Open images as numpy arrays using SCIFIO and Bio-Formats

scifio.py

#!/usr/bin/env python

#
# scifio.py - Open images as numpy arrays using SCIFIO and Bio-Formats.
#

# -- Settings --

max_mem_mb = '6144'
scifio_lifesci = False
bio_formats = True


# -- Bill of Materials --

imagej_version = '2.0.0-rc-71'
scifio_version = '0.38.2'
scifio_bf_compat_version = '4.0.0'
scifio_lifesci_version = '0.9.0'
bio_formats_version = '6.3.0'


# -- Functions --

def dtype_from_meta(image_meta):
    FormatTools = autoclass('io.scif.util.FormatTools')
    endianness = '<' if image_meta.isLittleEndian() else '>'
    pixel_types = {
        FormatTools.INT8: 'i1',
        FormatTools.UINT8: 'u1',
        FormatTools.INT16: 'i2',
        FormatTools.UINT16: 'u2',
        FormatTools.INT32: 'i4',
        FormatTools.UINT32: 'u4',
        FormatTools.FLOAT: 'f4',
        FormatTools.DOUBLE: 'f8'
    }
    pixel_type = pixel_types[image_meta.getPixelType()]
    return endianness + pixel_type

def read_images(scifio, image_path):
    import numpy
    from jnius import autoclass, cast

    # Initialize the SCIFIO reader.
    LocationService = autoclass('org.scijava.io.location.LocationService')
    location_service = cast(LocationService, scifio.get(LocationService))
    image_location = location_service.resolve(image_path)
    reader = scifio.initializer().initializeReader(image_location)
    meta = reader.getMetadata()

    images = []
    # Iterate over each nD image in the dataset.
    for i in range(0, reader.getImageCount()):
        # Query image type and dimensions.
        image_meta = meta.get(i)
        dtype = dtype_from_meta(image_meta)
        planar_axis_lengths = [image_meta.getAxisLength(p) for p in reversed(range(image_meta.getPlanarAxisCount()))]
        all_axis_lengths = list(reversed(image_meta.getAxesLengths()))

        # Iterate over each mD (m <= n; often m=2 or m=3) plane in the image.
        planes = []
        for p in range(0, reader.getPlaneCount(i)):
            b = reader.openPlane(i, p).getBytes()
            plane = numpy.frombuffer(bytes(b), dtype=dtype).reshape(planar_axis_lengths)
            planes.append(plane)

        image = numpy.concatenate(planes).reshape(all_axis_lengths)
        images.append(image)

    return images


# -- Main --

# Initialize SCIFIO with desired plugins.
import scyjava_config
scyjava_config.add_options('-Djava.awt.headless=true')
scyjava_config.add_options('-Xmx' + max_mem_mb + 'm')
endpoint = 'io.scif:scifio:{}'.format(scifio_version)
# Failed attempt to silence log4j and SLF4J warnings:
endpoint += '+org.slf4j:log4j-over-slf4j:1.7.28'
endpoint += '+org.slf4j:slf4j-simple:1.7.28'
if scifio_lifesci:
    endpoint += '+io.scif:scifio-lifesci:{}'.format(scifio_lifesci_version)
if bio_formats:
    endpoint += '+io.scif:scifio-bf-compat:{}'.format(scifio_bf_compat_version)
    endpoint += '+ome:formats-api:{}'.format(bio_formats_version)
    endpoint += '+ome:formats-bsd:{}'.format(bio_formats_version)
    endpoint += '+ome:formats-gpl:{}'.format(bio_formats_version)
scyjava_config.add_repositories({'scijava.public': scyjava_config.maven_scijava_repository()})
scyjava_config.add_endpoints(endpoint)
import scyjava
from jnius import autoclass
SCIFIO = autoclass('io.scif.SCIFIO')
scifio = SCIFIO()

# Dump the class path, for debugging.
#import re
#from jnius import autoclass
#System = autoclass('java.lang.System')
#java_class_path = System.getProperty('java.class.path')
#print('Java class path:')
#for element in java_class_path.split(':'):
#    print('\t' + re.sub('.*/', '', element))

# Read an image.
path = 'fiveD&pixelType=int16&axes=X,Y,Z,Channel,Time&lengths=17,7,2,3,5.fake'
#path = '/Users/curtis/data/blobs.gif'
images = read_images(scifio, path)
print('Image count = {}'.format(len(images)))
print('First image shape = {}'.format(images[0].shape))

# Clean up.
#scifio.getContext().dispose()

zzz-output.txt

$ python scifio.py
log4j:WARN No appenders could be found for logger (org.bushe.swing.event.EventService).
log4j:WARN Please initialize the log4j system properly.
log4j:WARN See http://logging.apache.org/log4j/1.2/faq.html#noconfig for more info.
Image count = 1
First image shape = (5, 3, 2, 7, 17)