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