def read_3D_java(sizeF1, sizeF2, sizeF3, filename="ser"):
"""
Reads in a Bruker 3D fid
sizeF1 x sizeF2 is the number of fid
sizeF3 is the number of data-points in the fid
uses java low level file access
"""
from java.io import RandomAccessFile
# from nmrtec.util.IO import SwapByte
import jarray
# read binary
dim(3)
chsize(int(sizeF1), int(sizeF2), int(sizeF3))
f = RandomAccessFile(filename, "r")
for i1 in range(sizeF1):
print(i1, end=' ')
for i2 in range(sizeF2):
for i3 in range(sizeF3):
x = f.readInt()
# x = SwapByte.swap(x) # uncoment if swapbyte is required
setval(i1 + 1, i2 + 1, i3 + 1, float(x)) # copy to 3D buffer
if ((sizeF3 % 256) != 0
): # pb with Bruker files, where size is always a 256 multiple
for i3 in range(((sizeF3 / 256) + 1) * 256 - sizeF3):
x = f.readInt()
def readFIBSEMdat(path, channel_index=-1, header=1024, magic_number=3555587570, asImagePlus=False, toUnsigned=True):
""" Read a file from Shan Xu's FIBSEM software, where two or more channels are interleaved.
Assumes channels are stored in 16-bit.
path: the file path to the .dat file.
channel_index: the 0-based index of the channel to parse, or -1 (default) for all.
header: defaults to a length of 1024 bytes
magic_number: defaults to that for version 8 of Shan Xu's .dat image file format.
isSigned: defaults to True, will subtract the min value when negative.
asImagePlus: return a list of ImagePlus instead of ArrayImg which is the default.
"""
ra = RandomAccessFile(path, 'r')
try:
# Check the magic number
ra.seek(0)
magic = ra.readInt() & 0xffffffff
if magic != magic_number:
msg = "magic number mismatch: v8 magic " + str(magic_number) + " != " + str(magic) + " for path:\n" + path
System.out.println(msg)
print msg
# Continue: attempt to parse the file anyway
# Read the number of channels
ra.seek(32)
numChannels = ra.readByte() & 0xff # a single byte as unsigned integer
# Parse width and height
ra.seek(100)
width = ra.readInt()
ra.seek(104)
height = ra.readInt()
# Read the whole interleaved pixel array
ra.seek(header)
bytes = zeros(width * height * 2 * numChannels, 'b') # 2 for 16-bit
ra.read(bytes)
# Parse as 16-bit array
sb = ByteBuffer.wrap(bytes).order(ByteOrder.BIG_ENDIAN).asShortBuffer()
bytes = None
finally:
ra.close()
#
shorts = zeros(width * height * numChannels, 'h')
sb.get(shorts)
sb = None
# Deinterleave channels and convert to unsigned short
# Shockingly, these values are signed shorts, not unsigned! (for first popeye2 squid volume, December 2021)
# With ASM: fast
channels = DAT_handler.deinterleave(shorts, numChannels, channel_index)
shorts = None
#
if toUnsigned:
for s in channels:
DAT_handler.toUnsigned(s)
# With python array sampling: very slow, and not just from iterating whole array once per channel
#seq = xrange(numChannels) if -1 == channel_index else [channel_index]
#channels = [shorts[i::numChannels] for i in seq]
if asImagePlus:
return [ImagePlus(str(i), ShortProcessor(width, height, s, None)) for i, s in enumerate(channels)]
else:
return [ArrayImgs.unsignedShorts(s, [width, height]) for s in channels]
def readFIBSEMdat(path, channel_index=-1, header=1024, magic_number=3555587570):
""" Read a file from Shan Xu's FIBSEM software, where two channels are interleaved.
Assumes channels are stored in 16-bit.
path: the file path to the .dat file.
channel_index: the 0-based index of the channel to parse, or -1 (default) for all.
header: defaults to a length of 1024 bytes
magic_number: defaults to that for version 8 of Shan Xu's .dat image file format.
"""
ra = RandomAccessFile(path, 'r')
try:
# Check the magic number
ra.seek(0)
if ra.readInt() & 0xffffffff != magic_number:
print "Magic number mismatch"
return None
# Read the number of channels
ra.seek(32)
numChannels = ra.readByte() & 0xff # a single byte as unsigned integer
# Parse width and height
ra.seek(100)
width = ra.readInt()
ra.seek(104)
height = ra.readInt()
print numChannels, width, height
# Read the whole interleaved pixel array
ra.seek(header)
bytes = zeros(width * height * 2 * numChannels, 'b') # 2 for 16-bit
ra.read(bytes)
print "read", len(bytes), "bytes" # takes ~2 seconds
# Parse as 16-bit array
sb = ByteBuffer.wrap(bytes).order(ByteOrder.BIG_ENDIAN).asShortBuffer()
shorts = zeros(width * height * numChannels, 'h')
sb.get(shorts)
# Deinterleave channels
# With Weaver: fast
channels = w.deinterleave(shorts, numChannels, channel_index)
# With python array sampling: very slow, and not just from iterating whole array once per channel
# seq = xrange(numChannels) if -1 == channel_index else [channel_index]
#channels = [shorts[i::numChannels] for i in seq]
# With clojure: extremely slow, may be using reflection unexpectedly
#channels = deinterleave.invoke(shorts, numChannels)
print len(channels)
# Shockingly, these values are signed shorts, not unsigned!
return [ArrayImgs.shorts(s, [width, height]) for s in channels]
finally:
ra.close()
def read_1D_java(size, filename="fid"):
"""
Reads in a Bruker 1D fid
size is the number of data-points in the fid
uses java low level file access
"""
from java.io import RandomAccessFile
# from nmrtec.util.IO import SwapByte
import jarray
# read binary
dim(1)
chsize(int(size))
f = RandomAccessFile(filename, "r")
for i in range(size):
x = f.readInt()
# x = SwapByte.swap(x) # uncoment if swapbyte is required
# print i,x
setval(i + 1, float(x)) # copy to 1D buffer
