32">5632</Attribute>
                                                        <Attribute Name="PIIM_PIXEL_DATA_REPRESENTATION_NUMBER" Group="0x1001" Element="0x8B02" PMSVR="IUInt16">3</Attribute>
                                                        <Attribute Name="PIIM_PIXEL_DATA_REPRESENTATION_ROWS" Group="0x2001" Element="0x115D" PMSVR="IUInt32">4608</Attribute>
                                                </DataObject>
                                                <DataObject ObjectType="PixelDataRepresentation">
                                                        <Attribute Name="DICOM_PIXEL_SPACING" Group="0x0028" Element="0x0030" PMSVR="IDoubleArray">&quot;0.00363636&quot; &quot;0.00363636&quot;</Attribute>
                                                        <Attribute Name="PIIM_DP_PIXEL_DATA_REPRESENTATION_POSITION" Group="0x101D" Element="0x100B" PMSVR="IDoubleArray">&quot;0&quot; &quot;0&quot; &quot;0&quot;</Attribute>
                                                        <Attribute Name="PIIM_PIXEL_DATA_REPRESENTATION_COLUMNS" Group="0x2001" Element="0x115E" PMSVR="IUInt32">3072</Attribute>
                                                        <Attribute Name="PIIM_PIXEL_DATA_REPRESENTATION_NUMBER" Group="0x1001" Element="0x8B02" PMSVR="IUInt16">4</Attribute>
                                                        <Attribute Name="PIIM_PIXEL_DATA_REPRESENTATION_ROWS" Group="0x2001" Element="0x115D" PMSVR="IUInt32">2560</Attribute>
                                                </DataObject>
                                                <DataObject ObjectType="PixelDataRepresentation">
                                                        <Attribute Name="DICOM_PIXEL_SPACING" Group="0x0028" Element="0x0030" PMSVR="IDoubleArray">&quot;0.00727273&quot; &quot;0.00727273&quot;</Attribute>
                                                        <Attribute Name="PIIM_DP_PIXEL_DATA_REPRESENTATION_POSITION" Group="0x101D" Element="0x100B" PMSVR="IDoubleArray">&quot;0&quot; &quot;0&quot; &quot;0&quot;</Attribute>
                                                        <Attribute Name="PIIM_PIXEL_DATA_REPRESENTATION_COLUMNS" Group="0x2001" Element="0x115E" PMSVR="IUInt32">1536</Attribute>
                                                        <Attribute Name="PIIM_PIXEL_DATA_REPRESENTATION_NUMBER" Group="0x1001" Element="0x8B02" PMSVR="IUInt16">5</Attribute>
                                                        <Attribute Name="PIIM_PIXEL_DATA_REPRESENTATION_ROWS" Group="0x2001" Element="0x115D" PMSVR="IUInt32">1536</Attribute>
                                                </DataObject>
                                                <DataObject ObjectType="PixelDataRepresentation">
                                                        <Attribute Name="DICOM_PIXEL_SPACING" Group="0x0028" Element="0x0030" PMSVR="IDoubleArray">&quot;0.0145455&quot; &quot;0.0145455&quot;</Attribute>
                                                        <Attribute Name="PIIM_DP_PIXEL_DATA_REPRESENTATION_POSITION" Group="0x101D" Element="0x100B" PMSVR="IDoubleArray">&quot;0&quot; &quot;0&quot; &quot;0&quot;</Attribute>
                                                        <Attribute Name="PIIM_PIXEL_DATA_REPRESENTATION_COLUMNS" Group="0x2001" Element="0x115E" PMSVR="IUInt32">1024</Attribute>
                                                        <Attribute Name="PIIM_PIXEL_DATA_REPRESENTATION_NUMBER" Group="0x1001" Element="0x8B02" PMSVR="IUInt16">6</Attribute>
                                                        <Attribute Name="PIIM_PIXEL_DATA_REPRESENTATION_ROWS" Group="0x2001" Element="0x115D" PMSVR="IUInt32">1024</Attribute>
                                                </DataObject>
                                                <DataObject ObjectType="PixelDataRepresentation">
                                                        <Attribute Name="DICOM_PIXEL_SPACING" Group="0x0028" Element="0x0030" PMSVR="IDoubleArray">&quot;0.0290909&quot; &quot;0.0290909&quot;</Attribute>
                                                        <Attribute Name="PIIM_DP_PIXEL_DATA_REPRESENTATION_POSITION" Group="0x101D" Element="0x100B" PMSVR="IDoubleArray">&quot;0&quot; &quot;0&quot; &quot;0&quot;</Attribute>
                                                        <Attribute Name="PIIM_PIXEL_DATA_REPRESENTATION_COLUMNS" Group="0x2001" Element="0x115E" PMSVR="IUInt32">512</Attribute>
                                                        <Attribute Name="PIIM_PIXEL_DATA_REPRESENTATION_NUMBER" Group="0x1001" Element="0x8B02" PMSVR="IUInt16">7</Attribute>
                                                        <Attribute Name="PIIM_PIXEL_DATA_REPRESENTATION_ROWS" Group="0x2001" Element="0x115D" PMSVR="IUInt32">512</Attribute>
                                                </DataObject>
                                        </Array>
                                </Attribute>
                                <Attribute Name="PIM_DP_IMAGE_COLUMNS" Group="0x301D" Element="0x1007" PMSVR="IUInt32">45056</Attribute>
                                <Attribute Name="PIM_DP_IMAGE_ROWS" Group="0x301D" Element="0x1006" PMSVR="IUInt32">35840</Attribute>
                                <Attribute Name="PIM_DP_SOURCE_FILE" Group="0x301D" Element="0x1000" PMSVR="IString">%FILENAME%</Attribute>
                        </DataObject>
                </Array>
        </Attribute>
        <Attribute Name="PIM_DP_UFS_BARCODE" Group="0x301D" Element="0x1002" PMSVR="IString">MzMxMTk0MA==</Attribute>
        <Attribute Name="PIM_DP_UFS_INTERFACE_VERSION" Group="0x301D" Element="0x1001" PMSVR="IString">3.0</Attribute>
        <Attribute Name="DICOM_SOFTWARE_VERSIONS" Group="0x0018" Element="0x1020" PMSVR="IStringArray">&quot;4.0.3&quot;</Attribute>
</DataObject>

Metadata(kind=MED_PHILIPS format=RAW buffer_size=25)
      level=1 mag=22 quality=80
Metadata(kind=MED_PHILIPS format=RAW buffer_size=25)
      level=2 mag=11 quality=80
Metadata(kind=MED_PHILIPS format=RAW buffer_size=26)
      level=3 mag=5.5 quality=80
Metadata(kind=MED_PHILIPS format=RAW buffer_size=27)
      level=4 mag=2.75 quality=80
Metadata(kind=MED_PHILIPS format=RAW buffer_size=28)
      level=5 mag=1.375 quality=80
Metadata(kind=MED_PHILIPS format=RAW buffer_size=29)
      level=6 mag=0.6875 quality=80
Metadata(kind=MED_PHILIPS format=RAW buffer_size=30)
      level=7 mag=0.34375 quality=80

[10]:

for code_stream_idx in range(0, cs.num_images):
    scs = cs.getSubCodeStream(code_stream_idx)
    img = decoder.decode(scs)
    plt.figure()
    plt.imshow(img.cpu())