def parse_TIFF_IFDs(filepath): """ Returns a generator of dictionaries of tags for each IFD in the TIFF file, as defined by the 'parseIFD' function above. """ ra = RandomAccessFile(filepath, 'r') try: # TIFF file format can have metadata at the end after the images, so the above approach can fail # TIFF file header is 8-bytes long: # (See: http://paulbourke.net/dataformats/tiff/tiff_summary.pdf ) # # Bytes 1 and 2: identifier. Either the value 4949h (II) or 4D4Dh (MM), # meaning little-endian and big-endian, respectively. # All data encountered past the first two bytes in the file obey # the byte-ordering scheme indicated by the identifier field. b1, b2 = ra.read(), ra.read() # as two java int, each one byte sized bigEndian = chr(b1) == 'M' parseNextInt = parseNextIntBigEndian if bigEndian else parseNextIntLittleEndian # Bytes 3 and 4: Version: Always 42 ra.skipBytes(2) # Bytes 5,6,7,8: IFDOffset: offset to first image file directory (IFD), the metadata entry for the first image. nextIFDoffset = parseNextInt(ra, 4) # offset to first IFD while nextIFDoffset != 0: ra.seek(nextIFDoffset) tags, nextIFDoffset = parseIFD(ra, parseNextInt) tags["bigEndian"] = bigEndian yield tags finally: ra.close()
def get(self, index): ra = None try: # Read cell origin and dimensions for cell at index cellMin = zeros(3, 'l') # long, 3 dimensions cellDims = zeros(3, 'i') # integer, 3 dimensions grid.getCellDimensions(index, cellMin, cellDims) # Unpack Cell origin (in pixel coordinates) x, y, z = cellMin # Unpack Cell dimensions: at margins, may be smaller than cell_width, cell_height width, height, _ = cellDims # ignore depth: it's 1 # Read cell from file into a byte array ra = RandomAccessFile(filepaths[z], 'r') read_width = width * bytesPerPixel bytes = zeros(read_width * height, 'b') # Initial offset to the Cell origin offset = (section_width * y + x) * bytesPerPixel n_read = 0 n_pixels = width * height # Read line by line while n_read < n_pixels: ra.seek(offset) ra.read(bytes, n_read, read_width) n_read += read_width offset += section_width * bytesPerPixel # Create a new Cell of the right pixel type return Cell(cellDims, cellMin, createAccess(bytes, bytesPerPixel)) except: print sys.exc_info() finally: if ra: ra.close()
def updateCmdForDeltaScanning(commandLine, Framework): originalScanFileFolderPath = CollectorsParameters.PROBE_MGR_INVENTORY_XMLENRICHER_FILES_FOLDER + XmlEnricherConstants.ORIGINAL_FOLDER_NAME originalScanFile = File(originalScanFileFolderPath, InventoryUtils.generateScanFileName(Framework)) if originalScanFile.exists(): scan = None try: try: buffer = jarray.zeros(0x24, 'b') fileSize = originalScanFile.length() if fileSize > 0x24: scan = RandomAccessFile(originalScanFile, "r") scan.readFully(buffer) if (buffer[0] == 0x1F) and ((buffer[1] & 0xFF) == 0x8B) and (buffer[2] == 0x08): scan.seek(fileSize - 8) scan.readFully(buffer, 0, 8) crc32 = getInt(buffer, 0) size = getInt(buffer, 4) deltaParams = ' -oldscanid:' + str(crc32) + ' -oldscansize:' + str(size) + ' ' index = String(commandLine).indexOf(ENTERPRISE_MODE) + String(ENTERPRISE_MODE).length() commandLine = commandLine[0:index] + deltaParams + commandLine[index + 1:] logger.debug('Scanner execution command updated to ', commandLine) except: logger.debugException("Failed to calculate CRC32 and size of zipped scan file " + originalScanFile.getAbsolutePath()) finally: if scan is not None: try: scan.close() except: pass return commandLine
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 read2DImageROI(path, dimensions, interval, pixelType=UnsignedShortType, header=0, byte_order=ByteOrder.LITTLE_ENDIAN): """ Read a region of interest (the interval) of an image in a file. Assumes the image is written with the first dimension moving slowest. path: the file path to the image file. dimensions: a sequence of integer values e.g. [512, 512, 512] interval: two sequences of integer values defining the min and max coordinates, e.g. [[20, 0], [400, 550]] pixeltype: e.g. UnsignedShortType, FloatType header: defaults to zero, the number of bytes between the start of the file and the start of the image data. Supports only these types: UnsignedByteType, UnsignedShortType, FloatType. Returns an ArrayImg of the given type. """ ra = RandomAccessFile(path, 'r') try: width, height = dimensions minX, minY = interval[0] maxX, maxY = interval[1] roi_width, roi_height = maxX - minX + 1, maxY - minY + 1 tailX = width - roi_width - minX #print minX, minY #print maxX, maxY #print roi_width, roi_height size = roi_width * roi_height n_bytes_per_pixel = pixelType().getBitsPerPixel() / 8 #print n_bytes_per_pixel bytes = zeros(size * n_bytes_per_pixel, 'b') # Read only the 2D ROI ra.seek(header + (minY * width + minX) * n_bytes_per_pixel) for h in xrange(roi_height): ra.readFully(bytes, h * roi_width * n_bytes_per_pixel, roi_width * n_bytes_per_pixel) ra.skipBytes((tailX + minX) * n_bytes_per_pixel) # Make an image roiDims = [roi_width, roi_height] if UnsignedByteType == pixelType: return ArrayImgs.unsignedBytes(bytes, roiDims) if UnsignedShortType == pixelType: shorts = zeros(size, 'h') ByteBuffer.wrap(bytes).order(byte_order).asShortBuffer().get(shorts) return ArrayImgs.shorts(shorts, roiDims) if FloatType == pixelType: floats = zeros(size, 'f') ByteBuffer.wrap(bytes).order(byte_order).asFloatBuffer().get(floats) return ArrayImgs.floats(floats, roiDims) finally: ra.close()
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 updateCmdForDeltaScanning(commandLine, Framework): originalScanFileFolderPath = CollectorsParameters.PROBE_MGR_INVENTORY_XMLENRICHER_FILES_FOLDER + XmlEnricherConstants.ORIGINAL_FOLDER_NAME originalScanFile = File(originalScanFileFolderPath, InventoryUtils.generateScanFileName(Framework)) if originalScanFile.exists(): scan = None try: try: buffer = jarray.zeros(0x24, 'b') fileSize = originalScanFile.length() if fileSize > 0x24: scan = RandomAccessFile(originalScanFile, "r") scan.readFully(buffer) if (buffer[0] == 0x1F) and ( (buffer[1] & 0xFF) == 0x8B) and (buffer[2] == 0x08): scan.seek(fileSize - 8) scan.readFully(buffer, 0, 8) crc32 = getInt(buffer, 0) size = getInt(buffer, 4) deltaParams = ' -oldscanid:' + str( crc32) + ' -oldscansize:' + str(size) + ' ' index = String(commandLine).indexOf( ENTERPRISE_MODE) + String( ENTERPRISE_MODE).length() commandLine = commandLine[ 0:index] + deltaParams + commandLine[index + 1:] logger.debug('Scanner execution command updated to ', commandLine) except: logger.debugException( "Failed to calculate CRC32 and size of zipped scan file " + originalScanFile.getAbsolutePath()) finally: if scan is not None: try: scan.close() except: pass return commandLine
def get(self, index): ra = None try: # Read cell origin and dimensions for cell at index cellMin = zeros(3, 'l') # long[3] cellDims = zeros(3, 'i') # integer[3] grid.getCellDimensions(index, cellMin, cellDims) # Unpack Cell origin (in pixel coordinates) x, y, z = cellMin # Unpack Cell dimensions: at margins, may be smaller than cell_width, cell_height width, height, _ = cellDims # ignore depth: it's 1 # Read cell from file into a byte array ra = RandomAccessFile(filepaths[z], 'r') read_width = width * bytesPerPixel bytes = zeros(read_width * height, 'b') # will contain the entire Cell pixel data # Initial offset to the Cell origin offset = (section_width * y + x) * bytesPerPixel n_pixels = width * height if width == section_width: # Read whole block in one go: cell data is continuous in the file ra.seek(offset) ra.read(bytes, 0, n_pixels * bytesPerPixel) else: # Read line by line n_read = 0 while n_read < n_pixels: ra.seek(offset) ra.read(bytes, n_read, read_width) n_read += read_width # ensure n_read advances in case file is truncated to avoid infinite loop offset += section_width * bytesPerPixel # Create a new Cell of the right pixel type return Cell(cellDims, cellMin, createAccess(bytes, bytesPerPixel)) except: print sys.exc_info() finally: if ra: ra.close()
class JESPrintableDocument(JESPrintable): def __init__(self, fileToPrint): self.fileName = fileToPrint self.today = SimpleDateFormat("yyyy.MM.dd HH:mm").format(Date()) self.textFont = Font("Monospaced", Font.PLAIN, 12) # We use a RandomAccessFile because Java likes to seek around and # print pages multiple times. self.raf = RandomAccessFile(self.fileName, "r") # These keep track of what pages we've found so far, # and where in the file the pages start. # Page 0's starts out filled, and the following pages' are filled # at the end of its predecessor. self.pagePointers = [] self.pageAfterEnd = None # Set the pointer for page 0. self.pagePointers.append(self.raf.getFilePointer()) def printPage(self, g, pform, pageIndex): if pageIndex < len(self.pagePointers): # We already know where this page starts. Seek there. self.raf.seek(self.pagePointers[pageIndex]) elif pageIndex >= self.pageAfterEnd: # We've found the end, and this page is after it. return JESPrintable.NO_SUCH_PAGE else: # We haven't gotten here yet. # Java will probably print each page multiple times, # and maybe even repeat pages after their successors, # but it should never print page n + 1 before page n. raise RuntimeError("Printing pages out of order") # Find our dimensions. minX = int(pform.getImageableX() + 10) width = int(pform.getImageableWidth() - 10) maxX = int(minX + width) midX = int(minX + width / 2) minY = int(pform.getImageableY() + 12) height = int(pform.getImageableHeight() - 12) maxY = int(minY + height) x, y = minX, minY # Title lines g.setColor(Color.black) # Left: filename titleString = "JES: " + os.path.basename(self.fileName) g.drawString(titleString, x, y) # Center: text pageNoString = "Page %d" % (pageIndex + 1) pageNoWidth = g.getFontMetrics().stringWidth(pageNoString) g.drawString(pageNoString, midX - (pageNoWidth / 2), y) # Right: date dateString = self.today dateWidth = g.getFontMetrics().stringWidth(dateString) g.drawString(dateString, maxX - dateWidth, y) # Line below header g.drawLine(minX, y + 6, maxX, y + 6) # OK, now the text. g.setColor(Color.black) g.setFont(self.textFont) # Generate as many lines as will fit in imageable area. y += 24 while y + 12 < maxY: line = self.raf.readLine() if line is None: # We've already printed the last line. # Don't print another page. self.pageAfterEnd = pageIndex + 1 return JESPrintable.PAGE_EXISTS try: g.drawString(line, x, y) except: # TBH I'm not sure what kind of exceptions happen here. # (If the line's too long, it'll just print over the margin.) # Unprintable characters maybe? g.drawString(' ', x, y) y = y + 12 if pageIndex + 1 == len(self.pagePointers): # Hey, we've discovered the pointer to the next page! # Let's add it to the list so the next print call works. self.pagePointers.append(self.raf.getFilePointer()) return JESPrintable.PAGE_EXISTS
writer.write(filepath, imp) # Parse the test file IFDs = list(parse_TIFF_IFDs(filepath)) # the tags of each IFD firstIFD = IFDs[0] print firstIFD ra = RandomAccessFile(filepath, 'r') try: # Read the image plane, compressed with packbits bytes_packedbits = zeros(sum(firstIFD["StripByteCounts"]), 'b') index = 0 for strip_offset, strip_length in zip(firstIFD["StripOffsets"], firstIFD["StripByteCounts"]): ra.seek(strip_offset) ra.read(bytes_packedbits, index, strip_length) index += strip_length print "Compressed:", bytes_packedbits # unpack bytes1 = unpackBits2(bytes_packedbits, firstIFD) bytes2 = unpackBits2(bytes_packedbits, firstIFD, use_imagereader=True) print "Decompressed jython:", bytes1 print "Decompressed imagej:", bytes2 # Check: if 0 == sum(a - b for a, b in zip(source_bytes, bytes1)): print "Image decompressed successfully by jython." if 0 == sum(a - b for a, b in zip(source_bytes, bytes2)): print "Image decompressed successfully by imagej." finally: ra.close()