def main():
imp = IJ.getFilePath("Select DCIMG file")
if not imp:
return
root, ext = os.path.splitext(imp)
if ext.lower() != '.dcimg':
cFrame = PlugInFrame('ERR DLG')
MessageDialog(cFrame, 'ERROR', 'Expected extension .dcimg')
return
#Lets start
fID = open(imp, 'rb')
hdr_bytes = read_header_bytes(fID)
hdr = parse_header_bytes(fID, hdr_bytes)
metadataStr = beginMetadata()
for key, value in hdr.iteritems():
metadataStr += addMetadataEntry(key, str(value))
metadataStr += endMetadata()
metadataDlg = HTMLDialog("DCIMG metadata", metadataStr, 0)
size = metadataDlg.getSize()
if size.width < 300:
size.width = 300
if size.height < 500:
size.height = 500
metadataDlg.setSize(size)
finfo = FileInfo()
finfo.fileName = imp
#finfo.width = hdr['xsize_req']
finfo.width = hdr['xsize']
finfo.height = hdr['ysize']
finfo.nImages = hdr['nframes']
finfo.offset = 232
finfo.fileType = hdr['bitdepth'] / 8 - 1 #Ugh
finfo.intelByteOrder = 1
#finfo.gapBetweenImages = int(hdr['bytes_per_img']*(1-float(hdr['xsize_req'])/float(hdr['xsize'])))
finfo.gapBetweenImages = 0
finfo.fileFormat = 1
finfo.samplesPerPixel = 1
finfo.displayRanges = None
finfo.lutSize = 0
finfo.whiteIsZero = 0
vs = VirtualStack()
finfo.virtualStack = vs
FileInfoVirtualStack(finfo)
imp.show()
finally:
cs.close()
# Approach 3: using low-level ImageJ libraries
from ij.io import FileInfo, FileOpener
fi = FileInfo()
fi.width = width
fi.height = height
fi.offset = headerSize + slice_offset
# ASSUMES images aren't ARGB, which would also have 32 as bit depth
# (There are other types: see FileInfo javadoc)
fi.fileType = {
8: FileInfo.GRAY8,
16: FileInfo.GRAY16_UNSIGNED,
24: FileInfo.RGB,
32: FileInfo.GRAY32_UNSIGNED
}[bitDepth]
fi.samplesPerPixel = 1
fi.nImages = num_slices
directory, filename = os.path.split(filepath)
fi.directory = directory
fi.fileName = filename
imp = FileOpener(fi).openImage() # returns an ImagePlus
imp.show()
# Approach 4: with low-level java libraries
from ij import ImagePlus, ImageStack
from ij.process import ByteProcessor, ShortProcessor, FloatProcessor
from java.io import RandomAccessFile
def open_Octopus_file():
# set up a file info structure
fi = FileInfo()
fi.fileFormat = fi.RAW
fi.fileType=FileInfo.GRAY16_UNSIGNED
fi.intelByteOrder = True
fi.nImages = 1
op = OpenDialog("Choose Octopus .dth file...", "")
if not op.getDirectory(): return False
# get the file extension
file_extension = re.search('(\.[a-z][a-z][a-z])', op.getFileName()).group(1)
if file_extension != ".dth":
dlg = GenericDialog("Warning")
dlg.addMessage("Please select an octopus .dth file")
dlg.showDialog()
return False
# now strip the filename into a stem and index
file_parse = re.match('([a-zA-z0-9_]*_)([0-9]+)\.dth', op.getFileName())
file_stem = file_parse.group(1)
file_index = int( file_parse.group(2) )
# ok now we need to parse the header info
header = get_Octopus_header(op.getDirectory(), file_stem, file_index)
fi.nImages = len(header['N'])
# check to see whether we have a bit depth, if not, assume 16-bit
if 'Bit_Depth' in header:
print header['Bit_Depth']
bit_depth = int(header['Bit_Depth'][0])
if bit_depth == 8: fi.fileType = FileInfo.GRAY8
else:
bit_depth = 16
# will assume that all files have the same size
fi.width = int( header['W'][0] )
fi.height = int( header['H'][0] )
file_timestamp = strftime("%a, %d %b %Y %H:%M:%S", gmtime(float(header['Time'][0])) )
# make a new imagestack to store the data
stack = ImageStack(fi.width, fi.height)
# finally, we need to make a list of files to import as sometimes we have
# non contiguous file numbers
try:
files = os.listdir(op.getDirectory())
except IOError:
raise IOError( "No files exist in directory: " + op.getDirectory())
filenums = []
for f in files:
# strip off the stem, and get the number
targetfile = re.match(file_stem+'([0-9]+)\.dth', f)
# only take thosefiles which match the formatting requirements
if targetfile:
filenums.append( int(targetfile.group(1)) )
# sort the file numbers
sorted_filenums = sorted(filenums)
# make a file stats string
file_stats_str = file_stem + '\n' + str(fi.width) +'x' + str(fi.height) + 'x' + \
str(len(sorted_filenums)) +' ('+str(bit_depth)+'-bit)\n' + file_timestamp
# now open a dialog to let the user set options
dlg = GenericDialog("Load Octopus Stream (v"+__version__+")")
dlg.addMessage(file_stats_str)
dlg.addStringField("Title: ", file_stem)
dlg.addNumericField("Start: ", 1, 0);
dlg.addNumericField("End: ", len(sorted_filenums), 0)
dlg.addCheckbox("Open headers", True)
dlg.addCheckbox("Contiguous stream?", False)
dlg.addCheckbox("8-bit unsigned", bit_depth==8)
dlg.showDialog()
# if we cancel the dialog, exit here
if dlg.wasCanceled():
return
# set some params
file_title = dlg.getNextString()
file_start = dlg.getNextNumber()
file_end = dlg.getNextNumber()
DISPLAY_HEADER = bool( dlg.getNextBoolean() )
# check the ranges
if file_start > file_end:
file_start, file_end = file_end, file_start
if file_start < 1:
file_start = 1
if file_end > len(sorted_filenums):
file_end = len(sorted_filenums)
# now set these to the actual file numbers in the stream
file_start = sorted_filenums[int(file_start)-1]
file_end = sorted_filenums[int(file_end)-1]
files_to_open = [n for n in sorted_filenums if n>=file_start and n<=file_end]
# if we've got too many, truncate the list
if (len(files_to_open) * fi.nImages * fi.width * fi.height) > (MAX_FRAMES_TO_IMPORT*512*512):
dlg = GenericDialog("Warning")
dlg.addMessage("This may use a lot of memory. Continue?")
dlg.showDialog()
if dlg.wasCanceled(): return False
IJ.log( "Opening file: " + op.getDirectory() + op.getFileName() )
IJ.log( file_stats_str + "\nFile range: " + str(files_to_open[0]) + \
"-" + str(files_to_open[-1]) +"\n" )
# make a results table for the metadata
# NOTE: horrible looping at the moment, but works
if DISPLAY_HEADER:
rt = ResultsTable()
# ok now we can put the files together into the stack
for i in files_to_open:
# open the original .dat file and get the stack
fi.fileName = get_Octopus_filename( op.getDirectory(), file_stem, i)
if os.path.isfile( fi.fileName ):
fo = FileOpener(fi)
imp = fo.open(False).getStack()
# put the slices into the stack
for im_slice in xrange( imp.getSize() ):
ip = imp.getProcessor( im_slice+1 )
if bit_depth == 8:
bi = ip.getBufferedImage()
else:
bi = ip.get16BitBufferedImage()
stack.addSlice( file_title, ip )
if DISPLAY_HEADER:
header = get_Octopus_header(op.getDirectory(), file_stem, i)
for n in xrange(len(header['N'])):
rt.incrementCounter()
for k in header.keys():
rt.addValue(k, parse_header( header[k][n] ) )
else:
break
# done!
output = ImagePlus('Octopus ('+file_stem+')', stack)
output.show()
if DISPLAY_HEADER:
rt.show("Octopus header metadata")
return True
metadataStr += addMetadataEntry('fileType', str(fileType))
metadataStr += addMetadataEntry('gapBetweenImages', str(gap+64))
if(metadataInconsistency > 0):
metadataStr += addMetadataEntry('Inconsistent METADATA', str(metadataInconsistency))
metadataStr += endMetadata()
metadataDlg = HTMLDialog("HIS parameters", metadataStr, 0)
size = metadataDlg.getSize()
if size.width < 300:
size.width = 300
if size.height < 300:
size.height = 300
metadataDlg.setSize(size)
finfo = FileInfo()
finfo.fileName = imp
finfo.width = width
finfo.height = height
finfo.nImages = frames
finfo.offset = offset+64
finfo.fileType = fileType-1
finfo.intelByteOrder = 1
finfo.gapBetweenImages = gap+64
finfo.fileFormat = 1
finfo.samplesPerPixel = 1
finfo.displayRanges = None
finfo.lutSize = 0
finfo.whiteIsZero = 0
vs = VirtualStack()
finfo.virtualStack = vs
FileInfoVirtualStack(finfo)